Journal of Theoretical and Computational Chemistry

In this work, HOMO-LUMO energy gap and the lowest excitation energy of poly [2,7-(9,9-dihexylfluorene)-co-alt-2,5-(decylthiophene) were performed by different methods. The obtained results indicate that TDDFT(B3LYP/6-31G*)//B3LYP/6-31G* calculations can be useful to provide reliable energetic and structural results of this polymer. The HOMO-LUMO predictions were not accurately obtained as compared to the experimental results. The inverse chain length approximation by using TDDFT(B3LYP/6-31G*)//B3LYP/6-31G* calculations provides energy gap of 2.50 eV, which is in an excellent agreement with the experimental data. However, it was found that the HOMO-LUMO energy gaps obtained from B3LYP calculations were still far from the experimental data.

HIV-1 RT catalyses the reverse transcription of viral genetic material (RNA) into double-stranded DNA, and is an important target of antiviral therapy in the treatment of AIDS. Better understanding of the structure, mechanism and functional role of residues involved in the resistance of HIV-1 RT against nucleoside-analog drugs may assist in the development of improved inhibitors, and also in understanding the effects of genetic variation on RT specificity and activity. In this study, firstly, molecular dynamics simulations (with CHARMM27) have been used to investigate binding interactions at the active site and the conformational behavior of the enzyme, then, mechanisms of deprotonation and DNA polymerization reactions have been modelled by the QM/MM method. A combined quantum mechanical and molecular mechanical (QM/MM) method (AM1/CHARMM) has been used to study the triphosphate substrate and the active site of HIV-1 reverse transcriptase complex structure, a virally-encoded enzyme. Free energy profiles for the reaction are also calculated. The obtained results provide important insight into the mechanistic activity of HIV-1 RT.

The notable three oxygen stacking that occurs upon binding of ribonucleoside substrate and phosphate nucleophile by human purine nucleoside phosphorylase (hPNP) enables the coupling of protein dynamic modes to compress this stack, squeezing the ribosyl O4' between ribosyl O5' and the nuclophilic O_P. Created primarily by the motion of active site residue H257, this compression dynamically lowers the barrier height for N9–C1' ribosidic bond cleavage by as much as 20%. As such, this compression constitutes a protein promoting vibration (PPV) (S. Nuñez et al.). Presently, we demonstrate charge fluctuations in the ribose and purine components of the ribonucleoside substrate, as well as specifically across the N9–C1' ribosidic bond, that are correlated with the PPV and can explain the decrease in reaction barrier height due to their facilitating cleavage of the ribosidic bond. hPNP apparently employs protein dynamics to push electrons, a finding that suggests that this coupling may be found more generally in enzymes that catalyze substitution and elimination reactions.

The origin of genuine (not statistically spurious) entropy-enthalpy compensation is investigated within standard liquid state statistical mechanics formalism. We treat two extreme cases of solvent-solute interaction: (1) those in which the changes "internal" to the solute dominate, and (2) those in which the solvent effect is dominant. They are evaluated in different ways, and lead to different predictions for compensation behavior. The first involves a conventional "thermodynamic perturbation" formalism.^1,2 The second case leads to an Ornstein–Zernicke-like relationship that predicts predominantly entropically driven changes in free energy of reaction.

A method for analyzing the topological relation of any two peptide fragments in a protein structure is given by making analogy of the two fragments with a braid. Knotted relations are analyzed by calculating polynomials for the two fragments separately and for the two as a whole, respectively. Twisting is calculated from the writhe number, which is a measure to the internal relative rotation during formation of the protein structure. Statistical analysis on the internal rotations of all known structures found that the relative rotation like a one-dimensional random walk with decreasing step lengths.

The intramolecular hydrogen bonding formation in ortho-substituted compounds of Acetanilide, ortho-hydroxy Acetanilide and ortho-nitro Acetanilide, was investigated using Density Functional Theory (DFT), Møller-Plesset second-order (MP2) method and "Atoms in Molecules (AIM)" theory. It was found that in each case, the cis isomer is more stable than the trans isomer and ortho-nitro Acetanilide forms a stronger hydrogen bond than ortho-hydroxy Acetanilide. The effects of hydrogen bonding on structural parameters of the considered systems were studied using Becke's functional (B3LYP) and at the ab initio MP2 level in conjunction with different basis sets and suitable structural factors. The results are in agreement with the results of AIM theory.

The conception of partial potential energy surface (PPES) is presented in this paper. PPES can be abstracted from complete potential energy surface (CPES), therefore, it can be constructed with ab initio quantum chemical method. For the systems of H+H₂→H₂+H, I+HI→IH+I and I^-+HI→IH+I^-, the construction and applications of PPES are proposed as typical examples. It can be seen that the applications of PPES demonstrate remarkable virtues in the analysis of reaction mechanism and the formation of scattering resonance states.

Theoretical justification for the preferential formation of an 18-membered cyclic oligopeptide 1 based on 5-(aminomethyl)-2-furancarboxylic acid (AMFC, 2), is attempted using ab initio quantum chemical calculations. The free energy values obtained from Hessian calculations show that while the formation of the higher order cyclized oligopeptides [HN–H₂C–(furan)–CO]_n with n=3,4, is energetically favorable, the formation of the cyclic dipeptide 3 is thermodynamically unfavorable. Inclusion of the solvent in calculations enhances this preference further. A plausible explanation for this is the proximity of repulsive charges on the furan O atoms in the dimer 3. Details of geometric parameters and Mulliken charges support this possibility. The repulsion is enhanced, as low frequency modes of nuclear motion that bring these O atoms closer are active at room temperature.

In this work, we investigate the intramolecular vibrational energy redistribution associated with the hydrogen transfer in a derivative of tropolone, namely 3,7-dichlorotropolone. Our quantum simulation is based on the Cartesian reaction surface Hamiltonian together with the multi-configurational time-dependent Hartree approach for the wave-packet propagation. We compare results for two model systems with 6 and 14 dimensions, respectively. The 6D model accounts for the most strongly coupled modes, whereas the 14D model includes further modes with significantly weaker couplings. The linear absorption spectrum of both models shows the development of an OH-stretching band. Furthermore the results show that despite the fact, that the additional modes in the 14D system couple significantly weaker, there are qualitative differences in the decay behavior of an OH-stretching excitation. Limitations of the present reaction surface approach are also discussed.

Density functional method was applied to the study of the highly efficient primary explosive 2-diazo-4,6-dinitrophenol (DDNP) in both gaseous tautomers and its bulk state. Two stable tautomers were located. It was found that the structure (I) with open diazo, i.e. with linear CNN, is more stable than that with diazo ring tautomer (II) of DDNP. The structure I is in good agreement with the structure in the bulk. The lattice energy is -89.01 kJ/mol, and this value drops to -83.29 kJ/mol when a 50% correction of the basis set superposition error was adopted. The frontier bands are quite flat. The carbon atoms in DDNP make up the upper valence bands. While the lower conduction bands mainly consist of carbon and diazo N atoms. The bond populations of C–N bonds (both C–Nitro and C–Diazo) are much less than those of the other bonds and the detonation may be initiated through the breakdown of C–N bonds.

Based on classical electrodynamics, the proper integral formula for general cases is adopted to estimate the electrostatic free energy difference between two given states, e.g. equilibrium and non-equilibrium states in the charging process of solute molecule in solution. With adequate consideration of the change of dielectric property in establishing the non-equilibrium state, the electrostatic free energy for this state can be obtained in a form differing from the traditional theories. The general formula of the solvent reorganization energy is derived according to the definition of the free energy difference between the non-equilibrium and equilibrium states due to the same electronic state of the solute molecule. Applying it to the two-sphere model and single-sphere model, we obtain the new expressions of the solvent reorganization energy, which are convenient to be used in practice. In the investigation of the return electron transfer of tetracyanoethylene-hexmethylbenzene system, good results can be obtained by using our expression when they are compared with those from the experiment.