Journal of Theoretical and Computational Chemistry

The peptide deformylase from Leptospira interrogans (LiPDF) shows many unusual characteristics. The substrate pocket of formate-bound complex adopts an open conformation. However, in the actinonin-bound LiPDF complex, a slightly open substrate pocket is observed. The opening is not large enough for the inhibitor, because the CD-loop restricts the access to the active site. To explore the conformational changes of the substrate pocket, we perform a 16,000 ps molecular dynamics simulation separately on the ligand-free LiPDF and actinonin-bound LiPDF. During the molecular dynamics simulations, extensive conformational changes have taken place. The comparison of the two MD results shows that the CD-loop, hydrophilic inhibitor, and hydrophobic cluster are necessary for the reopening of the substrate pocket. In addition, Tyr71 plays an important role in mediating the movements of CD-loop, and the transition of the substrate pocket from open to semi-open only occurs in the presence of an inhibitor, which are consistent with the experiment very well.

This paper focuses on the maximum generation issue. Molecular dynamics simulations have been employed to search the minimum energy configurations of eight types of structurally related polysilane dendrimers of various generations. Calculations reveal that for the studied dendrimers, the innermost Si–Si bonds adjoining the silicon atom at the center of the core structure are extended for steric relief with the amount of extension increasing with the number of generations due to the rise of the spatial hindrance inside these molecules.

The mechanistic study on the insertion of ethylene into the Zr–H bond of Cp₂ZrH₂ to give Cp₂Zr(H)(CH₂CH₃) is performed with the aid of density functional theory calculations. Two possible insertion pathways are proposed. One is the side-insertion and the other is the central-insertion. The rate-determining step is the ethylene insertion in the former path and formation of the adduct in the latter path. Our results of calculations predicted that the central-insertion path is preferred kinetically over the side-insertion path. Two types of Zr⋯H–C agostic interactions having different stabilities are described.

Quantum chemical calculations are used to estimate the bond dissociation energies (BDEs) for 15 thiol compounds. These compounds are studied by employing the hybrid density functional theory (B3LYP, B3PW91, B3P86, PBE0) methods and the complete basis set (CBS-Q) method together with 6-311G** basis set. It is demonstrated that B3P86 and CBS-Q methods are accurate for computing the reliable BDEs for thiol compounds. In order to test whether the non-local BLYP method suggested by Fu et al.¹⁹ is general for our study and whether B3P86 method has a low basis set sensitivity, the BDEs for seven thiol compounds are also calculated using BLYP/6-31+G* and B3P86 method with 6-31+G*, 6-31+G**, and 6-311+G** basis sets for comparison. The obtained results are compared with the available experimental results. It is noted that B3P86 method is not sensitive to the basis set. Considering the inevitable computational cost of CBS-Q method and the reliability of the B3P86 calculations, B3P86 method with a moderate or a larger basis set may be more suitable to calculate the BDEs of the C–SH bond for thiol compounds.

The glass transition temperature (T_g) values of three classes of vinyl polymers, i.e. polystyrenes, polyacrylates, and polymethacrylates, were predicted by using a quantitative structure–property relationship (QSPR) model constructed by back-propagation (BP) neural network. The four descriptors (the rigidness descriptor R_HR resulted by hydrogen-bonding moieties group and/or rings, the chain mobility n, the molecular average polarizability α, the net charge of the most negative atom q^-) were obtained directly from the polymers' monomer structures. Stepwise multiple linear regression analysis (MLRA) and artificial neural network (ANN) were used to generate the model. Simulated with the final optimum BP neural network [4–2–1], the results showed that the predicted T_g values were in good agreement with the experimental data, with a training set root-mean-square (rms) error of 20.478 K (R = 0.955) and a prediction set rms error of 20.174 K (R = 0.955).

Two kinds of nitrating reagents, a nitronium cation and a nitro radical (·NO₂), were used in the gaseous phase toluene mononitration reaction. The closed shell calculation for electrophilic substitution and open shell calculation for radical substitution were both performed in solventless, H₂O-solvated, and CH₃OH-solvated molecular reaction systems. In the series of electrophilic toluene nitration reactions, both ortho-nitro toluene (o-MNT) and para-nitro toluene (p-MNT) are more abundant products than meta-nitro toluene (m-MNT), no matter what solvent is used in the reaction system. The reaction energy barrier for obtaining each kind of mononitro toluene follows a stepwise decreasing trend when the reaction is carried out in the solventless, H₂O-solvated, and CH₃OH-solvated systems. In all radical toluene nitration reactions, solventless or solvated, m-MNT is the most abundant product. The energy barrier data also show that the nitration reaction is more feasible in a solvated than in a solventless system. H₂O has a more obvious solvent effect than CH₃OH in the ·NO₂ radical substitution reaction, and the H₂O-solvated system provides a lower activation energy reaction path.

We use the elements of the single particle density matrix in the atomic orbital basis as the basic variables and the simulated annealing method as the optimization tool to locate the global minima on the potential surfaces of polythiophene and polyselenophene oligomers (PT)_n, (PS)_n with n up to 100. A modified version of the Su–Schrieffer–Heeger Hamiltonian is used to generate the PES and the unitary transformation of the density variables as the bond lengths change during random reconfiguring moves. The cost effectiveness of the method is analyzed.

Quantitative structure–property relationship (QSPR) modeling is a powerful approach for predicting environmental behavior of organic pollutants with their structure descriptors. This study reports two optimal QSPR models for estimating water solubility (log S_W) and n-octanol/water partition coefficient (log K_OW) of chloric and alkyl benzene derivatives. Quantum chemical descriptors computed with density functional theory at B3LYP/6-31G(d) level and partial least squares (PLS) analysis with optimizing procedure were used for generating QSPR models for log S_W and log K_OW of chloric and alkyl benzene derivatives. The correlation coefficients of the optimal models for log S_W and log K_OW were 0.973 and 0.990, respectively. The results of internal cross-validation test and external validation test showed that both of the optimal models had high fitting precision and good predicting ability. The log S_W and log K_OW values predicted by the optimal models are very close to those observed. The PLS analysis indicated that chloric and alkyl benzene derivatives with larger electronic spatial extent and lower molecular total energy tend to be more hydrophobic and lipophilic, and smaller energy gap between the lowest unoccupied and the highest occupied molecular orbitals leads to larger dissolvability.

Steady-state cycle kinetics of single enzymes with competing substrates and multi-conformations is investigated. A large set of generalized Michaelis–Menten relations with similar structures is explored by introducing reasonable concepts of specificity constants, confirming the well-known belief that the specificity constants of an enzyme could be determined by studying the different substrates separately. The simple but general rigorous mathematical method used here makes the generalization to n substrates become straightforward, whereas the traditional King–Altman method can hardly be used in such a general case. Furthermore, the simple method introduced in the present paper can also be applied to a simple enzyme model with two or more conformations. It should be emphasized that the Michaelis–Menten steady-state flux is just the reciprocal of the mean waiting time for the occurrence of individual turnovers, which can be measured directly from the single-molecule experiment. And, we also point out how to test experimentally whether these reactions of different substrates occur at the same site of the enzyme in the single-molecule experiment.

Graph theory was successfully applied in developing a relationship between chemical structure and biological activity. The concept of distance in graphs is basic in the definition of various topological indices for chemical compounds, which determines some of the physicochemical properties of them. In this paper, we explain a method, using the concept of distance in the graph of zigzag polyhex nanotorus, which enables us to compute different topological indices simultaneously.

Density functional theory has been used to study Rh(I)-catalyzed hydroacylation of ethene or ethyne. All the intermediates and the transition states were optimized completely at the B3LYP/6-311++G(d,p) level (LANL2DZ(d) for Rh, P). Calculation results confirm that Rh(I)-catalyzed hydroacylation of ethene is exothermic and the total released energy is -54 kJ/mol, and that Rh(I)-catalyzed hydroacylation of ethyne is also exothermic and the total released energy is -122 kJ/mol. In Rh(I)-catalyzed hydroacylation, ethene and ethyne have similar reactivity. Rh(I)-catalyzed oxidative addition of aldehyde is the rate-determinating step for the Rh(I)-catalyzed hydroacylation of ethene or ethyne. Hydrogen transfer reaction is prior to the C–C bond-forming reaction for Rh(I)-catalyzed hydroacylation of ethene. Thus hydrogen transfer reaction and the C–C bond-forming reaction may be co-existed for Rh(I)-catalyzed hydroacylation of ethyne. The effect of solvent in the hydroacylation of ethyne is greater than that in the hydroacylation of ethene.

The conformational stability and electronic structures of novel H₂-(1) and Zn-tetraphenylporphyrin–[60]fullerene (2) dyads, in which the [60]fullerene is directly linked to the tetrapyrrolic rings by ethynylenephenylene subunits, have been studied by ab initio and density functional theory calculations. From the investigation on frontier molecular orbitals, it was found that the lowest unoccupied molecular orbital state of these supramolecules is localized on the fullerene and that the highest occupied molecular orbital state is localized on the porphyrin moiety. Molecular electrostatic potential maps clearly demonstrate the electron transfer phenomena from the porphyrin moiety to the fullerene in dyads 1 and 2.

The formation mechanism and photochromic property of a novel solid state Schiff base compound (E-isomer, C₂₁H₁₈I₂N₃O₂) derived from 4-aminoantipyrine and 3,5-diiodosalicylaldehyde is investigated in this work using density functional theory at the B3LYP/6-31l++G** level with and without solvent water presence. Our computational results show that the conversion in the gas phase is unlikely to occur and the solvent water is involved in the reaction to decrease the barrier height. We considered one to three water molecule participations in the water-catalyzed mechanism to produce the E-isomer. Time-dependent density functional theory (B3LYP/6-311+G*) is employed to examine the photochromic property of the molecule. A large Stokes shift between absorption and emission has been attributed to the intramolecular H-transfer (O–H⋯N to O⋯H–N) following photoexcitation of the enol species, suggesting that the keto form of the photoproduct structure plays the key role, in agreement with the experimental finding of stereoselectivity. Conceptual DFT reactivity indices are employed to rationalize the findings from the present study.

The greater number of parameters in the generalized Morse (GM) potential energy function, as compared with the conventional Morse (CM) potential, allows the former to be more flexible for curve fitting of experimental data. Owing to its simplicity, the CM function has been more widely adopted in molecular modeling softwares. Hence the conversion of the more accurate GM parameters into the commonly used CM parameter is useful for enhancing the latter. This paper proposes three methods for extracting the CM parameter from the GM parameters. The short-range relation was obtained by equating curvatures at the minimum well-depth, whereas the mid-range relation was obtained by equating equal energy integral from equilibrium to dissociation. The long-range relation was obtained by equating the CM parameter with the attractive index of the GM parameter.

The potential energy surface for the Kr–N₂O complex is calculated using the coupled-cluster singles and doubles with noniterative inclusion of connected triples [CCSD(T)] with a large basis set including midpoint bond functions. The interaction energies are obtained by the supermolecular approach with the full counterpoise correction for the basis set superposition error. The CCSD(T) potential is found to have two minima corresponding to the T-shaped and linear Kr–ONN structures. The geometry for the T-shaped configuration is very close to the experimental results. The two-dimensional discrete variable representation method is applied to calculate the rovibrational energy levels with N₂O at its ground and ν₃ excited states. The calculated transition frequencies and spectroscopic constants are in good agreement with the observed values.