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The Third International Conference on
Computational Science and Engineering (ICCSE-3)
28-30 November, 2016, Ho Chi Minh City, Vietnam
INVITED TALKS
1
The Third International Conference on
Computational Science and Engineering (ICCSE-3)
28-30 November, 2016, Ho Chi Minh City, Vietnam
I2.1
Recent Advances in Long-range Corrected (LC) DFT
KIMIHIKO HIRAO
Advanced Institute for Computational Science, RIKEN, Kobe, Japan
E-mail: [email protected]
DFT has emerged as a powerful computational tool for the chemical systems. It is simple and conceptual. KSDFT calculation takes about the same amount of time as a Hartree-Fock (HF) calculation, yet unlike HF, we get
a correlated result from KS-DFT. Many of the problems of KS-DFT have mostly been a consequence of not
having accurate functionals and potentials. Recently there has been considerable interest in the long-range
corrected (LC) DFT. In the LC scheme the exchange functional is partitioned with respect to the inter-electronic
separation into long-range and short-range parts using a standard error function. The LC solves many of DFT
problems: LC remedies the underestimation of Rydberg and core excitation energies and corresponding oscillator
strengths, the poor reproduction of charge-transfer excitations in TD-DFT calculations, and the overestimation of
linear and nonlinear polarizabilities of long-chain molecules in CP-DFT calculations. The LC successfully
provides a good description of weak van der Waals interactions as well as accurate reaction enthalpies and barrier
heights. The LC satisfies Koopmans’ theorem, which implies that the eigenvalues and eigenvectors connected to
the Kohn-Sham equation have a strict physical meaning.
The expensive time cost to evaluate the long-range HF exchange is a big obstacle to be overcome to be applied to
the large molecular systems and the solid state materials. Upon this problem, we propose a linear-scaling method
of the HF exchange integration, in particular, for the LC-DFT hybrid functional. Recent advances in LC-DFT will
be discussed.
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The Third International Conference on
Computational Science and Engineering (ICCSE-3)
28-30 November, 2016, Ho Chi Minh City, Vietnam
I2.2
Structural Variations and Chemical Bonding in Platinum
Complexes of Group 14 Heavier Tetrylene Homologues. Do
Divalent Tetrylenes(II) have Hidden Divalent Tetrylones(0)
Chemistry Character?
NGUYEN THI AI NHUNG
Department of Chemistry, Universit of Hue, Hue, Vietnam
Email: [email protected]
The structures of Pt(II) complexes containing the heavier homologues of germylene, stannylene, and plumbylene
[PtCl2−{NHEMe}] (Pt−NHE) with E = Ge to Pb, in which the ligand {NHEMe} retains one lone pair at the E central
atom as called heavier tetrylenes, have been computed using density functional theory calculations at the BP86
level with def2-SVP, def2-TZVPP, and TZ2P+ basis sets. The bonding of the complexes has been analyzed by
charge and energy decomposition analysis methods. The results of bonding analysis show that NHEMe ligands
exhibit donor-acceptor bonds with the  lone pair electrons of heavier NHEMe donated into the vacant orbital of
the metal fragment, and the Pt−E bonds having PtCl2←NHEMe strong -donation. The divalent heavier
tetrylenes(II) have the same role as the divalent heavier tetrylones(0) character since the ligand can retain the two
lone pairs at E atom. Currently experimental efforts are directed towards the synthesis of tetrylenes Pt(II)
complexes from natural products. Hence, the results in this study will provide an insight into the properties and
chemical bonding of complexes being synthesized.
(a) [PtCl2-{NHEMe}] (Pt−NHE)
(b) NHEMe (NHE)
E = Ge, Sn, Pb
Scheme 1: Overview of the compounds investigated.
Keywords: Density functional calculations, Bonding analysis, Carbenes, Germylenes, Stannylenes,
Plumbylenes, Platinum.
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The Third International Conference on
Computational Science and Engineering (ICCSE-3)
28-30 November, 2016, Ho Chi Minh City, Vietnam
I2.3
Stepwise Double Excited-State Proton Transfer
Is Not Possible in 7-Azaindole Dimer
NAWEE KUNGWAN
Department of Chemistry, Faculty of Science, Chiang Mai University,
Chiang Mai 50200, Thailand
Email: [email protected]
The nature of the excited-state double proton transfer in 7-Azaindole (7AI) dimer—whether it is stepwise or
concerted—has been under a fierce debate for two decades. Based on high-level computational simulations of
static and dynamic properties, we show that much of the earlier discussions was induced by inappropriate
theoretical modelling, which led to biased conclusions towards one or other mechanism. A proper topograhical
description of the excited-state potential energy surface of 7AI dimer in the gas phase clearly reveals that the
stepwise mechanism is not accessible due to kinetic and thermodynamic reasons. Single proton transfer can occur,
but when it does, an energy barrier blocks the transfer of the second proton and the dimer relaxes through internal
conversion. Double proton transfer takes place exclusively by an asynchronous concerted mechanism.
References
[1] Chemical Science, 2015, 6(10), 5762-5767
4
The Third International Conference on
Computational Science and Engineering (ICCSE-3)
28-30 November, 2016, Ho Chi Minh City, Vietnam
I2.4
Bridging Fundamental Chemistry/Physics and Reaction
Engineering - Applications and Computational Tools
LAM K. HUYNH
Department of Applied Chemistry, International University,
Vietnam National University – HCM City
Email: [email protected]
Computational modeling/simulation has served not only as a powerful post-facto tool for validating existing
principles and knowledge but also a strong predictive tool in the discovery of new knowledge in science and
engineering. Recent advances in information technology, algorithm, and scientific methods, which allow faster
and more accurate calculations for more realistic systems, have laid a solid foundation for bridging the time and
length scale from fundamental science to real engineering challenges. In this talk, I will demonstrate how to bridge
fundamental chemistry/physics & reaction engineering modeling in two domains/aspects: (1) gas-phase chemistry
and (2) complex chemical processes on surfaces (catalyst/material design). In gas-phase chemistry, an example
for understanding and modeling low-temperature combustion of hydrocarbon and alternative fuels will be
discussed in detail. Next, I will demonstrate how to design better catalysts for complex chemical systems such as
methanol conversion and water-gas shift reactions on Ni nanocatalysts. To facilitate the multiscale applications, I
will briefly present main features of our in-house computational tools, namely MultiSpecies-MultiChannel1
(MSMC) for complex gas-phase systems and Surfkin2 for gas-surface reactions.
Keywords: Multiscale, Modeling, Simulation, Gas-phase Chemistry, Materials Design, Thermodynamics and
Kinetics
References
[1] Duong, M. V.; Nguyen, H. T.; Truong, N.; Le, T. N. M.; Huynh, L. K. Multi-Species Multi-Channel (MSMC):
An Ab Initio-based Parallel Thermodynamic and Kinetic Code for Complex Chemical Systems. Int. J. Chem.
Kinet. 2015, 47 (9), 564-575; https://sites.google.com/site/msmccode/
[2] Le, T. N.; Liu, B.; Huynh, L. K. SurfKin: An ab initio kinetic code for modeling surface reactions. J. Comput.
Chem. 2014, 35 (26), 1890-9.
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The Third International Conference on
Computational Science and Engineering (ICCSE-3)
28-30 November, 2016, Ho Chi Minh City, Vietnam
I2.5
Skeletal Mechanisms Relevant to the Formation of Unsaturated
Intermediates in Combustion of Methyl Ester Fuel Surrogates
FAN-HSU KAO,1 HAIRONG TAO,2 KUANG C. LIN1
1
Department of Mechanical and Electro-Mechanical Engineering,
National Sun Yat-Sen University, Kaohsiung 80424, Taiwan
2
College of Chemistry, Beijing Normal University, Beijing, 100875, China
Email: [email protected]
In this study, a skeletal kinetic mechanisms for biodiesel fuel surrogates is developed for fuel oxidation that can
overcome the barrier of incorporating detailed chemistry to computational fluid dynamics (CFD) for fuel
combustion. This study begins from assembling mechanisms which are able to predict experimentally measured
methyl isobutyrate (MIB), polycyclic aromatic hydrocarbons (PAHs) and compound (C5H10). Then, we generate
a minimized skeletal mechanism using the path flux analysis method that determines a trade-off between the
accuracy and mechanism size. The newly derived compact mechanisms are examined in ignition delay time in 0D shock tube modeling, 1-D premixed burner flame, 1-D counterflow diffusion flame, and 2-D laminar diffusion
flame. We carry out the error analyses introduced by the removal of species and reactions from the detailed
mechanism. The rate of production (ROP) and sensitivity analysis (SA) are used to improve the predictions of
skeletal mechanisms. Moreover, the revised MIB skeletal mechanism are selected to be combined with the soot
sub model to obtain a skeletal mechanism which is able to predict the heavy PAHs and soot formation in pure
methane flame and methane/air diffusion flame doped with MIB.
Keywords: Biodiesel, Chemical Kinetic, Combustion, Computational Fluid Dynamics, Methyl Ester, Mechanism
Reduction, Polycyclic Aromatic Hydrocarbons, Soot.
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The Third International Conference on
Computational Science and Engineering (ICCSE-3)
28-30 November, 2016, Ho Chi Minh City, Vietnam
I2.6
Mechanisms and Kinetics of Some Reactions Related to Atmospheric and
Combustion Chemistry
NGUYEN THI MINH HUE
Faculy of Chemistry and Center for Computational Science, Hanoi National University of Education, 136 Xuan
Thuy, Cau Giay, Hanoi, Viet Nam
Email: [email protected]
In this talk we present our recent results obtained using both high accuracy molecular orbital and density functional
methods to determine the potential energy surfaces, and the kinetics and mechanisms of a series of gas phase
reactions involving small organic species and related to the atmospheric chemistry and combustion processes.
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The Third International Conference on
Computational Science and Engineering (ICCSE-3)
28-30 November, 2016, Ho Chi Minh City, Vietnam
I2.7
Computational Design for Advanced Materials in Environmental
Applications
SUPAWADEE NAMUANGRUK
Nanoscale simulation laboratory (SIM), NANOTEC, National Science and Technology Development Agency,
Klong Luang, Pathum Thani 12120, Thailand
E-mail: [email protected]
Understanding insight to the molecular level of chemical processes in nanomaterials is a key of development of
nanomaterials for specific purpose. Generally, the development of nanomaterials is essential in novel technologies
to address challenges related to the production, storage and efficient use of energy, as well as environmental
applications. However, the design, development and commercialization of a new material can take several
years. To accelerate functional material development, molecular simulation is a powerful tool that can help explore
the nanomaterial at a significantly faster rate and lower cost than it can typically be done experimentally. This
helps experimentalist focus only on the most promising materials. Here, deep understanding of the adsorption
and reaction mechanism of toxic compounds at nanoscale are shown by molecular modelling and simulations.
Through computational design and calculation, promising materials were suggested, such as catalysts for NOx
decomposition as well as adsorbents for elemental mercury (Hg 0) removal, before they are synthesized by
experimentalist.
Figure 1. Understanding synergetic effect of TiO2-supported silver nanoparticle as a sorbent for Hg0 removal
References
[1] Rungnim, C; Hannongbua, S; Promarak, V; Kungwan, N; Namuangruk, S. J. Hazardrous Mater. 310 (2016)
253-260.
[2] Rungnim, C.; Meeprasert, J.; Kunaseth, M.; Junkaew, A.; Khamdahsag, P.; Khemthong, P.; Pimpha, N.;
Namuangruk, S. Chem. Eng. J, 274 (2015) 132-142.
[3] Maitarad, P; Meeprasert, J.; Han, J.; Shi, L.; Limtrakul, J.; Zhang, D.; Namuangruk, S. Catal. Sci. Technol.
2016, DOI: 10.1039/C5CY02116B
[4] Meeprasert, J.; Junkaew, A.; Rungnim, Meeprasert, J.; C.; Kunaseth, M.; Namuangruk, S. Appl. Surf. Sci., 364
(2016) 166–175.
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The Third International Conference on
Computational Science and Engineering (ICCSE-3)
28-30 November, 2016, Ho Chi Minh City, Vietnam
I2.8
Ab-initio Methods for Time-Resolved Attosecond Dynamics of
Laser-Driven Many-Electron Molecules
THANH TUNG NGUYEN-DANG
Département de Chimie, Université Laval, Québec, G1K7P4, Qc, Canada
Email: [email protected]
Ultrafast spectroscopic and imaging schemes using short and intense laser pulses hold great promises in Chemical
Physics, as the matching of the durations of these pulses with the characteristic periods of molecular motions
means that one can take snapshots and videos of these motions on their natural time-scales. Molecular and/or
electronic processes unfolding under an ultrafast intense laser pulse are highly non-linear however, and their
descriptions require new non-perturbative theoretical and computational tools to be developed. After reviewing
these new challenges in theoretical chemistry, we will focus on the description of time-resolved multi-electron,
attosecond dynamics by an ab-initio approach, highlighting in particular the way a number of powerful tools of
stationary-state Quantum Chemistry can be adapted to suit the new context, that of time-dependent nonperturbative electron dynamics. Results of calculations on a number of few electron systems, in particular ionicchannel-resolved photoelectron spectra resulting from strong field molecular ionizations under a few-cycle NIR
and/or XUV pulse, will be shown to illustrate the concepts and methodological ideas developed throughout the
talk.
Keywords: Time-Dependent Quantum Mechanics, Electron Dynamics, Intense-Field Ionization, TDCI, Feshbach
Partitioning
9
The Third International Conference on
Computational Science and Engineering (ICCSE-3)
28-30 November, 2016, Ho Chi Minh City, Vietnam
I2.9
Inclusion Complexation of Insoluble Compounds with
Cyclodextrins
THANYADA RUNGROTMONGKOL
Structural and Computational Biology Research Group, Department of Biochemistry, Faculty of Science,
Chulalongkorn University, Bangkok 10330, Thailand
Email: [email protected]
Pinostrobin is widely found in the ginger family and adopted in traditional Thai medicine, while fisetin is abundant
in strawberry and mango. Besides the known antioxidant and anti-inflammatory properties of flavonoids,
pinostrobin shows the HIV-1 and HSV-1 antiviral activity and cytotoxic activity against tumor cells. Fisetin has
the cancer preventive properties and potential therapeutic use for the diabetic treatment. However, these
flavonoids show relatively low solubility and low physicochemical stability, leading to difficulties in
pharmaceutical and biomedical applications. By complexation with cyclodextrin, the solubility enhancement of
pinostrobin and fisetin is our main aim. Both experimental and theoretical approaches are applied. The complexes
between flavonoid and various cyclodextrins (both natural and modified cyclodextrins) are prepared, and followed
by measurement of the spectroscopic details and thermodynamics properties (1-3). The solubility of the inclusion
complexes is determined in comparison with the flavonoid alone. Besides the complex geometry obtained from
experiments, the molecular dynamics simulations are performed in order to investigate the structure and stability
of inclusion complex, as well as intermolecular interaction between each flavonoid and cyclodextrin (4,5). In
addition to the pharmaceutical and biomedical benefits, the results of this research would increase the values of
both flavonoid and cyclodextrin which are rich natural resources in Thailand with a consequence of local economy
development.
Keywords: Inclusion complex, Interaction, Stability, Anticancer activity
References
[1] Sangpheak W., Khuntawee W., Wolschann P., Pongsawasdi P. and Rungrotmongkol T. “Enhanced stability
of naringenin/2,6-dimethyl β-cyclodextrin inclusion complex: Molecular dynamics and free energy
calculations based on MM- and QMPBSA/GBSA” J. Mol. Graph Model, 50, 10–15 (2014).
[2] Sangpheak W., Kicuntod J., Schuster R., Rungrotmongkol T., Wolschann P., Kuawan N., Viernstein H.,
Mueller M. and Pongsawasdi P. “Physical properties and biological activities of hesperetin and naringenin in
complex with methylated β-cyclodextrin” Beilstein J. Org. Chem., 11, 2763–2773 (2015).
[3] Rungnim C., Phunpee S., Kunaseth M., Namuangruk S., Rungsardthong K., Rungrotmongkol T. and
Ruktanonchai U. “Co-solvation effect on the binding mode of the α-mangostin/β-cyclodextrin inclusion
complex” Beilstein J. Org. Chem., 11, 2306–2317 (2015).
[4] Nutho B., Khuntawee W., Rungnim C., Pongsawasdi P., Wolschann P., Karpfen A., Kungwan N. and
Rungrotmongkol T. “Binding mode and free energy prediction of fisetin/β-cyclodextrin inclusion complex”
Beilstein J. Org. Chem., 10, 2789–2799 (2014).
[5] Kicuntod J., Khuntawee W., Wolschann P., Pongsawasdi P., Kuawan N. and Rungrotmongkol T. “Inclusion
complexation of pinostrobin with various cyclodextrin derivatives” J. Mol. Graph Model, 63, 91–98 (2016).
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The Third International Conference on
Computational Science and Engineering (ICCSE-3)
28-30 November, 2016, Ho Chi Minh City, Vietnam
I2.10
Theoretical Rate Coefficient Calculation for Reactions of Criegee
Intermediate with Atmospheric Trace Gases
FRANK YIN, KAITO TAKAHASHI*
Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei 10617, Taiwan
E-mail: [email protected]
Atmospherically relevant carbonyl oxide R1R2COO, so-called Criegee intermediates (CIs), can have many
different forms depending on the substituents R1 and R2. These strong oxidizing species are the key intermediate
in the ozonolysis of different kinds of alkenes in the atmosphere. Due to CI’s active participation in atmospheric
chemistry, such as oxidation, aerosol formation and OH radical production, the atmospheric fate of this very
reactive species is a very important topic. However, presently there are no effective methods to measure the CI
concentration in the atmosphere. Thus the only way to know the CI concentration is through the rate of its
production and removal. Considering the abundance of water in the atmosphere, the reaction rate of CIs and
water vapor is a very important quantity to accurately model the removal rate of CI. In this study we theoretically
calculated the rate coefficient of the reaction between CI and atmospheric trace gases such as water vapor. By
comparing the results for (CH3)2COO as well as CH3CH2CHOO versus those for CH3CHOO we evaluate the
effect attaching additional methyl substitution in C3 CIs. Furthermore, by studying the reaction for CH 2CHCHOO
and CHCCHOO with water vapor, we evaluate the effect of the pi conjugation toward the reactivity.
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The Third International Conference on
Computational Science and Engineering (ICCSE-3)
28-30 November, 2016, Ho Chi Minh City, Vietnam
I2.11
Theoretical Study on the Catalytic Reduction Mechanism of NO
by CO catalyzed by Ag7Au6 Cluster
SIRIPORN JUNGSUTTIWONG,1 YUTTHANA WONGNONGWA,1 SUPAWADEE NAMUANGRUK2
1
Department of Chemistry andCenter of Excellence for Innovation in Chemistry, Faculty of Science, Ubon
Ratchathani University, Ubon Ratchathani 34190, Thailand.
2
National Nanotechnology Center, National Science and Technology Development Agency,
Klong Luang, Pathumthani 12120, Thailand
E-mail: [email protected]
The reaction mechanism of NO catalyzed by CO on Ag7Au6 cluster has been systematically investigated on the
ground and first excited states at the PBE/TZVP, lanl2dz level. This reaction is mainly divided into two reaction
stages, NO deoxygenation to generate N2O and then the deoxygenation of N2O with CO to form N2 and CO2. The
crucial reaction step deals with the NO deoxygenation to generate N2O catalyzed by Ag7Au6 cluster, in which the
deoxygenation of NO by CO reaction pathway is kinetically more preferable than that in the absence of CO. These
results can qualitatively explain the experimental finding of N2O, N2, NCO and CO2 species in the NO by CO
reaction.
Figure 1. The energy diagrams for the NO deoxygenation with CO catalyzed by Ag7Au6 Cluster
Keywords: catalytic reduction, NO by CO reaction, Ag7Au6 cluster
12
The Third International Conference on
Computational Science and Engineering (ICCSE-3)
28-30 November, 2016, Ho Chi Minh City, Vietnam
I2.12
Structural Evolution in Methylammonium Lead Iodide
CH3NH3PbI3
KHUONG P. ONG,1 TECK WEE GOH,2 GIANG XU,2 ALFRED HUAN1
1
Institute of High Performance Computing, Agency of Science, Technology and Research (A*STAR), 1
Fusionopolis Way, 138632, Singapore
2
Division of Physics and Applied Physics, School of Physical and Mathematical Sciences, Nanyang
Technological University, 21 Nanyang Link, 637371 Singapore
Email: [email protected]
Abstract
With the average growth of 40 percent per year, solar energy has been growing at a remarkable rate. The prospect
for sustaining such growth is based on the possible constraints on materials availability. Recently, the organometal
lead halide hybrid perovskite, with main focus on methylammonium lead iodide perovskite (MAPbI 3), has been
identified as a suitable candidate for use as active material in solar cells. Solar cell performance using this material
has seen tremendous progress, from power conversion efficiency of 3.8% to over 20% in a relatively short time
of dedicated photovoltaic research. Theoretical and experimental researches have achieved much of progress in
understanding electronic structures, chemical bonding, Rashba effect toward to optimizing the best performance
for MAPbI3. In this work, through first principle calculations we identify the mechanical origin of the structural
evolution and the interplay between the various MA cation orientations in the methylammonium lead iodide
perovskite (MAPbI3) to the band structures and optical properties of MAPbI3. Our study provides clear
understanding for the structural phase transitions and their influence on the performance of MAPbI3
Figure 1. Structural evolution in MAPbI3
Keywords: hybrid perovskite, photovoltaics, density functional theory, phase transitions, optical properties
13
The Third International Conference on
Computational Science and Engineering (ICCSE-3)
28-30 November, 2016, Ho Chi Minh City, Vietnam
I2.13
First Principles Study of Hydrogen Production and Storage
NACHIMUTHU SANTHANAMOORTHI, HSIN-NI CHIANG, PO-JUNG LAI,
JYH-CHIANG JIANG
Department of Chemical Engineering, National Taiwan University of Science and Technology, Taipei, 106,
Taiwan
Email: [email protected]
Abstract
In the current energy research, hydrogen, the most abundant element in the universe is considered as a “green
fuel” because, it burns cleanly without emitting any environmental pollutants and is considered as a most viable
energy source. H2 can be produced from different sources, e.g., coal, natural gas, liquefied petroleum gas (LPG),
propane, methane (CH4), dry biomass, biomass-derived liquid fuels (such as methanol, C2H5OH, biodiesel), as
well as from water. Among the liquid H2 sources, C2H5OH and water are good candidates due to its low toxicity
and easily available in nature etc,. Here we proposed H2 production from steam reforming by C2H5OH. Steam
reforming is the first step of the H2 production process involves a light hydrocarbon reacting with steam. The
second step, known as a water gas shift (WGS) reaction, the CO produced in the first reaction is reacted with
steam over a catalyst to form H2 and CO2. We used DFT methods to investigate the mechanism of the WGS
reaction on a model consisting of 3Cu atom-cluster on an 3Cu/α-Al2O3(0001) surface. Here we propose three
reaction mechanisms, such as redox, carboxyl and formate, have been examined and we found that the H2
formation barrier is extremely low, 0.65 eV, on this surface. However, storage of hydrogen under appropriate
conditions is the challenging problem in the modern research. In this present study we propose a new strategy in
which we considered three transition metal (TM) atoms with high, medium and low hydrogen adsorption energies.
These TM atoms are used to decorate the Boron doped graphene sheet and our results show that the activation
energies for H atom diffusion are much smaller than the previously reported values, indicating that a fast H
diffusion on this proposed surface can be achieved.
14
The Third International Conference on
Computational Science and Engineering (ICCSE-3)
28-30 November, 2016, Ho Chi Minh City, Vietnam
I2.14
Square-Triangle Solid-Solid Phase Transition
in 2D Simple System
VO VAN HOANG
Computational Physics Lab, HCM City Univ. of Technology,
Vietnam National Univ. HCM City, 268 Ly Thuong Kiet Street, District 10, HCM City, Vietnam
Email: [email protected]
Square-triangle solid-solid phase transition in 2D simple monatomic system is studied by molecular dynamics
(MD) simulation in models containing 6400 particles interacted via square potential [1]. Initial equilibrium models
with a square lattice structure obtained at low temperature are compressed step by step and we find a squaretriangle solid-solid phase transition in the system. Evolution of structure and various thermodynamic behaviors
upon compression is analyzed in details in order to study atomic mechanism of this solid-solid phase transition.
We find a quite new mechanism of formation of new phase (triangular one), i.e. nucleation of new phase is not
homogeneous. Atoms involving in triangles do not occur homogeneously throughout in the model, instead, they
form some separated domains in the parent phase. Further growth of these domains together with
formation/growth of new ones leads to the percolation of new phase. Our detailed MD simulation highlights the
situation related to the role of ‘liquidlike’ atoms in the nucleation of solid-solid phase transition found recently
[2,3]. Solid-solid phase transitions are important in science and technology including the earth science, diamond
and steel production or synthesis of ceramic materials, however, understanding of nature of these important phase
transitions at the atomic level is still poor. Therefore, detailed MD simulation in this direction is of great interest.
References
[1] M. Rechtsman et al., Phys. Rev. E 73, 011406 (2006).
[2] Yi Peng et al., Nature Mater. 14, 101 (2015).
[3] D.M. Hatch et al., Phys. Rev. Lett. 115, 185701 (2015).
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The Third International Conference on
Computational Science and Engineering (ICCSE-3)
28-30 November, 2016, Ho Chi Minh City, Vietnam
CONTRIBUTED TALKS
16
The Third International Conference on
Computational Science and Engineering (ICCSE-3)
28-30 November, 2016, Ho Chi Minh City, Vietnam
O2.1
Geometrical and Electronic Structures of MnSn−/0 (n =1 - 3)
Clusters from Computational Chemistry and Anion
Photoelectron Spectroscopy
VAN TAN TRAN, QUOC TRI TRAN
Department of Chemistry, Dong Thap University,
Cao Lanh City, Dong Thap, Viet Nam
Email: [email protected]
The geometrical and electronic structures of the MnSn−/0 (n = 1 - 3) clusters were probed by the photoelectron
spectroscopy a long time ago.[1] However, the reported photoelectron spectra are not fully understood. In this
work, the geometrical and electronic structures of MnSn−/0 (n = 1 - 3) clusters are investigated with the B3LYP
functional, ROHF/CCSD(T), CASSCF/NEVPT2, and CASSCF/CASPT2 methods.[2-4] The relative energies,
structural parameters, and harmonic vibrational frequencies and normal modes of the low-lying states of the most
important isomers of the studied clusters are reported. Also, the electron detachment energies of the anionic
clusters are calculated. Based on the computational results, the photoelectron spectra of MnS −, MnS2−, and MnS3−
are interpreted. The low-lying bands in the photoelectron spectra of MnS− cluster are assigned to the electron
detachments from the 7Σ+ anionic ground state. All features in the photoelectron spectra of MnS 2− cluster are
ascribed to the electron detachments from the 5Πg of the most stable linear SMnS− isomer and from the 7A1 of the
meta stable cyclic η2-MnS2− isomer. The photoelectron spectra of MnS3− cluster are explained by the electron
detachments from the most stable η2-(S2)MnS− and from the less stable η2-(S3)Mn− and triangle MnS3− isomers.
The Franck-Condon factor simulations based on the B3LYP geometrical structures and harmonic vibrational
frequencies and modes confirm the shapes of the low-lying bands in the photoelectron spectra of MnSn− (n = 1 3) clusters.
Figure 1. Geometries of the low-lying isomers of MnSn−/0 (n = 1 - 3) clusters
Keywords: MnSn−/0 (n = 1 - 3) clusters, geometrical structure, electronic structure, CASPT2, DFT
References
[1] N. Zhang, H. Kawamata, A. Nakajima, K. Kaya, J. Chem. Phys. 1996, 104, (1), 36.
[2] V.T. Tran, Q.T. Tran, M.F.A. Hendrickx, J. Phys. Chem. A 2015, 119, (22), 5626.
[3] V.T. Tran, Q.T. Tran, J. Phys. Chem. A 2016, 120, (20), 3670.
[4] V.T. Tran, Q.T. Tran, M.F.A. Hendrickx, Chem. Phys. Lett. 2015, 627, 121.
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The Third International Conference on
Computational Science and Engineering (ICCSE-3)
28-30 November, 2016, Ho Chi Minh City, Vietnam
O2.2
Data-Mining and Machine-Learning in Materials Science
PHAM TIEN LAM, 1, 2, 3, DAM HIEU CHI1, 3, 4, 5
1
Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa 923-1292, Japan
Institute for Solid State Physics, The University of Tokyo, Kashiwanoha 5-1-5, Kashiwa, Chiba 277-8581,
Japan
3
ESICMM, National Institute for Materials Science, 1-2-1 Sengen, Tsukuba, Ibaraki 305-0047, Japan
4
Center for Materials Research by Information Integration, National Institute for Materials Science, 1-2-1
Sengen, Tsukuba, Ibaraki 305-0047, Japan
5
JST, PRESTO, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
Email: [email protected]
2
Recently, the increasing volume of available experimental and quantum computational materials databases
together with the development of machine learning techniques open up a new opportunity to build automatic
methods for discovering new materials and new phenomena. In this talk, we give a short overview of the
application of data mining and machine-learning in material science. We discuss how machine learning can be
applied in predicting physical properties, finding the mechanism of a property or function (structure-property
relationship modeling), and exploring and visualizing in materials space. In order to apply machine-learning
algorithms materials science issues, we focus on the methods for encoding materials and finding materials
similarity. Our research demonstrates that knowledge of chemical physics on a materials system can be
automatically extracted from the experimental or calculated data using data mining techniques. Dimensional
reduction algorithms, e.g. principle component analysis (PCA) and manifold learning, is employed to discover
the low-dimensional embedding and the high-dimensional data. This new representation is used to visualize the
materials space and to find the pattern of material systems. It is shown that the machine-learned knowledge can
be utilized to construct simple models for predicting physical properties of a chemical system. By using advanced
regression algorithms, the parameters determining physical properties is derived from materials datasets.
18
The Third International Conference on
Computational Science and Engineering (ICCSE-3)
28-30 November, 2016, Ho Chi Minh City, Vietnam
O2.3
A Theoretical Investigation on Interactions of Cisplatin and a
Novel Derivative with the Nucleobase Guanine
PHAM VU NHAT
Department of Chemistry, College of Natural Sciences,
Can Tho University, Can Tho, Viet Nam
Email: [email protected]
Quantum chemical calculations are employed to examine the interactions of hydrolysis products of cisplatin and
a novel derivative cis-[PtCl2(iPram)(Hpz)] with the purine base site of DNA using guanine as a model reactant.
Thermodynamic parameters, electronic structures, bonding characteristics and spectroscopic properties of the
resulting complexes are investigated in the framework of density functional theory (B3LYP functional) along with
correlation consistent basis sets. Computed results show that these interactions are dominated by electrostatic
effects, namely H-bond contributions, and there exists a flow charge from H atoms of ligands to the O6 guanine.
Another remarkable finding is that the replacement of amine groups by larger ones accompanies with a moderate
reaction between PtII and guanine molecule.
Figure 1. Vibrational signatures of [Pt(iPram)(Hpz)(H2O)Cl]+ (above) and [Pt(iPram)(Hpz)(G)Cl]+ (below) in
their lowest-lying states
Keywords: Cisplatin, Density Functional Theory, Guanine, Anticancer, Hydrogen Bonding
19
The Third International Conference on
Computational Science and Engineering (ICCSE-3)
28-30 November, 2016, Ho Chi Minh City, Vietnam
O2.4
Density Functional Theory Modeling of Luminescent Properties
of Oligoatomic Silver Clusters in LTA Zeolite
NGO TUAN CUONG,1 PHAM HO MY PHUONG,2 NGUYEN THI MINH HUE1
1
Faculty of Chemistry and Center for Computational Science, Hanoi National University of Education, Vietnam
2
Institute for Computational Science and Technology, Ho Chi Minh City, Vietnam
Email: [email protected]
Optical spectra in the UV-VIS region of the hydrated doubly charged tetramer Ag42+ and hydrated multiply
charged hexamer Ag6p+ silver clusters encapsulated inside the sodalite cavity of LTA-type zeolite have been
systematically investigated using DFT, TD-DFT and CASSCF/CASPT2 methods. Absorption spectrum of
Ag42+(H2O)m cluster in sodalite cage reproducing the experimental absorption spectrum in the region from 300 to
600 nm. The average lengths of Ag-Ag and Ag-OH2 bonds are in good agreement with EXAFS results. The water
environment forces the silver tetramer to relocate in one side of the cavity instead of at its center as in the case of
non-hydrated [Ag4(Si24H24O36)]2+ cluster, and acts as ligands significantly splitting the energy levels of excited
states of the clusters. This causes the absorption spectra of the clusters to broaden and the emission to shift to the
green-yellow and red part of the visible region.
20
The Third International Conference on
Computational Science and Engineering (ICCSE-3)
28-30 November, 2016, Ho Chi Minh City, Vietnam
O2.5
Physical Insights of Coadsorption SO2 and CO2 in Metal–Organic
Framework Material Ni(bdc)(ted)0.5
DO NGOC SON, TA THI THUY HUONG
Ho Chi Minh City University of Technology,
VNU-HCM, Ho Chi Minh City, Vietnam
Email: [email protected]
Metal organic framework Ni(bdc)(ted)0.5 is a promising material for the simultaneous capture and reduction of the
harmful gases SO2 and CO2. Experiment found that SO2 competes much stronger than CO2 when they co-adsorb
in Ni(bdc)(ted)0.5; however, this observation still lacks the physical insights that can be explained through the
detailed analyses on the electronic structures obtained from the density functional theory calculations. More
details will be presented at the conference.
Keywords: Metal Organic Framework, Carbon Dioxide, Sulfur Dioxide, Electronic Structure, Density Functional
Theory
21
The Third International Conference on
Computational Science and Engineering (ICCSE-3)
28-30 November, 2016, Ho Chi Minh City, Vietnam
O2.6
Density-Functional Theory Studies on Activation and Reactions
of Light Alkanes over IrO2 (110) Surface
THONG LE MINH PHAM,1 JYH-CHIANG JIANG2
1
Institute of Research and Development, Duy Tan University, 03 Quang Trung, Da Nang, Viet Nam
Department of Chemical Engineering, National Taiwan University of Science and Technology, 43, Keelung
Road, Section 4, Taipei 106, Taiwan
Emails: [email protected]
2
The capability to activate light alkanes at mild temperature and selectively control the oxidation reactions are
defined the characteristic of an efficient catalyst for the direct oxidation of light alkanes to value-added products.
IrO2 (110) surface, which possesses coordinatively unsaturated iridium and oxygen sites, is expected to be a
potential catalyst to activate light alkanes at mild temperature. As a complement for experimental work, theoretical
investigation by periodic density functional theory (DFT) calculation with slab model has gradually become the
cornerstone for explaining and predicting atomic surface phenomena, such as adsorption, diffusion and chemical
reaction. In this work, we employed density functional theory calculations to explore the activation of methane
and ethane on the IrO2 (110) surface. The possible reaction pathways of methane and ethane on the IrO 2 (110)
surface were also investigated. Furthermore, the adsorption characeristics of CH x (x=1-4) and C2H6 on the IrO2
(110) surface were investigated by analysing plots of density of states (DOS) and electron density difference
(EDD) contours. Our work has provided an initial basis for understanding and designing efficient catalyst for the
direct conversion of methane and ethane to the valuable compounds under mild temperature.
Keywords: methane, ethane, C-H activation, IrO2(110), DFT
References
[1] J.J. Siirola, The Impact of Shale Gas in the Chemical Industry, AIChE Journal, 60 (2014) 810-819.
[2] Y. Yao, D. Graziano, M. Riddle, J. Cresko, E. Masanet, Greener Pathways For Energy-Intensive Commodity
Chemicals: Opportunities and Challenges, Current Opinion in Chemical Engineering, 6 (2014) 90-98.
[3] G. Centi, F. Cavani, F. Trifirò, Selective Oxidation by Heterogeneous Catalysis, Springer US, 2001.
[4] Pham, T. L. M.; Leggesse, E. G.; Jiang, J. C., Ethylene Formation by Methane Dehydrogenation and C-C
Coupling Reaction on a Stoichiometric IrO2 (110) Surface - a Density Functional Theory Investigation.
Catalysis Science & Technology 2015.
22
The Third International Conference on
Computational Science and Engineering (ICCSE-3)
28-30 November, 2016, Ho Chi Minh City, Vietnam
O2.7
Colloidal Semiconductor Nanomaterials and Their Optoelectronic
Applications
(STEVE) CUONG DANG
Centre of Excellence for Semiconductor Lighting and Displays,
School of Electrical and Electronic Engineering, The Photonics Institute (TPI),
Nanyang Technological University, 50 Nanyang Ave., 639 798, Singapore
Email: [email protected]
Colloidal semiconductor nanomaterials are unique material class having wide bandgap tune-ability, stability of
inorganic materials and low-cost, flexible manufacture of solution processing materials. Disruptive colloidal
quantum dot (QD) technology has found the way from the lab curiosities to the electronic products in shopping
centres. In this talk, we will discuss the current state of the art and the future of nanocrystal light emitting devices
covering all the intensity levels from quantum light emitters, light emitting diodes (LED) to lasers. At the single
particle levels, nanocrystals are artificial atoms and emitting single photons on demand, such long-sought quantum
sources are important for quantum technologies and quantum securities. Ensemble nanocrystal films can be
processed as active layers following the flexible organic LED architectures to be quantum dot LEDs (QLED) with
the stability advantages of inorganic active materials. Because of huge advantages in lighting and display
technologies, QLEDs are actively investigated in both academia and industry. Finally, the most advanced light
emitting devices (i.e. lasers) are now can be enabled by the most cost-effective technology (i.e. colloidal process)
thanks to semiconductor nanocrystals. Unlike current semiconductor lasers which require at least three different
technologies and materials to cover the red, green and blue colour, recent breakthroughs in the nanocrystal lasers
has promised “long sought” full-colour single-material lasers. Beside these conventional materials, new
semiconductor nanocrystals with novel structures such as nanoplatelets, quantum rings are actively investigated
from both material theoretical modelling and engineering communities.
23
The Third International Conference on
Computational Science and Engineering (ICCSE-3)
28-30 November, 2016, Ho Chi Minh City, Vietnam
POSTERS
24
The Third International Conference on
Computational Science and Engineering (ICCSE-3)
28-30 November, 2016, Ho Chi Minh City, Vietnam
P2.1
̅0) Surface
A Theoretical Study on Metal Atoms Doped ZnO (10𝟏
for CO Sensing
EN-WEI CHOU, SANTHANAMOORTHI NACHIMUTHU, JYH-CHIANG JIANG*
Department of Chemical Engineering, National Taiwan University of Science and Technology, Taipei, Taiwan
Email:[email protected]
Carbon monoxide (CO) is one of the most dangerous gases present in indoor and outdoor air. CO is highly toxic
gas which is colorless, odorless and difficult to dissolve in water. It is commonly found in the emission of
automobile exhausts and the burning of domestic fuels. [1] Hence, in order to maintain the indoor and outdoor air
quality and to detect early fires CO sensors are essential. Previously number of different types of CO sensors have
been designed. However, developing gas sensors for industrial environments is rather challenging because the
sensors must be both highly sensitive and selective. Recently, metal oxides (MOs) have attracted a great attention
for gas sensing because of their low-cost, high surface to volume ratios, excellent sensitivity, structural stability,
and good mechanical flexibility. [2] Among them, ZnO has been widely investigated for the detection of CO,
which can sense CO by means of chemisorption of oxygen with surface and further reaction occurs between
adsorbed oxygen and the analyze gas.[3] However, this reaction requires higher temperature. Previously, many
efforts have made to reduce the operating temperature, which include doping the metal oxide with noble metals
and applying an electrostatic field and found that doping metals on metal oxides is the most favorable. Hence, in
this study, we considered the doping of different metal atoms such as Cr (Chromium), Ni (Nickel), Ti (Titanium),
and Al (Aluminum) on ZnO and investigated their CO sensing behavior using density functional theory
calculations. We have calculated the adsorption energies of CO on different metal atoms doped ZnO surface and
also analyzed the electronic properties using density of states (DOS) as in Fig 1, and electron density difference
(EDD) contour plots. Our DFT results show that the d orbital of the dopant atoms strongly influences the
adsorption of CO on the surface. We found that metal atoms doping increases the adsorption energy of CO
compared to pure ZnO surface and among the different metal atoms, Ti atom doping has stronger CO adsorption
energy, which is due to the strong interaction between the surface and CO. The interaction between the metal
atoms and CO are confirmed by the DOS and EDD plots. Our results confirm that the sensing properties of an
oxide material can be modified by means of suitable doping and Ti doped ZnO will be the suitable material to
detect CO at room temperature.
̅𝟎) surface.
Figure 1. Adsorption of CO on Ti doped ZnO(10𝟏
Keywords: CO Sensing, Adsorption, Metal Oxides, Density Functional Theory, Doping
References
[1] H Gong, J Q Hua, J H Wang, C H Ong and F R Zhu, Sensors Actuators B, 2006, 115, 247–251.
[2] Z. Zhang, R. Zou, G. Song, L. Yu, Z. Chen, J. Hu, J. Mater. Chem. 2011, 21, 17360-17365.
[3] M Hijiri, L El Mir, S G Leonardi, N Donato and G Neri, Nanomaterials 2013, 3, 357-369.
25
The Third International Conference on
Computational Science and Engineering (ICCSE-3)
28-30 November, 2016, Ho Chi Minh City, Vietnam
P2.2
Double Carbon-Doped Hexagonal Boron-Nitride as Efficient
Metal-Free Catalysts for Oxygen Reduction Reaction:
A Theoretical Study
NGUYEN THI BICH DUYEN,1 TRAN NGUYEN LAN1,2
1
2
Ho Chi Minh City Institute of Physics, VAST, Ho Chi Minh City, Vietnam
Departments of Physics and Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
Email: [email protected]
Fuel cells have attracted significant attention due to their high efficiency and low pollution. Conventionally,
platinum (Pt) and its alloys have been used as catalysts to promote the chemical reactions. However, Pt-based
catalysts are expensive and unstable. Therefore, the development of cheap and stable catalysts for oxygen
reduction reaction (ORR) is crucial for large-scale commercial applications of fuel cells. Carbon-based catalysts
have been extensively investigated [1, 2]. Recently, hexagonal boron-nitride (h-BN) on metal-surface and hBN/graphene hybrid were shown to be efficient catalysts for ORR [3, 4]. In this study, we theoretically
demonstrate that C-doped h-BN can be alternatively used as novel and efficient catalysts for ORR. For theoretical
explanation, we used a model of C-doped BN nanoflakes (BNNFs). We found that all reactions can proceed via
the four-electron pathway, which is more efficient than the two-electron one. The waters formed are easily
released from the system and the initial structure of catalysts is able to recover after finishing OOR as well as
ready for the next catalytic process. Different reaction pathways and different doped positions (N or B atoms)
were considered. The most importantly, we show that the double C-doped BNNFs are more efficient than single
C-doped ones, which have been studied very recently [5, 6]. Our theoretical results are expected to be useful for
experiments.
O2
+4H++4e-
2H2O
Figure 1. The overall ORR via four-electron reaction pathway (O2 + 4H+ + 4e-  2H2O) using double C-doped
BNNFs as catalyst
Keywords: Metal-free catalysts, Boron nitride nanoflakes, Oxygen reduction reaction, Fuel cells
References
[1]. L. Zhang and Z. Xia, J. Phys. Chem. C 2010 115, 11170
[2]. L. Zhang, J. Niu, L. Dai, and Z. Xia, Langmuir 2012 28 7542
[3]. K. Uosaki, G. Elumalai, H. Noguchi, T. Masuda, A. Lyalin, A. Nakayama, and T. Taketsugu, J. Am. Chem.
Soc. 2014 136 6542
[4]. Q. Sun, C. Sun., A. Du, S. Dou, and Z. Li, Nanoscale 2016 8 24084
[5]. J. Zhao and Z. Chen, J. Phys. Chem. C 2015 119 26348
[6]. M. Gao, M. Adachi, A. Lyalin, and T. Taketsugu, J. Phys. Chem. C 2016 120 15993
26
The Third International Conference on
Computational Science and Engineering (ICCSE-3)
28-30 November, 2016, Ho Chi Minh City, Vietnam
P2.3
Capture of Carbon dioxide in Material of Institut Lavoisier-127
by Computational Chemistry Calculations
T. CHOKBUNPIAM,1 P. PONGSAJANUKUL,2 S. FRITZSCHE,3 S. ASSABUMRUNGRAT,4
S. WONGSAKULPHASATCH,5 T. BOVORNRATANARAKS,6 V. PARASUK2
1
Ramkhamhaeng University, Department of Chemistry, Faculty of Science, Bangkok 10240, Thailand
Chulalongkorn University, Computational Chemistry Unit Cell (CCUC), Department of Chemistry, Faculty of
Science, Bangkok 10330, Thailand
3
University of Leipzig, Institute of Theoretical Physics, Faculty of Physics and Geosciences, Postfach 100920,
D- 04009 Leipzig, Germany
4
Chulalongkorn University, Center of Excellence in Catalytic Reaction Engineering, Department of Chemical
Engineering, Faculty of Engineering, Bangkok 10330, Thailand
5
King Mongkut’s University of Technology North Bangkok, Department of Chemical Engineering, Faculty of
Engineering, Bangkok 10800, Thailand
6
Chulalongkorn University, Department of Physics, Faculty of Science, Bangkok 10330, Thailand
Email: [email protected]
2
Carbon dioxide (CO2) belongs to the most outstanding air pollutants that cause environment pollution and health
risk for human and animals. More important is its emission from industrial processes and from internal combustion
engines burning fossil fuels. Therefore, the porous metal organic frameworks namely Material of Institut Lavoisier
-127 (MIL-127) was investigated in this work for CO2 capture because of large surface area, high porosity and
high thermal stability [1]. The adsorption and diffusion of CO2 in the MIL-127 were studied by Molecular
Dynamics (MD) and Gibbs Ensemble Monte Carlo. Several interaction force fields have been calculated and an
optimal one has been proposed. The adsorption site of CO 2 was found at metal oxide of MIL-127. Moreover, the
self diffusion coefficient (around 2-3x10-9 m2/s) increases slightly with increasing concentration while at higher
concentrations it declines as a consequence of mutual hindrance of the CO2 molecules.
Figure 1. The structure of MIL-127 in 8 unit cells was constructed from X-Ray crystal data
Keywords: Material of Institut Lavoisier -127 (MIL-127), Carbon dioxide (CO2), Adsorption and diffusion
References
[1] Wongsakulphasatch, S.; Nouar, F.; Rodriguez, J.; Scott, L.; Le Guillouzer, C.; Devic, T.; Horcajada, P.;
Greneche, J. M.; Llewellyn, P. L.; Vimont, A.; Clet, G.; Daturi, M.; Serre, C. Direct Accessibility of MixedMetal (III/II) Acid Sites through the Green, Scalable and Rational Synthesis of Porous Metal Carboxylates.
Chem. Commun. 2015, 51, 10194-10197
27
The Third International Conference on
Computational Science and Engineering (ICCSE-3)
28-30 November, 2016, Ho Chi Minh City, Vietnam
P2.4
Boron and Nitrogen Doped Graphene as a Counter Electrode for
Iodine Reduction in Dye-Sensitized Solar Cells:
A Theoretical Study
KUAN-YU LIN, SANTHANAMOORTHI NACHIMUTHU, JYH-CHIANG JIANG
Department of Chemical Engineering, National Taiwan University of
Science and Technology, Taipei, Taiwan (R.O.C)
Email:[email protected]
Dye-sensitized solar cells (DSSCs) have attracted extensive attention due to their low cost, high efficiency, and
environmentally friendly nature [1]. Finding alternative counter electrodes which can replace expensive, corrosive
platinum (Pt) in DSSCs is one of the future avenues for improving DSSC performance and stability at a low cost.
Recently, extensive research has been devoted to the development of Pt-free counter electrodes using inorganic
metal compounds, conducting polymers, and carbon materials. [2-4] Among them, carbon based materials
including carbon nanotubes, and nanocarbon are considered because of their low cost, abundant, and stable in
corrosive electrolyte. However, the lower catalytic activity of pristine graphene hinders the practical applications
in DSSC electrocatalysts. Conversely, recent studies report that nitrogen-doped graphene could be the efficient
electrocatalyst for DSSCs, which improve the electrochemical activity of graphene without significant decrease
in conductivity. In order to improve the catalytic activity of graphene further, in this study, we considered doping
of both Boron and Nitrogen together and investigated its catalytic activity towards the reduction of Iodine using
density functional theory (DFT) calculations. The schematic representation of DSSC components are shown in
Figure 1. Among the considered possible adsorption sites, we found that I2 prefers to adsorb parallel to the boronnitrogen-doped graphene (BNG) surface. The calculated Iodine anion dissociating barrier in BNG surface (0.41
eV) is much lower than the boron-doped surface, indicating a reduction of Iodine in BNG surface is much faster
than boron doped graphene surface. This theoretical study can give a clear understanding of the catalytic
mechanism of iodine reduction reaction on BNG surface.
Figure 1: Schematic representation of I 2 decomposition on Boron-Nitrogen-doped Graphene (BNG) in DSSCs
Keywords: Dye-sensitized solar cells, Boron-nitrogen-doped graphene, I2 adsorption, iodine reduction, Density
functional theory.
References
[1] Gratzel M, Nature 2001, 414, 338-344.
[2] Anghel, B. Marsan B., Cevey Ha N. L., Pootrakulchote N., Zakeeruddin S. M. and Gratzel M., J. Am.
Chem. Soc. 2009, 131, 15976.
[3] Tsao, J. Burschka H. N., Yi C. Y., Kessler F., Nazeeruddin M. K. and Gratzel M., Energy Environ. Sci.
2011, 4, 4921.
[4] Cai X., Lv Z. B., Wu H. W., Hou S. C. and Zou D. C., J. Mater. Chem. 2012, 22, 9639.
28
The Third International Conference on
Computational Science and Engineering (ICCSE-3)
28-30 November, 2016, Ho Chi Minh City, Vietnam
P2.5
Multi-Scale Modeling and Simulation of Pyrolysis of Furan
TAM V.-T. MAI,1 LAM K. HUYNH2
1
Molecular Science and Nano-Materials Lab, Institute for Computational Science and Technology, SBI
Building, Quang Trung Software City, Tan Chanh Hiep Ward, District 12, Ho Chi Minh City, Vietnam.
2
International University, Vietnam National University – HCMC, Quarter 6, Linh Trung Ward, Thu Duc
District, Ho Chi Minh City, Vietnam.
Email: [email protected]
Furan compounds, key products of converting lignocellulosic biomass to biofuels, were recently shown promising
alternatives to petroleum-derived fuels. An integrated deterministic and stochastic model, within the master
equation/Rice–Ramsperger–Kassel–Marcus (ME/RRKM) framework, was used to characterize the temperatureand pressure-dependent behaviors of pyrolysis of furan – one of the most simple species of furan derivatives – in
a wide range of conditions (i.e., 500–2000 K & 0.001–100 atm). Here, using the potential energy surface and
molecular
properties
obtained
from
high-level
quantum
chemical
methodologies,
e.g.,
CCSD(T)/CBS//UMP2/aug-cc-pVDZ, macroscopic thermodynamic properties, species profiles and
phenomenological rate coefficients of the title reaction were satisfactorily derived with the corrections for
hindered internal rotation and tunneling treatments. Our calculated/simulated data are in excellent agreement with
experimental ones, in which the converging results obtained from both deterministic and stochastic approaches
reveal CO + propyne and C2H2 + ketene being of the main decomposition products via two parallel processes,
initiated by 1,2-H transfers that result in the formation of cyclic carbene intermediates. Such an agreement and
convergence suggest the multi-scale approaches can be confidently used as a post-facto as well as a predicting
tool in detailed chemical kinetic modeling/simulation for complex chemical reactions at different T-P conditions
served as the optimal process in the internal combustion engines.
Keywords: Furan, Biofuels, Pyrolysis, Kinetic Modeling/Simulation, Rate Constants.
29
The Third International Conference on
Computational Science and Engineering (ICCSE-3)
28-30 November, 2016, Ho Chi Minh City, Vietnam
P2.6
Detailed Kinetic Mechanism for CH3OO + NO Reaction:
A Combined Ab Initio Deterministic and Stochastic Study
NGUYEN T. HOAI,1,3 TAM V.-T. MAI, LAM K. HUYNH2
1
Institute for Computational Science and Technology, SBI Building, Quang Trung Software City, Tan Chanh
Hiep Ward, District 12, Ho Chi Minh City, Vietnam
2
International University, Vietnam National University – HCMC, Quarter 6, LinhTrung Ward, Thu Duc
District, Ho Chi Minh City, Vietnam
3
University of Technology, Vietnam National University – HCMC, Ly Thuong Kiet Street, 11 District, Ho Chi
Minh City, Vietnam
Email: [email protected]
In this study, the detailed kinetic mechanism of the CH3OO + NO reaction, an important reaction in the NO-toNO2 conversion relevant to recent NOx-emission control techniques and engine combustion modeling, was
intensively investigated using highly-accurate ab initio composite W1U methods (e.g., W1U and CBS-QB3) and
statistical Rice-Ramsperger-Kassel-Marcus/Master Equation (RRKM/ME) calculations. Within this framework,
the temperature- and pressure-dependent behaviors were intensively characterized using both deterministic and
stochastic approaches in a wide range of conditions (T = 298 – 1500 K, P = 7.6 – 76000 Torr). The comparison
of the computed thermodynamic results and NIST data shows very good agreement, with differences of
approximately 1 kcal/mol or less. The CH3O + NO2 was found to be the most dominant product channel in the
considered T-P range, which was found to be in excellent agreement with available kinetic data. The obtained
detailed sub-mechanism, consisting of thermodynamic and kinetic data for all species involved and elementary
reactions, respectively, can be confidently used for modeling the NOx-emission in the combustion of hydrocarbon
fuels.
Keywords: Kinetic mechanism, Peroxy radicals, Nitric oxide, Combustion modeling, Pressure-dependent,
Hydrocarbon fuels.
30
The Third International Conference on
Computational Science and Engineering (ICCSE-3)
28-30 November, 2016, Ho Chi Minh City, Vietnam
P2.7
Low-Temperature Oxidation of Biodiesel Molecules: Rate Rules
of Cyclization Reactions from Alkyl-Ester Hydroperoxy Radical
●
ROOH
XUAN T. LE,1, LAM K. HUYNH2
1
Institute for Computational Science and Technology at HCMC, Vietnam.
2
International University, Vietnam National University, HCM, Vietnam.
Email: [email protected]
In this article, the rate rules of cyclization reactions for the hydroperoxy alkyl-ester radical molecules have been
conducted for simple surrogates molecules in order to produce the primary characteristics/properties of biodiesel
molecules. All of the species were used accurate electronic structure calculations at the CBS-QB3 level of theory
combined with statistical mechanics and transition state theory to calculate high-pressure rate constants for
selected cyclization reactions, which then serve as the basis to develop rate rules for this type of reactions of alkylester hydroperoxy radicals. The cyclization reactions are believed to be responsible for the formation of cyclic
ether and hydroxyl radical in the titled fuel. These rate rules have been developed from a training set of reactions
that consist of all C1-C5 ester-alkyl hydroperoxy radical reactants. Our calculations demonstrated the –(C=O)O–
ester group in methyl/ethyl esters affect to process that form O–C bond and break O–OH bond, especially at
nearest carbon sites of the ester group. These effects can make the reactions occur slower/higher when compared
with hydrocarbon fuels. The derived rate rules are recommended to be used to effectively construct detailed kinetic
mechanisms for real biodiesel molecules.
Keywords: biodiesel surrogate, alkyl peroxy radical, high-pressure rate rules, low temperature oxidation,
cyclization reactions.
31
The Third International Conference on
Computational Science and Engineering (ICCSE-3)
28-30 November, 2016, Ho Chi Minh City, Vietnam
P2.8
Performance of B3PW91, PBE1PBE and OPBE Functionals in
Comparison to B3LYP for 13C NMR Chemical Shift Calculations
NGUYEN THANH SI, PHAM VU NHAT
Department of Chemistry, College of Natural Sciences, Can Tho University, Can Tho, Viet Nam
Email: [email protected]
The performance of density functionals B3PW91, PBE1PBE and OPBE are evaluated in comparison to the
B3LYP for the 13C NMR chemical shift calculations of 20 small molecules. We combine these functionals with
several basis sets including 6-311++G(d,p), 6-311++G(2d,2p), 6-311++G(3df,3pd) and cc-pVTZ to analyze the
effect on predicting 13C NMR chemical shifts. Our computed results show that the use of a simple expression
𝛿𝑠𝑐𝑎𝑙 = 0.9528𝛿𝑐𝑎𝑙𝑐 − 0.5986, where 𝛿𝑠𝑐𝑎𝑙 and 𝛿𝑐𝑎𝑙𝑐 are the calculated and the linearly scaled values of the 13C
chemical shifts, respectively, significantly improves the mean absolute deviations for a set of 75 chemical shifts
considered. In addition the B3PW91 is superior to the other three density functionals and the GIAO B3PW91/6311++G(2d,2p) is sufficient to determine accurate 13C chemical shifts. The 13C NMR chemical shifts of a larger
system, i.e. Taxol molecule, are also computed and compared with experimental values.
Maximum absolute error
Mean absolute deviation
R-square
18
0.9986
16
0.9985
14
0.9984
12
0.9983
10
0.9982
8
0.9981
6
0.998
4
0.9979
2
0.9978
0
0.9977
B3LYP
B3PW91
PBE1PBE
OPBE
Figure 1. Performance of different density functionals in combination with 6-311++G(2d,2p) for
chemical shift calculations of 20 small structures in comparison to experimentally observed values.
Keywords: Chemical Shift, Scaling Factor, NMR, DFT, GIAO
32
13
C NMR
The Third International Conference on
Computational Science and Engineering (ICCSE-3)
28-30 November, 2016, Ho Chi Minh City, Vietnam
P2.9
MSMC-GUI: An Interactive Tool for Data Munging and Analysis
for Chemical System
TRIET H.M. LE,1 SON T. DO,1 LAM K. HUYNH2
1
Department of Computer Science and Engineering, International University – Vietnam National University,
Ho Chi Minh City, Vietnam
2
Department of Biotechnology, International University – Vietnam National University, Ho Chi Minh City,
Vietnam
Email: [email protected]
Theoretical/computational chemistry has advanced so rapidly that it can serve as a post-facto and predictive tool
to study behaviors of various complex chemical/biological systems in a wide range of applications. Specifically,
ab initio approaches (i.e., from quantum chemistry to statistical mechanics) have been de-facto tools to estimate
reliable thermodynamic data [1] as well as describe kinetic/dynamic behaviors of complex chemical systems [2].
However, such approaches require numerous parameters, which turns out to be still complicated, tedious and
sometimes need certain degrees of users’ expertise. Within this framework, we present the Graphical User
Interface for our state-of-the-art Multi-Species Multi-Channel program [3] (MSMC-GUI) to facilitate ab initio
thermodynamic/kinetic calculations as well as on-the-fly analyses on High-Performance Computing (HPC)
platform. Therefore, our tool supports rigorous chemical data pre-/post-processing as well as HPC
submission/monitoring in an automatic and comprehensive manner (cf. Figure 1). The robustness of our tool has
been demonstrated with a wide range of chemical systems with different complexity. As a result, MSMC-GUI
provides the user a reliable and on-the-fly environment to fully exploit any chemical system of interest.
Figure 1. Workflow of MSMC-GUI for reaction data munging and analysis
Keywords: Computational Chemistry, Thermodynamics, Kinetics, Ab initio, High-Performance Computing, Data
Analysis, Computer Program
References
[1] McQuarrie, D. A., Statistical thermodynamics; Harper and Row: New York, 1973.
[2] Steinfeld, J. I., Francisco, J. S.; Hase, W. L., Chemical kinetics and dynamics; Prentice Hall Englewood Cliffs
(New Jersey), 1989; Vol. 3.
[3] Duong, M. V., Nguyen, H. T., Truong, N., Le, T. N. M.; Huynh, L. K., Int. J. Chem. Kinet. 2015, 47(9), 564575.
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The Third International Conference on
Computational Science and Engineering (ICCSE-3)
28-30 November, 2016, Ho Chi Minh City, Vietnam
P2.10
Effects of Metal Substitution in MIL-88A On Hydrogen
Adsorption: Computational Study
NGUYEN THI XUAN HUYNH1,2, O MY NA1, DO NGOC SON1
1
Ho Chi Minh City University of Technology, VNU-HCM, Ho Chi Minh City, Vietnam
2
Quy Nhon University, Quy Nhon City, Binh Dinh Province, Vietnam
Email: [email protected]
Metal Organic Frameworks (MOFs), a class of porous crystalline materials consisting of metal clusters and
organic ligands, is the most promising candidate for many applications such as gas storage and capture, gas
mixture separation, and drug delivery. MIL-88A has been evaluated for drug delivery and electrocatalysis but it
has not been tested for hydrogen storage. Moreover, we are interested in MIL-88A because of its high stability in
the humid environment and hence MIL-88A may be good for a long term usage for hydrogen storage. It was
known that creating open metal sites in the MOFs is one of the most effective strategies to enhance the adsorption
strength of hydrogen gas with the MOFs [1-3]. This strategy can be applied to MIL-88A by removing counteranions. In this work, we are concerned with the effects of transition metal substitution in MIL-88A on hydrogen
adsorption, which can be clarified by means of the van der Waals dispersion-corrected density functional theory
calculations. Furthermore, a quantitative assessment on the hydrogen uptake capacity is also considered through
grand canonical Monte Carlo simulations.
Keywords: Hydrogen Adsorption, Metal Organic Framework, Transition Metal, Electronic Structure, Density
Functional Theory
Acknowledgements
This research was funded by Ho Chi Minh City University of Technology under grant number TNCS-2015KHUD-33.
References
[1] T. T. T. Huong, P. N. Thanh, N. T. X. Huynh, and D. N. Son, VNU J. Sci. Math. – Phys. 2016, 32, 1, 67–85.
[2] D. a Gomez and G. Sastre, Phys. Chem. Chem. Phys. 2011, 13, 37, 16558–16568.
[3] J. L. C. Rowsell and O. M. Yaghi, Angew. Chem. Int. Ed. 2005, 44, 30, 4670–4679.
34
The Third International Conference on
Computational Science and Engineering (ICCSE-3)
28-30 November, 2016, Ho Chi Minh City, Vietnam
P2.11
Influence of the Hydrogen-Bond Geometry Controlling over
Excited State Intramolecular Proton Transfer of 10Hydroxybenzo[h]quinolone as Fluorescent Probes
WARINTHON CHANSEN, KHANITTHA KERDPOL, RATHAWAT DAENGNGERN,
NAWEE KUNGWAN
Department of Chemistry, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
Email: [email protected]
The excited state intramolecular proton transfer (ESIPT) reactions of 10-hydroxybenzo[h]quinolone (HBQ) and
its derivatives with different hydrogen-bonding geometries have been systematically investigated using a hybrid
density-functional theory (DFT) and its time-dependent DFT (TD-DFT) at B3LYP with TZVP basis set. ESIPT
can occur easily in the excited state with less required PT barrier. On-the-fly dynamics simulations in the firstexcited state are employed to determine reaction mechanisms and the time evolution of the ESIPT reaction. The
ESIPT times in all compounds take place within 100 fs.
Figure 1. Mechanism of excited state intramolecular proton transfer (ESIPT) for 10-hydroxybenzo[h]quinolone
(HBQ).
Keywords: Excited state intramolecular proton transfer, 10-hydroxybenzo[h]quinoline, Density-functional theory,
Time-dependent, Dynamics simulations
References
[1] Marty L. Martinez, William C. Cooper and Pi-Tai Chou, Chem. Phys. Lett. 1992, 193, 151-154.
[2] Bijan Kumar Paul and Nikhil Guchhait, J. Lumin. 2011, 131, 1918-1926.
[3] Meng Zhou, Jinfeng Zhao, Yanling Cui, Qianyu Wang, YumeiDai, Peng Song, and Lixin Xia,
J. Lumin. 2015, 161, 1-6.
[4] Giovanny A. Parada, Todd F. Markle, Starla D. Glover, Leif Hammarstrçm, Sascha Ott, and Burkhard Zietz,
Chem. Eur. J. 2015, 21, 6362-6366.
35
The Third International Conference on
Computational Science and Engineering (ICCSE-3)
28-30 November, 2016, Ho Chi Minh City, Vietnam
P2.12
Propane Dehydrogenation on Ni-based catalyst: DFT Study
TINNAKORN SAE-LEE1, ANCHALEE JUNKAEW2, SUPAWADEE NAMUANGRAK2,
NAWEE KUNGWAN1
1
Department of Chemistry, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
National Nanotechnology Center (NANOTEC), National Science and Technology Development Agency,
Pathumthani, 12120, Thailand.
Email: [email protected]
2
Propylene, a product from refining petroleum gas, is an important raw material for a variety of products.
Production of propylene via propane dehydrogenation (PDH) reaction is an interesting approach because this
method can raise a value and expand applications of propane. To date, platinum- (Pt-) and chromium- (Cr-) based
catalysts are widely used for PDH. Due to the high reactivity and good stability at high temperatures, nickel-(Ni)
based catalysts are one of effective catalysts used in various applications. Ni metal has the lower price than Pt and
it is more ecological friendly than Cr. Therefore, Ni is a good candidate for PDH reaction. However, its too high
reactivity results in hydrogenolysis process, breaking of C-C bond. This side reaction directly decreases the
selectivity of the Ni catalyst. Moreover, deep dehydrogenation reaction, which occurs during desorption of
propylene from the surface, leads to a coke formation which is a cause of the catalyst deactivation. In literatures,
doping Ni catalyst by gold (Au) can increase the reaction rate of PDH by reducing hydrogenolysis reaction [1,2].
In this work, the insight mechanisms of PDH and other possible side reactions on Ni-based catalysts have been
investigated by using DFT calculations implemented in VASP package. As a result, doping Au atoms on Ni
surface decreases the adsorption ability of propylene on the catalyst surface but it has no effect on the propane
adsorption.
Figure 1. PDH reaction on Ni catalyst
Keywords: “Propylene”, “Ni-based catalyst”, “PDH reaction”, “Hydrogenalysis reaction”, and “Deep
dehydrogenation”
References
[1] Yan Zhen, Goodman D. Wayne, Catalysis Letters 2012, 142, (5). 517-520.
[2] Yan Zhen, Yao Yunxi, Goodman D. Wayne, Catalysis Letters 2012, 142, (6). 714-717.
36
The Third International Conference on
Computational Science and Engineering (ICCSE-3)
28-30 November, 2016, Ho Chi Minh City, Vietnam
P2.13
Substituent Effects on Corrosion Inhibition Performance of Five
Natural Thiophene Derivatives: Density Functional Theory and
Molecular Dynamic Simulation Studies
TRUONG DINH HIEU1, DUY QUANG DAO2,*, THONG LE MINH PHAM2, THI CHINH NGO2,
NGUYEN PHAN TRUC XUYEN3, DINH TUAN4, MINH THONG NGUYEN5, PHAM CAM NAM6,*
1
Department of Chemistry, Hue University of Education, 34 Le Loi, Hue
Institute of Research and Development, Duy Tan University, 03 Quang Trung, Danang
3
Department of Environment and Chemical Engineering, Duy Tan University, 03 Quang Trung, Da Nang
4
Quality Assurance and Testing Centre 2, 01 Ngo Quyen, Danang
5
The University of Danang – Campus in Kon Tum, 704 Phan Dinh Phung, Kon Tum
6
The University of Danang - Danang University of Science and Technology, 54 Nguyen Luong Bang, Lien
Chieu, Danang
Emails: [email protected] (DQD); [email protected](PCN)
2
Corrosion inhibition performance of five thiophene derivatives extracted from natural products such as 2Acetylthiophene (AT), 2-Formylthiophene (FT), 2-Methyl-3-thiophenthiol (MTT), 2-Pentylthiophene (PT), 2Thenylthiol (TT) has been evaluated using Density functional theory (DFT). Quantum chemical parameters
characterizing the inhibition activity in gas phase and in aqueous phase were calculated using B3LYP, AFP-D
and M05-2X methods combined with 6-311G(d,p) basis set.
The obtained results show that the natural thiophene derivatives possess a good inhibition performance. Moreover,
it is showed that the thiophene derivatives with electron-releasing substituents like TT, MTT and PT have the
better corrosion inhibition activity than those with electron-withdrawing substituents like AT and FT (Figure 1).
The corrosion inhibition performance of these studied compounds can be classified in the decreasing trend: TT >
MTT > PT > AT > FT. This can be explained by the fact that electron-releasing substituents tend to a higher
electron density on thiophene ring and a better adsorption of inhibitors on metal surface, resulting to a higher
corrosion inhibition performance.
Figure 1. Optimized structures, HOMO, LUMO and electrostatic potential (ESP) structures of non-protonated
form of (a) AT, (b) FT, (c) PT, (d) TT and (e) MTT using APF-D/6-311G(d,p) model chemistry in gas phase.
(ESP structures are displayed at an isovalue of 0.15 and mapped in range from 0.13 to 0.15)
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The Third International Conference on
Computational Science and Engineering (ICCSE-3)
28-30 November, 2016, Ho Chi Minh City, Vietnam
Molecular dynamics simulations utilizing Monte Carlo simulated annealing procedure were further applied to
simulate the low adsorption configurations of the interaction of the thiophene molecules on the iron surface
(Figure 2).
(a) AT-Fe (110)
(b) FT-Fe (110)
(d) PT-Fe (110)
(e) TT-Fe (110)
(c) MTT-Fe (110)
Figure 2. Side views of equilibrium adsorption configurations of (a) AT, (b) FT (c) MTT (d) PT and (e) TT on
Fe(110) surface obtained using Monte Carlo simulations in the gas phase
Keywords: Thiophene, Green inhibitor, Iron, Metal corrosion, Natural products, DFT, Monte Carlo
38
The Third International Conference on
Computational Science and Engineering (ICCSE-3)
28-30 November, 2016, Ho Chi Minh City, Vietnam
P2.14
First Principles Calculation of the Hydrogen Adsorption on the
Different Pt Surfaces
TRAN THI THU HANH
Computational Physics Laboratory, Ho Chi Minh City University of Technology
268 Ly Thuong Kiet, Dist. 10, Ho Chi Minh, Vietnam
Email: [email protected]
The hydrogen adsorption on the Pt(111) and the missing row Pt(110)-(1x2) electrode surfaces has been intensively
investigated. To gain insight into detailed atomistic picture on the equilibrium coverage and structure, we have
constructed a lattice gas model by determining the on-site energy and the interaction parameters using the first
principles total-energy calculation. Therein atop, fcc, hcp and bridge sites for H/Pt(111) and the short bridge on
the ridge, the on-top on the micro facet, the hcp and the long bridge sites in the trough for H/Pt(110)-(1x2) are
covered by hydrogen atoms under various coverage conditions (0ML < Θ ≤ 1ML) and the total-energy
calculations are done for the (1x1), (2x2) and (3x3) cells. The total-energies of (3x3) cell, corrected by the zeropoint energy (ZPE), are found well fitted to the lattice gas model. With this model, the Monte Carlo (MC)
simulation has been performed. The first-principles calculation combined with MC simulation successfully
explains the interaction of H atoms on the Pt surfaces. The active sites of the hydrogen adsorption on the Pt(111)
and Pt(110)-(1x2) surfaces, which have been hitherto conceptually discussed but has not been shown by an
atomistic simulation, have been identified.
39
The Third International Conference on
Computational Science and Engineering (ICCSE-3)
28-30 November, 2016, Ho Chi Minh City, Vietnam
P2.15
A Theoretical Study on Charge Transport of Dithiolene Nickel
Complexes
VU THI THU HUONG, MINH THO NGUYEN
Department of Chemistry, KU Leuven, Celestijnenlaan 200F, B-3001, Leuven, Belgium
Email: [email protected]
Organic semiconducting materials play an important role in the fabrication of high performance organic electronic
devices. In the present work, we theoretically designed a series of organic semiconductors based on nickel
complexes. Their characteristics of charge transport were investigated using DFT computational approaches.
Based on the computed results, all compounds designed are found to be excellent candidates for ambipolar organic
semiconductors with low reorganization energies for both holes and electrons. The (I–V) characteristics and
transmission spectra of materials show that the replacement of benzene rings by thiophene rings results in an
increase of their HOMO and LUMO energy levels. HOMOs of compounds containing thiophene end-groups are
likely dominant for their conductance, while LUMOs of compounds containing benzene end-groups mainly affect
their conductance. The electron distribution in these frontier MOs is identified as the main reason which makes
the conductance the compounds of in the first series higher than those in the later series.
40
The Third International Conference on
Computational Science and Engineering (ICCSE-3)
28-30 November, 2016, Ho Chi Minh City, Vietnam
P2.16
Multiscale Simulations on Conformational Dynamics and
Membrane Interactions of the Non-structural 2 (NS2)
Transmembrane Domain
HUYNH MINH HUNG, TRAN DIEU HANG, MINH THO NGUYEN
Department of Chemistry, KU Leuven, Celestijnenlaan 200F, B-3001, Leuven, Belgium
Email: [email protected]
Hepatitis C virus (HCV) is one of the most crucial global health issues, in which the HCV non-structural protein
2 (NS2), particularly its three transmembrane segments, plays a crucial role in HCV assembly. Multiscale MD
simulations have been applied to investigate the preferred orientation of transmembrane domain of NS2 protein
(TNS2) in a POPC bilayer, structural stability and characteristic of intramembrane protein-lipid and proteinprotein interaction. Residues K27, R32, R43, H45, H47, R61 and K99 have been found to regularly contact with
the lipid headgroups. Our study indicates that NS2 protein adopts three trans-membrane segments with highly
stable α-helix structure in a POPC bilayer and a short helical luminal segment. While the first and second TM
segment involved in continuous helical domain, the third TM segment is however cleaved into two sub-segments
with different tilt angles via a kink at L87G88. Salt bridges K81-E45, R32-PO4 and R43-PO4 are determined as
the key factor to stabilize the structure of TM2 and TM3 which consist of charged residues located in the
hydrophobic region of the membrane.
41
The Third International Conference on
Computational Science and Engineering (ICCSE-3)
28-30 November, 2016, Ho Chi Minh City, Vietnam
P2.17
Free Radical Pathways Lading to the Formation of Nucleobases
from Formamide
HUYEN THI NGUYEN, HUYNH MINH HUNG, MINH THO NGUYEN
Department of Chemistry, KU Leuven, B-3001 Leuven, Belgium
Email: [email protected]
Modelling the complicated chemical reactions in the interstellar media and materials’ surfaces of Titan is
nontrivial. Since both the atmosphere and the surface are rich in organic molecules, the relevant chemistry may
have important implications for the origin of biomolecules. Prebiotic synthesis of DNA nucleobases from simple
molecules such as FM has been known for more than half a century, but the detailed mechanisms are still not
clear. In this study, new free radical pathways leading to the synthesis of purine, adenine, guanine, hypoxanthine,
xanthine, isoguanine, cytosine, uracil, and thymine were studied at B3LYP/6-311G(d,p) level of theory. The
pathways of formation of selected nucleobases demonstrate the importance of free radicals in the production of
key biomolecules under conditions appropriate for the interstellar medium or on Titan (low temperatures). The
pathways may be universal in nature and proceed without solvent requirements. Our calculations indicate that
radical pathways are characterized by smaller energy barriers as compared to previously reported pathways.
Overall, these results suggest that the chemistry on Titan's surface and/or the growth of organic particulates in the
haze layers in Titan's atmosphere likely involve free radicals. The inherent mechanisms demonstrate that
formation of important prebiotic precursors can be predicted. The reaction sequences reported in this study may
lead to the production and build-up of molecules with prebiotic relevance.
References
[1] Jeilani, Y.A., Nguyen, H.T., Newallo, D., Dimandja, J.-M.D., and Nguyen, M.T., Phys. Chem. Chem. Phys.
15 (2013) 21084-21093.
[2] Jeilani, Y.A., Nguyen, H.T., Cardelino, B.H., and Nguyen, M.T., Chem. Phys. Lett. 598 (2014) 58-64.
[3] Nguyen, H. T, Jeilani, Y. A., Hung, M. H., and Nguyen, M. T., J. Phys. Chem. A 119 (2015) 8871-8883.
42
The Third International Conference on
Computational Science and Engineering (ICCSE-3)
28-30 November, 2016, Ho Chi Minh City, Vietnam
P2.18
Catalytic Effects of Small Pure and Earth-Alkali Mixed Silicon
Clusters Sim-nMn (m = 3 – 4, n = 0 – 1) with M = Be, Mg, Ca
towards the Methanol Activation
TRAN DIEU HANG, MINH THO NGUYEN
Department of Chemistry, KU Leuven, Belgium
Email: [email protected]
The methanol activation pathways occurring on small pure and mixed silicon clusters Si m-nMn with M = Be, Mg,
Ca, and m = 3 – 4, n = 0 – 1 were investigated using quantum chemical computations (density functional theory
B3LYP/aug-cc-pVTZ and coupled-cluster theory CCSD(T)/CBS extrapolated from energies with the aug-ccpVnZ basis sets) to examine their thermodynamic and kinetic feasibilities. In all cases considered, the cleavage
of the O–H bond is favored over that of the C–H bond. The O–H bond cleavage in the presence of the singlet Si3
cluster is less thermodynamically preferred than on mixed Si2M clusters, even though it becomes more kinetically
favored. Replacement of one Si atom in the Si4 cluster with earth-alkaline metals substantially reduces the energy
barriers for both O–H and C–H dissociation paths. The most energetically preferred pathway for breaking the O–
H bond takes place on the Si3Ca cluster with a small energy barrier of only 2 kcal/mol. Most importantly, the
energy barriers for the O–H bond breaking on the singlet Si3, Si2Ca and Si3Ca clusters are found to be lower than
the previously reported results for metal clusters, catalytic metal surfaces, metal oxides…The small mixed Si
clusters thus appear to be good catalysts for methanol activation, and most probably in other dehydrogenation
processes from the X-H bonds of organic compounds. These findings suggest a further extensive search for doped
silicon clusters as realistic catalysts that can experimentally be prepared, for methanol activation particularly and
dehydrogenation processes generally.
Figure 1: Schematic potential energy profile illustrating the methanol dissociation reaction of methanol in the
presence of the singlet Si3Ca cluster. Relative energies in kcal/mol were obtained from CCSD(T)/CBS + ZPE
computations.
References
[1] Hang, T. D.; Hung, H. M.; Nguyen, H. T.; Nguyen, M. T. Structures, Thermochemical Properties, and Bonding
of Mixed Alkaline-Earth-Metal Silicon Trimers Si3M +/0/– with M = Be, Mg, Ca. J. Phys. Chem. A 2015, 119,
6493–6503.
[2] Hang, T. D, ; Nguyen, H. T. ; Nguyen, M. T. Methanol Activation Catalyzed by Small Earth-Alkali Mixed
Silicon Clusters Sim-nMn with M = Be, Mg, Ca and m = 3 – 4, n = 0 – 1. J. Phys. Chem. C, 2016, 120, 10442–
10451.
43
The Third International Conference on
Computational Science and Engineering (ICCSE-3)
28-30 November, 2016, Ho Chi Minh City, Vietnam
P2.19
Photoinduced Proton Transfer of 7-Hydroxyquinoline via
Intermolecular Hydrogen-Bonded Wire of Mixed Methanol and
Water: Theoretical Insights
K. KERDPOL1, R. DAENGNGERN1,2, J. MEEPRASERT2, S. NAMUANGRUK2, N. KUNGWAN1
1
Department of Chemistry, Faculty of Science, Chiang Mai University, 50200 Chiang Mai, Thailand
National Nanotechnology Center (NANOTEC), NSTDA, 111 Thailand Science Park, Pahonyothin Road,
Klong Luang, 12120 Pathum Thani, Thailand
Email: [email protected]
2
Intermolecular multiple proton transfer (PT) reactions of 7-hydroxyquinoline (7HQ) with mixed methanol and
water clusters, [7HQ(X)3 when X = M-methanol and W-water] (Fig. 1), both in ground (S0) and first excited (S1)
states have been studied by using density functional theory (DFT) at B3LYP and its time-dependent DFT with 631+G(d,p) basis set. For all complexes, the intermolecular hydrogen bonds involving PT process are strengthened
in the S1 state, confirmed by the short intermolecular hydrogen-bonded distances and the red-shift of the O–H
stretching vibrational frequencies especially the O–H proton donor of 7HQ. Therefore, PT may occur firstly via
the breaking O–H bond of 7HQ. Furthermore, the potential energy curves both in S0 and S1 states were calculated
to investigate the effect of different solvents surrounding 7HQ. PT reactions can occur easily in the S1 state due
to the low PT energy barrier. For pure solvent, the excited-stated proton transfer (ESPT) is likely to occur better
in methanol (4.22 kcal/mol) than water (6.67 kcal/mol). For mixed solvent, the ESPT energy barriers increase
gradually when replacing methanol with one up to three water molecules thus water may block ESPT reaction.
Figure 1. Scheme of (a) isolated 7-hydroxyquinoline (7HQ) and (b) 7HQ with a solvent wire (methanol and
water)
Keywords: “7-Hydroxyquinoline (7HQ)”, “Excited-Stated Proton Transfer (ESPT)”, “Mixed Methanol-Water”,
“B3LYP”, “Solvent Effect”
References
[1] K. Kerdpol, R. Daengngern, J. Meeprasert, S. Namuangruk, N. Kungwan, Theor. Chem. Acc., 2016, 135,
(208), 1-9.
[2] Y. Matsumoto, T. Ebata, N. Mikami, J. Phys. Chem. A., 2002, 106, (23), 5591-5599.
[3] Y. Cui, H. Zhao, J. Zhao, P. Li, P. Song, L. Xia, New. J. Chem., 2015, 39, 9910-9917.
44
The Third International Conference on
Computational Science and Engineering (ICCSE-3)
28-30 November, 2016, Ho Chi Minh City, Vietnam
P2.20
A DFT Study on Antioxidant Activity of Oxygenated Terpenoids
Extracted from Cleistocalyx operculatus
THI CHINH NGO1, DUY QUANG DAO1, PHAM CAM NAM2
2
1
Institute of Research and Development, Duy Tan University, 03 Quang Trung, Danang, Viet Nam
Department of Chemistry, Danang University of Science and Technology - The University of Danang, 54
Nguyen Luong Bang, Lien Chieu, Danang, Viet Nam
Email: [email protected]
Antioxidant capacity of 21 oxygenated monoterpenes and desquiterpenes extracted from buds of Cleistocalyx
operculatus [1] has been investigated in this study using density functional theory (Figure 1). Insight into the
theoretical mechanism of antioxidant activity of these compounds was clarified via three antioxidant mechanisms
including hydrogen atom transfer (HAT), single electron transfer followed by-proton transfer (SET-PT) and
sequential proton loss electron transfer (SPLET). The various calculated thermochemical parameters were
performed using density functional theory (DFT) method at (RO)B3LYP/6-311++G(2df,2p)//B3LYP/6311G(d,p) level of theory in the gas phase, ethanol and water.
As a result, falcarinol is the most effective antioxidant via both HAT and SPLET mechanisms. In fact, the BDE
in the gas phase of falcarinol is 66.5 kcal/mol which is much lower than the one of phenol. The presence of both
OH group and unsaturated double/triple bonds supports this molecule to have the good antioxidant properties.
Figure 1. Chemical structure of 21 oxygenated monoterpenes and desquiterpenes
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The Third International Conference on
Computational Science and Engineering (ICCSE-3)
28-30 November, 2016, Ho Chi Minh City, Vietnam
Keywords: Antioxidant, BDE, IE, HAT, SET-PT, SPLET, Natural compounds, Density functional theory.
References
[1] Ngo, T. C.; Dao, D. Q.; Thong, N. M.; Nam, P. C., Insight into the antioxidant properties of non-phenolic
terpenoids contained in essential oils extracted from the buds of Cleistocalyx operculatus: a DFT study. RSC
Advances 2016, 6, 30824-30834
[2] NIST Chemistry WebBook. http://webbook.nist.gov/chemistry/ 2015.
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The Third International Conference on
Computational Science and Engineering (ICCSE-3)
28-30 November, 2016, Ho Chi Minh City, Vietnam
P2.21
Etherification Mechanism of DMDHEU with Primary Alcohols in
Acidic Condition Studied with ab initio Quantum Chemistry
Methods
NGUYEN THUONG DANG, PHAM THANH QUAN, PHAM HONG PHUOC SANG
Faculty of Chemical Engineering – University of Technology – Vietnam National University, HCMC
Emails: [email protected] (NTD); [email protected] (PHPS)
This paper establishes the etherification mechanism of 4,5-dihydroxy-1,3-bis (hydroxymethyl) imidazolidin-2one (DMDHEU) with primary alcohols R-CH2OH in acidic condition using density functional theory B3LYP,
through surveying the effect of the substituent –R (R = H, CH3, CH2CH3, Vinyl, CH2NHCH3, CH2OCH3,
CH2Cl, MDHEU) and the effect of basis set (6-31g(d,p), 6-311g(d,p), 6-311++g(d,p)) on computational results.
The results indicate that the etherification reaction follows nucleophilic substitution unimolecular (SN1)
mechanism. Reactants and products form reactive intermediates with H+ and water, in this state H+ is occupied by
both alcohol and water or ether and water. This state has lower energy level compared to both of the following
cases: H+ is occupied only by water; and H+ is occupied only by the product/reactant. The substituent –R has a
significant impact on the amount of energy needed to convert the reactive intermediate into ether but shows no
effect on activation energy; while the basic set affects both activation energy and conversion energy.
Keywords: Etherification Reaction Mechanism, DMDHEU, Primary Alcohol, Effect of H+.
47
The Third International Conference on
Computational Science and Engineering (ICCSE-3)
28-30 November, 2016, Ho Chi Minh City, Vietnam
P2.22
Tiny Clusters Containing Transition Metals: Electronic
Structures and Insights into Their Anion Photoelectron Spectra
LE NHAN PHAM,1,2 MINH THO NGUYEN1
1
Department of Chemistry, KU Leuven Belgium
Department of Chemistry, University of Dalat, Lam Dong Vietnam
Email: [email protected]
2
Theoretical studies on clusters containing transition metals are one of the interesting and challenging topics. The
main reason is electronic structures of these systems need to be described with appropriate wavefunctions.
Usually, single reference wavefunctions can describes the electronic structure of many systems. For several
systems, single reference wavefunctions cannot be used efficiently with regards to correlation energy. In such
situations, multireference wavefunctions are believed to be an alternative. Therefore, in this work, we utilize single
reference and multireference quantum wavefunction types (DFT, RCCSD(T), CASSCF, MRCI, CASPT2 and
NEVPT2) to synergistically investigate the electronic structures of tiny clusters containing transition metals (VC2/0, ScSi2-/0 and TiGe2-/0). On the basis of their electronic structures, possible one-electron ionization processes,
which are the removals of one electron from anionic clusters, are predicted. These ionization energies, the socalled adiabatic and vertical detachment energy (ADE and VDE), are also calculated at several levels of theory
mentioned above. These calculated ADEs and VDEs provide reliable evidences to understand nature of all
experimental photoelectron bands in the spectra. In addition, multidimensional Franck-Condon simulations can
be employed to confirm electronic transitions and/or provide more details about experimental results.
Keyword: Clusters, transition metals, anion, photoelectron, excited state, ground state
48
The Third International Conference on
Computational Science and Engineering (ICCSE-3)
28-30 November, 2016, Ho Chi Minh City, Vietnam
P2.23
Solvent Control of Molecular Structure and Excited-State Proton
Transfer Process : Dynamics Simulations of
2-(2’-hydroxyphenyl) Benzimidazole (HBI)
CHANATKRAN PROMMIN, KHANITTHA KERDPOL , RATHAWAT DAENGNGERN,
NAWEE KUNGWAN
Department of Chemistry, Faculty of Science, Chiang Mai University,
Chiang Mai 50200, Thailand
Email: [email protected]
The excite-state intramolecular proton transfer (ESIPT) is one the most fundamental and important process due
to its photophysical properties. The applications of ESIPT are found in many applications such as organic light
emitting diodes, luminescent materials and fluorescent probes. As in fluorescent probes, one of the most widely
use dye is 2-(2'-hydroxyphenyl) benzimidazole (HBI). In this study, static calculations and dynamics simulations
of the excited-state proton transfer (ESPT) for HBI in several types of solvents were systematically examined by
density funcational theory (DFT) at B3LYP/6-31G method. In various kinds of isomers of HBI, ESPT can occur
both in the ground and excited state. It has also been recognized that this proton transfer is a very fast reaction and
the phototautomer is formed during the lifetime of the originally excited species. This may lead to a change in
physical or chemical properties of the molecule, which dictates its optical properties as fluorescent probe. Our
calculated results can explain the phenomena found in the experimental study in term of the weak sovolchromism
when protic solvents form an intermolecular hydrogen-bond with HBI
Figure 1. Principal photophysics of ESIPT Illustrated by 2-(2-hydroxyphenyl)-benzimidazole (HBI)
Keywords: : 2-(2'-hydroxyphenyl)benzimidazole (HBI), Excite-state intramolecular proton transfer (ESIntraPT),
Excite-state intermolecular proton transfer (ESInterPT), Density funcational theory
References
[1] R. Hossein, M. Nafiseh, and H. Fahemeh, Chem. Phys. 2014, 444, 66-76.
[2] R. Hossein, M. Nafiseh, and H. Fahemeh, Spectrochim. Acta A, 2014, 118, 228-238.
[3] D. Rathawat, and K. Nawee, Chem. Phys. Lett. 2014, 609, 147-154.
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The Third International Conference on
Computational Science and Engineering (ICCSE-3)
28-30 November, 2016, Ho Chi Minh City, Vietnam
P2.24
Dynamic Simulations on Hydrogen Bonding in the Excited State
of 3-hydroxyflavones and its Solvent Assistance
RUSRINA SALAEH, KHANITTHA KERDPOL, RATHAWAT DAENGNGERN, NAWEE KUNGWAN
Department of Chemistry, Faculty of Science, Chiang Mai University,Chiang Mai 50200, Thailand
Email: [email protected]
3-Hydroxyflavone (3HF) is composed of phenyl and pyranyl ring. This molecule belongs to a group of flavonoids,
which are responsible for the yellow color of petals. The photophysical change affected by intermolecular
hydrogen-bonded with protic solvent is very important information in the molecular level of this molecule to be
used as effective fluorescent probes for ions. In this work, the possible excited-state intra- and intermolecular
proton transfer (ESPT) reactions of 3HF in methanol, water, and ammonia have been theoretically studied both
static and dynamic calculations using density functional theory (DFT) and time-dependent density functional
theory (TD-DFT) methods. An analysis of the absorption and emission spectra as well as the time constant of
proton transfer was used to explain the optical changed with different solvents. The results demonstrate that the
enol and keto forms of 3HF can exist when a protic solvent is introduced. Both excited-state intra- and
intermolecular proton transfers can be competitive when increasing the polarity of solvent, resulting in slower
proton transfers.
Figure 1. Tautomerization of 3-hydroxyflavone (3HF) and 3-hydroxyflavone with solvent.
Keywords: 3-hydroxyflavone, intra- and intermolecular excited-state proton transfe, protic solvent, density
functional theory (DFT), time-dependent DFT (TD-DFT)
References
[1] Gunduz, S.; Goren, C. A.; and Ozturk, T, Org. Lett 2012, 14, 1476-1579.
[2] Sengupta, K. P.; Kasha, M, Org. Lett 1979, 68, 382.
[3] Klymchenko, S. A.; Demchenko, P. A., New. J. Chem 2004, 28, 687-692.
[4] Douhal, A.; Sanz, M.; Tormo L.; Organero A. J., Chem Phys Chem 2005, 6, 419-429.
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The Third International Conference on
Computational Science and Engineering (ICCSE-3)
28-30 November, 2016, Ho Chi Minh City, Vietnam
P2.25
The Effect of Co/Ni-Promoted on Edge Site of MoS2 Catalyst for
H2 Activation Mechanism using a Periodic DFT Study
CHANCHAI SATTAYANON,1 SUPAWADEE NAMUANGRUK,2 NAWEE KUNGWAN,1
MANASCHAI KUNASETH2
1
Department of Chemistry, Faculty of Science, Chiang Mai University, Chiang Mai , 50200, Thailand
National Nanotechnology Center (NANOTEC), National Science and Technology Development Agency
(NSTDA), Pathum Thani, 12120, Thailand
Emails: [email protected] (NK); [email protected] (MK)
2
Understanding the mechanism of molecular hydrogen (H2) activation on MoS-based catalysts is very important
for hydrotreating processes, which are crucial for hydrodesulfurization (HDS) and hydrodeoxygenation (HDO)
reactions. In this work, three major mechanisms of H2 activation (adsorption, dissociation and diffusion) on
NiMoS and CoMoS catalysts under HDS/HDO conditions were investigated by means of density functional theory
calculations. The results ofH2 adsorption on NiMoS and CoMoS catalysts revealed that H2 molecule preferred to
be adsorbed on metal atoms rather than the sulfide group, while the H 2 molecule adsorbed on CoMoS surface but
substantially weaker on NiMoS surface. In addition, the transition state calculation using improved nudged-elastic
band method indicated that the energy barrier of H 2 dissociation on NiMoS is lower than that of CoMoS, while
diffusion of dissociated hydrogen atoms on the surfaces of both catalysts occurred easily. In conclusion, the high
temperature and high pressure of H2 feedstock of HDS/HDO conditions are adequate for H2 dissociation and
diffusion on NiMoS and CoMoS.
Figure 1. Overview of H2 activation on both CoMoS and NiMoS catalysts
Keywords: Hydrogen adsorption, Hydrogen dissociation, NiMoS, CoMoS, Density functional theory
References
[1] Badawi, M.; Cristol, S.; Paul, J.-F.; Payen, E. Comptes Rendus Chimie 2009, 12, 754.
[2]Badawi, M.; Paul, J. F.; Payen, E.; Romero, Y.; Richard, F.; Brunet, S.; Popov, A.; Kondratieva, E.; Gilson,
J. P.; Mariey, L.; Travert, A.; Maugé, F. Oil Gas Sci. Technol. – Rev. IFP Energies nouvelles 2013, 68, 829.
[3] Ruinart de Brimont, M.; Dupont, C.; Daudin, A.; Geantet, C.; Raybaud, P. Journal of Catalysis 2012, 286,
153.
[4] Zhang, H.; Lin, H.; Zheng, Y. Applied Catalysis B: Environmental 2014, 160–161, 415.
[5] Prodhomme, P.-Y.; Raybaud, P.; Toulhoat, H. Journal of Catalysis 2011, 280, 178.
51
The Third International Conference on
Computational Science and Engineering (ICCSE-3)
28-30 November, 2016, Ho Chi Minh City, Vietnam
P2.26
Structure, Thermochemical Properties and Growth Sequence of
Aluminum Doped Silicon Clusters SinAlm (n = 1 – 11, m = 1 – 2)
and Their Anions
NGUYEN MINH TAM, MINH THO NGUYEN
1
Research Group of Computational Chemistry, Ton Duc Thang University, Vietnam
Email: [email protected]
A systematic examination of the aluminum doped silicon clusters, SinAlm with n = 1 – 11 and m = 1 – 2, in both
neutral and anionic states, is carried out using quantum chemical calculations. Lowest-energy equilibrium
structures of the clusters considered are identified on the basis of G4 energies. High accuracy total atomization
energies and thermochemical properties are determined for the first time using the G4 and CCSD(T)/CBS
(coupled-cluster theory with complete basis set up to n = 3) methods. In each size, substitution of Si atoms at
different positions of a corresponding pure silicon clusters by Al dopants invariably leads to a spectrum of distinct
binary structures but having similar shape and comparable energy content. Such an energetic degeneracy persists
in the larger cluster sizes, in particular for the anions. The equilibrium growth sequences for Al-doped Si clusters
emerge as follows: i) neutral singly doped SinAl clusters favor Al atom substitution into a Si position in the
structure of the corresponding cation Sin+1+, whereas the anionic SinAl- has one Si atom of the isoelectronic neutral
Sin+1 being substituted by the Al impurity, and ii) for doubly doped SinAl20/- clusters, the neutrals have the shape
of Sin+1 counterparts in which one Al atom substitutes a Si atom and the other Al adds on an edge or a face of it,
whereas the anions have both Al atoms substitute two Si atoms in the Si n+2+ frameworks. The higher stability of
the closed shell Si9Al- can be rationalized in terms of the jellium electron shell model.
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The Third International Conference on
Computational Science and Engineering (ICCSE-3)
28-30 November, 2016, Ho Chi Minh City, Vietnam
P2.27
Structure, Magnetism, and Dissociation Energy of Small
Bimetallic Cobalt-Chromium Oxide Cluster Cations
NGUYEN MINH TAM,1,2 HUNG TAN PHAM,3 NGO TUAN CUONG,4 NGUYEN THANH TUNG5
1
Research Group of Computational Chemistry, Ton Duc Thang University, Ho Chi Minh City, Vietnam
2
Faculty of Applied Sciences, Ton Duc Thang University, Ho Chi Minh City, Vietnam
3
Institute for Computational Science and Technology, Viet Nam
4
Center for Computational Science, Hanoi National University of Education, Viet Nam
5
Institute of Materials Science, Vietnam Academy of Science and Technology, Viet Nam
Email: [email protected]
The cationic clusters CoxCryO+m(x + y = 2, 3 and 1 ≤ m ≤ 4) are investigated using combined experimental
photodissociation mass spectrometry and density functional theory calculations. It is found that the clusters grow
preferentially through maximizing the number of metal–oxygen bonds with a favor on Cr sites. The size- and
composition-dependent magnetic behavior is discussed in relation with the local atomic magnetic moments. While
doped species show an oscillatory magnetic behavior, the total magnetic moment of pure cobalt and chromium
oxide clusters tends to enhance or reduce as increasing the oxygen content, respectively. The dissociation energies
for different evaporation channels are also calculated and compared with the experimental observations as well
as to suggest the stable patterns, as fingerprints for future photofragmentation experiments.
References
[1] Nguyen Thanh Tung, Nguyen Minh Tam, Minh Tho Nguyen, Ewald Janssens, Peter Lievens; Journal of
Chemical Physics, Vol. 141, 2014, 04431-04437.
[2] Hung Tan Pham, Ngo Tuan Cuong, Nguyen Minh Tam, Vu Dinh Lam, Nguyen Thanh Tung; Chemical Physics
Letters, Vol. 643, 2016, 77-83.
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The Third International Conference on
Computational Science and Engineering (ICCSE-3)
28-30 November, 2016, Ho Chi Minh City, Vietnam
P2.28
Theoretical Study of Small Scandium-Doped Silver Clusters
ScAgn with n= 1–7: σ-Aromatic Feature
LOC QUANG NGO, HUNG TAN PHAM, PHUONG MY HO-PHAM, MINH THO NGUYEN
Institute of Computational Science and Technology, Ho Chi Minh City, Viet Nam
Email: [email protected]
In this theoretical investigation, the geometry, chemical bonding and aromatic feature of silver cluster doped by
Sc are explored by the mean of DFT calculation. The planar shape is found for all ScAg n clusters. The growth
mechanism is illustrated as formation of the hexagonal and heptagonal metal cycles by increasing the number of
Ag atoms. Particularly, the ScAg6- and ScAg7 present the planar metal cyclic form in which Sc atom locates at the
central position of Ag6 and Ag7 cycles. The σ aromaticity is demonstrated by exist of strongly diatropic current
for both ScAg6-, ScAg7 and ScCu7 clusters. In Sc doped ScAgn clusters, the delocalized bonding pattern is found
as a connector between Sc and Agn host, as indicated by ELI_D analysis.
References
[1] H. T. Pham, L. Q. Ngo, M. P. Ho-Pham, M. T. Nguyen, J. Phys. Chem. A, 2016, 120, 7964–7972.
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The Third International Conference on
Computational Science and Engineering (ICCSE-3)
28-30 November, 2016, Ho Chi Minh City, Vietnam
P2.29
Mechanism of the Oxidation Process of 1,2-Naphthoquinone by
Hydroxyl Radicals in Water Studied using a DFT Approach
NGÔ QUANG LỘC,1 PHẠM HỒ MỸ PHƯƠNG1,2
1
2
Institute for Computational Science and Technology, Ho-Chi-Minh City (ICST), Vietnam
Faculty of Chemical Engineering, Ho Chi Minh City University of Technology (HCMUT), Vietnam
Email: [email protected]
The decomposition mechanism of 1,2-naphthoquinone in the presence of hydroxyl radicals and oxygen was
investigated by using DFT approach coupled with 6-311++G(d,p) basis set. The intermediates and transition state
as well as the energy profile for each reaction were discovered and calculated. Our results suggest that ring-open
and oxidization products such as: 2-formyl-Benzoic acid, catechol, benzene-1,2,3-triol, maleinaldehydic acid, and
a few oxo acids along with water and carbon dioxide are formed. A reaction coordinate for each major product is
then plotted to illustrate the changes in energy in the system. It is shown that most reactions are exothermic and
require low to mild input energy to overcome the classical barrier.
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The Third International Conference on
Computational Science and Engineering (ICCSE-3)
28-30 November, 2016, Ho Chi Minh City, Vietnam
P2.30
Effects of (-)-epigallocatechin-3-gallate (EGCG) on the
Oligomerization of Amyloid Beta (16-22) Hexamer: A Theoretical
Study
SON TUNG NGO,1,2 DUC TOAN TRUONG,3 NGUYEN MINH TAM1,2
1
Computational Chemistry Research Group, Ton Duc Thang University, Ho Chi Minh City
2
Faculty of Applied Sciences, Ton Duc Thang University, Ho Chi Minh City, Vietnam
3
Department of Theoretical Physics, University of Sciences, Ho Chi Minh City, Vietnam
Email: [email protected]
The (-)-epigallocatechin-3-gallate (EGCG), a small compound deriving from green tea, consists of the aromatic
rings that can form π-π stacking interactions with the amyloid beta (Aβ) residues able to prevent the formation of
Aβ oligomers. An extensive replica exchange molecular dynamics simulation was performed to investigate the
physical insight of the inhibition of EGCG on the Aβ16-22 hexamer. The changes in the structure of oligomers
when EGCG is present and absent were monitored and analyzed. REMD results indicate that EGCG not only
reduces the β-content of the oligomer over all considered snapshots, but also it decreases the β-sheet sizes with an
order of higher than two of the oligomers that correspond to the highly neurotoxic forms. Moreover, EGCG has
the possibility to accelerate the oligomerization process of the Aβ peptide, thus reduces the number of toxic
conformations of Aβ oligomer. The investigated inhibitor is bound to the peptide with the same level to curcumin,
but in a different scheme that EGCG creates strong electrostatic interactions to the receptor. The appearance of
EGCG tends to decrease the binding free energy between constituting monomers to the others of the Aβ 16-22
hexamer. In addition, the π-π stacking is indicated to be a critical factor of the non-bonded interaction between
EGCG and the peptide, which was investigated using quantum chemical methods (density functional theory with
the B97-D functional and the 6-311++G(d,p) basis set).
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The Third International Conference on
Computational Science and Engineering (ICCSE-3)
28-30 November, 2016, Ho Chi Minh City, Vietnam
P2.31
Electronic Structure and Thermochemical Parameters of the
Silicon-Doped Boron Clusters BnSi, with n = 8–14, and Their
Anions
LONG VAN DUONG,1 DANG THI TUYET MAI,2 MINH THO NGUYEN2
1
Institute for Computational Science and Technology (ICST), Quang Trung Software City, Ho Chi Minh City,
Viet Nam
2
Department of Chemistry, KU Leuven, Celestijnenlaan 200F, B-3001 Leuven, Belgium
Email: [email protected]
We performed a systematic investigation on silicon-doped boron clusters BnSi (n = 8–14) in both neutral and
anionic states using quantum chemical methods. Thermochemical properties of the lowest-lying isomers of BnSi0/–
clusters such as total atomization energies, heats of formation at 0 and 298 K, average binding energies,
dissociation energies, etc. were evaluated by using the composite G4 method. The growth pattern for B nSi0/– with
n = 8–14 is established as follows: (i) BnSi0/– clusters tend to be constructed by substituting B atom by Si-atom
or adding one Si-impurity into the parent Bn clusters with n to be even number, and (ii) Si favors an external
position of the Bn frameworks. Our theoretical results reveal that B 8Si, B9Si–, B10Si and B13Si– are systems with
enhanced stability due to having high average binding energies, second-order difference in energies and
dissociation energies. Especially, by analyzing the MOs, ELF, and ring current maps, the enhanced stability of
B8Si can be rationalized in terms of a triple aromaticity.
Keywords: Boron Clusters, Silicon-doped, Aromaticity, Ring Current
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The Third International Conference on
Computational Science and Engineering (ICCSE-3)
28-30 November, 2016, Ho Chi Minh City, Vietnam
P2.32
Aromatic Character of Planar Boron-based Clusters Revisited by
Ring Current Calculations
HUNG TAN PHAM,1 MINH THO NGUYEN2
2
1
Institute of Computational Science and Technology, Ho Chi Minh City, Viet Nam
Department of Chemistry, KU Leuven, Celestijnenlaan 200F, B-3001 Leuven, Belgium
Email: [email protected]
The planarity of small boron-based clusters is the result of an interplay between geometry, electron delocalization,
covalent bonding and stability. These compounds contain two different bonding patterns involving both σ and π
delocalized bonds, and up to now, their aromaticity has been assigned mainly using the classical (4N + 2) electron
count for both types of electrons. In the present study, we reexplored the aromatic feature of different types of
planar boron-based clusters making use of the ring current approach. The B 3+/-, B42-, B5+/-, B6, B7-, B82-, B9-, B102-,
B11-, B12, B13+, B142- and B162- are characterized by magnetic responses to be doubly σ and π aromatic species in
which the π aromaticity can be predicted using the (4N + 2) electron count. The triply aromatic character of B 12
and B13+ is confirmed. The π electrons of B182-, B19- and B202- obey the disk aromaticity rule with electronic
configuration of [1σ21π41δ42σ2] rather than the (4N + 2) count. The double aromaticity feature is observed for
boron hydride cycles including B@B5H5+, Li7B5H5 and M@BnHnq clusters from both the (4N + 2) rule and ring
current maps. The double π and σ aromaticity in carbon-boron planar cycles B7C-, B8C, B6C2, B9C-, B8C2 and
B7C3- is in conflict with the Huckel electron count. This is also the case for theions B 11C5+/- whose ring current
indicators suggest that they belong to the class of double aromaticity, in which the π electrons obey the disk
aromaticity characteristics. In many clusters, the classical electron count cannot be applied, and the magnetic
responses of the electron density expressed in terms of the ring current provide us with a more consistent criterion
for determining their aromatic character.
References
[1] H. T. Pham, K. Z. Lim, R. W. A. Havenith, M. T. Nguyen, Phys. Chem. Chem. Phys., 2016, 18, 1191911931.
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The Third International Conference on
Computational Science and Engineering (ICCSE-3)
28-30 November, 2016, Ho Chi Minh City, Vietnam
P2.33
Mn2@Si15: the Smallest Triple Ring Tubular Silicon Cluster
HUNG TAN PHAM,1 LONG VAN DUONG,1 NGUYEN MINH TAM,1
MINH THO NGUYEN2
1
Institute of Computational Science and Technology (ICST), Ho Chi Minh City, Viet Nam
2
Department of Chemistry, KU Leuven, Celestijnenlaan 200F, B-3001 Leuven, Belgium
Email: [email protected]
The smallest triple ring tubular silicon cluster Mn2@Si15 is reported for the first time. Theoretical structural
identification shows that the Mn2@Si15 tubular structure whose triple ring is composed by three five-membered
Si rings in anti-prism motif, is stable in high symmetry (D5h) and singlet ground state (1A1’). The dimer Mn2 is
placed inside the tubular along the C5 axis, and the Mn dopant form single Si–Mn bonds with Si skeleton, whereas
the Mn–Mn is characterized as a triple bond. The effect of Mn2 on the stability of the Si15 triple ring structure
arises from strong orbital overlap of Mn2 with Si15.
Reference
[1] H. T. Pham, T. T. Phan, N. M. Tam, D. V. Long, M. T. Nguyen, Phys. Chem. Chem. Phys., 2015, 17, 7566.
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The Third International Conference on
Computational Science and Engineering (ICCSE-3)
28-30 November, 2016, Ho Chi Minh City, Vietnam
P2.34
Effects of Bimetallic Doping on Small Cyclic and Tubular Boron
Clusters: B7M2 and B14M2 Structures with M = Fe,Co
HUNG TAN PHAM,1 MINH THO NGUYEN2
1
2
Institute of Computational Science and Technology, Ho Chi Minh City, Viet Nam
Department of Chemistry, KU Leuven, Celestijnenlaan 200F, B-3001 Leuven, Belgium
Email: [email protected]
Using density functional theory with the TPSSh functional and the 6-311+G(d) basis set, we extensively searched
for the global minima of two metallic atoms doped boron clusters B 6M2, B7M2, B12M2 and B14M2 with transition
metal element M being Co and Fe. Structural identifications reveal that B 7Co2, B7Fe2 and B7CoFe clusters have
global minima in a B-cyclic motif, in which a perfectly planar B7 is coordinated with two metallic atoms placed
along the C7 axis. The B6 cluster is too small to form a cycle with the presence of two metals. Similarly, the B 12
cluster is not large enough to stabilize the metallic dimer within a double ring 2xB6 tube. The doped B14M2 clusters
including B14Co2, B14Fe2 and B14CoFe have a double ring 2 x B7 tubular shape in which one metal atom is
encapsulated by the B14 tube and the other is located at an exposed position. Dissociation energies demonstrate
that while bimetallic cyclic cluster B7M2 prefers a fragmentation channel that generates the B 7 global minimum
plus metallic dimer, the tubular structure B14M2 tends to dissociate giving a bimetallic cyclic structure B 7M2 and
a B@B6 cluster. The enhanced stability of the bimetallic doped boron clusters considered can be understood from
the stabilizing interactions between the anti-bonding MOs of metal–metal dimers and the levels of a disk aromatic
configuration (for bimetallic cyclic structures), or the eigenstates of the B 14 tubular form (in case of bimetallic
tubular structure).
Reference
[1] H. T. Pham, M. T. Nguyen, Phys. Chem. Chem. Phys., 2015, 17, 17335.
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The Third International Conference on
Computational Science and Engineering (ICCSE-3)
28-30 November, 2016, Ho Chi Minh City, Vietnam
P2.35
Ab initio Chemical Mechanisms of SiHx+ (x = 1-3) Ions Reactions
with SiH4
TRONG NGHIA NGUYEN,1,2 M. C. LIN1
1
Center for Interdisciplinary Molecular Science, Department of Applied Chemistry, National Chiao Tung
University, Hsinchu 300, Taiwan. E-mail: M. C. Lin, [email protected]
2
Department of Physical Chemistry, Hanoi University of Science and Technology, No. 1, Dai Co Viet,
Ha Noi, Viet Nam.
E-mail: [email protected]
The mechanisms for reactions of SiH4 and SiHx+ (x = 1,2,3) ions, which are known to coexist under CVD
conditions, have been investigated by high level ab initio electronic structure calculations based on the
CCSD(T)/CBS//B3LYP/6-311++G(3df,2p),
CCSD(T)/CBS//CCSD/6-311++G(3df,2p),
and
CCSD(T)/CBS//CCSD(T)/6-311++G(d,p) methods. For the barrierless radical association processes, their
variational transition states have been characterized by the CASPT2//CASSCF method. Our results show that
SiH3+ ion mainly abstracts one of the H atoms in SiH4, while SiH+ and SiH2+ ions can both abstract the H or insert
into one of the Si-H bonds of SiH4. The abstraction reactions of SiHx+ (x = 1-3) ions with SiH4 occur by initial
association via complexes LM6 (HSi-H2SiH2+) , LM3 (H2Si-HSiH3+), and LM1 (H3Si-HSiH3+) with 33.4, 36.2,
and 35.6 kcal/mol bind energies to be followed by fragmentation giving SiH 2+ + SiH3 (41.9 kcal/mol), SiH3+ +
SiH3 (-1.2 kcal/mol), and SiH4 + SiH3+ (0.0 kcal/mol), respectively. The insertion reactions of SiH + and SiH2+ ions
with SiH4 occur via long-live intermediates, H2SiSiH3+ (-47.4 kcal/mol) and H3SiSiH3+ (-40.9 kcal/mol),
respectively, which can fragment to various smaller species as depicted by the PESs. The major products of the
reactions are Si2H3+ + H2; SiH3+ + SiH3 and H3SiSiH+ + H2; and SiH4 + SiH3+, respectively. The predicted results
by the different methods are close to one another; the predicted structural parameters and enthalpy changes agree
well with available data.
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Figure 1. Potential energy diagrams for the SiH+ and SiH2+ + SiH4 reactions computed at the
CCSD(T)/CBS//B3LYP/6-311++g(3df,2p) level. The values in the parentheses and brackets are calculated at the
CCSD(T)/CBS//CCSD/6-311++g(3df,2p) and CCSD(T)/CBS//CCSD(T)/6-311++g(d,p) levels of theory,
respectively.
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The Third International Conference on
Computational Science and Engineering (ICCSE-3)
28-30 November, 2016, Ho Chi Minh City, Vietnam
P2.36
Molecular Simulation of Covalent Organic Framework
Formation
VU H. NGUYEN, MICHAEL GRÜNWALD
*Department of Chemistry, The University of Utah
Email: [email protected]
Covalent organic frameworks (COFs) are highly porous, crystalline materials with applications in gas storage,
catalysis, and filtration. They consist of molecular building blocks held together by an intriguing balance of strong
covalent bonds and weaker stacking interactions. Despite much experimental effort, assembling COFs into
crystals that are ordered on length scales larger than tens of nanometers has remained a challenge. Here, we report
on our efforts to elucidate the thermodynamic and kinetic bottlenecks of COF-5 formation using coarse-grained
modeling and computer simulation. Our model captures important details of bond geometry and flexibility, but
retains the computationally efficacy necessary to access the large time and length scales of COF nucleation and
growth. Preliminary molecular dynamics results show a strong competition between covalent bond formation and
stacking interactions, consistent with experimental finding.
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The Third International Conference on
Computational Science and Engineering (ICCSE-3)
28-30 November, 2016, Ho Chi Minh City, Vietnam
P2.37
Ethane Activation on IrO2(110) surface: DFT and vdW-corrected
DFT study
THONG LE MINH PHAM,1 DUY QUANG DAO,1 DAI-VIET NGUYEN VO,2
PHAM CAM NAM,3 JYH-CHIANG JIANG4
1
Institute of Research and Development, Duy Tan University, 03 Quang Trung, Danang, Viet Nam
Centre of Excellence for Advanced Research in Fluid Flow, Universiti Malaysia Pahang, 26300 Gambang,
Kuantan, Pahang, Malaysia
3
Department of Chemistry, Danang University of Science and Technology - The University of Danang, 54
Nguyen Luong Bang, Lien Chieu, Danang, Viet Nam
4
Department of Chemical Engineering, National Taiwan University of Science and Technology, 43, Keelung
Road, Section 4, Taipei 106, Taiwan
Email: [email protected] (TLMP); [email protected] (JCJ)
2
Ethane, the second most abundant hydrocarbon in natural gas, has recently gained enormous attention as cheap
and reliable chemical feedstock owing to recent boom in shale gas and natural gas production.[1] The low-cost
supply of ethane derived from above-mentioned sources makes its chemical transformation into more valuable
products is of great economic attractiveness. Although ethane is chiefly used as raw material for ethylene
production by steam cracking in chemical industry,[2] the full extent of ethane utilization could also be
functionalization of ethane and selective conversion of ethane to ethylene, ethylene oxide, acid acetic,
acetaldehyde, acrolein, vinyl chloride, ethanol etc.[3-7] Moreover, Ethane adsorption and activation is the key
step in any heterogeneous catalytic processes involving in ethane chemical utilization. Therefore, it is absolutely
necessary to gain insight into molecular mechanism of ethane activation on heterogeneous catalytic surfaces. In
this work, theoretical calculations were performed to investigate ethane adsorption and activation on IrO2(110)
surface employing both conventional and vdW-corrected density functional theory (DFT). Ethane chemical
bonding to IrO2(110) surface is driven by agostic interaction of C-H bonds with Ircus, which is involved in electron
transfer from C–H bonding orbital to the empty d orbital of Ircus atom as well as back donation from the
Ircus -5d z2 orbital to the anti-bonding orbital of the C–H bond. The adsorption energy of ethane on IrO2(110)
surface calculated by PBE funtional is 0.5eV. Vdw-corrected DFT calculation results indicate that London
dispersion force enhances the adsorption energy of ethane on IrO2(110) surface by about 0.47-0.61 eV. Ethane
dissociation on IrO2(110) surface is thermodynamically and kinetically favorable reaction, whose reaction energy
and kinetic barrier calculated by PBE funtional are -1.13eV (-1.12eV by opt-B88 functional) and 0.50 eV (0.57eV
by opt-B88 functional), respectively. By enhancing ethane adsorption energy, London dispersion force facilitates
the precursor-mediated dissociation of ethane on IrO2(110) surface, which is expected to occur at relatively low
temperature.
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The Third International Conference on
Computational Science and Engineering (ICCSE-3)
28-30 November, 2016, Ho Chi Minh City, Vietnam
Figure 1. Electron density difference indicating agostic interaction between C 2H6 molecule and IrO2 (110)
surface and Potential energy diagram for C2H6 dissociation reaction on IrO2 (110) surface
Table 1. Adsorption energies and structural parameters of the most stable C2H6 adsorption configuration on IrO2
(110) calculated by PBE and vdW-corrected DFT functionals
DFT functionals
Eads (eV)
d(Ir…C) (Å)
r(C-C) (Å)
r(C-H) (Å)
PBE
0.50
2.70, 2.71
1.53
1.15, 1.15, 1.10
vdW-DF
0.67
2.84, 2.83
1.55
1.13, 1.13 , 1.10
vdW-DF2
0.72
2.95, 2.94
1.55
1.13, 1.13, 1.10
optPBE-vdW
0.97
2.71, 2.70
1.54
1.15, 1.15, 1.10
optB88-vdW
1.12
2.71, 2.70
1.54
1.15, 1.15, 1.10
optB86b-vdW
1.21
2.68, 2.67
1.54
1.15, 1.15, 1.10
Keywords: Ethane adsorption, C-H activation, precursor-mediated mechanism, IrO2(110), vdW-corrected DFT
References
[1] J.J. Siirola, The impact of shale gas in the chemical industry, AIChE Journal, 60 (2014) 810-819.
[2] Y. Yao, D. Graziano, M. Riddle, J. Cresko, E. Masanet, Greener pathways for energy-intensive commodity
chemicals: opportunities and challenges, Current Opinion in Chemical Engineering, 6 (2014) 90-98.
[3] G. Centi, F. Cavani, F. Trifirò, Selective Oxidation by Heterogeneous Catalysis, Springer US, 2001.
[4] J. Gao, D. Zhou, Y. Wu, T. Wu, Direct conversion of ethane to ethylene oxide over NiAgYO catalyst, Catalysis
Communications, 30 (2013) 51-55.
[5] D.J. Xiao, E.D. Bloch, J.A. Mason, W.L. Queen, M.R. Hudson, N. Planas, J. Borycz, A.L. Dzubak, P. Verma,
K. Lee, F. Bonino, V. Crocellà, J. Yano, S. Bordiga, D.G. Truhlar, L. Gagliardi, C.M. Brown, J.R. Long,
Oxidation of ethane to ethanol by N2O in a metal–organic framework with coordinatively unsaturated iron(II)
sites, Nat Chem, 6 (2014) 590-595.
[6] P. Verma, K.D. Vogiatzis, N. Planas, J. Borycz, D.J. Xiao, J.R. Long, L. Gagliardi, D.G. Truhlar, Mechanism
of Oxidation of Ethane to Ethanol at Iron(IV)–Oxo Sites in Magnesium-Diluted Fe2(dobdc), Journal of the
American Chemical Society, 137 (2015) 5770-5781.
[7] Z. Zhao, Y. Yamada, Y. Teng, A. Ueda, K. Nakagawa, T. Kobayashi, Selective Oxidation of Ethane to
Acetaldehyde and Acrolein over Silica-Supported Vanadium Catalysts Using Oxygen as Oxidant, Journal of
Catalysis, 190 (2000) 215-227.
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The Third International Conference on
Computational Science and Engineering (ICCSE-3)
28-30 November, 2016, Ho Chi Minh City, Vietnam
P2.38
Formation of Two-Dimensional Amorphous Silicon Carbide
from the Melt
LE NGUYEN TUE MINH, VO VAN HOANG
Computational Physics Lab, HCM City Univ. of Technology
268 Ly Thuong Kiet Street, District 10, HochiMinh City-Vietnam
Email: [email protected]
The glass formation of two-dimensional Silicon Carbide with the Tersoff interatomic potential is studied by
molecular dynamics (MD) simulation. Supercooled and glassy states are obtained by cooling from the melt.
Structural properties are investigated via partial radial distribution function (PRDF), coordination number and
ring distributions. Structural defects and their role in structure and properties of two-dimensional SiC have been
analyzed and discussed. We also show temperature dependence of various thermodynamic quantities of the
system. Calculations show that although amorphous two-dimensional SiC also exhibits honeycomb-like structure
(sixfold rings are main structural blocks), Si and C atoms are randomly distributed in the rings unlike that found
for crystalline counterpart. In addition, amorphous two-dimensional SiC contains a large amount of structural
defects which may lead to quite different physico-chemical behaviors compared to those of crystalline one.
Keywords: Glass Formation, Two-Dimensional Silicon Carbide, Structural Defects
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The Third International Conference on
Computational Science and Engineering (ICCSE-3)
28-30 November, 2016, Ho Chi Minh City, Vietnam
P2.39
A Synergistic Effect of Hydrogenation and SCN Treatments
of Ag-loaded TiO2 NPs on Water Splitting
T. T WANG, P. RAGHUNATH, M. C. LIN*
Center for Interdisciplinary Molecular Science, Department of Applied Chemistry,
National Chiao Tung University, Hsinchu 300, Taiwan
Emails: [email protected] (PR); [email protected] (MCL)
Although silver is less reactive as a catalyst for water splitting than Pt and Au, Choi et al. [ACS Catal. 2016, 6,
821] have revealed that the SCN-treatment of Ag-loaded on TiO2 nanoparticles enhances its hydrogen production
efficiency by 4 times. In this work, we have discovered that the hydrogenation of TiO2 NPs further enhances the
efficiency of AgSCN/TiO2 by a factor of 3 with an overall solar to hydrogen efficiency of 7.0% using a Pyrex
tube with a <3.25 W Xe-lamp from a 500W Xe-lamp.
Experimentally, the hydrogenated TiO2 (H:TiO2) NPs were first prepared with 3 hours of hydrogenation at 300
ºC with 150 Torr methanol vapor as H source. Silver ion from AgNO 3 was reduced on H:TiO2 NPs in methanol
solution with 30 min Xe-lamp irradiation. For water splitting reaction, 30 mg substrate was dissolved in a reactor
with 60ml DIW and 20% methanol as sacrificial reagent. For Ag/H:TiO 2 NPs, H2 production rate was found to
increase by 15 times over that of H:TiO2 (see Fig. 1). SCN treatment of Ag/H:TiO2 further enhanced the efficiency
by 3 times. H2 production rate remained unchanged after 6 consecutive weeks of durability test (carried out once
per week), including a full week solar irradiation, revealing the durability of the AgSCN/H:TiO2 system.
Computationally, we have investigated the adsorption of SCN and the reaction of H on Ag-loaded anatase
TiO2(101) surface using spin-polarized density functional theory (DFT) employing the PBE functional. The SCN
adsorption energy for on the Ag/TiO2 was found to be 43.0 kcal/mol for 1 SCN on 1Ag and 60.2 kcal/mol for 2
SCN on 3Ag atoms. H atom can directly form an N−H bond with large exothermicity (-67.9 kca/mol) when
compared to an S−H bond (-46.9 kca/mol). The results show that, an additional H atom can directly abstract the
H atom of TiO2-1Ag-SCNH or TiO2-1Ag-S(H)CN to release H2 through 10.2 or 4.6 kcal/mol barriers,
respectively. In the case of 2 SCN on 3 Ag loaded TiO2, H2 elimination from 2 N−H and 2 S−H sides required
52.8 kcal/mol and 6.9 kcal/mol, respectively. The predicted densities of states show several prominent new
impurity states in the band gap of AgSCN/H:TiO2.
a)
80
TiO2
HTiO2
AgTiO2
AgSCNTiO2
AgHTiO2
AgSCNHTiO2
70
60
[H2] /mol
50
40
30
20
10
0
0
20
40
60
80
100
Time /min
Figure 1. a) Hydrogen production rate comparison for TiO2, H:TiO2, Ag/TiO2, AgSCN/TiO2, Ag/H:TiO2,
AgSCN/H:TiO2 as labelled. b) Schematic diagram of H atom binding on SCN and H2 elimination by DFT method.
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The Third International Conference on
Computational Science and Engineering (ICCSE-3)
28-30 November, 2016, Ho Chi Minh City, Vietnam
P2.40
Theoretical Study of the Influence of Saturated Hydrocarbons
Over Dye Adsorption in Dyes-Sensitized Solar Cells Application
THI M. T. NGUYEN,1 HA H. DO,1 NGUYEN-NGUYEN PHAM-TRAN1,2
1
Institute for Computational Science And Technology at Ho Chi Minh City, Quang Trung Software City, SBI
Building. Street No. 3, Tan Chanh Hiep Ward, District 12, HCMC.
2
Laboratory of Computational Chemistry, Faculty of Chemistry, University of Science, Vietnam National
University – Ho Chi Minh City,227 Nguyen Van Cu, District 5, HCMC.
E-mail: [email protected]
Three organic dyes, named 2-4, were designed followed D-π-A model, the most common dye formation has been
used in dye-sensitized solar cells (DSSCs). Without heterocycles in the conjugations, theoretical dye molar
extinction coefficients in DMF were merely different, 340.3 (2) and 340.4 nm (3 and 4) with PCM model at TDDFT/MPW1K/6-31G* level. Furthermore, the study carried out the influence of alkyl chains on dye adsorption
onto TiO2 semiconductor surface with (1 0 1) direction. With the prolongation of alkyl chains in charge pushing
groups, from four to eight saturated carbons, these dyes adsorbed at the interfaces without regulation. To
investigate the dependence of adsorption positions, each dye adsorption was modeled in two forms. Adsorption
energies were ~ 0.9 kcal/mol (2), ~ 18.5 kcal/mol (3) and ~ -15.8 kcal/mol (4). The energy deviations between
two adsorbed positions were not significant (~ 0.001- 0.01 kcal/mol). Based on the computational results, with
the purpose of experimental backup, we suggested that prolonging alkyl chains mainly prevented dye aggregation
and the use of longer alkyl chains to improve the power conversion efficiencies (PCEs) were not regular.
Moreover, the adsorbed positions were negligibly dependent on sizes of alkyl chains and it was considered as the
minor influence to dye adsorption.
Keywords: DSSCs, PCEs, DSC, PCM, TD-DFT, D-π-A
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The Third International Conference on
Computational Science and Engineering (ICCSE-3)
28-30 November, 2016, Ho Chi Minh City, Vietnam
P2.412
Density Functional Studies on Mechanisms of Alkaline
Hydrolysis Reactions of Lactam Antibiotics Models
NGUYEN HOA MI,1 NGUYEN THI NGOC HONG,1 SEIJI MORI2
1
VNU University of Science, Ha Noi, Vietnam
2
Ibaraki University, Japan
Email: [email protected]
β-Lactam resistance of methicillin-resistant Staphylococcus aureus (MRSA), a pathogenic bacterium that causes
staph infections, represents a serious threat to public health. Previous researches indicated that the mechanism of
β-lactam resistance was related to the process of cleaving the C-N bond of β-lactam ring. Numerous researches
were devoted to the hydrolytic ring-opening reaction mechanism of β-lactam, which proved that the mechanism
of enzymatic hydrolysis is similar to that of alkaline hydrolysis.
Mechanism of the alkaline hydrolysis reactions of lactam models were proposed to take place in two basic steps:
The first step of the reaction mechanism involves the nucleophilicity of the hydroxyl ion group to promote the CO bond formation. The second step involves the simultaneous breaking of C–N bond and a proton transfer from
a hydroxyl group to nitrogen atom to yield the product (Figure 1).
CH2 n
O
C
NH
CH2
O
C
CH2
n
NH
O
C
CH2
n
NH
O
C
O
O
H
H
O
n
NH
H
-
Figure 1. Acylation mechanism in which the lactam carbonyl is attacked by (OH ) in solution.
All calculations were carried out with the Gaussian 09 package. Geometry optimizations in soluiton were carried
out the B3LYP-D3 method with 6-311+G** basis set. The alkaline hydrolysis reaction was performed in aqueous
phase using the self-consistent reaction field (SCRF) method based on SMD theory with water solvent
(ε=78.3553).
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The Third International Conference on
Computational Science and Engineering (ICCSE-3)
28-30 November, 2016, Ho Chi Minh City, Vietnam
P2.42
QSPR Studies of Organic Dyes Using First-Principles and
Artificial Neuron Network:
Predicting Tools for Energy Conversion Efficiency of DyesSensitized Solar Cells
Phuc T. N. Tu, 1, Thanh N. Tran,1 Loan T. T. Nguyen,1 Van K. T. Nguyen,1
Thi M. T. Nguyen,2 Nguyen-Nguyen Pham-Tran1,2
1
Laboratory of Computational Chemistry, Faculty of Chemistry, University of Science, Vietnam National
University – Ho Chi Minh City,227 Nguyen Van Cu, District 5, HCMC.
2
Institute for Computational Science And Technology at Ho Chi Minh City, Quang Trung Software City, SBI
Building. Street No. 3, Tan Chanh Hiep Ward, District 12, HCMC.
E-mail: [email protected]
Abstract
In this work, we take the advantage of computational chemistry, as well as chemoinformatic in solving practical
problems of developing high potential organic dyes for dye-sensitized solar cells (DSSC) application. The
outcome of our project is to build a good QSPR (Quantitative Structure Property Relationships) model of series
organic dyes which has accurately predicting energy conversion efficiency of DSC based on parameter-free from
first principles calculations. This will be a powerful support tool for virtual screening and testing new dyes for
DSC and suggesting the promising candidates for actual experimental synthesis.
Keywords: Chemoinformatic, QSPR, DSC, ANN, GA, First principles calculations
70