Download Chemistry in Computers: from Educational Tools to

Chemistry in Computers:
From Educational Tools
to Computational Chemistry
Rituraj Kalita
Sr. Lecturer in Chemistry, Cotton College, Guwahati
(web-page: www.geocities.com/riturajkalita)
Presentation Prepared in: May, 2006
Chemistry in Computers – Why?
• Chemistry is a science of mobile three-dimensional
entities (species) such as molecules, radicals, ions &
macromolecules etc., and of their mutual interactions.
Two-dimensional and static figures on paper or on the
blackboard can’t properly explain or represent these!
• So, chemistry-education is greatly facilitated with
in-computer visual models and visual software-packages,
say in stereochemistry & organic-reaction mechanisms.
• The branch of computational chemistry (also called
theoretical chemistry) utilizes quantum mechanics to
theoretically calculate thermodynamic, spectroscopic &
kinetic properties of chemical species, existing or even
hypothetical. This job requires immense computations!
Visual Models & Packages:
Those Pre-built for You
• There remains several multimedia software packages for
aiding in one’s chemistry learning, either available in the
market or even freely obtainable on the internet.
• These packages include visual models of molecules that
can be rotated / translated by the user, and moving visual
models of reactions such as of SN1 & SN2 reaction-types.
• The internationally reputed chemistry textbooks for the
degree & postgraduate levels also, nowadays, provide a
CD containing such visual models relevant to the book,
• Such a multimedia package has also been developed at
the Chemistry Department of Pandu College, Guwahati!
Pre-built Visual Models:
A Rotating Model of Iodo-Methane
Visual Models & Packages:
To be Built by You
• Packages discussed above do not offer a facility for
creating your own visual models, or for modifying the
existing ones.
• In contrast, drawing packages such as ISIS/Draw and
modelling packages such as ArgusLab allows you to
create your own molecular-structure drawings/ models.
• Any such drawing or modelling package is based on the
idea that a molecule or radical can be represented by
specifying the nuclear-framework only, i.e., only by the
specification of the identities and positions of each of the
constituent nuclei. The electrons constantly keep moving
to form the electron-cloud, and so are un-specifiable. So,
there, you need to draw out only the nuclear-framework.
The Drawing Package ISIS/Draw:
Drawing Structures for Word-Processors
• Ever needed to draw chemical structures using Microsoft
Word or PageMaker? Or using Paint? It’s too difficult.
• ISIS/Draw is meant for that purpose: to draw chemical
structures for putting them into a word-processor
document such as an news-essay, or into a presentation
(e.g., power-point) file to present in front of a gathering.
• ISIS/Draw is developed by MDL Information Systems
Inc. (USA), and is available to anybody as a freeware.
• To get ISIS/Draw from the internet, search for ISIS/Draw
in a search engine (e.g., www.google.com), locate the
home-page (it is now www.mdli.com) of MDL, and
download ISIS/Draw (and its help-system)
The Modelling Package ArgusLab:
3-D Visual Models of Molecular Systems
• ISIS/Draw does not give you a full-fledged 3-D model of
the structure you’ve drawn. The picture formed can’t be
rotated to understand its 3-dimensional intricacies!
• So we may use ArgusLab, a leading Chemical Modelling
Software , to draw in it proper visual models.
• ArgusLab is developed by Planaria Software, (www.
planaria-software.com), and is available for free.
• ArgusLab allows us to draw structures as if on paper,
substitute, move, and delete atoms, and fix distances in
space. We can here grow structures with complete
control of stereochemistry. Even drug-macromolecule
docking could be performed in ArgusLab now .
Demonstration of ArgusLab v4.0
(Demonstration is to be performed by the instructor)
Drawing a Molecular-Structure Model
Saving a Molecular-Structure Model in Disk
Opening a Pre-Saved Molecular-Structure File
Viewing Structure Model in Different Views
Showing and Hiding Hydrogen Atoms, Rotating
Substituting and Deleting Atoms
The Basis Behind the Visual View:
Hidden Nuclear-Framework Mathematics
• In case of any visual molecular model worth this term,
the view isn’t preserved in the form a image (picture) file
as it would have made 3-D rotations rather impossible!
• The visual model is actually preserved as a text file (with
extensions .xyz, .c3d or .mop etc.) that contains list of the
identities (H, C, N, O etc.) & position-coordinates of all
the constituent nuclei, and also the molecular net charge.
• The model-viewer software-package such as ArgusLab,
ORTEP or Protein Explorer can read such data from
such molecular-model text file, and then generates the
visual view instantaneously to be viewed by the user.
The Basis Behind the Visual View:
An Actual Nuclear-Framework Expression
• In the following molecular model file of the .xyz type,
the identities of the nuclei and their Cartesian (x,y,z)
position-coordinates are kept listed (1 line for 1 nucleus)
• The unit of distance for the position-coordinates is
Angstrom (10–10 m) as a universally accepted convention
The Basis Behind the Visual View:
Two Types of Framework Specifications
• The above specification isn’t, however, the only possible
way of specification for the molecular nuclear-framework.
• Such Cartesian specifications are used in case of .xyz
(XYZ type) and .c3d (Chem-3D type) files. However in
the .mop (Mopac type) files etc., specification is in another
way, called the z-matrix relative-coordinates specification.
• In this way, a nuclear position is specified relative to a
bond-distance, a bond-angle and a dihedral-angle with
respect to some other (pre-specified) nuclei. This way is,
obviously, closer to any chemist’s heart.
• The angles are kept, by universal convention, in degrees.
The Basis Behind the Visual View:
Z-Matrix Type Coordinates-Specification
The Mathematical Basis of the Visual:
Computational Chemistry Flies Herefrom
• For any computational chemistry computation-package to
theoretically calculate the properties of any molecule or
any other chemical species, the molecule or chemical
species must be specified to it in a definitive manner.
• The afore-mentioned mathematical aspect of the
(molecular) model serves exactly this purpose. Thus the
computational software knows what species to calculate.
• A computational software-package (such as PC-GAMESS,
a freeware) is a very powerful tool at the hand of chemists.
Using it along with a PC for several hours, they can
calculate properties of (not-so-big) chemical species even
without doing any experiment! Even the pre-assumed
molecular structure may be made better via optimization.
Does Computational Chemistry Work?
A Study of a Silly Chemical Reaction
• As we can see here, computational chemistry can really
predict whether two molecules will react or not!
• Prediction is faster and better for small ones.
• To do that, we need to make a model of the moleculecombination (supermolecule) with the molecules far
apart, then ask the package for a structure-optimization.
• For larger molecules, meaningful computation requires
more accurate level of computations: this means much
more computer-time (hours for ~50 atom supermolecule)
• To find that NH3 & BF3 will react with DE~65 kJ mol–1,
forming N-B coordinate bond ~2 Ao long etc., takes only
less than a minute using PC-Gamess in a Pentium-II PC
Computational Chemistry Working:
Some Works that PC-GAMESS Does Are
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Calculation of molecular energies at diff. level of accuracy.
Calculation of molecular electronic wavefunctions.
Calculation of dipole moments and electron density.
Optimization of the pre-assumed molecular structure.
Calculation of vibrational normal modes, vibrational
frequencies and IR-spectra intensities.
• Prediction of reactivity and reaction-path (with mechanism).
(Instructor to do a Demonstration of PC-Gamess Operation)