Journal of Theoretical and Computational Chemistry

Employing density functional theory (DFT) and time-dependent density functional theory (TDDFT) calculations in combination with the semiclassical nuclear ensemble method, we have simulated the photoabsorption spectra of the four canonical DNA nucleobases in aqueous solution. In order to model the effects of solvation, for each nucleobase, a number of solvating water molecules were explicitly included in the simulations, and additionally, the bulk solvent was represented by a continuous polarizable medium. We find that the effect of the solvation shell in general is significant, and its inclusion improves the realism of the spectral simulations. The involvement of lone electron pairs in the hydrogen bonding with the solvating water molecules has the effect of systematically increasing the energies of vertical excitation into the $n{\pi }^{*}$-type states. Apart from a systematic blue shift of around $0.3$eV observed in the absorption peaks, the calculated photoabsorption spectra reproduce the measured ones with good accuracy. The photoabsorption spectra are dominated by excited states with $\pi {\pi }^{*}$ and partial $\pi {\pi }^{*}$ character. No low-energy charge transfer states are observed with the use of the CAM-B3LYP and M06-2X functionals.

The possible paths of dimethyl ether (DME) synthesis from methanol over hydrated $\gamma$-Al₂O₃(110) in vacuum and liquid paraffin have been investigated by using density functional theory (DFT). Over hydrated $\gamma$-Al₂O₃(110), the three possible paths of methanol dehydration to DME have been investigated by the DFT method in vacuum and liquid paraffin. DME synthesis from methanol is carried out along the same pathway 2CH₃OH(g) $+$ 2* $\to$ 2CH₃OH* $\to$ 2CH₃O* $+$ 2H* $\to$ CH₃OCH₃* $+$ H₂O* in vacuum and liquid paraffin, and the step of highest energy barrier is the reaction of 2CH₃O* $\to$ CH₃OCH₃* $+$ O*. The energy barrier of the step in liquid paraffin is higher than that in vacuum by 0.33eV. The surface acid strength in liquid paraffin decreases over $\gamma$-Al₂O₃(110) surface comparing with vacuum, showing that stronger surface acid strength benefits to DME synthesis. Our result is in consistent with the experiment results.

In this work, the reaction mechanisms for the selective catalytic reduction (SCR) of nitrogen oxides (NO_x) with NH₃ on a (MnO)${}^{2+}$/ZSM-5 catalyst were investigated based on the density functional theory (DFT) method. Our calculations showed that the NH₃ could strongly adsorb on the (MnO)${}^{2+}$/ZSM-5 catalyst as compared to NO. The proposed reaction pathway, NH₃(ads)$\to$NH${}_2+$H$\to$NH₂(ads) $+$ NO(ads)$\to$ NH₂NO$\to$NHNO $+$ H$\to$N${}_2+$H₂O, was more favorable with smaller activation barrier (1.40eV) of the rate-determining step. The compared reaction process that the adsorbed NH₃ reacted directly with adsorbed NO was difficult to happen for the higher activation barrier. Meanwhile, the framework oxygen participated in the oxidation process from ammonia to NH₂, thereby increasing its availability for the reaction. In addition, the regeneration process of active site in the presence of NH₃ and NO₂ was explored, and the rate-limiting step possessed an activation barrier of 1.46eV. The NH₂NO species was formed as the crucial intermediate and subsequently decomposed into the N₂ and H₂O.

Ionic liquids (ILs) especially their mixtures are of high interest within the different scientific societies due to their amazing properties. In this regard, a number of attempts have been made to measure, correlate, estimate and calculate the properties of ILs in the neat or mixture forms. Among the different possible predictive methods, artificial neural networks (ANNs) are widely used because of their unique and amazing capabilities for prediction of different parameters. With respect to this paper, a feed-forward ANN model is proposed to model the densities of different binary mixtures of ILs/ethanol. The proposed network is trained and tested with 1078 binary data points gathered by mining into the different published literatures. The data gathered from previously published literatures are separated into two different subsets namely training and testing. The statistical error analysis has shown that the proposed neural network correlated the binary densities with the overall mean absolute percentage error (MAPE), average relative deviation percentage error (ARD%), minimum relative deviation percent (RDmin%), maximum relative deviation Percent (RDmax%) and correlation coefficient ($R^2)$ of 1.5%, $-$0.1%, $-$13.0%, 15.0% and 0.9712, respectively.

The electronic transport properties of hybrid nanoribbons constructed by substituting zigzag graphane nanoribbons (ZGaNRs) into zigzag graphene nanoribbons (ZGNRs) are investigated with the non-equilibrium Green’s function method and the density functional theory. Both symmetric and asymmetric ZGNRs are considered. The electronic transport of symmetric and asymmetric ZGNR-based hybrid nanoribbons behave distinctly differently from each other even in the presence of the same substitution positions of ZGaNRs. Moreover, the electronic transport of these hybrid systems is found to be enhanced or weakened compared with pristine ZGNRs depending on the substitution position and proportion. Our results suggest that such hybridization is an effective approach to modulate the transport properties of ZGNRs.

We investigate the effects of vacancies on the electronic and magnetic properties in fully-hydrogenated boron nitride sheet by performing first-principles calculation. Our results reveal that this sheet fosters magnetic materials with finite magnetic moment under certain vacancies. This phenomenon can be explained by the charge redistribution in which the unpaired electrons in bands determine the magnitude of magnetic moment and thus the ground state of the systems. The magnetic moment can be tuned from 0 to 2 by introducing different vacancies. This picture explicitly demonstrates that the type of vacancy plays an important role in determining nonmagnetic or magnetic materials of fully-hydrogenated boron nitride sheet, indicating their functionalities and possible applications in spintronics.

In the first part of this paper, a comprehensive theoretical study of molecular structure, stability, intramolecular hydrogen bond (IMHB) and $\pi$-electron delocalization ($\pi$-ED) of the enol and thiol tautomers of 3-thioxopropanal (TPA) in the ground state is performed. In this regard, all of the plausible conformations of TPA at M06-2X/6-311$++$G(d,p) are optimized and a variety of theoretical levels are employed to identify the global minimum. Our calculations show that E1 is the most stable form that is in contrast to the results of Gonzalez et al. [J Phys Chem 101: 9710, 1997]. In order to elucidate this duality, the IMHB and $\pi$-ED of chelated forms (E1 and T1) have been extensively investigated. So, it is found that both of the IMHB analysis and $\pi$-ED concepts emphasize on the E1, as the global minimum. In the second part of this study, a set of simple electron-withdrawing and electron-donating substituents such as CN, F, Cl, CH3 and NH2 have been considered to evaluate their effects on the IMHB of the first singlet excited state of E1 and T1 at TD-DFT/6–311$++$G(d,p) level of theory. According to our analysis, it was found that the IMHB strength of the excited states are much weaker than the ground states. Surprisingly, the IMHB of thiol derivatives is stronger than the enol ones in contrast to the ground state. Furthermore, the substitution effects in the ground and excited states are significantly different. Finally, various linear correlations between the IMHB energies with geometrical, topological and molecular orbital parameters are obtained.

Interactions between P-selectin, expressed on activated endothelium, and its counterpart P-selectin glycoprotein ligand-1 (PSGL-1), expressed on leukocytes, play a pivotal role in adhesive events that recruit circulating leukocytes toward inflamed or injured tissues. Atomistic understanding of the association and dissociation of these bonds under blood flow is necessary to define the underlying mechanism. In this study, steered molecular dynamics (SMD) simulations were applied to investigate the conformational changes of P-LE/SGP-3 construct (an effective binding unit of the P-selectin/PSGL-1 complex) under stretching with constant velocity. In the present simulations, a self-built force field parameterization was developed for sulfated tyrosine by using force field toolkit of Visual Molecular Dynamics (VMD) program. A dissociation mechanism was represented by analyzing the nonbonded energies between interface residues. The results indicate that the salt bridges between P-LE and SGP-3 and the hydrogen bonds between ion Ca${}^{2+}$ and residue fucose of glycan group of PSGL-1 and also between sulfated tyrosine residues are the most effective bonds in binding. Finally, potential of mean force (PMF) was calculated by averaging the outcomes of eight independent runs and the results were discussed.

The structures, electronic properties, bonding characters and UV–Vis spectra of $3d$ ($d^1$–$d^{10}$) transition-metal phthalocyanines (TMPcs) molecules have been studied with different density function theory (DFT) methods. The calculated structural parameters agree well with previous experimental or theoretical values. Natural Population Analysis (NPA) charge revealed that $4s$–$3d∕4p$ hybridizations occur when $3d$ TM atoms are involved in chemical bondings. The spin magnetic moments of TMPcs are mainly from the contribution of $3d$ electrons. Conceptual density functional theory (CDFT) results indicate that $3d$ TMPcs molecules are willing to accept further electrons. The TM–N chemical bonds show very weak covalent nature, and are consistent with bond order analyses. Time-dependent density function theory (TD-DFT) calculations were carried out to simulate the UV–Vis spectra, and corresponding electronic transfers for dominant peaks were also obtained.

We theoretically study, from the thermodynamic point of view, the possibility of the two degradation pathways of antitumor drug of imexon. According to the theoretical results obtained at DFT level in both gas and aqueous phases, the two degradation pathways of imexon are characterized by negative reaction Gibbs free energies. It has been found that 4-imino-5-methylene-imidazolidin-2-one is the favored degradation product of imexon.

Herein, the focus of this work has been on calculating the geometries, relative energies and electronic properties of all possible prototropic tautomers of 4-imino-5-methylene-imidazolidin-2-one using the DFT and MP2 levels. The bulk water environment has been simulated by continuum model using Solvation Model based on Density (SMD). The UV spectra of two dominant tautomers of 4-imino-5-methylene-imidazolidin-2-one are also predicted using time-dependent density functional theory and the results are compared with the available experimental data. The comparison of the simulated and the experimental absorption spectra has allowed us to accurately characterize the predominant tautomer of the degradation product in aqueous medium.