Showing papers on "Hydrogen bond published in 2006"

Hydrogen Bonding - New Insights

Abstract: I. Characterization of Hydrogen Bonding: From van der Waals Interactions to Covalency, R. Parthasarathi and V. Subramanian II. Intramolecular Hydrogen Bonds. Methodologies and Strategies for their Strength Evaluation, Giuseppe Buemi III. Changes of Electron Properties in the Formation of Hydrogen Bonds, Luis F. Pacios IV. Weak to Strong Hydrogen Bonds, Han Myoung Lee, N. Jiten Singh, Kwang S. Kim V. The Nature of the C-H...X Intermolecular Interactions in Molecular Crystals. A Theoretical Perspective, Fernando Mota, Emiliana D'Oria VI. Weak hydrogen bonds involving transition elements, Maria Jose Calhorda VII. Contribution of CH**X Hydrogen Bonds to Biomolecular Structure, Steve Scheiner VIII. Neutral Blue-Shifting and Blue-Shifted Hydrogen Bonds, Eugene S. Kryachko IX. Hydrogen-Hydrogen Bonding: the Non-Electrostatic Limit of Closed-Shell Interaction Between two Hydrogen Atoms (A Review), Cherif F. Matta X. Potential Energy Shape for the Proton Motion in Hydrogen Bonds Reflected in Infrared and NMR Spectra, Gleb S. Denisov, Janez Mavri and Lucjan Sobczyk XI. Molecular Geometry - Distant Consequences of H-Bonding, Tadeusz M. Krygowski and Joanna E. Zachara XII. Topology of X-ray charge density of hydrogen bonds, Tibor S. Koritsanszky XIII. Structure-Property Relations for Hydrogen-Bonded Solids, Andrzej Katrusiak XIV. Unrevealing the Nature of Hydrogen Bonds: p -Electron delocalization Shapes H-Bond Features. Intramolecular and Intermolecular Resonance-Assisted Hydrogen Bonds, Slawomir J.Grabowski and Jerzy Leszczynski

Structural conformation and vibrational spectroscopic studies of 2,6-bis(p-N,N-dimethyl benzylidene)cyclohexanone using density functional theory

Abstract: NIR-FT Raman and FT-IR spectra of the crystallized 2,6-bis (p-N,N-dimethyl benzylidene)cyclohexanone (C24H28N2O) have been recorded in the region 3200–500 and 4000–400 cm−1, respectively. The spectral interpretation has been done following full structure optimization and vibrational wavenumber calculations based on the density functional theory (DFT) using the standard B3LYP/6-31G* basis set. The predicted vibrational spectra are in excellent agreement with the experiment, permitting an unambiguous assignment for the unusual downshifting of νCO caused by expanded conjugation effects in the dienone system. The optimized geometry clearly demonstrates the ‘half-chair’ conformation of the central nonheterocyclic ring. The ring CH stretching vibrational modes involving aromatic hydrogen atoms participating in steric interaction have been observed with low intensities. There are valid structural and spectral bases for the enhancement of its bioactivity due to full charge transfer reaction by the substitution of the electron-donating 4-dimethylamino group into the aryl rings. The existence of intramolecular, CH…O, improper, blue-shifted hydrogen bond was investigated by means of the natural bonding orbitals (NBO) analysis. There are also slight dissimilarities in the bond lengths and endocyclic bond angles of both phenyl rings due to the effect of the heavy substitution. The characteristic ring modes have also been assigned in detail. Copyright © 2006 John Wiley & Sons, Ltd.

Characterising the Electronic Structure of Ionic Liquids: An Examination of the 1‐Butyl‐3‐Methylimidazolium Chloride Ion Pair

Abstract: In this paper we analyse the electronic properties of gas-phase 1-butyl-3-methylimidazolium Cl ion pairs, [C(4)C(1)im]Cl, in order to deepen our understanding of ionic liquids in general. Examination of charge densities, natural bond orbitals (NBO), and delocalised molecular orbitals computed at the B3LYP and MP2/6-31(++)G(d,p) levels have enabled us to explain a number of experimental phenomena: the relative acidity of different sites on the imidazolium ring, variations in hydrogen-bond donor and acceptor abilities, the apparent contradiction of the hydrogen-bond-donor parameters for different types of solute, the low probability of finding a Cl(-) anion at the rear of the imidazolium ring and the expansion of the imidazolium ring in the presence of a strong hydrogen-bond acceptor. The unreactive but coordinating environment and large electrochemical window have also been accounted for, as has the strong electron-donating character of the carbon atoms to the rear of the ring in associated imidazolylidenes. The electronic structure of the [C(4)C(1)im](+) cation is best described by a C(4)==C(5) double bond at the rear, and a delocalised three-centre 4 e(-) component across the front (N(1)-C(2)-N(3)) of the imidazolium ring; delocalisation between these regions is also significant. Hydrogen-bond formation is driven by Coulombic stabilisation, which compensates for an associated destabilisation of the electronic part of the system. Interactions are dominated by a large positive charge at C(2) and the build up of pi-electron density above and below the ring, particularly that associated with the double bond between C(4) and C(5). The NBO partial charges have been computed and compared with those used in a number of classical simulations.

Molecular Recognition in the Selective Oxygenation of Saturated C-H Bonds by a Dimanganese Catalyst

Abstract: Although enzymes often incorporate molecular recognition elements to orient substrates selectively, such strategies are rarely achieved by synthetic catalysts. We combined molecular recognition through hydrogen bonding with C-H activation to obtain high-turnover catalytic regioselective functionalization of sp 3 C-H bonds remote from the –COOH recognition group. The catalyst contains a Mn(μ-O) 2 Mn reactive center and a ligand based on Kemp9s triacid that directs a –COOH group to anchor the carboxylic acid group of the substrate and thus modify the usual selectivity for oxidation. Control experiments supported the role of hydrogen bonding in orienting the substrate to achieve high selectivity.

Vibrational Spectroscopic Studies of Aqueous Interfaces: Salts, Acids, Bases, and Nanodrops

Abstract: The ubiquitous nature of water makes the study of water both practical and relevant. Yet in this advanced technological age, many important, fundamental questions remain unanswered about water and the aqueous interface. As we learn more about water, more questions arise. The fact that water molecules strongly hydrogen bond to one another explains, at the most basic level, the inherently high boiling point of water. Moreover, the surface structure of water, directly related to the hydrogen bonding between water molecules, is unique. It is the nature of the hydrogen bond that makes understanding water and aqueous interfaces such a challenge: hydrogen bonding is dynamic and is a strong intermolecular force, yet it is considerably weaker than a covalent bond. Due to the experimental and theoretical challenges presented by the hydrogen bond, the scientific community is far from a full understanding of bulk and surface water. In this review, we focus on spectroscopic studies of surface water structure as it is affected by salts, acids, and ammonia. Cluster studies contribute to understanding the aqueous interface, and these are discussed along with studies of aqueous nanodrops.

Thermodynamics of Hydrogen Bonding in Hydrophilic and Hydrophobic Media

Abstract: The thermodynamics of hydrogen bond breaking and formation was studied in solutions of alcohol (methanol, ethanol, 1-propanol) molecules. An extensive series of over 400 molecular dynamics simulations with an aggregate length of over 900 ns was analyzed using an analysis technique in which hydrogen bond (HB) breaking is interpreted as an Eyring process, for which the Gibbs energy of activation ΔG⧧ can be determined from the HB lifetime. By performing simulations at different temperatures, we were able to determine the enthalpy of activation ΔH⧧ and the entropy of activation TΔS⧧ for this process from the Van't Hoff relation. The equilibrium thermodynamics was determined separately, based on the number of donor hydrogens that are involved in hydrogen bonds. Results (ΔH) are compared to experimental data from Raman spectroscopy and found to be in good agreement for pure water and methanol. The ΔG as well as the ΔG⧧ are smooth functions of the composition of the mixtures. The main result of the calculations ...

Testing the conformational hypothesis of passive membrane permeability using synthetic cyclic peptide diastereomers.

Abstract: Little is known about the effect of conformation on passive membrane diffusion rates in small molecules. Evidence suggests that intramolecular hydrogen bonding may play a role by reducing the energetic cost of desolvating hydrogen bond donors, especially amide N−H groups. We set out to test this hypothesis by investigating the passive membrane diffusion characteristics of a series of cyclic peptide diastereomers based on the sequence cyclo[Leu-Leu-Leu-Leu-Pro-Tyr]. We identified two cyclic hexapeptide diastereomers based on this sequence, whose membrane diffusion rates differed by nearly two log units. Results of solution NMR studies and hydrogen/deuterium (H/D) exchange experiments showed that membrane diffusion rates correlated with the degree of intramolecular hydrogen bonding and H/D exchange rates. The most permeable diastereomer, cyclo[d-Leu-d-Leu-Leu-d-Leu-Pro-Tyr] (1), exhibited a passive membrane diffusion rate comparable to that of the orally available drug cyclosporine A.

Theoretical Investigations on Chalcogen−Chalcogen Interactions: What Makes These Nonbonded Interactions Bonding?

Abstract: To understand the intermolecular interactions between chalcogen centers (O, S, Se, Te), quantum chemical calculations on pairs of model systems were carried out. For the oxygen derivatives, one of the components of the supermolecules consists of dimethyl ether, while the second component is either dimethyl ether (1) or ethynyl methyl ether (2) or methyl cyanate (3). The model calculations were also extended to the sulfur (4−6), selenium (7−9), and tellurium congeners (10−12). The MP2/SDB-cc-pVTZ, 6-311G* level of theory was used to derive the geometrical parameters and the global energies of the model systems. A detailed analysis based on symmetry adapted perturbation theory (SAPT) reveals that induction and dispersion forces contribute to the bonding in each case. For 1−3 the electrostatic energy also contributes to the intermolecular bonding, but not for 4−12. The NBO analysis reveals that the interaction in the dimers 1−3 is mainly due to weak hydrogen bonding between methyl groups and chalcogen center...

Hydrogen Bonding without Borders: An Atoms-in-Molecules Perspective

Abstract: It is shown that the electron density at the hydrogen bond critical point increases approximately linearly with increasing stabilization energy in going from weak hydrogen bonds to moderate and strong hydrogen bonds, thus serving as an indicator of the nature and gradual change of strength of the hydrogen bond for a large number of test intermolecular complexes.

Cooperativity in hydrogen-bonded interactions: ab initio and "atoms in molecules" analyses.

Abstract: The H2CO···(HF)n (n = 1, ..., 9) complexes were investigated using the MP2 method and the following basis sets: 6-311++G(d,p), aug-cc-pVDZ and aug-cc-pVTZ. It was found that the cooperativity effect enhances significantly the F−H···O hydrogen bond; in some of cases one can detect the covalent nature of hydrogen bonding. To deepen the nature of the interactions investigated, the scheme of decomposition of the interaction energy was applied; for stronger H-bonds where the coopearativity is more important, the delocalization energy term increases. The ratio of delocalization energy to electrostatic energy increases for stronger hydrogen bonds where the proton···acceptor distance is shorter. The Bader theory was also applied, and it was found that for stronger H-bonds the electronic energy density at the proton···acceptor bond critical point is negative and may be attributed to the partly covalent interaction.

Ion‐Pair Formation in the Ionic Liquid 1‐Ethyl‐3‐methylimidazolium Bis(triflyl)imide as a Function of Temperature and Concentration

Abstract: The structures and ion-pair formation in the ionic liquid (IL) 1-ethyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide are studied by a combination of FTIR measurements and DFT calculations. We could clearly distinguish imidazolium cations that are completely H-bonded to anions from those that are single H-bonded in ion pairs. Ion-pair formation already occurs in the neat IL and rises with temperature. Ion-pair formation is strongly promoted by dilution of the IL in chloroform. In these weakly polar environments ion pairs H-bonded via C(2)H are strongly favored over those H-bonded via C(4,5)H. This finding is in agreement with DFT (gas phase) calculations, which show a preference for ion pairs H-bonded via C(2)H as a result of the acidic C(2)H bond.

A structural investigation of the N-B interaction in an o-(N,N-dialkylaminomethyl)arylboronate system

Abstract: o-(Pyrrolidinylmethyl)phenylboronic acid (4) and its complexes with bifunctional substrates such as catechol, alpha-hydroxyisobutyric acid, and hydrobenzoin have been studied in detail by X-ray crystallography, (11)B NMR, and computational analysis. The N-B interactions in analogous boronic acids and esters have been extensively cited in molecular recognition and chemosensing literature. The focal point of this study was to determine the factors that are pertinent to the formation of an intramolecular N-B dative bond. Our structural study predicts that the formation of an N-B dative bond, and/or solvent insertion to afford a tetrahedral boronate anion, depends on the solvent and the complexing substrate present. Specifically, from (11)B NMR studies, complexation of 4 with electron-withdrawing and/or vicinally bifunctionalized substrates promotes both the formation of N-B dative bonds and the solvation of sp(2) boron to a tetrahedral sp(3) boronate. In the solid state, the presence of an N-B dative bond in the complex of 4 and catechol (7) depends on the solvent from which it crystallizes. From chloroform, an N-B bond was observed, whereas from methanol, a methoxylated boronate was formed, where the methoxy group is hydrogen-bonded with the neighboring tertiary ammonium ion. The structural optimization of compounds 4 and 7 using density functional theory in a simulated water continuum also predicts that complexation of 4 and catechol promotes either the formation of an N-B bond or solvolysis if 1 equiv of water is present. The conclusion from this study will help in the design of future chemosensing technologies based on o-(N,N-dialkylaminomethyl)arylboronate scaffolds that are targeting physiologically important substances such as saccharides, alpha-hydroxycarboxylates, and catecholamines.

Unusual Hydrogen Bonding in Water-Filled Carbon Nanotubes

Abstract: We present the first experimental vibrational spectroscopy study providing direct evidence of a water phase inside single-walled carbon nanotubes that exhibits an unusual form of hydrogen-bonding due to confinement. Water adopts a stacked-ring structure inside nanotubes, forming intra- and inter-ring hydrogen bonds. The intra-ring hydrogen bonds are bulk-like while the inter-ring hydrogen bonds are relatively weak, having a distorted geometry that gives rise to a distinct OH stretching mode. The experimentally observed infrared mode at 3507 cm-1 is assigned to vibrations of the inter-ring OH-groups based on detailed atomic-level modeling. The direct observation of unusual hydrogen bonding in nanotubes has potential implications for water in other highly confined systems, such as biological channels and nanoporous media.

Hydrogen bonding and the cryoprotective properties of glycerol/water mixtures.

Abstract: Molecular dynamics simulations and infrared spectroscopy were used to determine the hydrogen bond patterns of glycerol and its mixtures with water. The ability of glycerol/water mixtures to inhibit ice crystallization is linked to the concentration of glycerol and the hydrogen bonding patterns formed by these solutions. At low glycerol concentrations, sufficient amounts of bulk-like water exist, and at low temperature, these solutions demonstrate crystallization. As the glycerol concentration is increased, the bulk-like water pool is eventually depleted. Water in the first hydration shell becomes concentrated around the polar groups of glycerol, and the alkyl groups of glycerol self-associate. Glycerol−glycerol hydrogen bonds become the dominant interaction in the first hydration shell, and the percolation nature of the water network is disturbed. At glycerol concentrations beyond this point, glycerol/water mixtures remain glassy at low temperatures and the glycerol−water hydrogen bond favors a more linea...

Cooperative End-to-End and Lateral Hydrogen-Bonding Motifs in Supramolecular Thermoplastic Elastomers

Abstract: To a large extent, the mechanical properties of polymers are determined by the strength of the physical interactions between chains. Thermoplastic elastomers (TPE’s) make sophisticated use of reversible physical interactions.1 They consist of polymer chains in which strongly interacting segments alternate with weakly interacting segments to give rise to microphase-separated materials with a soft block/hard block morphology. When the hard blocks contain urethane and/or urea groups, strong and specific hydrogen-bonding interactions2 lead to useful properties, such as a high modulus for a given hard block content. In recent years, highly directional physical interactions have been applied in a fundamentally different way to form supramolecular polymers.3 In this novel class of materials, endfunctionalization of unimers with functional groups that associate via noncovalent interactions such as multiple hydrogen bonds4,5 or coordinative bonds6 results in a strong increase of the virtual molecular weight and in concurrent changes of mechanical and rheological properties. The use of directional hydrogen bonding within the hard blocks of TPE’s has been studied by Stadler and co-workers,7 who used telechelic hydrogen-bonded polyisobutylenes with relatively weak end-to-end interactions between urazole groups and between benzoic acid groups. Recently, Bouteiller et al.8 have studied poly(dimethylsiloxane)s with bisurea end groups which aggregate laterally. The authors concluded that aggregation of the end groups into 3-D crystalline domains results in elastomeric behavior, while the formation of hydrogen bonds without crystallization was not sufficient to obtain tensile properties. Similar conclusions were drawn by Rowan et al.,9 who noticed that even very weak end-to end interactions can be used to obtain polymers with film-forming properties when the end groups phase segregate. Here, we study the effect of combining very strong end-toend association via ureidopyrimidinone (UPy) quadruple hydrogen bonding10 and directional lateral aggregation via the urea (U) and urethane (T) hydrogen bonding motifs11 to give supramolecular thermoplastic elastomers with 1-D aggregation of dimerized end groups. Hydroxy-telechelic poly(ethylene butylene) (PEB, Mn ) 3500 g/mol, Mw/Mn ) 1.06, degree of functionalization 1.92) was functionalized with lateral hydrogen-bonding functionalities (UU-PEB-U-U and U-T-PEB-T-U), with end-to-end hydrogenbonding functionalities (UPy-PEB-UPy), and functionalized with both lateral and end-to-end functionalities (UPy-U-PEB-U-UPy and the previously reported5 UPy-T-PEB-T-UPy) (Scheme 1). The resulting materials were characterized with DSC, AFM, dynamic mechanical measurements, and tensile testing. The parent hydroxy-telechelic PEB is a liquid at room temperature which shows purely viscous behavior in oscillatory shear experiments. Incorporation at the chain ends of functional groups capable of lateral aggregation via 3 or 4 hydrogen bonds leads to the formation of elastic solids, with melting points that increases from 45 °C for U-T-PEB-T-U to 129 °C for the U-UPEB-U-U material. The former is a single segment of a segmented, PEB-based poly(urethane-urea) recently reported by Wilkes et al.,2b while the latter material can be considered a PEB analogue of the bisurea-functionalized PDMS reported by Bouteiller.8 In line with the highly directional nature of the hydrogen bonding of UPy moieties, direct functionalization of PEB with the UPy quadruple hydrogen bonding unit in UPyPEB-UPy gives rise to a noticeable increase in viscosity at 40 °C from 10 to 7 × 103 Pa‚s, but it does not lead to the formation of a material with a discernible melting point. The viscosity changes are in line with end-to-end linking of PEB by directional quadruple hydrogen bonds between UPy functional groups, considering that the degree of functionalization of 1.92 of the starting material limits the average number of end-linked unimers to ∼50. A master curve of oscillatory shear experiments on UPy-PEBUPy (Figure 1) confirms the directional end-to-end nature of UPy-UPy hydrogen bonding as the storage and loss moduli show terminal relaxation behavior with slopes of 0.96 and 2.05, demonstrating the absence of long-lived lateral interactions. Nevertheless, the formation of supramolecular polymer chains by linear association of unimers results in an entanglement network with characteristic lifetime of 1 s at 40 °C, evident from a viscoelastic transition at higher frequencies. A dramatic enhancement of mechanical properties was observed when end-to-end and lateral interactions were combined in UPy-U-PEB-U-UPy. In contrast to UPy-PEB-UPy, this material is an elastic solid, with a melting point of 129 °C. The * Corresponding authors. E-mail: r.p.sijbesma@tue.nl; e.w.meijer@tue.nl. Scheme 1. Hydrogen-Bonded Telechelic PEB’s

Tetrahedral structure or chains for liquid water.

Abstract: It has been suggested, based on x-ray absorption spectroscopy (XAS) experiments on liquid water [Wernet, Ph., et al. (2004) Science 304, 995–999], that a condensed-phase water molecule’s asymmetric electron density results in only two hydrogen bonds per water molecule on average. The larger implication of the XAS interpretation is that the conventional view of liquid water being a tetrahedrally coordinated random network is now replaced by a structural organization that instead strongly favors hydrogen-bonded water chains or large rings embedded in a weakly hydrogen-bonded disordered network. This work reports that the asymmetry of the hydrogen density exhibited in the XAS experiments agrees with reported x-ray scattering structure factors and intensities for Q > 6.5 A−1. However, the assumption that the asymmetry in the hydrogen electron density does not fluctuate and is persistent in all local molecular liquid water environments is inconsistent with longer-ranged tetrahedral network signatures present in experimental x-ray scattering intensity and structure factor data for Q < 6.5 A−1. polarizability tetrahedral liquid x-ray absorption spectroscopy x-ray scattering hydrogen-bonding

Histidines, heart of the hydrogen ion channel from influenza A virus: toward an understanding of conductance and proton selectivity.

Abstract: The heart of the H+ conductance mechanism in the homotetrameric M2 H+ channel from influenza A is a set of four histidine side chains. Here, we show that protonation of the third of these imidazoles coincides with acid activation of this transmembrane channel and that, at physiological pH, the channel is closed by two imidazole–imidazolium dimers, each sharing a low-barrier hydrogen bond. This unique construct succeeds in distributing a pair of charges over four rings and many atoms in a low dielectric environment to minimize charge repulsion. These dimers form with identical pKas of 8.2 ± 0.2, suggesting cooperative H+ binding and clearly illustrating high H+ affinity for this channel. The protonation behavior of the histidine side chains has been characterized by using solid-state NMR spectroscopy on the M2 transmembrane domain in fully hydrated lipid bilayers where the tetrameric backbone structure is known. Furthermore, electrophysiological measurements of multichannel and single-channel experiments confirm that these protein constructs are functional.

Hydrogen Sensors Based on Conductivity Changes in Polyaniline Nanofibers

Abstract: Hydrogen causes a reversible decrease in the resistance of a thin film of camphorsulfonic acid doped polyaniline nanofibers. For a 1% mixture of hydrogen in nitrogen, a 3% decrease in resistance is observed (DeltaR/R = -3%). The hydrogen response is completely suppressed in the presence of humidity. In contrast, oxygen does not inhibit the hydrogen response. A deuterium isotope effect on the sensor response is observed in which hydrogen gives a larger response than deuterium: (DeltaR/R)H/(DeltaR/R)D = 4.1 +/- 0.4. Mass sensors using nanofiber films on a quartz crystal microbalance also showed a comparable deuterium isotope effect: DeltamH/DeltamD = 2.3 +/- 0.2 or DeltanH/DeltanD = 4.6 +/- 0.4 on a molar basis. The resistance change of polyaniline nanofibers is about an order of magnitude greater than conventional polyaniline, consistent with a porous, high-surface-area nanofibrillar film structure that allows for better gas diffusion into the film. A plausible mechanism involves hydrogen bonding to the amine nitrogens along the polyaniline backbone and subsequent dissociation. The inhibitory effect of humidity is consistent with a stronger interaction of water with the polyaniline active sites that bind to hydrogen. These data clearly demonstrate a significant interaction of hydrogen with doped polyaniline and may be relevant to recent claims of hydrogen storage by polyaniline.

Synthesis of MIL-102, a Chromium Carboxylate Metal−Organic Framework, with Gas Sorption Analysis

Abstract: A new three-dimensional chromium(III) naphthalene tetracarboxylate, CrIII3O(H2O)2F{C10H4(CO2)4}1.5·6H2O (MIL-102), has been synthesized under hydrothermal conditions from an aqueous mixture of Cr(NO3)3·9H2O, naphthalene-1,4,5,8-tetracarboxylic acid, and HF. Its structure, solved ab initio from X-ray powder diffraction data, is built up from the connection of trimers of trivalent chromium octahedra and tetracarboxylate moieties. This creates a three-dimensional structure with an array of small one-dimensional channels filled with free water molecules, which interact through hydrogen bonds with terminal water molecules and oxygen atoms from the carboxylates. Thermogravimetric analysis and X-ray thermodiffractometry indicate that MIL-102 is stable up to ∼300 °C and shows zeolitic behavior. Due to topological frustration effects, MIL-102 remains paramagnetic down to 5 K. Finally, MIL-102 exhibits a hydrogen storage capacity of ∼1.0 wt % at 77 K when loaded at 3.5 MPa (35 bar). The hydrogen uptake is discussed...

C[sbnd]H[sbnd]O Hydrogen Bonding in Crystals

Abstract: An overview is given on C-H-O hydrogen bonding in the solid state Following a short survey of the early literature, the general properties of C-H-O bonding are discussed The structural characteristics and some physical consequences of C-H-O bonds are described A number of special systems are discussed in greater detail; these include water acceptors, inclusion complexes, and some biological structures

Quantitative classification of covalent and noncovalent H-bonds.

Abstract: The covalent nature of interactions within various hydrogen bonded molecular aggregates has been characterized by the two entirely different computational methods: Bader analysis of the electron density and variation-perturbation partitioning of the intermolecular interaction energy. Analysis of 34 complexes representing different types of hydrogen bonds indicates that the proton-acceptor distance ∼1.8 A and the ratio of delocalization and electrostatic terms ∼0.45 constitutes approximately a borderline between covalent and noncovalent hydrogen bonds. The latter ratio could be used to characterize quantitatively the degree of the covalent nature of transition state interactions with active site residues, a quantity essential for an enzyme catalytic activity.

Solvent induced polymorphism in supramolecular 1,3,5-benzenetribenzoic acid monolayers.

Abstract: This work presents a scanning tunneling microscopy (STM) based study of benzenetribenzoic acid (BTB) monolayer structures at the liquid−solid interface. On graphite(0001) the tailored molecules self-assemble into 2D supramolecular host systems, suitable for the incorporation of other nanoscopic objects. Two crystallographically different BTB structures were foundboth hydrogen bonded networks. A specific structure was deliberately selected by solvent identity. One of the BTB polymorphs is a 6-fold chicken-wire structure with circular, approximately 2.8 nm wide cavities. The other structure exhibits an oblique unit cell and a different hydrogen bonding pattern. The large cavity size of the chicken-wire structure was made possible through comparatively strong 2-fold hydrogen bonds between carboxylic groups. In addition, the low conformational flexibility of BTB was supportive to combat the tendency for dense packing.

The effect of an external magnetic field on the structure of liquid water using molecular dynamics simulation

Abstract: Through a series of molecular dynamics simulations based on the flexible three-centered water model, this study analyzes the structural changes induced in liquid water by the application of a magnetic field with a strength ranging from 1to10T. It is found that the number of hydrogen bonds increases slightly as the strength of the magnetic field is increased. This implies that the size of a water cluster can be controlled by the application of an external magnetic field. The structure of the water is analyzed by calculating the radial distribution function of the water molecules. The results reveal that the structure of the water is more stable and the ability of the water molecules to form hydrogen bonds is enhanced when a magnetic field is applied. In addition, the behavior of the water molecules changes under the influence of a magnetic field; for example, the self-diffusion coefficient of the water molecules decreases.

About the choice of the protogenic group in polymer electrolyte membranes: Ab initio modelling of sulfonic acid, phosphonic acid, and imidazole functionalized alkanes.

Abstract: The possible use of sulfonic acid, phosphonic acid, or imidazole as the protogenic group in polymer electrolyte membranes for fuel cells operating at intermediate temperature (T>100 degrees C) and very low humidity conditions is examined by comparing specific molecular properties obtained with first principles based electronic structure calculations. Potential energy profiles determined at the B3LYP/6-311G** level for rotation of imidazole, phosphonic acid and sulfonic acid functional groups on saturated heptyl chains revealed that the torsional barriers are 3.9, 10.0, and 15.9 kJ mol-1, respectively; indicating that the imidazole is clearly the most labile when tethered to an alkyl chain. Minimum energy conformations (B3LYP/6-311G**) of methyl dimers of each of the acids indicated that the binding of the pairs of the acids is greatest in the phosphonic acids and lowest for the imidazoles. Comparison of the ZPE corrected total energies of the methyl acid dimers with corresponding pairs consisting of the conjugate acid and conjugate base revealed that the energy penalty in transferring the proton (from acid to acid) was greatest for imidazole (120.1 kJ mol-1) and least for the phosphonic acid (37.2 kJ mol-1). This result is in agreement with experimentally measured proton conductivities of acid-functionalized heptyl compounds under dry conditions and further underpins the observation that phosphonic acid possesses the best amphoteric character critical in achieving proton conductivity when no solvent (i.e. water) is present. Finally, BSSE corrected binding energies were computed for the methyl acids with a single water molecule and indicated that while the magnitude of the interaction of the sulfonic and phosphonic acids with water are similar (47.3 and 44.4 kJ mol-1, respectively), the binding is much weaker to the imidazole (28.8 kJ mol-1). This result suggests that the oxo-acids will probably retain water better under very low humidity conditions and that the dynamics of the hydrogen bonding of the first hydration water molecules will be more constrained with -SO3H and -PO3H2 than imidazole.