Explanation of Ionic Sequences in Various Phenomena. VI. The Formation and Destruction of Helices in Bovine Plasma Albumin in Neutral and Acidic Solutions

Abstract

The structure of bovine plasma albumin (BPA) was examined by optical rotatory dispersion studies at both low (pH 1.5 and 2.0) and high (pH 9.0) pH values in various aqueous salt solutions. The resulting cationic sequences were compared to those observed by Pedersen for values of the sedimentation constant. At pH 9.0 the destruction of the “helix” produces an acidic sequence. The relative pH position of the “helix” transition, the fact that addition of salt increases the apparent helical content of BPA, and the observed acidic-type of sequence rule out the possibility of (1)ionic bonds between carboxylate and ?-amino groups, (2) hydrophobic bonds, or (3) hydrogen bonds between peptide linkages as major contributing forces in the formation of the helix. The stability of the “helix” in BPA between pH 3.0 and 9.0 must therefore be due to hydrogen bonds between carboxylate ions and hydroxyl groups such as those of serine, threonine, and tyrosine. Repulsive forces between the positively charged groups on BPA strengthen these bonds by preventing the expanded form of BPA from collapsing. At pH 2.0 two types of sequences were observed: The s⁰ _{20, w}, [α]_D and a₀ values gave an acidic-type cationic sequence. The b₀ (helix content), λ_c and [λ]₂₃₃ values gave essentially a nonpolar sequence. The nonpolar or hydrophobic salting-out sequences show that the formation of hydrophobic bonds at pH 2.0 hinders the formation of the helix or folded structure. The acidic sequences show that hydrogen bonds between carboxylic acid groups stabilize both the apparent helix or helices and the intermolecular aggregation of the BPA molecules. From a comparison of the S⁰ ₂₀,w values and the helical content of BPA at pH 9.0 it is also concluded that the formation of these apparent helices or folded structures expands or stiffens the BPA molecule.     

Vibrational analysis of sodium α-, β- and γ-hydroxybutyrates. Inter- and intramolecular hydrogen bonds

The infrared and Raman spectra of sodium α-, β- and γ-hydroxybutyrates and their deuterated analogues are examined in the 4000-100 cm⁻¹ range and an assignment of the fundamental vibrations is given. Based on the localization of the asymmetric stretching vibrations ν_asOH and the out-of-plane vibration γOH, inter- and/or intramolecularly hydrogen-bonded forms are proposed: the low frequencies of ν_asOH (<3200 cm⁻¹) and high frequencies of γOH (≈800 cm⁻¹) argue in favour of the existence of intramolecular hydrogen bonding. Sodium α-hydroxybutyrate exhibits as a chelate ring with an intramolecular hydrogen bond between hydroxyl and carboxyl groups, whereas sodium, β-hydroxybutyrate has the two association forms with inter- and intramolecular hydrogen bonds. Sodium γ-hydroxybutyrate exists as a hydrogen-bonded polymer, with an intermolecular hydrogen bond between the hydroxyl groups and between the hydroxyl and carbonyl groups. At a crystallization temperature above 50°C, only the α- salt showed a structural change indicating the existence of intra- and intermolecular hydrogen bonds. This result is confirmed by differential scanning analysis.     

Neutral and ionic hydrogen bonding in Schiff bases

Low-temperature, high-resolution X-ray studies of charge distributions in the three Schiff bases, the dianil of 2-hydroxy-5-methylisophthaldehyde, 3,5-dinitro-N-salicylidenoethylamine and 3-nitro-N-salicylidenocyclohexylamine, have been carried out. These structures exhibit interesting weak interactions, including two extreme cases of intramolecular hydrogen bonds that are ionic N(+)-H...O- and neutral O-H...N in nature. These two types of hydrogen bond reflect differences in geometrical parameters and electron density distribution. At the level of geometry, the neutral O-H...N hydrogen bond is accompanied by an increase in the length of the C(1)-O(1) bond, opening of the ipso-C(1) angle, elongation of the aromatic C-C bonds, shortening of the C(7)-N(2) bond and increased length of the C(1)-C(7) bond, relative to the ionic hydrogen bond type. According to the geometrical and critical point parameters, the neutral O-H...N hydrogen bond seems to be stronger than the ionic ones. There are also differences between charge density parameters of the aromatic rings consistent with the neutral hydrogen bond being stronger than the ionic ones, with a concomitant reduction in the aromaticity of the ring. Compounds with the ionic hydrogen bonds show a larger double-bond character in the C-O bond than appears in the compound containing a neutral hydrogen bond; this suggests that the electronic structure of the former pair of compounds includes a contribution from a zwitterionic canonical form. Furthermore, in the case of ionic hydrogen bonds, the corresponding interaction lines appear to be curved in the vicinity of the hydrogen atoms. In the 3-nitro-N-salicylidenocyclohexylamine crystal there exists, in addition to the intramolecular hydrogen bond, a pair of intermolecular O...H interactions in a centrosymmetric dimer unit.     

The assignment of IR absorption bands due to free hydroxyl groups in cellulose

Interpretation of the IR hydroxyl absorption bands in cellulose has been limited to the inter- and intramolecularly hydrogen-bonded hydroxyl groups in the crystalline form. This paper attempts to assign IR frequencies due to ‘free‘ or non-hydrogen bonded hydroxyl groups by using a curve fitting method. The almost completely methylated cellulose derivatives of tritylcellulose (previously used in related studies) exhibited small IR bands due to hydroxyl groups. The IR bands were assumed to appear under stereohindered conditions and thus resulted in a mixture of bands which included the contribution of free hydroxyl groups. The curve fitting method deconvoluted the IR bands into three bands in the OH stretching region: they were interpreted in terms of free or hydrogen bonded hydroxyl groups. The assignments were confirmed by comparison of an almost completely methylated derivative with partially methylated derivatives having different degrees of substitution. In addition, intramolecular hydrogen bonds involving OH at the C-3, C-2 and C-6 positions were shown to be easily formed, even between extremely small numbers of unsubstituted hydroxyl groups present, and thus cause perturbation of the specific deconvoluted band. This revised version was published online in August 2006 with corrections to the Cover Date.     

Structural characteristics of phenol formaldehyde novolak resin depending on polycondensation type using molecular simulation

Phenol formaldehyde novolak resins have various structures depending on the polycondensation types. Their structures were characterized using molecular mechanics and molecular dynamics. Dimer, tetramer, hexamer, octamer, and decamer of the resins with the ortho–ortho, ortho–para, and para–para sequences were calculated. The ortho–ortho resins have the structural characteristics of intramolecular hydrogen bonds between hydroxyl groups of the adjacent phenolic units. For the ortho–para and para–para resins, the intramolecular hydrogen bonds are formed mainly between hydroxyl groups of the backbone phenolic units. The para–para resins also have intramolecular hydrogen bonds between hydroxyl groups of the branched phenolic units. A factor determining the structural characteristics of the resins was found to be the geometry of the basic unit (dimer). The order of the end‐to‐end distances between hydrogen atoms on the para‐position of the basic units of the resins is ortho–ortho resin < ortho–para resin < para–para resin. The calculational results were found to be consistent with the gel permeation chromatography (GPC) analysis. Copyright © 2001 John Wiley & Sons, Ltd.     

Hydrophobic Effects in Adsorptive Protein Immobilization

In an aqueous environment, noncovalent polar bonding (i.e., through ionic, charge transfer, or hydrogen bonds) may be assumed to be relatively weak because of thestrong chargesolvating and hydrogen-bonding ability of water. It has been suggested, the refore, that apolar (hydrophobic) forces may be the most important single factor providing the driving force for noncovalent intermolecular interactions in an aqueous milieu [1, 2]. However, in aqueous solutions electrostatic interaction may become important when the pertaining charges are shielded by accompanying hydrophobic groups from the quenching effect of water [1]. In this connection it may be pointed out that, on account of the low dielectric constant of the hydrophobic interior of a protein, intramolecular interaction of oppositely charged surface groups can be strong indeed [3].     

Ionic hydrogen bonds controlling two-dimensional supramolecular systems at a metal surface

Hydrogen-bond formation between ionic adsorbates on an Ag(111) surface under ultrahigh vacuum was studied by scanning tunneling microscopy/spectroscopy (STM/STS), X-ray photoelectron spectroscopy (XPS), near-edge X-ray absorption fine structure (NEXAFS), and molecular dynamics calculations. The adsorbate, 1,3,5-benzenetricarboxylic acid (trimesic acid, TMA), self-assembles at low temperatures (250-300 K) into the known open honeycomb motif through neutral hydrogen bonds formed between carboxyl groups, whereas annealing at 420 K leads to a densely packed quartet structure consisting of flat-lying molecules with one deprotonated carboxyl group per molecule. The resulting charged carboxylate groups form intermolecular ionic hydrogen bonds with enhanced strength compared to the neutral hydrogen bonds; this represents an alternative supramolecular bonding motif in 2D supramolecular organization.     

Synergy of intramolecular hydrogen-bonding network in myo-inositol 2-monophosphate: theoretical investigations into the electronic structure, proton transfer, and pKa

This work demonstrates the pivotal role that an intramolecular hydrogen-bonding network (intra-HBN) plays in the determination of the conformation of myo-inositol 2-monophosphate (Ins(2)P1), a member of the inositol phosphate family of compounds, which are important participants in the role that phosphates play in biological and environmental chemistry. For biologically significant compounds that contain phosphate and hydroxyl groups, Ins(2)P1 is a model system for studying both the primary forces that determine their conformations and their chemical properties from the effect of phosphate group addition. We performed ab initio calculations to determine the intra-HBN within important thermally accessible conformations for neutral Ins(2)P1 and its anions, Ins(2)P1(1-) and Ins(2)P1(2-). The results show that the global minima prefer 1a/5e structures where the phosphate group is in the axial position with all -OH groups in the equatorial positions. The calculations of transition state structures for ring inversion at each ionization state predict an activation energy of 18.16 kcal/mol for the neutral species in water, while the activation energy is lower for the charged compounds, 15.62 kcal/mol for Ins(2)P1(1-) and 12.48 kcal/mol for Ins(2)P1(2-). The pK(a) values of Ins(2)P1 were calculated by modeling the solvent as a polarizable continuum medium (PCM) and as explicit solvent molecules. These values are in good agreement with experimental data. A novel four-center pattern of hydrogen bonding was found to stabilize the system. The intramolecular proton transfer across a low barrier hydrogen bond between the charged phosphate and hydroxyl groups was found to occur under standard conditions with an activation energy that is less than 0.5 kcal/mol.     

Spectroscopic Evidence for Clusters of Like‐Charged Ions in Ionic Liquids Stabilized by Cooperative Hydrogen Bonding

Direct spectroscopic evidence for hydrogen‐bonded clusters of like‐charged ions is reported for ionic liquids. The measured infrared O?H vibrational bands of the hydroxyethyl groups in the cations can be assigned to the dispersion‐corrected DFT calculated frequencies of linear and cyclic clusters. Compensating the like‐charge Coulomb repulsion, these cationic clusters can range up to cyclic tetramers resembling molecular clusters of water and alcohols. These ionic clusters are mainly present at low temperature and show strong cooperative effects in hydrogen bonding. DFT‐D3 calculations of the pure multiply charged clusters suggest that the attractive hydrogen bonds can compete with repulsive Coulomb forces.     

Modulation of the relative reactivities of carbohydrate secondary hydroxyl groups. Modification of the hydrogen bond network

An approach towards the control of the relative regioselectivity of the secondary hydroxyl groups is presented. Original protecting groups, which are capable of specific intramolecular hydrogen bonds and are likely to modulate the partial charges of the oxygen atoms, have been developed. Qualitative NMR experiments confirmed the existence of the expected hydrogen bonds and shed light on the perturbation of the cooperative intramolecular hydrogen bond network. Further reactivity studies are presented and confirm the potential of protecting group-mediated regioselective functionalization of carbohydrates.     

Unique role of ionic liquid [bmin][BF4] during curcumin-surfactant association and micellization of cationic, anionic and non-ionic surfactant solutions

Hydrophilic ionic liquid, 1-butyl-3-methylimidazolium tetrafluoroburate, modified the properties of aqueous surfactant solutions associated with curcumin. Because of potential pharmaceutical applications as an antioxidant, anti-inflammatory and anti-carcinogenic agent, curcumin has received ample attention as potential drug. The interaction of curcumin with various charged aqueous surfactant solutions showed it exists in deprotonated enol form in surfactant solutions. The nitro and hydroxyl groups of o-nitrophenol interact with the carbonyl and hydroxyl groups of the enol form of curcumin by forming ground state complex through hydrogen bonds and offered interesting information about the nature of the interactions between the aqueous surfactant solutions and curcumin depending on charge of head group of the surfactant. IL[bmin][BF4] encouraged early formation of micelle in case of cationic and anionic aqueous surfactant solutions, but slightly prolonged micelle formation in the case of neutral aqueous surfactant solution. However, for curcumin IL [bmin][BF4] favored strong association (7-fold increase) with neutral surfactant solution, marginally supported association with anionic surfactant solution and discouraged (～2-fold decrease) association with cationic surfactant solution.     

Single particle and pair dynamics in water-formic acid mixtures containing ionic and neutral solutes: nonideality in dynamical properties

A series of molecular dynamics simulations of water-formic acid mixtures containing either an ionic solute or a neutral hydrophobic solute has been performed to study the extent of nonideality in the dynamics of these solutes for varying composition of the mixtures. The diffusion coefficients of the charged solutes, both cationic and anionic, are found to show nonideal behavior with variation of composition, and similar nonideality is also observed for the diffusion and orientational relaxation of solvent molecules in these mixtures. The diffusion coefficient of a neutral hydrophobic solute, however, decreases monotonically with increase in water concentration. We have also investigated some of the pair dynamical properties such as water-water and water-formic acid hydrogen bond relaxation and residence dynamics of water molecules in water and formic acid hydration shells. The lifetimes of water-water hydrogen bonds are found to be longer than those between formic acid carbonyl oxygen-water hydrogen bonds, whereas the lifetimes of formic acid hydroxyl hydrogen-water hydrogen bonds are longer than those of water-water hydrogen bonds. In general, the hydrogen bond lifetimes for both water-water and water-formic acid hydrogen bonds are found to decrease with increase in water concentration. Residence times of water molecules also show the same trend with increase in formic acid concentration. Interestingly, these pair dynamical properties show a monotonic dependence on composition without any maximum or minimum and behave almost ideally with respect to changes in the composition of the mixtures. The present calculations are performed with fixed-charge nonpolarizable models of the solvent and solute molecules without taking into account many-body polarization effects in an explicit manner.     

Biodegradable gemini surfactants. Correlation of area per surfactant molecule with surfactant structure

Values of the area per surfactant molecule of various single chain and gemini quaternary ammonium surfactants containing biodegradable amide and ester groups are obtained from the surface tension measurements and they are mutually compared. It was found that surfactant molecules with the ester group in their structure occupy smaller area at the air/water interface than the corresponding molecules with the amide group, mainly due to the higher conformational flexibility of ester groups. In decreasing the area per surfactant molecule value, hydrogen bonding (both inter- and intramolecular) plays a significant role when amide groups are present in the spacer of a gemini molecule. They must be separated by a polymethylene chain or a flexible group such as cyclohexane which is short enough to allow intramolecular hydrogen bonds. The flexible cyclohexane group with the amide group in single chain surfactants may lead to the formation of intermolecular hydrogen bonds among surfactant molecules which also results in the reduction of the area per surfactant molecule.     

Hydrogen Isotope Absorption in Unary Oxides and Nitrides with Anion Vacancies and Substitution

The absorption states of hydrogen isotopes in various ceramic materials were investigated by density functional theory. For pristine ceramic materials, main-group oxides do not form any bond with a hydrogen atom. However, transition metal oxides form hydroxyl groups and absorb hydrogen atoms. Main-group and transition metal nitrides form ionic bonds between a hydrogen atom and the surrounded cation. For anion-deficient ceramic materials, hydrogen atoms are negatively charged because of excess electrons induced by anion vacancies, and ionic bonds form with the surrounded cation, which stabilizes the hydrogen absorption state. N substitutional doping into oxides introduces an electron hole, while O substitutional doping into the nitrides introduces an excess of electrons. Therefore, hydrogen isotopes form covalent bonds in N-substituted oxides, and form hydride ions in O-substituted nitrides. Thus, Al₂O₃, SiO₂, CrN, and TiN are promising materials as hydrogen permeation barriers.     

Cyclic Octamer of Hydroxyl-functionalized Cations with Net Charge Q=+8e Kinetically Stabilized by a ‘Molecular Island’ of Cooperative Hydrogen Bonds

Cyclic octamers are well-known structural motifs in chemistry, biology and physics. These include covalently bound cyclic octameric sulphur, cylic octa-alkanes, cyclo-octameric peptides as well as hydrogen-bonded ring clusters of alcohols. In this work, we show that even calculated cyclic octamers of hydroxy-functionalized pyridinium cations with a net charge Q=+8e are kinetically stable. Eight positively charged cations are kept together by hydrogen bonding despite the strong Coulomb repulsive forces. Sufficiently long hydroxy-octyl chains prevent “Coulomb explosion” by increasing the distance between the positive charges at the pyridinium rings, reducing the Coulomb repulsion and thus strengthen hydrogen bonds between the OH groups. The eightfold positively charged cyclic octamer shows spectroscopic properties similar to those obtained for hydrogen-bonded neutral cyclic octamers of methanol. Thus, the area of the hydrogen bonded OH ring represents a ‘molecular island’ within an overall cationic environment. Although not observable, the spectroscopic properties and the correlated NBO parameters of the calculated cationic octamer support the detection of smaller cationic clusters in ionic liquids, which we observed despite the competition with ion pairs wherein attractive Coulomb forces enhance hydrogen bonding between cation and anion.     

带电组氨酸侧链与DNA碱基间非键作用强度的理论研究

采用MP2方法和6-31+G(d,p)基组优化得到了带有一个正电荷的组氨酸侧链与4个DNA碱基间形成的18个氢键复合物的气相稳定结构, 从文献中获取了组氨酸侧链与DNA碱基间形成的12个堆积和T型复合物的气相稳定结构, 使用包含基组重叠误差(BSSE)校正的MP2方法和aug-cc-pVTZ基组及密度泛函理论M06-2X-D3方法和aug-cc-pVDZ基组计算了这些复合物的结合能. 研究结果表明, 包含BSSE校正的M06-2X-D3方法和aug-cc-pVDZ基组能够给出较准确的结合能; 气相条件下, 组氨酸侧链与同种DNA碱基间的离子氢键作用明显强于堆积作用和T型作用, 组氨酸侧链最易通过离子氢键与胞嘧啶C和鸟嘌呤G作用形成氢键复合物, 组氨酸与胞嘧啶C和鸟嘌呤G间的T型作用强于与腺嘌呤A和胸腺嘧啶T间的离子氢键作用; 水相条件下, 组氨酸侧链与同种DNA碱基间的离子氢键作用仍明显强于堆积作用和T型作用, 组氨酸侧链更易与胞嘧啶C和鸟嘌呤G相互作用形成氢键复合物, 但是最强的组氨酸侧链与胞嘧啶C间的T型作用明显弱于与腺嘌呤A和胸腺嘧啶T间的离子氢键作用, 说明水相条件下组氨酸侧链与DNA碱基间主要通过离子氢键作用形成氢键复合物.     

Preparation, solid-state characterization, and computational study of a crown ether attached to a squaramide

[structure: see text] Crystals of a disecondary squaramide covalently linked to a crown ether presents a great variety of inter- and intramolecular nonbonded interactions including C-H/pi contacts, C-H...O and N-H...O hydrogen bonds, and pi-pi stacking between squaramide rings. Latter interaction, the stacking between squaramide rings, can be considered as an experimental evidence for the proposed aromaticity of squaramide when it is forming hydrogen bonds, either as acceptor or donor.     

Stereospecific anionically promoted transannular hydride shifts in medium-ring hydroxy ketones. Probe of their reversibility and the potential for regiocontrol

Examples are provided of stereospecific transannular oxidation-reduction processes involving the conjugate bases of delta-hydroxy ketones in a nine-membered ring setting. The ability to control the direction of these equilibria by proper modulation of the solvent environment and level of hydroxyl group protection is demonstrated. MM3-derived steric energies of the isomer pairs suggest that the equilibrium distributions are the outcome of the extent to which intramolecular hydrogen bonding forces are disrupted by polar solvent molecules when present.     

Hydrogen-bonded dimers of tetra-urea calix[4]arenes stable in THF

[structure: see text]. Whereas tetra-urea derivatives of tetra-alkoxy calix[4]arenes 1 exist as single molecules in THF, dimeric hydrogen-bonded capsules are exclusively found for the corresponding calix[4]arene derivatives 3 and 2 with two or four free hydroxyl groups. Comparison with the rigidified tetra-urea 5 suggests that this increased stability of the dimers is due to the stabilization of their four-fold symmetry by intramolecular hydrogen bonds between the phenolic hydroxyl groups.     

Hydrogen-bonded clusters and solvate structures in the supercritical CO2-water-o-hydroxybenzoic acid system: the car-parrinello molecular dynamics

Hydrogen-bonded clusters and solvate structures formed by o-hydroxybenzoic acid (o-HBA) and water in supercritical CO₂ were studied (T = 318 K, 348 K, ρ = 0.7 g/cm³). The atom-atom radial distribution functions, coordination numbers, average numbers of hydrogen bonds for individual atomic groups, and power spectrum were calculated by the Car-Parrinello molecular dynamics. Despite the high polarity of the cosolvent, the hydroxyl group of o-HBA predominantly forms intramolecular hydrogen bond, while hydrogen bonds with water involve only the atoms of carboxyl groups. The temperature effect on the stability of these bonds showed itself in different ways. The intermolecular interactions of o-HBA with carbon dioxide were found to be weaker than those with water. It was established that the Lewis acid-Lewis base interactions between CO₂ and the hydroxyl group of the solute increase with increasing temperature. Instantaneous configurations illustrating the temperature effects on the molecular structures were obtained.