Journal of Molecular Structure-theochem最新文献

The hydrogen bonding interactions between cysteine and urea were studied with density functional theory (DFT) regarding their geometries, energies, vibrational frequencies, and topological features of the electron density. The quantum theory of atoms in molecules (QTAIM) and natural bond orbital (NBO) analyses were employed to elucidate the interaction characteristics in the complexes. Multiple hydrogen bonds (H-bonds) are formed in one complex since both cysteine and urea have multiple sites as H-bond donor or acceptor. Most of intermolecular H-bonds involve O atom of cysteine/urea moiety as proton acceptors. The H-bond involving O atom of urea moiety as proton acceptor and hydroxyl of cysteine moiety as proton donor is the strongest one, which is attributed to a partial covalent character. The H-bonds involving the CH group of cysteine moiety as proton donor are very weak and show small blue shifts, while other H-bonds are red-shifting ones. Both hydrogen bonding interaction and structural deformation are responsible for the stability of Cys–Urea complexes, and the complexes involving either the strongest H-bond or the smallest deformation are not the stable ones. Analysis of various physically meaningful contributions arising from the energy decomposition procedures shows that the orbital interaction of H-bond is predominant during the formation of complex. The cooperative effects happened in complexes have also been discussed. Relationships between the topological properties (electron density ρ_b and its Laplacian ∇²ρ_b) at the bond critical point (BCP) of H-bond and structural parameter (δR) as well as the second-perturbation energies E(2) have also been discussed.

In this paper, the polarizable continuum model (PCM) is used to investigate the effect of solvent on the geometry, vibrational frequencies, IR intensities, Raman scattering activities, solvation free energies and the dipole moment of sulfanilamide. Hartee–Fock (HF), B3LYP and MP2 are employed for all models, both in gas phase and in solution, with basis sets up to 6-311+G(d,p) for HF and B3LYP and 6-31G(d) for MP2. A new SMD model is also used for solvation energy and dipole moment calculations. Some significant changes are observed in the dihedral angles but no noticeable changes appear in vibrational frequencies when sulfanilamide is solvated. Moreover, solvent effects on infrared intensities and Raman scattering activities are quite considerable and they increase as one goes from lower to higher dielectric constant. With PCM, both the solvation free energy and dipole moment of sulfanilamide increase when going from non-polar to polar solvents but no noticeable changes are observed among polar solvents. However, with SMD the solvation free energies are 15.5–33.0 kJ/mol and 9.6–19.7 kJ/mol higher than those of PCM for polar and non-polar solvent, respectively.

A new quantitative method for predicting and calculating the heat of detonation for a series of nitro paraffins and nitramines employing the natural bond orbital (NBO) charge analysis and ¹⁵N NMR chemical shifts of the nitro group is established. All calculations, including optimizations, charge analysis and ¹⁵N_Nitro NMR chemical shifts, were performed using density functional (DFT) methods with 6-311+G(d,p) basis set. The results show a linear correlation between the nitro group charges and C/N-nitro bond lengths. The latter reflect the strength of the corresponding bond and thus the stability of the nitro compounds. A strong correlation was observed between the heat of detonation with the charge and ¹⁵N NMR chemical shift on the nitro group in nitramines and nitro paraffins. Nitro compounds with a higher heat of detonation have less negative nitro group charges, (Q_Nitro) and a lower value for the ¹⁵N_Nitro chemical shift in analogous compounds. From the quantitative models, the heat of detonation increase when the Q_Nitro values (positive coefficient) are larger and decrease when the ¹⁵N_Nitro NMR chemical shift (negative coefficient) is higher. The present work provides consistent models (mean square error prediction values below 0.14 MJ kg⁻¹) in a systematic way for quick estimation of heats of detonation – with or without experimental data – for a wide range of energetic materials. This practical approach is particularly useful as a tool for the design of high-energy density materials.

Chlorinated benzoates are widely spread in the environment and are subject to anaerobic degradations, where chlorinated benzoates are used as electron acceptor by certain groups of anaerobic bacteria and the energy of the reduction reactions is used by bacteria for growth. The energies, namely the change of Gibbs energy of the reduction reaction (Δ_rG), are predicted here using quantum chemistry calculations, where the gas-phase properties, including the enthalpies of formation, the Gibbs free energies, and the acidities, are predicted at the G3XMP2 level, and the solvent effects are modelled using the polarizable conductor model (C-PCM) model. The predicted gas-phase enthalpies of formation and acidities of monochlorinated benzoic acids are in excellent agreement with the experimental measurements, and the aqueous phase pK_a prediction shows that chlorinated benzoic acids will exist as benzoates almost exclusively in the natural environment (pH ∼7).

Theoretical investigation has been carried out for the electronic structures, optical properties and electron transition mechanism of R-substituted 2-phenylbenzoxazole complexes (nb) and derived phenolic Schiff bases (na) (n = 1, R = CH₃; n = 2, R = N(CH₃)₂; n = 3, R = Cl; n = 4, R = NO₂). In the gas phase, the ground and excited states were fully optimized at the B3LYP/cc-pVDZ, HF/cc-pVDZ and CIS/cc-pVDZ, respectively. For each derivative, two conformations are available, one with a downward hydrogen (H2) and the other with an upward hydrogen, and the former one is more stable than the latter one. Absorption and emission spectra of all species were calculated by the time-dependent density functional theory (TD-DFT) based on the ground and excited states geometries. The absorption and emission spectra were consistently blue shifted in going from na to nb. The solvent effects on molecular geometries and optical properties were characterized in several solvents from B3LYP/cc-pVDZ and HF/cc-pVDZ calculations employing the Onsager model within the framework of the self-consistent reaction field (SCRF) theory. The SCRF calculations provide reliable information regarding the solvent effects on the geometries and optical properties of the conjugate compounds.

In this article, we apply the quasi-classical trajectory (QCT) method to study the reaction $\text{O}\left({}^3\text{P}\right)+{\text{H}}_2(\nu =0\text{,}j=0)\to \text{OH}+\text{H}$ on the ³A′ and ³A″ potential energy surfaces (PESs). Information of the vector correlations revealing the product alignment and orientation on the two different triplet PESs has been provided. The results of the calculations show that the products not only align strongly along the direction perpendicular to reagent initial relative vector k, but also orient along the direction of the negative y-axis, with stronger product polarizations being observed on the ³A″ PES at the collision energy smaller than 24 kcal/mol and on the ³A′ PES at the collision energy bigger than 24 kcal/mol. On both PESs, especially on the ³A″ PES, the products show preference for backward scattering which becomes weaker as collision energy increases.

During the computation, 15 complexes for nitrosamine–formic acid (Z, E), and nitrosamine–formamide were found. For all of the methods, containing B3LYP/6-311++(2d,2p), B3LYP/aug-cc-pVDZ and B3LYP/aug-cc-pVTZ, the complexes of Z-1 and F-1 are the most stable ones. The order of hydrogen bond strengths are as follows: O–H⋯O > N–H⋯O > N–H⋯N > C–H⋯O > C–H⋯N. Results show that the proton stretching between a donor and an acceptor affects the strength of hydrogen bond. In some cases, eight-member ring is formed due to the resonance-assisted hydrogen bonds (RAHB) mechanism. AIM analyses at the hydrogen bond critical points show maximum electron density (ρ) for O–H⋯O, and minimum electron density for C–H⋯O.

The hydrogen bond (H-bond) interaction of 1:1 supermolecular complexes of protonated adrenaline (PAd⁺) with formate anion and its derivatives (denoted as RCOO⁻, RH, CH₃, CH₂F, CH₂Cl, and CH₂Br) has been investigated by performing density functional theory calculations at the B3LYP/6-31G+(d) level. We obtained the most stable three conformations for each complex, which are denoted as PAd⁺–RCOO⁻(I), PAd⁺–RCOO⁻(II), PAd⁺–RCOO⁻(III), respectively, and calculated the interaction energy between PAd⁺ and RCOO⁻. In all PAd⁺–RCOO⁻ complexes, PAd⁺–CH₃COO⁻ is found to be the most favorable energetically. There exists low-barrier hydrogen bond (LBHB) in PAd⁺–HCOO⁻(III), PAd⁺–CH₂FCOO⁻(III), PAd⁺–CH₂ClCOO⁻(III), and PAd⁺–CH₂Br⁻(III) complexes. The solvent effects on the geometry and energy of the complexes are also considered by using the polarizable continuum model (PCM) model in aqueous solvent. It is found that PAd⁺–R⁻ complexes in solution are significantly less stable than those in the gas-phase. The theoretical results for the present model systems will be useful for experimental researchers working in this field.

The stable structures of (AgBr)_n (n ⩽ 6) are optimized by using density functional method, and the basis set effect is also investigated. Our initial structures are the stable structures of (AgX)_n (X = Cl, Br, I, n ⩽ 6) obtained from the results of genetic algorithm. It is found that the most stable structures of (AgBr)_n are planar rings for n ⩽ 4 and three-dimensional structures for n > 4, with (AgBr)₃ the most stable one. For the ground state structures of (AgBr)_n, the chemical bonds are studied and electronic structures also explored.

Approaches, using density functional theory (DFT), to calculate accurate adiabatic and vertical carbon 1s core electron binding energies (CEBE) of some alkanes, alkenes, alkynes and methyl- and fluorine-substituted benzenes are investigated.

The approaches tested can be schematized as follows; $\Delta E_{\text{KS}}(\text{PW}86\times -\text{PW}91\text{c}/\text{TZP}+C_{\text{rel}})//\text{DFT}(\text{PW}86\times -\text{PW}91c/\text{TZP})$ where ΔE_KS is the difference between the Kohn–Sham total energy of the core–hole cation M⁺, E_KS(M⁺), and the Kohn–Sham total energy of the neutral ground state molecule M, E_KS(M). The geometry of M is optimized with DFT(PW86x-PW91c/TZP). For the adiabatic C1s CEBE calculation, the geometry of M⁺ is optimized whereas, for the vertical C1s CEBE calculation, the geometry of M⁺ is identical to the neutral ground state molecule M. C_rel represents relativistic corrections. We tested two cases; C_rel = 0 eV, and C_rel = 0.05 eV. The relativistic correction turned out to be not necessary, because inclusion of the relativistic correction always increased deviation. The current results suggest a systematic error in the calculations that is fortuitously offset by the neglect of relativistic effects. The best approach resulted in average absolute deviations (maximum absolute deviations) from adiabatic experimental values of 0.045 eV (0.130 eV) for calculations of the corresponding C1s CEBE of the alkanes, alkenes, and substituted benzenes for 120 cases. The absolute uncertainty in the experimental measurements is estimated to be 0.03 eV. The average absolute deviation of 0.045 eV is close to the magnitude of the experimental uncertainty. Agreement between theory and experiment is better for adiabatic C1s CEBE than for vertical C1s CEBE.