Structural properties of liquid water

Monte Carlo simulations of molecular configurations of liquid water in theNVT-ensemble atT=298 K using unit cells containing 125 and 1000 molecules were, carried out. Comparison of experimental and calculated radial distribution functions suggests the existence of two types of spatial ordering in water. Structural properties of low-energy molecular clusters and associates of closed cycles of H-bonds were determined. The properties of the network of H-bonds can be described by a set of fundamental constants and one free parameter,viz., the probability of bond formation. The existence of long-range correlations in spatial arrangement of both the molecules and the cycles of bonds was established. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 5, pp. 841–851, May, 1999.     

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.     

Density functional theory and topological analysis on the hydrogen bonds in cysteine–propanoic acid complexes

The complexes formed via hydrogen bonding interactions between cysteine and propanoic acid have been studied at the density three-parameter hybrid functional DFT-B3LYP/6-311++G(d,p) level regarding their geometries, energies, vibrational frequencies, and topological features of the electron density. The quantum theory of atoms in molecules (QTAIM) and natural bond orbital (NBO) analysis was employed to elucidate the interaction characteristics in cysteine–propanoic acid (Cys–Prop) complexes. More than 10 kinds of hydrogen bonds (H-bonds) including intra- and inter-molecular H-bonds have been found in Cys–Prop complexes. The results show that both the strength of H-bonds and the deformation are important factors for the stability of Cys–Prop complexes. The strongest H-bonds (O2H^A···O1^B and O2H^A···O1^B) exist in the most stable Cys–Prop complex. The stronger H-bonds formed between hydroxyl and O (or N) atom usually stronger than those involve C (or S) atom. Relationships between the electron density (ρ) of BCP and H-bond length as well as the Fock matrix element (F _ij) has also been investigated and used to study the nature of H-bonds. Moreover, the results show that the change of the bond length linearly correlates with the corresponding frequency shift.     

Crystallographic and conformational analysis of two novel trans-azo benzene compounds

The molecular and crystal structure of (E)-2-Acetyl-4-(2-bromophenyldiazenyl)phenol (1) and (E)-2-Methyl-4-(o-tolyldiazenyl)phenol (2) were characterized and determined by single crystal X-ray diffraction method besides spectroscopic means. The periodic organization of 1 is stabilized by C–H···O type weak H-bond and Br···O type weak halogen bonding and thus, a two dimensional puckered network is established almost parallel to () the plane. Molecules of 2 are linked into C(7) chains generated by translation along the [1 0 1] direction with the aid of O–H···N type H-bonds, and these chains are strengthened by C–H···π interactions involving o-tolylphenol ring. Quantum chemical studies at B3LYP/6-311 ++G(d,p) level reveal that potential barrier of the compounds around Ar–N torsions is of double minimum character unless it is defected by the presence of o-substituent groups in the vicinity of the azo bridge. The results from crystallographic and quantum chemical studies suggest that azo benzene compounds may adapt non-planar geometry apart from the most stable planar conformation, which is located on the secondary minima of double potential barrier regarding rotational motion around Ar–N bonds.     

Molecular and quantum mechanical studies on the monomer recognition of a highly-regular β-helical antifreeze protein

The possible interaction models for an antifreeze protein from Tenebrio molitar (TmAFP) have been systematically studied using the methods of molecular mechanics, molecular dynamics and quantum chemistry. It is hoped that these approaches would provide insights into the nature of interaction between protein monomers through sampling a number of interaction possibilities and evaluating their interaction energies between two monomers in the course of recognition. The results derived from the molecular mechanics indicate that monomerś β-sheets would be involved in interaction area and the side chains on two p-faces can match each other at the two-dimensional level. The results from molecular mechanics and ONIOM methods show that the strongest interaction energy could be gained through the formation of H-bonds when the twoβ-sheets are involved in the interaction model. Furthermore, the calculation of DFT and analysis of van der Waals bond charge density confirm further that recognition between the two TCTs mainly depends on inter-molecular hydroxyls. Therefore, our results demonstrate that during the course of interaction the most favorable association of TmAFPs is via their β-sheets.     

Combined DFT with NBO and QTAIM studies on the hydrogen bonds in (CH<Subscript>3</Subscript>OH)<Subscript><Emphasis Type="Italic">n</Emphasis></Subscript> (<Emphasis Type="Italic">n</Emphasis> = 2–8) clusters

The (CH₃OH) _n (n = 2–8) clusters formed via hydrogen bond (H-bonds) interactions have been studied systemically by density functional theory (DFT). The relevant geometries, energies, and IR characteristics of the intermolecular OH···O H-bonds have been investigated. The quantum theory of atoms in molecule (QTAIM) and natural bond orbital (NBO) analysis have also been applied to understand the nature of the hydrogen bonding interactions in clusters. The results show that both the strength of H-bonds and the deformation are important factors for the stability of (CH₃OH) _n clusters. The weakest H-bond was found in the dimer. The strengths of H-bonds in clusters increase from n = 2 to 8, moreover, the strengths of H-bonds in (CH₃OH) _n (n = 4–8) clusters are remarkably stronger than those in (CH₃OH) _n (n = 2, 3) clusters. The small differences of the strengths of H-bonds among (CH₃OH) _n (n = 6–8) clusters indicate that a partial covalent character is attributed to the H-bonds in these clusters. The linear relationships between the electron density of BCP (ρ_b) and the H···O bond length of H-bonds as well as the second-perturbation energies E(2) have also been investigated and used to study the nature of H-bonds, respectively.     

X-ray structural investigation of gossypol and its derivatives XXIII autoclathrates based on a mixed gossypol — 1,4-Dioxane matrix

Gossypol forms various complexes with the isomeric dioxanes. The clathrate with 1,4-dioxane is the only complex of gossypol in which the intrinsic symmetry of the gossypol molecule — the symmetry of a twofold axis — is retained. In this complex, two out of the three 1,4-dioxane molecules belonging to each gossypol molecule participate in the construction of a mixed H-bound gossypol -dioxane matrix, while the third molecule plays the part of guest, the guest molecules having no H-bonds with the host matrix and undergoing desolvation at 108–110°C.     

Theoretical study of bifurcated bent blue-shifted hydrogen bonds CH<Subscript>2</Subscript>···Y

Ab initio quantum chemistry methods were applied to study the bifurcated bent hydrogen bonds Y··· H₂CZ (Z = O, S, Se) and Y···H₂CZ₂ (Z = F, Cl, Br) (Y = Cl⁻, Br⁻) at the MP2/6-311++G(d,p) and MP2/6-311++G(2df,2p) levels. The results show that in each complex there are two equivalent blue-shifted H-bonds Y···H-C, and that the interaction energies and blue shifts are large, the energy of each Y···H-C H-bond is 15–27 kJ/mol, and Δr(CH) = −0.1 − −0.5 pm and Δv(CH) = 30 − 80 cm⁻¹. The natural bond orbital analysis shows that these blue-shifted H-bonds are caused by three factors: large rehybridization; small direct intermolecular hyperconjugation and larger indirect intermolecular hyperconjugation; large decrease of intramolecular hyperconjugation. The topological analysis of electron density shows that in each complex there are three intermolecular critical points: there is one bond critical point between the acceptor atom Y and each hydrogen, and there is a ring critical point inside the tetragon YHCH, so these interactions are exactly H-bonding.     

Representation of Electrical Conductances for Polyvalent Electrolytes by the Quint-Viallard Conductivity Equation. Universal Curves of Limiting Conductances and Walden Products of Electrolytes in Mixed Solvents. Part 5. Symmetrical 2:2, 3:3 and Unsymmetrical 1:2, 2:1 and 1:3 Type Electrolytes

Conductivities of symmetrical and unsymmetrical electrolytes of 2:2, 3:3, 1:2, 2:1 and 1:3 types in ethanol–water and the 1,4-dioxane–water mixtures were analyzed using the Quint-Viallard conductivity equation and taking into account the ion association effect. The molar limiting conductances and the ion association constants were reexamined for various multivalent electrolytes. One non-aqueous system, methanol–ethylene glycol mixtures, was also considered. The limiting conductances were also examined in the framework of universal curves of limiting conductances and the excess Walden products introduced by the author. These new concepts in the analysis of conductance data allow the estimation of values of limiting conductances of electrolytes or ions, to give an indication about the quality of the conductivity measurements and the type of interactions expected in the systems. It was found that for any type of electrolyte only one universal curve of limiting conductances exists. In the water-rich mixtures, attractive interactions (structure-making effects) are expected when electrolytes are added to mixtures with ethanol or with 1,4-dioxane. In contrast, in ethylene glycol–methanol-rich mixtures repulsive interactions (structure-breaking effects) are more likely.     

A dielectric study of the structure of propylene glycol

The dielectric spectra of propylene glycol over the frequency and temperature ranges 10 mHz–75 GHz and 175–423 K, respectively, were analyzed using the Dissado-Hill cluster model. A correlation between relaxation processes of breaking and formation of intermolecular H-bonds in clusters was obtained. A correlation of fluctuation processes of synchronous exchange of molecules between neighboring clusters corresponded to the redistribution of H-bonds between them. The Dissado-Hill theory was used to determine the integral relaxation times, n _DH and m _DH parameters and calculate the mean dipole moments of propylene glycol clusters and the energy characteristics of processes of their rearrangement. The mean dipole moments of clusters (23617–18.65 D) were compared with those of molecules in the liquid phase (3.67–3.03 D). The apparent activation enthalpy of processes of cluster rearrangements decreased from 141.8 to 25.2 kJ/mol, the activation energy decreased from 46.03 to 18.47 kJ/mol, and the energy of orientation dipole-dipole interactions, from 3.78 to 3.45 kJ/mol as the temperature increased.     

IR spectroscopic study of molecular associates of mesogenic cyanophenyls

Molecular association greathy affects the physicochemical properties of mesogenic cyanophenyls, which are currently widely used as molecular materials for optoelectronics. This paper reports on a polythermal IR spectroscopic study of molecular association for mesogenic alkyl/alkoxycyanobiphenyls and their hydrated and heteroaromatic analogs in nonpolar solutions, low-temperature inert matrices, and molecular condensate layers in the temperature ranges of 5–10 and 80–330 K. Correlation of the thermodynamic parameters of association with molecular structure of cyanophenyls is established. M. V. Lomonosov Moscow State University. Translated fromZhurnal Strukturnoi Khimii, Vol. 39, No. 3, pp. 395–400, May–June, 1998. This work was carried out in the framework of the Federal Program “Universities of Russia” and the International Scientific Collaboration Program OMMEL.     

Modes of coordination and stereochemistry of the NO3 − anions in inorganic nitrates

Stereochemical features of 950 nitrate groups in the structures of 365 inorganic nitrates were analyzed using TOPOS software. The types of coordination of nitrate groups are systematized by means of Voronoi-Dirichlet polyhedra and the method of intersecting spheres. Terminal coordination (53% of the total number of nitrate groups), most of all terminal bidentate coordination (47%) was found to prevail. Bridging nitrate groups occur less frequently (20%). A considerable number of nitrate groups are not incorporated in the coordination sphere of the complexing atom but form H-bonds or bonds of mainly ionic nature (27%). A number of metal cations show clear-cut tendency for a certain mode of coordination of the NO₃ group. Criteria for classification of nitrate groups into four types (slightly distorted groups and groups with monodentate, bidentate and asymmetric type distortion) are proposed. Structural features of nitrate groups depending on the mode of coordination are considered. The geometry of mono- or bidentate nitrate groups can differ appreciably from the typical one because of participation of terminal oxygen atoms in ionic or hydrogen bonds. Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 3, pp. 429–440, March, 2008.     

Recent Advances in the Description of the Structure of Water, the Hydrophobic Effect, and the Like-Dissolves-Like Rule

 Following a critical survey of the vast recent literature, the state of the art may be summarized as follows: (A) Water structure. The key is appreciating the next-nearest neighbour aspect. Thus, liquid water may be conceived as a fluctuating mixture of broadly two groups of structure elements: (i) an open ice-I_h-type outer neighbour bonding at about 4.5 ? and (ii) a dense ice-II-type outer neighbour bonding at about 3.4 ?. On the other hand, the nearest neighbour distance of about 2.8 ? and the number of these neighbors (4) is very similar in the solid and liquid state. The characterization of the two states may be directed either by the geometry of the H-bonds (more linear H-bonds in (i) and more bent H-bonds in (ii) or by the bonding forces operating (H-bonding favours the ordered open state (i), oxygen–oxygen interactions favour the random dense state (ii). Basically, the nature of liquid water can be understood in terms of a competition between H-bond (Coulomb) and dispersion (van der Waals) forces. Since the bonding characteristics in crystalline phases carry over to the liquid state, any molecular dynamics (MD) model of the liquid would have first of all to reproduce well the ice polymorph structures under appropriate thermodynamic conditions.     

Ab initio HF and DFT calculations on an organic non-linear optical material

The molecular geometric optimization, vibrational frequencies, and gauge-including atomic orbital (GIAO) ¹H and ¹³C chemical shift values of 3-[(1E)-N-ethylethanimidoyl]-4-hydroxy-6-methyl-2H-pyran-2-one have been investigated by using ab initio Hartree–Fock (HF) and density functional method (B3LYP: Becke-3-Lee–Yang–Parr) with 6–31G(d) and 6–31++G(d,p) basis sets. Also, the first hyperpolarizabilities have been calculated at the HF and B3LYP levels employing the corresponding basis sets. To understand this phenomenon in the context of molecular orbital picture, we examined the molecular HOMOs and molecular LUMOs generated via HF and B3LYP levels. The computed vibrational frequencies are used to determine the types of molecular motions associated with each of the experimental bands observed. Data of 3-[(1E)-N-ethylethanimidoyl]-4-hydroxy-6-methyl-2H-pyran-2-one display significant second-order molecular nonlinearity and provide the basis for design of efficient nonlinear optical materials.     

Structure of guest-host complexes of β-cyclodextrin with arenes: a quantum-chemical study

The structure of β-cyclodextrin (β-CD), as well as the structure and energetics of β-CD-naphthalene, β-CD-fluorene, β-CD-phenanthrene, β-CD-cyclohexane (1:1), and β-CD-naphthalene (2:2) inclusion complexes was studied by the semiempirical MNDO/PM3 method. Calculations of a β-CD-naphthalene-cyclohexane (1:1:1) complex were also performed. The minimum heat of formation was found for the symmetric β-CD conformation withC ₇ symmetry axis. The structure is stabilized by the ring of interunit H-bonds formed by the protons of the 2-OH groups and the O atoms of the 3′-OH groups of the glucose units. Preferableness of this orientation of interunit H-bonds was confirmed byab initio calculations of the molecule of α-(1–4)-glucobiose (maltose) in the MP2/6-31G(d,p)//6-31G(d,p) approximation. The formation of any inclusion compounds of β-CD with arenes is energetically favorable: the complexation energy varies in the range −9 to −12 kcal mol⁻¹. Among complexes with naphthalene, that of composition 2:2 is the most energetically favorable, which is in agreement with experimental data. In this complex, β-CD exists as a dimer of the “head-to-head” type, in which both partners are linked by a system of H-bonds. The structure of the “head-to-head” dimer of β-CD was simulated byab initio calculations of the H-bonded dimer of α-d-glucose in the RHF/6-31G(d,p) approximation. In the dimer, both components are linked by a pair of H-bonds formed by the protons of the 3-OH groups and the O atoms of the, 2-OH groups. The dimerization energies obtained fromab initio and semiempirical MNDO/PM3 and AM1 calculations differ by about 2.5 times (8.6vs 3.2 and 3.8 kcal mol⁻¹, respectively).     

C–H...O and C–H...N interactions in RNA structures

Small molecule studies indicate that C–H...X interactions (X: O,N) constitute weak H-bonds. We have performed a comprehensive analysis of their occurrence and geometry in RNA structures. Here, we report on statistical properties of the total set of interactions identified and discuss selected motifs. The distance/angle distribution of all interactions exhibits an excluded region where the allowed C–H...X angle range increases with an increasing H...X distance. The preferred short C–H...X interactions in RNA are backbone-backbone contacts between neighbour nucleotides. Distance/angle distributions generated for various interaction types can be used for error recognition and modelling. The axial C2′(H)...O4′ and C5′(H)...O2′ interactions connect two backbone segments and form a seven-membered ring that is specific for RNA. An AA base pair with one standard H-bond and one C–H...N interaction has been identified in various structures. Despite the occurrence of short C–H...X contacts their free energy contribution to RNA stability remains to be assessed. Received: 17 May 1998 / Accepted: 4 August 1998 / Published online: 2 November 1998     

Structural properties of liquidN-methylformamide

Monte Carlo simulation of liquidN-methylformamide was carried out at 298 K. The atom-atom spatial distribution functions, concentrations of closed cycles of H-bonds, radial distribution functions of geometric centers of the cycles, and other characteristics of the system of hydrogen bonds and the network built of the lines connecting neighboring molecules were calculated. The effects of electrostatic and van der Waals interactions as well as molecular conformations on the regularities of mutual arrangement of the molecules were investigated. It was found that open chains of H-bonds dominate over closed cycles. Spatial structure of liquidN0methylformamide is determined by packing of the molecules and steric factors and is close to the structure of a random closely packed system of soft spheres. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 2, pp. 235–247, February, 2000.     

The influence of universal and specific interactions on structural properties of liquid formamide

Monte Carlo simulation of the structure of liquid formamide at 298 K was carried out. Intermolecular interactions were calculated using five different potentials. No essential changes in the spatial structure and topological properties of the network of hydrogen bonds of liquid formamide occur upon varying the electrostatic intermolecular interactions, strength of H-bonds, and temperature. Fragments of crystal structure are partly retained in liquid formamide. It was found that the network of H-bonds is structurally inhomogeneous and contains long-lived associates of closed cycles of H-bonds as well as tree-like and chain-like structures. The energy, topological, and statistical characteristics of closed cycles of H-bonds were determined. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 12, pp. 2227–2236, December, 1999.     

Membrane-active properties and antiradical activity of gossypol and its derivatives

A novel asymmetric gossypol derivative was synthesized. The antioxidant activity of gossypol and certain of its derivatives at the aldehyde groups and the interaction of these compounds with model membranes were studied. It was shown that the antiradical and membrane activities of the gossypol derivatives were determined by the structure of the substituent and that gossypol and its derivatives were partially localized in the lipid bilayer and possibly induced formation of a new interdigitating phase. Published in Khimiya Prirodnykh Soedinenii, No. 3, pp. 265–266, May–June, 2008.