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.     

Hydration profiles of aromatic amino acids: conformations and vibrations of L-phenylalanine-(H2O)n clusters

IR-UV double resonance spectroscopy and ab initio calculations were employed to investigate the structures and vibrations of the aromatic amino acid, L-phenylalanine-(H(2)O)(n) clusters formed in a supersonic free jet. Our results indicate that up to three water molecules are preferentially bound to both the carbonyl oxygen and the carboxyl hydrogen of L-phenylalanine (L-Phe) in a bridged hydrogen-bonded conformation. As the number of water molecules is increased, the bridge becomes longer. Two isomers are found for L-Phe-(H(2)O)(1), and both of them form a cyclic hydrogen-bond between the carboxyl group and the water molecule. In L-Phe-(H(2)O)(2), only one isomer was identified, in which two water molecules form extended cyclic hydrogen bonds with the carboxyl group. In the calculated structure of L-Phe-(H(2)O)(3) the bridge of water molecules becomes larger and exhibits an extended hydrogen-bond to the pi-system. Finally, in isolated L-Phe, the D conformer was found to be the most stable conformer by the experiment and by the ab initio calculation.     

Construction of halogen and hydrogen bond‐based multicomponent nanostructures at liquid‐solid interface

The cooperative effect of hydrogen and halogen bonds on the 2‐dimensional molecular arrangement of highly oriented pyrolytic graphite has been studied by scanning tunneling microscopy. The scanning tunneling microscopy observations demonstrate that the self‐assembled hydrogen‐bonded molecular chicken‐wire networks of trimesic acid have been significantly transformed after annealing and the introduction of tribromobenzene guest molecules. Bromine atoms and carboxyl groups were found to form 2 different multicomponent structures via hydrogen and halogen bonds. Owing to the effect of halogen and hydrogen bonds, tribromobenzene with trimesic acid formed the 3‐fold symmetry networks.     

Special features of the hydration of siderophores of the ferrichrome family

An investigation of the hydration of the siderophore ferrichrome A has been carried out by the Monte-Carlo method. It has been shown that the ligands and the iron atom interact weakly with water. The four carbonyl groups of the peptide ring of the molecule, with which hydrogen bonds are formed by six water molecules, and the side-chain carboxyl groups, with each of which a hydrogen bond is formed by one water molecule, interact most strongly with the aqueous phase. Evaluations of the free energy of hydration of the molecule have been carried out. The different activities of the siderophores of the ferrichrome family have been explained on the basis of the calculations. It has been postulated that the bonding of ferrichromes to a membrane receptor is effected by means of the peptide ring of the molecule. The transport of ferrichrome A through the interior of a membrane is energetically considerably more difficult than that of ferrichrome, since it is associated with dehydration of the side-chain carboxyl groups of the molecule.Translated from Teoreticheskaya i Éksperimental'naya Khimiya, Vol. 24, No. 2, pp. 167–172, March–April, 1988.     

Formation of solvate structures by the <Emphasis Type="Italic">ortho</Emphasis>-, <Emphasis Type="Italic">meta</Emphasis>-, and <Emphasis Type="Italic">para</Emphasis>-isomers of hydroxybenzoic acid in supercritical fluid

The solvate structures formed by the ortho-, meta-, and para-isomers of hydroxybenzoic acid (o-HBA, m-HBA, and p-HBA) with a polar co-solvent (methanol at a concentration of 0.030 and 0.035 mole fractions) in supercritical carbon dioxide at a constant density of 0.7 g/cm³ and temperatures of 318 and 328 K have been studied by the classic molecular dynamics. It has been determined that a stable hydrogen-bonded complex with the co-solvent forms via the hydrogen of the carboxyl group for all isomers. The probability of this complex existence is high at all temperatures and concentrations. In the o-HBA molecule, the other functional groups are engaged in the intramolecular hydrogen bond, but not involved in interactions with methanol. It has been found that m-HBA and p-HBA can be involved in hydrogen bonds with methanol via hydroxyl hydrogen and oxygen atoms; they are characterized by the presence of one more co-solvent molecule (rarely, two molecules) in their solvation shell and intermittent formations/breakages of hydrogen bonds via other functional groups. These bonds are far less stable, and their formation is sensitive to change of temperature and co-solvent concentration. It has been concluded that the degree of selective solvation of m-HBA and p-HBA by co-solvent molecules is approximately the same, but the rate of structural rearrangements in the nearest environment of m-HBA is higher than that of p-HBA.     

Crystal structure of 1:1 Complexes between urea and two crown ether derivatives of phthalic acid, 2,3,5,6,8,9,11,12,14,15-decahydrobenzo[1,4,7,10,13,16]hexaoxacyclo-octadecin-18,19-dicarboxylic acid (i) and 2,3,5,6,8,9,11,12-octahydro-benzo[1,4,7,10,13]pentaoxacyclopentadecin-15,16-dicarboxylic acid (II)

The crystal structures of the titlke compounds have been determined by X-ray diffraction. Urea, I crystallizes in the triclinic PI space group with cell dimensions a = 8.336(2), b = 11.009(2), c = 13.313(2) Å, α = 105.55(3), β = 103.62(3), γ = 104.63(3)° and Z = 2 final R value 0.072 for 2105 observations. Urea, II crystallizes in the orthorhombic P2₁2₁2₁ space group with cell dimensions a = 8.750(2), b = 10.844(3) and c = 21.215(3) Å and Z = 4, final R value 0.083 for 599 observations. All the hydrogen atoms were located in the complex urea, I ; urea molecules form hydrogen bonded dimers about centers of symmetry, these dimers are sandwiched between macrocyclic rings forming one simple and one bifurcated hydrogen bond from the “endo” hydrogen atoms to the ether oxygen atoms. These units are held by hydrogen bonding between the urea molecules and carboxylic acids in two other units; these hydrogen bonds are cyclic involving eight atoms -(N-H(exo)…O(keto)-C-O-H…O(urea)-C)-. Only one carboxylic acid group per molecule takes part in these hydrogen bonds, the other forms a short, 2.490(7) Å, internal bond to the acceptor keto oxygen atom. N(H)…O bonds range from 2.930(7) to 3.206(7) Å, O(H)…O is 2.475(6) Å. In the complex urea, II each urea is hydrogen bonded to three different host molecules and vice versa; the urea “endo” hydrogen atoms bond to the ether oxygen atoms, while both “exo” hydrogen atoms take part in cyclic hydrogen bonds to carboxylic acids. There is not internal hydrogen bond. N(H)…O bonds range from 2.83 to 3.26(2) A and the O-…O bonds are 2.55 and 2.56(2) Å.     

Crystal structure of the alcoholates and the ansolvate of PNU-97018, an angiotensin II receptor antagonist

The title compound, PNU-97018 [systemic name: 2-butyl-3,6,7,8,9,11-hexahydro-6,9-dimethyl-3-([2'-(2H-tetrazol-5-yl)[1,1'-biphenyl]-4-yl]methyl)-6,9-ethano-4H-imidazo[4,5-d]-pyridazino[1,2-a]pyridazin-4-one] is a newly developed angiotensin II receptor antagonist. The compound and its methanolate and ethanolate were characterized by X-ray crystallography and thermal analysis. The methanolate and ethanolate crystals have an almost identical molecular conformation and crystal packing. In both alcoholates, each alcohol molecule is fixed to the compound with a molar ratio of 1 : 1 by a hydrogen bond between the hydroxyl group of the alcohol molecule and the tetrazole group of the compound. The hydroxyl group of each alcohol molecule further links with the imidazole ring of the neighboring compound by hydrogen bond to form a hydrogen-bond network in both alcoholates. A tunnel-like structure that includes alcohol molecules is formed in each alcoholate. The ansolvate crystal showed completely different thermal and X-ray crystallographic characteristics from the alcoholates, where the compound molecules were directly linked by hydrogen bonds between the tetrazole group of a molecule and the imidazole ring of the neighboring molecule. The position of the hydrogen atom in the tetrazole ring was different between the ansolvate and alcoholates. Unlike alcoholates, a layer structure stacked on the b-c plane was observed in the ansolvate crystal. It was concluded that the molecular conformation and the arrangement of the compound molecules were largely different between ansolvate and alcoholate crystals.     

Properties of a water layer on hydrophilic and hydrophobic self-assembled monolayer surfaces: A molecular dynamics study

The microscopic behaviors of a water layer on different hydrophilic and hydrophobic surfaces of well ordered self-assembled monolayers (SAMs) are studied by molecular dynamics simulations. The SAMs consist of 18-carbon alkyl chains bound to a silicon(111) substrate, and the characteristic of its surface is tuned from hydrophobic to hydrophilic by using different terminal functional groups ( CH 3 , COOH). In the simulation, the properties of water membranes adjacent to the surfaces of SAMs were reported by comparing pure water in mobility, structure, and orientational ordering of water molecules. The results suggest that the mobility of water molecules adjacent to hydrophilic surface becomes weaker and the molecules have a better ordering. The distribution of hydrogen bonds indicates that the number of water-water hydrogen bonds per water molecule tends to be lower. However, the mobility of water molecules and distribution of hydrogen bonds of a water membrane in hydropho- bic system are nearly the same as those in pure water system. In addition, hydrogen bonds are mainly formed between the hydroxyl of the COOH group and water molecules in a hydrophilic system, which is helpful in understanding the structure of interfacial water.     

DNA sequencing with titanium nitride electrodes

We construct a hydrogen‐bond based metal–molecule–metal junction, which contains two identical “reader” molecules, one single DNA base as a bridged molecule, and two titanium nitride electrodes. Hydrogen bonds are formed between “reader” molecules and DNA base, whereas titanium–sulfur bonds are formed between “reader” molecules and titanium nitride electrodes. We perform electronic structure calculations for both the bare bridged molecule and the full metal–molecule–metal system. The projected density of states shows that when the molecule is connected to the titanium nitride electrode, the energy levels of the bridged molecule are shifted, with an indirect effect on the hydrogen bonds. This is similar to the case for a gold electrode but with a more pronounced effect. We also calculate the current–voltage characteristics for the molecular junctions containing each DNA base. Results show that titanium nitride as an electrode can generate distinct conductance for each DNA base, providing an alternative electrode for DNA sequencing. © 2013 Wiley Periodicals, Inc.     

Structure and dynamics of methanol in water: a quantum mechanical charge field molecular dynamics study

An ab initio quantum mechanical charge field molecular dynamics simulation was carried out for one methanol molecule in water to analyze the structure and dynamics of hydrophobic and hydrophilic groups. It is found that water molecules around the methyl group form a cage-like structure whereas the hydroxyl group acts as both hydrogen bond donor and acceptor, thus forming several hydrogen bonds with water molecules. The dynamic analyses correlate well with the structural data, evaluated by means of radial distribution functions, angular distribution functions, and coordination number distributions. The overall ligand mean residence time, τ identifies the methanol molecule as structure maker. The relative dynamics data of hydrogen bonds between hydroxyl of methanol and water molecules prove the existence of both strong and weak hydrogen bonds. The results obtained from the simulation are in excellent agreement with the experimental results for dilute solution of CH(3)OH in water. The overall hydration shell of methanol consists in average of 18 water molecules out of which three are hydrogen bonded.     

甘氨酸与间硝基苯甲酸加合物的合成及晶体结构

The title 1:1 adduct, has been prepared and a large single crystal with dimensions of 5 mm×50 mm×20 mm was obtained by slow-cooling method. It produces the green radiation at 532 nm under the irradiation of Nd~3+: YAG laser beam at 1064nm. The crystal structure of this potential non-linear optical material was determined by X-ray diffraction method. The crystal is orthorbombic, space group Pca2_1, with a=2.2701(5) nm, b=0.5852(2) nm, c=0.7815(2) nm, Z=4; final R is 0.054 for 702 observed reflections. The intermolecular hydrogen bonds are formed between the amino and carboxyl groups of glycines, which connect the glycine molecules to form two-dimensional network parallel to the (100) plane, while the intermolecular hydrogen bonds between the carboxyl group of glycine and the carboxyl group of m-nitrobenzoic acid let the latter link to above mentioned two-dimensional network.     

Shape of 4S- and 4R-hydroxyproline in gas phase

The alpha-amino acids 4(S)-hydroxyproline and 4(R)-hydroxyproline have been studied under isolation conditions in gas phase using laser-ablation molecular-beam Fourier transform microwave spectroscopy. Two conformers of each molecule have been detected in the jet-cooled rotational spectrum. The most stable conformer in both molecules exhibits an intramolecular N...H-O hydrogen bond (configuration 1) between the hydrogen atom of the carboxylic group and the nitrogen atom. The second conformer is characterized by an intramolecular N-H...O=C hydrogen bond (configuration 2). The conformers of 4(R)-hydroxyproline adopt a C(gamma)-exo puckering, while those of 4(S)-hydroxyproline present a C(gamma)-endo ring conformation. These ring conformations, which show the same propensity observed in collagen-like peptides, are stabilized by additional intramolecular hydrogen bonds involving the 4-hydroxyl group, with the exception of the most stable form of 4(S)-hydroxyproline for which a n-pi interaction between the oxygen atom of the 4-hydroxyl group and the carboxyl group carbon seems to be established. A gauche effect could be also contributing to stabilize the observed conformers.     

The effect of aqueous solutions of trimethylamine-N-oxide on pressure induced modifications of hydrophobic interactions

To understand the mechanism of protein protection by the osmolyte trimethylamine-N-oxide (TMAO) at high pressure, using molecular dynamics (MD) simulations, solvation of hydrophobic group is probed in aqueous solutions of TMAO over a wide range of pressures relevant to protein denaturation. The hydrophobic solute considered in this study is neopentane which is a considerably large molecule. The concentrations of TMAO range from 0 to 4 M and for each TMAO concentration, simulations are performed at five different pressures ranging from 1 atm to 8000 atm. Potentials of mean force are calculated and the relative stability of solvent-separated state over the associated state of hydrophobic solute are estimated. Results suggest that high pressure reduces association of hydrophobic solutes. From computations of site-site radial distribution function followed by analysis of coordination number, it is found that water molecules are tightly packed around the nonpolar particle at high pressure and the hydration number increases with increasing pressure. On the other hand, neopentane interacts preferentially with TMAO over water and although hydration of neopentane reduces in presence of this osmolyte, TMAO does not show any tendency to prevent the pressure-induced dispersion of neopentane moieties. It is also observed that TMAO molecules prefer a side-on orientation near the neopentane surface, allowing its oxygen atom to form favorable hydrogen bonds with water while maintaining some hydrophobic contacts with neopentane. Analysis of hydrogen-bond properties and solvation characteristics of TMAO reveals that TMAO can form hydrogen bonds with water and it reduces the identical nearest neighbor water molecules caused by high hydrostatic pressures. Moreover, TMAO enhances life-time of water-water hydrogen bonds and makes these hydrogen bonds more attractive. Implication of these results for counteracting effect of TMAO against protein denaturation at high pressures are discussed.     

Bile pigment complexes with cyclodextrins: electronic and vibrational circular dichroism study

Chiral recognition of bilirubin IX-α, biliverdin IX-α, and bilirubin ditaurate dianions by cyclodextrins was studied using a combination of vibrational and electronic circular dichroism. Biliverdin forms inclusion complexes with β-cyclodextrin and β-methylcyclodextrin. Bilirubin bonds to both cyclodextrins by means of hydrogen bonds and only shallow inclusions that are restricted by the presence of COO⁻ in the pigment structure. Bilirubin ditaurate complexes are realized by a weak inclusion of the whole molecule, or some part of it, into the cyclodextrin cavity and stabilization of the conformation by hydrogen bonds. Bilirubin and bilirubin ditaurate can be recognized by cyclodextrin and methylcyclodextrin in the form of opposite conformers. Spectroscopic characteristics of the different conformations of the bile pigments were obtained for the first time by vibrational circular dichroism techniques.     

Crystal and molecular structure of the “asymmetric” ethylenediamine-N,N-di-3-propionic acid monohydrate

A new complexing agent the “asymmetric” ethylenediamine-N,N-di-3-propionic acid (as.EDDP) is obtained. The crystal structure of the new compound is determined by single-crystal X-ray diffraction. C₈H₁₆N₂O₄·H₂O crystals are monoclinic; space group P2₁/c, a = 12.7416(4) Å, b = 6.5470(2) Å, c = 12.1908(4) Å, β = 93.100(1)°, Z = 4, ρ _x = 1.454 mg/m³, and R ₁ (I > 2.0σ(I)) = 0.0326. In the solid form, the as.EDDP molecule has a double betaine structure: The intramolecular hydrogen bonds with the betaine proton of the tertiary nitrogen atom are formed with the participation of one oxygen atom of the carboxyl group of each 3-propionic fragment, which forms two N(1)-H(1N)-bonded six-membered H-cycles. The intermolecular hydrogen bonds are formed between the three hydrogen atoms of the protonated primary nitrogen atom and the oxygen atoms of the 3-propionic fragments of three other as.EDDP molecules. The water molecule participates in the formation of intermolecular hydrogen bonds with the oxygen atom of one carboxyl group of the molecule.     

Bildung und Eigenschaften von Aoylphosphinen. III. Molekül- und KristallStruktur von Dipivaloylphosphin

Syntheses and Properties of Acylphosphines. III. Molecular and Crystal Structure of Dipivaloylphosphine In the reaction of tris(trimethylsilyl)phosphine with pivaloyl chloride two Si? P bonds are cleaved and dipivaloyltrimethylsilylphosphine is formed. Reaction with methanol yields dipivaloylphosphine. N.m.r. investigations show a tautomeric equilibrium between keto and enol form as in β-diketones. The substance crystallizes in the orthorhombic space group Pmmn with molecules in two crystallographically different sites [cell parameters: a = 14.04(1), b = 13.82(1), c = 6.28(2) Å]. An X-ray structure determination (R = 5.0%) proves the existence of the enol form in the solid, in that (1.) the molecular symmetry is mm 2(C_2v), (2.) P? C bonds are shortened and C? O bonds are elongated, and (3.) we find a symmetric hydrogen bridge with a very short O? O distance. Bond lengths and angles are compared with those of other β-diketones. The packing of molecules is studied in detail.     

A Novel Lead- bis (4-Chloro-2-Methylphenoxy)- Acetate Polymeric Complex

The bis (4-chloro-2-methylphenoxy)acetato lead (II) monohydrate infinite polymer was synthesized and characterized by elemental analysis and infrared spectroscopy. The crystal and molecular structure has been determined and the bond valences were computed. Molecules of the monomer, each occupying an asymmetric unit, are connected by the inversion center and a polymer chain is created by Pb(2O)Pb rings in spiro arrangement. The lead atom is seven coordinate by four oxygen atoms from two chelating carboxyl groups, one water molecule, and two oxygen atoms provided by symmetry generated carboxyl groups. Each carboxyl group acts as a bidentate ligand toward one metal atom and as a monodentate ligand with respect to a second. The lead-oxygen distances are spread over a wide range of values. One molecule of (4-chloro-2-methylphenoxy)acetate in the monomer is close to planarity, and the second is bent. All 4-chloro-2-methylphenoxy groups are almost parallel. The polymer infinite chains are assembled by weak hydrogen bonds to a layered structure.     

Geometric structure of a molecule of Epitalon tetrapeptide: A molecular-dynamics simulation

Variation of the geometric parameters of a molecule of Epitalon tetrapeptide (Ala-Glu-Asp-Gly) over a period of 1500 ps was simulated by the method of molecular dynamics using AMBER force field. The structure of the molecule is stabilized by two salt bridges formed by the N-terminal nitrogen atom and oxygen atoms of Asp and Glu side chains. The biological effect of Epitalon was attributed to formation of salt or hydrogen bonds involving one or several ionizable functional groups of the molecules.     

油纸复合介质中水分子扩散行为的分子动力学模拟

对不同温度下水分子在油纸复合介质中的扩散行为进行了分子动力学模拟研究. 通过分析水分子与纤维素形成的氢键发现, 油中的水分子在模拟过程中会逐渐扩散到纤维素内并与之形成氢键, 而纤维素内的水分子则与纤维素形成氢键后被束缚于纤维素中. 通过分析水分子的扩散系数发现, 由于油和纤维素的极性不同, 使得水分子在油和纤维素两种单介质中的扩散行为有较大差别, 而在复合介质中的扩散系数受水分子在油和纤维素中的比例影响较大, 两者表现出很强的相关性. 水分子和两介质的相互作用与两介质的极性也存在很大的关系, 且不同温度下水分子与两介质的相互作用能和水分子在油和纤维素中的比例也表现出了较强的相关性. 不同温度下水分子的不同分布弱化了温度对扩散系数的影响.     

Gas chromatographic, quentum-chemical, and molecular statistical studies of cluster adsorption of water and methanol molecules on hydrophilic surface sites of hydrophobic adsorbents

The comprehensive theoretical and experimental study of the adsorption of water and methanol molecules on active sites (carboxyl and phenol hydroxyl groups) on the graphitized thermal carbon black is performed. It is shown that microclusters formed upon the adsorption of these molecules on such sites are characterized by the cyclic structure comprising 4–5 molecules similar to that whose existence was revealed previously in liquid water and on the surface of silver iodide. The analysis of the studied adsorption clusters demonstrated that the formation of such cycles is governed primarily by the hydrogen bonding; however, a definite role is played also by energy effects associated with the changes in the state of molecular motion during adsorption. It is shown that the generalized Langmuir equation derived from molecular statistical considerations provides for better reproducing of the experimental isotherm within a wider surface coverage range, thus making it possible to consistently interpret data on structural and energetic characteristics of adsorption systems obtained by gas chromatography and quentum-chemical method.