4-硝基-1,3-丁二烯基胺分子的氢键效应

在从头计算的水平上, 利用杂化密度泛函理论研究了溶剂对4-硝基-1,3-丁二烯基胺分子的几何结构、分子内的电荷分布和电荷转移态的能量漂移的影响. 在四种极性溶剂中, 我们构造了包括氢键作用的超分子结构. 分别研究了由极化连续模型模拟的溶剂和溶质分子的长程相互作用, 溶剂和溶质分子的氢键作用, 以及溶剂和溶质分子的整体作用对分子结构和性质的影响. 研究结果表明氢键作用引起了溶质分子结构和性质的较大变化, 从而将明显地影响该类分子的非线性光学性质. 因此, 在模拟溶剂效应时需要考虑氢键作用.     

水溶液中氢键寿命的定义和弛豫机理

氢键弛豫过程决定水溶液中分子的动力学行为,氢键寿命作为理论和实验结果中一个重要的参数通常用以描述溶液中的氢键动力学性质.本文采用SPC/E-P2和SPC/E-OPLS两种力场方法对二甲基亚砜(DMSO)水溶液体系进行分子动力学模拟,计算了四种不同定义下的氢键寿命,并进行了对比阐述,连续性氢键寿命Tc和基于动力学平衡方法下的氢键寿命TR较短,它们忽略了不成功的氢键交换过程,稳定态模型下的氢键寿命TPR能够真实体现氧键转换过程,可作为标度衡量其它量值.间歇性氢键寿命T相对最长,重复统计了氢键成功交换后的恢复概率.随着二甲基亚砜浓度增大,TC、TI、TR和TPR不断增大,分子平动扩散系数在中等浓度达到极小,说明氢键寿命与分子活动性无决定性关联,同类型氢键在不同浓度下的寿命差异表明氢键寿命具有分子环境依赖性;水分子和二甲基亚砜分子氢键个数降低,氢键受激角度扭曲和拉伸概率下降,TC和TR不断接近,氢键交换受体密度降低使氢键交换速率下降,TPR不断增大,氢键寿命与其周围氢键密度密切相关.TI与TPR的比值体现了氢键交换的局域性,其变化趋势与分子平动活动性趋势相同.两种力场下氢键寿命的差异也说明氢键的寿命具有明显的理论模型依赖性.     

葡萄糖水溶液氢键结构和动力分析

利用分子动力学模拟方法研究了不同浓度下葡萄糖水溶液的氢键结构和氢键生存周期. 分析了参与i个氢键(分子内、分子间、所有类型)的葡萄糖分子和水分子的百分比分布. 研究发现存在一个特征数N, 参与N个氢键的分子的比例最高, 当iN时, 参与i个氢键的分子的比例随着浓度的增加而减小. 还分析了不同类型氢键(葡萄糖分子内、葡萄糖分子间、水分子间、葡萄糖分子与水分子间、所有类型)的连续和截断自相关函数, 并计算了对应的氢键生存周期.     

液态水体系间2种氢键判别标准的比较分析

采用从头算分子动力学软件CPMD对64个水分子体系在330K温度下氢键成键情况进行了系统分析.结果表明:应用氢键的能量判别标准与几何判别标准存在明显的差别,因此,研究氢键特征时应该根据体系特点选择合适的氢键判别标准.     

BIC和HA体系的氢键驱动的HOPG表面手性自组装分子动力学模拟

5-（苄氧基）-间苯二甲酸衍生物（BIC）与庚醇（HA）分子在高定向热解石墨（HOPG）表面吸附,通过氢键等弱相互作用会形成具有手性特征的二维网络结构。对该过程进行分子动力学模拟,通过几何结构、能量、氢键数目、氢键键长、氢键键角等特征性参数的定量分析,并与实验结果比照,进行氢键与手性自组装结构的形成趋势和稳定性的相关性研究。     

特殊缔合体系TFE水溶液分子动力学模拟

三氟乙醇(TFE)水溶液是一类特殊的缔合体系. 采用分子动力学模拟方法结合核磁共振化学位移研究了TFE水溶液体系全浓度范围的氢键网络, 并对动力学模拟结果和核磁共振化学位移进行了比较. 从径向分布函数(RDF)发现, TFE水溶液中存在着强氢键, 而体系中的C—H…O弱相互作用较为明显, 也不能忽略. 氢键网络分析发现TFE 水溶液体系的氢键大致分为以下三个区域: 在水富集区域, 水分子倾向于自身缔合形成稳定的簇结构, 随着TFE 浓度的增加, 水的有序结构受到破坏, 水分子和TFE分子发生交叉缔合作用形成氢键; 在TFE富集区域, 水分子较少, TFE分子自身通过氢键形成多缔体结构. 此外, 分子动力学统计的平均氢键数的变化和文献报导的核磁共振化学位移变化趋势相同, 实验和理论的结果吻合较好.     

多肽中氢键强度的理论研究

用B3LYP/6-31G^*法优化了多肽分子的几何构型,计算了各个构型的电荷分布和氢键酸度,进而对多肽分子中的氢键强度进行了研究.结果表明,多肽分子中氢键的强度同时取决于形成氢键的H…O原子间距R和N-H…O之间的键角β;多肽分子倾向于形成R值小、β值大的大环氢键.3₁₀螺旋结构的多肽分子中的氢键具有协同效应,分子越大,分子中氢键越多,氢键的协同效应越强.     

甘油水溶液氢键特性的分子动力学模拟

为了研究低温保护剂溶液的结构和物理化学特性, 以甘油为保护剂, 采用分子动力学方法, 对不同浓度的甘油和水的二元体系进行了模拟. 得到了不同浓度的甘油水溶液在2 ns内的分子动力学运动轨迹, 通过对后1 ns内运动轨迹的分析, 得到了各个原子对的径向分布函数和甘油分子的构型分布. 根据氢键的图形定义, 分析了氢键的结构和动力学特性. 计算了不同浓度下体系中平均每个原子(O和H)和分子(甘油和水)参与氢键个数的百分比分布及其平均值. 同时还计算了所有氢键、水分子之间的氢键以及甘油与水分子之间的氢键的生存周期.     

2-[(4-氯苯基亚氨基)甲基]-8-羟基喹啉质子转移的理论研究

研究了2-[(4-氯苯基亚氨基)甲基]-8-羟基喹啉的三种质子转移途径: 分子内质子转移、水分子辅助质子转移和甲醇分子辅助质子转移. 以该席夫碱化合物的晶体结构作为模型, 在B3LYP/6-31＋G(d)水平上, 优化得到稳定态和过渡态的几何构型. 对三类质子转移前后的结构、能量、红外光谱、化学位移进行研究, 结果表明水分子辅助质子转移和甲醇分子辅助质子转移中, 水和甲醇分子利用氢键作用参与质子转移过程, 形成七元环状过渡态, 大大降低了反应的能垒, 有利于质子的转移, 氢键在降低活化能方面起着重要作用.     

基于双嘧啶和双巴比妥酸的氢键组装体的理论研究

用AM1方法对双嘧啶和双巴比妥酸以及二者以1:1的摩尔比通过分子间多重氢键自组织形成的二体进行了几何构型优化,得到氢键键能。并在此基础上用INDO-CI方法讨论了三者的UV-Vis光谱,结果与实验值符合得很好,证实了多重氢键导致新的超分子聚集体的生成,并讨论了氢键在超分子聚集体形成过程中的作用本质。     

An ab initio molecular dynamics study on hydrogen bonds between water molecules

The quantitative estimation of the total interaction energy of a molecular system containing hydrogen bonds (H bonds) depends largely on how to identify H bonding. The conventional geometric criteria of H bonding are simple and convenient in application, but a certain amount of non-H bonding cases are also identified as H bonding. In order to investigate the wrong identification, we carry out a systematic calculation on the interaction energy of two water molecules at various orientation angles and distances using ab initio molecular dynamics method with the dispersion correction for the Becke-Lee-Yang-Parr (BLYP) functionals. It is shown that, at many orientation angles and distances, the interaction energies of the two water molecules exceed the energy criterion of the H bond, but they are still identified as H-bonded by the conventional "distance-angle" criteria. It is found that in these non-H bonding cases the wrong identification is mainly caused by short-range interaction between the two neighbouring water molecules. We thus propose that, in addition to the conventional distance and angle criteria of H bonding, the distance d(H···H) between the two neighbouring hydrogen atoms of the two water molecules should also be taken as a criterion, and the distance r(O···H) between the hydrogen atom of the H-bond donor molecule and the oxygen atom of the acceptor molecule should be restricted by a lower limit. When d(H···H) and r(O···H) are small (e.g., d(H···H) < 2.0 ? and r(O···H) < 1.62 ?), the repulsion between the two neighbouring atoms increases the total energy of the two water molecules dramatically and apparently weakens the binding of the water dimer. A statistical analysis and comparison of the numbers of the H bonds identified by using different criteria have been conducted on a Car-Parrinello ab initio molecular dynamics simulation with dispersion correction for a system of 64 water molecules at near-ambient temperature. They show that the majority of the H-bonds counted by using the conventional criteria combined with the d(H···H) criterion and the restriction of r(O···H) match what is identified by the binding energy criteria (e.g., E ≤ -10 kJ/mol), while some of them still have a binding energy that exceeds the energy criterion, indicating that the complicated quantum effects in H bonding can only be described by the three geometric parameters to a certain extent.     

Dynamics of halide ion-water hydrogen bonds in aqueous solutions: dependence on ion size and temperature

We have carried out a series of molecular dynamics simulations to investigate the dynamics of X(-)-water (X = F, Cl, Br, and I) and water-water hydrogen bonds in aqueous alkali halide solutions at room temperature and also of Cl(-)-water and water-water hydrogen bonds at seven different temperatures ranging from 238 to 318 K. The hydrogen bonds are defined by using a set of configurational criteria with respect to the anion(oxygen)-oxygen and anion(oxygen)-hydrogen distances and the anion(oxygen)-oxygen-hydrogen angle for an anion(water)-water pair. The results of the hydrogen bond dynamics are obtained for two different cutoff values for the angular criterion. In both cases, similar dynamical behavior of the hydrogen bonds is found with respect to their dependence on ion size and temperature. The fluoride ion-water hydrogen bonds are found to break at a much slower rate than water-water hydrogen bonds, while the lifetimes of chloride and bromide ion-water hydrogen bonds are found to be shorter than those of fluoride ion-water ones but still longer than water-water hydrogen bonds. The short-time dynamics of iodide ion-water hydrogen bonds is found to be slightly faster, while its long-time dynamics is found to be slightly slower than the corresponding water-water hydrogen bond dynamics. Correlations of the observed dynamics of anion(water)-water hydrogen bonds with those of rotational and translational diffusion and residence times of water molecules in ion(water) hydration shells are also discussed. With variation of temperature, the lifetimes of both Cl(-)-water and water-water hydrogen bonds are found to show Arrhenius behavior with a slightly higher activation energy for the Cl(-)-water hydrogen bonds.     

Hydrogen bond and residence dynamics of ion-water and water-water pairs in supercritical aqueous ionic solutions: dependence on ion size and density

We have carried out a series of molecular dynamics simulations to investigate the hydrogen bond and residence dynamics of X(-)-water (X=F, Cl, and I) and pairs in aqueous solutions at a temperature of 673 K. The calculations are done at six different water densities ranging from 1.0 to 0.15 g cm(-3). The hydrogen bonds are defined by using a set of configurational criteria with respect to the anion(oxygen)-oxygen and anion(oxygen)-hydrogen distances and the anion(oxygen)-oxygen-hydrogen angle for an anion(water)-water pair. The F(-)-water hydrogen bonds are found to have a longer lifetime than all other hydrogen bonds considered in the present study. The lifetime of Cl(-)-water hydrogen bonds is shorter than that of F(-)-water hydrogen bonds but longer than the lifetime of water-water hydrogen bonds. The lifetimes of I(-)-water and water-water hydrogen bonds are found to be very similar. Generally, the lifetimes of both anion-water and water-water hydrogen bonds are found to be significantly shorter than those found under ambient conditions. In addition to hydrogen bond lifetimes, we have also calculated the residence times and the orientational relaxation times of water molecules in ion(water) hydration shells and have discussed the correlations of these dynamical quantities with the observed dynamics of anion(water)-water hydrogen bonds as functions of the ion size and density of the supercritical solutions.     

Structure and dynamics of water at the interface with phospholipid bilayers

We have performed two molecular-dynamics simulations to study the structural and dynamical properties of water at the interface with phospholipid bilayers. In one of the simulations the bilayer contained neutral phospholipid molecules, dioleoylphosphatidylcholine (DOPC); in the second simulation the bilayer contained charged lipid molecules, dioleoylphosphatidylserine (DOPS). From the density profile of water we observe that water next to the DOPS bilayer is more perturbed as compared to water near the DOPC bilayer. Using an energetic criterion for the determination of hydrogen bonding we find that water molecules create strong hydrogen bonds with the headgroups of the phospholipid molecules. Due to the presence of these bonds and also due to the confinement of water, the translational and orientational dynamics of water at the interface are slowed down. The degree of slowing down of the dynamics depends upon the location of water molecules near a lipid headgroup.     

Trigger bond analysis of nitroaromatic energetic materials using wiberg bond indices

The identification of trigger bonds, bonds that break to initiate explosive decomposition, using computational methods could help direct the development of novel, “green” and efficient high energy density materials (HEDMs). Comparing bond densities in energetic materials to reference molecules using Wiberg bond indices (WBIs) provides a relative scale for bond activation (%ΔWBIs) to assign trigger bonds in a set of 63 nitroaromatic conventional energetic molecules. Intramolecular hydrogen bonding interactions enhance contributions of resonance structures that strengthen, or deactivate, the C NO₂ trigger bonds and reduce the sensitivity of nitroaniline‐based HEDMs. In contrast, unidirectional hydrogen bonding in nitrophenols strengthens the bond to the hydrogen bond acceptor, but the phenol lone pairs repel and activate an adjacent nitro group. Steric effects, electron withdrawing groups and greater nitro dihedral angles also activate the C NO₂ trigger bonds. %ΔWBIs indicate that nitro groups within an energetic molecule are not all necessarily equally activated to contribute to initiation. %ΔWBIs generally correlate well with impact sensitivity, especially for HEDMs with intramolecular hydrogen bonding, and are a better measure of trigger bond strength than bond dissociation energies (BDEs). However, the method is less effective for HEDMs with significant secondary effects in the solid state. Assignment of trigger bonds using %ΔWBIs could contribute to understanding the effect of intramolecular interactions on energetic properties. © 2018 Wiley Periodicals, Inc.     

Time‐dependent density functional theory study on the electronic excited‐state geometric structure,infrared spectra,and hydrogen bonding of a doubly hydrogen‐bonded complex

The geometric structures and infrared (IR) spectra in the electronically excited state of a novel doubly hydrogen‐bonded complex formed by fluorenone and alcohols, which has been observed by IR spectra in experimental study, are investigated by the time‐dependent density functional theory (TDDFT) method. The geometric structures and IR spectra in both ground state and the S₁ state of this doubly hydrogen‐bonded FN‐2MeOH complex are calculated using the DFT and TDDFT methods, respectively. Two intermolecular hydrogen bonds are formed between FN and methanol molecules in the doubly hydrogen‐bonded FN‐2MeOH complex. Moreover, the formation of the second intermolecular hydrogen bond can make the first intermolecular hydrogen bond become slightly weak. Furthermore, it is confirmed that the spectral shoulder at around 1700 cm^?1 observed in the IR spectra should be assigned as the doubly hydrogen‐bonded FN‐2MeOH complex from our calculated results. The electronic excited‐state hydrogen bonding dynamics is also studied by monitoring some vibraitonal modes related to the formation of hydrogen bonds in different electronic states. As a result, both the two intermolecular hydrogen bonds are significantly strengthened in the S₁ state of the doubly hydrogen‐bonded FN‐2MeOH complex. The hydrogen bond strengthening in the electronically excited state is similar to the previous study on the singly hydrogen‐bonded FN‐MeOH complex and play important role on the photophysics of fluorenone in solutions. © 2009 Wiley Periodicals, Inc. J Comput Chem 2009     

Interactions between hydrophobic and ionic solutes in aqueous guanidinium chloride and urea solutions: lessons for protein denaturation mechanism

In order to clarify the mechanism of denaturant-induced unfolding of proteins we have calculated the interactions between hydrophobic and ionic species in aqueous guanidinium chloride and urea solutions using molecular dynamics simulations. Hydrophobic association is not significantly changed in urea or guanidinium chloride solutions. The strength of interaction between ion pairs is greatly diminished by the guanidinium ion. Although the changes in electrostatic interactions in urea are small, examination of structures, using appropriate pair functions, of urea and water around the solutes show strong hydrogen bonding between urea's carbonyl oxygen and the positively charged solute. Our results strongly suggest protein denaturation occurs by the direct interaction model according to which the most commonly used denaturants unfold proteins by altering electrostatic interactions either by solvating the charged residues or by engaging in hydrogen bonds with the protein backbone. To further validate the direct interaction model we show that, in urea and guanidinium chloride solutions, unfolding of an unusually stable helix (H1) from mouse PrPC (residues 144-153) occurs by hydrogen bonding of denaturants to charged side chains and backbone carbonyl groups.