Journal of Theoretical and Computational Chemistry

The fate of hexachlorobenzene (HCB) in soil represents a critical environmental problem. Once HCB has reached the soil it will interact with soil constituents, especially soil organic matter (SOM). The understanding of this interaction is important for choosing effective remediation procedures. Here we report a study of binding of HCB to a test set of molecules, which was developed to mimic representative functional groups of SOM. The binding energy of complexes formed by HCB and the test set molecules were investigated at different levels of theory. Effects of different types of dispersion correction to DFT, basis sets and DFT-functionals have been studied. Moreover, the general ability of dispersion-corrected DFT to represent this interaction has been benchmarked against methods such as MP2 and CCSD. As a result the B3LYP-D3 dispersion correction combined with the 6-311++G(2d,2p) basis set was found to be a compromise between accuracy and efficiency and it is recommended for studying this type of non-covalent interaction. Moreover, the performance of the GROMOS force field in the description of this interaction has been tested.

In this paper, 21 substituents with various electron donating and electron withdrawing characters were placed in available positions of irigenin in order to study their effect on the O–H bond dissociation enthalpy (BDE) via DFT/B3LYP method. Results indicated the substituents in X₃ and X₄ positions have exerted stronger influence upon BDE values of irigenin derivatives when compared with same substituents in X₁ and X₂ positions. The results show that intramolecular hydrogen bond effects are able to considerably stabilize the parents and radicals. The natural bond orbital (NBO) analysis results also confirmed the intramolecular hydrogen bond stabilization. The formation of strong intramolecular hydrogen bonds in several radicals results in low BDEs. The 3-OH BDE values for substituents in X₂ position have linear dependencies with Hammett constants (Fig. 2 and Eq. (2)). Found dependencies are suitably linear, that can be important for the synthesis of novel antioxidants based on irigenin.

In this work, the electronic structure and properties of the ruthenanaphthalenes, and ring-fused B–N ruthenabenzenes isomers have been explored using the hybrid density functional mpw1pw91 theory. These calculations show more stability in isomers with Ru–N bond. This is compatible with principles of minimum energy and minimum polarizability. Molecular orbital analysis shows increase of hardness in isomers with Ru–B bonds rather than Ru–N isomers. Also, calculations show that magnitude of the first hyperpolarizability tensor of all molecules is rather moderate. Nucleus-independent chemical shift analysis (NICS) has been used for studying of aromaticity in these species.

The inhibition performance of 10 imidazoline molecules with number of carbon from 15 to 21 of hydrocarbon straight-chain was studied by weight-loss method and theoretical approaches. The main purpose was to build a quantitative structure–activity relationship (QSAR) between the structural properties and the inhibition efficiencies, and then to predict efficiencies of new corrosion inhibitors. The quantum chemical calculation suggested that the active region of imidazoline molecules was located on the imidazoline ring and hydrophilic group, and active sites were concentrated on the nitrogen atoms of the molecules and carbon atoms of hydrophilic group. A model in accordance with the real experimental solution was built in the molecular dynamics, and the equilibrium configuration indicated that the imidazoline molecules were adsorbed on Fe(110) surface in parallel manner. Descriptors for QSAR model building were selected by principal component analysis (PCA) and the model was built by the support vector machine (SVM) approach, which shows good performance since the value of correlation coefficient (R) was 0.99 and the root mean square error (RMSE) was 0.94. Additionally, six new imidazoline molecules were theoretically designed and the inhibition efficiencies of three molecules were predicted to be more than 86% by the established QSAR model.

The ground-state geometries of 2-cyano-5-(4-(phenyl(4-vinylphenyl)amino)phenyl) penta-2,4-dienoic acid (TC4) derivatives have been optimized by using density functional theory (DFT) at B3LYP/6-31G** level of theory. The effect of bridge has been investigated on the electronic and charge transfer properties. The distortion between triphenylamine unit and acceptor moieties revealed there would be recombination barrier. The excitation energies have been computed by time dependent DFT at PCM-CAM-B3LYP/6-31G** and PCM-LC-BLYP/6-31G** level of theories. The absorption spectrum of TC4 computed at PCM-CAM-B3LYP/6-31G** level of theory is in good agreement with the experimental evidence while PCM-LC-BLYP/6-31G** level of theory underestimate it. The electron injection, electronic coupling constant and light harvesting efficiency (LHE) improved by elongating the bridge. The superior electron injection, electronic coupling constant, LHE, LUMO lying above the conduction band of TiO₂ and HOMO below the redox couple compared to parent molecule revealed that new designed materials would be efficient photosensitizers.

The vertex and edge bipartization problems are to find the minimum number of vertices and edges, respectively, whose removal makes the graph bipartite. It is well-known that these problems are NP hard even for cubic graph. In this paper, a result is proved by which it is possible to find a fast algorithm for computing the edge bipartization number of (3,6)-fullerenes.

First-principle density functional calculations have been carried out to explore the mechanism of the BF₃-catalyzed intramolecular coupling between a C(sp³)-H bond in the α-position of such heteroatom as O and an electron-deficient alkene that has an electron-withdrawing substitute, e.g. acetal or carbonyl [McQuaid KM, Sames D, J Am Chem Soc131:402, 2009]. The computations not only confirmed the previously proposed mechanism that coordination of BF₃ (as Lewis acid catalyst) to the acetal oxygen atom triggers 1,5-hydride transfer from the α-C(sp³)-H bond to the alkenic carbon, followed by 1,6-cyclization (C–C bond formation) between the carbon atom of the as-formed oxacarbenium and another alkenic carbon atom, but also disclosed that the 1,5-hydride transfer step is rate-limiting and the cyclization step accounts for the stereoselectivity. In addition, the following substituent effects were disclosed, i.e. the efficacy of intramolecular coupling can be significantly improved by introducing a more electron-donative amino group as the closest neighbor of the hydride donor, but retarded by introducing a less electron-withdrawing –CO₂Me group as the closest neighbor of the hydride acceptor or by introducing an aromatic phenyl linkage, instead of the saturated linkages exploited in experiments, between the two reacting groups.

The first dehydration of protonated glycerol taking place at its secondary site was investigated by density functional calculations by considering different conformations of glycerol. Five parallel reaction pathways via different conformers of protonated glycerol were found. One of these pathways leads to a direct formation of protonated 3-hydroxylpropanal (HPA), another one of these pathways produces protonated glycidol, and the other three produce protonated 3-hydroxy-1,1-propanediol (HPD). One of these pathways producing protonated HPD was found to have obviously larger relative reaction rate than other pathways. The dehydration of protonated HPD to afford protonate HPA requires a rather low reaction barrier (12 kcal/mol). These results show that the production of HPA via a stepwise process with protonated HPD as a key intermediate, is energetically favorable than via a one-step concerted process producing HPA.

The electronic spectra of HNCSe were studied by performing multireference ab initio calculations at CASPT2 level of theory taking into account spin-orbit (SO) coupling. Our highly accurate calculation indicated that theoretically determined geometric parameters and harmonic vibrational frequencies for the ground state X¹A′ are consistent with observed experimental data. We present the oscillator strengths, electronic and structural changes accompanying the excitation process. The bonding characteristics in the low-lying excited states were analyzed on the basis of the valence molecular orbitals (MOs). And the excited states of HNCSe exist in the complex of Se and HNC radical pair. According to our calculations, the ground-state of HNCSe⁺ is linear, and the value of the ionization potential of HNCSe has been found. The existence of bound excited anion states has been found for the first time in HNCSe^-.

Developing small molecule inhibitors of human immunodeficiency virus type 1 (HIV-1) fusion has attracted significant interest. Recently, Jiang have reported several natural and synthetic N-substituted pyrrole derivatives targeting gp41 that are experimentally shown to inhibit cell–cell fusion in the low micromolar range. In order to help gain insight on the binding mechanism, we carried out computational study to help identify possible binding modes and to characterize structures of binding complexes. Detailed gp41-molecule binding interactions and free energies of binding are obtained through molecular dynamics (MD) simulation and MM-PBSA calculation. Specific molecular interactions in the gp41-inhibitor complexes are identified. Current computational study complements the corresponding experimental investigation and provides theoretical understanding on the binding mechanism which is helpful for further refinement of small molecule inhibitors of gp41.

A density functional theory (DFT) study was performed on distribution of skeletal aluminum and Brønsted acid (B-acid) sites as well as the acid strength in ZSM-48 zeolite. The correlation between Si/Al molar ratio and the general acid strength was also investigated. The calculations were performed based on 51T and 90T cluster models by using two-layered ONIOM schemes (B3LYP/6-31G (d,p): AM1) method. The former 51T cluster is used for the calculation of single-Al substitution and the latter is for the multi-Al substitution study. The properties of Si/Al substitution energy, deprotonation energy, bridging hydroxyl stretching vibration frequency and adsorption energy for the probe molecule were calculated and used to measure Brønsted acid location and strength. As the result shows, T2 is the most readily to be replaced by Al and the Brønsted acids prefer to be formed at Al2–O7–Si3 site. Al2–O6–Si2 is the highest in Brønsted acid strength. Besides, the acid strength weakens with the decrease of Si/Al.

A great deal of theoretical work has been carried out to investigate the properties of the six lowest singlet electronic states of N₂O molecule: the ground state X¹A′; the excited states 1¹A′′, 2¹A′, 2¹A′′, 3¹A′ and 3¹A′′. Multireference configuration interaction (MRCI) approach has been used to compute the full-dimensional potential energy surfaces of the six lowest states employing aug-cc-pVQZ minus g orbital basis set. It was found that such of highly accurate potential yields excellent results of bond dissociation and vertical excitation energies in comparison with the experimental values. Several important symmetry and nonsymmetry related conical intersections in linear and bent geometries have been discussed. Of particular interest is the location of conical intersections between the 2¹A′(¹Δ) and 3¹A′(¹Π) states, and between the 1¹A′′(¹Σ^-) and 3¹A′′(¹Π) states in linear geometry, as well as conical intersection between the X¹A′ and 2¹A′ states in bent geometry. The corresponding transition dipole moment surfaces have also been computed, connecting the ground electronic state to the lowest five excited states. Detailed discussion on the vector properties of the dipole transition has been presented specifically in the vicinity of the conical intersections.