三唑烯醇手性识别的分子力学研究

近十几年来 ,解决不同类型手性化合物的分离是手性色谱发展的前沿领域 [1～ 3] ,对手性识别机理的研究也逐渐引起重视 [4 ,5] ,但由于缺乏手性固定相和手性化合物分子复合体的单晶数据 ,有关手性分离机理的通用定量解释方法很不完善 .采用分子模型设计和理论计算方法 ,研究 CSPs与手性化合物复合体的三维结构性质 ,不仅易于获得 CSPs与 R-体、S-体之间能量的差值 ,而且能直观地得出手性识别发生的位置、作用力的性质及其大小 ,这对于新型 CSPs的设计 ,药物动力学研究和药物分子设计具有十分重要的意义 .本文利用分子力学方法研究了手性…     

Role of the uranyl oxo group as a hydrogen bond acceptor

Density functional theory calculations have been used to evaluate the geometries and energetics of interactions between a number of uranyl complexes and hydrogen bond donor groups. The results reveal that although traditional hydrogen bond donors are repelled by the oxo group in the [UO(2)(OH(2))(5)](2+) species, they are attracted to the oxo groups in [UO(2)(OH(2))(2)(NO(3))(2)](0), [UO(2)(NO(3))(3)](-), and [UO(2)Cl(4)](2-) species. Hydrogen bond strength depends on the equatorial ligation and can exceed 15 kcal mol(-1). The results also reveal the existence of directionality at the uranyl oxo acceptor, with a weak preference for linear U═O---H angles.     

The role of hydrogen bonding in water-metal interactions

The hydrogen bond interaction between water molecules adsorbed on a Pd <111> surface, a nucleator of two dimensional ordered water arrays at low temperatures, is studied using density functional theory calculations. The role of the exchange and correlation density functional in the characterization of both the hydrogen bond and the water-metal interaction is analyzed in detail. The effect of non local correlations using the van der Waals density functional proposed by Dion et al. [M. Dion, H. Rydberg, E. Schr?der, D. C. Langreth and B. I. Lundqvist, Phys. Rev. Lett., 2004, 92, 246401] is also studied. We conclude that the choice of this potential is critical in determining the cohesive energy of water-metal complexes. We show that the interaction between water molecules and the metal surface is as sensitive to the density functional choice as hydrogen bonds between water molecules are. The reason for this is that the two interactions are very similar in nature. We make a detailed analogy between the water-water bond in the water dimer and the water-Pd bond at the Pd <111> surface. Our results show a strong similarity between these two interactions and based on this we describe the water-Pd bond as a hydrogen bond type interaction. These results demonstrate the need to obtain an accurate and reliable representation of the hydrogen bond interaction in density functional theory.     

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.     

In situ FTIR study of the adsorption geometry of bisulfate accepted ions on a platinum electrode

It is shown that a better understanding of the geometry of adsorbed bisulfate species on the surface is gained by monitoring simultaneously more than one vibrational mode of the molecule. We propose that in the double layer region the bisulfate ions are adsorbed via an oxygen atom of its SO₃ unit with the Pt-O-S linkage along the surface normal. In the oxide region the bisulfate ions are adsorbed on the oxygen covered surface of the platinum electrode via the hydrogen atom by hydrogen bonding with the hydrogen bond showing a significant tilt (approximately 60° ).     

The explicit interactions of five-membered saturated heterocyclics containing one and two heteroatoms with single water molecule

In this article, the hydrogen bonding interaction between saturated five-membered heterocyclic molecules and water has been investigated. Molecular orbital and density functional theory methods have been used to evaluate the stabilization energies associated with the adduct formation between heterocyclic molecules and water. The hydrogen bond acceptor ability of O, S, Se, and N as members of five-membered ring has been analyzed. The effect of the presence of second heteroatom N in the ring on the hydrogen bond interaction has also been evaluated. Atoms in molecules theory calculations were carried out to characterize the hydrogen bond through the changes in electron density and Laplacian of electron density. A natural energy decomposition analysis and natural bond orbital analysis is also performed to understand the nature of hydrogen bonding interaction in monohydrated five-membered heterocyclic adducts.     

Glycosidic linkage,N‐acetyl side‐chain,and other structural properties of methyl 2‐acetamido‐2‐deoxy‐β‐d‐glucopyranosyl‐(1→4)‐β‐d‐mannopyranoside monohydrate and related compounds

The crystal structure of methyl 2‐acetamido‐2‐deoxy‐β‐d ‐glycopyranosyl‐(1→4)‐β‐d ‐mannopyranoside monohydrate, C₁₅H₂₇NO₁₁·H₂O, was determined and its structural properties compared to those in a set of mono‐ and disaccharides bearing N‐acetyl side‐chains in βGlcNAc aldohexopyranosyl rings. Valence bond angles and torsion angles in these side chains are relatively uniform, but C—N (amide) and C—O (carbonyl) bond lengths depend on the state of hydrogen bonding to the carbonyl O atom and N—H hydrogen. Relative to N‐acetyl side chains devoid of hydrogen bonding, those in which the carbonyl O atom serves as a hydrogen‐bond acceptor display elongated C—O and shortened C—N bonds. This behavior is reproduced by density functional theory (DFT) calculations, indicating that the relative contributions of amide resonance forms to experimental C—N and C—O bond lengths depend on the solvation state, leading to expectations that activation barriers to amide cis–trans isomerization will depend on the polarity of the environment. DFT calculations also revealed useful predictive information on the dependencies of inter‐residue hydrogen bonding and some bond angles in or proximal to β‐(1→4) O‐glycosidic linkages on linkage torsion angles ? and ψ. Hypersurfaces correlating ? and ψ with the linkage C—O—C bond angle and total energy are sufficiently similar to render the former a proxy of the latter.     

Computational evidence for methyl-donated hydrogen bonds and hydrogen-bond networking in 1,2-ethanediol-dimethyl sulfoxide

The 1:1 complex of 1,2-ethanediol with dimethyl sulfoxide was studied using density functional theory. A network of three hydrogen bonds holds the complex together, including two in which each methyl group donates to the same hydroxyl oxygen. Four lines of evidence support the existence of methyl-donated hydrogen bonds. The interaction energy is 36 +/- 5 kJ/mol using Becke's three parameter hybrid theory with the 1991 nonlocal correlation functional of Perdew and Wang, and a moderately large basis set (B3PW91/6-311++G**//B3PW91/6-31+G**). To determine the energy of each hydrogen bond, a relaxed potential energy scan was performed in a smaller basis set to break the weaker hydrogen bonds by forced systematic rotation of the methyl groups. Two cross-checking analyses show cooperative effects that cause individual hydrogen bond energies in the network to be nonadditive. When one methyl hydrogen bond is broken, the remaining interactions stabilize the complex by storing an additional 2-3 kJ/mol. With all hydrogen bonds intact, the O[bond]H...O[bond]S hydrogen bond contributes 26 +/- 2 kJ/mol stability, and each weak methyl bond stores 5 +/- 2 kJ/mol.     

Copper hydroperoxo species activated by hydrogen-bonding interaction with its distal oxygen

A novel copper(II)[bond]OOH complex with functional ligand that can form a hydrogen bond with the distal oxygen of hydroperoxide has been designed and prepared as a structural/functional model of dopamine beta-hydroxylases, whose spectroscopic characterization and decomposition rates have indicated that the hydroperoxide is activated through the hydrogen-bonding interaction with the distal oxygen.     

Adsorption of acetaldehyde on ice as seen from computer simulation and infrared spectroscopy measurements

Detailed investigation of the adsorption of acetaldehyde on I(h) ice is performed under tropospheric conditions by means of grand canonical Monte Carlo computer simulations and compared to infrared spectroscopy measurements. The experimental and simulation results are in a clear accordance with each other. The simulations indicate that the adsorption process follows Langmuir behavior in the entire pressure range of the vapor phase of acetaldehyde. Further, it was found that the adsorption layer is strictly monomolecular, and the adsorbed acetaldehyde molecules are bound to the ice surface by only one hydrogen bond, typically formed with the dangling H atoms at the ice surface, in agreement with the experimental results. Besides this hydrogen bonding, at high surface coverages dipolar attraction between neighboring acetaldehyde molecules also contributes considerably to the energy gain of the adsorption. The acetaldehyde molecules adopt strongly tilted orientations relative to the ice surface, the tilt angle being scattered between 50° and 90° (i.e., perpendicular orientation). The range of the preferred tilt angles narrows, and the preference for perpendicular orientation becomes stronger upon saturation of the adsorption layer. The CH(3) group of the acetaldehyde molecules points as straight away from the ice surface within the constraint imposed by the tilt angle adopted by the molecule as possible. The heat of adsorption at infinitely low coverage is found to be -36 ± 2 kJ/mol from the infrared spectroscopy measurement, which is in excellent agreement with the computer simulation value of -34.1 kJ/mol.     

4-Amino-3-（p-chlorophenyl）-5-（p-methoxybenzyl）-4H-1,2,4-triazole：X-ray and DFT-calculated Structures

The title compound, 4-amino-3-(p-chlorophenyl)-5-(p-methoxybenzyl)-4H-1,2,4- triazole I , C16H15ClN4O), has been determined using X-ray diffraction techniques and the molecular structure has also been optimized at the B3LYP/6-31 G(d, p) level using density functional theory (DFT). The triazole ring exhibits dihedral angles of 41.61(15)o and 80.73(11)o with the phenyl rings. The molecules are linked principally by N–H…N hydrogen bonds involving the amino NH2 group and a triazole N atom, forming C(5) chains which are further linked to give a two-dimensional network of molecules. The N–H…N hydrogen bonding is supported by C–H…N hydrogen bond and C–H…π interaction. Intermolecular N–H…N and C–H…N hydrogen bonds produce R22(9), R44(10) and R44(20) rings.     

邻二氮杂苯-水复合物氢键相互作用的理论研究

The hydrogen bond structure and interaction energy on the ground state of pyridazine and water complex are studied with B3LYP and MP2 method. All calculations show that there are strong interactions for a hydrogen bond N…H-O and large red-shifts for the symmetric H-O stretching vibrational frequencies in the pyridazine and water complex. The first singlet 1(n, π ) and 1(π,π) vertical excitations of the monomer pyridazine and the hydrogen bond between a pyridazine molecule and a water molecule have been investigated with time-dependent density functional theory TDB3LYP method.     

Analysis of the structures,energetics, and vibrational frequencies for the hydrogen-bonded interaction of nucleic acid bases with Carmustine pharmaceutical agent: a detailed computational approach

In the present study, it is attempted to scrutinize the hydrogen bonding interaction between Carmustine drug and DNA pyrimidine bases by means of density functional theory calculations regarding their geometries, binding energies, vibrational frequencies, and topological features of the electron density in the gas phase and the water solution. Based on the density functional theory results, it is found that the process of intermolecular interaction between Carmustine drug and nucleobases is exothermic and all of the optimized configurations are stable. Furthermore, the negative stability energy represented by a polarizable continuum model shows the significant increase in the solubility of the nucleobase after hydrogen bonding intermolecular interaction in the presence of water solvent. It is also found that the intermolecular hydrogen bonds between drug and the nucleobases play the significant role in the stability of the physisorption configurations. Hydrogen bond energies for hydrogen-bonded complexes are obtained from Espinosa method and the atoms-in-molecules theory are also applied to get a more precise insight into the nature of the intermolecular hydrogen bond interactions.     

Conformational preferences and cis-trans isomerization of L-lactic acid residue

The conformational study on N-acetyl- N'-methylamide of l-lactic acid (Ac-Lac-NHMe, the Lac dipeptide) is carried out using ab initio HF and density functional methods with the self-consistent reaction field method to explore its backbone conformational preferences and cis-trans isomerization for the depsipeptide with an ester bond in the gas phase and in solution. In the gas phase and in chloroform, the conformation tB with a trans depsipeptide bond is most preferred for the Lac dipeptide, whose backbone torsion angles are phi approximately -150 degrees and psi approximately -5 degrees , juxtaposed to those of the 3 10-helical structure. The larger shift in phi is brought to reduce the repulsion between the two carbonyl carbons of the acetyl and NHMe groups. However, the polyproline II-like tF conformation becomes more populated and the relative stability of conformation tB decreases significantly as the solvent polarity increases. This may be ascribed to weakening a C(5) hydrogen bond between the depsipeptidyl oxygen and the carboxyl amide hydrogen that plays a role in stabilizing the conformation tB in the gas phase and in chloroform. The cis populations about the depsipeptide bond are nearly negligible in the gas phase and in solution. The rotational barriers to the cis-trans isomerization of the depsipeptide bond for the Lac dipeptide are calculated to be about 11 kcal/mol, which is about half of those for the Ala dipeptide, although they increase somewhat with the increase of solvent polarity. The cis-trans isomerization of the depsipeptide bond proceeds through either clockwise or anticlockwise rotations with torsion angles of about +90 degrees or -90 degrees , respectively, in the gas phase and in solution, whereas it has been known that the isomerization proceeds through only the clockwise rotation for alanyl and prolyl peptide bonds. The pertinent distances between the depsipeptidyl oxygen and the carboxyl amide hydrogen can describe the role of this hydrogen bond in stabilizing the transition state structures in the gas phase and in solution.     

Rotational spectroscopy and molecular structure of 1,1,2-trifluoroethylene and the 1,1,2-trifluoroethylene-hydrogen fluoride complex

Fourier transform microwave rotational spectra in the 6-22 GHz region are obtained for the complex formed between 1,1,2-trifluoroethylene and hydrogen fluoride, including the normal isotopomer, the two singly substituted 13C species, and the complex obtained with DF. A unique planar structure for the complex is determined from a combined analysis of the rotational constants derived from the spectra and atomic positions obtained using Kraitchman [Am. J. Phys. 21, 17 (1953)] substitution coordinates. Consistent with this structure, no hyperfine splitting of rotational lines due to the nuclear quadrupole coupling interaction is observed for the D-containing species. Although the primary interaction in the complex is a hydrogen-fluorine hydrogen bond, as is the case for all previously studied Lewis acid-fluoroethylene complexes, the CF2CHF-HF complex adopts a distinctly different geometry in which both the primary and secondary interactions occur between the HF molecule and a F atom and a H atom, respectively, bonded to the same carbon of CF2CHF. The 2.020(41) A hydrogen bond has hydrogen fluoride as the donor and 1,1,2-trifluoroethylene as the acceptor and forms a 109.0(13) degrees C-F...H angle. The secondary interaction between the hydrogen fluoride F atom and the H atom geminal to the acceptor F atom causes the hydrogen bond to deviate 41.6(51) degrees from linearity. Structural comparisons with analogous complexes formed with mono- and difluorinated ethylenes suggest that the primary hydrogen bond strength and the fluoroethylene fluorine atom basicity both decrease with increasing fluorine substitution. In the course of this work, it was necessary to obtain additional rotational spectra for the 1,1,2-trifluroethylene monomer and to improve the precision of the values of the structural parameters for this molecule.     

Influence of bonded-phase coverage in reversed-phase liquid chromatography via molecular simulation I. Effects on chain conformation and interfacial properties

Particle-based Monte Carlo simulations were employed to examine the effects of bonding density on molecular structure in reversed-phase liquid chromatography. Octadecylsilane stationary phases with five different bonding densities (1.6, 2.3, 2.9, 3.5, and 4.2 mumol/m(2)) in contact with a water/methanol (50/50 mol%) mobile phase were simulated at a temperature of 323 K. The simulations indicate that the alkyl chains become more aligned and form a more uniform alkyl layer as coverage is increased. However, this does not imply that the chains are highly ordered (e.g., all-trans conformation or uniform tilt angle), but rather exhibit a broad distribution of conformations and tilt angles at all bonding densities. At lower densities, significant amounts of the silica surface are exposed leading to an enhanced wetting of the stationary phase. At high densities, the solvent is nearly excluded from the bonded phase and persists only near the residual silanols. An enrichment in the methanol concentration and a disruption in the mobile phase's hydrogen bond network are observed at the interface as bonding density is increased.     

Methyl 2‐O‐β‐l‐fucopyranosyl α‐d‐glucopyranoside monohydrate: a synchrotron study

The structure of the title compound, C₁₃H₂₄O₁₀·H₂O, is stabilized by hydrogen bonds situated adjacent to the glycoside linkage. A direct intramolecular hydrogen bond is present between the fucopyranosyl ring O atom and a glucopyranoside OH group, and a bridging water molecule mediates a hydrogen‐bond‐based interaction from a fucopyranosyl OH group to the methoxy O atom. The conformation of the disaccharide is described by the glycosidic torsion angles ϕ_H = −41° and ψ_H = −2°.     

A theoretical study on the excited‐state intramolecular proton transfer mechanism of 4′‐dimethylaminoflavonol chemosensor

In this work, density functional theory (DFT) and time‐dependent density functional theory (TDDFT) methods are used to explore the excited‐state intramolecular proton transfer (ESIPT) mechanism of a novel system 4′‐dimethylaminoflavonol (DAF). By analyzing the molecular electrostatic potential (MEP) surface, we verify that the intramolecular hydrogen bond in DAF exists in both the S₀ and S₁ states. We calculate the absorption and emission spectra of DAF in two solvents, which reproduce the experimental results. By comparing the bond lengths, bond angles, and relative infrared (IR) vibrational spectra involved in the hydrogen bonding of DAF, we confirm the hydrogen‐bond strengthening in the S₁ state. For further exploring the photoexcitation, we use frontier molecular orbitals to analyze the charge redistribution properties, which indicate that the charge transfer in the hydrogen‐bond moiety may be facilitating the ESIPT process. The constructed potential energy curves in acetonitrile and methylcyclohexane solvents with shortened hydrogen bond distances demonstrate that proton transfer is more likely to occur in the S₁ state due to the lower potential barrier. Comparing the results in the two solvents, we find that aprotic polar and nonpolar solvents seem to play similar roles. This work not only clarifies the excited‐state behaviors of the DAF system but also successfully explains its spectral characteristics.     

Cooperativity in a cycloalkane-1,2/1,3-polyol corona: Topological hydrogen bonding in 1,2-diol motifs

A corona, consisting of 18 carbon atoms bearing 12 hydroxy groups in a continuous hydrogen-bonded chain, is built up by alternating degenerate conformations of alternating alkane-1,2-diol and 1,3-diol motifs. Geometries, proton nuclear magnetic resonance shifts and interaction energies for the dodecahydroxycyclo-octadecane and selected fragments are determined by density functional calculations at the B3LYP/6-311+G(d,p) level. Cooperative effects of O–H⋯O–H bonding are evident from the simple juxtaposition of these two motifs with a common OH group in butane-1,2,4-triol conformers. Bracketing a 1,2-diol motif with two 1,3-diol motifs in hexane-1,3,4,6-tetrol leads to a structure in which the 1,2-diol motif displays a bond critical point for hydrogen bonding. This is associated with enhancement of the shift of the hydrogen-bonded OH proton and of the corresponding H⋯O interaction energy. The full corona has a complete outer ring of O–H⋯O–H bond paths, and an inner ring of bond paths, due to C–H⋯H–C hydrogen–hydrogen bonding, which result in a central ring critical point. The topological O–H⋯O–H hydrogen bond, never seen in simple alkane-1,2-diols, is associated with cooperative enhancement of the H⋯O interaction energy, but this is not a necessary condition for a bond path: values for topological C–H⋯H–C hydrogen–hydrogen bonds can be as low as −0.4 kcal mol⁻¹.