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.     

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.     

Hydrogen bond interactions in sulfamerazine: DFT study of the O-17, N-14, and H-2 electric field gradient tensors

Hydrogen bond (HB) interactions are studied in the real crystalline structure of sulfamerazine by density functional theory (DFT) calculations of the electric field gradient (EFG) tensors at the sites of O-17, N-14, and H-2 nuclei. One-molecule (single) and four-molecule (cluster) models of sulfamerazine are created by available crystal coordinates and the EFG tensors are calculated in both models to indicate the influence of HB interactions on the tensors. Directly relate to the experiments, the calculated EFG tensors are converted to the experimentally measurable nuclear quadrupole resonance (NQR) parameters, quadrupole coupling constant (qcc) and asymmetry parameter (η_Q). The evaluated NQR parameters reveal that due to contribution of the target molecule to N–HN and N–HO types of HB interactions, the EFG tensors at the sites of various nuclei are influenced from single model to the target molecule in cluster. Additionally, O2, N4, and H2 nuclei of the target molecule are significantly influenced by HB interactions, consequently, they have the major contributions to HB interactions in cluster model of sulfamerazine. The calculations are performed employing B3LYP method and 6-311++G** basis set using GAUSSIAN 98 suite of program.     

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.     

B24N24 nanocages: a GIAO density functional theory study of 14N and 11B nuclear magnetic shielding and electric field gradient tensors

Abstract  

Density functional theory (DFT) calculations were performed to determine boron-11 and nitrogen-14 nuclear magnetic resonance (NMR) and nuclear quadrupole resonance (NQR) spectroscopy parameters in the three most stable B₂₄N₂₄ fullerenes for the first time. The considered samples were first allowed to relax entirely, and then the NMR and NQR calculations were performed on the geometrically optimized models. The calculations of the ¹¹B and ¹⁴N nuclear magnetic shielding tensors and electric field gradient tensors employed the Gaussian 98 software implementation of the gauge-including atomic orbital (GIAO) method using the Becke3, Lee-Yang-Parr (B3LYP) DFT level and 6-311G** and 6-311++G** standard basis sets in each of the three optimized forms, and converted the results to experimentally measurable NMR parameters.The calculated NMR chemical shieldings of the three cages show significant differences, providing a way to identify these clusters. The evaluated NQR parameters of the ¹¹B and ¹⁴N nuclei in the clusters are also reported and discussed.     

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.     

B<Subscript>24</Subscript>N<Subscript>24</Subscript> nanocages: a GIAO density functional theory study of <Superscript>14</Superscript>N and <Superscript>11</Superscript>B nuclear magnetic shielding and electric field gradient tensors

Abstract  Density functional theory (DFT) calculations were performed to determine boron-11 and nitrogen-14 nuclear magnetic resonance (NMR) and nuclear quadrupole resonance (NQR) spectroscopy parameters in the three most stable B₂₄N₂₄ fullerenes for the first time. The considered samples were first allowed to relax entirely, and then the NMR and NQR calculations were performed on the geometrically optimized models. The calculations of the ¹¹B and ¹⁴N nuclear magnetic shielding tensors and electric field gradient tensors employed the Gaussian 98 software implementation of the gauge-including atomic orbital (GIAO) method using the Becke3, Lee-Yang-Parr (B3LYP) DFT level and 6-311G** and 6-311++G** standard basis sets in each of the three optimized forms, and converted the results to experimentally measurable NMR parameters.The calculated NMR chemical shieldings of the three cages show significant differences, providing a way to identify these clusters. The evaluated NQR parameters of the ¹¹B and ¹⁴N nuclei in the clusters are also reported and discussed. Graphical abstract        

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.     

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型(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中具有相同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叠误差(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.     

Hydrogen-Bonding Interaction in a Complex of Amino Acid with <Emphasis Type="Italic">N</Emphasis>,<Emphasis Type="Italic">N</Emphasis>-Dimethylformamide Studied by DFT Calculations

Theoretical studies on hydrogen-bonded complexes between amino acids (glycine, alanine and leucine) and N,N-dimethylformamide (DMF) in gas phase have been carried out using density functional theory (DFT) and ab initio calculations at the B3LYP/6-311++G** and MP2/6-311++G** theory levels. The structures, binding energy, stretching frequency and bond characteristics of the mentioned complexes were calculated. The NH₂ and COOH groups of amino acids form different types of hydrogen bonds with the DMF molecule, as well as alkyl side chains. High binding energy suggests multiple hydrogen bonds present in one complex. The nearly linear OH???O and NH???O contacts are stronger than a conventional hydrogen bond interaction with their H???O separation between 1.74 and 2.14 Å. The weaker CH???O H-bond is also discussed as being a crucial interaction in biological systems involving amino acids. The formation of this interaction results in a blue shift in the CH stretching frequency.     

DFT investigation of sites of protonation of antitumor of 2‐(4‐aminophenyl)benzazoles in the gas phase and in solution

The proton affinity on each of the possible sites in the antitumor 2‐(4‐aminophenyl)benzazoles has been calculated at the B3LYP/6‐311G** level of theory in the gas phase and in solution. The N₃‐site of protonation is found to be strongly favored over the NH₂‐site for the studied compounds both in gas phase and in solution. The stability of N₃‐protonated species is explained by the resonance interaction of the NH₂‐group with the heterocyclic ring. The potential energy surface (PES) for the protonation process was studied at the density functional theory (DFT)/B3LYP/6‐311++G** level of theory. Solvent effects on the PES were also examined using two models: Onsager self‐consistent field and polarizable continuum model (PCM). © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

Intramolecular hydrogen bond in 3‐imino‐propenylamine isomers: AIM and NBO studies

The molecular structure and intramolecular hydrogen bond energy of 18 conformers of 3‐imino‐propenyl‐amine were investigated at MP2 and B3LYP levels of theory using the standard 6‐311++G** basis set. The atom in molecules or AIM theory of Bader, which is based on the topological properties of the electron density (ρ), was used additionally and the natural bond orbital (NBO) analysis was also carried out. Furthermore calculations for all possible conformations of 3‐imino‐propenyl‐amin in water solution were also carried out at B3LYP/6‐311++G** and MP2/6‐311++G** levels of theory. The calculated geometrical parameters and conformational analyses in gas phase and water solution show that the imine–amine conformers of this compound are more stable than the other conformers. B3LYP method predicts the IMA‐1 as global minimum. This stability is mainly due to the formation of a strong N? H···N intramolecular hydrogen bond, which is assisted by π‐electrons resonance, and this π‐electrons are established by NH2 functional group. Hydrogen bond energies for all conformers of 3‐imino‐propenyl‐amine were obtained from the related rotamers methods. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010     

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.     

Intramolecular hydrogen bonding in 3‐imino‐propenylamine: Theoretical investigations

Intramolecular H‐bonds existing for derivatives of 3‐imino‐propenylamine have been studied using the B3LYP/6‐311++G** level of theory. The nature of these interactions, known as resonance‐assisted hydrogen bonds, has been discussed. Vibrational frequencies for α‐derivatives were calculated at the same level of theory. The topological properties of the electron density distributions for N? H···N intramolecular bridges have been analyzed in terms of the Bader theory of atoms in molecules (AIM). Calculation for 3‐imino‐propenylamine derivatives in water solution were also carried out at B3LYP/6‐311++G** level of theory. Finally, the analysis of hydrogen bond in this molecule and their derivatives by quantum theory of natural bond orbital methods fairly support the ab initio results. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2009     

Theoretical Study on Hydrogen Interaction between 5-Fluorouracil and Glycine

The geometries,electronic structure,IR spectrum and other properties of hydrogen interaction between 5-fluorouracil and glycine were studied at the B3LYP/6-31+G* level.Single point energy calculations were executed at the B3LYP/6-311++G** and B3LYP/aug-cc-pvdz levels,and natural bond orbital (NBO) analysis was carried out at the B3LYP/6-31+G* level.Finally,the hydrogen bonds were discussed via AIM electronic density topology analysis.     

Theoretical Study on Vibrational Spectra,Detonation Properties and Pyrolysis Mechanism for Cyclic 2-Diazo-4,6-dinitrophenol

Based on the full optimized molecular geometrical structures at the DFT-B3LYP/6-311+G** level, there exists intramolecular hydrogen bond interaction for cyclic 2-diazo-4,6-dinitrophenol. The assigned infrared spectrum is obtained and used to compute the thermodynamic properties. The results show that there are four main characteristic regions in the calculated IR spectra of the title compound. The detonation velocities and pressures are also evaluated by using Kamlet-Jacobs equations based on the calculated density and condensed phase heat of formation. Thermal stability and the pyrolysis mechanism of 2-diazo-4,6-dinitrophenol are investigated by calculating the bond dissociation energies at the B3LYP/6-311+G** level.     

Quantum-chemical Study on the Structures and Properties of Uracil-BX3 （X = F, Cl） Complexes

1 INTRODUCTION The intermolecular interaction of bases in DNA or RNA is of immense interest and significance to che- mists and biologists alike. The interactions of these bases with metal cations, solvent molecules and other small molecules or ions would affect the struc- ture and biological properties or recognition process,which has been investigated widely[1～8]. Boron contained compounds are electron deficient com- pounds and have been extensively used as catalysts in chemical react…     

Theoretical studies of uracil–(H2O)n (n = 1–7) clusters by ab initio and ABEEMσπ/MM fluctuating charge model

Uracil–(H₂O)_n (n = 1–7) clusters were systemically investigated by ab initio methods and the newly constructed ABEEMσπ/MM fluctuating charge model. Water molecules have been gradually placed in an average plane containing uracil. The geometries of 38 uracil–water complexes were obtained using B3LYP/6-311++G** level optimizations, and the energies were determined at the MP2/6-311++G** level with BSSE corrections. The ABEEMσπ/MM potential model gives reasonable properties of these clusters when comparing with the present ab initio data. For interaction energies, the root mean square deviation is 0.96 kcal/mol, and the linear coefficient reaches 0.997. Furthermore, the ABEEMσπ charges changed when H₂O interacted with the uracil molecule, especially at the sites where the hydrogen bond form. These results show that the ABEEMσπ/MM model is fine giving the overall characteristic hydration properties of uracil–water systems in good agreement with the high-level ab initio calculations.     

Bifurcate hydrogen bonds. Interaction of intramolecularly H-bonded systems with Lewis bases

The structure and the hydrogen bonding in the systems formed by the intramolecularly H-bonded systems, namely, maltol (3-hydroxy-2-methyl-4-pyrone), 5, 2,4,6-trinitrophenol, 6, acetylacetone enol, 7, with Lewis bases, phosgene, 8, dioxane, 9, and DMSO, 10, have been studied by density functional theory (B3LYP) and MP2 using the 6-311G* basis set. The continuum solvent effect was simulated by IEF-PCM model. The hydrogen bond analysis using the atoms in molecules (AIM) method was applied by using the MP2(full)/6-311++G** electron density to establish the nature of the bifurcate hydrogen bond (BHB) in these systems as well as contributory factors for its stabilization. The nature of interaction in the intermolecular H-complexes formed by compounds 5- 7 with the Lewis bases 8- 10 was shown to depend on the strength of the intramolecular hydrogen bond O...H and the strength of the base. The critical values of the CO...H and NO...H angles for which the formation of BHB is possible, have been determined.