NMR Parameters and Vibrational Investigation of 2-Dicyanovinyl-5-（4-ethoxyphenyl） thiophene by ab initio HF and DFT Calculations

Optimized geometry and harmonic vibrational frequency of 2-dicyanovinyl-5-(4- ethoxyphenyl)thiophene (C16H12N2OS) are calculated at the HF/6-31++G(d,p) and B3LYP/6- 311++G(d,p) levels. Mulliken charges in the ground state are also calculated. The research shows the presence of intermolecular interaction in the title compound. The scaled harmonic vibrational frequencies have been compared with experimental FT-IR spectra. A detailed interpretation of the infrared spectra of the title compound is reported. The theoretical spectrograms for IR spectra of the title compound have been constructed. The isotropic chemical shift computed by 13C and 1H NMR analyses also shows good agreement with the experimental observations.     

Reaction of C2HCl2＋O2： Combined TR-FTIR Spectroscopy and Electronic Structure

The product channels and mechanisms of the C2HC12＋O2 reaction are investigated by step-scan time-resolved Fourier transform infrared emission spectroscopy and the G3MP2// B3LYP/6-311G（d,p） level of electronic structure calculations. Vibrationally excited products of HCI, CO, and CO2 are observed in the IR emission spectra and the product vibrational state distribution are determined which shows that HCI and CO are vibrationally excited with the nascent average vibrational energy estimated to be 59.8 and 51.8 kJ/mol respectively. In combination with the G3MP2//B3LYP/6-311G（d,p） calculations, the reaction mechanisms have been characterized and the energetically favorable reaction pathways have been suggested.     

Studies on the Structures and Spectra of Benzothiophene Oligomers

Theoretical studies on a series of oligobenzothiophenes were carded out with the AM 1 and DFT methods. Based on B3LYP/6-31G（D） optimized geometries, the electronic spectra, IR spectra and NMR spectra of the oligomers were calculated by INDO/CIS, AM1 and B3LYP/6-31G（D） methods, respectively. The energy gaps decrease, and the absorption in elec- tronic spectra exhibits a red-shift as polymerization increases. The IR frequencies are little affected by the polymerization and substituents. The ^13C chemical shifts are changed to be upfield since the electron-donating groups increase the electron density of carbon atoms but remain unchanged with the increase of polymerization.     

IR and Raman Vibrational Assignments for Metal-free Phthalocyanine from Density Functional B3LYP／6-31G（d） Method

Vibrational (IR and Raman) spectra for the metal-free phthalocyanine (H2Pc) have been comparatively investigated through experimental and theoretical methods. The frequencies and intensities were calculated at density functional B3LYP level using the 6-3 IG(d) basis set. The calculated vibrational frequencies were scaled by the factor 0.9613 and compared with the experimental result. In the IR spectrum, the characteristic IR band at 1008.cm^-1 is interpreted as C-N (pyrrole) in-plane bending vibration, in contrast with the traditional assigned N-H in-plane or out-of-plane bending vibration. The band at 874 cm^-1 is attributed to the isoindole deformation and aza vibration. In the Raman spectrum, the bands at 540, 566, 1310, 1340, 1425, 1448 and 1618 cm^-1 are also re-interpreted. Assignments of vibrational bands in the IR and Raman spectra are given based on density functional calculations for the first time. The present work provides valuable information to the traditional empirical assignment and will be helpful for further investigation of the vibration spectra of phthalocyanine analogues and their metal complexes.     

Theoretical Investigations into the Intermolecular Hydrogen-bonding Interactions between Azacyclopentane-2-one and N-Methylol Ethanone

The structures of the complexes formed between N-methylol ethanone(model molecule of ceramide) and azacyclopentane-2-one(the model molecule of azone) have been fully optimized at the B3LYP/6-311++G** level.The intermolecular hydrogen bonding interaction energies have been calculated by using the B3LYP/6-311++G**,B3LYP/6-311++G(2df,2p),MP2(full)/6-311++G** and MP2(full)/6-311++G(2df,2p) methods,respectively.The results show that strong O–H···O=C,N–H···O=C and C–H···O=C hydrogen bonds could exist between azacyclopentane-2-one and N-methylol ethanone.The formation of the complexes might change the conformation of ceramide molecule and thus cause better percutaneous permeation for the drugs.This is perhaps the origin of the permeation enhances the activity of azone for medicament,as is in accordance with the experimental results.The hydrogen-bonding interactions follow the order of(a) (c) (b) (d) (g) ≈(e) ≈(i) (h) (f).The analyses of frequency,NBO,AIM and electron density shift are used to further reveal the nature of the complex formation.In the range of 263.0~328.0 K,the complex is formed via an exothermic reaction,and the solvent with lower temperature and dielectric constant is favorable to this process.     

亚烷基锡烯与乙烯环加成反应机理的理论研究

The mechanism of a cycloaddition reaction between singlet alkylidenestannylene and ethylene has been investigated with MP2/3-21 G^* and B3LYP/3-21 G* methods, including geometry optimization and vibrational analysis for the involved stationary points on the potential energy surface. Energies for the involved conformations were calculated by CCSD(T)//MP2/3-2 IG^* and CCSD(T)//B3LYP/3-21G^* methods, respectively. The results show that the dominant reaction pathway of the cycloaddition is that an intermediate (INT) is firstly formed between the two reactants through a barrier-free exothermic reaction of 39.7 kJ/mol, and the intermediate then isomerizes to a four-membered ring product (P2.1) via a transition state TS2.1 with a barrier of 66.8 kJ/mol.     

FT-IR, Raman and NMR Spectra, Molecular Geometry, Vibrational Assignments, ab initio and Density Functional Theory Calculations for Diethyl Phthalate

Phthalate acid esters (PAEs) possess endocrine disruptive effects and can produce reproductive and developmental toxicities. In this paper, both experimental and theoretical studies on FT-IR, Raman and 1H NMR spectra of diethyl phthalate (DEP) have been carried out. The geometrical structure of DEP was optimized at the HF/6-31G*, HF/6-311G**, B3LYP/6-31G*, and B3LYP/6-311G** levels, respectively. The harmonic vibrational frequencies, IR intensity, Raman activity and 1H NMR chemical shifts have been computed at the B3LYP/6-31G* and B3LYP/6-311G** levels. Anharmonic corrections to frequencies were obtained by means of second-order perturbation theory (PT2) at the B3LYP/6-31G* level. Based on potential energy distribution (PED), the vibrational assignments have also been performed. The theoretical calculation values were compared with the experimental observations and the results indicate they are in excellent agreement.     

Theoretical Study on the High Energy Density Compound Hexanitrohexaazatricyclotetradecanedifuroxan

Density functional theory （DFT） has been employed to study the molecular geometries, electronic structures, infrared （IR） spectra, and thermodynamic properties of the high energy density compound hexanitrohexaazatricyclotetradecanedifuroxan （HHTTD） at the B3LYP/6-31G^＊＊ level of theory. The calculated results show that there are four conformational isomers （α, β, γ and δ） for HHTTD, and the relative stabilities of four conformers were assessed based on the calculated total energies and the energy-gaps between the frontier molecular orbitals. The computed harmonic vibrational frequencies are in reasonable agreement with the available experimental data. Thermodynamic properties derived from the IR spectra on the basis of statistical thermodynamic principles are linearly correlated with the temperature. Detonation performances were evaluated by using the Kamlet-Jacobs equations based on the calculated densities and heats of formation. It was found that four HHTTD isomers with the predicted densities of ca. 2 g·cm^-3, detonation velocities near 10 km·s^-1, and detonation pressures over 45 GPa, may be novel potential candidates of high energy density materials （HEDM）. These results may provide basic information for the molecular design of HEDM.     

Synthesis and Infrared Spectra Computation of Sterically Congested 2,2-Disubstituted Indane-1,3-dione Derivatives

Sterically congested 2,2-disubstituted indane-1,3-dione derivatives have been syn-thesized and characterized by 1H NMR,13C NMR,FT-IR and elemental analysis.The B3LYP/HF calculations for computation of IR spectra have been carried out for the title compounds at the 6-31G and 6-311++G basis set levels.Predicted vibrational frequencies have been assigned and compared with the experimental FT-IR spectra and they are supported each other.     

Correlation effects on the structure and dynamics of the H3O+ hydrate: B3LYP/MM and MP2/MM MD simulations

Two combined quantum mechanics/molecular mechanics (QM/MM) molecular dynamics (MD) simulations, namely B3LYP/MM and MP2/MM, have been performed to investigate the possible influence of electron correlation on the structure and dynamics of the H(3)O(+) hydrate. In comparison to the previously published HF/MM results, both B3LYP/MM and MP2/MM simulations clearly reveal stronger H(3)O(+)-water hydrogen bond interactions, which are reflected in a slightly greater compactness of the H(3)O(+) hydrate. However, the B3LYP/MM simulation, although providing structural details very close to the MP2/MM data, shows an artificially slow dynamic nature of some first shell water molecules as a consequence of the formation of a long-lived H(3)O(+)···H(2)O hydrogen bonding structure.     

Experimental and theoretical investigation of the first overtone spectrum of 1,3,5-trinitrotoluene

Vibrational overtone spectroscopy is a powerful tool for studying intramolecular and intermolecular interactions. We report on a combined experimental and modeling study of the C-H stretch first overtone of bulk 1,3,5-trinitrotoluene (TNT) and TNT on fumed-silica powder. We recorded the overtone spectra by laser photoacoustic spectroscopy and compared them with those predicted with the harmonically coupled anharmonic oscillator model in the 5600-6600 cm(-1) region. The model systems included single molecules and hybrid quantum and molecular mechanical (QM:MM) clusters to account for the effects of intermolecular interactions on the observed spectra. We performed the hybrid QM:MM calculations at the HF/6-31+G(d,p), B3LYP/6-31+G(d,p), and MP2/6-31+G(d,p) levels of theory and with the universal force field (UFF) to account for van der Waals and electrostatic effects from surrounding molecules. Overtone spectra calculated from the MP2 level of theory, using a HF/3-21+G* calculation to assign molecular charges in the MM layer, and the Merz-Singh-Kollman population analysis for assigning partial charge in the QM layer and determining the transition dipole moment agreed best with the experimental data.     

Characteristics of CO3(2-)-water hydrogen bonds in aqueous solution: insights from HF/MM and B3LYP/MM MD simulations

Two combined quantum mechanics/molecular mechanics (QM/MM) molecular dynamics simulations, namely HF/MM and B3LYP/MM, have been performed to investigate the local hydration structure and dynamics of carbonate (CO(3)(2-)) in dilute aqueous solution. With respect to the QM/MM scheme, the QM region, which contains the CO(3)(2-) and its surrounding water molecules, was treated at HF and B3LYP levels of accuracy, respectively, using the DZV+ basis set, while the rest of the system is described by classical MM potentials. For both the HF/MM and B3LYP/MM simulations, it is observed that the hydrogen bonds between CO(3)(2-) oxygens and their nearest-neighbor waters are relatively strong, i.e., compared to water-water hydrogen bonds in the bulk, and that the first shell of each CO(3)(2-) oxygen atom somewhat overlaps with the others, which allows migration of water molecules among the coordinating sites to exist. In addition, it is observed that first-shell waters are either "loosely" or "tightly" bound to the respective CO(3)(2-) oxygen atoms, leading to large fluctuations in the number of first-shell waters, ranging from 1 to 6 (HF/MM) and 2 to 7 (B3LYP/MM), with the prevalent value of 3. Upon comparing the HF and B3LYP methods in describing this hydrated ion, the latter is found to overestimate the hydrogen-bond strength in the CO(3)(2-)-water complexes, resulting in a slightly more compact hydration structure at each of the CO(3)(2-) oxygens.     

Combined quantum mechanical/molecular mechanical study on the pentacoordinated ferric and ferrous cytochrome P450cam complexes

The pentacoordinated ferric and ferrous cytochrome P450(cam) complexes have been investigated by combined quantum mechanical/molecular mechanical (QM/MM) calculations in the presence of a protein/solvent environment and by QM calculations on the isolated QM regions with use of density functional theory. The B3LYP functional has been found more reliable than the BLYP and BHLYP functionals for estimating the relative state energies. The B3LYP/CHARMM calculations with an all-electron basis set for iron give high-spin ground states for the title complexes, in agreement with experiment. The comparison of the B3LYP/CHARMM results of the entire protein system with the B3LYP calculations on the naked QM regions shows that the amount of stabilization by the protein environment is largest for the intermediate-spin states, followed by the high-spin states of the complexes. The calculation of M?ssbauer parameters in the presence of the enzyme environment confirms the double occupation of the d(xz) orbital in the quintet spin state of the ferrous complex, consistent with the computed QM/MM energies in the enzyme environment, while the d(x)2(-)(y)2 orbital is doubly occupied in the gas-phase quintet state.     

Comparison of polarizable continuum model and quantum mechanics/molecular mechanics solute electronic polarization: study of the optical and magnetic properties of diazines in water

A combination of the polarizable continuum model (PCM) and the hybrid quantum mechanics/molecular mechanics (QM/MM) methodology, PCM-MM/QM, is used to include the solute electronic polarization and then study the solvent effects on the low-lying n→π(?) excitation energy and the (15)N nuclear magnetic shielding of pyrazine and pyridazine in aqueous environment. The results obtained with PCM-MM/QM are compared with two other procedures, i.e., the conventional PCM and the iterative and sequential QM/MM (I-QM/MM). The QM calculations are made using density functional theory in the three procedures. For the excitation energies, the time-dependent B3LYP/6-311+G(d) model is used. For the magnetic shielding, the B3LYP/aug-pcS2(N)/pcS2(C,O,H) is used with the gauge-including atomic orbitals. In both cases, i.e., PCM-MM/QM and I-QM/MM, that use a discrete model of the solvent, the solute is surrounded by a first shell of explicit water molecules embedded by an electrostatic field of point charges for the outer shells. The best results are obtained including 28 explicit water molecules for the spectral calculations and 9 explicit water molecules for the magnetic shielding. Using the PCM-MM/QM methodology the results for the n→π(?) excitation energies of pyridazine and pyrazine are 32,070 ± 80 cm(-1) and 32,675 ± 60 cm(-1), respectively, in good agreement with the corresponding I-MM/QM results of 32,540 ± 80 cm(-1) and 32,710 ± 60 cm(-1) and the experimental results of 33,450-33,580 cm(-1) and 32,700-33,300 cm(-1). For the (15)N magnetic shielding, the corresponding numbers for the gas-water shifts obtained with PCM-MM/QM are 47.4 ± 1.3 ppm for pyridazine and 19.7 ± 1.1 ppm for pyrazine, compared with the I-QM/MM values of 53.4?±?1.3 ppm and 19.5 ± 1.2 ppm and the experimental results of 42-54 ppm and 17-22 ppm, respectively. The agreement between the two procedures is found to be very good and both are in agreement with the experimental values. PCM-MM/QM approach gives a good solute polarization and could be considered in obtaining reliable results within the expected QM/MM accuracy. With this electronic polarization, the solvent effects on the electronic absorption spectra and the (15)N magnetic shielding of the diazines in water are well described by using only an electrostatic approximation. Finally, it is remarked that the experimental and theoretical results suggest that the (15)N nuclear magnetic shielding of any diazine has a clear dependence with the solvent polarity but not directly with the solute-solvent hydrogen bonds.     

Conformational space of 4,4′-methoxypropylstilbene molecule

Quantum-chemical simulation of the ground state [the density function B3LYP/6-31G, B3LYP/6-31G(d), and B3LYP/6-31+G(d,p) and the perturbation theory MP2/6-31G(d) methods] and the transition states [the B3LYP/6-31G(d) method] of 4,4′-methoxypropylstilbene molecule has been performed. Using the Ellinger MM2 force field method, the potentials of internal rotation have been obtained for each rotational degree of freedom of the molecule. The B3LYP simulation has revealed the planarity of the conjugated system and the orthogonal position of the alkyl substituent, whereas the benzene rings have deviated by about 20° with respect to the double bond plane according to the MP2 data. Three transition states of the molecule corresponding to the saddle points of the first and the second orders have been revealed. The stationary points have been identified by means of vibrational analysis.     

Force-field parameters for the simulation of tetrahedral intermediates of serine hydrolases

CHARMM force-field parameters are reported for the tetrahedral intermediate of serine hydrolases. The fitting follows the standard protocol proposed for CHARMM22. The reference data include ab initio (RHF/6-31G*) interaction energies of complexes between water and the model compound 1,1-dimethoxyethoxide, torsional profiles of related model compounds from correlated ab initio (MP2/6-311+G*//B3LYP/6-31+G*) calculations, as well as molecular geometries and vibrational frequencies from density functional theory (B3LYP/6-31+G*). The optimized parameters reproduce the target data well. Their utility is demonstrated by a QM/MM study of the tetrahedral intermediate in Bacillus subtilis lipase A, and by classical molecular modeling of enantioselectivity in Pseudomonas aeruginosa lipase and its mutants.     

Toward accurate barriers for enzymatic reactions: QM/MM case study on p-hydroxybenzoate hydroxylase

The hydroxylation reaction catalyzed by p-hydroxybenzoate hydroxylase has been investigated by quantum mechanical/molecular mechanical (QM/MM) calculations at different levels of QM theory. The solvated enzyme was modeled (approximately 23,000 atoms in total, 49 QM atoms). The geometries of reactant and transition state were optimized for ten representative pathways using semiempirical (AM1) and density functional (B3LYP) methods as QM components. Single-point calculations at B3LYP/MM optimized geometries were performed with local correlation methods [LMP2, LCCSD(T0)] and augmented triple-zeta basis sets. A careful validation of the latter approach with regard to all computational parameters indicates convergence of the QM contribution to the computed barriers to within approximately 1 kcal mol(-1). Comparison with the available experimental data supports this assessment.     

A combined QM/MM molecular dynamics simulations study of nitrate anion (NO3-) in aqueous solution

The structural and dynamical properties of NO3- in dilute aqueous solution have been investigated by means of two combined quantum mechanics/molecular mechanics (QM/MM) molecular dynamics simulations, namely HF/MM and B3LYP/MM, in which the ion and its surrounding water molecules were treated at HF and B3LYP levels of accuracy, respectively, using the DZV+ basis set. On the basis of both HF and B3LYP methods, a well-defined first hydration shell of NO3- is obtainable, but the shell is quite flexible and the hydrogen-bond interactions between NO3- and water are rather weak. With respect to the detailed analysis of the geometrical arrangement and vibrations of NO3-, the experimentally observed solvent-induced symmetry breaking of the ion is well reflected. In addition, the dynamical information, i.e., the bond distortions and shifts in the corresponding bending and stretching frequencies as well as the mean residence time of water molecules surrounding the NO3- ion, clearly indicates the "structure-breaking" ability of this ion in aqueous solution. From a methodical point of view it seems that both the HF and B3LYP methods are not too different in describing this hydrated ion by means of a QM/MM simulation. However, the detailed analysis of the dynamics properties indicates a better suitability of the HF method compared to the B3LYP-DFT approach.