Towards an unified hydrogen-bond theory

Beyond Badger's Rule: The Origins and Generality of the Structure-Spectra Relationship of Aqueous Hydrogen Bonds

The structure of hydrogen bonded networks is intimately intertwined with their dynamics. Despite the incredibly wide range of hydrogen bond strengths encountered in water clusters, ion-water clusters, and liquid water, we demonstrate that the previously reported correlation between the change in the equilibrium bond length of the hydrogen bonded OH covalent bond and the corresponding shift in its harmonic frequency in water clusters is much more broadly applicable. Surprisingly, this correlation describes the ratios for both the equilibrium OH bond length/harmonic frequency and the vibrationally averaged bond length/anharmonic frequency in water, hydronium water, and halide water clusters. Consideration of harmonic and anaharmonic data leads to a correlation of -19 ± 1 cm^-1/0.001 Å. The fundamental nature of this correlation is further confirmed through the analysis of ab initio Molecular Dynamics (AIMD) trajectories for liquid water. We demonstrate that this simple correlation for both harmonic and anharmonic systems can be modeled by the response of an OH bond to an external field. Treating the OH bond as a Morse oscillator, we develop analytic expressions, which relate the ratio of the shift in the vibrational frequency of the hydrogen-bonded OH bond to the shift in OH bond length, to parameters in the Morse potential and the ratio of the first and second derivatives of the field-dependent projection of the dipole moment of water onto the hydrogen-bonded OH bond. Based on our analysis, we develop a protocol for reconstructing the AIMD spectra of liquid water from the sampled distribution of the OH bond lengths. Our findings elucidate the origins of the relationship between the molecular structure of the fleeting hydrogen-bonded network and the ensuing dynamics, which can be probed by vibrational spectroscopy.

Oxidative addition of carbon dioxide into mesoionics

This work examines the prospect of making stable mesoionic compounds of the type mesomeric betaine R+-CO2- from direct oxidative additions of carbon dioxide to suitably-delocalized singlet carbene moieties, with bold objectives of carbon sequestration and overall energy storage. A set of possible candidates for such mesoionic compounds is theoretically explored through DFT calculations, inspecting coupling paths, thermodynamic and kinetic stabilities, and geometric and electronic structural features. Among others, the addressed cationic parts include aromatic rings in their broader sense, phenalene systems, and odd linear polyenic chains. Various structurally-close neutral alternatives such as oxiranones or carbene-acid forms are also considered. In the linear polyenic chain family, there is stark contrast between 4N + 1 and 4N - 1 lengths, with ensuing substantial consequences for stabilities and structures. Amino substitutions can favor mesoionic arrangements through their cation-stabilizing π-donor properties, further supported by possible strong intramolecular hydrogen bonds, but they can also contribute to weaken their kinetic stability through the existence of stable neutral imino alternatives. All in all, mesoionics including tropylium, phenalene, or 4N + 1 odd polyene frames as cationic parts could be reasonable targets.

Structural organization and phase behaviour of meta-substituted dioctadecylaminobenzoquinones at the air/water interface

The structural organization and phase behaviour of an amphiphilic zwitterionic quinonemonoimine at the air/water interface are presented. Brewster angle microscopy reveals multiple co-existing phases are observed over the entire isotherm while grazing incidence X-ray diffraction (GIXD) shows that these comprise both tilted, untilted and multilayer structures with crystalline headgroups. Despite the heterogeneity, the phase transitions are highly reversible over multiple cycles.

π-Hydrogen bonding and aromaticity: a systematic interplay study

Quantum DFT calculations, corrected for long-range interactions, have been carried out on complex models formed between HF as a proton donor and 2-methylene-2H-indene derivatives as proton acceptors. Using various exocyclic X substitutions, mutual effects of the aromaticity and the strength of the resulting π-hydrogen bond (after its evaluation by AIM methodology) have been investigated. The results show that the aromaticity of 6-membered rings and the hydrogen bond strength increase upon increasing the electron-donating character of the X-substituents. Based on some aromaticity indices (HOMA, FLU, SA and NICS(1)zz), it has been shown that the formation of a π-hydrogen bond causes an increase of aromaticity of the 6-membered ring. Also, the strength of the resulting π-hydrogen bond (with an energy of about 4.0 to 7.0 kcal mol-1) depends on the aromaticity of the 6-membered ring and increases with an increase in the aromaticity. In addition, a linear relationship was found between the most negative value of the molecular electrostatic potential (Vmin) and the HOMA, which confirms that the Vmin in the region of the studied ring could be used as a new index to estimate the amount of aromaticity. The electronic properties of the complexes have also been evaluated by means of the molecular electrostatic potential (MEP), the atoms in molecules (AIM) and the natural bond orbital (NBO) analyses.

Charge-assisted hydrogen bonding as a cohesive force in soil organic matter: water solubility enhancement by addition of simple carboxylic acids

Weak bonds between molecular segments and between separate molecules of natural organic matter (OM) govern OM solubility, adsorption, supramolecular association in solution, and complexation with metal ions and oxides. We tested the hypothesis that especially strong hydrogen bonds, known as (negative) charge-assisted hydrogen bonds, (-)CAHB, contribute significantly to OM cohesion and play a role in the water solubility of solid-phase OM. The (-)CAHB, exemplified by structures such as (-CO2HO2C-)- and (-CO2HO-)-, may form between weak acids with similar proton affinity, and is shorter, more covalent, and much stronger than ordinary hydrogen bonds. Using a high-organic reference soil, we show that (-)CAHBs within the solid OM phase (intra-OM) are disrupted by solutions of aliphatic and aromatic acids, resulting in enhanced solubility of OM. The aromatic acids included naturally occurring plant exudate compounds. At constant pH and ionic strength, OM solubility increased with added organic acid concentration and molecular weight. Polar compounds incapable of forming (-)CAHBs, such as alkanols, acetonitrile, and dimethyl sulfoxide, were ineffective. Solubility enhancement showed behavior consistent with (-)CAHB theory and published observations-namely, (i) that formate is more effective than acetate due to its tendency to form stronger (-)CAHBs; (ii) that solubility enhancement peaks at pH ∼5-6, where the product of the concentration of the interacting carboxylate ions reaches a maximum; and (iii) that elution of acetate or formate through soil columns releases hydroxide ion, consistent with formation of (-)CAHBs between added acid and free weak acid groups on the solid OM. The results support the hypothesis that the (-)CAHB contributes to the cohesion of OM in the solid state.

Discovery of Quinazolines That Activate SOS1-Mediated Nucleotide Exchange on RAS

Proteins in the RAS family are important regulators of cellular signaling and, when mutated, can drive cancer pathogenesis. Despite considerable effort over the last 30 years, RAS proteins have proven to be recalcitrant therapeutic targets. One approach for modulating RAS signaling is to target proteins that interact with RAS, such as the guanine nucleotide exchange factor (GEF) son of sevenless homologue 1 (SOS1). Here, we report hit-to-lead studies on quinazoline-containing compounds that bind to SOS1 and activate nucleotide exchange on RAS. Using structure-based design, we refined the substituents attached to the quinazoline nucleus and built in additional interactions not present in the initial HTS hit. Optimized compounds activate nucleotide exchange at single-digit micromolar concentrations in vitro. In HeLa cells, these quinazolines increase the levels of RAS-GTP and cause signaling changes in the mitogen-activated protein kinase/extracellular regulated kinase (MAPK/ERK) pathway.

Hydrogen Bonding in Amorphous Alkaline Earth Carbonates

Amorphous intermediates play a crucial role during the crystallization of alkaline earth carbonates. We synthesized amorphous carbonates of magnesium, calcium, strontium, and barium from methanolic solution. The local environment of water and the strength of hydrogen bonding in these hydrated modifications were probed with Fourier transform IR spectroscopy, ¹H NMR spectroscopy, and heteronuclear correlation experiments. Temperature-dependent spin-lattice (T1) relaxation experiments provided information about the water motion in the amorphous materials. The Pearson hardness of the respective divalent metal cation predominantly determines the strength of the internal hydrogen-bonding network. Amorphous magnesium carbonate deviates from the remaining carbonates, as it contains additional hydroxide ions, which act as strong hydrogen-bond acceptors. Amorphous calcium carbonate exhibits the weakest hydrogen bonds of all alkaline earth carbonates. Our study provides a coherent picture of the hydrogen bonding situation in these transient species and thereby contributes to a deeper understanding of the crystallization process of carbonates.

Hydrogen bonding from a valence bond theory perspective: the role of covalency

A valence bond theory based method has been developed to decompose hydrogen bond energies into contributions from geometry, electrostatics, polarization and charge transfer. This decomposition method has been carried out for F-HFH, F-HOH2, F-HNH3, HO-HOH2, HO-HNH3, and H2N-HNH3. Localized valence bond self-consistent field (L-VBSCF) and localized breathing orbital valence bond (L-BOVB) calculations were performed at the PBEPBE/aug-cc-pVDZ optimized geometries. It is shown that inclusion of valence bond structures that explicitly include charge transfer account for at least 32% (likely over half) of the hydrogen bond energy of all systems studied, indicating the dominant role of covalency. This is in agreement with calculated bond lengths, geometry deformation energies, and polarization energies. Electrostatic effects were found to play only a minor role in contrast to some widely held ideas regarding the nature of hydrogen bonding.

Extremely Strong Halogen Bond. The Case of a Double-Charge-Assisted Halogen Bridge

The stable model of a double (±)charge-assisted halogen bridge has been built on the basis of searches of the Crystal Structure Database. The model, investigated by DFT theory, consists of quinuclidine-like cation derivatives and a set of simple anions. These charged fragments form halogen-bonded complexes of which the energy of complexation in some cases reaches 100 kcal/mol. Even for such strong interactions, the QTAIM characteristics are similar to those of the more classic, relatively weak halogen bonds. An important effect of complexation is the charge transfer measured by means of QTAIM and NBO. It can also be supposed, on the basis of detailed structural and QTAIM analysis, that the delocalization of the charge in a quinuclidine moiety occurs through space and not necessarily along formal bonds. The analysis of only partially charged and fully neutral counterparts of a double (±)charge-assisted halogen bridge shows significantly weaker bonding, being less than 10 kcal/mol.

Homo-Conjugation of Low Molecular Weight Organic Acids Competes with Their Complexation with Cu(II)

Dissolved organic matter (DOM) controls the bioavailability and toxicity of heavy metals in aquatic environments. The observation of decreased conditional binding constants with increasing DOM concentration is not well documented, which may result in significant uncertainties in heavy metal behavior modeling and risk assessment. We used eight low molecular weight organic acids (LMOC) with representative structures to simulate DOM molecules. The interactions between LMOC molecules resulted in the decreased Cu(II)-LMOC binding with increasing LMOC concentrations, but higher pH values than theoretical calculation after mixing LMOC solutions of different pHs. We thus proposed homoconjugation between LMOC molecules through negative charge-assisted H-bond ((-)CAHB). A mathematic model was developed to describe Cu(II)-LMOC complexation ( K_C) and LMOC homoconjugation ( K_LHL). The increased competition of LMOC homoconjugation over Cu(II)-LMOC complexation, as suggested by the increased ratios of K_LHL/ K_C, resulted in the apparently decreased Cu(II)-LMOC binding with the increased LMOC concentration. Similar concentration-dependent binding was also observed for DOM. With the identified homoconjugation between DOM molecules, some of the literature data with concentration-dependent behavior may be re-evaluated. This is the first work that quantitatively identified homoconjugation among organic molecules. Both the modeling concepts and results provide useful information in investigating the environmental roles of DOM in mediating metal bioavailability and transport.

An Electron Density Source-Function Study of DNA Base Pairs in Their Neutral and Ionized Ground States†

The source function (SF) decomposes the electron density at any point into contributions from all other points in the molecule, complex, or crystal. The SF "illuminates" those regions in a molecule that most contribute to the electron density at a point of reference. When this point of reference is the bond critical point (BCP), a commonly used surrogate of chemical bonding, then the SF analysis at an atomic resolution within the framework of Bader's Quantum Theory of Atoms in Molecules returns the contribution of each atom in the system to the electron density at that BCP. The SF is used to locate the important regions that control the hydrogen bonds in both Watson-Crick (WC) DNA dimers (adenine:thymine (AT) and guanine:cytosine (GC)) which are studied in their neutral and their singly ionized (radical cationic and anionic) ground states. The atomic contributions to the electron density at the BCPs of the hydrogen bonds in the two dimers are found to be delocalized to various extents. Surprisingly, gaining or loosing an electron has similar net effects on some hydrogen bonds concealing subtle compensations traced to atomic sources contributions. Coarser levels of resolutions (groups, rings, and/or monomers-in-dimers) reveal that distant groups and rings often have non-negligible effects especially on the weaker hydrogen bonds such as the third weak CH⋅⋅⋅O hydrogen bond in AT. Interestingly, neither the purine nor the pyrimidine in the neutral or ionized forms dominate any given hydrogen bond despite that the former has more atoms that can act as source or sink for the density at its BCP. © 2018 Wiley Periodicals, Inc.

Specific features of supramolecular organisation and hydrogen bonding in proline cocrystals: a case study of fenamates and diclofenac

New zwitterionic cocrystals of fenamate drugs and diclofenac with the naturally occurring amino acid l-proline have been obtained and thoroughly characterised by a variety of experimental and theoretical techniques.

Theoretical investigation on ESIPT mechanism for a novel Sal-3,4-benzophen system

In this work, we theoretically investigate the properties of excited state process for a novel salicylidene sal-3,4-benzophen (Sal-3,4-B) system, which contains two intramolecular hydrogen bonds (O1-H2[Formula: see text]N3 and O4-H5[Formula: see text]N6). Based on the density functional theory (DFT) and time-dependent DFT (TDDFT) methods, we find these two hydrogen bonds should be strengthened in the S1 state, while the O4-H5[Formula: see text]N6 one could be largely affected upon the excitation process. Analyses about infrared (IR) vibrational spectra about hydrogen bond moieties also confirm this viewpoint. Frontier molecular orbitals (MOs) depict the nature of electronic excited state and support the excited state intramolecular proton transfer (ESIPT) reaction.Two kinds of stepwise potential energy curves of Sal-3,4-B in the S1 state demonstrate that only one proton could be transferred. Also based on constructing potential energy curves, the synergetic situation could be eliminated. Due to the specific ESIPT mechanism for Sal-3,4-B, we successfully explain the previous experiment and provide a reasonable attribution to the second emission peak of experiment.

A Critical Check for the Role of Resonance in Intramolecular Hydrogen Bonding

Although resonance-assisted H-bonds (RAHBs) are well recognized, the role of π resonance in RAHBs is controversial, as the seemingly enhanced H-bonds in unsaturated compounds may result from the constraints imposed by the σ skeleton. Herein the block-localized wave function (BLW) method, which can derive optimal yet resonance-quenched structures with related physiochemical properties, was employed to examine the correlation between π resonance and the strength of intramolecular RAHBs. Examination of a series of paradigmatic molecules with RAHBs and their saturated analogues showed that it is inappropriate to compare a conjugated system with its saturated counterpart, as they may have quite different σ frameworks. Nevertheless, comparison between a conjugated system and its resonance-quenched (i.e., electron-localized) state, which have identical σ skeletons, shows that in all studied cases, π resonance unanimously reduces the bonding distance by 0.111-0.477 Å, strengthens the bonding by 40-56 %, and redshifts the D-H vibrational frequency by 104-628 cm^-1 . Furthermore, there is an excellent correlation between hydrogen-bonding strength and the classical Coulomb attraction between the hydrogen-bond donor and the acceptor, which suggests that the dominant role of the electrostatic interaction in H-bonds and RAHBs originates from the charge flow from H-bond donors to acceptors through π conjugation.

Sorption of ionizable and ionic organic compounds to biochar, activated carbon and other carbonaceous materials

The sorption of ionic and ionizable organic compounds (IOCs) (e.g., pharmaceuticals and pesticides) on carbonaceous materials plays an important role in governing the fate, transport and bioavailability of IOCs. The paradigms previously established for the sorption of neutral organic compounds do not always apply to IOCs and the importance of accounting for the particular sorption behavior of IOCs is being increasingly recognized. This review presents the current state of knowledge and summarizes the recent advances on the sorption of IOCs to carbonaceous sorbents. A broad range of sorbents were considered to evaluate the possibility to read across between fields of research that are often considered in isolation (e.g., carbon nanotubes, graphene, biochar, and activated carbon). Mechanisms relevant to IOCs sorption on carbonaceous sorbents are discussed and critically evaluated, with special attention being given to emerging sorption mechanisms including low-barrier, charge-assisted hydrogen bonds and cation-π assisted π-π interactions. The key role played by some environmental factors is also discussed, with a particular focus on pH and ionic strength. Overall the review reveals significant advances in our understanding of the interactions between IOCs and carbonaceous sorbents. In addition, knowledge gaps are identified and priorities for future research are suggested.

Characterization of Ionizable Groups' Environments in Proteins and Protein-Ligand Complexes through a Statistical Analysis of the Protein Data Bank

We conduct a statistical analysis of the molecular environment of common ionizable functional groups in both protein-ligand complexes and inside proteins from the Protein Data Bank (PDB). In particular, we characterize the frequency, type, and density of the interacting atoms as well as the presence of a potential counterion. We found that for ligands, most guanidinium groups, half of primary and secondary amines, and one-fourth of imidazole neighbor a carboxylate group. Tertiary amines bind more rarely near carboxylate groups, which may be explained by a crowded neighborhood and hydrophobic character. In comparison to the environment seen by the ligands, inside proteins, an environment enriched in main-chain atoms is found, and the prevalence of direct charge neutralization by carboxylate groups is different. When the ionizable character of water molecules and phenolic or hydroxyl groups is accounted, considering a high-resolution dataset (less than 1.5 Å), charge neutralization could occur for well above 80% of the ligand functional groups considered, but for tertiary amines.

Activity and Reactivity of Pyrogenic Carbonaceous Matter toward Organic Compounds

Pyrogenic carbonaceous matter (PCM) includes environmental black carbon (fossil fuel soot, biomass char), engineered carbons (biochar, activated carbon), and related materials like graphene and nanotubes. These materials contact organic pollutants due to their widespread presence in the environment or through their use in various engineering applications. This review covers recent advances in our understanding of adsorption and chemical reactions mediated by PCM and the links between these processes. It also covers adsorptive processes previously receiving little attention and ignored in models such as steric constraints, physicochemical effects of confinement in nanopores, π interactions of aromatic compounds with polyaromatic surfaces, and very strong hydrogen bonding of ionizable compounds with surface functional groups. Although previous research has regarded carbons merely as passive sorbents, recent studies show that PCM can promote chemical reactions of sorbed contaminants at ordinary temperature, including long-range electron conduction between molecules and between microbes and molecules, local redox reactions between molecules, and hydrolysis. PCM may itself contain redox-active functional groups that are capable of oxidizing or reducing organic compounds and of generating reactive oxygen species (ROS) from oxygen, peroxides, or ozone. Amorphous carbons contain persistent free radicals that may play a role in observed redox reactions and ROS generation. Reactions mediated by PCM can impact the biogeochemical fate of pollutants and lead to useful strategies for remediation.

Crystal structure of 2-(aza-niumylmeth-yl)pyridinium bis(hydrogen squarate)

The asymmetric unit of the title compound, C6H10N22+·2C4HO4-, comprises two hydrogen squarate (Hsq-; systematic name: 2-hy-droxy-3,4-dioxo-cyclo-butano-late) anions and a 2-(aza-niumylmeth-yl)pyridinium dication. The squaric acid mol-ecules each donate an H atom to the N atoms of the pyridine ring and the amino-methyl units of a 2-(amino-meth-yl)pyridine mol-ecule, forming the 1:2 salt. The Hsq- anions are linked by strong O-H⋯O hydrogen bonds and an N-H⋯O hydrogen bond links the 2-(aza-niumylmeth-yl)pyridinium cation to one of the squaric acid anions. The crystal structure features additional N-H⋯O and O-H⋯O hydrogen bonds, π-π stacking and unusual weak C-O⋯π(ring) inter-actions.

Estimation of kinetic and thermodynamic ligand-binding parameters using computational strategies

Kinetic and thermodynamic ligand–protein binding parameters are gaining growing importance as key information to consider in drug discovery. The determination of the molecular structures, using particularly x-ray and NMR techniques, is crucial for understanding how a ligand recognizes its target in the final binding complex. However, for a better understanding of the recognition processes, experimental studies of ligand–protein interactions are needed. Even though several techniques can be used to investigate both thermodynamic and kinetic profiles for a ligand–protein complex, these procedures are very often laborious, time consuming and expensive. In the last 10 years, computational approaches have enormous potential in providing insights into each of the above effects and in parsing their contributions to the changes in both kinetic and thermodynamic binding parameters. The main purpose of this review is to summarize the state of the art of computational strategies for estimating the kinetic and thermodynamic parameters of a ligand–protein binding.

Polymer-Nucleic Acid Interactions

Gene therapy is an important therapeutic strategy in the treatment of a wide range of genetic disorders. Polymers forming stable complexes with nucleic acids (NAs) are non-viral gene carriers. The self-assembly of polymers and nucleic acids is typically a complex process that involves many types of interaction at different scales. Electrostatic interaction, hydrophobic interaction, and hydrogen bonds are three important and prevalent interactions in the polymer/nucleic acid system. Electrostatic interactions and hydrogen bonds are the main driving forces for the condensation of nucleic acids, while hydrophobic interactions play a significant role in the cellular uptake and endosomal escape of polymer-nucleic acid complexes. To design high-efficiency polymer candidates for the DNA and siRNA delivery, it is necessary to have a detailed understanding of the interactions between them in solution. In this chapter, we survey the roles of the three important interactions between polymers and nucleic acids during the formation of polyplexes and summarize recent understandings of the linear polyelectrolyte-NA interactions and dendrimer-NA interactions. We also review recent progress optimizing the gene delivery system by tuning these interactions.

Extensive analysis of N-H...O hydrogen bonding in four classes of phosphorus compounds: a combined experimental and database study

The N-H...O hydrogen bond is the characteristic interaction in the crystal structures of N-benzyl-P-phenyl-N'-(p-tolyl)phosphonic diamide, C₂₀H₂₁N₂OP or (C₆H₅)P(O)(NHCH₂C₆H₅)(NHC₆H₄-p-CH₃), (I), diphenylphosphinic 1-methylpropylamide, C₁₆H₂₀NOP or (C₆H₅)₂P(O)[NHCH(CH₃)(C₂H₅)], (II), (S)-1-phenylethylammonium N-[(S)-1-phenylethyl]phenylphosphonamidate, C₈H₁₂N⁺·C₁₄H₁₅NO₂P^- or [S-(C₆H₅)CH(CH₃)NH₃][(C₆H₅)P(O){S-NHCH(CH₃)(C₆H₅)}(O)], (III), and (4-methylbenzyl)ammonium diphenylphosphinate, C₈H₁₂N⁺·C₁₂H₁₀O₂P^- or [4-CH₃-C₆H₄CH₂NH₃][(C₆H₅)₂P(O)(O)], (IV). This article focuses on the N-H...O hydrogen bonds by considering the structures of (I), (II), (III) and (IV), and reviewing their analogous compounds, including 43 (C)P(O)(N)₂, 102 (C)₂P(O)(N), 31 (C)P(O)(N)(O) and 96 (C)₂P(O)(O) structures, deposited in the Cambridge Structural Database (CSD). For the structures with a (C)P(O)(N)₂ segment, only neutral hydrogen bonds were found in the CSD. The other three classes of compounds included both neutral and `charge-assisted' hydrogen bonds, and the (C)₂P(O)(O) structures were particularly noticeable for a high number of cation-anion compounds. The overall tendencies of N...O distances in neutral and cation-anion compounds were compared. The N-H...O hydrogen-bond angles were also analyzed for the four classes of phosphorus compounds.

Insight into the orientational versatility of steroid substrates-a docking and molecular dynamics study of a steroid receptor and steroid monooxygenase

Numerous steroids are essential plant, animal, and human hormones. The medical and industrial applications of these hormones require the identification of new synthetic routes, including biotransformations. The metabolic fate of a steroid can be complicated; it may be transformed into a variety of substituted derivatives. This may be because a steroid molecule can adopt several possible orientations in the binding pocket of a receptor or an enzyme. The present study, based on docking and molecular dynamics, shows that it is indeed possible for a steroid molecule to bind to a receptor binding site in two or more orientations (normal, head-to-tail reversed, upside down). Three steroids were considered: progesterone, dehydroepiandrosterone, and 7-oxo-dehydroepiandrosterone. Two proteins were employed as hosts: the human mineralocorticoid receptor and a bacterial Baeyer-Villiger monooxygenase. When the steroids were in nonstandard orientations, the estimated binding strength was found to be only moderately diminished and the network of hydrogen bonds between the steroid and the host was preserved.

Cooperative vibrational properties of hydrogen bonds in Watson–Crick DNA base pairs

For the AT pair, Symst and Strech peaks further shift toward the red, giving the H-bonds an amplified effect (orange arrows).

Effect of inorganic–organic surface modification of calcium sulfate whiskers on mechanical and thermal properties of calcium sulfate whisker/poly(vinyl chloride) composites

(A) CSW modified by coupling agent and (B) CSW modified by NaOH and coupling agent.

H-Bond: Τhe Chemistry-Biology H-Bridge

H-bonding, as a non covalent stabilizing interaction of diverse nature, has a central role in the structure, function and dynamics of chemical and biological processes, pivotal to molecular recognition and eventually to drug design. Types of conventional and non conventional (H-H, dihydrogen, H- π, CH- π, anti- , proton coordination and H-S) H-bonding interactions are discussed as well as features emerging from their interplay, such as cooperativity (σ- and π-) effects and allostery. Its utility in many applications is described. Catalysis, proton and electron transfer processes in various materials or supramolecular architectures of preorganized hosts for guest binding, are front-line technology. The H-bond-related concept of proton transfer (PT) addresses energy issues or deciphering the mechanism of many natural and synthetic processes. PT is also of paramount importance in the functions of cells and is assisted by large complex proteins embedded in membranes. Both intermolecular and intramolecular PT in H-bonded systems has received attention, theoretically and experimentally, using prototype molecules. It is found in rearrangement reactions, protein functions, and enzyme reactions or across proton channels and pumps. Investigations on the competition between intra- and intermolecular H bonding are discussed. Of particular interest is the H-bond furcation, a common phenomenon in protein-ligand binding. Multiple H-bonding (H-bond furcation) is observed in supramolecular structures.

Resonance-Assisted Hydrogen Bonding as a Driving Force in Synthesis and a Synthon in the Design of Materials

Resonance-assisted hydrogen bonding (RAHB), a concept introduced by Gilli and co-workers in 1989, concerns a kind of intramolecular H-bonding strengthened by a conjugated π-system, usually in 6-, 8-, or 10-membered rings. This Review highlights the involvement of RAHB as a driving force in the synthesis of organic, coordination, and organometallic compounds, as a handy tool in the activation of covalent bonds, and in starting moieties for synthetic transformations. The unique roles of RAHB in molecular recognition and switches, E/Z isomeric resolution, racemization and epimerization of amino acids and chiral amino alcohols, solvatochromism, liquid-crystalline compounds, and in synthons for crystal engineering and polymer materials are also discussed. The Review can provide practical guidance for synthetic chemists that are interested in exploring and further developing RAHB-assisted synthesis and design of materials.