A systematic investigation of hydrogen-bonding effects on the 17O, 14N, and 2H nuclear quadrupole resonance parameters of anhydrous and monohydrated cytosine crystalline structures: a density functional theory study

A systematic computational study was carried out to characterize the 17O, 14N, and 2H nuclear quadrupole resonance (NQR) parameters in the anhydrous and monohydrated cytosine crystalline structures. To include the hydrogen-bonding effects in the calculations, the most probable interacting molecules with the central molecule in the crystalline phase were considered in the pentameric clusters of both structures. To calculate the parameters, couples of the methods B3LYP and B3PW91 and the basis sets 6-311++G** and CC-pVTZ were employed. The mentioned methods calculated reliable values of 17O, 14N, and 2H NQR tensors in the pentameric clusters, which are in good agreements with the experiment. The different influences of various hydrogen-bonding interactions types, N-H...N, N-H...O, and O-H...O, were observed on the 17O, 14N, and 2H NQR tensors. Lower values of quadrupole coupling constants and higher values of asymmetry parameters in the crystalline monohydrated cytosine indicate the presence of stronger hydrogen-bonding interactions in the monohydrated form rather than that of crystalline anhydrous cytosine.     

Study of hydrogen bonds in crystalline 5-nitrouracil. Density functional theory calculations of the O-17, N-14, and H-2 nuclear quadrupole resonance parameters

Hydrogen bond interaction properties of backbone uracil was studied in crystalline structure of 5-nitrouracil. To this aim the electric field gradient tensors were calculated at the level of density functional theory in two single (non-hydrogen bonded) and cluster (hydrogen-bonded four-molecule) models of 5-nitrouracil. The electric field gradient tensors at the sites of O-17, N-14, and H-2 nuclei were converted to the experimentally measurable nuclear quadrupole resonance spectroscopy parameters, quadrupole coupling constant and asymmetry parameter. The results indicated different hydrogen bond interaction properties at the sites of various nuclei and also the protective role of ?NO₂ group for contribution of O1 to hydrogen bond interactions in comparison with uracil. The density functional theory calculations were performed using GAUSSIAN 98 package employing B3LYP method and 6-311G** and 6-311++G** basis sets.     

Density functional theory study of nitrogen‐14 nuclear quadrupole coupling parameters of L‐histidine: hydrogen‐bonded system

The calculations of nitrogen‐14 nuclear quadrupole parameters, nuclear quadrupole coupling constant, χ, and asymmetry parameter, η, of L‐His were done in two distinct environments: one as a free fully optimized molecule, an isolated molecule with the geometrical parameters taken from X‐ray, and the other in the orthorhombic and monoclinic solid states. The most probable interacting molecules with the central molecule in the crystalline phase were considered in the hexameric clusters to include hydrogen‐bonding effects in the calculations. The computations were performed with PW91P86/6‐31++G** and B3LYP6‐31++G** methods using the Gaussian 98 program. The good agreement between the nitrogen‐14 quadrupole parameters of the free His and imidazole molecules with their microwave available data demonstrates that the applied level of theory and the 6‐31++G** basis set are suitable to obtain reliable electric field gradient values. In the solid state, the shifts of quadrupole coupling parameters from the monomer to the solid phase are reasonably well reproduced for the amino and imino sites of imidazole ring in a hexameric cluster. That implies the fact that the hexameric cluster worked effectively to generate the results which are compatible with the experiment. The quadrupole coupling constant values of –N⁺H₃ group are in fair agreement with the experiment. This discrepancy is due to the absences of vibrational effects and the rotation of –N⁺H₃ group around N–C(α) bond. Copyright © 2012 John Wiley & Sons, Ltd.     

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.     

Partial proton transfer in a molecular complex: assessments from both the donor and acceptor points of view

Microwave spectra have been observed for the gas phase complexes (CH(3))(3)(14)N-H(14)NO(3) and (CH(3))(3)(15)N-H(14)NO(3) and rotational and nuclear quadrupole coupling constants are reported. The structure and binding energy have also been calculated at the MP2 level of theory using the 6-311++G(d,p) and 6-311++G(2df,2pd) basis sets both with and without corrections for basis set superposition error. The HNO(3) forms a near-linear hydrogen bond to the amine nitrogen with a rather short hydrogen bond distance of about 1.5-1.6 ? (depending on the basis set and method of computation). The C(3) axis of the trimethylamine lies in the plane of the nitric acid. For both the H(14)NO(3) and the (CH(3))(3)(14)N moieties of the parent species, the component of the nuclear quadrupole coupling tensor perpendicular to the molecular symmetry plane, χ(cc), is sensitive to the electronic structure at the corresponding nitrogen but independent of relative orientation within the plane. Its value, therefore, provides a convenient experimental measure of the degree of proton transfer within the complex. For the HNO(3), χ(cc) lies 62% of the way between those of free HNO(3) and aqueous NO(3)(-), indicating a substantial degree of proton transfer. A similar comparison of the quadrupole coupling constant of (CH(3))(3)N in the (CH(3))(3)N-HNO(3) complex with those of free (CH(3))(3)N and (CH(3))(3)NH(+) indicates only about 31% proton transfer, about half that determined from the HNO(3) coupling constant. Though surprising at first, this disparity is to be expected if the quadrupole coupling constants vary nonlinearly with the position of the proton relative to the donor and acceptor atoms. Calculations of the (14)N nuclear quadrupole coupling constants as a function of proton position using density functional theory are reported and confirm that this is the case. We suggest that when proton transfer is assessed according to changes in individual monomer molecular properties, the overall process may be best described in terms of a dual picture involving proton release by the acid and proton acquisition by the base.     

Theoretical 13C chemical shift, 14N, and 2H quadrupole coupling- constant studies of hydrogen bonding in L-alanylglycine dipeptide

(13)C chemical shieldings and (14)N and (2)H electric field gradient (EFG) tensors of L-alanylglycine (L-alagly) dipeptide were calculated at RHF/6-31 + + G** and B3LYP/6-31 + + G** levels of theory respectively. For these calculations a crystal structure of this dipeptide obtained from X-ray crystallography was used. Atomic coordinates of different clusters containing several L-alagly molecules were used as input files for calculations. These clusters consist of central and surrounding L-alagly molecules, the latter forming short, strong, hydrogen bonds with the central molecule. Since the calculations did not converge for these clusters, the surrounding L-alagly molecules were replaced by glycine molecules. In order to improve the accuracy of calculated chemical shifts and nuclear quadrupole coupling constants (NQCCs), different geometry-optimization strategies were applied for hydrogen nuclei. Agreement between calculated and experimental data confirms that our optimized coordinates for hydrogen nuclei are more accurate than those obtained by X-ray diffraction.     

Nuclear quadrupole hyperfine structure in the microwave spectrum of HCl-N2O: electric field gradient perturbation of N2O by HCl

The microwave spectra of six isotopomers of HCl-N(2)O have been obtained in the 7-19 GHz region with a pulsed molecular beam, Fourier transform microwave spectrometer. The nuclear quadrupole hyperfine structure due to all quadrupolar nuclei is resolved and the spectra are analyzed using the Watson S-reduced Hamiltonian with the inclusion of nuclear quadrupole coupling interactions. The spectroscopic constants determined include rotational constants, quartic and sextic centrifugal distortion constants, and nuclear quadrupole coupling constants for each quadrupolar nucleus. Due to correlations of the structural parameters, the effective structure of the complex cannot be obtained by fitting to the spectroscopic constants of the six isotopomers. Instead, the parameters for each isotopomer are calculated from the A and C rotational constants and the chlorine nuclear quadrupole coupling constant along the a-axis, chi(aa). There are two possible structures; the one in which hydrogen of HCl interacts with the more electronegative oxygen of N(2)O is taken to represent the complex. The two subunits are approximately slipped parallel. For H (35)Cl-(14)N(2)O, the distance between the central nitrogen and chlorine is 3.5153 A and the N(2)O and HCl subunits form angles of 72.30 degrees and 119.44 degrees with this N-Cl axis, respectively. The chlorine and oxygen atoms occupy the opposite, obtuse vertices of the quadrilateral formed by O, central N, Cl, and H. Nuclear quadrupole coupling constants show that while the electric field gradient of the HCl subunit remains essentially unchanged upon complexation, there is electronic rearrangement about the two nitrogen nuclei in N(2)O.     

DFT calculations of <Superscript>14</Superscript>N, <Superscript>17</Superscript>O,and <Superscript>2</Superscript>H NQR parameters: Investigation of hydrogen bond interactions in sulfapyridine crystalline structure

DFT calculations of electric field gradient (EFG) tensors at the sites of ¹⁴N, ¹⁷O, and ²H nuclei are carried out to characterize the hydrogen bond (HB) interactions in the sulfapyridine crystal structure. One-molecule (monomer) and hydrogen-bonded hexameric cluster models of sulfapyridine are constructed according to available X-ray coordinates where the proton positions are optimized. Then, EFG tensors are calculated for both monomer and target molecule in the hexameric cluster of sulfapyridine to show the effect of HB interactions on the tensors. The calculated EFG tensors are converted to the experimentally measurable nuclear quadrupole resonance (NQR) parameters: quadrupole coupling constant (C _Q ) and asymmetry parameter (η _Q ). The results reveal different contribution of various nuclei to N-H⋯N and N-H⋯O HB interactions in the cluster where the N2 and O1 have major contributions. The computations are performed with B3LYP and B3PW91 functionals DFT method and 6-311+G* and 6-311++G** standard basis sets using the Gaussian 98 package.     

Density functional theory investigation of hydrogen bonding effects on the oxygen, nitrogen and hydrogen electric field gradient and chemical shielding tensors of anhydrous chitosan crystalline structure

A systematic computational investigation was carried out to characterize the 17O, 14N and 2H electric field gradient, EFG, as well as 17O, 15N, 13C and 1H chemical shielding tensors in the anhydrous chitosan crystalline structure. To include the hydrogen-bonding effects in the calculations, the most probable interacting molecules with the target molecule in the crystalline phase were considered through a hexameric cluster. The computations were performed with the B3LYP method and 6-311++G(d,p) and 6-31++G(d,p) standard basis sets using the Gaussian 98 suite of programs. Calculated EFG and chemical shielding tensors were used to evaluate the 17O, 14N and 2H nuclear quadrupole resonance, NQR, and 17O, 15N, 13C and 1H nuclear magnetic resonance, NMR, parameters in the hexameric cluster, which are in good agreement with the available experimental data. The difference between the calculated NQR and NMR parameters of the monomer and hexamer cluster shows how much hydrogen bonding interactions affect the EFG and chemical shielding tensors of each nucleus. These results indicate that both O(3)-H(33)...O(5-3) and N-H(22)...O(6-4) hydrogen bonding have a major influence on NQR and NMR parameters. Also, the quantum chemical calculations indicate that the intra- and intermolecular hydrogen bonding interactions play an essential role in determining the relative orientation of EFG and chemical shielding principal components in the molecular frame axes.     

Characterization of intermolecular interactions in crystalline aspirin: A computational NQR study

A computational study at the level of density functional theory was carried out to characterize the ¹⁷O and ²H nuclear quadrupole resonance (NQR) spectroscopy parameters in crystalline aspirin. To include O? H···O and C? H···O hydrogen bonding effects in the calculations, the most probable interacting molecules with the target molecule in the crystalline phase were considered through a pentamer cluster. The NQR calculations were performed with BLYP, B3LYP, and M06 functionals employing 6‐311++G** and Jensen's polarization‐consistent pcJ‐1 basis sets. Linear correlations are observed between the calculated ¹⁷O and ²H NQR parameters and the hydrogen bond strengths, suggesting the possibility of estimating hydrogen bonding information from calculated NQR data. Different contributions of various nuclei to hydrogen bonding interactions and observed trends of calculated NQR parameters are well justified by atoms in molecules analyses at the BCPs of these interactions. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2012     

An investigation of hydrogen-bonding effects on the nitrogen and hydrogen electric field gradient and chemical shielding tensors in the 9-methyladenine real crystalline structure: a density functional theory study

Hydrogen-bonding effects in the real crystalline structure of 9-methyladenine, 9-MA, were studied using calculated electric field gradient, EFG, and chemical shielding, CS, tensors for nitrogen and hydrogen nuclei via density functional theory. The calculations were carried out at the B3LYP and B3PW91 levels with the 6-311++G basis set via the Gaussian 98 package. Nuclear quadrupole coupling constants, C(Q), and asymmetry parameters, eta(Q), are reported for (14)N and (2)H. The chemical shielding anisotropy, Deltasigma, and chemical shielding isotropy, sigma(iso), are also reported for (15)N and (1)H. The difference between the calculated parameters of the monomer and heptameric layer-like cluster 9-MA shows how much H-bonding interactions affect the EFG and CS tensors of each nucleus. This result indicates that N(10) (imino nitrogen) has a major role in H-bonding interactions, whereas that of N(9) is negligible. There is good agreement between the present calculated parameters and reported experimental data. Although some discrepancies were observed, this could be attributed to the different conditions which were applied for calculation and the experiments.     

Study of hydrogen bonds in N-methylacetamide by DFT calculations of oxygen, nitrogen, and hydrogen solid-state NMR parameters

Solid-state nuclear magnetic resonance (NMR) parameters of ¹⁷O, ¹⁴N/¹⁵N, and ²H/¹H nuclei were evaluated in two available neutron crystalline structures of N-methylacetamide (NMA) at 250 and 276 K, NMA-I and NMA-II, respectively. Density functional theory calculations were performed by B3LYP method and 6-311++G** and IGLO-II type basis sets to calculate the electric field gradient (EFG) and chemical shielding (CS) tensors at the sites of mentioned nuclei. In order to investigate hydrogen bonds (HBs) effects on NMR tensors, calculations were performed on four-model systems of NMA: an optimized isolated gas-phase, crystalline monomers, crystalline dimers, and crystalline trimers. Comparing the calculated results reveal the influence of N–H···O=C and C–H···O=C HB types on the NMR tensors which are observable by the evaluated parameters including quadrupole coupling constant, C _Q, and isotropic CS, σ _iso. Furthermore, the results demonstrate more influence of HB on the EFG and CS tensors of NMA at 276 K rather than that of 250 K.     

Phonon-driven proton transfer in 3,5-pyridine dicarboxylic acid studied by 2H, 14N, and 17O nuclear quadrupole resonance

Hydrogen bonding in crystalline 3,5-pyridine dicarboxylic acid has been studied by (2)H, (14)N, and (17)O nuclear quadrupole resonance. The (2)H and (17)O data show the presence of two distinct hydrogen bonds, a "normal" O-H···O bond and a short, strong N···H···O bond, with significantly different NQR parameters. In the latter, the temperature variation of the (14)N nuclear quadrupole resonance (NQR) parameters is related to the phonon-driven proton transfer in the N···H···O hydrogen bond. The temperature dependence of the N···H and H···O distances in the N···H···O hydrogen bond is extracted from the (14)N NQR data.     

14N NQR study of polymorphism and hydrogen bonding in molecular complex isonicotinamide-oxalic acid (2:1)

The complete (14)N nuclear quadrupole resonance (NQR) spectra have been measured in the two polymorphic crystalline phases of the molecular complex isonicotinamide-oxalic acid (2:1) by nuclear quadrupole double resonance. The observed NQR frequencies, quadrupole coupling constants, and asymmetry parameters (η) have been assigned to the two nitrogen positions (ring and amide) in a molecule on the basis of the intensity and multiplicity of the double resonance signals. The NQR data for the ring nitrogen in both polymorphic phases deviate from the correlation relations observed in substituted pyridines. This deviation is analyzed in a model, where it is assumed that an additional electric charge on the nitrogen atom changes the NQR parameters. The model suggests that this additional electric charge is negative so that the N···H-O hydrogen bond seem to be partially ionic, of the type N(-)···H-O.     

High-resolution microwave spectrum of the weakly bound helium-pyridine complex

High-resolution rotational spectra of the helium-pyridine dimer were obtained using a pulsed molecular beam Fourier transform microwave spectrometer. Thirty-nine R-branch (14)N nuclear quadrupole hyperfine components of a- and c-type dipole transitions were observed and assigned. The following spectroscopic parameters were obtained: rotational constants A=3875.2093(48) MHz, B=3753.2514(45) MHz, and C=2978.4366(81) MHz; quartic centrifugal distortion constants D(J)=0.124 08(55) MHz, D(JK)=0.1200(43) MHz, D(K)=-0.2451(25) MHz, d(1)=0.004 27(27) MHz, and d(2)=0.000 16(10) MHz; sextic centrifugal distortion constants H(J)=0.003 053(35) MHz, H(JK)=-0.006 598(47) MHz, and H(K)=0.004 11(59) MHz; (14)N nuclear quadrupole coupling constants chi(aa)((14)N)=-4.7886(76) MHz, chi(bb)((14)N)=1.4471(76) MHz, and chi(cc)((14)N)=3.3415(43) MHz. Our analyses of the rotational and (14)N quadrupole coupling constants show that the He atom binds perpendicularly to the aromatic plane of C(5)H(5)N with a displacement angle of approximately 7.0 degrees away from the c axis of the pyridine monomer, toward the nitrogen atom. Results from an ab initio structure optimization on the second order Moller-Plesset level are consistent with this geometry and gave an equilibrium well depth of 86.7 cm(-1).     

Gas-Phase Conformational Map of the Amino Acid Isovaline

Four conformers of the non-proteinogenic α-amino acid isovaline, vaporized by laser ablation, are characterized by Fourier-transform microwave techniques in a supersonic expansion. The comparison between the experimental rotational and ¹⁴N nuclear quadrupole coupling constants and the ab initio calculated ones provides conclusive evidence for the identification of the conformers. The most stable species is stabilized by an N−H⋅⋅⋅O =C intramolecular hydrogen bond and a cis-COOH interaction, whereas the higher-energy conformers exhibit an N⋅⋅⋅H−O intramolecular hydrogen bond and trans-COOH, as in other aliphatic amino acids. The spectroscopic data herein reported can be used for the astrophysical purpose in a possible detection of isovaline in space.     

Gas-phase structure of N,N-dimethylglycine.

Three conformers of the neutral amino acid N,N-dimethylglycine [(CH3)2NCH2COOH] were detected in a supersonic expansion by a combination of laser ablation (LA) and molecular-beam Fourier transform microwave (MB-FTMW) spectroscopy. A bifurcated methyl-to-carbonyl (C--HO==C) weak intramolecular hydrogen bond might stabilise the most stable conformer of C(s) symmetry. The second most stable conformer of C1 symmetry has a hydrogen bond between the hydroxyl group and the lone pair at the nitrogen atom (NH--O). The r(s) and r0 structures were derived for this conformer from the rotational data for the parent and six minor 13C, 15N and OD isotopomers. A third conformer exhibits a cis-carboxyl functional group and C1 symmetry. Ab initio MP2/6-311++G(d,p) predictions of the spectroscopic parameters were useful in analysing the spectra. In particular, the agreement of the nuclear quadrupole coupling constants with those calculated was conclusive in identifying the different conformers.     

Effect of methyl groups substitution on the strength of intramolecular hydrogen bonding of naphthazarin: DFT and NBO studies

A density functional theory (DFT) study-based method B3LYP/6-311++G** was carried out to investigate the methyl groups substitution effect on the structure and the strength of intramolecular hydrogen bonding in naphthazarin (NZ) (5,8-dihydroxy-1,4-naphthoquinone). The full geometry optimization of molecular structures, the difference between the energies of hydrogen-bonded and non-hydrogen-bonded rotamers, and the proton chemical shift of the hydroxyl groups in NZ and its methyl substituents obtained at the B3LYP/6-311++G** level. The vibrational frequencies of all samples and their deuterated analogues were calculated at the same theoretical level. The ¹H chemical shifts for NZ and its methyl substituents were computed at the B3LYP/6-311++G** level using the gauge-including atomic orbital method. Furthermore, in order to investigate the changes in bond order, electron density, electron delocalization, and steric effects caused by methyl substituents, natural bond orbital analysis were carried out at the B3LYP/6-311++G** level. After comparing these effective parameters in methyl substituents with those of their parent, NZ, we concluded that, in general, intramolecular hydrogen bonding strength increases by substituting methyl groups in the different positions of NZ.     

Hydrogen bonding affects the [NiFe] active site of Desulfovibrio vulgaris Miyazaki F hydrogenase: a hyperfine sublevel correlation spectroscopy and density functional theory study

Pulse electron paramagnetic resonance and hyperfine sublevel correlation spectroscopy have been used to investigate nitrogen coordination of the active site of [NiFe] hydrogenase of Desulfovibrio vulgaris Miyazaki F in its oxidized "ready" state. The obtained (14)N hyperfine (A = [+1.32, +1.32, +2.07] MHz) and nuclear quadrupole (e(2)qQ/h = -1.9 MHz, eta = 0.37) coupling constants were assigned to the N(epsilon) of a highly conserved histidine (His88) by studying a hydrogenase preparation in which the histidines were (15)N labeled. The histidine is hydrogen-bonded via its N(epsilon)-H to the nickel-coordinating sulfur of a cysteine (Cys549) that carries an appreciable amount of spin density. Through the hydrogen bond a small fraction of the spin density ( approximately 1%) is delocalized onto the histidine ring giving rise to an isotropic (14)N hyperfine coupling constant of about 1.6 MHz. These conclusions are supported by density functional calculations. The measured (14)N quadrupole coupling constants are related to the polarization of the N(epsilon)-H bond, and the respective hydrogen bond can be classified as being weak.     

气相中O3与HSO自由基间的氢键复合物

气相中O3与HSO自由基之间的相互作用及其反应在大气化学中非常重要.在DFT-B3LYP/6-311++G**和MP2/6-311++G**水平上求得O3+HSO复合物势能面上的稳定构型,B3LYP方法得到了三种构型(复合物Ⅰ,Ⅱ和Ⅲ),而MP2方法只能得到一种构犁(复合物Ⅱ).在复合物Ⅰ和Ⅲ中,HSO单元中的1H原子作为质子供体.与O3分子中的端基O原子作为质子受体相互作用,形成红移氢键复合物;而在复合物Ⅱ中,虽与复合物Ⅰ和Ⅲ中具有相间的质子供体和质子受体,却形成了蓝移氢键复合物.B3LYP/6-311++G**水平上计算的单体间相互作用能的计算考虑了基组重甍误差(BSSE)和零点振动能(ZPVE)校正,其值在-3.37到-4.55 kJ·mol-1之间.采用自然键轨道理论(NBO)对单体间相互作用的本质进行了考查,并通过分子中原子理论(AIM)分析了三种复合物中氢键的电子密度拓扑性质.