Study of a hydrogen-bombardment process for molecular cross-linking within thin films

A low-energy hydrogen bombardment method, without using any chemical additives, has been designed for fine tuning both physical and chemical properties of molecular thin films through selectively cleaving C-H bonds and keeping other bonds intact. In the hydrogen bombardment process, carbon radicals are generated during collisions between C-H bonds and hydrogen molecules carrying ～10 eV kinetic energy. These carbon radicals induce cross-linking of neighboring molecular chains. In this work, we focus on the effect of hydrogen bombardment on dotriacontane (C(32)H(66)) thin films as growing on native SiO(2) surfaces. After the hydrogen bombardment, XPS results indirectly explain that cross-linking has occurred among C(32)H(66) molecules, where the major chemical elements have been preserved even though the bombarded thin film is washed by organic solution such as hexane. AFM results show the height of the perpendicular phase in the thin film decreases due to the bombardment. Intriguingly, Young's modulus of the bombarded thin films can be increased up to ～6.5 GPa, about five times of elasticity of the virgin films. The surface roughness of the thin films can be kept as smooth as the virgin film surface after thorough bombardment. Therefore, the hydrogen bombardment method shows a great potential in the modification of morphological, mechanical, and tribological properties of organic thin films for a broad range of applications, especially in an aggressive environment.     

Liquid structure of acetic acid-water and trifluoroacetic acid-water mixtures studied by large-angle X-ray scattering and NMR

The structures of acetic acid (AA), trifluoroacetic acid (TFA), and their aqueous mixtures over the entire range of acid mole fraction xA have been investigated by using large-angle X-ray scattering (LAXS) and NMR techniques. The results from the LAXS experiments have shown that acetic acid molecules mainly form a chain structure via hydrogen bonding in the pure liquid. In acetic acid-water mixtures hydrogen bonds of acetic acid-water and water-water gradually increase with decreasing xA, while the chain structure of acetic acid molecules is moderately ruptured. Hydrogen bonds among water molecules are remarkably formed in acetic acid-water mixtures at xA相似文献   

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.     

Helical molecular programming: supramolecular double helices by dimerization of helical oligopyridine-dicarboxamide strands

Helically preorganized oligopyridine-dicarboxamide strands are found to undergo dimerization into double helical supramolecular architectures. Dimerization of single helical strands with five or seven pyridine rings has been characterized by NMR and mass spectrometry in various solvent/ temperature conditions. Solution studies and stochastic dynamic simulations consistently show an increasing duplex stability with increasing strand length. The double helical structures of three different dimers was characterized in the solid phase by X-ray diffraction analysis. Both aromatic stacking and hydrogen bonding contribute the double helical arrangement of the oligopyridinedicarboxamide strand. Inter-strand interactions involve extensive face-to-face overlap between aromatic rings, which is not possible in the single helical monomers. Most hydrogen bonds occur within each strand of the duplex and stabilize its helical shape. Some inter-strand hydrogen bonds are found in the crystal structures. Dynamic studies by NMR as well as by molecular modeling computations yield structural and kinetic information on the double helices and on monomer-dimer interconversion. In addition, they reveal the presence of a spring-like extension/compression as well as rotational displacement motions.     

The role of hydrogen bonding in supercooled methanol

The role of hydrogen bonding on the microscopic properties of supercooled methanol has been analyzed by means of molecular dynamics simulations. Thermodynamic, structural, and dynamical properties have been investigated in supercooled methanol. The results have been compared with those of an ideal methanol-like system whose molecules have the same dipole moment as the methanol but lack sites for hydrogen bonding. Upon cooling the methanol samples, translational relaxation times increase more rapidly than reorientational ones. This effect is much more important when hydrogen bonds are suppressed. Suppression of hydrogen bonds also results in lower critical temperatures for diffusion and for several characteristic relaxation time constants. The anisotropy of individual dynamics and the existence of dynamical heterogeneities have also been investigated.     

A C alpha-H...O hydrogen bond in a membrane protein is not stabilizing

Hydrogen bonds involving a carbon donor are very common in protein structures, and energy calculations suggest that Calpha-H...O hydrogen bonds could be about one-half the strength of traditional hydrogen bonds. It has therefore been proposed that these nontraditional hydrogen bonds could be a significant factor in stabilizing proteins, particularly membrane proteins as there is a low dielectric and no competition from water in the bilayer core. Nevertheless, this proposition has never been tested experimentally. Here, we report an experimental test of the significance of Calpha-H...O bonds for protein stability. Thr24 in bacteriorhodopsin, which makes an interhelical Calpha-H...O hydrogen bond to the Calpha of Ala51, was changed to Ala, Val, and Ser, and the thermodynamic stability of the mutants was measured. None of the mutants had significantly reduced stability. In fact, T24A was more stable than the wild-type protein by 0.6 kcal/mol. Crystal structures were determined for each of the mutants, and, while some structural changes were seen for T24S and T24V, T24A showed essentially no apparent structural alteration that could account for the increased stability. Thus, Thr24 appears to destabilize the protein rather than stabilize. Our results suggest that Calpha-H...O bonds are not a major contributor to protein stability.     

Hydrogen Bond Fluctuations Control Photochromism in a Reversibly Photo‐Switchable Fluorescent Protein

Reversibly switchable fluorescent proteins (RSFPs) are essential for high‐resolution microscopy of biological samples, but the reason why these proteins are photochromic is still poorly understood. To address this problem, we performed molecular dynamics simulations of the fast switching Met159Thr mutant of the RSFP Dronpa. Our simulations revealed a ground state structural heterogeneity in the chromophore pocket that consists of three populations with one, two, or three hydrogen bonds to the phenolate moiety of the chromophore. By means of non‐adiabatic quantum mechanics/molecular dynamics simulations, we demonstrated that the subpopulation with a single hydrogen bond is responsible for off‐switching through photo‐isomerization of the chromophore, whereas two or more hydrogen bonds inhibit the isomerization and promote fluorescence instead. While rational design of new RSFPs has so far focused on structure alone, our results suggest that structural heterogeneity must be considered as well.     

On the possibility of detecting low barrier hydrogen bonds with kinetic measurements

Recent experimental evidence has pointed to the possible presence of a short, strong hydrogen bond in the enzyme-substrate transition states in some biochemical reactions. To date, most experimental measures of these short, strong hydrogen bonds have monitored their equilibrium properties. In this work we show that kinetic measurements can also be used to detect the presence of short, strong hydrogen bonds. In particular, we find nontrivial differences among rate constant ratios of protonated to deuterated hydrogen bonds between strong and weak hydrogen bonds for proton transfer between donor-acceptor sites. We quantify this kinetic isotope effect by performing dynamical calculations of these rate constants by computing reactive flux through a dividing surface. This reactive flux is computed by evolving trajectories on an effective quantum mechanical potential energy surface.     

Ultrafast structural dynamics of water induced by dissipation of vibrational energy

In the liquid phase, water molecules form a disordered fluctuating network of intermolecular hydrogen bonds. Using both inter- and intramolecular vibrations as structural probes in ultrafast infrared spectroscopy, we demonstrate a two-stage structural response of this network to energy disposal: vibrational energy from individually excited water molecules is transferred to intermolecular modes, resulting in a sub-100 fs nuclear rearrangement that leaves the local hydrogen bonds weakened but unbroken. Subsequent energy delocalization over many molecules occurs on an approximately 1 ps time scale and is connected with the breaking of hydrogen bonds, resulting in a macroscopically heated liquid.     

alpha- and beta-FOX-7, polymorphs of a high energy density material, studied by X-ray single crystal and powder investigations in the temperature range from 200 to 423 K

The alpha-beta phase transition in the novel energetic material 1,1-diamino-2,2-dinitroethylene, C2H4N4O4 (FOX-7), has been studied by single-crystal X-ray investigations at five different temperatures over the 200-393 K range. In these investigations, the positions of the hydrogen atoms were experimentally determined without any geometric constraints. In addition, X-ray powder investigations using the Guinier technique have been performed to characterize the beta-phase up to 423 K. The alpha-beta phase transition at 389 K is first order, shows a discontinuous increase of the molar volume and entropy (DeltaV = 1.75 cm3/mol, X-ray investigation; DeltaS = 1.5 cal/K mol, DSC analysis), and can be classified as displacive. The hitherto unknown structure of beta-FOX-7 was solved at 393 K and showed simple structural relations to the alpha-polymorph. The characteristic bonding in wave-shaped layers is now found for beta-FOX-7 (P2(1)2(1)2(1), z = 4, a= 6.9738(7) A, b = 6.635(1) A, c = 11.648(2) A, 393 K), as well as for alpha-FOX-7 (P2(1)/n, z = 4, a = 6.9467(7) A, b = 6.6887(9) A, c = 11.350(1) A, beta = 90.143(13) degrees , 373 K). Interestingly, whereas the intramolecular C-C, C-N, N-O, and N-H bond distances remain nearly unchanged for both polymorphs over the whole temperature range from 200 to 393 K, the two nitro groups deviate strongly from the molecular plane formed by the two carbon and two amino nitrogen atoms. In alpha-FOX-7 at 373 K, the nitro groups are twisted -47 and +6 degrees with respect to the carbon-carbon bond, but in beta-FOX-7 at 393 K, these twist angles are changed to -36 and +20 degrees . Within the layers, the FOX-7 molecules show strong pi-conjugation and extensive intra- and intermolecular hydrogen bonding. In this investigation, we have been able to show that alpha- and beta-FOX-7 build up different nets of intermolecular hydrogen bonds. In alpha-FOX-7, each oxygen atom of the nitro groups is involved in two hydrogen bonds resulting in two intramolecular and six intermolecular hydrogen bonds. But in beta-FOX-7 this coordination changes, and half of the oxygen atoms build up two and the other half build up three hydrogen bonds leading to two intramolecular and eight intermolecular hydrogen bonds. The average intermolecular hydrogen bond distance increases slightly from 2.31 A in alpha-FOX-7 to 2.52 A in beta-FOX-7. The C-NO2 bonds are of particular interest because they are referred to as the detonation trigger. It has been suggested that these bonds could be strengthened by the extensive intermolecular hydrogen bonding within the layers in both polymorphs. Such bond strengthening via cooperative effects was proposed in earlier DFT calculations on FOX-7 and may be one key to understanding its low sensitivity and high activation energy to impact.     

Is inhibition process better described with MD(QM/MM) simulations? The case of urokinase type plasminogen activator inhibitors

Urokinase plasminogen activator (uPA) is an enzyme involved in cancer growth and metastasis. Therefore, the design of inhibitors of uPA is of high therapeutic value, and several chemical families have been explored, even if none has still emerged, emphasizing the need of a rationalized approach. This work represents a complete computational study of uPA complexed with five inhibitors, which present weak similarities. Molecular dynamics simulations in explicit solvent were conducted, and structural analyses, along with molecular mechanics (MM)/Poisson-Boltzmann surface area free energies estimations, yield precious structure-activity relationships of these inhibitors. Besides, we realized supplemental QM/MM computations that improved drastically the quality of our models providing original information on the hydrogen bonds and charge transfer effects, which are, most often, neglected in other studies. We suggest that these simulations and analyses could be reproduced for other systems involving protein/ligand molecular recognitions.     

Hydrogen‐bonding interactions in the active site of a low molecular weight protein‐tyrosine phosphatase

Molecular dynamics simulation of the Michaelis complex, phospho‐enzyme intermediate, and the wild‐type and C12S mutant have been carried out to examine hydrogen‐bonding interactions in the active site of the bovine low molecular weight protein‐tyrosine phosphatase (BPTP). It was found that the S_γ atom of the nucleophilic residue Cys‐12 is ideally located at a position opposite from the phenylphosphate dianion for an inline nucleophilic substitution reaction. In addition, electrostatic and hydrogen‐bonding interactions from the backbone amide groups of the phosphate‐binding loop strongly stabilize the thiolate anion, making Cys‐12 ionized in the active site. In the phospho‐enzyme intermediate, three water molecules are found to form strong hydrogen bonds with the phosphate group. In addition, another water molecule can be identified to form bridging hydrogen bonds between the phosphate group and Asp‐129, which may act as the nucleophile in the subsequent phosphate hydrolysis reaction, with Asp‐129 serving as a general base. The structural difference at the active site between the wild‐type and C12S mutant has been examined. It was found that the alkoxide anion is significantly shifted toward one side of the phosphate binding loop, away from the optimal position enjoyed by the thiolate anion of the wild‐type enzyme in an S_N2 process. This, coupled with the high pK_a value of an alcoholic residue, makes the C12S mutant catalytically inactive. These molecular dynamics simulations provided details of hydrogen bonding interactions in the active site of BPTP, and a structural basis for further studies using combined quantum mechanical and molecular mechanical potential to model the entire dephosphorylation reaction by BPTP. © 2000 John Wiley & Sons, Inc. J Comput Chem 21: 1192–1203, 2000     

Controllable Scission and Seamless Stitching of Metal–Organic Clusters by STM Manipulation

Scanning tunneling microscopy (STM) manipulation techniques have proven to be a powerful method for advanced nanofabrication of artificial molecular architectures on surfaces. With increasing complexity of the studied systems, STM manipulations are then extended to more complicated structural motifs. Previously, the dissociation and construction of various motifs have been achieved, but only in a single direction. In this report, the controllable scission and seamless stitching of metal–organic clusters have been successfully achieved through STM manipulations. The system presented here includes two sorts of hierarchical interactions where coordination bonds hold the metal–organic elementary motifs while hydrogen bonds among elementary motifs are directly involved in bond breakage and re‐formation. The key to making this reversible switching successful is the hydrogen bonding, which is comparatively facile to be broken for controllable scission, and, on the other hand, the directional characteristic of hydrogen bonding makes precise stitching feasible.     

On the mutual diffusion properties of ethanol-water mixtures

The structural organization, the number of hydrogen bonds (H bond), and the self- and mutual diffusion coefficients of ethanol-water mixtures were studied by molecular dynamics simulation. It was found that both the numbers of H bonds per water and per ethanol decrease as the mole fraction of ethanol increases. The composition dependences and the relationships between the self- and the mutual diffusion coefficients were further discussed. The self-diffusion coefficient of water has a large drop as the concentration of ethanol increases from 0 to 0.3 and then it nearly keeps constant, while that of ethanol has a minimum around ethanol mole fraction of 0.5. The mutual diffusion coefficient could be divided into two parts, the kinematic factor and the thermodynamic factor. Both the kinematic and thermodynamic factors for ethanol-water mixtures were calculated. It was found that the change trend of mutual diffusion coefficients with the composition is mainly dependent on the thermodynamic factors.     

The inhibitory effects of vinylphosphonate-linked thymidine dimers on the unidirectional translocation of PcrA helicase along DNA: a molecular modelling study

The PcrA DNA helicases are important bacterial enzymes and quintessential examples of molecular motors. Through conformational changes caused by ATP hydrolysis, they move along the template double helix, breaking the hydrogen bonds holding the two strands together, and separating the template chains so that the genetic information can be accessed. The flexibility of the DNA backbone is essential for the unidirectional translocation of PcrA. A modified DNA substrate with reduced backbone rotational flexibility (via an incorporated vinylphosphonate linkage) has previously been designed and tested as a helicase substrate. The results show that a single modification on the backbone is sufficient to inhibit the activity of PcrA. In this paper a range of molecular simulation methods have been applied to examine the structural origins of this inhibitory effect, as it tests our theories of the mechanism of action of this motor. We observe that the chemical modification has different effects on the energetics of DNA translocation through the protein as it reaches different sub-sites.     

一维链状配位聚合物{[Cu(H2bttc)(H2O)3]·3H2O}n的非等温反应动力学和晶体结构

为研究配位聚合物{[Cu(H₂bttc)(H₂O)₃]·3H₂O}_n(H₂bttc=1，2，4，5-benzenetetracarboxylate)的热分解机理和非等温反应动力学进行了DSC和TG-DTG热分析。由热分析结果和FTIR光谱推测了其热分解机理；将Kissinger法、Ozawa法、积分法和微分法得到的动力学参数进行比较确定了第一个失重过程最可能的动力学模型函数。配位聚合物的X射线单晶结构分析表明它由 [Cu(H₂bttc)(H₂O)₃]_n分子链组成，并有客体水分子通过分子间氢键附着在分子链上。这一结构特点与热分析结果相一致。还有一种氢键将分子链连接起来形成二维框架，这一框架在失去配位水和结晶水后到553 K开始分解。     

Two-dimensional infrared spectroscopy study on phase transition and structural variations of a hydrogen-bonded liquid crystal

Infrared (IR) spectra have been measured for a liquid crystal (LC) consisting of one trans-butene diacid (BD) molecule as a proton donor and two 4-(2,3,4-tridecyloxybenzoyloxy)-4'-stilbazoles (DBS) molecules as a proton acceptor (DBS:BD:DBS) linked together with each other by inter-molecular hydrogen bonds over a temperature range from 20 to 120 degrees C to explore its phase transition and heat-induced structural variations. The temperature-dependent IR spectra have shown that the inter-molecular hydrogen bonds are stable in the liquid crystalline phase but become slightly decoupled with temperature increasing. Two kinds of two-dimensional (2D) correlation spectroscopy, variable-variable (VV) and sample-sample (SS) 2D spectroscopy, have been employed to analyze the observed temperature-dependent spectral variations more efficiently. The SS 2D correlation analysis in the spectral range of 2700-1800 cm(-1) has demonstrated that a change in hydrogen bonds in the LC starts from 40 degrees C, which is not clarified by differential scanning calorimetry (DSC) and conventional IR and Raman spectroscopic analyses. On the other hand, the phase transition of LC revealed by SS 2D spectroscopy in the specific spectral regions of 1750-1650 and 3000-2700 cm(-1) is in a good agreement with that revealed by DSC for the heating process. The VV 2D correlation spectroscopy analysis has provided information about the structural variations of inter-molecular hydrogen bonds. The different species of hydrogen-bonded and free -COOH and -COO- groups in the LC have been clarified by the VV 2D correlation analysis. It has also elucidated the specific order of the temperature-induced structural changes in the intra- and inter-molecular hydrogen bonds concerning with the -COOH and/or -COO- groups in the LC.     

On the molecular mechanism of drug intercalation into DNA: a simulation study of the intercalation pathway, free energy, and DNA structural changes

Intercalation into DNA (insertion between a pair of base pairs) is a critical step in the function of many anticancer drugs. Despite its importance, a detailed mechanistic understanding of this process at the molecular level is lacking. We have constructed, using extensive atomistic computer simulations and umbrella sampling techniques, a free energy landscape for the intercalation of the anticancer drug daunomycin into a twelve base pair B-DNA. A similar free energy landscape has been constructed for a probable intermediate DNA minor groove-bound state. These allow a molecular level understanding of aspects of the thermodynamics, DNA structural changes, and kinetic pathways of the intercalation process. Key DNA structural changes involve opening the future intercalation site base pairs toward the minor groove (positive roll), followed by an increase in the rise, accompanied by hydrogen bonding changes of the minor groove waters. The calculated intercalation free energy change is -12.3 kcal/mol, in reasonable agreement with the experimental estimate -9.4 kcal/mol. The results point to a mechanism in which the drug first binds to the minor groove and then intercalates into the DNA in an activated process, which is found to be in general agreement with experimental kinetic results.     

Protein wrapping: a molecular marker for association, aggregation and drug design

In this tutorial review we survey the concept of protein wrapping from a physico-chemical perspective. Wrapping is introduced as an indicator of the packing quality of protein structure. Thus, while a well-wrapped protein is sustainable in isolation, a poorly wrapped protein is reliant on binding partnerships to maintain its structural integrity. At a local level, wrapping is indicative of the extent of solvent exposure of the amide-carbonyl hydrogen bonds of the protein backbone. Poorly wrapped hydrogen bonds, the so-called dehydrons, are shown to represent structural vulnerabilities. These singularities are sticky, hence promoters of protein associations. We also focus on severely under-wrapped protein structures that belong to an order/disorder twilight. Such proteins are shown to be prone to aggregate. Finally, we survey the recent exploitation of dehydrons as targetable features to promote specificity in drug-based cancer therapy. Dehydrons prove to be valuable targets to reduce side effects and enhance drug safety.     

On the nature of organic catalysis "on water"

A molecular origin of the striking rate increase observed in a reaction on water is studied theoretically. A key aspect of the on-water rate phenomenon is the chemistry between water and reactants that occurs at an oil-water phase boundary. In particular, the structure of water at the oil-water interface of an oil emulsion, in which approximately one in every four interfacial water molecules has a free ("dangling") OH group that protrudes into the organic phase, plays a key role in catalyzing reactions via the formation of hydrogen bonds. Catalysis is expected when these OH's form stronger hydrogen bonds with the transition state than with the reactants. In experiments more than a 5 orders of magnitude enhancement in rate constant was found in a chosen reaction. The structural arrangement at the "oil-water" interface is in contrast to the structure of water molecules around a small hydrophobic solute in homogeneous solution, where the water molecules are tangentially oriented. The latter implies that a breaking of an existing hydrogen-bond network in homogeneous solution is needed in order to permit a catalytic effect of hydrogen bonds, but not for the on-water reaction. Thereby, the reaction in homogeneous aqueous solution is intrinsically slower than the surface reaction, as observed experimentally. The proposed mechanism of rate acceleration is discussed in light of other on-water reactions that showed smaller accelerations in rates. To interpret the results in different media, a method is given for comparing the rate constants of different rate processes, homogeneous, neat and on-water, all of which have different units, by introducing models that reduce them to the same units. The observed deuterium kinetic isotope effect is discussed briefly, and some experiments are suggested that can test the present interpretation and increase our understanding of the on-water catalysis.