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从实验和理论两个方面研究了Z型和E型对甲氧基苯甲醛肟晶体的熔点、 结构、 红外光谱和分子间相互作用. 在E型和Z型晶体中, 对甲氧基苯甲醛肟分子分别呈二聚体重复单元和双链Zigzag结构排列. 研究结果表明, 电荷分布变化引起的静电相互作用差别、 形成氢键的方式和强度以及晶体中分子排列方式导致的范德华作用不同是造成Z型和E型对甲氧基苯甲醛肟固体熔点、 红外光谱等物理性质差别的根本原因. 相似文献
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复杂缔合体系NMA-H2O的1H NMR研究 总被引:1,自引:0,他引:1
N-甲基乙酰胺(NMA)是最简单的肽键模型分子,广泛地被用来研究氢键相互作用.采用外标法测量了不同温度下NMA-H2O缔合体系的1H NMR数据,通过磁化率校正得到了混合物的准确化学位移数据.然后用量子化学计算的结果确定体系的缔合形式,运用化学缔合理论建立模型,对模型进行降维,减少模型参数;再采用最小二乘法,联合遗传算法(GA)和Levenberg-Marquardt算法对模型参数进行全局寻优,求解得到了缔合平衡常数和缔合平衡的ΔH和ΔS.此外,还采用密度泛函理论(DFT)计算了NMA-H2O的几种主要缔合形式在298 K的ΔH,计算结果与化学缔合模型得到的结果和文献吻合较好. 相似文献
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用DFT方法在B3LYP/6-311++G (d,p)水平下研究了甲醇线性和环状分子簇. 对于不同大小的分子簇之间定义了协同因子. 计算得到的协同因子可以验证氢键的强协同效应, 环状分子簇之间的协同效应远远大于线性分子簇. 做为理论验证和比较, 热力学模型分别采用含氢键缔合的格子流体状态方程(LFHB), 以及含氢键协同效应的LFHB, 关联醇-惰性体系的1H核磁共振化学位移. 考虑协同效应的关联结果优于原始的LFHB. 比较量子化学计算的和热力学模型中采用的协同因子, 认为甲醇和乙醇在溶液中更可能大部分以线性缔合形式存在. 相似文献
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DFT和热力学研究氢键协同效应及对关联1H NMR的影响 总被引:1,自引:0,他引:1
用DFT方法在B3LYP/6—311 G(d,p)水平下研究了甲醇线性和环状分子簇.对于不同大小的分子簇之间定义了协同因子,计算得到的协同因子可以验证氢键的强协同效应,环状分子簇之间的协同效应远远大于线性分子簇,做为理论验证和比较,热力学模型分别采用含氢键缔合的格子流体状态方程(LFHB),以及含氢键协同效应的LFHB,关联醇一惰性体系的^1H核磁共振化学位移.考虑协同效应的关联结果优于原始的LFHB,比较量子化学计算的和热力学模型中采用的协同因子,认为甲醇和乙醇在溶液中更可能大部分以线性缔合形式存在。 相似文献
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利用从头计算方法计算了鸟苷与联苯酰基胺离子反应生成C8加成物的NMR化学位移, 结果与实验所测到的NMR化学位移符合得很好, 并且根据原子-键电负性均衡方法中的σπ模型(ABEEM σπ)计算所得到的电荷与NMR化学位移也有很好的对应关系; 但采用相同的方法计算腺苷与联苯酰基胺离子反应生成的亚胺加成物时, 得到的NMR化学位移与实验值在个别关键的碳原子处有很大差别. 根据研究得到的结果推测, 实验上得到的构型不仅仅是亚胺加成物, 而可能是一种含有亚胺和氮杂形式加成物的混合物. 相似文献
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利用光谱实验结合计算机模拟技术研究了药物恩诺沙星(Enrofloxacin,EFLX)与牛乳铁蛋白(Bovine lactoferrin,BLF)的相互作用机理。测定反应体系的结合参数、能量转移参数及热力学函数,考察EFLX对BLF分子构象的影响,并模拟EFLX-BLF结合反应的分子模型。结果表明,药物分子与牛乳铁蛋白的相互作用表现为动态结合过程,结合强度适中,EFLX与BLF分子的结合距离r值较小,说明发生了能量转移现象。EFLX影响BLF的结构域微区构象,降低结合位域的疏水性。荧光相图技术解析出EFLX与BLF反应构象型态的变迁为"二态模型"。EFLX-BLF的热力学参数表明两者间是以氢键和范德华力为主的分子间作用。分子建模结果显示,EFLX与BLF的相互作用主要为氢键和范德华力,兼有疏水作用力。计算机分子模拟与实验测试获得了一致性结果。 相似文献
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利用太赫兹时域光谱和低频拉曼光谱仪研究了丙氨酸晶体在0.2-2.6 THz 范围内的太赫兹吸收和拉曼散射光谱. 研究表明: 在该低频范围有四个振动模式, 其中两个只具有拉曼活性, 其余两个同时具有红外和拉曼活性. 基于B3LYP杂化密度泛函的自洽场晶体轨道法对丙氨酸周期性结构进行了理论研究和光谱计算. 通过比较实验和理论结果, 指认了实验光谱特征峰所属的不可约表示. 通过理论计算得到的图形, 得出在此低频范围的振动模式主要包含分子间氢键的扭转和摇摆运动. 相似文献
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Schmidt J Hoffmann A Spiess HW Sebastiani D 《The journal of physical chemistry. B》2006,110(46):23204-23210
We present an analysis of bulk (1)H NMR chemical shifts for a series of biochemically relevant molecular crystals in analogy to the well-known solvent NMR chemical shifts. The term bulk shifts denotes the change in NMR frequency of a gas-phase molecule when it undergoes crystallization. We compute NMR parameters from first-principles electronic structure calculations under full periodic boundary conditions and for isolated molecules and compare them to the corresponding experimental fast magic-angle spinning solid-state NMR spectra. The agreement between computed and experimental lines is generally very good. The main phenomena responsible for bulk shifts are packing effects (hydrogen bonding and pi-stacking) in the condensed phase. By using these NMR bulk shifts in well-ordered crystalline model systems composed of biologically relevant molecules, we can understand the individual spectroscopic signatures of packing effects. These local structural driving forces, hydrogen bonding, pi-stacking, and related phenomena, stand as a model for the forces that govern the assembly of much more complex supramolecular aggregates. We show to which accuracy condensed-phase ab initio calculations can predict structure and structure-property relationships for noncovalent interactions in complex supramolecular systems. 相似文献
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《Journal of computational chemistry》2018,39(19):1335-1343
Accurate lattice energies of organic crystals are important i.e. for the pharmaceutical industry. Periodic DFT calculations with atom‐centered Gaussian basis functions with the Turbomole program are used to calculate lattice energies for several non‐covalently bound organic molecular crystals. The accuracy and convergence of results with basis set size and k‐space sampling from periodic calculations is evaluated for the two reference molecules benzoic acid and naphthalene. For the X23 benchmark set of small molecular crystals accurate lattice energies are obtained using the PBE‐D3 functional. In particular for hydrogen‐bonded systems, a sufficiently large basis set is required. The calculated lattice energy differences between enantiopure and racemic crystal forms for a prototype set of chiral molecules are in good agreement with experimental results and allow the rationalization and computer‐aided design of chiral separation processes. © 2018 Wiley Periodicals, Inc. 相似文献
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Biliškov N Kojić-Prodić B Mali G Molčanov K Stare J 《The journal of physical chemistry. A》2011,115(14):3154-3166
Hydrogen bonding and proton transfer in the solid state are studied on the crystals of isostructural anhydrous potassium and rubidium complex chloranilates by variable-temperature single crystal X-ray diffraction, solid state (1)H NMR and IR spectroscopies, and periodic DFT calculations of equilibrium geometries, proton potentials, and NMR chemical shifts. Their crystal structures reveal neutral molecules of chloranilic acid and its dianions connected into a chain by O-H···O hydrogen bond. A strong hydrogen bond with a large-amplitude movement of the proton with NMR shift of 13-17 ppm and a broad continuum in IR spectra between 1000 and 500 cm(-1) were observed. Periodic DFT calculations suggest that proton transfer is energetically more favorable if it occurs within a single pair of chloranilate dianion and chloranilic acid molecule but not continuously along the chains of long periodicity. The calculated chemical shifts confirm the assumption that the weak resonance signals observed at lower magnetic fields pertain to the case when the proton migrates to the acceptor side of the hydrogen bond. The detected situation can be described by a partial proton transfer. 相似文献
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Using multiple computational tools, we examine five candidate crystal structures for β-carbonic acid, a molecular crystal of environmental and astrophysical significance. These crystals comprise of hydrogen bonded molecules in either sheetlike or chainlike topologies. Gas phase quantum calculations, empirical force field based crystal structure search, and periodic density functional theory based calculations and finite temperature simulations of these crystals have been carried out. The infrared spectrum calculated from density functional theory based molecular dynamics simulations compares well with experimental data. Results suggest crystals with one-dimensional hydrogen bonding topologies (chainlike) to be more stable than those with two-dimensional (sheetlike) hydrogen bonding networks. We predict that these structures can be distinguished on the basis of their far infrared spectra. 相似文献
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Precise theoretical predictions of NMR parameters are helpful for the spectroscopic identification of complicated biological molecules, especially for the carbon shielding tensors in amino acids. The (13)C shielding tensors of various crystalline amino acids and peptides have been calculated using the gauge-including projector augmented wave (GIPAW) method based on two different periodic structure models, namely that deduced from available crystallographic data and that from theoretically optimized structures. The incorporation of surrounding lattice effects is found to be crucial in obtaining reliable predictions of (13)C shielding tensors that are comparable to the experimental data. This is accomplished by refining the experimental crystallographic data of the amino acids and peptides at the GGA/PBE level by which more accurate intramolecular C--H bond lengths and intermolecular hydrogen-bonding interactions are obtained. Accordingly, more accurate predictions of (13)C shielding tensors comparable to the experimental results (within a maximum deviation of +/-10 ppm) were achieved, rendering more explicit (13)C shielding tensors assignments for solid biological systems particularly for amino acids with multiple carboxyl carbons, such as asparagine, glutamine, and glutamic acid. 相似文献
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The hydrogen-bond interaction can be studied using a variety of spectroscopic and crystallographic techniques, as well as
theoretical studies based on quantum chemical principles, semi-empirical procedures, and statistical interpretations. A degree
of specificity, along with flexibility, provides H-bonded systems with a variety of unusual and interesting physical, chemical
and biological properties. Neutron diffraction is the method of choice for obtaining high-precision data on hydrogen-atom
positions and hydrogen-bond stereo-chemistry in crystals. Neutron inelastic scattering can provide information on the dynamics
of H-bonded systems. High-precision neutron diffraction studies on a variety of crystal hydrates, amino acids and small peptides,
development of semi-empirical potential functions for bent-hydrogen bonds, and statistical analysis of H-bond populations
associated with various donor and acceptor groups are some of the investigations on hydrogen bonding, carried out at Trombay
during the past three decades. 相似文献
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采用分子模拟方法研究了正交晶系冰晶(020)生长面在不同浓度甘油水溶液中的生长情况. 通过统计分析氢键数、 密度分布函数、 均方根偏差和原子间径向分布函数研究了水分子和甘油分子的动态行为. 结果表明, 甘油分子在水溶液中可与水分子形成大量氢键, 这使水分子间的氢键作用受到抑制, 降低了水分子的扩散性, 致使冰晶不易成核和生长; 另外, 一些甘油分子可代替水分子吸附在晶面上, 甚至占据晶格位点, 这种行为打破了冰晶的对称性并且降低了冰晶的生长速率. 因此, 甘油可同时在晶面和液相中抑制冰晶的生长. 相似文献
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Halogen bonding, a specific intermolecular noncovalent interaction, plays crucial roles in fields as diverse as molecular recognition, crystal engineering, and biological systems. This paper presents an ab initio investigation of a series of dimeric complexes formed between bromobenzene and several electron donors. Such small model systems are selected to mimic halogen bonding interactions found within crystal structures as well as within biological molecules. In all cases, the intermolecular distances are shown to be equal to or below sums of van der Waals radii of the atoms involved. Halogen bonding energies, calculated at the MP2/aug-cc-pVDZ level, span over a wide range, from -1.52 to -15.53 kcal/mol. The interactions become comparable to, or even prevail over, classical hydrogen bonding. For charge-assisted halogen bonds, calculations have shown that the strength decreases in the order OH- > F- > HCO2- > Cl- > Br-, while for neutral systems, their relative strengths attenuate in the order H2CS > H2CO > NH3 > H2S > H2O. These results agree with those of the quantum theory of atoms in molecules (QTAIM) since bond critical points (BCPs) are identified for these halogen bonds. The QTAIM analysis also suggests that strong halogen bonds are more covalent in nature, while weak ones are mostly electrostatic interactions. The electron densities at the BCPs are recommended as a good measure of the halogen bond strength. Finally, natural bond orbital (NBO) analysis has been applied to gain more insights into the origin of halogen bonding interactions. 相似文献