Journal of Theoretical and Computational Chemistry

Density functional theory (DFT) was used to investigate the reaction mechanisms of ruthenium(II)-catalyzed hydroacylation of isoprene with benzaldehyde, and o-methoxyl, m-methoxyl and p-methoxyl benzaldehyde. All intermediates and transition states were entirely optimized at the B3LYP/6-31G(d,p) level (LANL2DZ(f) for Ru). The results demonstrated that the hydroacylation had two different catalytic cycles (path I and II), path II was more favorable than path I. Ru(II)-catalyzed hydroacylation began from the first catalytic cycle, and the nucleophilic reaction was the rate-determining step. The activation barriers of hydrogen migration were the highest in two catalytic cycles, so the hydrogen migration was the rate-determining step. The activation barrier of hydrogen migration could be broken down to two parts: the free energy of exchange ($\mathrm{\Delta }{G}_{\mathrm{\text{ex}}}$) and the relative free energy of transition state ($\mathrm{\Delta }G$). The ligand exchange energy ($\mathrm{\Delta }{G}_{\mathrm{\text{ex}}}$) had more contribution to the activation barrier than the relative free energy of transition state ($\mathrm{\Delta }G$), so the ligand exchange would control these hydroacylation. Furthermore, our calculations also described the substituent effect, and the results indicated that four aldehydes showed different chemical reactivity, and benzaldehyde and m-methoxyl benzaldehyde were predicted to have the best reactivity in ruthenium hydride-catalyzed hydroacylation.

The all-atom model of the photosynthetic core complex composed of the light-harvesting system (LH1) and the reaction center (RC) from a thermophilic purple bacterium Thermochromatium tepidum is constructed. We compare the structural parameters of this complex embedded into the lipid bilayer to those reported for the recently resolved crystal structure of the LH1–RC. We focus on the local structure of the binding sites of the calcium ions regulating stability and optical spectra of the core complex. We show the differences between the computationally derived model and the crystal structure at the extramembrane region of the LH1 polypeptides where the calcium binding sites are located.

Current knowledge about Chagas disease, the potentially life-threatening illness caused by the protozoan parasite (Trypanosoma cruzi), has led to the development of new drugs and the understanding of their mode of action. The Conceptual Density-Functional Theory was applied to determine the active center sites of trypanocidal compounds, extended by the Molecular Docking analysis to identify the most favorable ligand conformation when bound to the active site of cruzain. Results such as CHELPG charges, Fukui function, MESP, and Molecular Docking analysis are reported and discussed in the present investigation. Whereas, a close agreement with experimental results was found to explain the possibility of studying the receptor-binding mode using these different axes.

The addition reaction of germylenoid H₂GeFMgF with ethylene (C₂H₄) was first investigated in this work. All of the stationary points were optimized using the M062X method in conjunction with the 6-311$+$G (d, p) basis set and the corresponding energies were calculated using the QCISD method with the 6-311$++$G (d, p) basis set. The calculated results demonstrated that there are two different channels in the addition reaction of H₂GeFMgF with C₂H₄, while only the channel I is feasible once the C₂H₄ approaches H₂GeFMgF in the proper conditions. The solvent effect upon the addition reaction was also investigated using PCM model. The results demonstrated that the tetrahydrofuran (THF) solvent could accelerate the addition reaction.

A variety of organic donor–acceptor–donor materials based on thienylbenzothiadiazole (BTD$ii=1$–5) combined with different $\pi$-conjugated systems are studied by density functional theory (DFT) and time-dependent DFT (TD-DFT) for the ground- and excited-state properties, respectively, using B3LYP and the 6-31G(d, p) basis set. The effect of different electron-donor groups on the structural, electronic and optoelectronic properties is studied. To provide for the bandgap and to guide the synthesis of novel low bandgap materials, we applied quantum chemistry techniques to calculate the difference in the highest occupied molecular orbital (HOMO) and lowest occupied molecular orbital LUMO energies. However, we have studied the effect of the reduction and oxidation properties on the electronic excitation transitions for all compounds. The emission energies have been obtained from TD-DFT calculations performed on the excited-state optimized S₁ geometries. The theoretical results suggest that both the introduction of electron-donor groups and the doping process contribute significantly to the electronic and optoelectronic properties of the alternating donor–acceptor–donor conjugated systems studied.

This work describes a procedure for the numerical calculation of third virial coefficients of simple linear molecules. The method is applied to nitrogen using a site–site model pair-potential and the triple dipole term. Values of volumetric and acoustic second and third virial coefficients of nitrogen are reported over a wide range of temperature and compared with experimental data of several authors. The effect of including the quadrupole–quadrupole energy to the pair potential is investigated and the results suggest that the contributions of the quadrupole moment to second and third virial coefficients are non-negligible at low temperatures.

Biosynthesis of polyterpenoid and related molecules are largely accomplished via mevalonate pathway. One of the vital steps in this pathway is the inter-conversion of two intermediates isopentenyl pyrophosphate (IPP) and dimethylallyl pyrophosphate (DMAPP) catalyzed by IPP:DMAPP isomerase (IDI). The crystal structure of the enzyme, bound to the substrate analogues and inhibitors, revealed possible mechanism of this inter-conversion; however, none of them could affirm the true nature of the transition state through which the process is taking place. Our DFT study on the pathway of this isomerization reaction at the active site of the enzyme suggests a favorable concerted mechanism that occurs through a single transition structure without generating any carbocation intermediate. In this mechanism, the Cys-67 residue acts as proton donor whereas Glu-116 acts as proton acceptor. The mechanism also reveals the active involvement of other two components present at the active site. A crystallographic water molecule (Wat508) and Glu-87 assist to reprotonate the conjugate base of cysteine residue through a proton shuttle mechanism while forming the transition structure of the isomerization reaction.

Molecular dynamics simulations are applied to investigate the cylindrical polyelectrolyte brushes in monovalent and multivalent salt solutions. By varying the salt valence and concentration, the brush thickness, shape factor of grafted chains, and distributions of monomers and ions in the solutions are studied. The simulation results show that the single osmotic pressure effect in the brush leads to changes in conformation in the presence of monovalent salt, while the ion exchange effect induces the collapse of the brushes in the multivalent salt solutions. Furthermore, the snapshots combined with the distributions of the end-monomers and the mean bond angles demonstrate a nonuniform stretching picture of the grafted chains, which is different with the chains tethered on the planar surface. The charge ratios between the ions trapped in the brush and the monomers are also calculated to elucidate the details of ion exchange process.

The charge transport properties of perylene diimide (PDI) and its fluorinated derivatives were explored by density functional theory (DFT) coupled with the incoherent charge-hopping model. The geometric structure, reorganization energy, frontier molecule orbital, electron affinity (EA), ionization potential (IP), transfer integral as well as the anisotropic mobility were discussed. By attaching fluorine atoms to the bay region of PDI, the p-type material converts to the n-type or ambipolar ones (difluorinated-perylene diimide (DF-PDI) and tetraflurinated-perylene diimide (TF-PDI)). The electron mobility of difluorinated-perylene diimide (DF-PDI) (0.33cm² V${}^{-1}$ s${}^{-1})$ is much larger than its corresponding hole mobility (0.0008cm² V${}^{-1}$ s${}^{-1})$ due to its lower LUMO energy and more efficient pack-stacking, hence it could be a candidate of n-type organic semiconductor (OSC). The introduction of strong electron-withdrawing substituents (such as fluorine) to the perylene-based OSC materials is a promising strategy for the high-performance n-type OSCs. Besides, the three molecules exhibit remarkable anisotropic behaviors. Both the hole and electron maximal mobilities occur in the parallel $\pi$–$\pi$ stacking dimers.