Towards an unified hydrogen-bond theory

The advanced treatment of hydrogen bonding in quantum crystallography

Although hydrogen bonding is one of the most important motifs in chemistry and biology, H-atom parameters are especially problematic to refine against X-ray diffraction data. New developments in quantum crystallography offer a remedy. This article reports how hydrogen bonds are treated in three different quantum-crystallographic methods: Hirshfeld atom refinement (HAR), HAR coupled to extremely localized molecular orbitals and X-ray wavefunction refinement. Three different compound classes that form strong intra- or intermolecular hydrogen bonds are used as test cases: hydrogen maleates, the tripeptide l-alanyl-glycyl-l-alanine co-crystallized with water, and xylitol. The differences in the quantum-mechanical electron densities underlying all the used methods are analysed, as well as how these differences impact on the refinement results.

What is specific in adsorption of perfluoroalkyl acids on carbon materials?

Various activated carbon products show wide variability in adsorption performance towards perfluoroalkyl acids (PFAAs) and predictive tools are largely missing. In order to gain a better understanding on the adsorption mechanisms of PFAAs, perfluorooctanoic acid (PFOA) was compared with its fluorine-free analogon octanoic acid (OCA) as well as phenanthrene (nonionic) in terms of their response towards changes in carbon surface chemistry. For this approach, a commercial activated carbon felt (ACF) with high content of acidic surface groups was modified by amino-functionalisation as well as thermal defunctionalisation in H₂ (yielding DeCACF). While improvement by amino-functionalisation was moderate, defunctionalisation drastically enhanced adsorption of PFOA and other PFAAs. In comparison, OCA and phenanthrene were much less affected. Electrostatic interactions and charge compensation provided by positively charged surface sites (quantified by their anion exchange capacity) are obviously more crucial for PFAAs than for common organic acids (such as the tested OCA). A possible reason is their exceptionally strong acidity with pK_a < 1. Nevertheless, at the best modified ACF material (DeCACF) the sorption coefficients (K_d) for PFOA and perfluorooctylsulfonic acid (PFOS) at environmentally relevant concentrations reach the range of 10⁷ L/kg which is outstanding. DeCACF provides a surface with overall low polarity (low O-content), low density of acidic sites causing electrostatic repulsion, but nevertheless a sufficient density of charge-balancing sites for organic anions. The results of the present study contribute to an optimized selection of adsorbents for PFAA adsorption from water considering also various salt matrices and the presence of natural organic matter.

Intramolecular O-H⋯S hydrogen bonding in threefold symmetry: Line broadening dynamics from ultrafast 2DIR-spectroscopy and ab initio calculations

The dynamics of intramolecular hydrogen-bonding involving sulfur atoms as acceptors is studied using two-dimensional infrared (2DIR) spectroscopy. The molecular system is a tertiary alcohol whose donating hydroxy group is embedded in a hydrogen-bond potential with torsional C₃-symmetry about the carbon-oxygen bond. The linear and 2DIR-spectra recorded in the OH-stretching region of the alcohol can be simulated very well using Kubo's line shape theory based on the cumulant expansion for evaluating the linear and nonlinear optical response functions. The correlation function for OH-stretching frequency fluctuations reveals an ultrafast component decaying with a time constant of 700 fs, which is in line with the apparent decay of the center line slopes averaged over absorption and bleach/emission signals. In addition, a quasi-static inhomogeneity is detected, which prevents the 2DIR line shape to fully homogenize within the observation window of 4 ps. The experimental data were then analyzed in more detail using a full ab initio approach that merges time-dependent structural information from classical molecular dynamics (MD) simulations with an OH-stretching frequency map derived from density functional theory (DFT). The latter method was also used to obtain a complementary transition dipole map to account for non-Condon effects. The 2DIR-spectra obtained from the MD/DFT method are in good agreement with the experimental data at early waiting delays, thereby corroborating an assignment of the fast decay of the correlation function to the dynamics of hydrogen-bond breakage and formation.

When are two hydrogen bonds better than one? Accurate first-principles models explain the balance of hydrogen bond donors and acceptors found in proteins

Hydrogen bonds (HBs) play an essential role in the structure and catalytic action of enzymes, but a complete understanding of HBs in proteins challenges the resolution of modern structural (i.e., X-ray diffraction) techniques and mandates computationally demanding electronic structure methods from correlated wavefunction theory for predictive accuracy. Numerous amino acid sidechains contain functional groups (e.g., hydroxyls in Ser/Thr or Tyr and amides in Asn/Gln) that can act as either HB acceptors or donors (HBA/HBD) and even form simultaneous, ambifunctional HB interactions. To understand the relative energetic benefit of each interaction, we characterize the potential energy surfaces of representative model systems with accurate coupled cluster theory calculations. To reveal the relationship of these energetics to the balance of these interactions in proteins, we curate a set of 4000 HBs, of which >500 are ambifunctional HBs, in high-resolution protein structures. We show that our model systems accurately predict the favored HB structural properties. Differences are apparent in HBA/HBD preference for aromatic Tyr versus aliphatic Ser/Thr hydroxyls because Tyr forms significantly stronger O–H⋯O HBs than N–H⋯O HBs in contrast to comparable strengths of the two for Ser/Thr. Despite this residue-specific distinction, all models of residue pairs indicate an energetic benefit for simultaneous HBA and HBD interactions in an ambifunctional HB. Although the stabilization is less than the additive maximum due both to geometric constraints and many-body electronic effects, a wide range of ambifunctional HB geometries are more favorable than any single HB interaction.

Correlated wavefunction theory predicts and high-resolution crystal structure analysis confirms the important, stabilizing effect of simultaneous hydrogen bond donor and acceptor interactions in proteins.

Lactic Acid Spectroscopy: Intra- and Intermolecular Interactions

Lactic acid, a relevant molecule in biology and the environment, is an α-hydroxy acid with a high propensity to form hydrogen bonds, both internally and to other hydrogen-bond-accepting molecules. This work includes the novel recording of infrared spectra of gas-phase lactic acid using Fourier transform infrared spectroscopy, and the vibrational absorption features of lactic acid are assigned with the aid of computationally simulated vibrational spectra with anharmonic corrections. Theoretical chemistry methods are used to relate intramolecular hydrogen-bond strengths to the relative stability of lactic acid conformers. The formation of hydrogen-bonded lactic acid dimers and 1:1 water complexes is investigated by simulated vibrational spectra and calculated thermodynamic parameters for the lactic acid monomer and dimer and its water complex in the gas phase. The results of this study are discussed in the context of environmental chemistry with an emphasis on indoor environments.

Configurational and Constitutional Dynamics of Enamine Molecular Switches

Dual configurational and constitutional dynamics in systems based on enamine molecular switches has been systematically studied. pH-responsive moieties, such as 2-pyridyl and 2-quinolinyl units, were required on the "stator" part, also providing enamine stability through intramolecular hydrogen-bonding (IMHB) effects. Upon protonation or deprotonation, forward and backward switching could be rapidly achieved. Extension of the stator π-system in the 2-quinolinyl derivative provided a higher E-isomeric equilibrium ratio under neutral conditions, pointing to a means to achieve quantitative forward/backward isomerization processes. The "rotor" part of the enamine switches exhibited constitutional exchange ability with primary amines. Interestingly, considerably higher exchange rates were observed with amines containing ester groups, indicating potential stabilization of the transition state through IMHB. Acids, particularly BiIII , were found to efficiently catalyze the constitutional dynamic processes. In contrast, the enamine and the formed dynamic enamine system showed excellent stability under basic conditions. This coupled configurational and constitutional dynamics expands the scope of dynamic C-C and C-N bonds and potentiates further studies and applications in the fields of molecular machinery and systems chemistry.

Tuning the Binding Strength of Even and Uneven Hydrogen-Bonded Arrays with Remote Substituents

We investigated the tunability of hydrogen bond strength by altering the charge accumulation around the frontier atoms with remote substituents. For pyridine···H2O with NH2 and CN substituted at different positions on pyridine, we find that the electron-withdrawing CN group decreases the negative charge accumulation around the frontier atom N, resulting in weakening of the hydrogen bond, whereas the electron-donating NH2 group increases the charge accumulation around N, resulting in strengthening of the hydrogen bond. By applying these design principles on DDAA-AADD, DADA-ADAD, DAA-ADD, and ADA-DAD hydrogen-bonded dimers, we find that the effect of the substituent is delocalized over the whole molecular system. As a consequence, systems with an equal number of hydrogen bond donor (D) and acceptor (A) atoms are not tunable in a predictable way because of cancellation of counteracting strengthening and weakening effects. Furthermore, we show that the position of the substituent and long-range electrostatics can play an important role as well. Overall, the design principles presented in this work are suitable for monomers with an unequal number of donor and acceptor atoms and can be exploited to tune the binding strength of supramolecular building blocks.

(R)-10-Hydroxystearic Acid: Crystals vs. Organogel

The chiral (R)-10-hydroxystearic acid ((R)-10-HSA) is a positional homologue of both (R)-12-HSA and (R)-9-HSA with the OH group in an intermediate position. While (R)-12-HSA is one of the best-known low-molecular-weight organogelators, (R)-9-HSA is not, but it forms crystals in several solvents. With the aim to gain information on the structural role of hydrogen-bonding interactions of the carbinol OH groups, we investigated the behavior of (R)-10-HSA in various solvents. This isomer displays an intermediate behavior between (R)-9 and (R)-12-HSA, producing a stable gel exclusively in paraffin oil, while it crystallizes in other organic solvents. Here, we report the X-ray structure of a single crystal of (R)-10-HSA as well as some structural information on its polymorphism, obtained through X-ray Powder Diffraction (XRPD) and Infrared Spectroscopy (IR). This case study provides new elements to elucidate the structural determinants of the microscopic architectures that lead to the formation of organogels of stearic acid derivatives.

Inter- vs. Intramolecular Hydrogen Bond Patterns and Proton Dynamics in Nitrophthalic Acid Associates

Noncovalent interactions are among the main tools of molecular engineering. Rational molecular design requires knowledge about a result of interplay between given structural moieties within a given phase state. We herein report a study of intra- and intermolecular interactions of 3-nitrophthalic and 4-nitrophthalic acids in the gas, liquid, and solid phases. A combination of the Infrared, Raman, Nuclear Magnetic Resonance, and Incoherent Inelastic Neutron Scattering spectroscopies and the Car-Parrinello Molecular Dynamics and Density Functional Theory calculations was used. This integrated approach made it possible to assess the balance of repulsive and attractive intramolecular interactions between adjacent carboxyl groups as well as to study the dependence of this balance on steric confinement and the effect of this balance on intermolecular interactions of the carboxyl groups.

Hydrogen-bonded host-guest systems are stable in ionic liquids

We show that H-bonded host–guest systems associate in ionic liquids (ILs), pure salts with melting point below room temperature, in which dipole–dipole electrostatic interactions should be negligible in comparison with dipole-charge interactions. Binding constants (K_a) obtained from titrations of four H-bonded host–guest systems in two organic solvents and two ionic liquids yield smaller yet comparable K_a values in ionic liquids than in organic solvents. We also detect the association event using force spectroscopy, which confirms that the binding is not solely due to (de)solvation processes. Our results indicate that classic H-bonded host–guest supramolecular chemistry takes place in ILs. This implies that strong H-bonds are only moderately affected by surroundings composed entirely of charges, which can be interpreted as an indication that the balance of Coulombic to covalent forces in strong H-bonds is not tipped towards the former.

Understanding colossal barocaloric effects in plastic crystals

Plastic crystal neopentylglycol (NPG) exhibits colossal barocaloric effects (BCEs) with record-high entropy changes, offering exciting prospects for the field of solid-state cooling through the application of moderate pressures. Here, we show that the intermolecular hydrogen bond plays a key role in the orientational order of NPG molecules, while its broken due to thermal perturbation prominently weakens the activation barrier of orientational disorder. The analysis of hydrogen bond strength, rotational entropy free energy and entropy changes provides insightful understanding of BCEs in order-disorder transition. External pressure reduce the hydsrogen bond length and enhance the activation barrier of orientational disorder, which serves as a route of varying intermolecular interaction to tune the order-disorder transition. Our work provides atomic-scale insights on the orientational order-disorder transition of NPG as the prototypical plastic crystal with BCEs, which is helpful to achieve superior caloric materials by molecular designing in the near future.

Enhanced affinity of racemic phosphorothioate DNA with transcription factor SATB1 arising from diastereomer-specific hydrogen bonds and hydrophobic contacts

Phosphorothioate modification is commonly introduced into therapeutic oligonucleotides, typically as a racemic mixture in which either of the two non-bridging phosphate oxygens is replaced by sulfur, which frequently increases affinities with proteins. Here, we used isothermal titration calorimetry and X-ray crystallography to investigate the thermodynamic and structural properties of the interaction between the primary DNA-binding domain (CUTr1) of transcription factor SATB1 and dodecamer DNAs with racemic phosphorothioate modifications at the six sites known to contact CUTr1 directly. For both the modified and unmodified DNAs, the binding reactions were enthalpy-driven at a moderate salt concentration (50 mM NaCl), while being entropy-driven at higher salt concentrations with reduced affinities. The phosphorothioate modifications lowered this susceptibility to salt, resulting in a significantly enhanced affinity at a higher salt concentration (200 mM NaCl), although only some DNA molecular species remained interacting with CUTr1. This was explained by unequal populations of the two diastereomers in the crystal structure of the complex of CUTr1 and the phosphorothioate-modified DNA. The preferred diastereomer formed more hydrogen bonds with the oxygen atoms and/or more hydrophobic contacts with the sulfur atoms than the other, revealing the origins of the enhanced affinity.

Ion and water transport reasonably involves rotation and pseudorotation: measurement and modeling the temperature dependence of small-angle neutron scattering from aqueous SrI2

X-ray and neutron scattering have provided insight into the short range (<8 Å) structures of ionic solutions for over a century. For longer distances, single scattering bands have, however, been seen. For the non-hydrolyzing salt SrI2 in aqueous (D2O) solution, a structure sufficient to scatter slow neutrons has been seen to persist down to a concentration of 0.1 mol L-1 where the measured average spacing between scatterers is over 20 Å. Theoretical studies of such long distance solution structures are difficult, and these difficulties are discussed. The width of the distribution in distances between the scatterers (ions, ion pairs, etc.) remains less than 10 Å, which approximates the average size of the ions and their first hydration shell. Here, we measure the temperature dependence from 10 °C to 90 °C of the small angle neutron scattering (SANS) by a 0.5 molar SrI2 solution in D2O and find that this surprisingly narrow distribution of the distances remains constant within experimental uncertainty. This structure of the ions in the solution appears to endure because changes in interion distances along any single spatial dimension require displacements near the size of a water molecule. Together, the experimental measurements support a rotatory mechanism for simultaneous ion transport and water countertransport. Since rotation minimizes displacement of the solution framework, it is suggested that water transport alone also involves rotation of multimolecular structures, and that the interpretation of single-molecule water rotation is confounded by pseudorotation that results from paired picosecond proton exchanges. It is pointed out that NMR-determined millisecond to microsecond proton exchange times of chelated-metal-ion bound waters and the much faster chelate rotational correlation times around 10 picoseconds, both of which require making and breaking of hydrogen bonds, are difficult to impossible to reconcile.

Negative cooperativity upon hydrogen bond-stabilized O2 adsorption in a redox-active metal-organic framework

The design of stable adsorbents capable of selectively capturing dioxygen with a high reversible capacity is a crucial goal in functional materials development. Drawing inspiration from biological O2 carriers, we demonstrate that coupling metal-based electron transfer with secondary coordination sphere effects in the metal-organic framework Co2(OH)2(bbta) (H2bbta = 1H,5H-benzo(1,2-d:4,5-d')bistriazole) leads to strong and reversible adsorption of O2. In particular, moderate-strength hydrogen bonding stabilizes a cobalt(III)-superoxo species formed upon O2 adsorption. Notably, O2-binding in this material weakens as a function of loading, as a result of negative cooperativity arising from electronic effects within the extended framework lattice. This unprecedented behavior extends the tunable properties that can be used to design metal-organic frameworks for adsorption-based applications.

Design of Nonideal Eutectic Mixtures Based on Correlations with Molecular Properties

In this work, a statistical analysis was performed to reveal how the molecular properties are correlated with the nonideal behavior observed in eutectic mixtures. From this, a statistical model, combined with theory and experimental results, was developed to predict the nonideal behavior of a specific set of eutectic mixtures, consisting of quaternary ammonium bromides with dicarboxylic acids and polyols. The combination of this analysis and this model can be considered as a first step toward the a priori design of eutectic mixtures. The analysis performed is based on principal components. The descriptors used for this are molecular properties of the constituents of these mixtures. The molecular properties are a combination of experimental, theoretical, and computed properties. The analysis reveals that there are strong correlations between the nonideality of the mixtures and a measure of the acidity of the hydrogen bond donating protons, the displacement of the bromide anion, and the bulkiness of the quaternary ammonium salt. Our analysis highlights the design rules of deep eutectic systems (DES), enabling control over the extent of the liquid window. Our model enables prediction of the eutectic temperature for a range of related mixtures.

Imine or Enamine? Insights and Predictive Guidelines from the Electronic Effect of Substituents in H-Bonded Salicylimines

Imine and enamine bonds decorate the skeleton of numerous reagents, catalysts, and organic materials. However, it is difficult to isolate at will a single tautomer, as dynamic equilibria occur easily, even in the solid state, and are sensitive to electronic and steric effect, including π-conjugation and H-bonding. Here, using as model Schiff bases generated from salicylaldehydes and TRIS in a set of linear free energy relationships (LFER), we disclose how the formation of either imines or enamines can be controlled and provide a comprehensive framework that captures the structural underpinning of this prediction. This work highlights the potentiality of tailor-made designs en route to compounds with desirable functionality.

Crystal structure of a new phen-yl(morpholino)methane-thione derivative: 4-[(morpholin-4-yl)carbothioyl]benzoic acid

4-[(Morpholin-4-yl)carbothioyl]benzoic acid, C12H13NO3S, a novel phen-yl(morpholino)methane-thione derivative, crystallizes in the monoclinic space group P21/n. The morpholine ring adopts a chair conformation and the carb-oxy-lic acid group is bent out slightly from the benzene ring mean plane. The mol-ecular geometry of the carb-oxy-lic group is characterized by similar C-O bond lengths [1.266 (2) and 1.268 (2) Å] as the carboxyl-ate H atom is disordered over two positions. This mol-ecular arrangement leads to the formation of dimers through strong and centrosymmetric low barrier O-H⋯O hydrogen bonds between the carb-oxy-lic groups. In addition to these inter-molecular inter-actions, the crystal packing consists of two different mol-ecular sheets with an angle between their mean planes of 64.4 (2)°. The cohesion between the different layers is ensured by C-H⋯S and C-H⋯O inter-actions.

The promoted dissolution of copper oxide nanoparticles by dissolved humic acid: Copper complexation over particle dispersion

Humic substances are the dominant dissolved organic matter fraction in the aqueous phase of environmental media. They would inevitably react with chemicals released into the environment. The influence of dissolved humic acid (DHA) on the dissolution and dispersion of copper oxide nanoparticles (CuO NPs, 50 nm, 49.57 mg L^-1) was therefore investigated in the present study. In addition to dispersing CuO NPs and reducing the size of the aggregates, the amount of released Cu from CuO NPs was found to increase over time with increasing concentrations of DHA, 96% of which was present as organic complexes after 72 h. At DHA concentrations exceeding 16.09 mg C L^-1, the complexation coefficients of DHA with Cu and the adsorptivity of CuO NPs to DHA were both reduced due to increased homo-conjugation of DHA as promoted by negative charge-assisted H-bond. Although the adsorption capacity of DHA kept increasing up to 57.07 mg C L^-1, the hydrodynamic diameter and ζ-potential were similar and the percentages of total released Cu continued to increase linearly to 4.92% at higher levels of DHA (30.13-57.07 mg C L^-1). Thereupon, DHA promoted the dissolution of CuO NPs in a concentration-dependent fashion. The driving force was complexation of Cu by DHA, rather than the balancing between the exposed and the covered surface area of the CuO NPs due to DHA adsorption. Our findings facilitate understanding the underlying mechanisms on how DHA impacts the CuO NPs environmental behavior (or fate) as well as on their kinetics.

Theoretical study of intramolecular hydrogen bond in selected symmetric "proton sponges" on the basis of DFT and CPMD methods

"Proton sponges," derivatives of prototypic 1,8-bis(dimethylamino)naphthalene (DMAN), exhibit remarkable basicity, which made them interesting for various experimental and theoretical studies. The details of bridged proton dynamics in protonated DMAN and its derivative denoted as TMGN (1,8-bis(tetramethylguanidino)naphthalene) were investigated on the basis of density functional theory (DFT) and Car-Parrinello molecular dynamics (CPMD) methods. Special attention was paid to the effects of symmetry of the molecular skeleton and the type of substituent on the bridged proton neighborhood statistics and dynamics. The metric parameter analyses of hydrogen bridge provided us with a conclusion that proton migration events in TMGNH⁺ are less numerous than in DMANH⁺, which can be rationalized by noticing the slower dynamics of large substituents of TMGN with respect to the smaller -N(Me)₂ groups of DMAN. The atomic velocity power spectra served as computational models of the vibrational signatures associated with the presence of the intramolecular hydrogen bond. A broad feature was registered for hydrogen bonds present in both compounds. The computations were verified by experimental data available.

Symmetry and 1H NMR chemical shifts of short hydrogen bonds: impact of electronic and nuclear quantum effects

Electronic and nuclear quantum effects determine the symmetry and highly downfield ¹H NMR chemical shifts of short hydrogen bonds.

Hydrogen atoms in bridging positions from quantum crystallographic refinements: influence of hydrogen atom displacement parameters on geometry and electron density

Hydrogen atom positions can be obtained accurately from X-ray diffraction data of hydrogen maleate salts via Hirshfeld atom refinement.

Role of substituents on resonance assisted hydrogen bonding vs. intermolecular hydrogen bonding

Resonance assisted hydrogen bond (RAHB) ring can be weakened/opened by a strong electron-donor (ED) group.

Electronic effects in tautomeric equilibria: the case of chiral imines from d-glucamine and 2-hydroxyacetophenones

A one-pot procedure for preparing a series of chiral imines by direct condensation of d-glucamine with 2-hydroxyacetophenones is described. Under conventional acetylation an unexpected mixture of two different peracetylated molecules is obtained, one with an open enamine structure, and the other incorporating an N-acetyl-1,3-oxazolidine into the acyclic skeleton. Surprisingly, both molecules coexist within the crystal's unit cell, as inferred from single-crystal X-ray analysis of a 5-bromo-substituted aryl derivative. Moreover, the 1,3-oxazolidine ring exists as rotational conformers (E,Z) owing to the restricted rotation around the N-acetyl bond. The equilibrium involving imine and enamine structures has been assessed in detail, providing in addition linear free-energy relationships between the tautomerization constants (K_T) and the electronic effect of the substituents.

Synthesis, Structural Characterization, and Biological Activities of Organically Templated Cobalt Phosphite (C4H14N2)[Co(H2PO3)4]∙2H2O

A novel hybrid phosphite (C4H14N2)[Co(H2PO3)4]∙2H2O was synthesized with 1,4-diaminobutane (dabn) as a structure-directing agent using slow evaporation method. Single crystalX-ray diraction analysis showed that it crystallizes in the P-1 triclinic space group, with the following unit cell parameters (Å, °) a = 5.4814 (3), b = 7.5515 (4), c = 10.8548 (6), α = 88.001 (4), β = 88.707 (5), = 85.126 (5), and V= 447.33 (4) Å3. The crystal structure was built up from corner-sharing [CoO6]octahedrons, forming chains parallel to [001], which are interconnected by H2PO3-pseudo-tetrahedral units. The diprotonated 1,4-butanediammonium molecules, residing between the parallel chains, interacted with the inorganic moiety via hydrogen bonds leading thus to the formation of the 3D crystal structure. The Fourier transform infrared spectrum showed characteristic bands corresponding to the phosphite group and the organic molecule. The thermal decomposition of the compound consisted mainly of the loss of the organic moiety and the water molecules. The biological tests exhibited significant activity against Candida albicans and Escherichia coli strains in all used concentrations, while less activity was pronounced when tested against Staphylococcus epidermidis and Saccharomycescerevisiae, while there was no activity against the nematode model Steinernema feltiae.

Intramolecular Hydrogen Bonds in Selected Aromatic Compounds: Recent Developments

A review of intramolecular hydrogen bonding in ortho-hydroxyaryl Schiff bases, ortho-hydroxyaryl Mannich bases, dipyrrins, ortho-hydroxyaryl ketones, ortho-hydroxyaryl amides, and 4-Bora-3a,4a-diaza-s-indacene (BODIPY) dyes with tautomeric sensors as substituents is presented in this paper. Ortho-hydroxy Schiff and Mannich base derivatives are known as model molecules for analysing the properties of intramolecular hydrogen bonding. The compounds under discussion possess physicochemical features modulated by the presence of strong intramolecular hydrogen bonds. The equilibrium between intra- and inter-molecular hydrogen bonds in BODIPY is discussed. Therefore, the summary can serve as a knowledge compendium of the influence of the hydrogen bond on the molecular properties of aromatic compounds.

Isotopic-Perturbation NMR Study of Hydrogen-Bond Symmetry in Solution: Temperature Dependence and Comparison of OHO and ODO Hydrogen Bonds

Is a hydrogen bond symmetric, with the hydrogen centered between two donor atoms, or is it asymmetric, with the hydrogen closer to one but jumping to the other? The NMR method of isotopic perturbation has been used to distinguish these. Previous evidence from isotope shifts implies that a wide variety of dicarboxylate monanions are asymmetric, present as a rapidly equilibrating mixture of tautomers. However, calculations of hydrogen trajectories across an anharmonic potential-energy surface could reproduce the observed isotope shifts in a phthalate monoanion. Therefore, it was concluded that those isotope shifts are instead consistent with isotope-induced desymmetrization on a symmetric potential-energy surface. To distinguish between these two interpretations, the ¹⁸O-induced isotope effects on the ¹³C NMR chemical shifts of cyclohexene-1,2-dicarboxylate monoanion in chloroform-d and on the ¹⁹F NMR chemical shifts of difluoromaleate monoanion in D₂O have been investigated. In both cases the isotope effects are larger at lower temperature and also with deuterium in the hydrogen bond. It is concluded that these behaviors are consistent with the perturbation of an equilibrium between asymmetric tautomers and inconsistent with isotope-induced desymmetrization on a symmetric potential-energy surface.

Quantum Stabilization of the Frustrated Hydrogen Bonding Structure in the Hydrogen Fluoride Trimer

We performed ab initio path integral molecular dynamics (PIMD) and molecular dynamics (MD) simulations to discuss the thermal and nuclear quantum effects on the stabilities of hydrogen bonding network in a hydrogen fluoride trimer (HF)₃ cluster. By the conventional molecular orbital calculation, the (HF)₃ cluster has an equilateral triangle shape, which has a frustration in the chemical structure of the hydrogen bonds, whereas the hydrogen bonding structure of a hydrogen fluoride dimer (HF)₂ cluster is nearly perpendicular to the acceptor molecule. The ratio of the triangular structures with the three hydrogen bondings in the PIMD simulation is larger than that in the MD one, whereas nonhydrogen bonding conformations such as a dimerlike structure are often found in MD simulation. The nuclear quantum effect stabilizes the frustrated hydrogen bonding network of the triangular (HF)₃ cluster.

Water in protein hydration and ligand recognition

This review describes selected basics of water in biomolecular recognition. We focus on a qualitative understanding of the most important physical aspects, how these change in magnitude between bulk water and protein environment, and how the roles that water plays for proteins arise from them. These roles include mechanical support, thermal coupling, dielectric screening, mass and charge transport, and the competition with a ligand for the occupation of a binding site. The presence or absence of water has ramifications that range from the thermodynamic binding signature of a single ligand up to cellular survival. The large inhomogeneity in water density, polarity and mobility around a solute is hard to assess in experiment. This is a source of many difficulties in the solvation of protein models and computational studies that attempt to elucidate or predict ligand recognition. The influence of water in a protein binding site on the experimental enthalpic and entropic signature of ligand binding is still a point of much debate. The strong water‐water interaction in enthalpic terms is counteracted by a water molecule's high mobility in entropic terms. The complete arrest of a water molecule's mobility sets a limit on the entropic contribution of a water displacement process, while the solvent environment sets limits on ligand reactivity.

The Nature of Hydrogen Bonds: A Delineation of the Role of Different Energy Components on Hydrogen Bond Strengths and Lengths

Hydrogen bonds are a complex interplay between different energy components, and their nature is still subject of an ongoing debate. In this minireview, we therefore provide an overview of the different perspectives on hydrogen bonding. This will be done by discussing the following individual energy components: 1) electrostatic interactions, 2) charge-transfer interactions, 3) π-resonance assistance, 4) steric repulsion, 5) cooperative effects, 6) dispersion interactions and 7) secondary electrostatic interactions. We demonstrate how these energetic factors are essential in a correct description of the hydrogen bond, and discuss several examples of systems whose energetic and geometrical features are not captured by easy-to-use predictive models.

Synthesis, Structural Characterization, and Biological Activities of Organically Templated Cobalt Phosphite (C4N2H14)[Co(H2PO3)4]·2H2O

A novel hybrid phosphite (C4N2H14)[Co(H2PO3)4]·2H2O was synthesized with 1,4- diaminobutane (dabn) as a structure-directing agent using slow evaporation method. Single crystal X-ray diffraction analysis showed that it crystallizes in the P\-1 triclinic space group, with the following unit cell parameters (Å, °) a = 5.4814 (3), b = 7.5515 (4), c = 10.8548 (6), α = 88.001 (4), β = 88.707 (5), γ = 85.126 (5), and V = 447.33 (4) Å3. The crystal structure was built up from corner-sharing [CoO6]-octahedrons, forming chains parallel to [001], which are interconnected by H2PO3− pseudo-tetrahedral units. The diprotonated 1,4-butanediammonium molecules, residing between the parallel chains, interacted with the inorganic moiety via hydrogen bonds leading thus to the formation of the 3D crystal structure. The Fourier transform infrared spectrum showed characteristic bands corresponding to the phosphite group and the organic molecule. The thermal decomposition of the compound consisted mainly of the loss of the organic moiety and the water molecules. The biological tests exhibited significant activity against Candida albicans and Escherichia coli strains in all used concentrations, while less activity was pronounced when tested against Staphylococcus epidermidis and Saccharomyces cerevisiae, while there was no activity against the nematode model Steinernema feltiae.

Enhancement of Atmospheric Nucleation by Highly Oxygenated Organic Molecules: A Density Functional Theory Study

New particle formation (NPF) by gas-particle conversion is the main source of atmospheric aerosols. Highly oxygenated organic molecules (HOMs) and sulfuric acid (SA) are important NPF participants. 2-Methylglyceric acid (MGA), a kind of HOMs, is a tracer of isoprene-derived secondary organic aerosols. The nucleation mechanisms of MGA with SA were studied using density functional theory and atmospheric cluster dynamics simulation in this study, along with that of MGA with methanesulfonic acid (MSA) as a comparison. Our theoretical works indicate that the (MGA)(SA) and (MGA)(MSA) clusters are the most stable ones in the (MGA) _i(SA) _j ( i = 1-2, j = 1-2) and (MGA) _i(MSA) _j ( i = 1-2, j = 1-2) clusters, respectively. Both the formation rates of (MGA)(SA) and (MGA)(MSA) clusters are quite large and could have significant contributions to NPF. The results imply that the homomolecular nucleation of MGA is unlikely to occur in the atmosphere, and MGA and SA can effectively contribute to heteromolecular nucleation mainly in the form of heterodimers. MSA exhibits properties similar to SA in its ability to form clusters with MGA but is slightly weaker than SA.