Comparison of experimental and density functional study on the molecular structure, infrared and Raman spectra and vibrational assignments of 6-chloronicotinic acid

The experimental and theoretical study on the structures and vibrations of 6-chloronicotinic acid (6-CNA, C(6)H(4)ClNO(2)) are presented. The Fourier transform infrared spectra (4,000-50 cm(-1)) and the Fourier transform Raman spectra (3,500-50 cm(-1)) of the title molecule in solid phase have been recorded, for the first time. The geometrical parameters and energies have been obtained for all four conformers from DFT (B3LYP) with different basis sets calculations. There are four conformers, C1, C2, C3, and C4 for this molecule. The computational results diagnose the most stable conformer of 6-CNA as the C1 form. The vibrations of the two stable and two unstable conformers of 6-CNA are researched with the aid of quantum chemical calculations. The molecular structure, vibrational frequencies, infrared intensities and Raman scattering activities and theoretical vibrational spectra were calculated a pair of molecules linked by the intermolecular OH...O hydrogen bond. The spectroscopic and theoretical results are compared to the corresponding properties for 6-CNA stable monomers and dimer of C1 conformer.     

Structure and conformational dynamics of the cyclopropanecarbaldehyde molecule in the ground (S<Superscript>b0</Superscript>) and lowest excited (T<Superscript>b1</Superscript> and S<Superscript>b1</Superscript>) electronic states

The structure and conformational dynamics of nonrigid cyclopropanecarbaldehyde (CPCA) molecule in the ground (S^b0) and lowest excited triplet (T^b1) and singlet (S^b1) electronic states were calculated using the MP2, DFT, CASSCF, CASPT2, and CCSD quantum chemical methods. According to ab initio calculations, in the S^b0 electronic state there are two symmetrical (cis and trans) conformers of the CPCA molecule. Excitation of the CPCA molecule to the ?1 and S1 electronic states causes significant structural changes: carbonyl CCHO fragment becomes nonplanar, cyclopropane fragment rotates around the C–C bond, thus changing the relative positions of the formyl and cyclopropane fragments. Using sections of the potential energy surfaces (PES) of the CPCA molecule in the T^b1 and S^b1 states, we calculated the torsion and inversion wave functions and vibrational transition energies. The results obtained suggest a strong coupling of the torsion and inversion motions in the T^b1 and S^b1 excited states.     

Vibrational and electronic spectra of benzophenone in different phase states: Ab initio calculations and experiment

An ab initio method has been used to perform quantum mechanical calculations of the formation energy of different conformers of benzophenone: planar molecule, twisted molecule, planar molecule dimer, twisted molecule dimer; electronic and vibrational spectra of these conformers were also obtained. An assessment of the medium (solvent) influence on the optimal geometry, dipole moment and stability of different forms of benzophenone was performed in the self-consistent reaction field approximation. It is shown that the twisted conformer is more stable than the planar one (the difference of free energies is 32 kJ/mol for free molecules) and it becomes even more stable with the increase in solvent polarity. The calculated electronic and vibrational spectra agree well with the experimental data and properly reflect the complication of the vibrational spectrum when passing from the gaseous phase to the condensed state of benzophenone. The difference between spectral properties of the two dimer forms allows their identification from the spectra and qualitative explanation of the observed peculiarities of phosphorescence of the amorphous phase of benzophenone by the stabilization of different conformers.     

NMR, UV, FT-IR, FT-Raman spectra and molecular structure (monomeric and dimeric structures) investigation of nicotinic acid N-oxide: A combined experimental and theoretical study

In this work, the experimental and theoretical UV, NMR, and vibrational features of nicotinic acid N-oxide (abbreviated as NANO, C(6)H(5)NO(3)) were studied. The ultraviolet (UV) absorption spectrum of studied compound that dissolved in water was examined in the range of 200-800nm. FT-IR and FT-Raman spectra in solid state were observed in the region 4000-400cm(-1) and 3500-50cm(-1), respectively. The (1)H and (13)C NMR spectra in DMSO were recorded. The geometrical parameters, energies and the spectroscopic properties of NANO were obtained for all four conformers from density functional theory (DFT) B3LYP/6-311++G(d,p) basis set calculations. There are four conformers, C(n), n=1-4 for this molecule. The computational results identified the most stable conformer of title molecule as the C1 form. The complete assignments were performed on the basis of the total energy distribution (TED) of the vibrational modes, calculated with scaled quantum mechanics (SQM) method. (13)C and (1)H nuclear magnetic resonance (NMR) chemical shifts of the molecule were calculated by using the gauge-invariant atomic orbital (GIAO) method. The electronic properties, such as excitation energies, absorption wavelengths, HOMO and LUMO energies, were performed by CIS approach. Finally the calculation results were applied to simulate infrared, Raman, and UV spectra of the title compound which show good agreement with observed spectra.     

Structure and protonation of some indolizine derivatives studied by ab initio MO calculations

Some gauge invariant atomic orbitals-coupled-perturbed Hartree-Fock (GIAO-CPHF) calculations were performed for seven indolizine derivatives and their monoprotonated forms. Chemical shift, molecular geometry, and charge distribution data are reported for each molecule. The calculations support the results of nuclear magnetic resonance (NMR) spectroscopy measurements showing that protonation occurs preferentially at N1. The good agreement between the calculated and observed ¹³C and ¹⁵N chemical shifts show that such calculations can be used for chemical shift assignment purposes. Cation structures and probable sites for electrophilic reaction or second protonation are also discussed.     

Characteristics of the hydrogen bond and the structure of Н-complexes of <Emphasis Type="Italic">p</Emphasis>-n-propyloxybenzoic acid and <Emphasis Type="Italic">p</Emphasis>-n-propyloxy-<Emphasis Type="Italic">p</Emphasis>′-cyanobiphenyl

The conformational properties of p-n-propyloxybenzoic acid and p-n-propyloxy-p′-cyanobiphenyl molecules, which can exhibit liquid crystalline properties in the formation of Н-complexes, are studied (DFT/B3LYP)/cc-pVTZ method). It is found that a molecule of p-n-propyloxybenzoic acid has 16 conformers that can be divided into four groups with respect to relative energies (0 kcal/mol, 1.6 kcal/mol, 6.5 kcal/mol, and 8.1 kcal/mol), and a molecule of p-n-propyloxy-p′-cyanobiphenyl has six conformers with relative energies of 0 kcal/mol (two conformers, φ(С_Ph–O–C–C)=180°) and 1.6 kcal/mol (four conformers, φ(С_Ph–O–C–C)=64.4°). In all conformers of the 3-AOCB molecule, phenyl rings are turned at 35° relative to each other. A conformation with the planar arrangement of two rings has a higher energy by 1.5 kcal/mol. Barriers to the internal rotation of different groups are determined and it is established that the structural nonrigidity of the molecules is mainly due to the possible rotation of the–C₂Н₅ moiety about the C–C bond. It is shown that with increasing temperature the vibrational amplitudes of the OC₃H₇ substituent, which enhance the probabilities of transitions between the conformers, become appreciably larger. It is found that p-n-propyloxybenzoic acid and p-n-propyloxy-p′-cyanobiphenyl can form Н-complexes with the medium hydrogen bond. Two types of the structural organization of Н-complexes are considered: linear and angular. The similarity of energies of Н-complexes with different structures (NBO analysis) can be the reason for the occurrence of two liquid crystalline subphases of p-n-propyloxybenzoic acid and p-n-propyloxy-p′-cyanobiphenyl system.     

Interpretation of vibrational and NMR spectra of allyl acrylate: An evidence for several conformers

The mid-IR, far-IR, and Raman spectra of allyl acrylate were measured and interpreted with support of the B3LYP/aug-cc-pVDZ calculated anharmonic vibrational spectra followed by the potential energy distribution analysis. The experimental ¹H and ¹³C NMR spectra of allyl acrylate dissolved in CDCl₃ or C₆D₆ were interpreted by means of the B3LYP/aug-cc-pVDZ-su2 calculated NMR chemical shifts and J(¹H,¹H) and J(¹H,¹³C) coupling constants. Exactly ten stable allyl acrylate conformers (five s-cis and five s-trans) were found after careful B3LYP/aug-cc-pVDZ and MP2/aug-cc-pVDZ scan of the conformational space. The experimental IR and Raman spectra are in good agreement with the theoretical spectra of the most stable conformers 1 with a presence of the second stable conformer 2, both exhibiting cis arrangement of the acrylic moiety. There are however two bands in the IR spectra, at ca. 1270 and 1260 cm⁻¹, that definitely indicate the conformers with trans arrangement of the acrylic moiety to be present in liquid allyl acrylate. The bands at ca. 2990 and 1650 cm⁻¹ are suggested to be due to Fermi resonances engaging CH and CC stretching vibrations, respectively. The careful inspection of the room temperature ¹H and ¹³C NMR spectra of allyl acrylate suggest that a dominating form of the allyl acrylate molecule in an inert solvent exhibits the cis conformation of the acrylic moiety and an extended allyl group.     

Isomerism and Vibrational Spectra of Alkali Metal Perrhenates: Ab Initio CISD+Q Calculations

The equilibrium geometric parameters, isomerization energies, force fields, vibrational frequencies and intensities in the IR spectra of MReO₄ molecules (M = Li, Na, K) are calculated by the configuration interaction method including all singly and doubly excited configurations with Davidson's correction for quartic excitations in expanded basis sets using effective relativistic core potentials. The calculations indicate that the chemical bonds between the metal atoms and the ReO₄ anion group are highly polar. It is found that the MReO₄ molecule has two isomers. The basic isomer with C_2v symmetry has bidentate b coordination of the M⁺ cation to the ReO ₄ ^- anion. The excited isomer is of C_3v symmetry and corresponds to monodentate m coordination of M⁺. The low relative energies of the m isomers (17-29 kJ/mole) and the low energy barriers to the intramolecular mb rearrangements (5-11 kJ/mole) indicate that MReO₄ molecules are structurally nonrigid systems where the M–XO₄ chemical bonds are polytopic. The results of calculations are compared with the available literature data on the structure and vibrational spectra of MReO₄ molecules.     

DFT study of CH<Subscript>4</Subscript> adsorption on the (5,0), (4,4), (5,5) and (6,6) single-walled carbon nanotubes. Calculated binding energies,NMR and NQR parameters

Behavior of a single CH₄ molecule adsorbed on external surface of H-capped (4,4) (5,5), (6,6) and (5,0) single-walled carbon nanotubes (SWCNTs) is studied via B97D hybrid density functional and 6-31G* basis set. Binding energies clearly exhibit adsorption dependence on tube diameter. ¹³C and ¹H chemical shielding tensors are calculated at the B971 level using GIAO method. The ¹H and ¹³C(CH₄) NMR results reveal that chemical shielding due to CH₄ molecule adsorption are also dependent upon the nanotube electronic structure, and radius. ²H nuclear quadrupole coupling constants, C Q, and asymmetry parameter, η, reveal the remarkable effect of CH4 adsorption on electronic structure of the SWCNTs.     

Ab initio and DFT studies on 1-(thionitrosomethylene) hydrazine: conformers, energies, and intramolecular hydrogen-bond strength

In the current study, we present an intramolecular HB, molecular structure, π-electrons delocalization and vibrational frequencies analysis of 25 possible conformers of 1-(thionitrosomethylene) hydrazine by means of DFT (B3LYP), MP2 methods in conjunction with the 6-311++G** and augmented correlation-consistent polarized-valence triple-zeta basis sets and G2MP2 theoretical level. The influence of the solvent on the stability order of conformers and the strength of intramolecular hydrogen-bonding was considered using the Tomasi’s polarized continuum model. Statistical analyses of quantitative definitions of aromaticity, nucleus independent chemical shift, harmonic oscillator model of aromaticity, aromatic fluctuation index, and the π-electron delocalization parameter (Q) as a geometrical indicator of a local aromaticity, evaluated for this conformers. Further verification of the obtained transition state structures were implemented via intrinsic reaction coordinate (IRC) analysis. Calculations of the ¹H NMR chemical shift at GIAO/B3LYP/6-311++G** levels of theory are also presented. The calculated highest occupied molecular orbital (MO) and lowest unoccupied MO energies show that charge transfer occur within the molecule. Hydrogen-bond energies for H-bonded conformers were obtained from Espinosa method and the natural bond orbital theory and the atoms in molecules theory were also applied to get a more precise insight into the nature of such H-bond interactions.     

Internal dynamics of flexible molecules: Cyclohexane

Summary The international motions of a single cyclohexane molecule are studied by molecular dynamics calculations. Classical trajectories are calculated by integrating Newton's equation of motion. The potential functions used are essentially the same as in Allinger's MM2 program which is widely applied for calculations on conformational energies of organic molecules.Geometries and relative energies are reported for all stable low energy conformers and some transition states of cyclohexane. Vibrational frequencies of classical oscillations of individual bonds — computed for ethane as reference system — are close to the experimental values.Two trajectories of the molecular dynamics of cyclohexane were simulated. In the first we were able to follow the process of ring inversion: chair twisted forms inverted chair. The reaction path is analysed in detail and compared with static approaches. The second trajectory shows the correlated reorientation of the possible twisted forms alone. This process is known as pseudorotation.Dedicated to Prof. Dr. Karl Schlögl     

Synthesis, spectroscopic characterization, crystal structures, theoretical studies, and antibacterial evaluation of two novel N-phosphinyl ureas

Abstract  

Two novel N-phosphinyl ureas containing different substituents were synthesized and characterized by ¹H, ¹³C, and ³¹P NMR, IR, UV, mass spectroscopy, and elemental analysis. The crystal structures of these compounds were determined by X-ray crystallography. The structure of one compound exhibits the presence of two independent forms of the molecule with equal occupancy in the lattice and theoretical data reveal the same stabilization energies for these conformers. The title molecules have anti conformation with respect to the C=O and P=O bonds, whereas the other compound shows syn configuration. Quantum chemical calculations were applied to clarify this conformational behavior. Furthermore, the molecular geometry and vibrational frequencies of the new derivatives in the ground state were calculated by using the Hartree–Fock (HF) and density functional method (B3LYP) with 6-31+G** and 6-311+G** basis sets and compared with experimental values. The new derivatives were additionally tested in view of their antibacterial properties.     

Solvent effects on dimeric self-association of 2-pyrrolidinone: An ab initio study

Full geometry optimizations were carried out for 2-pyrrolidinone (2-Py) and its dimer structures at the DFT (B3LYP) and HF levels in the gas phase and in solution. Additionally, single-point MP2/6-31G^** calculations were performed on the HF/6-31G^** optimized geometries. The self-association of 2-Py in 1,4-dioxane (=2.21) and in water (=78.54) were studied using the self-consistent reaction field (SCRF) theory. The calculated relative free energies (G) for the dimerization processes predict the cyclic dimer (CD) to be more stable than the open dimer (OD) at all levels of theory in the gas phase and in solution. The results show that, at least for the properties of the hydrogen-bonded systems studied in this work, the B3LYP/6-31G^** calculations give better results than the HF and MP2 calculations with the same basis set. The data obtained from this study were compared with the corresponding experimental results when available.     

Application of J(C,H) coupling constants in conformational analysis

Conformational equilibria for a number of methyl substituted 1,3-dioxanes 1, 1,3-oxathianes 2 and 1,3-dithianes 3 were calculated at the HF and DFT levels of theory. In addition to the chair conformers also the energetically adjacent twist conformers were considered and the positions of the corresponding conformational equilibria estimated. On the basis of the global energy minima of conformers, participating in the conformational equilibria, the ¹J_C,Hax,equ coupling constants were calculated using the GIAO method and compared with the experimental values obtained from ¹³C,¹H coupled ¹³C NMR spectra. The Perlin effect, the influence of the solvent and the suitability of this NMR parameter for assigning the conformational equilibria present are critically discussed.     

Ab initio calculations of the geometry and polarizabilities of bisphenyls having aliphatic substituents

Ab initio geometry optimization and polarizability calculations of a series of bisphenyls, which are the model compounds of chemically different polycarbonates using HF/6‐31G and 6‐31G** basis sets are presented. Calculated absolute value of the conformationally averaged optical anisotropy (〈γ²〉) of diphenyl propane, a model analog of bisphenol A polycarbonate, is higher than the corresponding experimental value in the dilute solution phase. The calculations have reproduced the relative trend in the optical anisotropy for the different bisphenyl model compounds in a manner similar to those using semiclassical approach, by incorporation of the condensed phase polarizabilities and quantum chemically calculated geometry structure into the valence optical scheme. Individual contributions to the gas phase polarizability and optical anisotropy of the model compounds for various dihedral conformers, because of the presence of different aliphatic chemical groups, are correctly predicted by the calculations here. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Multidimensional tunneling dynamics of proton transfer in malonaldehyde molecule and its isotopomers

The twenty-one-dimensional Hamiltonian of malonaldehyde molecule and a number of its isotopomers (H/D, ¹³C/¹²C) was reconstructed in the low-energy region (<3000 cm^–1). Parameters of the Hamiltonian were obtained from quantum-chemical calculations of the energies, equilibrium geometries, and eigenvectors and eigenfrequencies of normal vibrations at the stationary points corresponding to the ground state and transition state. Despite substantial variation of the barrier height calculated using different quantum-chemical methods (from 2.8 to 10.3 kcal mol^–1), the corresponding potential energy surfaces can be matched with high accuracy by scaling only one parameter (the semiclassical parameter , which defines the scales of potential, energy, and action). Scaling invariance allows optimization of the Hamiltonian in such a way that the calculated ground-state tunneling splitting coincides with the experimental value. The corresponding potential barrier height is estimated at 4.34±0.4 kcal mol^–1. The quantum dynamics problem was solved using the perturbative instanton approach without reducing the number of degrees of freedom. The role of all transverse vibrations in proton tunneling is characterized. Vibration-tunneling spectrum is calculated for the ground state and low-lying excited states and mode-specific isotope effects are predicted.     

Internal field of polymer crystals: Polarizability tensor of the methylene group from the birefringence of paraffin crystal

Using the concept of a point dipole lattice, it is shown that the internal field of induced dipoles can be calculated for crystals comprised of simple chain molecules. The only structure which must be taken into account accurately is that of the chain molecule itself. From the calculations, reliable values of the polarizability tensor of the CH₂ unit are deduced from the birefringence of the paraffin crystal. In addition, it is shown that birefringence measurements provide a method for demonstrating the consistency of polarizability data so that no detailed structural information is needed. For the CH₂ unit, it is found by both methods that α^∥ ? α^? = ? 0.63 with respect to the chain direction [the units of polarizability α are 10^?24 cm³ (cgs)]. The most probable anisotropies for the bond polarizabilities are α ? α = 0.30, α ? α = ? 0.62.     

Theoretical studies of l-ascorbic acid (vitamin C) and selected oxidised, anionic and free-radical forms

Calculations were carried out at the restricted and unrestricted B3LYP/6-311++G(d,p) and B3LYP/EPR-II levels for two conformers (1 and 2) of l-ascorbic acid and their respective oxidation products to di- and monodehydroascorbates. For the didehydroascorbates, corresponding to Conformer 1, free radical properties are compared with previously published calculations in the gaseous and aqueous solution states and with experimental EPR values. Calculated molecular structures, EPR and vibrational spectral and energetic properties are reported including some proposed changes to previous EPR assignments. Conformer 2 of l-ascorbic acid is predicted to have lower energy than Conformer 1, under the method and basis sets used, by between 11 and 26 kJ mol⁻¹ and is stabilised by internal hydrogen bonding. For particular monodehydroascorbates, formed by loss of H from the chain CH(OH) group, calculated properties of conformers of five neutral mono-radicals and the corresponding five anionic di-radicals are reported. Relaxed potential energy surface (PES) scans were carried out for two proton transfer processes and relative energies of stable minima and barriers between them determined. The physiological significance of the protective oxidation of l-ascorbic acid by free radicals is briefly described.