Journal of Theoretical and Computational Chemistry

B3LYP/6-311++G(d,p) and B3LYP/6-31G(d,p) theoretical levels combined with topological calculations based on the theory of atoms in molecules (AIM) were used to study the formation of intermolecular interactions on heterocyclic hydrogen-bonded complexes formed by ethylene oxide, sulfide oxide, 2,5-dihydrofuran, thiophene, and the hydrofluoric acid. As observed, the electrophilic attack of the hydrofluoric acid occur aligned to the n lone pair of the heteroatom of the cyclic systems, the modeled structure of the hydrogen-bonded complexes is interpreted in terms of the intermolecular parameters of the (n ⋯ HF) hydrogen bond, such as its R(n ⋯ HF) distance, ΔE^C binding energy, and the new υ(n ⋯ HF) stretching vibrational mode. From these criteria, a relationship between the strength (R, ΔE^C and υ) of the hydrogen bonds and its nonlinearity deviation was verified, which is formed by a secondary interaction between the hydrofluoric acid and axial hydrogen atoms of the cyclic structure. Moreover, even though the Bader's electronic density partitioning has been projected with low dependence from ab initio wave functions, it is shown here that the 6-31G(d,p) basis sets characterized the secondary interaction in geometrical point of view, as well as by means of the AIM protocol through the specific calculation of bond critical points between the fluoride and the axial hydrogen atoms.

The complex singlet and triplet potential energy surfaces (PESs) of the [C₂N₂O₂] system are performed at the B3LYP and Gaussian-3//B3LYP levels in order to investigate the possibility of the carbyne radical CCN in removal of nitrogen dioxide. Thirty minimum isomers and 36 transition states are located. Starting from the very energy-rich reactant RCCN + NO₂, the terminal C-attack adduct NCCN(O)O (singlet at -48.6 and triplet at -48.1 kcal/mol) is first formed on both singlet and triplet PESs. Subsequently, the singlet NCCN(O)O takes an O-transfer to form the intermediate singlet cis-NCC(O)NO (-120.1), which can lead to the fragments NCCO + NO (-94.4) without barrier. The simpler evolution of the triplet NCCN(O)O is the direct N–O rupture to form the final fragmentation NCCNO + ³O (-31.0). However, the lower lying products ³NCNO + CO (-103.3) and NCNCO + ³O (-86.5) are kinetically much less competitive. All the involved transition states for the generation of NCCO + NO and NCCNO + ³O lie much lower than the reactants, and it indicates that this reaction can proceed effectively even at low temperatures. We expect that the reaction CCN + NO₂ can play a role in both combustion and interstellar processes. Comparison is made between the CCN + NO₂ and CH + NO₂ reaction mechanisms.

The heats of formation (HOFs) for 15 thiol compounds are calculated by employing the hybrid density functional theory (B3LYP, B3PW91, B3P86) methods with 6-311G** basis set and the complete basis set (CBS-Q) method. It is demonstrated that the B3P86 and CBS-Q methods are accurate to compute the reliable HOFs for thiol compounds. In order to test whether the B3P86 method has a low basis set sensitivity, the HOFs for six thiol compounds are also calculated by using the B3P86 method with 6-31+G*, 6-31+G**, and 6-311+G** basis sets for comparison. We also extend our study by employing the nonlocal BLYP method together with 6-31+G* basis set to calculate the HOFs for thiol compounds. The obtained results are compared with the experimental results. It is noted that the B3P86 method is not sensitive to the basis sets. Considering the inevitably computational cost of CBS-Q method and the reliability of the B3P86 calculation, the B3P86 method with a moderate or a larger basis set such as 6-311G** and 6-311+G** may be more suitable to calculate the HOFs of thiol compounds. In addition, we believe that the maximum error associated with the calculated HOFs is less than 6 kcal/mol for the B3P86/6-311G** method and it is expected that the error bar is more likely 1–5 kcal/mol for the HOFs of thiol compounds.

In the present paper, the antifungal activity of some 1-benzylbenzimidazole derivatives were evaluated against yeast Saccharomyces cerevisiae. The tested compounds displayed in vitro antifungal activity and minimum inhibitory concentration (MIC) was determined for all the compounds. Quantitative structure–activity relationship (QSAR) has been used to study the relationships between inhibitory activity and lipophilicity parameters (log P). A variety of lipophilicity parameters (log P_Hyper, CS log P, mi log P, A log P, IA log P, C log P, log P_Kow, and X log P) were calculated using different software products, and experimentally determined ("shake-flask" method). On the basis of correlations, the nonlinear structure–activity models were derived between the log 1/c_MIC and two different lipophilicity parameters. Four high-quality QSAR models were found to have a good predictive ability and a close agreement between the experimental and predicted values was obtained.

Microring electrodes are useful for the investigation of electrode kinetics due to their large perimeter-to-area ratio and compact nature but have hitherto been limited in application due to the absence of the underpinning theory. In this review, the analytical solutions, approximate expressions, and numerical solutions of transient chronoamperometric current at a microring electrode under diffusion control are discussed. The steady and non-steady-state current for microring electrode for an EC' reaction are also discussed. Tabular compilations of dimensionless current are provided.

Adsorption of solvent or organic compounds at a metal/interface is characterized by a wide spectrum of interactions governing the phenomenon under effective fields of order ≈ 10⁷V/cm. A generalized spin-1 Ising Hamiltonian was formulated by considering various interactions under molecular field approximation (MFA) to arrive at a three-state model of adsorption isotherm (i.e. the joint adsorption of two different organic compounds in the presence of solvent molecules). A general multi-state model was deduced heuristically and an expression for the charge at which maximum adsorption (θ_max) occurs derived explicitly for a three-state site parity model that incorporates short-range interaction energies, functional dependence of permanent and induced dipole moments of the organic adsorbate, and the solvent and substrate interactions.

Trypsin is one of the most important enzymes and plays important roles in the regulation of biological processes. The newly developed trypsin–inhibitor interaction potential model based on atom-bond electronegativity equalization method fused into molecular mechanics (ABEEM/MM) was employed to study complexes of trypsin and its inhibitors. Some structural properties, including root-mean-square deviations (RMSD) of bond length, bond angle and key dihedral, and coordinated RMS Shifts of atoms and hydrogen bond, were studied using ABEEM/MM method and compared with OPLS-AA force-field. At the same time, comparative study on the charges of the hydrogen atoms at the tail of the ligand was also discussed in order to investigate the effect of hydrogen bond between trypsin and its ligand. This work demonstrates that ABEEM/MM model can well reproduce good structures for these trypsin–inhibitor complexes with rather small RMSD of bond length, bond angles, key dihedrals, and RMS Shifts of atomic coordinates with respect to the experimental crystal structures, compared with the results from the OPLS-AA method. The charges obtained by ABEEM/MM model are in good accordance with those from an ab initio calculation. Moreover, both the polarization and the salt-bridge effects have been taken into account. It is shown that ABEEM charges can properly describe the electrostatic interactions between the protein trypsin and its inhibitors.

We postulate that the adiabatic electron affinity of SF₆ is 2.40(10) eV, obtained from the photodetachment onset, 3.2(1) eV and a rearrangement energy of 0.8(1) eV. This eliminates the perceived "SF₆ density functional enigma". All of the experimental electron affinities are evaluated and 14 significantly different values selected to construct empirical anionic Morse potentials. These values are (in eV): 2.40(10) 2.20(10), 2.00(10), 1.80(10), 1.60(10), 1.20(10), 1.07(7), 0.93(10), 0.80(10), 0.63(10), 0.43(10), 0.30(10), 0.10(10), and 0.0(2). Comparisons are made to theoretical calculations and relative bond orders. The calculated electron affinities of SF₆ are: density functional, 1.6–3.0 eV; ab initio, -1.0–2.2 eV; semiempirical, 0.1–2.2 eV, and for SF₅ is 0.3–3.8 eV. Curves calculated using semiempirical, density functional and ab initio procedures are similar to the anionic Morse potentials. This work attempts to correct for differences in the EA calculated for this species.

A series of atomic energy formulas that relate atomic energies to the electrostatic potentials V₀ at nuclei are obtained by a series of polynomial and series fits of V₀ versus nuclear charge (Z). Density functional and Hartree–Fock V₀ are used for a series of fits that involve an isoelectronic series of anions, cations, and neutral ground state atoms to approximate atomic energies. Comparisons to the exact energies were performed in order to demonstrate the efficacy of the rigorous expressions.

In this paper, we present the results from model real-time quantum dynamical calculations of the proton transfer in green fluorescent protein (GFP) regarding four electronic states (labeled A, A*, I, I*). A coupled-states quantum wavepacket method has been used, which involves split-operator and fast FFT algorithms. The model potential energy surfaces are based upon data derived from experimental results with some modifications. Several important processes in GFP have been simulated, which include the photo-absorption and proton transfer in the excited state, the isotope effect and the recurrence time for proton motion in the excited state. The origin of the early-time (prompt) stimulated emission is tentatively explained in terms of off-resonance excitation as well as the contribution from the fastest component for proton transfer in GFP.

The effect of gas adsorption on the electronic properties of MgO and Ca-doped MgO is investigated using ab initio molecular dynamics method. The equilibrium position, adsorption energy, charge transfer, and electronic band structure of MgO and Ca-doped MgO (001) surface in the presence of H₂, O₂, and CO were calculated. It was found that CO and O₂ affect the electronic properties of MgO and Ca-doped MgO, extensively. The MgO and Ca-doped MgO can exhibit semiconductor behavior with a band gap which is smaller than that of the MgO after CO and O₂ adsorption. The obtained results indicate that Ca doping increase the activity and the conductivity of MgO (001) surface.

Elevated cholesterol levels are a primary risk factor for the development of coronary artery disease. Dietary changes associated with drug therapy can reduce high serum cholesterol levels and dramatically decrease the risk of stroke and overall mortality. HMG-CoA reductase is an important molecular target of hypolipemic drugs, known as statins, which are effective in the reduction of cholesterol serum levels, attenuating cholesterol synthesis in-liver by competitive inhibition regarding the substrate HMG-CoA. In this paper, we have focused on computer-aided molecular design using density functional theory, flexible docking, molecular dynamics as well as ADME, and synthetic accessibility analyses in order to propose novel potential HMG-CoA reductase inhibitors, designed by bioisosteric modifications which are promising for the treatment of hypercholesterolemia.

The Bessel discrete variable representation (DVR) method is tested to describe the interaction of atomic hydrogen with intense laser fields by numerically solving the time-dependent Schrödinger equation. Using the Bessel functions of the first kind, the singular terms, r^-2 or r^-1 at the origin, in the kinetic energy operators are analytically solved. As an illustration example, the high-order harmonic generation (HOHG) spectra in atomic hydrogen is calculated in length and acceleration forms. From the numerical results, it is concluded that this simple Bessel DVR may be a useful method for describing the interaction of atomic hydrogen with intense laser fields.

The electronic band structure, metallization, structural phase transition, and superconductivity of cubic zinc blende type GaAs and InAs are investigated. The equilibrium lattice constant, bulk modulus, and the phase transition pressure at which the compounds undergo structural phase transition from ZnS to NaCl are predicted from the total energy calculations. The density of states at the Fermi level (N(E_F)) get enhanced after metallization, which leads to the superconductivity in GaAs and InAs. The superconducting transition temperatures (T_c) of GaAs and InAs are obtained as a function of pressure for both the ZnS and NaCl structures. GaAs and InAs come under the class of pressure-induced superconductors. When pressure is increased T_c increases in both the normal and high pressure-structures. The dependence of T_c on electron–phonon mass enhancement factor λ shows that GaAs and InAs are electron–phonon-mediated superconductors. Also, it is found that GaAs and InAs retained in their normal structure under high pressure give appreciably high T_c.

Two of the three previously (the polyshell and polychair) proposed model structures for surface water are thermodynamically analyzed finding the excess surface enthalpy for air adsorption of the polyshell network close to the experimental one. The surface roughness of the model polyshell network is also close to experiment. The previously postulated Hydrogen Bond Formation Theory of Surface Activity, rests on the shell and chair structures, acquires predictive value for the calculation of the surface tensions of aqueous solutions of n-alkanols. The proposed models based on the contribution of hydrogen bonds and clusters to the thermodynamic properties are shown to allow useful quantitative estimations of some properties of the water–gas interphase.

The reactions between nitrile oxides and alkenes are of considerable interest in organic synthesis as the resulting heterocycles are versatile intermediates for the synthesis of natural products and biologically active compounds. In this paper, we design a series of reactions of phosphonyl nitrile oxides with acrylonnitrile, which can give 2:1 cycloaddition products with no crystal structure released so far, and present a detailed theoretical study on the mechanism of the 2:1 1, 3-dipolar cycloaddition reaction, which has been explored with density functional theory calculations at B3LYP/6-31G* level. The results reveal that the following mechanism is quite possible. Firstly, it starts as a normal 1,3-dipolar cycloaddition reaction to produce a regiospecific 1:1 product. Subsequently, highly reactive diisopropanyl phosphonyl nitrile oxide sequentially reacts with the aforementioned regiospecific 1:1 product and gives the corresponding cycloadduct. Further study is underway to expand the scope of this methodology, as well as to ascertain mechanistic details of the cycloaddition process.

Reaction paths are studied with the help of diabatic potential-energy surfaces coupled in a generic external field. We show that all putative geometrical and topological features of two-dimensional (2D) potential-energy surfaces for an isomerization can be generated with a model consisting of strictly diabatic harmonic 2D wells coupled in a static (yet uniform) external field. For a large class of three-state models, we provide a phase diagram of possible topologies in the relevant parameter space for three-state models. By following the shift in diabatic electronic amplitudes (denoted by {|c_k|²}) in coherent quantum states produced in the field, we assess whether the models within each phase can produce reaction paths visiting regions of configurational space that are structurally similar to the diabatic transition state.

The density matrix theory is used to calculate the fluorescence depletion spectra and the internal conversion (IC) times of rhodamine-700 (R-700) in methanol, ethanol, and DMSO solvents. The calculated IC times from S_x to S₁ states of R-700 in methanol, ethanol, and DMSO solvents are about 20, 33, and 70 fs, respectively. The times of the excited solvation processes for R-700 in methanol, ethanol, and DMSO solvents are about 8.0, 7.0, and 3.0 ps, respectively.

We present an alternative and accurate solution of the radial Schrödinger equation for the Hellmann potential within the framework of the asymptotic iteration method. We show that the bound state energy eigenvalues can be obtained easily for any n and ℓ values without using any approximations required by other methods. Our results are compared with the findings of other methods.

A new hybrid vairational-perturbational MRCISD(TQ) approach is applied to the problem of singlet–triplet and singlet–singlet separation in methylene using several basis sets. The inclusion of higher excitations beyond single and double excitations can predict more accurate splitting energies between states as well as closer single-point energies to available full CI results when the small basis set is used. Comparisons with MRCISD and MRCCSD treatments indicate that MRCISD(TQ) can lead to reliable predictions of the splitting energies when larger bases are employed.

Applying Kinetic Monte Carlo (KMC) technique, we investigated the influence of temperature and step-width on the step-flow growth of a (2D + 1) semiconductor-like uniform-spacing stepped model with inverse Ehrlich–Schwoebel (iES) barrier. The relation between diffusion length (R) and half of step width (L/2) was established to characterize the transition temperature T_c for switching between the random deposition growth and step-flow growth on surface. When temperature is lower than T_c, the surface growth mode is dominated by random deposition growth. As temperature approaches to T_c, the surface growth mode gradually switches to step-flow growth. However, only when the temperature is much higher than T_c, the random deposition growth is completely replaced by the step-flow growth. It is found that the step-width effect has a profound influence on surface growth mode in the transition region. The surface morphology undergoes a kinetic step-flow growth to form step-edge aggregation by either increasing temperature or decreasing the step width.

New species with molecular formula Si₂NS, not yet observed experimentally, are described theoretically for the first time. Various levels of calculations are applied to obtain the structures, energies, dipole moments, vibrational spectra, rotational constants, and isomerization of Si₂NS species. A total of 15 minima which are connected by 21 interconversion transition states on the potential energy surface are located at the DFT/B3LYP/6-311G(d) level of theory. And at the higher (single point) CCSD(T)/6-311+G(2d)//QCISD/6-311G(2d)+ZPVE level of theory, the global state of 1 (at 0.0 kcal/mol) corresponds to a nonlinear SiNSiS with a ²A′ electronic state. The next most stable isomer of 2 (only 3.7 kcal/mol higher 1) possesses a rhomboidal-type structure similar to the global state of Si₂NO. This is followed by another local minimum of 6 (at 43.8 kcal/mol above 1) which is a nonlinear SiNSSi form with a ²A′ electronic state. Note that both 1 and 6 have the important Si≡N triple bonding. Too, the analog of (NCCS) NSiSiS is unstable due to the higher energy of its own. The bonding natures of the relevant species are also discussed. An analysis of the bonding properties and structural similarities and differences between C₂NO, C₂NS, SiCNO, and Si₂NO is also carried out.

The quantitative structure–activity relationship (QSAR) of troxacitabine prodrugs with antitumor activity has been studied by using the density functional theory (DFT), molecular mechanics (MM2), and statistical methods. The established QSAR model shows not only significant statistical quality, but also predictive ability, with the square of adjusted correlation coefficient and the square of the cross-validation coefficient (q² = 0.807). The antitumor activity is expressed as pIC₅₀, which is defined as the negative value of the logarithm of necessary molar concentration of a compound to cause 50% growth inhibition against the human non-small-cell lung cancer cell line SW1573. It appears to be mainly governed by two factors (or original variables), i.e. the calculated hydrophobic coefficient (C log P) of whole molecule and the net charges of the first atom of substituent R (Q_FR), although three descriptors, i.e. C log P, (C log P)², and Q_FR, were selected in our multiple linear regression model. The factor C log P shows parabolic relation to pIC₅₀ and its suitable range is around 5.6, and the other factor Q_FR shows a significant negative correlation with pIC₅₀. In this paper, a detailed discussion on these two factors was carried out, and their close correlation with the action mechanism of these prodrugs was reasonably revealed. Such results can offer some useful theoretical references for understanding the action mechanism and directing the molecular design of this kind of compound with antitumor activity.

The binding energies, geometries, ⁷Li magnetic shielding, and electric field gradient tensors of hydrogenated lithium clusters, Li_nH_m (m ≤ n ≤ 4), were studied via density functional theory approach. We optimized the structures using B3LYP functional and 6-311++G (2d,2p) basis set. The calculated binding energies of lithium hydride clusters indicate that hydrogenation energy of Li_nH_m clusters decreases as the number of hydrogen atoms within the cluster increases. Our calculations also showed that for n = 4 clusters, the three-dimensional structure is more stable than the planar one. The study of the trends in the ⁷Li magnetic shielding isotropy, σ_iso, and anisotropies, Δσ, values are explained in terms of the interplay between the electronic and geometrical effects. The variations in the ⁷Li nuclear quadrupole coupling constants, χ, and their associated asymmetry parameters, η_Q, for different isomers of the lithium hydride clusters and the influence of hydrogenation on the EFG tensors are also discussed. For n = 4, we obtained a noticeable difference in the χ value from the planar to the three-dimensional structures. The atoms in molecules (AIM) analysis at the Li–H bond critical point reveals remarkably different topographical properties of the charge density and associated Laplacian fields for the planar and three-dimensional lithium hydride clusters.

An iteration method of functional theory is used to solve Poisson equation self-consistently in order to determine the retarded and advanced Green's function of a molecular system. The approach is demonstrated using a system with a spherical potential. The retarded and advanced Green's functions are calculated and the determined current–voltage results compare well with experimental data for the system involving Coulomb potential. The approach is expected to find wide applications in general systems.