Methanol in its own gravy. A PCM study for simulation of vibrational spectra

For studying both hydrogen bond and dipole-dipole interactions between methanol molecules (self-association) the geometry of clusters of increasing numbers of methanol molecules (n = 1,2,3) were optimized and also their vibrational frequencies were calculated with quantum chemical methods. Beside these B3LYP/6-311G** calculations, PCM calculations were also done for all systems with PCM at the same quantum chemical method and basis set, for considering the effect of the liquid continuum on the cluster properties. Comparing the results, the measured and calculated infrared spectra are in good accordance.     

A computational NQR study on the hydrogen-bonded lattice of cytosine-5-acetic acid

A computational study at the level of density functional theory (DFT) employing 6-311++G** standard basis set was carried out to evaluate nuclear quadrupole resonance (NQR) spectroscopy parameters in cytosine-5-acetic acid (C5AA). Since the electric field gradient (EFG) tensors are very sensitive to the electrostatic environment at the sites of quadruple nuclei, the most possible interacting molecules with the target one were considered in a five-molecule model system of C5AA using X-ray coordinates transforming. The hydrogen atoms positions were optimized and two model systems of original and H-optimized C5AA were considered in NQR calculations. The calculated EFG tensors at the sites of (17)O, (14)N, and (2)H nuclei were converted to their experimentally measurable parameters, quadrupole coupling constants and asymmetry parameters. The evaluated NQR parameters reveal that the nuclei in original and H-optimized systems contribute to different hydrogen bonding (HB) interaction. The comparison of calculated parameters between optimized isolated gas-phase and crystalline monomer also shows the relationship between the structural deformation and NQR parameters in C5AA. The basis set superposition error (BSSE) calculations yielded no significant errors for employed basis set in the evaluation of NQR parameters. All the calculations were performed by Gaussian 98 package of program.     

An investigation of keto–enol tautomerism in N-vinyl-2-, and 3-pyrrolidinones using ab initio and density functional theory calculations

We investigated the protomeric tautomerism of N-vinyl-2-pyrrolidinone (NV2P) and N-vinyl-3-pyrrolidinone (NV3P) molecules, and considered the three neutral tautomers for NV2P (1a, 1b, 1c) and the five for NV3P (2a, 2b, 2c, 2d, 2e). Full geometry optimizations were carried out at the HF/6-31G**, HF/6-31+G** and B3LYP/6-31+G** levels in the gas phase and in water. Additionally, single-point MP2/6-31+G** calculations were performed on the HF/6-31+G** optimized geometries. The tautomerization processes in water (=78.54) were studied using the self-consistent reaction field theory. According to our estimations, the tautomerization of NV2P and NV3P molecules are not strongly influenced by the polar solvents, the improvement of the basis set quality and the electron correlation effects in the gas phase and in water. The calculated relative free energies (ΔG) predict that 1a and 2a are the energetically preferred tautomers in the gas phase and in water.     

Ring inversion, structural stability and vibrational assignments of sulfolane c-C4H8SO2 and 3-sulfolene c-C4H6SO2

The structural stability of sulfolane (tetrahydrothiophene1,1-dioxide) and 3-sulfolene (dihydrothiophene1,1-dioxide) was investigated by DFT-B3LYP and ab initio MP2 calculations with 6-311+G**) basis set. The calculated symmetric ring-puckering potential of 3-sulfolene at the B3LYP level is consistent with a flat minimum that corresponds to a planar ring but at the MP2 level with a double minimum with a low barrier of about 193calmol(-1) to ring planarity in reasonable agreement with experimental results. From the calculations at the two levels of theory sulfolane was predicted to exist predominantly in the twist conformation. The vibrational wavenumbers were calculated at the MP2/6-31G** level of theory and the potential energy distributions PED among the symmetry coordinates of the normal modes were computed for the low-energy structure of the molecules. Complete vibrational assignments were provided on the basis of the calculated PED values. The experimental infrared and Raman spectra of the two molecules were compared to the calculated ones.     

An Ab Initio Study of the Complexes Formed by the Positive Acetylene Ion with the Hydrogen and Nitrogen Molecules and the Argon Atom

The complexes formed by the positive acetylene ion with the hydrogen molecule, the nitrogen molecule, and the argon atom are investigated with ab initio calculations using the 6-311G** and the 6-31+G(2df,2pd) basis sets. MP2/6-311G** energies and optimum geometries are obtained, as well as single-point MP3, MP4, and QCISD(T) energies with the MP2/6-311G** optimized geometries. Single-point calculations are performed with the 6-31+G(2df,2pd) basis set at MP2/6-311G** optimized geometries.     

Solution and solid-state effects on NMR chemical shifts in sesquiterpene lactones: NMR, X-ray, and theoretical methods

Selected guaianolide type sesquiterpene lactones were studied combining solution and solid-state NMR spectroscopy with theoretical calculations of the chemical shifts in both environments and with the X-ray data. The experimental (1)H and (13)C chemical shifts in solution were successfully reproduced by theoretical calculations (with the GIAO method and DFT B3LYP 6-31++G**) after geometry optimization (DFT B3LYP 6-31 G**) in vacuum. The GIPAW method was used for calculations of solid-state (13)C chemical shifts. The studied cases involved two polymorphs of helenalin, two pseudopolymorphs of 6α-hydroxydihydro-aromaticin and two cases of multiple asymmetric units in crystals: one in which the symmetry-independent molecules were connected by a series of hydrogen bonds (geigerinin) and the other in which the symmetry-independent molecules, deprived of any specific intermolecular interactions, differed in the conformation of the side chain (badkhysin). Geometrically different molecules present in the crystal lattices could be easily distinguished in the solid-state NMR spectra. Moreover, the experimental differences in the (13)C chemical shifts corresponding to nuclei in different polymorphs or in geometrically different molecules were nicely reproduced with the GIPAW calculations.     

A study on the intermolecular hydrogen bonds of alpha-glycylglycine in its actual crystalline phase using ab initio calculated 14N and 2H nuclear quadrupole coupling constants

alpha-Glycylglycine in its actual crystalline phase is studied by ab initio calculated nuclear quadrupole coupling constants. These physical quantities are computed for 2H and 14N in the hydrogen bonds. The type of hydrogen bond is the N-H...O type. The computations are performed with the RHF and B3LYP methods and 6-31++G** and 6-311++G** basis sets using the Gaussian 98 program. Values of the calculated nuclear quadrupole coupling constants are shown in Tables 1-3. The aim of this work is the study of 2H and 14N quadrupole coupling constants which contribute in the CON2H...O=CN2H type of hydrogen bond. The computed nuclear quadrupole coupling constants of 2H nuclei meet the related experimental values. In addition, the computed chi value of 14N belonging to the -CO-14NH- group agrees well with values obtained experimentally. However, there are some discrepancies between calculated 14N chi values of the N+H3 residue and experiments. Also, the values of these physical parameters are calculated for >C2H2 of alpha-glycylglycine in its crystalline phase. Calculations for these parameters are carried out in a single molecule using X-ray diffraction coordinates, too.     

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.     

Conformational analysis and comparison between theoretical and experimental vibrational spectra for chloroacetyl isocyanate

The conformational stability and vibrational infrared and Raman spectra of chloroacetyl isocyanate (CH2ClCONCO) were investigated by ab initio MP2 and density functional B3LYP calculations using the 6-311 + + G** basis set. From the potential energy scans of the internal rotations of both the halomethyl and the isocyanate rotors, chloroacetyl isocyanate was predicted to exist predominantly in a mixture of the cis-cis (chlorine atom and NCO group eclipse C=O bond) and the gauche-cis (one hydrogen atom and NCO group eclipse C=O bond) conformations with a comparable relative stability. The vibrational wavenumbers of each of the two conformers of the molecule were computed at DFT-B3LYP/6-311 + + G** level. Normal coordinate calculations were carried out to obtain the potential energy distributions (PED) among the symmetry coordinates of the normal modes for each of the stable conformers of chloroacetyl isocyanate. The theoretical vibrational assignments are compared with experimental ones and a ratio of observed/calculated wavenumbers of about 0.97-1.04 was obtained.     

The influence of protecting the hydroxyl group of β-oxy-α-diazo carbonyl compounds in the competition between Wolff rearrangement and [1,2]-hydrogen shift. Density functional theory study and topological analysis of the charge density

The influence of protecting the hydroxyl group of a β-oxy-α-diazo carbonyl compound on the competition between the Wolff rearrangement (WR) and the [1,2]-hydrogen shift (HS) was investigated theoretically. Stationary points on the potential-energy surface were located with the B3LYP density functional and the 6-31G** basis set. For the basic system geometry optimisations at B3LYP/6-311+G** were performed to validate the reliability of the B3LYP/6-31G** calculations. Single-point energy calculations were carried out at the B3LYP/6-311+G** level on the B3LYP/6-31G**-optimised geometries. Further insight into the processes was achieved with the aid of the theory of “atoms in molecules” of Bader. The calculated energy barriers qualitatively predicted the yields of HS and WR obtained experimentally. In order to rationalise the calculated energy barriers, it was necessary to take into account not only the electronegativity of the protective groups but also the alignment of the migrating groups with the depletion sites at the carbene centre. Further, when the hydroxyl group was not protected the existence of an intramolecular hydrogen bond played an important role in both HS and WR. Received: 30 December 1998 / Accepted: 7 May 1999 / Published online: 4 October 1999     

An Ab Initio Study of C2H2.H2, C2H2.N2, and C2H2.Ar Complexes

Ab initio calculations at the post Hartree–Fock level were performed on complexes of acetylene with hydrogen, nitrogen, and argon. Total energies, optimum geometries, and binding energies were calculated, using the 6-311G** and the 6-31+G(2df,2pd) basis sets. Calculations showed the complexes to be more stable than the separate entities, with the exception of the acetylene–hydrogen complex.     

Spectroscopic, electronic structure and natural bond orbital analysis of o-fluoronitrobenzene and p-fluoronitrobenzene: a comparative study

Experimental FTIR, FT-Raman and FT-NMR spectroscopic studies of o-fluoronitrobenzene and p-fluoronitrobenzene have been carried out. A detailed quantum chemical calculations have been performed using DFT/B3LYP method with 6-311++G** and 6-31G** basis sets. Complete vibrational analyses of the compounds were performed. The temperature dependence of thermodynamic properties has been analysed. The atomic charges, electronic exchange interaction and charge delocalisation of the molecule have been performed by natural bond orbital (NBO) analysis. Molecular electrostatic surface potential (MESP), total electron density distribution and frontier molecular orbitals (FMOs) are constructed at B3LYP/6-311++G** level to understand the electronic properties. The charge density distribution and site of chemical reactivity of the molecules have been obtained by mapping electron density isosurface with electrostatic potential surfaces (ESP). The electronic properties, HOMO and LUMO energies were measured by time-dependent TD-DFT approach. (1)H and (13)C NMR spectra were recorded and (1)H and (13)C nuclear magnetic resonance chemical shifts of the molecule were calculated. The (1)H and (13)C nuclear magnetic resonance (NMR) chemical shifts of the molecules in chloroform solvent and in gas phase were calculated by using the Gauge-Independent Atomic Orbital (GIAO) method and are found to be in good agreement with experimental values. The theoretical parameters obtained at B3LYP levels have been compared with the experimental values.     

Structural and spectroscopic studies on 2-pyranones

Experimental methods of infrared, Raman and electronic absorption spectroscopy and DFT calculations using B3LYP functionals and 6-31G** and 6-311++G** basis sets have been used to understand the structural and spectral characteristics of 2-pyranones, 6-phenyl-4-methylsulfanyl-2-oxo-2H-pyran and 6-phenyl-4-methylsulfanyl-2-oxo-2H-pyran-3-carbonitrile in the electronic ground (S₀) and first excited (S₁) states. Information about the size, shape, charge density distribution and site of chemical reactivity of the molecules has been obtained by mapping electron density isosurface with electrostatic potential surfaces (ESP). Based on TD-DFT calculations using 6-31+G**5D basis set, an assignment of absorption peaks in the UV–VIS region has been suggested. The S₁ state is found to be a ¹(π,π*) state. A complete vibrational analysis has been attempted on the basis of experimental infrared and Raman spectra and calculated frequency and intensity of the vibrational bands and potential energy distribution over the internal coordinates. Characteristic vibrational bands of the 2-pyranone ring and methylsulfanyl and carbonyl groups have been identified.     

Substituent effects on structural stability of formyl ketene and analysis of vibrational spectra of formyl haloketenes and formyl methylketene.

The conformational behavior and the structural stability of formyl fluoroketene, formyl chloroketene and formyl methylketene were investigated by utilizing quantum mechanical DFT calculations at B3LYP/6-31I + + G** and ab initio calculations at MP2/6-311 + + G** levels. The three molecules were predicted to have a planar s-cis<-->s-trans conformational equilibrium. From the calculations, the direction of the conformational equilibrium was found to be dependent on the nature of the substituting group. In formyl haloketenes, the cis conformation, where the C=O group eclipses the ketenic group, was expected to be of lower energy than the trans conformer. In the case of formyl methylketene the conformational stability was reversed and the trans form (the aldehydic hydrogen eclipsing the ketenic group) was calculated to be about 2 kcal mol(-1) lower in energy than the cis form. The calculated cis-trans energy barrier was found to be in the order: fluoride (15.3 kcal mol(-1)) > chloride (13.1 kcal mol(-1)) > methyl (11.7 kcal mol(-1). Full optimization was performed at the ground and the transition states of the molecules. The vibrational frequencies for the stable conformers of the three ketenic systems were computed at the DFT-B3LYP level, and the zero-point corrections were included into the calculated rotational barriers. Complete vibrational assignments were made on the basis of both normal coordinate calculations and comparison with experimental results of similar molecules.     

Computational treatment of the microsolvation of neutral and zwitterionic forms of alanine

B3LYP/6-31++G** and MP2/6-31++G**//B3LYP/6-31++G** calculations are reported for the structures of neutral alanine–(H₂O)_n and zwitterionic alanine–(H₂O)_n clusters where n = 2–10. Optimized geometries and energies were obtained. In general, with an increasing number of water molecules, the hydrated zwitterionic form becomes more thermodynamically stable. In the presence of six or seven water molecules, the energetics indicate that the two forms may coexist. Eight water molecules are sufficient to computationally guarantee the reported experimental observation of zwitterionic dominance in solution.     

Theoretical and experimental NMR study of protopine hydrochloride isomers

The 1H and 13C NMR chemical shifts of cis- and trans-protopinium salts were measured and calculated. The calculations of the chemical shifts consisted of conformational analysis, geometry optimization (RHF/6-31G** method) and shielding constants calculations (B3LYP/6-31G** method). Based on the results of the quantum chemical calculations, two sets of experimental chemical shifts were assigned to the particular isomers. According to the experimental results, the trans-isomer is more stable and its population is approximately 68%.     

Nonempirical Description of the Atmospherically Important Anionic Species. II. Hydrated Ozone Anions

Ozone–water clusters are nonempirically modeled in the complete active space self-consistent field approximation (CASSCF) with the energetic estimates obtained at the multiconfiguration quasidegenerate perturbation theory level (MCQDPT) with 6–31++G** basis set. Coordination of a neutral ozone molecule to small water clusters is either surface or interior, with the binding energy of the order of a weak hydrogen bond. Upon localization of an excess electron, the hydration of ozone becomes strong. The adiabatic affinities of water–ozone clusters and the energies of electron detachment from their anions, depending on the number of water molecules, estimate the electron hydration and vertical electron detachment thresholds of water or ice that superficially coordinates minor amounts of ozone.     

Infrared predissociation spectroscopy of ammonia cluster cations (NH3)n+ (n=2-4) produced by vacuum-ultraviolet photoionization

Infrared predissociation spectroscopy of vacuum ultraviolet-pumped ion (IRPDS-VUV-PI) is performed on ammonia cluster cations (NH3)n+ (n=2-4) that are produced by VUV photoionization in supersonic jets. The structures of (NH3)2+ and (NH3)4+ are determined through the observation of infrared spectra and vibrational calculations based on ab initio calculations at the MP2/6-31G** and 6-31++G** levels. (NH3)2+ is found to be of the "hydrogen-transferred" form having the (H3N+-...NH2) composition. In contrast, (NH3)4+ exhibits the "head-to-head" dimer cation (H3...NH3+ core structure, where the positive charge is shared between two ammonia molecules in the core, and two other molecules are hydrogen bonded onto the core. An unequivocal assignment of the infrared spectrum of (NH3)3+ has not been achieved, because the presence of two isomeric structures could be suggested by the observed spectrum and theoretical calculations.     

Quadrupole coupling constants of deuterons in molecular clusters Ca<Superscript>2+</Superscript>(D<Subscript>2</Subscript>O)<Subscript><Emphasis Type="Italic">n</Emphasis></Subscript> (<Emphasis Type="Italic">n</Emphasis> = 6, 8, 10, 18)

Characteristic features of the structure of Ca²⁺ hydration shells were considered. The results of quantum chemical calculations were compared with experimental data obtained from the study of nuclear magnetic relaxation of deuterons in aqueous solutions of calcium salts. The influence of the basis set and computational procedure on the calculated ²D quadrupole couling constants (QCC) in isolated water molecule was investigated. The ²D QCC in molecular clusters (D₂O)₅ and Ca²⁺(D₂O) _n (n =6, 8, 10, 18) were calculated using the B3LYP/6-31++G** density functional method.     

A theoretical investigation of the plausibility of reactions between ammonia and carbonyl species (formaldehyde, acetaldehyde, and acetone) in interstellar ice analogs at ultracold temperatures

We have reexamined the reaction between formaldehyde and ammonia, which was previously studied by us and other workers in modestly sized cluster calculations. Larger model systems with up to 12H(2)O were employed, and reactions of two more carbonyl species, acetaldehyde and acetone, were also carried out. Calculations were performed at the B3LYP/6-31+G** level with bulk solvent effects treated with a polarizable continuum model; limited MP2/6-31+G** calculations were also performed. We found that while the barrier for the concerted proton relay mechanism described in previous work remains modest, it is still prohibitively high for the reaction to occur under the ultracold conditions that prevail in dense interstellar clouds. However, a new pathway emerged in more realistic clusters that involves at least one barrierless step for two of the carbonyl species considered here: ammonia reacts with formaldehyde and acetaldehyde to form a partial charge transfer species in small clusters (4H(2)O) and a protonated hydroxyamino intermediate species in large clusters (9H(2)O, 12H(2)O); modest barriers that decrease sharply with cluster size are found for the analogous processes for the acetone-NH(3) reaction. Furthermore, if a second ammonia replaces one of the water molecules in calculations in the 9H(2)O clusters, deprotonation can occur to yield the same neutral hydroxyamino species that is formed via the original concerted proton relay mechanism. In at least one position, deprotonation is barrierless when zero-point energy is included. In addition to describing the structures and energetics of the reactions between formaldehyde, acetaldehyde, and acetone with ammonia, we report spectroscopic predictions of the observable vibrational features that are expected to be present in ice mixtures of different composition.