A Computational Understanding of Solvent Effect on the Structure,Electronic, Thermochemical,and Spectroscopic Properties of Ni(η2‐C6H4)(H2PCH2CH2PH2) Complex

Here we report the density functional calculations of the molecular parameters including the energy, geometries, electric dipole moments, vibrational IR frequencies, and ¹H and ¹³C NMR chemical shifts of Ni(η²‐C₆H₄ )(H₂PCH₂CH₂PH₂ ) (a benzyne complex). Based on the polarizable continuum model (PCM ), the effect of polarity of the solvent on these parameters was explored. The wavenumbers of υ(C1–C2 ) as well as the ¹H and ¹³C NMR chemical shift values of complex in various solvents were calculated and correlated with the Kirkwood–Bauer–Magat equation (KBM ), the solvent acceptor numbers (ANs ), and the linear solvation energy relationship (LSER ). The bonding interaction between the benzyne and Ni(H₂PCH₂CH₂PH₂ ) fragment was analyzed by means of the energy decomposition analysis (EDA ). The character of the Ni–C bonds of the molecules was analyzed by natural bond orbital (NBO ) analysis. Also, Monte Carlo simulations were used for the calculation of the total energy and solvation free energy of the complex in water.     

Solvent effect of aqueous media on properties of glycine: Significance of specific and bulk solvent effects,and geometry optimization in aqueous media

Geometries of the normal (N) and zwitterionic (Z) forms of glycine (gly) and their complexes gly.(H₂O)_n, n = 0–2, were fully optimized in gas phase and aqueous media, and transition states located between the corresponding N and Z forms. The geometry was also optimized and vibrational spectra calculated for the gly.(H₂O)₃ complex of Z glycine. Density functional theory at the B3LYP/AUG‐cc‐pVDZ level was employed for the geometry optimization calculations in gas phase and aqueous media while single point energy calculations were performed at the MP2/AUG‐cc‐pVDZ level in each case. Solvation in bulk water was treated using the polarizable continuum model (PCM). Zero‐point energy correction to total energy and thermal energy correction to enthalpy were obtained at the B3LYP/AUG‐cc‐pVDZ level of theory in both gas phase and bulk aqueous media and these corrections were also considered to be valid for the corresponding single point energy calculations performed at the MP2/AUG‐cc‐pVDZ level of theory. When geometries of the complexes of glycine with water molecules are optimized in aqueous media, the calculated properties are found to be appreciably modified with respect to those obtained by gas phase geometry optimization followed by solvation in aqueous media. For several vibrational frequencies, the agreement between the calculated and experimentally observed results is improved appreciably when both the specific and bulk solvent effects are considered in combination with full geometry optimization in aqueous media. For certain vibrational frequencies, mode assignments have also been modified. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2008     

Molecular structure, vibrational spectra and HOMO, LUMO analysis of yohimbine hydrochloride by density functional theory and ab initio Hartree-Fock calculations

Yohimbine hydrochloride (YHCl) is an aphrodisiac and promoted for erectile dysfunction, weight loss and depression. The optimized geometry, total energy, potential energy surface and vibrational wavenumbers of yohimbine hydrochloride have been determined using ab initio, Hartree–Fock (HF) and density functional theory (DFT/B3LYP) method with 6-311++G(d,p) basis set. A complete vibrational assignment is provided for the observed Raman and IR spectra of YHCl. The UV absorption spectrum was examined in ethanol solvent and compared with the calculated one in gas phase as well as in solvent environment (polarizable continuum model, PCM) using TD-DFT/6-31G basis set. These methods are proposed as a tool to be applied in the structural characterization of YHCl. The calculated highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) with frontier orbital gap are presented.     

Molecular analysis of water clusters: Calculation of the cluster structures and vibrational spectrum using density functional theory

Density functional theory (DFT) is applied to obtain absorption spectra at THz frequencies for molecular clusters of H₂O. The vibrational modes of the clusters are calculated. Coupling among molecular vibrational modes explains their spectral features associated with THz excitation. THz excitation is associated with vibrational frequencies which are here calculated within the DFT approximation of electronic states. This is done for both isolated molecules and collections of molecules in a cluster. The principal result of the paper is that a crystal-like cluster of 38 water molecules together with a continuum solvent background is sufficient to replicate well the experimental vibrational frequencies.     

Conformational Distributions of N‐Acetyl‐L‐cysteine in Aqueous Solutions: A Combined Implicit and Explicit Solvation Treatment of VA and VCD Spectra

The conformational distributions of N‐acetyl‐L ‐cysteine (NALC) in aqueous solutions at several representative pH values are investigated using vibrational absorption (VA), UV/Vis, and vibrational circular dichroism (VCD) spectroscopy, together with DFT and molecular dynamics (MD) simulations. The experimental VA and UV/Vis spectra of NALC in water are obtained under strongly acid, neutral, and strongly basic conditions, as well as the VCD spectrum at pH 7 in D₂O. Extensive searches are carried out to locate the most stable conformers of the protonated, neutral, deprotonated, and doubly deprotonated NALC species at the B3LYP/6‐311++G(d,p) level. The inclusion of the polarizable continuum model (PCM) modifies the geometries and the relative stabilities of the conformers noticeably. The simulated PCM VA spectra show significantly better agreement with the experimental data than the gas‐phase ones, thus allowing assignment of the conformational distributions and dominant species under each experimental condition. To further properly account for the discrepancies noted between the experimental and simulated VCD spectra, PCM and the explicit solvent model are utilized. MD simulations are used to aid the modelling of the NALC–(water)_N clusters. The geometry optimization, harmonic frequency calculations, and VA and VCD intensities are computed for the NALC–(water)_3,4 clusters at the B3LYP/6‐311++G(d,p) level without and with the PCM. The inclusion of both explicit and implicit solvation models at the same time provides a decisively better agreement between theory and experiment and therefore conclusive information about the conformational distributions of NALC in water and hydrogen‐bonding interactions between NALC and water molecules.     

Density functional theory study of the rotational barriers,conformational preference,and vibrational spectra of 2-formylfuran and 3-formylfuran

The torsional potentials, molecular structures, conformational stability, and vibrational wavenumbers for the rotational isomers of 2-formylfuran and 3-formylfuran are computed using the density functional theory (B3LYP) method with the 6-31+G* basis set. All structures are fully optimized and the optimized geometries, rotational constants, dipole moments, and energies are presented. From the computations, both 2-formylfuran and 3-formylfuran are predicted to exist predominantly in trans conformation with a cis–trans rotational barrier of 11.19 kcal/mol and 8.10 kcal/mol, respectively. The vibrational wavenumbers and the corresponding vibrational assignments of the molecules in the C _s symmetry are examined and the infrared spectra of the molecules are simulated using the wavenumbers and the corresponding intensities obtained from the computations. The effect of solvents on the conformational stability of all the molecules in nine different solvents (heptane, chloroform, tetrahydrofuran, dichloroethane, acetone, ethanol, methanol, dimethylsulfoxide, and water) is investigated. The integral equation formalism in the polarizable continuum model (IEF-PCM) is used for all solution phase computations.     

Density functional studies of hydrogen-bonded systems: II. Solvation of the H2O–CO complex by a nonpolar solvent

A dielectric continuum approach (SCIPCM) in the framework of density functional theory has been applied to study the structures, energetics and vibrational spectra of hydrogen-bonded H₂O–CO and H₂O–OC complexes in a non-polar solvent. The dielectric constants for Ar (1.63), Kr (1.83) and Xe (2.19) were used in order to mimic the low-temperature matrix isolation experiments. We have found that calculations which include a dielectric reaction field around the complexes are able to reproduce the experimentally observed spectral changes. The correction of the calculated interaction energy for the basis set superposition error is discussed in the framework of the self-consistent reaction field approach.     

Structural and spectral properties of 3-substitutedphenyl-1,5-diphenylformazans: A quantum chemical study

The structural and optical properties of 3-substitutedphenyl-1,5-diphenylformazans are studied by quantum chemical methods. The density functional theory (DFT) is employed to optimize the ground state geometries of formazans substituted with different electron donating and withdrawing groups in both gas and solvent phases. The absorption spectra of formazan derivatives are calculated using time dependent density functional theory (TD-DFT). The polarizable continuum model (PCM) calculations of 3-substitutedphenyl-1,5-diphenylformazans are performed for bulk solvent effects. The geometrical parameters, vibrational frequencies, and relative stabilities of isomers of 3-substitutedphenyl-1,5-diphenylformazans are studied. The results obtained by TD-DFT calculations reveal that the substitution of electron withdrawing and donating substituents affects the absorption spectra of 3-substitutedphenyl-1,5-diphenylformazans. The calculated maximum absorption wavelengths (λ_max) are highly consistent with the experimental values as found from UV-vis spectra.     

Three novel dipicolinate complexes with the pyridine-2,6-dimethanol – A combined structural,spectroscopic, antimicrobial and computational study

Three new dipicolinate complexes, [M(dmp)(dpc)]·H₂O [M = Co(II) (1); Zn(II) (2); Ni(II) (3); dmp: pyridine-2,6-dimethanol; dpc: dipicolinate or pyridine-2,6-dicarboxylate], were synthesized and combined with experimental and theoretical study on molecular, vibrational and electronical properties. The central M(II) ion in all complexes is bonded to dpc and dmp ligands through pyridine nitrogen atom together with two oxygen atom, forming the distorted octahedral geometry. The complex molecules, connected via O–H⋯O hydrogen bonds, form a supramolecular structure. The complexes were also screened for antimicrobial activity against human pathogenic Gram-positive, Gram-negative bacteria and fungi. Among the tested microorganisms, Streptococcus pneumoniae was the most sensitive strain, especially to H₂dpc and its complexes. The EPR spectra of Cu²⁺ doped polycrystalline complexes indicate that the paramagnetic center has a rhombic symmetry. Although the supramolecular interactions have some influences on the molecular geometry in solid state phase, calculated data show that the predicted geometries can reproduce the structural parameters. The electronic station in the frontier orbitals of the dipicolinate complexes calculated from the experimental data is compared to the results of time-depended DFT calculations with the polarizable continuum model and UV–Vis spectrum of the complexes has been discussed on this basis. Calculated vibrational frequencies using the DFT and HF method are consistent with the experimental IR data.     

Density functional theory studies on the structure,spectra (FT-IR,FT-Raman,and UV) and first order molecular hyperpolarizability of 2-hydroxy-3-methoxy-N-(2-chloro-benzyl)-benzaldehyde-imine: Comparison to experimental data

The infrared and Raman spectra of 2-hydroxy-3-methoxy-N-(2-chloro-benzyl)-benzaldehyde-imine (HMCBI) have been recorded and analyzed. Density functional calculations at B3LYP/6-311++G(d,p) level were carried out to study the equilibrium geometries and vibrational spectra of HMCBI. The calculations revealed that the optimized geometry closely resembled the experimental XRD data. The calculated vibrational spectra were analyzed on the basis of the potential energy distribution (PED) of each vibrational mode, which allowed us to obtain a quantitative as well as qualitative interpretation of IR and Raman spectra. The ¹H nuclear magnetic resonance (NMR) chemical shifts of the molecule in the ground state were calculated by Gauge independent atomic orbital (GIAO) method. Information about size, shape, charge density distribution and site of chemical reactivity of the molecules has been obtained by mapping electron density isosurface with electrostatic potential surface. Based on optimized ground state geometries, the NBO analysis has been done to study donor–acceptor (bond–antibond) interactions. The TD-DFT method has been used to calculate energies, oscillator strengths of electronic singlet–singlet transitions and the absorption wavelengths. Solvent effects were considered using the polarizable continuum model (PCM). Good consistency is found between the calculated results and experimental data for the electronic absorption. The calculated first hyperpolarizability may be attractive for further studies on non-linear optical properties of materials.     

Theoretical study on the solvent effect of the nitrosyl cation (NO+) generating reaction

Nitrosyl cation (NO⁺) generating reaction HONO + H⁺ → NO⁺ + H₂O has been theoretically investigated by B3LYP and high‐electron‐correlation QCISD methods with 6‐31G (d,p) basis set. The solvent effects on the geometries, reaction path properties, energies, thermodynamic, and kinetic characters in four solvents (benzene, tetrahydrofuran, acetonitrile, and water) have been calculated using self‐consistent reaction field (SCRF) approach with the polarizable continuum model (PCM). The results show that the activation energy barriers and the relative energies of the products are decreased with increase of the polarities of the solvents, and the reaction is favored in polar solvents thermodynamically and kinetically. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Structural and spectral properties of 4-bromo-1-naphthyl chalcones: a quantum chemical study

The structural and optical properties of 4-bromo-1-naphthyl chalcones (BNC) have been studied by using quantum chemical methods. The density functional theory (DFT) and the singly excited configuration interaction (CIS) methods were employed to optimize the ground and excited state geometries of unsubstituted and substituted BNC with different electron withdrawing and donating groups in both gas and solvent phases. Based on the ground and excited state geometries, the absorption and emission spectra of BNC molecules were calculated using the time-dependent density functional theory (TDDFT) method. The solvent phase calculations were performed using the polarizable continuum model (PCM). The geometrical parameters, vibrational frequencies, and relative stability of cis- and trans-isomers of unsubstituted and substituted BNC molecules have been studied. The results from the TDDFT calculations reveal that the substitution of electron withdrawing and electron donating groups affects the absorption and emission spectra of BNC.     

Intermolecular interactions in uracil–nitrous acid complexes: structures,binding energy,topological properties,and nuclear magnetic resonance study

Molecular interactions between uracil and nitrous acid (U–NA) [C₄N₂O₂H₄? NO₂H] have been studied using B3LYP, B3PW91, and MP2 methods with different basis sets. The optimized geometries, harmonic vibrational frequencies, charge transfer, topological properties of electron density, nucleus‐independent chemical shift (NICS), and nuclear magnetic resonance one‐ and two‐bonds spin–spin coupling constants were calculated for U–NA complexes. In interaction between U and NA, eight cyclic complexes were obtained with two intermolecular hydrogen bonds N(C)HU…N(O) and OH_NA…O_U. In these complexes, uracil (U) simultaneously acts as proton acceptor and proton donor. The most stable complexes labeled, UNA1 and UNA2, are formed via NH bond of U with highest acidity and CO group of U with lowest proton affinity. There is a relationship between hydrogen bond distances and the corresponding frequency shifts. The solvent effect on complexes stability was examined using B3LYP method with the aug‐cc‐pVDZ basis set by applying the polarizable continuum model (PCM). The binding energies in the gas phase have also been compared with solvation energies computed using the PCM. Natural bond orbital analysis shows that in all complexes, the charge transfer takes place from U to NA. The results predict that the Lone Pair (LP)(O)_U → σ*(O? H) and LP(N(O)_NA → σ*(N(C)? H)_U donor–acceptor interactions are most important interactions in these complexes. Atom in molecule analysis confirms that hydrogen bond contacts are electrostatic in nature and covalent nature of proton donor groups decreases upon complexation. The relationship between spin–spin coupling constant (^1hJ_H…_Y and ^2hJ_H…_Y) with interaction energy and electronic density at corresponding hydrogen bond critical points and H‐bonds distances are investigated. NICS used for indicating of aromaticity of U ring upon complexation. © 2013 Wiley Periodicals, Inc.     

水环境对GC和AT碱基对质子转移的影响

采用B3LYP/DZP++的方法研究了第一水化层作用和连续化处理的水溶剂作用对鸟嘌呤-胞嘧啶(GC)碱基对和腺嘌呤-胸腺嘧啶(AT)碱基对质子转移反应的影响. GC和AT碱基对在连续化水溶剂作用下,均发生单质子转移(SPT1)和分步的双质子转移(DPT),而在第一水化层5 个水分子的作用下(GC·5H₂O,AT·5H₂O)或同时考虑第一水化层作用和连续化水溶剂作用(GC·5H₂O+PCM,AT·5H₂O+PCM)时,GC和AT碱基对的质子转移均只得到单质子转移反应(SPT1). 单质子转移过程中的活化能变化情况表明：第一水化层对GC和AT碱基对结构和质子转移影响较大,水环境对碱基对的作用主要发生在第一水化层.     

Density functional theory studies of conformational stabilities and rotational barriers of 2- and 3-thiophenecarboxaldehydes

The molecular structures, conformational stabilities, and infrared vibrational wavenumbers of 2-thiophenecarboxaldehyde and 3-thiophenecarboxaldehyde are computed using Becke-3–Lee–Yang–Parr (B3LYP) with the 6-311++G** basis set. From the computations, cis-2-thiophenecarboxaldehyde is found to be more stable than the transfer conformer with an energy difference of 1.22 kcal/mol, while trans-3-thiophenecarboxaldehyde is found to be more stable than the cis conformer by 0.89 kcal/mol. The computed dipole moments, structural parameters, relative stabilities of the conformers and infrared vibrational wavenumbers of the two molecules coherently support the experimental data in the literature. The normal vibrational wavenumbers are characterized in terms of the potential energy distribution using the VEDA4 program. The effect of solvents on the conformational stability of the molecules in nine different solvents is investigated using the polarizable continuum model.     

Vibrational study of fluorobenzene and its solvation with methanol via polarized Raman measurements and quantum chemical calculations

Raman spectra of neat fluorobenzene (C₆H₅F, FB) and its binary mixtures with methanol (CH₃OH, M) at varying mole fractions of FB from 0.1 to 0.9 were recorded in order to understand the influence of intermolecular interaction on spectral features corresponding to some selected vibrational bands of FB in the region 1200-450 cm⁻¹. Only few vibrational bands of fluorobenzene show a significant change in their peak position in going from neat liquid to the complexes. The 803, 829 and 994 cm⁻¹ bands show blue shift upon complexation which indicates significant amount of charge transfer between the reference molecule and the solvent. However, the linewidths do not show any appreciable change. Density functional theory (DFT) calculations were performed employing B3LYP method and high level basis set 6-311++G(d,p) to obtain the ground state geometry of neat FB and its hydrogen bonded complexes with methanol in gas phase. In order to account for the solvent effect and also to realize a condition quite close to the experiment, polarizable continuum model (PCM) calculations considering bulk solvation as well as explicit (specific plus bulk) solvation approaches were also performed. A detailed vibrational assignment of the various normal modes has been performed on the basis of potential energy distribution (PED) calculations. Depolarization ratios for the different vibrational bands were calculated and the values match nicely with the depolarization ratio determined from the experimental data.     

Local mode interpretation of the CH and CD stretching vibrational manifolds of isotopic ethylenes,C2H3D and C2HD3

The IR spectra of C₂H₃D and C₂HD₃ have been studied up to 3 quanta of excitation of CH and CD stretching (<9500 cm⁻¹). Observed vibrational wavenumbers are well reproduced in terms of a local mode model, which involves different Fermi resonance interactions in each molecule. Equivalent harmonic and anharmonic parameters determined from refinements to 65 vibration levels in C₂H₃D and 33 in C₂HD₃ are in excellent agreement with each other, and also with those determined for other isotopic ethylenes.     

Solvent effect on the stability and properties of platinum-substituted borirene and boryl isomers: The polarizable continuum model

The structure and properties of platinum borirene complex trans-[Cl(PMe₃)₂Pt{μ-BN(SiMe₃)₂C=C}Ph] and its isomer the platinum boryl complex trans–[Cl(PMe₃)₂PtBN(SiMe₃)₂C≡CPh] were investigated theoretically. The solvent effect on the stability, structural parameters, frontier orbital energies, HOMO–LUMO gaps, and hardness of isomers was investigated using the polarizable continuum model (PCM). It was found that borirene isomer is the most stable isomer in the gas phase and solvent. The calculated results show that the presence of solvent reduces the frontier orbital energy of the studied molecules. Geometries obtained from calculations were used to perform NBO analysis.     

Raman spectra of single H2O molecules isolated in cavities of crystals

The vibrational (Raman) spectra of H₂O molecules isolated in cavities of beryl, cordierite, bikitaite, natrolite, scolecite, lawsonite, and hemimorphite have been measured in the temperature range of 4–295 K. The influence of van der Waals and hydrogen bonds on the values of frequency, intensity, and half-width of stretching and bending modes of H₂O is considered. The spectra of translational vibrations of H₂O molecules in crystal cavities are discussed. For the firsts time, the ratio between the frequencies of translation and stretching vibrations of H₂O and the dependence of frequencies of bending vibrations on the angle H-O-H in H₂O molecule are presented.     

Quantum‐chemical,IR, NMR,and X‐ray diffraction studies on 2‐(4‐chlorophenyl)‐1‐methyl‐ 1H‐benzo[d]imidazole

The title molecule, 2‐(4‐chlorophenyl)‐1‐methyl‐1H‐benzo[d]imidazole (C₁₄H₁₁ClN₂), was prepared and characterized by ¹H NMR, ¹³C NMR, IR, and single‐crystal X‐ray diffraction. The molecular geometry, vibrational frequencies, and gauge including atomic orbital (GIAO) ¹H and ¹³C NMR chemical shift values of the title compound in the ground state have been calculated by using the Hartree‐Fock (HF) and density functional theory (DFT/B3LYP) method with 6‐31G(d) basis sets, and compared with the experimental data. The calculated results show that the optimized geometries can well reproduce the crystal structural parameters, and the theoretical vibrational frequencies and GIAO ¹H and ¹³C NMR chemical shifts show good agreement with experimental values. The energetic behavior of the title compound in solvent media has been examined using B3LYP method with the 6‐31G(d) basis set by applying the Onsager and the polarizable continuum model (PCM). Besides, molecular electrostatic potential (MEP), frontier molecular orbitals (FMO) analysis, and nonlinear optical (NLO) properties of the title compound were investigated by theoretical calculations. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011