Theoretical studies of structure, function and reactivity of molecules--a personal account

Abstract

Last few decades theoretical/computational studies of structure, function and reactivity of molecules have been contributing significantly in chemistry by explanation of experimental results, better understanding of underlying principles and prediction of the unknown experimental outcome. Accuracy needed in chemistry has long been established, but due to high power dependency of such accurate methods on the molecular size, it has been a major challenge to apply theoretical methods to large molecular systems. In the present article we will review some examples of such applications. One is theoretical study of growth/formation of carbon nanostructures such as fullerenes and carbon nanotubes, using quantum mechanical molecular dynamics method. For growth of single walled carbon nanotube from transition metal cluster, we have demonstrated continued growth of attached nanotube, cap formation and growth from small carbon fragments. For homogeneous catalysis we presented results of studies on N(2) activation by Zr complexes. For biomolecular reactions we use active site and protein models and show that in some catalyses the protein environment is involved in reactions and changes the preferred pathway, and in some other case the effect is modest. The review is concluded with a perspective.

Fig. 1

The schematic representation of multi-layered ONIOM method.

Fig. 2

“Shrinking Hot Giant” mechanism of fullerene formation from small carbon fragments. The self-assembly (size-up) process took place through different stages: nucleation of polycyclic structures from entangled polyyne chains, 2. repeated growth via “octopus-on-the-rock” structures, consisting of the familiar ring condensation of carbon chains and rings attached to the hexagon and pentagon containing nucleus as well as the chain-growth by addition of more C₂ fragments to the peripherals, and finally 3. cage closure where polyyne chains reach over the opening and “zip” them closed. Only giant fullerenes are formed. The size-down or shrinking process very slowly loses C₂ fragments from giant fullerenes by “pop-out” events to produce smaller fullerenes.

Fig. 3

DFTB/MD simulations of growth of SWNT from Fe₃₈ cluster. (A) Continued growth model. (B) Cap growth model.

Fig. 4

Activation of N₂ using two zirconium complexes. (A) Structure of the Fryzuk complex Fr_1 and the Chirik complex 4_Ch_1. (B) The relative energy of the Chirik end-on dimer complex relative to the side-on dimer complex, for different number of methyl groups on the cyclopentadienyl ligand. (C) Comparison of potential energy profile for the activation of the first two hydrogen molecules by Chirik and Fryzuk complexes. (Adapted from Bobadova-Parvanova et al., Ref. . Reprinted with permission. Copyright 2006 American Chemical Society.)

Fig. 5

Schematic representation of strategy of ONIOM approaches to effects of protein environments on enzymatic reactions.

Fig. 6

Mechanism of enzymatic reaction of indole 2,3-dioxygenase (IDO) and tryptophan 2,3-dioxygenase (TDO). (A) the reaction catalyzed by IDO and TDO. (B) X-ray structure of TDO. (C) Previously proposed mechanism of the enzymatic reaction, (D) The new mechanism based on the present study. (Adapted from Chung et al., Ref. . Reprinted with permission. Copyright 2008 American Chemical Society.)

Fig. 7

Mechanism of biosynthesis of antibiotics in isopenicillin N synthase (IPNS). (A) The reaction catalyzed by IPNS. (B) Structure of IPNS protein and active site. (C) Potential energy profiles of oxidation of ACV substrate by IPNS, using the active site model (DFT, black) and the protein model (DTF:MM, blue), with some detailed explanation of the effects of protein environments.

Fig. 8

Mechanism of radical carbon skeleton rearrangement catalyzed by B12-dependent methylmalonyl-CoA mutase (MMCM). (A) The reaction catalyzed by MMCM. (B) Stepwise and concerted pathways for the Co–C bond cleavage and hydrogen transfer stages of the reaction.

Fig. 9

The mechanism of efficient firefly bioluminescence via adiabatic transition state and seam of sloped conical intersection. (A) The reaction that generate the excited state of oxyluciferin that emit the light. (B) X-ray structure of luciferase. (C) The calculated overall reaction pathway, shown in red. (D) Topology of two potential energy surfaces in the vicinity of minimum energy conical intersection, MECI. (Adapted from Chung et al., Ref. . Reprinted with permission. Copyright 2008 American Chemical Society.)