Journal of Theoretical and Computational Chemistry

The energetic, electronic and structural properties of defective g-C₃N₄-zz3 nanotubes are considered based on spin-polarized density-functional theory calculations. Nine basic system types with vacancy defects are characterized by their stabilization energies and band gaps. It is found that the nitrogen atom denoted as N3 is the most favorable atom for a vacancy defect. In all cases, local bond reconstruction occurs in the presence of vacancy defects. The role of C/N bond rotations on the above properties has been also investigated. The results show that N1–C3 bond rotation is the most favorable rotational defect. In addition, the electronic properties of the semiconducting g-C₃N₄-zz3 nanotube with defects have been studied using band structure and density of states plots.

The formation of carbon disulfide (CS₂) and ammonia (NH₃) from the thermal decomposition products of thiourea has been studied with MP2, and hybrid module-based density functional theory methods (B3LYP, MPW1PW91 and PBE1PBE), each in conjunction with five different basis sets (6-31+G(2d,2p), 6-311++G(2d,2p), DGDZVP, DGDZVP2 and DGTZVP). The free energy changes and activation energies for all the five primitive reactions involved in the formation of CS₂ and NH₃ have been compared and discussed. The results indicate that CS₂ is most likely formed in a consecutive reaction path that consists of the addition of hydrogen sulfide (H₂S) to isothiocyanic acid (HNCS) to generate carbamodithioic acid and subsequent decomposition of carbamodithioic acid. By contrast, thiocyanic acid (HSCN) as the structural isomer of isothiocyanic acid is not likely the source of CS₂.

In this work, the interaction of C₂₀ with N₂X₂ (X = H, F, Cl, Br, Me) molecules has been explored using the B3LYP, M062x methods and 6-311G(d,p) and 6-311+G(d,p) basis sets. The interaction energies (IEs) obtained with standard method were corrected by basis set superposition error (BSSE) during the geometry optimization for all molecules at the same levels of theory. It was found C₂₀…N₂H₂ interaction is stronger than the interaction of other N₂X₂ (X = F, Cl, Br, Me) with C₂₀. Highest occupied and lowest unoccupied molecular orbitals (HOMO and LUMO, respectively) levels are illustrated by density of states spectra (DOS). The nucleus-independent chemical shifts (NICSs) confirm that C₂₀…N₂X₂ molecules exhibit aromatic characteristics. Geometries obtained from DFT calculations were used to perform NBO analysis. Also, ¹⁴N NQR parameters of the C₂₀…N₂X₂ molecules are predicted.

The cationic complexes of Asparagine (Asn), M⁺(Asn), with M⁺ = Li⁺, Na⁺, K⁺, Cs⁺, and H⁺, are models for studying the interaction between cations and Asn. Ab initio molecular dynamics (AIMD) method is employed to simulate their behavior at finite temperatures. Structural transformation between conformers is observed, which becomes progressively easier as the cation varies from Li⁺, to Na⁺, K⁺, Cs⁺, and H⁺. The fluctuation of the M⁺–N and M⁺–O distances and rotation of torsional angles are significant even at room temperature for K⁺, Cs⁺ and H⁺. Vibrational profiles based on AIMD trajectories provide insights into the broadening and shifts in relative intensities observed in the vibrational spectra measured by infrared multi-photon dissociation (IRMPD) experiments.

Theoretical investigations on Au and S substituted poly (2,3-di-(4′-hydroxyphenyl)-1,4-phenylene ethynyl) as a molecular wire have been carried out by incorporating the external electric field (EF). The results demonstrate that both geometric and electronic structures of conjugated molecular wire are sensitive to EF. The Z component of the dipole moment and total dipole moment increases continuously since EF polarizes the molecule. Static EF modifies the frontline molecular orbitals and HLG. The I-V curve indicates the symmetrical trend respect to the original point.

A newly developed AMBER compatible force field with coupled backbone torsion potential terms (AMBER03^2D) is utilized in a folding simulation of a mini-protein Trp-cage. Through replica exchange and direct molecular dynamics (MD) simulations, a multi-step folding mechanism with a synergetic folding of the hydrophobic core (HPC) and the α-helix in the final stage is suggested. The native structure has the lowest free energy and the melting temperature predicted from the specific heat capacity C_v is only 12 K higher than the experimental measurement. This study, together with our previous study, shows that AMBER03^2D is an accurate force field that can be used for protein folding simulations.

The extensive search for the global minimum structure of at the B3LYP/LANL2DZ level of the theory revealed that is the ground state. Molecular orbital (MO) analysis reveal that delocalized partial σ and δ bonding in makes partial (σ- and δ-) aromaticity. The multiple d-orbital aromaticities are responsible for a three-center metal–metal bond of the triangular Re₃. We also search the pyramidal Re₃Li²⁺, Re₃X³⁺ (X = Be, Mg and Ca) and Re₃Y (Y = Al and Ga) clusters containing to reveal that the was preserved perfectly in all-metal compounds, which also possess partially σ- and δ-multiple aromatic characters.

The structures of Ca²⁺ hydrates in the interlayer space of montmorillonites (MMT) were studied by periodic density functional theory (DFT) calculations under the GGA/PBE approximation. Affected by the internal surfaces, which are rich of negative charge, the Ca²⁺ hydration exhibits different behaviors from that in gas phase. The Ca²⁺ is located at the six-oxygen-ring (SOR) on the internal surface in dry MMT, while the incoming water molecules bind with the Ca²⁺, the O atoms on surface, and/or with each other. The water molecules have a tendency of forming a hydrogen bond (HB) network that connects the upper and lower surfaces. Attracted by surrounding water molecules, the Ca²⁺ gradually moves outward with increasing number of water molecules. Moreover, the hydration energy (E_H) of Ca²⁺ is determined not only by the interaction between Ca²⁺ and H₂O, but also by that among Ca²⁺, H₂O and the surfaces. As a result, the E_H has only small changes for additional incoming water molecules, in contrast to the great and monotonic decrease in gas phase.

This paper describes systemically a theoretical research on the interaction of alkali-metal cations (Li⁺, Na⁺, K⁺ and Rb⁺) with five different crown ether derivatized thiophenes using density functional theory (DFT). The fully optimized geometries have been performed with real frequencies which indicate the minima states. The optimized structures and electronic properties, such as HOMO and LUMO energies, bandgaps of the free ligands L (L₁-L₅), the complexes L/M⁺ (Li⁺, Na⁺, K⁺ and Rb⁺) have been performed at B3LYP/6-31+G(d,p) and Lanl2DZ level. Natural bond orbital (NBO) and frequency analysis are discussed on the basis of the optimized geometric structures. The main driving forces of the coordination in host–guest molecules are investigated, the electron-donating O offers lone pair electrons to the contacting LP* (1-center valence antibond lone pair) of alkali-metal cations. In addition, the transition energies are calculated by the time-dependent density functional theory (TD-DFT).

The molecular structures and electron affinities of the R–S/R–S^-(R=CH₃, C₂H₅, n-C₃H₇, n-C₄H₉, n-C₅H₁₁, i-C₃H₇, i-C₄H₉, t-C₄H₉) species have been studied using 17 pure and hybrid density functionals (five generalized gradient approximation (GGA) methods, six hybrid GGAs, one meta GGA method and five hybrid meta GGAs). The basis set used in this work is of double-ζ plus polarization quality with additional diffuse s- and p-type functions, denoted by DZP++. The geometries are fully optimized with each DFT method and discussed. Harmonic vibrational frequencies are found to be within 3.5% of available experimental values for most functionals. Three different types of the neutral-anion energy separations have been presented. The theoretical electron affinities of alkylthio radicals are in good agreement with the experiment data. The M06 method is very good for the adiabatic electron affinity calculations, and the average absolute error is 0.0439 eV. The HCTH method performs better for EA prediction. The M06-HF, mPWPW91, VSXC and B98 are also reasonable. The most reliable adiabatic electron affinities are predicted to be 1.864 eV (CH₃S), 1.946 eV (C₂H₅S), 1.959 eV (n-C₃H₇S), 1.970 eV (n-C₄H₉S), 1.982 eV (n-C₅H₁₁S), 2.053 eV (i-C₃H₇S), 1.991 eV (i-C₄H₉S) and 2.100 eV (t-C₄H₉S) at the M06/DZP++ level of theory, respectively.

The outer membrane protein TolC of Escherichia coli forms a channel-tunnel pore spanning the periplasmic space and outer membrane, serving as the main exit duct for bacteria multidrug resistance and protein export. Many aspects of the transport mechanism of TolC are still unclear. Here, we have investigated the substrate permeability and gating mechanism of TolC by calculating the potential of mean forces (PMFs) for transporting sodium ion and doxorubicin through TolC using the adaptive biasing force (ABF) method. The transport mechanism is turned out to be substrate dependent. It is found that the periplasmic gate is required to open for the passage of both Na⁺ and doxorubicin, but the conformational gating does not lead to permeation barrier for Na⁺ at this region. The extracellular loops and K283 residues cause permeation barriers for Na⁺ at the extracellular entrance, but not for doxorubicin due to the extensive interactions between the drug molecule and the protein. TolC exhibits high conformational flexibility during the transport of Na⁺, while doxorubicin seems to be able to stabilize TolC in the resting state with the periplasmic gate closed. The association of the TolC docking domain of AcrB does not lower the permeation barrier for doxorubicin at the periplasmic gate, while the gate opening induces the dissociation of the TolC–AcrB complex.

Here we investigate the kinetic model for the large deformation theory of hydrogel under the outside stimulations. We present the large deformation dynamical model in the following two points. (1) The phase transition caused by the deformation gradient is concerned, which makes the model more integral. (2) Based on the steady-state model, the time-dependent large deformation model is proposed and the time developing process is investigated. Considering the force of the large deformation, we introduce the heat equation to express the transformation of the chemical potential. The extended model can be used to describe the development of the large deformation. We present numerical examples of the cylindrical hydrogel for one- and two-dimensional cases under pressure and stretch. Besides, some key parameters are studied to test the model.

Permeability assessment is an important procedure in the drug development process, and drug partitioning in membrane bilayer is related to permeability. To investigate the pH dependence on drug partitioning, the process of different ionization state of ibuprofen passing across POPC bilayer was studied using molecular dynamics simulation. The results show that both atomic charge scheme and ionization state of the drug affect the value and shape of energy profile when passing across the POPC bilayer. The neutral ibuprofen (ibuprofen under acidic condition) has a much lower energy barrier as compared with the anionic ibuprofen (ibuprofen under basic condition). Meantime, hydrogen bond analysis also certifies that it is easy for neutral ibuprofen to pass from bulk water to bilayer center. Our calculation suggests that the ionization state of ibuprofen may be changed between neutral and anionic state when passing across membrane: it may be ionized outside the membrane and neutralized inside the membrane.