Journal of Theoretical and Computational Chemistry

We present results of a detailed numerical investigation of the phase separation kinetic process of the macromolecular microsphere composite (MMC) hydrogel. Based on the Flory-Huggins-de Gennes-like reticular free energy, we use the time-dependent Ginzburg–Landau (TDGL) mesoscopic model (called MMC-TDGL model) to simulate the phase separation process. Domain growth is investigated through the pair correlation function. Then we obtain the time-dependent characteristic domain size, which reflects the growth kinetics of the MMC hydrogel. The results indicate that the growth law based on the MMC-TDGL equation is consistent with the modified Lifshitz–Slyozov theory.

Thermal conductivity is one of the most important properties of materials especially liquids. Thermal conductivity is highly interesting since it is the main parameter required for most heat-transfer calculations or design of industrial equipments such as heat exchangers. Unfortunately, thermal conductivity is extremely hard to be experimentally measured due to some operational issues which shifted the researchers’ interest toward proposing a correlation to predict this property. In the light of this limitation, in the current study, a four-parameter correlation based on critical temperature ($T_c)$, critical pressure ($P_c)$ and acentric factor ($\omega )$ of substances is proposed to predict thermal conductivity of liquids. In this way, 956 experimental data points collected from previously published literatures were divided into two different subsets, namely training and testing subsets, in the first stage and then used to find the optimum values of fitting parameters of the proposed correlation. Based on the obtained results of error analysis, it can be concluded that the proposed correlation has capability of both extrapolating and correlating the thermal conductivity of liquids.

The deamination reaction of 8-oxoguanine (8-oxoG) catalyzed by 8-oxoguanine deaminase (8-oxoGD) plays a critically important role in the DNA repair activity for oxidative damage. In order to elucidate the complete enzymatic catalysis mechanism at the stages of 8-oxoguanine binding, departure of 2-hydroxy-1H-purine-6,8(7H,9H)-dione from the active site, and formation of 8-oxoxanthine, extensive combined QM(PM3)/MM molecular dynamics simulations have been performed. Computations show that the rate-limiting step corresponds to the nucleophilic attack from zinc-coordinate hydroxide group to free 8-oxoguanine. Through conformational analyses, we demonstrate that Trp115, Trp123 and Leu119 connect to O₈@8-oxoguanine with hydrogen bonds, and we suggest that mutations of tryptophan (115 and 123) to histidine or phenylalanine and mutation of leucine (119) to alanine could potentially lead to a mutant with enhanced activity. On this ground, a proton transfer mechanism for the formation of 8-oxoxanthine was further discussed. Both Glu218 and water molecule could be used as proton shuttles, and water molecule plays a major role in proton transfer in substrate. On the other hand, comparative simulations on the deamination of guanine and isocytosine reveal that, for the helping of hydrogen bonds between O₈@8-oxoguanine and enzyme, O₈@8-oxoguanine is the fastest to be deaminated among the three substrates which are also supported by the experimental kinetic constants.

By combining group representation theory with density functional theory (DFT) investigations, we reveal that (BCO)$n$ systems have three nonoverlapping level sequences and the energy level diagrams in each level sequence have the same general arrangement of level. The stability of monocyclic carbon boronyl–boron carbonyl mixed clusters [(BCO)${}_{6-n}$(CBO)_n] ($n=0$–6) systems are theoretically investigated based on DFT. MO analysis reveals that the delocalized nature of delocalized $\pi$ valence orbitals within the –CBO groups is a key factor for the increase in the stability of (BCO)${}_{6-n}$(CBO)_n($n=0$–6) with increasing $n$. The order of stability of (BCO)${}_{6-n}$(CBO)_n($n=2$, 3 and 4) isomers is explained by recursion analysis at charge distribution. The determined order of stability is consistent with the energy order.

A robust extrapolation model requiring few input parameters to predict the kinetic constants characterizing the curing behavior of NR vulcanized in presence of sulfur and two accelerants (TBSS and DPG) at different concentrations is discussed. The numerical model based on the reproduction of rheometer curves by means of the well-known Han’s kinetic model, which describes with kinetic base the most important NR vulcanization phases, namely curing initiation, formation of matured crosslinked polymer and reversion. The derived mathematical model is a closed form exponential function depending on only three kinetic constants. The procedure proposed is a two-step one. In the first step, kinetic constants of NR in the presence of single activators (i.e. either only with S and TBBS or S and DPG) are estimated by means of an interactive trial and error optimization software (GURU) that proceeds in approximating more and more strictly normalized experimental rheometer curves with Han’s function. Four different concentrations of S and TBSS (or S and DPG) are assumed as calibration points. In the second step, from the results obtained previously, kinetic constants for NR with any S-TBBS-DPG concentration of technical relevance are deduced by means of standard mathematical extrapolation. The procedure is benchmarked on 16 different S-TBBS-DPG concentrations at two temperatures (150${}^{\circ }$C and 180${}^{\circ }$C), for which both experimental data are available and kinetic constants are previously derived with GURU. Quite good agreement is found, meaning that the approach may be useful for practical purposes, because expensive and cumbersome experimental investigations can be avoided.

The objective of this study was to determine the physicochemical properties of the oligomers of procyanidins (PCs) including PA1, PA2, PB1, PB2, PC1 and a B-type tetramer, taking into account of their conformations related to the interflavan links using the density functional theory (DFT). This information may provide useful insight into the potential effect of physicochemical properties on the absorption of PCs. The results indicate that A-type and B-type PCs in all of their conformations tend to be more stable in water than in octanol, showing a hydrophilic character due to their negative log $P$ values, which increase with the degree of polymerization (DP). The studied PCs, including the B-type tetramer, can achieve an appropriate molecular size (i.e. width and length) that can allow them to pass through the pores in the paracellular route in the human small intestine. The factor that could limit the absorption of the PC oligomers with increases in size is the higher number of hydroxyl groups exposed to the outside of the molecule due to their potential to interact with other molecules, which is based on electrostatic potential maps.

Zeno and anti-Zeno effects in the evolution of the multi-photonic dissociation dynamics of the diatomic molecule HBr${}^{+}$ owing to repeated measurements demand if the system in the initial state have been studied. The effects have been calculated numerically for the case of vibrational population transfer and dissociation dynamics of HBr${}^{+}$ taking it as a model. We use time-dependent Fourier grid Hamiltonian (TDFGH) method as a mathematical tool in presence of intense radiation field as perturbation. The effects have been explored through a probable mechanism of population transfer from the ground vibrational state to the different upper vibrational states which ultimately go to the dissociation continuum. The results show significant differences in the mechanism of population transfer and the significant role of time interval of measurement ($\tau )$ in Zeno and anti-Zeno effects. In case of survival probability of ground vibrational states, there is Zeno effect when the frequency of the laser to which the molecule is submitted is near the vibrational $v=0$ to $v=1$ resonance, while there is anti-Zeno effect if it is far from this resonance.

Poisson–Boltzmann (PB) model is a widely used implicit solvent approximation in biophysical modeling because of its ability to provide accurate and reliable PB electrostatic salvation free energies ($\mathrm{\Delta }{G}_{\mathrm{\text{el\_solv}}})$ as well as electrostatic binding free energy ($\mathrm{\Delta }\mathrm{\Delta }{G}_{\mathrm{\text{el}}})$ estimations. However, a recent study has warned that the 0.5Å grid spacing which is normally adopted can produce unacceptable errors in $\mathrm{\Delta }\mathrm{\Delta }{G}_{\mathrm{\text{el}}}$ estimation with the solvent excluded surface (SES) (Harris RC, Boschitsch AH and Fenley MO, Influence of grid spacing in Poisson–Boltzmann equation binding energy estimation, J Chem Theory Comput 19: 3677–3685, 2013). In this work, we investigate the grid dependence of the widely used PB solver DelPhi v6.2 with molecular surface (MS) for estimating both electrostatic solvation free energies and electrostatic binding free energies. Our results indicate that, for the molecular complex and components the absolute errors of $\mathrm{\Delta }\mathrm{\Delta }{G}_{\mathrm{\text{el\_solv}}}$ are smaller than that of $\mathrm{\Delta }{G}_{\mathrm{\text{el\_solv}}}$, and grid spacing of 0.8Å with DelPhi program ensures the accuracy and reliability of $\mathrm{\Delta }\mathrm{\Delta }{G}_{\mathrm{\text{el\_solv}}}$; however, the accuracy of $\mathrm{\Delta }\mathrm{\Delta }{G}_{\mathrm{\text{el}}}$ largely relies on the order of magnitude of $\mathrm{\Delta }\mathrm{\Delta }{G}_{\mathrm{\text{el}}}$ itself rather than that of $\mathrm{\Delta }{G}_{\mathrm{\text{el\_solv}}}$ or $\mathrm{\Delta }\mathrm{\Delta }{G}_{\mathrm{\text{el\_solv}}}$. Our findings suggest that grid spacing of 0.5Å is enough to produce accurate $\mathrm{\Delta }\mathrm{\Delta }{G}_{\mathrm{\text{el}}}$ for molecules whose $\mathrm{\Delta }\mathrm{\Delta }{G}_{\mathrm{\text{el}}}$ are large, but finer grids are needed when $\mathrm{\Delta }\mathrm{\Delta }{G}_{\mathrm{\text{el}}}$ is very small.