Showing papers on "Hydrogen bond published in 2011"
3,322 citations
TL;DR: In this paper, a novel definition for the hydrogen bond is proposed, which takes into account the theoretical and experimental knowledge acquired over the past century, and six criteria are listed that could be used as evidence for the presence of a hydrogen bond.
Abstract: A novel definition for the hydrogen bond is recommended here. It takes into account the theoretical and experimental knowledge acquired over the past century. This def- inition insists on some evidence. Six criteria are listed that could be used as evidence for the presence of a hydrogen bond.
1,367 citations
TL;DR: In this paper, a new definition of the hydrogen bond is proposed, which emphasizes the need for evidence, and a list of criteria has been provided, and these can be used as evidence for hydrogen bond formation.
Abstract: The term "hydrogen bond" has been used in the literature for nearly a century now. While its importance has been realized by physicists, chemists, biologists, and material sci- entists, there has been a continual debate about what this term means. This debate has inten- sified following some important experimental results, especially in the last decade, which questioned the basis of the traditional view on hydrogen bonding. Most important among them are the direct experimental evidence for a partial covalent nature and the observation of a blue-shift in stretching frequency following X-HY hydrogen bond formation (XH being the hydrogen bond donor and Y being the hydrogen bond acceptor). Considering the recent experimental and theoretical advances, we have proposed a new definition of the hydrogen bond, which emphasizes the need for evidence. A list of criteria has been provided, and these can be used as evidence for the hydrogen bond formation. This list is followed by some char- acteristics that are observed in typical hydrogen-bonding environments.
809 citations
TL;DR: The dual characteristic of the CH/π hydrogen bond is the basis for ubiquitous existence of this force in various fields of chemistry and extends to the specificity of molecular recognition or selectivity in organic reactions, polymer science, surface phenomena and interactions involving proteins.
Abstract: The CH/π hydrogen bond is an attractive molecular force occurring between a soft acid and a soft base. Contribution from the dispersion energy is important in typical cases where aliphatic or aromatic CH groups are involved. Coulombic energy is of minor importance as compared to the other weak hydrogen bonds. The hydrogen bond nature of this force, however, has been confirmed by AIM analyses. The dual characteristic of the CH/π hydrogen bond is the basis for ubiquitous existence of this force in various fields of chemistry. A salient feature is that the CH/π hydrogen bond works cooperatively. Another significant point is that it works in nonpolar as well as polar, protic solvents such as water. The interaction energy depends on the nature of the molecular fragments, CH as well as π-groups: the stronger the proton donating ability of the CH group, the larger the stabilizing effect. This Perspective focuses on the consequence of this molecular force in the conformation of organic compounds and supramolecular chemistry. Implication of the CH/π hydrogen bond extends to the specificity of molecular recognition or selectivity in organic reactions, polymer science, surface phenomena and interactions involving proteins. Many problems, unsettled to date, will become clearer in the light of the CH/π paradigm.
701 citations
TL;DR: Recently, a recommendation has been made to the International Union of Pure and Applied Chemistry (IUPAC) suggesting an updated definition of the term hydrogen bond, which will be discussed in greater detail.
Abstract: A hydrogen bond is an interaction wherein a hydrogen atom is attracted to two atoms, rather than just one, and acts like a bridge between them. The strength of this attraction increases with the increasing electronegativity of either of the atoms, and in the classical view, all hydrogen bonds are highly electrostatic and sometimes even partly covalent. Gradually, the concept of a hydrogen bond has become more relaxed to include weaker and more dispersive interactions, provided some electrostatic character remains. A great variety of very strong, strong, moderately strong, weak, and very weak hydrogen bonds are observed in practice. Weak hydrogen bonds are now invoked in several matters in structural chemistry and biology. While strong hydrogen bonds are easily covered by all existing definitions of the phenomenon, the weaker ones may pose a challenge with regard to nomenclature and definitions. Recently, a recommendation has been made to the International Union of Pure and Applied Chemistry (IUPAC) suggesting an updated definition of the term hydrogen bond. This definition will be discussed in greater detail.
478 citations
TL;DR: The AMOEBA force field performs well across different environments and phases, and the key algorithms involved in the electrostatic model and a protocol for developing parameters are detailed to facilitate extension to additional molecular systems.
Abstract: An empirical potential based on permanent atomic multipoles and atomic induced dipoles is reported for alkanes, alcohols, amines, sulfides, aldehydes, carboxylic acids, amides, aromatics, and other small organic molecules. Permanent atomic multipole moments through quadrupole moments have been derived from gas phase ab initio molecular orbital calculations. The van der Waals parameters are obtained by fitting to gas phase homodimer QM energies and structures, as well as experimental densities and heats of vaporization of neat liquids. As a validation, the hydrogen bonding energies and structures of gas phase heterodimers with water are evaluated using the resulting potential. For 32 homo- and heterodimers, the association energy agrees with ab initio results to within 0.4 kcal/mol. The RMS deviation of the hydrogen bond distance from QM optimized geometry is less than 0.06 A. In addition, liquid self-diffusion and static dielectric constants computed from a molecular dynamics simulation are consistent wit...
389 citations
TL;DR: A combined experimental and theoretical study of the air–water interface is reported using surface-selective heterodyne-detected vibrational sum frequency spectroscopy to focus on the ‘free OD’ transition found only in the topmost water layer, finding a remarkably fast onset of bulk-phase behaviour on crossing from the air into the water phase.
Abstract: Surface phenomena at the air–water interface are of vital importance in many situations, from oceanography to atmospheric and environmental chemistry. An unanswered question in the field is how thin is the interfacial region — or how soon do the properties of bulk liquid water reappear as the interface is crossed. Using spectroscopy to probe the 'free OD' vibrational mode of water molecules with an oxygen–deuterium bond protruding from the surface and theoretical modelling to interpret the results, Stiopkin et al. find that water molecules straddling the interface form hydrogen bonds that are only slightly weaker than those in bulk water. This suggests a remarkably rapid onset of bulk-phase behaviour, and an extremely short 'healing length' for the interface on crossing from the air into the water phase. The air–water interface is perhaps the most common liquid interface. It covers more than 70 per cent of the Earth’s surface and strongly affects atmospheric, aerosol and environmental chemistry. The air–water interface has also attracted much interest as a model system that allows rigorous tests of theory, with one fundamental question being just how thin it is. Theoretical studies have suggested a surprisingly short ‘healing length’ of about 3 angstroms (1 A = 0.1 nm), with the bulk-phase properties of water recovered within the top few monolayers1,2,3. However, direct experimental evidence has been elusive owing to the difficulty of depth-profiling the liquid surface on the angstrom scale. Most physical, chemical and biological properties of water, such as viscosity, solvation, wetting and the hydrophobic effect, are determined by its hydrogen-bond network. This can be probed by observing the lineshape of the OH-stretch mode, the frequency shift of which is related to the hydrogen-bond strength4,5,6. Here we report a combined experimental and theoretical study of the air–water interface using surface-selective heterodyne-detected vibrational sum frequency spectroscopy to focus on the ‘free OD’ transition found only in the topmost water layer. By using deuterated water and isotopic dilution to reveal the vibrational coupling mechanism, we find that the free OD stretch is affected only by intramolecular coupling to the stretching of the other OD group on the same molecule. The other OD stretch frequency indicates the strength of one of the first hydrogen bonds encountered at the surface; this is the donor hydrogen bond of the water molecule straddling the interface, which we find to be only slightly weaker than bulk-phase water hydrogen bonds. We infer from this observation a remarkably fast onset of bulk-phase behaviour on crossing from the air into the water phase.
375 citations
TL;DR: The first pulsed field gradient nuclear magnetic resonance (PFG-NMR) study of DESs found the diffusion mechanism was found to be the same as for ionic liquids with discrete anions, which highlights that the molecular structure of the hydrogen bond donor can greatly affect the mobility of the whole system.
Abstract: Deep Eutectic Solvents (DESs) are a novel class of solvents with potential industrial applications in separation processes, chemical reactions, metal recovery and metal finishing processes such as electrodeposition and electropolishing. Macroscopic physical properties such as viscosity, conductivity, eutectic composition and surface tension are already available for several DESs, but the microscopic transport properties for this class of compounds are not well understood and the literature lacks experimental data that could give a better insight into the understanding of such properties. This paper presents the first pulsed field gradient nuclear magnetic resonance (PFG-NMR) study of DESs. Several choline chloride based DESs were chosen as experimental samples, each of them with a different associated hydrogen bond donor. The molecular equilibrium self-diffusion coefficient of both the choline cation and hydrogen bond donor was probed using a standard stimulated echo PFG-NMR pulse sequence. It is shown that the increasing temperature leads to a weaker interaction between the choline cation and the correspondent hydrogen bond donor. The self-diffusion coefficients of the samples obey an Arrhenius law temperature-dependence, with values of self-diffusivity in the range of [10−10–10−13 m2 s−1]. In addition, the results also highlight that the molecular structure of the hydrogen bond donor can greatly affect the mobility of the whole system. While for ethaline, glyceline and reline the choline cation diffuses slower than the associated hydrogen bond donor, reflecting the trend of molecular size and molecular weight, the opposite behaviour is observed for maline, in which the hydrogen bond donor, i.e. malonic acid, diffuses slower than the choline cation, with self-diffusion coefficients values of the order of 10−13 m2 s−1 at room temperature, which are remarkably low values for a liquid. This is believed to be due to the formation of extensive dimer chains between malonic acid molecules, which restricts the mobility of the whole system at low temperature (<30 °C), with malonic acid and choline chloride having almost identical diffusivity values. Diffusion and viscosity data were combined together to gain insights into the diffusion mechanism, which was found to be the same as for ionic liquids with discrete anions.
374 citations
TL;DR: In this article, the authors report ab initio path integral molecular dynamics studies on the quantum nature of the hydrogen bond and show that quantum nuclear effects weaken weak hydrogen bonds but strengthen relatively strong ones.
Abstract: Hydrogen bonds are weak, generally intermolecular bonds, which hold much of soft matter together as well as the condensed phases of water, network liquids, and many ferroelectric crystals. The small mass of hydrogen means that they are inherently quantum mechanical in nature, and effects such as zero-point motion and tunneling must be considered, though all too often these effects are not considered. As a prominent example, a clear picture for the impact of quantum nuclear effects on the strength of hydrogen bonds and consequently the structure of hydrogen bonded systems is still absent. Here, we report ab initio path integral molecular dynamics studies on the quantum nature of the hydrogen bond. Through a systematic examination of a wide range of hydrogen bonded systems we show that quantum nuclear effects weaken weak hydrogen bonds but strengthen relatively strong ones. This simple correlation arises from a competition between anharmonic intermolecular bond bending and intramolecular bond stretching. A simple rule of thumb is provided that enables predictions to be made for hydrogen bonded materials in general with merely classical knowledge (such as hydrogen bond strength or hydrogen bond length). Our work rationalizes the influence of quantum nuclear effects, which can result in either weakening or strengthening of the hydrogen bonds, and the corresponding structures, across a broad range of hydrogen bonded materials. Furthermore, it highlights the need to allow flexible molecules when anharmonic potentials are used in force field-based studies of quantum nuclear effects.
363 citations
TL;DR: It is seen that the substitution of fluorines in systems containing smaller halogens results in electrostatic potentials resembling those of systems with larger halogens, with correspondingly stronger interaction energies, and it is shown that aromatic fluorine substitutions affect the optimal geometries of the halogen-bonded complexes.
Abstract: In the past several years, halogen bonds have been shown to be relevant in crystal engineering and biomedical applications. One of the reasons for the utility of these types of noncovalent interactions in the development of, for example, pharmaceutical ligands is that their strengths and geometric properties are very tunable. That is, substitution of atoms or chemical groups in the vicinity of a halogen can have a very strong effect on the strength of the halogen bond. In this study we investigate halogen-bonding interactions involving aromatically-bound halogens (Cl, Br, and I) and a carbonyl oxygen. The properties of these halogen bonds are modulated by substitution of aromatic hydrogens with fluorines, which are very electronegative. It is found that these types of substitutions have dramatic effects on the strengths of the halogen bonds, leading to interactions that can be up to 100% stronger. Very good correlations are obtained between the interaction energies and the magnitudes of the positive electrostatic potentials (σ-holes) on the halogens. Interestingly, it is seen that the substitution of fluorines in systems containing smaller halogens results in electrostatic potentials resembling those of systems with larger halogens, with correspondingly stronger interaction energies. It is also shown that aromatic fluorine substitutions affect the optimal geometries of the halogen-bonded complexes, often as the result of secondary interactions.
352 citations
TL;DR: How the synergistic activity of cellulases was enhanced by altering the hydrogen bond network within crystalline cellulose fibrils was demonstrated, which led to an enhancement in apparent cellulase activity and unique insight into the nature of cellulose recalcitrance.
Abstract: Conversion of lignocellulose to biofuels is partly inefficient due to the deleterious impact of cellulose crystallinity on enzymatic saccharification. We demonstrate how the synergistic activity of cellulases was enhanced by altering the hydrogen bond network within crystalline cellulose fibrils. We provide a molecular-scale explanation of these phenomena through molecular dynamics (MD) simulations and enzymatic assays. Ammonia transformed the naturally occurring crystalline allomorph I(β) to III(I), which led to a decrease in the number of cellulose intrasheet hydrogen bonds and an increase in the number of intersheet hydrogen bonds. This rearrangement of the hydrogen bond network within cellulose III(I), which increased the number of solvent-exposed glucan chain hydrogen bonds with water by ~50%, was accompanied by enhanced saccharification rates by up to 5-fold (closest to amorphous cellulose) and 60-70% lower maximum surface-bound cellulase capacity. The enhancement in apparent cellulase activity was attributed to the "amorphous-like" nature of the cellulose III(I) fibril surface that facilitated easier glucan chain extraction. Unrestricted substrate accessibility to active-site clefts of certain endocellulase families further accelerated deconstruction of cellulose III(I). Structural and dynamical features of cellulose III(I), revealed by MD simulations, gave additional insights into the role of cellulose crystal structure on fibril surface hydration that influences interfacial enzyme binding. Subtle alterations within the cellulose hydrogen bond network provide an attractive way to enhance its deconstruction and offer unique insight into the nature of cellulose recalcitrance. This approach can lead to unconventional pathways for development of novel pretreatments and engineered cellulases for cost-effective biofuels production.
TL;DR: In this article, a detailed analysis of Hirshfeld surfaces and fingerprint plots facilitates a comparison of intermolecular interactions, which are crucial in building different supramolecular architectures.
Abstract: Mononuclear copper(II) and nickel(II) complexes, [(C5H6N2)Cu(IDA)(H2O)] (1) and (C5H7N2)2[Ni(IDA)2(H2O)] (2) [H2IDA = iminodiacetic acid; C5H6N2 = 4-aminopyridine; C5H7N2 = protonated 2-aminopyridine], have been synthesized, and their crystal structures were solved using single crystal X-ray diffraction data. A detailed analysis of Hirshfeld surfaces and fingerprint plots facilitates a comparison of intermolecular interactions, which are crucial in building different supramolecular architectures. Molecules are linked by a combination of N–H···O, O–H···O and C–H···O hydrogen bonds into two-dimensional framework, whose formation is readily analyzed in terms of substructures of lower dimensionality with zero finite zero-dimensional dimeric units as the building blocks within the structures. Moreover, the aromatic molecules that are engaged in lone pair···π interactions with the noncoordinated carbonyl moieties play a crucial role in stabilizing the self-assembly process observed for both complexes. Intricate...
TL;DR: In this paper, the hydrogen bond interaction energy (E HB ) of HF⋯HR (R = H, Li, Al, Cl, CCH) complexes under external electric fields is investigated in terms of the bonding distance and of several properties at the bond critical point.
TL;DR: Although ionic liquids consist solely of anions and cations and Coulomb forces are the dominating interaction, local and directional interaction such as hydrogen bonding has significant influence on the structure and properties of ionic liquid.
Abstract: Potential applications of ionic liquids depend on the properties of this class of liquid material. To a large extent the structure and properties of these Coulomb systems are determined by the intermolecular interactions among anions and cations. In particular the subtle balance between Coulomb forces, hydrogen bonds and dispersion forces is of great importance for the understanding of ionic liquids. The purpose of the present paper is to answer three questions: Do hydrogen bonds exist in these Coulomb fluids? To what extent do hydrogen bonds contribute to the overall interaction between anions and cations? And finally, are hydrogen bonds important for the physical properties of ionic liquids? All these questions are addressed by using a suitable combination of experimental and theoretical methods including newly synthesized imidazolium-based ionic liquids, far infrared spectroscopy, terahertz spectroscopy, DFT calculations, differential scanning calorimetry (DSC), viscometry and quartz-crystal-microbalance measurements. The key statement is that although ionic liquids consist solely of anions and cations and Coulomb forces are the dominating interaction, local and directional interaction such as hydrogen bonding has significant influence on the structure and properties of ionic liquids. This is demonstrated for the case of melting points, viscosities and enthalpies of vaporization. As a consequence, a variety of important properties can be tuned towards a larger working temperature range, finally expanding the range of potential applications.
TL;DR: Cooperation between two distinct noncovalent interactions leads to unusual effects on receptor selectivity, a result of fundamental differences in the interactions of halogen- and hydrogen-bond donor groups with anions.
Abstract: Studies of a series of urea-based anion receptors designed to probe the potential for anion recognition through combinations of hydrogen and halogen bonding are presented. Proton- and fluorine-NMR spectroscopy indicates that the two interactions act in concert to achieve binding of certain anions, a conclusion supported by computational studies. Replacement of the halogen-bond donating iodine substituent by fluorine (which does not participate in halogen bonding) enables estimation of the contribution of this interaction to the free energy of anion binding. Evidence for attractive contacts between anions and electron-deficient arenes arising from the use of perfluoroarene-functionalized ureas as control receptors is also discussed. The magnitude of the free energy contribution of halogen bonding depends both on the geometric features of the group linking the hydrogen- and halogen-bond donor groups and on the identity of the bound anion. The results are interpreted in relation to fundamental features of the halogen-bonding interaction, including its directionality and unusual preference for halides over oxoanions. Cooperation between two distinct noncovalent interactions leads to unusual effects on receptor selectivity, a result of fundamental differences in the interactions of halogen- and hydrogen-bond donor groups with anions.
TL;DR: Mechanistic investigations indicate that the reaction proceeds via nucleophilic attack of the phthalimide on an aromatic radical cation, as opposed to the electrophilic aromatic amination that has been reported for other I(III) amination reactions.
Abstract: The development of a novel intermolecular oxidative amination reaction, a synthetic transformation that involves the simultaneous functionalization of both a N–H and C–H bond, is described. The process, which is mediated by an I(III) oxidant and contains no metal catalysts, provides a rapid and green method for synthesizing protected anilines from simple arenes and phthalimide. Mechanistic investigations indicate that the reaction proceeds via nucleophilic attack of the phthalimide on an aromatic radical cation, as opposed to the electrophilic aromatic amination that has been reported for other I(III) amination reactions. The application of this new reaction to the synthesis of a variety of substituted aniline derivatives is demonstrated.
TL;DR: NMR based evidence for intramolecular hydrogen bonding in several ‘beyond rule of five’ oral drugs is described and the propensity for these drugs to form intramolescular hydrogen bonds could be predicted for through modelling the lowest energy conformation in the gas phase.
Abstract: Utilising ‘beyond rule of five’ chemical space is becoming increasingly important in drug design, but is usually at odds with good oral absorption. The formation of intramolecular hydrogen bonds in drug molecules is hypothesised to shield polarity facilitating improved membrane permeability and intestinal absorption. NMR based evidence for intramolecular hydrogen bonding in several ‘beyond rule of five’ oral drugs is described. Furthermore, the propensity for these drugs to form intramolecular hydrogen bonds could be predicted for through modelling the lowest energy conformation in the gas phase. The modulation of apparent lipophilicity through intramolecular hydrogen bonding in these molecules is supported by intrinsic cell permeability and intestinal absorption data in rat and human.
TL;DR: The present study indicates that there is no ice-like structure at the surface, but that there are water pairs interacting with a strong hydrogen bond at the outermost surface, and confirms that the major source of the isotope effect on the water χ((2)) spectra is the intramolecular anharmonic coupling, i.e., Fermi resonance.
Abstract: The energetically unfavorable termination of the hydrogen-bonded network of water molecules at the air/water interface causes molecular rearrangement to minimize the free energy. The long-standing question is how water minimizes the surface free energy. The combination of advanced, surface-specific nonlinear spectroscopy and theoretical simulation provides new insights. The complex χ(2) spectra of isotopically diluted water surfaces obtained by heterodyne-detected sum frequency generation spectroscopy and molecular dynamics simulation show excellent agreement, assuring the validity of the microscopic picture given in the simulation. The present study indicates that there is no ice-like structure at the surface—in other words, there is no increase of tetrahedrally coordinated structure compared to the bulk—but that there are water pairs interacting with a strong hydrogen bond at the outermost surface. Intuitively, this can be considered a consequence of the lack of a hydrogen bond toward the upper gas phas...
TL;DR: Hydrogen-bond-activated C-N bond cleavage of allylic amines was realized in Pd-catalyzed allylic alkylation to form the C-C bond product.
Abstract: Hydrogen-bond-activated C–N bond cleavage of allylic amines was realized in Pd-catalyzed allylic alkylation to form the C–C bond product. The method could be expanded to a series of allylic amines and carbonyl compounds with excellent results. It provides a new and convenient access to C–C bond formation based on Pd-catalyzed allylic alkylation of allylic amines by using only inexpensive alcohol solvents.
TL;DR: Urea m-values for protein folding and other protein processes are quantitatively interpreted and predicted using these urea interaction potentials or Kp values, which reveal that urea accumulates moderately at amide O and weakly at aliphatic C, whereas GB is excluded from both.
Abstract: To explain the large, opposite effects of urea and glycine betaine (GB) on stability of folded proteins and protein complexes, we quantify and interpret preferential interactions of urea with 45 model compounds displaying protein functional groups and compare with a previous analysis of GB. This information is needed to use urea as a probe of coupled folding in protein processes and to tune molecular dynamics force fields. Preferential interactions between urea and model compounds relative to their interactions with water are determined by osmometry or solubility and dissected using a unique coarse-grained analysis to obtain interaction potentials quantifying the interaction of urea with each significant type of protein surface (aliphatic, aromatic hydrocarbon (C); polar and charged N and O). Microscopic local-bulk partition coefficients Kp for the accumulation or exclusion of urea in the water of hydration of these surfaces relative to bulk water are obtained. Kp values reveal that urea accumulates moderately at amide O and weakly at aliphatic C, whereas GB is excluded from both. These results provide both thermodynamic and molecular explanations for the opposite effects of urea and glycine betaine on protein stability, as well as deductions about strengths of amide NH—amide O and amide NH—amide N hydrogen bonds relative to hydrogen bonds to water. Interestingly, urea, like GB, is moderately accumulated at aromatic C surface. Urea m-values for protein folding and other protein processes are quantitatively interpreted and predicted using these urea interaction potentials or Kp values.
Journal Article•
TL;DR: Density functional theory calculations showed that the transfer of hydrogen from surface hydroxyls to the molecule and its interaction with surface hydoxyls substantially lowered the activation barrier for rotational motion across the surface.
Abstract: Stop or Go on Oxide Surfaces Direct studies of surface diffusion with instruments such as the scanning tunneling microscope (STM) have often focused on species on metal surfaces, but surface diffusion can play an important role for reactions on metal oxide surfaces. Li et al. (p. 882) used STM and density functional theory calculations to study how catechol (a benzene ring bearing two −OH groups) diffuses on the surface of the rutile phase of titanium dioxide. Both mobile and immobile species were observed on the time scale of minutes while making repeated STM scans. Hydrogen atom transfers between surface OH groups and the molecule changed the interaction energy between the molecule and the surface, and hence the barrier for diffusion. The diffusion barrier for an organic molecule on a hydroxylated metal oxide surface depends on hydrogen bond formation. Direct studies of how organic molecules diffuse on metal oxide surfaces can provide insights into catalysis and molecular assembly processes. We studied individual catechol molecules, C6H4(OH)2, on a rutile TiO2(110) surface with scanning tunneling microscopy. Surface hydroxyls enhanced the diffusivity of adsorbed catecholates. The capture and release of a proton caused individual molecules to switch between mobile and immobile states within a measurement period of minutes. Density functional theory calculations showed that the transfer of hydrogen from surface hydroxyls to the molecule and its interaction with surface hydroxyls substantially lowered the activation barrier for rotational motion across the surface. Hydrogen bonding can play an essential role in the initial stages of the dynamics of molecular assembly.
TL;DR: Natural bond orbital analysis, energy decomposition, and visualization of total electron density shifts reveal other similarities and differences between the three sorts of molecular interaction.
Abstract: When PH3 is paired with NH3, the two molecules are oriented such that the P and N atoms face one another directly, without the intermediacy of a H atom Quantum calculations indicate that this attraction is due in part to the transfer of electron density from the lone pair of the N atom to the σ* antibond of a P–H covalent bond Unlike a H-bond, the pertinent hydrogen is oriented about 180° away from, instead of toward, the N, and the N lone pair overlaps with the lobe of the P–H σ* orbital that is closest to the P In contrast to halogen bonds, there is no requirement of a σ-hole of positive electrostatic potential on the P atom, nor is it necessary for the two interacting atoms to be of differing potential In fact, the two atoms can be identical, as the global minimum of the PH3 homodimer has the same structure, characterized by a P ⋅⋅⋅ P attraction Natural bond orbital analysis, energy decomposition, and visualization of total electron density shifts reveal other similarities and differences between the three sorts of molecular interaction
TL;DR: The spin-polarized density of states reveals a strong hybridization of frontier orbitals of NO(2) and NO(3) with the electronic states around the Fermi level of GO, and gives rise to the strong acceptor doping by these molecules and remarkable charge transfers from molecules to GO, compared to NO and N( 2)O(4) adsorptions on GO.
Abstract: The interactions of nitrogen oxides NO(x) (x = 1,2,3) and N(2)O(4) with graphene and graphene oxides (GOs) were studied by the density functional theory. Optimized geometries, binding energies, and electronic structures of the gas molecule-adsorbed graphene and GO were determined on the basis of first-principles calculations. The adsorption of nitrogen oxides on GO is generally stronger than that on graphene due to the presence of the active defect sites, such as the hydroxyl and carbonyl functional groups and the carbon atom near these groups. These active defect sites increase the binding energies and enhance charge transfers from nitrogen oxides to GO, eventually leading to the chemisorption of gas molecules and the doping character transition from acceptor to donor for NO(2) and NO. The interaction of nitrogen oxides with GO with various functional groups can result in the formation of hydrogen bonds OH⋅⋅⋅O (N) between -OH and nitrogen oxides and new weak covalent bonds C⋅⋅⋅N and C⋅⋅⋅O, as well as the H abstraction to form nitrous acid- and nitric acidlike moieties. The spin-polarized density of states reveals a strong hybridization of frontier orbitals of NO(2) and NO(3) with the electronic states around the Fermi level of GO, and gives rise to the strong acceptor doping by these molecules and remarkable charge transfers from molecules to GO, compared to NO and N(2)O(4) adsorptions on GO. The calculated results show good agreement with experimental observations.
TL;DR: In this paper, four organic compounds based on substituted coumarin derivatives were synthesized and characterized by X-ray structural studies with a detailed analysis of Hirshfeld surface and fingerprint plots facilitating a comparison of intermolecular interactions in building different supramolecular architectures.
Abstract: Four organic compounds based on substituted coumarin derivatives (1–4) have been synthesized and characterized by X-ray structural studies with a detailed analysis of Hirshfeld surface and fingerprint plots facilitating a comparison of intermolecular interactions in building different supramolecular architectures. The X-ray study reveals that in the molecular packing C–H···O, π···π, and carbonyl (lone pair)···π interactions cooperatively take part. The recurring feature of the self-assembly in all the compounds is the appearance of the molecular ribbon through weak hydrogen bonding. These hydrogen bonded ribbons further stacked into molecular layers by π···π forces. The mode of cooperativity of the weak C–H···O and π···π forces is such that they operate in mutually perpendicular directions — hydrogen bonding in the plane of the molecule at their edges and π-stacking perpendicular to the molecular plane. Investigation of intermolecular interactions and crystal packing via Hirshfeld surface analyses reveals...
TL;DR: Principal component analysis of the data showed that partitioning was a dominating mechanism for uncharged solutes in HILIC, and correlations between functional groups and interactions were observed, which confirms that the HilIC retention mechanism is partly contributed by adsorption mechanisms involving electrostatic interaction and multipoint hydrogen bonding.
TL;DR: It is shown that almost buried polar atoms--a common feature on protein binding sites--tend to form hydrogen bonds that are shielded from water, affording a novel tool to interpret and predict structure-kinetics relationships.
Abstract: Time scale control of molecular interactions is an essential part of biochemical systems, but very little is known about the structural factors governing the kinetics of molecular recognition. In drug design, the lifetime of drug–target complexes is a major determinant of pharmacological effects but the absence of structure–kinetic relationships precludes rational optimization of this property. Here we show that almost buried polar atoms—a common feature on protein binding sites—tend to form hydrogen bonds that are shielded from water. Formation and rupture of this type of hydrogen bonds involves an energetically penalized transition state because it occurs asynchronously with dehydration/rehydration. In consequence, water-shielded hydrogen bonds are exchanged at slower rates. Occurrence of this phenomenon can be anticipated from simple structural analysis, affording a novel tool to interpret and predict structure–kinetics relationships. The validity of this principle has been investigated on two pairs of...
TL;DR: The results of molecular simulation of water in silica nanopores at full hydration and room temperature find that water forms two distinct molecular layers at the interface and exhibits uniform, but somewhat lower than bulk liquid, density in the core region.
Abstract: We report the results of molecular simulation of water in silica nanopores at full hydration and room temperature. The model systems are approximately cylindrical pores in amorphous silica, with diameters ranging from 20 to 40 A. The filled pores are prepared using grand canonical Monte Carlo simulation and molecular dynamics simulation is used to calculate the water structure and dynamics. We found that water forms two distinct molecular layers at the interface and exhibits uniform, but somewhat lower than bulk liquid, density in the core region. The hydrogen bond density profile follows similar trends, with lower than bulk density in the core and enhancements at the interface, due to hydrogen bonds between water and surface non-bridging oxygens and OH groups. Our studies of water dynamics included translational mean squared displacements, orientational time correlations, survival probabilities in interfacial shells, and hydrogen bond population relaxation. We found that the radial-axial anisotropy in translational motion largely follows the predictions of a model of free diffusion in a cylinder. However, both translational and rotational water mobilities are strongly dependent on the proximity to the interface, with pronounced slowdown in layers near the interface. Within these layers, the effects of interface curvature are relatively modest, with only a small increase in mobility in going from the 20 to 40 A diameter pore. Hydrogen bond population relaxation is nearly bulk-like in the core, but considerably slower in the interfacial region.
TL;DR: It was found that there are not any distinct differences between RAHBs and the other intramolecular hydrogen bonds, and the CVB index based on the ELF method as well as the total electron energy density at the bond critical point of the proton-acceptor distance may be treated as universal descriptors of the hydrogen bond strength.
Abstract: B3LYP/aug-cc-pVTZ calculations were performed on the species with intramolecular O–H···O hydrogen bonds. The Quantum Theory of Atoms in Molecules (QTAIM) and the Electron Localization Function (ELF) method were applied to analyze these interactions. Numerous relationships between ELF and QTAIM parameters were found. It is interesting that the CVB index based on the ELF method as well as the total electron energy density at the bond critical point of the proton–acceptor distance (Hbcp) may be treated as universal descriptors of the hydrogen bond strength, they are also useful to estimate the covalent character of this interaction. There are so-called resonance-assisted hydrogen bonds (RAHBs) among the species analyzed here. It was found that there are not any distinct differences between RAHBs and the other intramolecular hydrogen bonds.
TL;DR: Ab initio calculations have been carried out in a systematic investigation of P···N pnicogen complexes H( 2)XP:NXH(2) for X ═ H, CH(3), NH(2), OH, F, and Cl, as well as selected complexes with different substituents X bonded to P and N.
Abstract: Ab initio calculations have been carried out in a systematic investigation of P···N pnicogen complexes H2XP:NXH2 for X ═ H, CH3, NH2, OH, F, and Cl, as well as selected complexes with different substituents X bonded to P and N. Binding energies for complexes H2XP:NXH2 range from 8 to 27 kJ mol–1 and increase to 39 kJ mol–1 for H2FP:N(CH3)H2. Equilibrium structures have a nearly linear A–P–N arrangement, with A being the atom directly bonded to P. Binding energies correlate with intermolecular N–P distances as well as with bonding parameters obtained from AIM and SAPT analyses. Complexation increases 31P chemical shieldings in complexes with binding energies greater than 19 kJ mol–1. One-bond spin–spin coupling constants 1pJ(N–P) across the pnicogen interaction exhibit a quadratic dependence on the N–P distance for complexes H2XP:NXH2, similar to the dependence of 2hJ(X–Y) on the X–Y distance for complexes with X–H···Y hydrogen bonds. However, when the mixed complexes H2XP:NX′H2 are included, the curvature...
TL;DR: Simple alkyl-substituted pillar[5]arenes can form stable interpenetrated complexes with neutral bis(imidazole) guests utilizing multiple C-H···O(N) hydrogen bond and C- H···π interactions.