Vibrational spectra of alpha-amino acids in the zwitterionic state in aqueous solution and the solid state: DFT calculations and the influence of hydrogen bonding

The zwitterionic forms of the two simplest alpha-amino acids, glycine and l-alanine, in aqueous solution and the solid state have been modeled by DFT calculations. Calculations of the structures in the solid state, using PW91 or PBE functionals, are in good agreement with the reported crystal structures, and the vibrational spectra computed at the optimized geometries provide a good fit to the observed IR and Raman spectra in the solid state. DFT calculations of the structures and vibrational spectra of the zwitterions in aqueous solution at the B3-LYP/cc-pVDZ level were found to require both explicit and implicit solvation models. Explicit solvation was modeled by inclusion of five hydrogen-bonded water molecules attached to each of the five possible hydrogen-bonding sites in the zwitterion and the integration equation formalism polarizable continuum model (IEF-PCM) was employed, providing a satisfactory fit to observed IR and Raman spectra. Band assignments are reported in terms of potential-energy distributions, which differ in some respects to those previously reported for glycine and l-alanine.     

The influence of hydrogen bonding on the physical properties of ionic liquids

Potential applications of ionic liquids depend on the properties of this class of liquid material. To a large extent the structure and properties of these Coulomb systems are determined by the intermolecular interactions among anions and cations. In particular the subtle balance between Coulomb forces, hydrogen bonds and dispersion forces is of great importance for the understanding of ionic liquids. The purpose of the present paper is to answer three questions: Do hydrogen bonds exist in these Coulomb fluids? To what extent do hydrogen bonds contribute to the overall interaction between anions and cations? And finally, are hydrogen bonds important for the physical properties of ionic liquids? All these questions are addressed by using a suitable combination of experimental and theoretical methods including newly synthesized imidazolium-based ionic liquids, far infrared spectroscopy, terahertz spectroscopy, DFT calculations, differential scanning calorimetry (DSC), viscometry and quartz-crystal-microbalance measurements. The key statement is that although ionic liquids consist solely of anions and cations and Coulomb forces are the dominating interaction, local and directional interaction such as hydrogen bonding has significant influence on the structure and properties of ionic liquids. This is demonstrated for the case of melting points, viscosities and enthalpies of vaporization. As a consequence, a variety of important properties can be tuned towards a larger working temperature range, finally expanding the range of potential applications.     

Effect of hydrogen bonding on the physicochemical properties and bilayer self-assembly formation of N-(2-hydroxydodecyl)-L-alanine in aqueous solution

The aggregation behavior of N-(2-hydroxydodecyl)-L-alanine (C12HAla) and N-(n-dodecyl)-L-alanine (C12Ala) was studied in aqueous buffer (pH 12) over a concentration range above their critical aggregation concentration (cac). The C12HAla amphiphile has two cacs in contrast to only one cac value for C12Ala. The micropolarity and microviscosity of the aggregates were studied by use of pyrene and 1,6-diphenyl-1,3,5-hexatriene, respectively, as fluorescent probes. Dynamic light scattering was used to measure the average hydrodynamic diameter and size distribution of the aggregates. Large size, high microviscosity, and low micropolarity values of the aggregates suggested the formation of bilayer structures in dilute solutions of C12HAla. In contrast, C12Ala was observed to form micelles. Transmission electron micrographs of dilute and moderately concentrated solutions of C12HAla revealed the existence of spherical vesicles and branching tubular structures, respectively. Comparison of the aggregation behavior of these amphiphiles to that of C12Ala and the FT-IR spectrum suggested that intermolecular hydrogen-bonding interactions between adjacent hydrocarbon chains through the -OH and -NH- groups of C12HAla are responsible for bilayer formation. The mechanism of nanotube formation was discussed. The temperature dependence of aggregate formation of the amphiphile also was investigated.     

3,4,5-三羟基苯甲酸二聚体氢键结构性质

分子间相互作用在生物和材料等科学中发挥着关键作用,研究分子间相互作用的本质意义重大。氢键是分子间相互作用的一种主要形式,在确定分子构象和晶体结构以及生物分子尤其是核酸和蛋白质的结构功能中起着重要作用[1-3]。苯甲酸衍生物广泛存在于生物大分子内,与生物活性离子通过氢键作用等改变生物活性分子的活性功能,研究苯甲酸衍生物分子间氢键相互作用对于了解生物体内的化学现象具有重要意义。研究表明菱角的抗肿瘤作用明显,实验上已经从菱角中成功提取了活性单体化合物:3,4,5-三羟基苯甲酸二聚体[4],理论研究标题化合物的氢键结构与氢…     

The influence of hydrogen bonding on the preparation and mechanical properties of PS-diblock copolymer blends

In this article, the preparation of nanosized core-shell particles to induce ductility in polystyrene (PS) is described. FTIR spectroscopy, solid-state NMR spectroscopy, and DSC were used to examine the extent of miscibility of PS and poly(butylacrylate)-b-polyolefin diblock copolymers in a blend in which PS was chemically modified by copolymerization with 0.5–5 mol % of p-(hexafluoro-2-hydroxy isopropyl) styrene (HFS). Hydrogen bonding between the hydroxyl-groups and the carbonyl-groups of polybutylacrylate enhanced the miscibility and lead to randomly distributed polyolefin particles surrounded by a homogeneous PBA/PS matrix. Morphological parameters such as the size of the dispersed phase or extent of interpenetration between the components are controllable simply by changing the amount of interacting groups in the blend. The mechanical properties of the prepared blends were also studied. The intrinsic deformation behavior was investigated by compression tests, whereas the microscopic mode of deformation was studied by time-resolved small-angle X-ray scattering. It was shown that the macroscopic strain at break depends to a large extent on the diblock copolymer content and the degree of demixing between the rubber shell and PS matrix. Brittle behavior was observed for PS blends that contain more than 3 mol % HFS and show complete miscibility between the PS matrix and acrylate shell. For the blends showing partial miscibility, the compression tests demonstrated a pronounced decrease in strain softening with increasing diblock copolymer concentration. Furthermore, it was illustrated that dependent on the degree of demixing the microscopic deformation mode changes from crazing to cavitation induced shear yielding. © 2004 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 42: 2137–2160, 2004     

The hydrogen bond in the solid state

The hydrogen bond is the most important of all directional intermolecular interactions. It is operative in determining molecular conformation, molecular aggregation, and the function of a vast number of chemical systems ranging from inorganic to biological. Research into hydrogen bonds experienced a stagnant period in the 1980s, but re-opened around 1990, and has been in rapid development since then. In terms of modern concepts, the hydrogen bond is understood as a very broad phenomenon, and it is accepted that there are open borders to other effects. There are dozens of different types of X-H.A hydrogen bonds that occur commonly in the condensed phases, and in addition there are innumerable less common ones. Dissociation energies span more than two orders of magnitude (about 0.2-40 kcal mol(-1)). Within this range, the nature of the interaction is not constant, but its electrostatic, covalent, and dispersion contributions vary in their relative weights. The hydrogen bond has broad transition regions that merge continuously with the covalent bond, the van der Waals interaction, the ionic interaction, and also the cation-pi interaction. All hydrogen bonds can be considered as incipient proton transfer reactions, and for strong hydrogen bonds, this reaction can be in a very advanced state. In this review, a coherent survey is given on all these matters.     

Vibrational spectra and structures of urazole and 4-methylurazole: DFT calculations of the normal modes in aqueous solution and in the solid state,and the influence of hydrogen bonding

Solid-state IR and Raman as well as aqueous solution state Raman spectra are reported for urazole, 4-methylurazole and their deuterated derivatives. DFT calculations, at the B3-LYP/cc-pVTZ level, established that the structures and vibrational spectra of the molecules can be interpreted using models with hydrogen-bonded water molecules, in conjunction with the polarizable continuum solvation method. The vibrational spectra were computed at the optimised molecular geometry in each case, enabling normal coordinate analysis, which yielded satisfactory agreement with the experimental IR and Raman data. Computed potential energy distributions of the normal modes provided detailed vibrational assignments. Solid-state pseudopotential-plane-wave DFT calculations, using the PW91 functional were also carried out, reflecting the importance of intermolecular hydrogen bonding in the solid state.     

Synthesis of a biphenyl library for studies of hydrogen bonding in the solid state

A biphenyl library incorporating amide and sulfonamide groups has been synthesised via microwave-mediated Suzuki-Miyaura couplings. Many derivatives were crystallised from dichloromethane/methanol and analysed by single crystal X-ray diffraction. An interesting structure was obtained for N-(4′-methylbiphenyl-4-yl)acetamide with Z′=6 and hydrogen-bonding networks of the type N-H^…O in the unit cell.     

The influence of intermolecular interactions in n-pentane-alkane-1-ol systems on their physicochemical properties

The Helmholtz energy of dipole-dipole interaction (ΣΔ_d F) and its long-range (Δ_d F°) and short-range (Δ_d F*) components were calculated for n-pentane-alkane-1-ol (from methanol to dodecane-1-ol) systems at 298.15 K using the Winkelmann statistical model theory of liquid dielectrics. It was shown that the longer the alkane-1-ol hydrocarbon radical, the greater the extent to which the properties of the systems with n-pentane were determined by the structure of n-alkane.     

Self-assembly of helical supramolecular channels from chiral aminopyrimidine hydrogen bonding motifs in the solid state

The H-bond mediated self-assembly of the chiral C₂-symmetric bis-(2-amino-4-chloro-pyrimidines) 3 and 4 allows for the molecular recognition directed generation of helical superstructures. In the former case, unoccupied channel structures defined by the cylindrical interior of the derived supramolecular helix result, as revealed by X-ray crystallographic analysis using a synchrotron source. Upon crystallization, racemic 3 spontaneously resolves to form homochiral crystals exhibiting a helical packing motif identical to that determined for optically pure 3. The data provide insight into the interplay of the different structural and interactional features of the molecular components to the generation of the channel structure and suggest design strategies toward porous organic molecular solids of variable size.     

Hydrogen bonding of adenine with benzoic acids in the solid state. An FTIR study

Complex formation by hydrogen bonding, in the solid-state, between adenine and benzoic acid derivatives, was studied by IR spectroscopy.     

The influence of intramolecular hydrogen bonding on the structure and E ↔ Z photoisomerization of urocanic acid derivatives

The molecular structures and E ? Z photoisomerization reactions of methyl urocanate and several urocanamides were investigated. All of the Z isomers possess intramolecular hydrogen bonds. The intramolecular hydrogen bonds may influence the efficiency of photoisomerization but do not totally inhibit its occurrence. The relative energies of the electronic absorption of the E and Z isomers depends on the mode of hydrogen bonding and are accurately predicted in the case of methyl urocanate using INDO/S-CI calculations. The solvent dependence of the absorption spectra of methyl urocanate can be related to the effects of inter- and intramolecular hydrogen bonding.     

Model pharmaceutical co-crystallization: Guest-directed assembly of caffeine and aromatic tri-hydroxy and dicarboxylic acids into different heteromolecular hydrogen bonding networks in solid state

Three model pharmaceutical caffeine-containing co-crystals of 1,3,5-trihydroxybenzene (phloroglucinol), isophthalic acid and 5-hydroxyisophthalic acid were synthesized and characterized via single-crystal X-ray diffraction. The three crystalline forms reported are an anhydrous co-crystal and other two are co-crystal hydrates. Also their binding properties were studied by UV-vis analysis. In each of these structures, an organised intermolecular hydrogen bonding motif was observed. A comparison of hydrogen bonding motifs in the crystal sheets was presented.     

The structure of glibenclamide in the solid state

The structure of glibenclamide, 5‐chloro‐N‐(2‐{4‐[(cyclohexylamino)carbonyl] aminosulfonyl}phenyl) ethyl)‐2‐methoxybenzamide, an important antidiabetic drug, has been studied both in solution and in the solid state by a combination of NMR spectroscopy and theoretical calculations. The possibility that glibenclamide suffers a tautomerization under melting to afford a desmotrope was rejected. Copyright © 2012 John Wiley & Sons, Ltd.     

The influence of solvation on short strong hydrogen bonds: a density functional theory study of the Asp-His interaction in subtilisins

The effect of a structural water molecule on the electronic nature of the His64-Asp32 hydrogen bond in subtilisins is examined by DFT calculations; the structural water is found to favor a short strong hydrogen bond in the catalytic triad in sharp contrast to some current beliefs.     

The interaction of solid surfaces in aqueous systems

The interaction between two high-grade polished fused silica plates separated by a thin layer of aqueous LiCl, NaCl and KCl solution, respectively, was determined by means of a selfdeveloped method. Concerning the repulsion created by overlap of the electrical double layers excellent agreement with the DLVO theory down to separation of about 5 nm were found. For still smaller separations a relatively strong additional repulsion arises which according to experimental evidence might be assigned to the overlap of hydration layers emanating chiefly from the alkali metal halide ions adsorbed onto the silica surfaces. Our results agree well with those obtained by Israelachvili et al. and Pashley, who used mica sheets.     

Alteration of the physicochemical properties of catalysts based on aqueous solutions of Mo-V-P heteropoly acids in redox processes

Selective catalytic oxidation of various organic substrates with O₂ in the presence of aqueous solutions of Mo-V-P heteropoly acids (HPA) is carried out via two stages in separate reactors. In stage (1), a substrate is oxidized into a desired product while HPA is reduced. The reduced form of HPA is oxidized with O₂ in stage (2). A set of the physicochemical properties of the homogeneous catalyst has been found to alter continuously during these redox processes. Using a solution of the modified high-vanadium HPA (H₁₂P₃Mo₁₈V₇O₈₅), we demonstrate that the density, viscosity, and pH of this solution reach their maxima after reaction (1) and attain their minima after reaction (2). On the contrary, the redox potential of the solution is minimum after reaction (1), and maximum after reaction (2). All alterations of the physicochemical properties of the catalyst are found to be completely reversible.     

Intermolecular charge transfer and hydrogen bonding in solid furan

The calculated structures of furan as a monomer, a dimer that was isolated from the crystal structure, and the full crystal structure have been thoroughly investigated by a combination of density functional theory (DFT) calculations and inelastic neutron scattering (INS) measurements. To improve our understanding of the nature and magnitude of the intermolecular interactions in the solid, the atoms in molecules (AIM) theory has been applied to the dimer and a cluster of eight monomers. After a careful topological study of the theoretical charge density and of its Laplacian, we have established the existence of C-H...pi, C-H...O, and H...H interactions between adjacent molecules in solid furan. The electron distribution has also been analyzed by performing natural bond orbital (NBO) calculations for the monomer and a H-bonded dimer. When the hydrogen bond is established between two adjacent furan rings, some electron charge is transferred from the pi electronic system of one furan ring to the other molecule in the dimer. This result provides a model of the interaction between end groups of neighboring chains of polyfuran and could be applicable to other conjugated polymers where the pi system is responsible for their conducting properties. To determine how the intermolecular bonds in the solid affect the vibrational dynamics in the periodic system, INS data were analyzed by performing molecular and periodic density functional calculations. Reasonable agreement is achieved, although we note that the poorest agreement is for modes involving hydrogen atoms.     

Transport properties of solid state crown ether channel systems

Single crystals of [(H₂O)⊂(DB18C6)(μ₂-H₂O)_2/2][(H₃O)⊂(DB18C6)(μ₂-H₂O)_2/2]I₃ 1 were shown to possess ideally stacked crown ether molecules which form channels running in one direction through the solid state structure. By immersion of single crystals of 1 into NaOH, ion exchange takes place to yield the compound [(Na)⊂(DB18C6)(μ₂-H₂O)_2/2][(Na)⊂(DB18C6)(μ₂-OH)_2/2]I₃ 2, with slightly but significantly different cell parameters. Both compounds were tested for transport properties through these channels by using two different devices, one for water transport, the other for NaOH transport, through single crystals of 1 and 2, respectively. The results indicate that transport can take place via a hopping mechanism.