吡咯与HX(X=F,Cl,Br)分子间多种氢键的电子密度拓扑研究

采用密度泛函B3LYP/6-311＋＋G(d,p)方法, 对吡咯与HX (X＝F, Cl, Br)形成的经典氢键和π型氢键, 从其几何参数、电子密度的拓扑性质和电子积分等方面进行了研究. 在对π型氢键的讨论中我们将π电子与σ电子分离, 得到了π型氢键体系的π电子的密度等值线和拉普拉斯量等值线图以及各原子的π电子积分, 形象地说明了π型氢键的作用本质.     

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.     

Hydrogen bond and halogen bond inside the carbon nanotube

The hydrogen bond and halogen bond inside the open-ended single-walled carbon nanotubes have been investigated theoretically employing the newly developed density functional M06 with the suitable basis set and the natural bond orbital analysis. Comparing with the hydrogen or halogen bond in the gas phase, we find that the strength of the hydrogen or halogen bond inside the carbon nanotube will become weaker if there is a larger intramolecular electron-density transfer from the electron-rich region of the hydrogen or halogen atom donor to the antibonding orbital of the X-H or X-Hal bond involved in the formation of the hydrogen or halogen bond and will become stronger if there is a larger intermolecular electron-density transfer from the electron-rich region of the hydrogen or halogen atom acceptor to the antibonding orbital of the X-H or X-Hal bond. According to the analysis of the molecular electrostatic potential of the carbon nanotube, the driving force for the electron-density transfer is found to be the negative electric field formed in the carbon nanotube inner phase. Our results also show that the X-H bond involved in the formation of the hydrogen bond and the X-Hal bond involved in the formation of the halogen bond are all elongated when encapsulating the hydrogen bond and halogen bond within the carbon nanotube, so the carbon nanotube confinement may change the blue-shifting hydrogen bond and the blue-shifting halogen bond into the red-shifting hydrogen bond and the red-shifting halogen bond. The possibility to replace the all electron nanotube-confined calculation by the simple polarizable continuum model is also evaluated.     

Some measures for making halogen bonds stronger than hydrogen bonds in H2CS-HOX (X = F, Cl, and Br) complexes

The properties and applications of halogen bonds are dependent greatly on their strength. In this paper, we suggested some measures for enhancing the strength of the halogen bond relative to the hydrogen bond in the H(2)CS-HOX (X = F, Cl, and Br) system by means of quantum chemical calculations. It has been shown that with comparison to H(2)CO, the S electron donor in H(2)CS results in a smaller difference in strength for the Cl halogen bond and the corresponding hydrogen bond, and the Br halogen bond is even stronger than the hydrogen bond. The Li atom in LiHCS and methyl group in MeHCS cause an increase in the strength of halogen bonding and hydrogen bonding, but the former makes the halogen bond stronger and the latter makes the hydrogen bond stronger. In solvents, the halogen bond in the Br system is strong enough to compete with the hydrogen bond. The interaction nature and properties in these complexes have been analyzed with the natural bond orbital theory.     

取代基对N—H…O＝C氢键三聚体中氢键强度的影响

使用MP2方法研究了氢键三聚体中N-H…O=C氢键强度,探讨了氢键受体分子中不同取代基对N-H…O=C氢键强度的影响.研究表明,不同取代基对氢键三聚体中N-H…O=C氢键强度的影响是不同的:取代基为供电子基团,氢键键长r(H…O)缩短,氢键强度增强;取代基为吸电子基团,氢键键长r(H…O)伸长,氢键强度减弱.自然键轨道(NBO)分析表明,N-H…O=C氢键强度越强,氢键中氢原子的正电荷越多,氧原子的负电荷越多,质子供体和受体分子间的电荷转移越多.供电子基团使N-H…O=C氢键中氧原子的孤对电子n(O)对N-H的反键轨道σ~*(N-H)的二阶相互作用稳定化能增加,吸电子基团使这种二阶相互作用稳定化能减小.取代基对与其相近的N-H…O=C氢键影响更大.     

取代基对N-H…O=C氢键三聚体中氢键强度的影响

使用MP2方法研究了氢键三聚体中N—H…O=C氢键强度, 探讨了氢键受体分子中不同取代基对N—H…O=C氢键强度的影响. 研究表明, 不同取代基对氢键三聚体中N—H…O=C氢键强度的影响是不同的: 取代基为供电子基团, 氢键键长r(H…O)缩短, 氢键强度增强; 取代基为吸电子基团, 氢键键长r(H…O)伸长, 氢键强度减弱. 自然键轨道(NBO)分析表明, N—H…O=C氢键强度越强, 氢键中氢原子的正电荷越多, 氧原子的负电荷越多, 质子供体和受体分子间的电荷转移越多. 供电子基团使N—H…O=C氢键中氧原子的孤对电子n(O)对N—H的反键轨道滓*(N—H)的二阶相互作用稳定化能增加, 吸电子基团使这种二阶相互作用稳定化能减小. 取代基对与其相近的N—H…O=C氢键影响更大.     

The effect of hydrogen bonding on structural parameters ii. an ab initio study of the monohydrated formamide molecule

Four hydrogen-bonded formamide-water complexes have been studied by ab initio calculations, two where the amino group acts as a donor and two where the carbonyl oxygen is an acceptor. The results indicate that the effect on the conjugated NCO fragment depends on both the type and the energy of the hydrogen bond formed. Although, in all cases the formation of a hydrogen bond leads to increased conjugation, expressed as a shortening of the CN bond and a corresponding lengthening of the CO bond, there is a significant difference in the effect of the two types of hydrogen bonds. This difference may be explained by changes in the electron populations. In two of the complexes the effect of varying the hydrogen bond length has been studied in some detail. It is found that the effect on the conjugated system depends on the length of the hydrogen bond, and analytical expressions have been found for the variations of the CO and CN bond lengths with changes in the hydrogen bond length. Potential functions for the N-H β O and O-H β O hydrogen bonds have also been derived.     

Relevance of hydrogen bond definitions in liquid water

To evaluate the relevance of treating the hydrogen bonds in liquid water as a digital (discrete) network and applying topological analyses, a framework to optimize the fitting parameters in various hydrogen bond definitions of liquid water is proposed. Performance of the definitions is quantitatively evaluated according to the reproducibility of hydrogen bonding in the inherent structure. Parameters of five popular hydrogen bond definitions are optimized, for example. The optimal choice of parameters for the hydrogen bond definitions accentuates the binary nature of the hydrogen bonding and the intrinsic network topology of liquid water, especially at the low temperature region. The framework provides a solid basis for network analyses, which have been utilized for water, and is also useful for designing new hydrogen bond definitions.     

Identification of hydrogen bonds using quantum electrodynamics

A method for the identification of hydrogen bonds was investigated from the viewpoint of the stress tensor density proposed by Tachibana and following other works in this field. Hydrogen bonds are known to exhibit common features with ionic and covalent bonds. In quantum electrodynamics, the covalent bond has been demonstrated to display a spindle structure of the stress tensor density. Importantly, this spindle structure is also seen in the hydrogen bond, although the covalency is considerably weaker than in a typical covalent bond. Distinguishing it from the ionic bond is most imperative for the identification of the hydrogen bond. In the present study, the directionality of the hydrogen bond is investigated as the ionic bond is nearly isotropic, while the hydrogen bond exhibits the directionality. It was demonstrated that the hydrogen bond can be distinguished from the ionic bond using the angle dependence of the largest eigenvalue of the stress tensor density.     

高分子共混物中氢键的作用Ⅱ.氢键对高分子共混物性能的影响以及引入方法

高分子共混物中氢键的存在能促进共混组分具有更好的可混和性.因此,研究高分子共混物中的氢键对高分子的共混改性具有重要的理论和实用价值.本文是<高分子共混物中氢键的Ⅰ.氢键的特征描述以及影响因素>的下篇,将继续介绍高分子共混物中氢键的作用,主要包括氢键对高分子共混物性能的影响以及主要的引入氢键的方法.特别地,本文通过将高分子共混物分为合成高分子与合成高分子共混物,合成高分子与天然高分子共混物以及合成高分子与其它物质共混物,总结了氢键存在对共混物性能的影响.     

Theoretical study on the bromomethane-water 1:2 complexes

Bromomethane-water 1:2 complexes have been theoretically studied to reveal the role of hydrogen bond and halogen bond in the formation of different aggregations. Four stable structures exist on the potential energy surface of the CH3Br(H2O)2 complex. The bromine atom acts mainly as proton acceptor in the four studied structures. It is also capable of participating in the formation of the halogen bond. The properties and characteristics of the hydrogen bond and the halogen bond are investigated employing several different quantum chemical analysis methods. Cooperative effects for the pure hydrogen bonds or the mixed hydrogen bonds with halogen bonds and the possibility of describing cooperative effects in terms of the topological analysis of the electronic density or the charge-transfer stabilization energy are discussed in detail. An atoms-in-molecules study of the hydrogen bond or the halogen bond in the bromomethane-water 1:2 complexes suggests that the electronic density topology of the hydrogen bond or the halogen bond is insensitive to the cooperative effect. The charge-transfer stabilization energy is proportional to the cooperative effect, which indicates the donor-acceptor electron density transfer to be mainly responsible for the trimer nonadditive effect.     

Correlated proton motion in hydrogen bonded systems: tuning proton affinities

The theorem of matching proton affinities (PA) has been widely used in the analysis of hydrogen bonds. However, most experimental and theoretical investigations have to cope with the problem that the variation of the PA of one partner in the hydrogen bond severely affects the properties of the interface between both molecules. The B3LYP/d95+(d,p) analysis of two hydrogen bonds coupled by a 5-methyl-1H-imidazole molecule showed that it is possible to change the PA of one partner of the hydrogen bond while maintaining the properties of the interface. This technique allowed us to correlate various properties of the hydrogen bond directly with the difference in the PAs between both partners: it is possible to tune the potential energy surface of the bonding hydrogen atom from that of an ordinary hydrogen bond (localized hydrogen atom) to that of a low barrier hydrogen bond (LBHB, delocalized hydrogen atom) just by varying the proton affinity of one partner. This correlation shows clearly that matching PAs are of lesser importance for the formation of a LBHB than the relative energy difference between the two tautomers of the hydrogen bond.     

Characterization of intramolecular hydrogen bonds by atomic charges and charge fluxes

The electronic charge redistribution and the infrared intensities of the two types of intramolecular hydrogen bonds, O-H···O and O-H···π, of o-hydroxy- and o-ethynylphenol, respectively, together with a set of related intermolecular hydrogen bond complexes are described in terms of atomic charges and charge fluxes derived from atomic polar tensors calculated at the B3LYP/cc-pVTZ level of theory. The polarizable continuum model shows that both the atomic charges and charge fluxes are strongly dependent on solvent. It is shown that their values for the OH bond in an intramolecular hydrogen bond are not much different from those for the "free" OH bond, but the changes are toward the values found for an intermolecular hydrogen bond. The intermolecular hydrogen bond is characterized not only by the decreased atomic charge but also by the enlarged charge flux term of the same sign producing thus an enormous increase in IR intensity. The overall behavior of the charges and fluxes of the hydrogen atom in OH and ≡CH bonds agree well with the observed spectroscopic characteristics of inter- and intramolecular hydrogen bonding. The main reason for the differences between the two types of the hydrogen bond lies in the molecular structure because favorable linear proton donor-acceptor arrangement is not possible to achieve within a small molecule. The calculated intensities (in vacuo and in polarizable continuum) are only in qualitative agreement with the measured data.     

Study of the selective catalysis of metalloporphyrins for 2-methyl-butane oxidation with PhIO under mild conditions

Nine ironporphyrins and eight manganeseporphyrins were synthesized, and their selective catalysis for the oxidation of the secondary and tertiary carbon–hydrogen bonds of 2-methyl-butane with PhIO was studied. The proportion of the oxidation product of tertiary carbon–hydrogen bond to the one of secondary carbon–hydrogen bond was 3:1 when ironporphyrins were used as catalysts, and 2.3:1 when manganeseporphyrins were used as catalysts. The research showed that the substituting groups on the porphyrin rings influenced the catalytic selectivity of metalloporphyrins for the oxidation of the secondary and tertiary carbon–hydrogen bonds as well as the reaction yields. The electron-attracting groups on benzene rings of ironporphyrins increased the catalytic selectivity of ironporphyrins for the tertiary carbon–hydrogen bond oxidation and the reaction speeds, and the electron-releasing groups increased the catalytic selectivity for secondary carbon–hydrogen bond oxidation and reduced the reaction speeds. Both electron-attracting and -releasing groups on benzene rings of manganeseporphyrins enhanced the catalytic selectivity of manganeseporphyrins for the secondary carbon–hydrogen bond oxidation.     

Nature of the Hydrogen Bond Enhanced Halogen Bond

The factors responsible for the enhancement of the halogen bond by an adjacent hydrogen bond have been quantitatively explored by means of state-of-the-art computational methods. It is found that the strength of a halogen bond is enhanced by ca. 3 kcal/mol when the halogen donor simultaneously operates as a halogen bond donor and a hydrogen bond acceptor. This enhancement is the result of both stronger electrostatic and orbital interactions between the XB donor and the XB acceptor, which indicates a significant degree of covalency in these halogen bonds. In addition, the halogen bond strength can be easily tuned by modifying the electron density of the aryl group of the XB donor as well as the acidity of the hydrogen atoms responsible for the hydrogen bond.     

Toward assessing the position-dependent contributions of backbone hydrogen bonding to beta-sheet folding thermodynamics employing amide-to-ester perturbations

An amide-to-ester backbone substitution in a protein is accomplished by replacing an alpha-amino acid residue with the corresponding alpha-hydroxy acid, preserving stereochemistry, and conformation of the backbone and the structure of the side chain. This substitution replaces the amide NH (a hydrogen bond donor) with an ester O (which is not a hydrogen bond donor) and the amide carbonyl (a strong hydrogen bond acceptor) with an ester carbonyl (a weaker hydrogen bond acceptor), thus perturbing folding energetics. Amide-to-ester perturbations were used to evaluate the thermodynamic contribution of each hydrogen bond in the PIN WW domain, a three-stranded beta-sheet protein. Our results reveal that removing a hydrogen bond donor destabilizes the native state more than weakening a hydrogen bond acceptor and that the degree of destabilization is strongly dependent on the location of the amide bond replaced. Hydrogen bonds near turns or at the ends of beta-strands are less influential than hydrogen bonds that are protected within a hydrophobic core. Beta-sheet destabilization caused by an amide-to-ester substitution cannot be directly related to hydrogen bond strength because of differences in the solvation and electrostatic interactions of amides and esters. We propose corrections for these differences to obtain approximate hydrogen bond strengths from destabilization energies. These corrections, however, do not alter the trends noted above, indicating that the destabilization energy of an amide-to-ester mutation is a good first-order approximation of the free energy of formation of a backbone amide hydrogen bond.     

Hydrogen bonding in selected vanadates: a Raman and infrared spectroscopy study

Water plays an important role in the stability of minerals containing the deca and hexavanadates ions. A selection of minerals including pascoite, huemulite, barnesite, hewettite, metahewettite, hummerite has been analysed. Infrared spectroscopy combined with Raman spectroscopy has enabled the spectra of the water HOH stretching bands to be determined. The use of the Libowitsky type function allows for the estimation of hydrogen bond distances to be determined. The strength of the hydrogen bonds can be assessed by these hydrogen bond distances. An arbitrary value of 2.74A was used to separate the hydrogen bonds into two categories such that bond distances less than this value are considered as strong hydrogen bonds whereas hydrogen bond distances greater than this value are considered relatively weaker. Importantly infrared spectroscopy enables the estimation of hydrogen bond distances using an empirical function.     

Theoretical Studies on the Hydrogen Bond Transfer and Proton Transfer between Anamorphoses of the Dihydrated Glycine Complex

The conversion between anamorphoses of the dihydrated glycine complex was studied by means of B3LYP/6-31++G**. It was found that proton transfer was accompanied by hydrogen bond transfer in the process of conversion between different kinds of anamorphoses. With proton transfer, the electrostatic action was notably increased and the hydrogen-bonding action was evidently strengthened when the dihydrated neutral glycine complex converts into dihydrated zwitterionic glycine complex. The activation energy required for hydrogen bond transfer between dihydrated neutral glycine complexes is very low (6.32 kJ·mol-1); however, the hydrogen bond transfer between dihydrated zwitterionic glycine complexes is rather difficult with the required activation energy of 13.52 kJ·mol-1 due to the relatively strong electrostatic action. The activation energy required by proton transfer is at least 27.33 kJ·mol-1, higher than that needed for hydrogen bond transfer. The activation energy for either hydrogen bond transfer or proton transfer is in the bond-energy scope of medium-strong hydrogen bond, so the four kinds of anamorphoses of the dihydrated glycine complex could convert mutually.     

Hydrogen bond structural group constants

The ability of functional groups to act as hydrogen bond acids and bases can be obtained from either equilibrium constants for 1:1 hydrogen bonding or overall hydrogen bond constants. Either method leads to structural constants for hydrogen bonding that in some way are analogous to substituent constants. Extensive lists of these functional group constants are reported. It is shown that those derived from overall hydrogen bond constants are the more useful in analyses of physicochemical and biochemical properties.     

Cooperativity between the Dihydrogen Bond and the N⋅⋅⋅HC Hydrogen Bond in LiH–(HCN)n Complexes

The cooperativity between the dihydrogen bond and the N???HC hydrogen bond in LiH–(HCN)_n (n=2 and 3) complexes is investigated at the MP2 level of theory. The bond lengths, dipole moments, and energies are analyzed. It is demonstrated that synergetic effects are present in the complexes. The cooperativity contribution of the dihydrogen bond is smaller than that of the N???HC hydrogen bond. The three‐body energy in systems involving different types of hydrogen bonds is larger than that in the same hydrogen‐bonded systems. NBO analyses indicate that orbital interaction, charge transfer, and bond polarization are mainly responsible for the cooperativity between the two types of hydrogen bonds.