Theoretical Study On Structure Of Chiral Molecules And Transition Process Between Enantiomers Under Environment

Chirality is a very important intrinsic property of the natural biological molecules,which is also considered to be directly related to the origin of life. The structuralstability of the enantiomer of chiral molecules as well as the conformation transitionupon the environment is closely associated with some basic life processes. And it alsoplays an important role in drug development and delivery. It has been currentlyreceived much attention in physics, chemistry, material science and life science fields.In this thesis, we synthetically used the density functional theory, density functionaltight binding method developed on this basis, and down to the semi-empirical abinitio as well as the classical molecular dynamics simulation methods, in order tostudy the structures of typical chiral molecules and the feature under environment,including the transition process between enantiomers upon the confinement. Thespecific research work mainly includes the following four parts:Firstly, reliable structural information of extremal points in a reaction isimportant but difficult to achieve in molecular chiral transitions under confinementdue to the complex molecular interactions. In this part, based on statistical results of anumber of classical molecular dynamics simulations, we expounded the completechiral transition process of a difluorobenzo[c]phenanthrene molecule (C18H12F2, calledD molecule) within a single-walled boron-nitride nanotube involves at least fiveextremal point structures, showing a unique feature of chiral transition in the confinedenvironment and suggesting an alternative to conventional first-principles calculationsto determine the complex potential energy surface of intermolecular interactions.Secondly, the transition process between chiral difluorobenzo[c]phenanthrenemolecule (C18H12F2, D molecule) enantiomers within non-polar fullerene C260has been studied based on ONIOM method, which combined the density functional theoryand the semi-empirical ab initio method, in order to explore the impact ofconfinement on the transition process of chiral enantiomers. We found that blue shiftoccurred generally in infrared and Raman spectra of D molecule under confinementenvironment, compared with those of isolated systems. Meanwhile, six types ofparticular patterns representing overall movement of D molecules appeared in0-60cm-1band. Interestingly, energy barrier of D molecule chiral transformation under saidconfinement ambience is elevated by15.88kcal·mol-1compared to those underisolated conditions, which means this confinement conditions can facilitate thestability of chiral molecular enantiomers. Moreover, in the confinement system, frontorbital energy of D molecule is lower than that of C260fullerene, so that D molecule isfurther stabilized due to the protection of fullerene matrix, in terms of reactivity. It isconcluded that confinement environment in nanoscale will have an impact onenantiomer transformation process of chiral molecules. These results may instructchiral medicine molecules transport and even the stability of chiral enantiomers.Thirdly, to further explore the factors that affect the structural stability, thehyperconjugation effect on molecular structural stability is studied by performing firstprinciples density functional theory calculations on the tert-butyl and its derived C4Hn(n=4-10) isomer structures. Four of the isomer structures with n=7-10were found toshow hyperconjugation similar to that in the tert-butyl, with hyperconjugation orbitalenergies decreasing with the increase of the number of hydrogen atoms participatingin the hyperconjugation (PIH). The distribution of charge carried by the PIH hydrogenatoms is uniform, which reveals a delocalization character in the electronic structures;and the PIH hydrogen atoms are found responsible for the main IR spectrum peakrelating to C-H stretching vibration. These findings may provide some regularknowledge on hyperconjugation.Finally, to promote possible applications of graphene in molecular identificationbased on stacking efects, in particular in recognizing aromatic amino acids and evensequencing nucleobases in life sciences, we study the interaction between graphenesegments and diferent cyclic organic hydrocarbons including benzene (C6H6),cyclohexane (C6H12), benzyne (C6H4), cyclohexene (C6H10),1,3-cyclohexadiene(C6H8(1)) and1,4-cyclohexadiene (C6H8(2)), using the density-functionaltight-binding (DFTB) method. The results present obviously diferent characteristics in Raman vibrational and ultraviolet visible absorption spectra of the small moleculesadsorbed on the graphene sheet. That are both spectra involve clearly diferentcharacteristic peaks, belonging to the diferent small molecules upon adsorption, withthe ones of ionized molecules being more substantial. Further analysis shows that theadsorptions are almost all due to the presence of dispersion energy in neutral casesand involve charge transfer from the graphene to the small molecules. In contrast, themain binding force in the ionic adsorption systems is the electronic interaction. Theresults present clear signatures that can be used to recognize diferent kinds ofaromatic hydrocarbon rings on graphene sheets. We expect that our findings will behelpful for designing molecular recognition devices using graphene.