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Graduate Category:EngineeringandTechnology DegreeLevel:PhDinChemicalEngineering AbstractID#1106 Multi-ScaleMolecularModelingofTetracyclicRosetteNanotubes ArthurGonzales III, Belete Legesse, TakeshiYamazaki, Hicham Fenniri* Abstract Results Rosettenanotubes(RNTs)aresoftorganicnanomaterialsselfassembledunderaqueousconditionsfromWatson-Crickinspired guanine-cytosine(G∧C)hybridbuildingblockswithcomplementary hydrogenbondingsites.Thesematerialshavesubstantialdesign flexibilityandarangeofapplications,whichispartlyattributedto theirdiversesurfacefunctionalizationandachemically/physically tunablechannelforguestmoleculeloading.Severalstudieshave establishedtheirbiocompatibilityandapplicationsinnanomedicine suchasincoatingsformedicaldevices,materialsfortissue engineering andfordrugdisplayanddelivery. Withnovelapplicationsinmind,particularly,drugdelivery,anew tetracyclicG∧Cmotif,theyGC,wasdesignedtoselfassembleinto RNTinwater. ToaidinthecharacterizationofthisnewRNT,multiscalemolecularmodelingtechniqueswereappliedtopredictits structureinwater.Moleculardynamics(MD),molecularmechanics (MM),andthestatisticalmechanicaltheoryofsolvation,alsoknown asthe3dimensionalreferenceinteractionsitemodel(3D-RISM) theorywere appliedtopredicttheconformationofRNTs.MMwas usedtodeterminethepossibleconformationsoftheindividual motifs.Fromthese,RNTmodelswerebuiltandMDsimulations were runtodeterminethestabilityandprobablestructureofthe nanotubes.TheresultssuggestthattheyGC motifcaneitherforma 6-memberedor7-memeberedringstacks.3D-RISMintegral equationswerethensolvedforthesystemtodeterminethe energeticsandtoproposeaself-assemblypathwayfortheRNTs. Currently,experimentsare beingdonetoverifythestructureofthe RNTs. TheMDsimulationssuggestthat A thereare morethanonepossible RNTconfigurations.Indeed,visually theRNTformedfrom7-membered ringslookmorestableasthecircular structureofthe6-memberedrosette deforms.AndtrajectoryRMSDsof thenitrogenatomsalsoindicatesthe samething. B C Thefinalmodelsofthetwosystems are shownbelow. System1:6-memberedrosette • Diameter =19Å • StackingDistance=3.8Å • Staggered Angle =12.8° D System2:7-memberedrosette Figure 2. MD simulation results. Middle rosette of System 1 (A) and System 2 (B). RMSD of the trajectories of the nitrogen atoms of the middle rosettes of System 1 (C) and System 2 (D). • Diameter =25Å • StackingDistance=3.9Å • Staggered Angle =12.2° Introduction A B C D 3D-RISManalysisofthefinalRNT modelsshowsanegativelytrending associationfreeenergy,which indicatesformationofrosettefrom withavailable motifsisspontaneous. Andboththe6-memberedrosette andthe7-memberedoneare possible. 0 1 2 3 4 5 6 7 0 -10 -20 -30 Sys tem 1 Sys tem 2 -40 -50 -60 Motif N umber Figure 4. Association free energy of the two systems. Conclusion Methods • 2 RNTs were then built from the minimized motifs and minimized. • 100 ns MD simulations were run to determine the stability and the most probable structure of the RNTs. • 3D-RISM was used to determine the energetics and to propose a selfassembly pathway for the RNTs. B Figure 3. Final RNT models. Rosette of System 1 (A) and System 2 (B). Twenty-ring stack RNTs of System 1 (C) and System 2 (D). Objectives • Get the possible conformations for yGC-RNTs using molecular mechanics (MM) and molecular dynamics (MD) simulations • Analyze energies using Macromodel (Schrodinger MM package) and 3D-RISM theory A As s ociation Free Energy (kcal/ mol) Th o u san d s TheyGC wasdesignedsothatanRNT withalarge channelcouldformand accommodateahostmoleculeinits cavitythatisbetween19-26Å in diameter. 6-memberedand7-memberedRNTsweremodeledusingmolecular mechanicaltechniquesandbothwerefoundtobeprobableconfigurations. EnergeticsanalysispredictsthatformationofRNTsfromavailablemotifsin solutiongoesthroughamotifbymotifadditionandisspontaneousat300K. Experimentsare currentlybeingdonetoverifythestructureoftheRNTs. C Figure 1. yGC motif (A), rosette formed by 6 yGC motifs (B), and a twenty-ring-stack RNT, hydrogen atoms are hidden for clarity (C). Suggested References 1. J. Am. Chem. Soc. 2001, 123 (16), 3854. 2. ChemPhysChem, 2010, 11, pp 361-367