When does a hydrogen bond become a van der Waals interaction? a topological answer

The hydrogen bond (H-bond) is among the most important noncovalent interaction (NCI) for bioorganic compounds. However, no “energy border” has yet been identified to distinguish it from van der Waals (vdW) interaction. Thus, classifying NCIs and interpreting their physical and chemical importance remain open to great subjectivity. In this work, the “energy border” between vdW and H-bonding interactions was identified using a dimer of water, as well as for a series of classical and nonclassical H-bonding systems. Through means of the quantum theory of atoms in molecules and in particular the source function, it was possible to clearly identify the transition from H-bonding to vdW bonding via analysis of the electronic structure. This “energy border” was identified both on elongating the interatomic interaction and by varying the contact angle. Hence, this study also redefines the “critic angle” previously proposed by Galvão et al. (J. Phys. Chem. A 2013, 117, 12668). Consequently, such “energy border” through an analysis of atomic basins volume variation was possible to identify the end of long-range interactions. © 2019 Wiley Periodicals, Inc.     

van der Waals状态方程与溶液理论

阐明了van der Waals状态方程与溶液理论间的密切关系。由van der Waals状态方程中的内压力和自由体积简捷地导得Scatchard-Hildebrand正规溶液理论、无热溶液理论和Flory-Huggins聚合物溶液理论。表明这些理论都是建立在van der Waals流体的基础上,为进一步改进这些理论提供了一条切实可行的思路。     

分子间van der Waals能的估算方法

本文采用Ｌｅｎｎａｒｄ－Ｊｏｎｅｓ势能公式推导了气体分子内压力的表达式，进而得到用ｖａｎｄｅｒＷａａｌｓ系数ａ、ｂ表达的实际气体分子间的ｖａｎｄｅｒＷａａｌｓ能，即Ｄ＝１０ａ／９πｂ。对一些气体进行了计算，并与实验结果进行了对比。     

van der Waals团簇ArHCl的光电离研究

用同步辐射光源和光电离质谱研究了分子束中ArHClvanderWaals（vdW）团簇的光电离过程．测量结果表明，分子束中的ArHCl的浓匠与气源压力近似满足如下关系式：a（ArHCl）％＝179×10-8.首次给出了ArHCl团簇的光电高效率曲线，并测得ArHCl 的出现势为12.52±0.03eV。根据实验测量的HCl和ArHCl的电高能，计算出Ar－HCl 的解高能为022±0.03eV.用Gaussian－94w量化程序计算出解高能约为0.16eV.实验表明当团簇内的Ar电离时，ArHCl 质谱峰强度明显低于预计的强度，是由于体系电离后发生了电荷转移及解离过程．     

ChemInform Abstract: AunHgm Clusters: Mercury Aurides,Gold Amalgams,or van der Waals Aggregates?

ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.     

Experimental Quantification of Halogen⋅⋅⋅Arene van der Waals Contacts

Crystallographic and computational studies suggest the occurrence of favourable interactions between polarizable arenes and halogen atoms. However, the systematic experimental quantification of halogen⋅⋅⋅arene interactions in solution has been hindered by the large variance in the steric demands of the halogens. Here we have synthesized molecular balances to quantify halogen⋅⋅⋅arene contacts in 17 solvents and solvent mixtures using ¹H NMR spectroscopy. Calculations indicate that favourable halogen⋅⋅⋅arene interactions arise from London dispersion in the gas phase. In contrast, comparison of our experimental measurements with partitioned SAPT0 energies indicate that dispersion is sufficiently attenuated by the solvent that the halogen⋅⋅⋅arene interaction trend was instead aligned with increasing exchange repulsion as the halogen increased in size (ΔG_X⋅⋅⋅_Ph=0 to +1.5 kJ mol⁻¹). Halogen⋅⋅⋅arene contacts were slightly less disfavoured in solvents with higher solvophobicities and lower polarizabilities, but strikingly, were always less favoured than CH₃⋅⋅⋅arene contacts (ΔG_Me⋅⋅⋅_Ph=0 to −1.4 kJ mol⁻¹).     

van der Waals气体状态方程对于实际气体pV_m-p曲线的解释

为加深对物理化学中实际气体行为的认识,通过van der Waals方程对不同温度下实际气体的pV_m-p曲线进行了解释。     

The molecular structure and conformation of 1,1′-dimethyl-bicyclopropyl

The molecular structure and conformation of 1,1′-dimethyl-bicyclopropyl have been studied by the gas electron diffraction method, extended by normal coordinate and molecular mechenics calculations. The experimental data are in accordance with all molecules having the gauche conformation, with a dihedral angle of 58°.     

6,6′-Dimethoxygossypol: molecular structure,crystal polymorphism,and solvate formation

6,6′-Dimethoxygossypol (DMG) is a naturally occurring derivative of gossypol that is found in relatively high concentration in some Gossypium barbadense cotton varieties. Like gossypol, DMG forms an equimolar solvate with acetic acid, but it was not known if, like gossypol, the compound would also form clathrates with other molecules. To test for this, the compound was crystallized from different solvents. Four new structures of DMG were found that include two polymorphic and two solvated forms. The polymorphs include two monoclinic structures with P2₁/c and C2/c space groups (P1 and P2, respectively). Packing of the DMG molecules P1 is similar to packing of the gossypol molecules in the P1 polymorphic form of gossypol. The DMG molecules in P2 pack in a highly ordered arrangement that has not been previously observed among gossypol structures. DMG forms equimolar solvates with water (S1) and cyclohexanone (S2). Both structures are triclinic with P [`1]P \bar {1} space groups. The DMG molecules in S2 assemble in a manner that is similar to the gossypol molecules of gossypol–cyclohexanone (1:1), and the DMG molecules in S1 pack in a manner that is similar to the DMG molecules in DMG–acetic acid (1:1) as well as the gossypol molecules in gossypol–acetic acid (1:1). Although DMG is not as versatile a host compound as gossypol, it still forms solvates under many crystallization conditions. Consequently, some care is needed to be sure that one understands exactly which form is recovered when the compound is isolated.     

Solution structure of a DNA duplex containing a guanine-difluorotoluene pair: a wobble pair without hydrogen bonding?

The incorporation of synthetic nucleoside analogues into DNA duplexes provides a unique opportunity to probe both structure and function of nucleic acids. We used 1H and 19F NMR and molecular dynamics calculations to determine the solution structures of two similar DNA decamer duplexes, one containing a central G-T mismatched or "wobble" base pair, and one in which the thymine in this base pair is replaced by difluorotoluene (a thymine isostere) creating a G-F pair. Here, we show that the non-hydrogen-bonding G-F pair stacks relatively well into the helix and that the distortions caused by each non-Watson-Crick G-T or G-F base pair are quite localized to a three base pair site around the mismatch. A detailed structural analysis reveals that the absence of hydrogen bonding introduces more dynamic motion into the G-F pair relative to G-T and permits the G-F pair to exhibit stacking and conformational features characteristic of both a Watson-Crick base pair (on the guanine containing strand) and a wobble base pair (on the strand containing the difluorotoluene). We used these results to posit a rationale for recognition and repair of mismatch sites in DNA.     

The Weak Interaction on CO2 …CO van der Waals Complex : A Theoretical Study

The geometries of van der Waals complex CO2…CO were optimized at DFT and second-order Moller-Plesset perturbation(MP2) levels with the large basis set,three stable structures were found.The most stable structure has a T-shape geometry in which the CO lies along the C2 axis of CO2,with the two C atoms direct contact and R(C…C)=0.3227nm.The corresponding energies of the most stable structure were calculated by means of MP2,MP4D,MP4DQ,MP4SDTQ,MP4SDQ,CCSD and CCSD(T) methods,The BSSE (basis set superposition error) wads eliminated by the Boys-Bernardi counterpoise correction(CP) method.According to thermodynamics data.van der Waals complex CO2…CO can found at a low temperature and or a high pressure,There is a little charge transferred between the two interacted subunits.In the most stable structure,CO2 is the acceptor and CO is the donor.     

The crystal and molecular structures of 1,1′-divinyl-2,2′-biimidazolyl

The crystal and molecular structures of 1,1-divinyl-2,2-biimidazolyl (L) were determined by x-ray crystallographic analysis. It was established that the molecule of L has crystallographic symmetry 2 and a cisoid conformation with an angle of rotation of 128° between the imidazole rings. The length of the C²-C² bond is increased to 1.485(11) Å compared with the length of the analogous bond in unsubstituted 2,2-biimidazolyl (1.423 Å). Localization of the N=C multiple bond is observed [1.297(9) Å]. The other N-C bonds of the ring are almost equalized (1.374 Å) and are close to the standard values for bonds of the C _sp ²-N type in imidazoles. The angle between the plane of the heterocycle and the plane passing through the atoms of the vinyl group amounts to 7°.N. S. Kurnakov Institute of General and Inorganic Chemistry, Russian Academy of Sciences, 117907 Moscow. Irkutsk Institute of Organic Chemistry, Siberian Branch, Russian Academy of Sciences, 664033 Irkutsk. Translated fromIzvestiya Akademii Nauk, Seriya Khimicheskaya, No. 6, pp. 1376–1380, June, 1992.     

New results for the formation of a muoniated radical in the Mu + Br2 system: a van der Waals complex or evidence for vibrational bonding in Br-Mu-Br?

New evidence is presented for the observation of a muoniated radical in the Mu + Br(2) system, from μSR longitudinal field (LF) repolarisation studies in the gas phase, at Br(2) concentrations of 0.1 bar in a Br(2)/N(2) mixture at 300 K and at 10 bar total pressure. The LF repolarisation curve, up to a field of 4.5 kG, reveals two paramagnetic components, one for the Mu atom, formed promptly during the slowing-down process of the positive muon, with a known Mu hyperfine coupling constant (hfcc) of 4463 MHz, and one for a muoniated radical formed by fast Mu addition. From model fits to the Br(2)/N(2) data, the radical component is found to have an unusually high muon hfcc, assessed to be ～3300 MHz with an overall error due to systematics expected to exceed 10%. This high muon hfcc is taken as evidence for the observation of either the Br-Mu-Br radical, and hence of vibrational bonding in this H[combining low line]-L[combining low line]-H[combining low line] system, or of a MuBr(2) van der Waals complex formed in the entrance channel. Preliminary ab initio electronic structure calculations suggest the latter is more likely but fully rigorous calculations of the effect of dynamics on the hfcc for either system have yet to be carried out.     

Mercury-rare gas van der Waals complexes: From the lightest HgHe to the heaviest HgXe

Mercury helium and mercury xenon van der Waals complexes have been observed in a supersonic free jet expansion by laser-induced fluorescence in the vicinity of the Hg(³P₁¹S₀) transition. The helium complex very weakly bonded in the ground state (D₀ = 8 ± 1 cm⁻¹) exhibited a simple rotational structure. The strongly bonded xenon complex has shown a clear example of isotopic broadening in its vibronic spectra.     

Carbamohydrazonothioate derivative—experimental and theoretical explorations of the crystal and molecular structure

Structural Chemistry - The structural studies of carbamohydrazonothioate derivative and its hydrochloride solvate are the aim of hereunder presented research. The combination of the...     

Synthesis and x-ray crystal structure of a stable α-chlorooxetane

The Barton modification of the Hunsdiecker reaction is the key step in the preparation of 3,5-anhydro-5R-chloro-1,2-O-isopropylidenexylofuranose (1), a stable α-chlorooxetane.