Characterization of Low-Barrier Hydrogen Bonds. 1. Microsolvation Effects. An ab Initio and DFT Investigation

Hydroxide Chemoselectivity Changes with Water Microsolvation

Solvent molecules are known to affect chemical reactions, especially if they interact with one or more of the reactants or catalysts. In ion microsolvation, i.e., solvent molecules in the first solvation sphere, strong electronic interactions are created, leading to significant changes in charge distribution and consequently on their nucleophilicity/electrophilicity and acidity/basicity. Despite a long history of research in the field, fundamental issues regarding the effects of ion microsolvation are still open, especially in the condensed phase. Using reactions between hydroxide and relatively stable quaternary ammonium salts as an example, we show that water microsolvation can change hydroxide's chemoselectivity by differently affecting its basicity and nucleophilicity. In this example, the hydroxide reactivity as a nucleophile is less affected by water microsolvation than its reactivity as a base. These disparities are discussed by calculating and comparing oxidation potentials and polarizabilities of the different water-hydroxide clusters.

Double proton transfer in hydrated formic acid dimer: Interplay of spatial symmetry and solvent-generated force on reactivity

The double proton transfer (DPT) reaction in the hydrated formic acid dimer (FAD) is investigated at molecular-level detail. For this, a global and reactive machine learned (ML) potential energy surface (PES) is developed to run extensive (more than 100 ns) mixed ML/MM molecular dynamics (MD) simulations in explicit molecular mechanics (MM) solvent at MP2-quality for the solute. Simulations with fixed – as in a conventional empirical force field – and conformationally fluctuating – as available from the ML-based PES – charge models for FAD show a significant impact on the competition between DPT and dissociation of FAD into two formic acid monomers. With increasing temperature the barrier height for DPT in solution changes by about 10% (∼1 kcal mol⁻¹) between 300 K and 600 K. The rate for DPT is largest, ∼1 ns⁻¹, at 350 K and decreases for higher temperatures due to destabilisation and increased probability for dissociation of FAD. The water solvent is found to promote the first proton transfer by exerting a favourable solvent-induced Coulomb force along the O–H⋯O hydrogen bond whereas the second proton transfer is significantly controlled by the O–O separation and other conformational degrees of freedom. Double proton transfer in hydrated FAD is found to involve a subtle interplay and balance between structural and electrostatic factors.

Simulation of double proton transfer in formic acid dimer by reactive ML potential in explicit molecular mechanics water solvent.

ABEEM/MM OH- Models for OH-(H2O)n Clusters and Aqueous OH-: Structures, Charge Distributions, and Binding Energies

Based on the atom-bond electronegativity equalization method fused into molecular mechanics (ABEEM/MM), two fluctuating charge models of OH^--water system were proposed. The difference between these two models is whether there is charge transfer between OH^- and its first-shell water molecules. The structures, charge distributions, charge transfer, and binding energies of the OH^-(H₂O)_n (n = 1-8, 10, 15, 23) clusters were studied by these two ABEEM/MM models, the OPLS/AA force field, the OPLS-SMOOTH/AA force field, and the QM methods. The results demonstrate that two ABEEM/MM models can search out all stable structures just as the QM methods, and the structures and charge distributions agree well with those from the QM calculations. The structures, the charge transfer, and the strength of hydrogen bonds in the first hydration shell are closely related to the coordination number of OH^-. Molecular dynamics simulations on the aqueous OH^- solution are performed at 298 and 278 K using ABEEM/MM-I model. The MD results show that the populations of three-, four-, and five-coordinated OH^- are 29.6%, 67.1%, and 3.4% at 298 K, respectively, and those of two-, three-, four-, and five-coordinated OH^- are 10.8%, 44.9%, 39.2%, and 4.9% at 278 K, respectively; the average hydrogen bond lengths and the hydrogen bond angle in the first shell increase with the temperature decreasing.

Resonance Raman spectroscopic and density functional theoretical study on microsolvated 2-Thiocytosine clusters with polar solvents

Microsolvation effects on the excited state deactivation dynamics of 2-thiocytosine (2tC) were studied in hydrogen-bonded 2tC clusters with protic solvents using resonance Raman, FT-IR, FT-Raman, UV-vis spectroscopy combining with density functional theoretical calculation. Two protic solvents, water (H₂O) and methanol (MeOH), and one aprotic solvent, acetonitrile (MeCN), were used to investigate the 2tC(H₂O)_1-5, 2tC(MeOH)_1-5, and 2tC(MeCN)_1-3 microsolvated clusters. In CH₃OH and H₂O solvents, most of the Raman shifts were due to the vibration modes of 2tC(solvent)_n (solvent = H₂O, CH₃OH; n = 1-4) clusters via intermolecular NH⋯O hydrogen bonds (HB). The intermolecular >NH⋯O hydrogen bond interactions, which are the key constituents of stable thione structure of 2tC, revealed the spectra difference of 2tC in CH₃CN, CH₃OH and H₂O. With the aid of electronic structural and vibration frequency calculations, the observed Raman spectra were assigned to the low energy isomers of 2tC(solvent)₂ (solvent = H₂O, CH₃OH) clusters in water and methanol and 2tC(CH₃CN) in acetonitrile solvents. 2tC(solvent)₂ clusters in water and methanol may prohibit or promote excited state proton transfer reaction from sulfur atom to neighbor nitrogen atom due to the hydrogen bonding chain between 2tC and protic solvent molecules. Our experimental and theoretical studies confirmed that the hydrogen bond sites were located on the specified functional group SCNH of 2tC with solvent molecules.

Enormous Hydrogen Bond Strength Enhancement through π-Conjugation Gain: Implications for Enzyme Catalysis

Surprisingly large resonance-assistance effects may explain how some enzymes form extremely short, strong hydrogen bonds to stabilize reactive oxyanion intermediates and facilitate catalysis. Computational models for several enzymic residue-substrate interactions reveal that when a π-conjugated, hydrogen bond donor (XH) forms a hydrogen bond to a charged substrate (Y^-), XH can become significantly more π-electron delocalized, and this "extra" stabilization may boost the [XH···Y^-] hydrogen bond strength by ≥15 kcal/mol. This reciprocal relationship departs from the widespread pK_a concept (i.e., the idea that short, strong hydrogen bonds form when the interacting moieties have matching pK_a values), which has been the rationale for enzymic acid-base reactions. The findings presented here provide new insight into how short, strong hydrogen bonds could form in enzymes.

Solvent effect on hydrogen bonded Tyr⋯Asp⋯Arg triads: Enzymatic catalyzed model system

The hydrogen bond plays a vital role in structural arrangement, intermediate state stabilization, materials function, and biological activity of certain enzymatic reactions. The solvent and electronic effects on hydrogen bonds are illustrated employing the polarizable contimuum model at B3LYP/6-311++G(d,p) level. Geometry optimizations reflect the significant solvent and electronic effect. The proton departs spontaneously upon oxidation from the hydroxyl group of tyrosyl in hydrogen bonded Tyr⋯Asp⋯Arg triads in both gas phase and solvents. The electron transfer isomers are observed for anionic triads, no matter what the solvent is. The difference of distance between two hydrogen bonds is enlarged in solvent as compared to that in gas phase. The electronic effect on IR spectra is distinctive. The tyrosyl fragment tends to be oxidized and the arginine moiety is easier to bind an excess electron. The variations of chemical shift and spin-spin coupling constant are more significant upon electron transfer than upon solvent dielectric constant. The augmentation of solvent dielectric constant stabilizes the system, enhances the difference of isomers, and increases the vertical ionization potential and vertical electron affinity values.

Hydration effect on proton transfer in melamine-cyanuric acid complex

Self-assembly of melamine-cyanuric acid (MC) leads to urinary tract calculi and renal failure. The hydration effects on molecular geometry, the IR spectra, the frontier molecular orbital, the energy barrier of proton transfer (PT), as well as the stability of MC were explored by density functional theory (DFT) calculations. The intramolecular PT breaks the big π-conjugated ring of melamine or converts the p-π conjugation (:N-C'=O) to π-π conjugation (O=C-N=C') of cyanuric acid. The intermolecular PT varies the coupling between melamine and cyanuric acid from pure hydrogen bonds (Na…HNd and NH…O) to the cooperation of cation…anion electrostatic interaction (NaH(+)…Nd (-)) and two NH…O hydrogen bonds. Distinct IR spectra shifts occur for Na…HNd stretching mode upon PT, i.e., blue-shift upon intramolecular PT and red-shift upon intermolecular PT. It is expected that the PT would inhibit the generation of rosette-like structure or one-dimensional tape conformer for the MC complexes. Hydration obviously effects the local geometric structure around the water binding site, as well as the IR spectra of NH…O and N…HN hydrogen bonds. Hydration decreases the intramolecular PT barrier from ~45 kcal mol(-1) in anhydrous complex to ~11.5 kcal mol(-1) in trihydrated clusters. While, the hydration effects on intermolecular PT barrier is slight. The relative stability of MC varies slightly by hydration due to the strong hydrogen bond interaction between melamine and cyanuric acid fragments. Graphical Abstract Hydration effect on proton transfer in melamine-cyanuric acid complex.

The crucial role of water in shaping low-barrier hydrogen bonds

Low-barrier hydrogen bonds (LBHBs) are key components in a range of chemical processes, often appearing in metal-mediated catalytic applications.

Strong, low-barrier hydrogen bonds may be available to enzymes

The debate over the possible role of strong, low-barrier hydrogen bonds in stabilizing reaction intermediates at enzyme active sites has taken place in the absence of an awareness of the upper limits to the strengths of low-barrier hydrogen bonds involving amino acid side chains. Hydrogen bonds exhibit their maximal strengths in isolation, i.e., in the gas phase. In this work, we measured the ionic hydrogen bond strengths of three enzymatically relevant model systems in the gas phase using anion photoelectron spectroscopy; we calibrated these against the hydrogen bond strength of HF2(-), measured using the same technique, and we compared our results with other gas-phase experimental data. The model systems studied here, the formate-formic acid, acetate-acetic acid, and imidazolide-imidazole anionic complexes, all exhibit very strong hydrogen bonds, whose strengths compare favorably with that of the hydrogen bifluoride anion, the strongest known hydrogen bond. The hydrogen bond strengths of these gas-phase complexes are stronger than those typically estimated as being required to stabilize enzymatic intermediates. If there were to be enzyme active site environments that can facilitate the retention of a significant fraction of the strengths of these isolated (gas-phase), hydrogen bonded couples, then low-barrier hydrogen bonding interactions might well play important roles in enzymatic catalysis.

THE COOPERATIVITY BETWEEN HYDROGEN AND HALOGEN BONDS

The cooperativity between hydrogen bonds and halogen bonds in X–HCN–Y ( X: C2H2, H2O, NH3, HCI, HCN, HF; Y: HF, BrF, Br2 is analyzed with MP2/6-311++G(d, p) and DFT/6-311++G(d, p) calculations using the B3LYP and mPW1PW91 hybrid functionals. The results from the quantum chemical calculations are typically clustered in groups according to the Y-ligand. By choosing the X–HCN–HF group as reference it is possible to describe the interaction between the hydrogen and the halogen bond with a two-parameter model. The value of the first parameter of the model describes the contribution of the X -ligand to the interbond cooperativity in the reference cluster. The second parameter of our model quantifies the changes in interbond cooperativity upon varying the Y -ligand. This simple model can be used to predict the cooperativity in X–HCN–Y trimers with reasonable accuracy and thereby to organize the results systematically. It is further shown that the conclusions drawn from this ordering scheme are independent from the computational method and thereby generally applicable.

The role of CS₂ in CS₂/NMP mixed solvent in weakening the hydrogen bond of OH-N in coal: a DFT investigation

The interaction processes of trace amounts of N-methyl-2-pyrrolidinone (NMP), CS(2)/NMP (1:1 by volume) and pure NMP solvent with the hydrogen bond of OH⋯N in coal were constructed and simulated by density functional theory methods. The distances and bond orders between the main related atoms, and the hydrogen bond energy of OH⋯N were calculated. The calculated results show that pure NMP solvent does not weaken the hydrogen bond of OH⋯N in coal. However, trace amounts of NMP and CS(2)/NMP (1:1 by volume) have a strong capacity to weaken the hydrogen bond of OH⋯N in coal. The H2-N3 distances are elongated from 1.87 Å to 3.80 Å and 3.44 Å, the bond orders of H2-N3 all disappear, and the corresponding hydrogen bond energies of OH⋯N in coal decrease from 45.72 kJ mol(-1) to 7.06 and 11.24 kJ mol(-1), respectively. These results show that CS(2) added to pure NMP solvent plays an important role in releasing the original capacity of NMP to weaken the hydrogen bond of OH⋯N in coal, in agreement with experimental observations.

On the Origin of Red and Blue Shifts of XH and CH Stretching Vibrations in Formic Acid (Formate Ion) and Proton Donor Complexes

Complexes between formic acid or formate anion and various proton donors (HF, H(2)O, NH(3), and CH(4)) are studied by the MP2 and B3LYP methods with the 6-311++G(3df,3pd) basis set. Formation of a complex is characterized by electron-density transfer from electron donor to ligands. This transfer is much larger with the formate anion, for which it exceeds 0.1 e. Electron-density transfer from electron lone pairs of the electron donor is directed into sigma* antibonding orbitals of X--H bonds of the electron acceptor and leads to elongation of the bond and a red shift of the X--H stretching frequency (standard H-bonding). However, pronounced electron-density transfer from electron lone pairs of the electron donor also leads to reorganization of the electron density in the electron donor, which results in changes in geometry and vibrational frequency. These changes are largest for the C--H bonds of formic acid and formate anion, which do not participate in H-bonding. The resulting blue shift of this stretching frequency is substantial and amounts to almost 35 and 170 cm(-1), respectively.

Analysis of pH-dependent elements in proteins: geometry and properties of pairs of hydrogen-bonded carboxylic acid side-chains

A rather frequent but so far little discussed observation is that pairs of carboxylic acid side-chains in proteins can share a proton in a hydrogen bond. In the present article, quantum chemical calculations of simple model systems for carboxyl-carboxylate interactions are compared with structural observations from proteins. A detailed structural analysis of the proteins deposited in the PDB revealed that, in a subset of proteins sharing less than 90% sequence identity, 19% (314) contain at least one pair of carboxylic acids with their side-chain oxygen atoms within hydrogen-bonding distance. As the distance between those interacting oxygen atoms is frequently very short ( approximately 2.55 A), many of these carboxylic acids are suggested to share a proton in a strong hydrogen bond. When situated in an appropriate structural environment (low dielectric constant), some might even form a low barrier hydrogen bond. The quantum chemical studies show that the most frequent geometric features of carboxyl-carboxylate pairs found in proteins, and no or symmetric ligation, are also the most stable arrangements at low dielectric constants, and they also suggest at medium and low pH a higher stability than for isosteric amide-carboxylate pairs. The presence of these pairs in 119 different enzymes found in the BRENDA database is set in relation to their properties and functions. This analysis shows that pH optima of enzymes with carboxyl-carboxylate pairs are shifted to lower than average values, whereas temperature optima seem to be increased. The described structural principles can be used as guidelines for rational protein design (e.g., in order to improve pH or temperature stability).

Application of classical molecular dynamics for evaluation of proton transfer mechanism on a protein

Proton transfer reactions on surfaces are prevalent in biology, chemistry and physics. In the present study, we employed classical Molecular Dynamics simulations to search for the presence of transient configurations that enable proton transfer, or proton sharing, between adjacent carboxylate groups on the protein surface. The results demonstrate that, during random fluctuations of the residues on the surface, there are repeated situations in which nearby carboxylates either share a common proton through a hydrogen bond, or are connected by a few water molecules that form conducting networks. These networks do not extend out of the common Coulomb cage of the participating residues and the lifetimes of the bridged structures are sufficiently long to allow passage of a proton between the carboxylates. The detection of domains capable of supporting a rapid proton transfer on a protein supports the notion that clusters of carboxylates are the operative elements of proton collecting antennae, as in bacteriorhodopsin, cytochrome c oxidase or the photosynthetic reaction center.

Double proton transfer and one-electron oxidation behavior in double H-bonded glycinamide-glycine complex in the gas phase

The behaviors of double proton transfer (DPT) occurring in a representative glycinamide-glycine complex have been investigated employing the B3LYP/6-311++G** level of theory. Thermodynamic and especially kinetic parameters, such as tautomerization energy, equilibrium constant, and barrier heights have been discussed, respectively. The relevant quantities involved in the DPT process including geometrical changes, interaction energies, and deformation energies have also been studied. Analogous to that of tautomeric process assisted with a formic acid molecule, the participation of a glycine molecule favors the proceeding of the proton transfer (PT) for glycinamide compared with that without mediator-assisted case. The DPT process proceeds with a concerted mechanism rather than a stepwise one because no zwitterionic complexes have been located during the DPT process. The barrier heights are 12.14 and 0.83 kcal/mol for the forward and reverse directions, respectively. However, both of them have been reduced by 3.10 and 2.66 kcal/mol to 9.04 and -1.83 kcal/mol with further inclusion of zero-point vibrational energy (ZPVE) corrections, where the disappearance of the reverse barrier height implies that the reverse reaction should proceed with barrierless spontaneously, analogous to those of DPTs occurring between glycinamide and formic acid (or formamide). Additionally, the oxidation process for the double H-bonded glycinamide-glycine complex has also been investigated. The oxidated product is characterized by a distonic radical cation due to the fact that one-electron oxidation takes place on glycine fragment and a proton has been transferred from glycine to glycinamide fragment spontaneously. As a result, the vertical and adiabatic ionization potentials for the neutral complex have been determined to be about 8.71 and 7.85 eV, respectively, where both of them have been reduced by about 0.54 (1.11) and 0.75 (1.13) eV relative to those of isolated glycinamide (glycine) due to the formation of the intermolecular H-bond.

Theoretical study of the symmetry of the (OH...O)- hydrogen bonds in vinyl alcohol-vinyl alcoholate systems

The interactions between substituted vinyl alcohols and vinyl alcoholates (X = NH(2), H, F, Cl, CN) are studied at the B3LYP/6-311++G(d,p) level of theory. In a first step, the conformation of the monomers is investigated and the proton affinities (PA(A(-))) of the enolates are calculated. The enols and enolates are held together by strong (OH...O)(-) hydrogen bonds, the hydrogen bond energies ranging from 19.1 to 34.6 kcal mol(-1). The optimized O...O distances are between 2.414 and 2.549 A and the corresponding OH distances from 1.134 and 1.023 A. The other geometry parameters such as C[double bond]C or CO distances also indicate that, in the minimum energy configuration, the hydrogen bonds are characterized by a double well potential. The Mulliken charges on the different atoms of the proton donors and proton acceptors and the frequencies of the nu(OH) stretching vibrations agree with this statement. All the data indicate that the hydrogen bonds are the strongest in the homomolecular complexes. The transition state for hydrogen transfer is located with the transition barrier estimated to be about zero. Upon addition of the zero-point vibration energies to the total potential energy, the barrier vanishes. This is a characteristic feature of low-barrier hydrogen bonds (LBHBs). The hydrogen bond energies are correlated to the difference 1.5 PA(AH) - PA(A(-)). The correlation predicts different energies for homomolecular hydrogen bonds, in agreement with the theoretical calculations. Our results suggest that a PA (or pK(a)) match is not a necessary condition for forming LBHBs in agreement with recent data on the intramolecular hydrogen bond in the enol form of benzoylacetone (J. Am. Chem. Soc. 1998, 120, 12117).

Chemical information from the source function

The source function, which enables one to equate the value of the electron density at any point within a molecule to a sum of atomic contributions, has been applied to a number of cases. The source function is a model-independent, quantitative measure of the relative importance of an atom's or group's contribution to the density at any point in a system, and it represents a potentially interesting tool to provide chemical information. It is shown that the source contribution from H to the electron density rho(b) at the bond critical point in HX diatomics decreases with increasing X's electronegativity, and that this decrease is a result of significant changes in the Laplacian distribution within the H-basin. It is also demonstrated that the source function from Li to rho(b) in LiX diatomics is a more sensitive index of atomic transferability than it is the lithium atomic energy or population. The observed changes are such as to ensure a constant percentage source contribution from Li to rho(b) throughout the LiX series, rather than a constant source as one would expect in the limit of perfect atomic transferability. Application of the source function to planar lithium clusters has revealed that the source function clearly discriminates between a nonnuclear electron density maximum and a maximum associated to a nucleus, on the basis of the relative weight of the source contributions from the basin associated to the maximum and from the remaining basins in the cluster. The source function has also allowed for a classification of hydrogen bonds in terms of characteristic source contributions to the density at the H-bond critical point from the H involved in the H-bond, the H-donor D, and the H-acceptor A. The source contribution from the H appears as the most distinctive marker of the H-bond strength, being highly negative for isolated H-bonds, slightly negative for polarized assisted H-bonds, close to zero for resonance-assisted H-bonds, and largely positive for charge-assisted H-bonds. The contributions from atoms other than H, D, and A strongly increase with decreasing H-bond strength, consistently with the parallel increased electrostatic character of the interaction. The correspondence between the classification provided by the Electron Localization Function topologic approach and by the source function has been highlighted. It is concluded that the source function represents a practical tool to disclose the local and nonlocal character of the electron density distributions and to quantify such a locality and nonlocality in terms of a physically sound and appealing chemical partitioning.

A nucleophile activation dyad in ribonucleases. A combined X-ray crystallographic/ab initio quantum chemical study

Ribonucleases (RNases) catalyze the cleavage of the phosphodiester bond in RNA up to 10(15)-fold, as compared with the uncatalyzed reaction. High resolution crystal structures of these enzymes in complex with 3'-mononucleotide substrates demonstrate the accommodation of the nucleophilic 2'-OH group in a binding pocket comprising the catalytic base (glutamate or histidine) and a charged hydrogen bond donor (lysine or histidine). Ab initio quantum chemical calculations performed on such Michaelis complexes of the mammalian RNase A (EC ) and the microbial RNase T(1) (EC ) show negative charge build up on the 2'-oxygen upon substrate binding. The increased nucleophilicity results from stronger hydrogen bonding to the catalytic base, which is mediated by a hydrogen bond from the charged donor. This hitherto unrecognized catalytic dyad in ribonucleases constitutes a general mechanism for nucleophile activation in both enzymic and RNA-catalyzed phosphoryl transfer reactions.

Symmetry of O-H-O and N-H-N hydrogen bonds in 6-hydroxy-2-formylfulvene and 6-aminofulvene-2-aldimines

The symmetry of the hydrogen bonds in 6-hydroxy-2-formylfulvene and two N,N'-diaryl-6-aminofulvene-2-aldimines is probed by the NMR technique of isotopic perturbation. Observed deuterium-induced 13C NMR isotope shifts at several positions can be attributed to a combination of an intrinsic shift and the perturbation of a tautomeric equilibrium. The most dramatic are at the aldehydic or aldiminic carbon signals, where the observed isotope shift for the unlabeled carbon is +376 or +223 ppb. This large downfield shift is contrary to the small upfield shift expected for a four-bond intrinsic shift and can be attributed only to a perturbation shift. Therefore these intramolecular hydrogen bonds are asymmetric, the proton resides in a double-minimum potential surface, and each molecule exists as a pair of rapidly interconverting tautomers, regardless of solvent. The symmetry of the hydrogen bond is not governed only by the O-O or N-N distance. It is proposed that symmetric hydrogen bonds can be observed in crystalline phases but not as yet in solution because the disorder of the solvation environment induces an asymmetry of the hydrogen bond, whereas a crystal can guarantee a symmetric environment. These results provide no insight into the source of the stabilization attributed to low-barrier hydrogen bonds if they lack the special feature of symmetry.

The charge density distribution in a model compound of the catalytic triad in serine proteases

Combined low temperature (28(1) K) X-ray and neutron diffraction measurements were carried out on the co-crystallised complex of betaine, imidazole, and picric acid (1). The experimental charge density was determined and compared with ab initio theoretical calculations at the B3LYP/6-311G(d,p) level of theory. The complex serves as a model for the active site in, for example, the serine protease class of enzymes, the so-called catalytic triad. The crystal contains three short strong N-H...O hydrogen bonds (HBs) with dN...O < 2.7 A. The three HBs have energies above 13 kcalmol(-1), although the hydrogen atoms are firmly localized in the "nitrogen wells". This suggests that low-barrier hydrogen bonding in catalytic enzyme reactions may be a sufficient, but not a necessary, condition for obtaining transition-state stabilization. Structural analysis (e.g., covalent N-H bond lengthening) indicates that the hydrogen bond between H3A and 08 of imidazole and betaine respectively (HB2) is slightly stronger than the bond between H1A and O1A of imidazole and picric acid (HB1), although HB1 is shorter than HB2: (dN...O(HB1)= 2.614(1) A, dN...O(HB2) = 2.684(1) A, dH...O(HB1) = 1.630(1) A, dH...O(HB2)= 1.635(1) A, dN-H(HB1) = 1.046(1) A, dN-H(HB2) = 1.057(1) A). Furthermore, the charge density analysis reveals that HB2 has a larger covalent character than HB1, with considerable polarization of the density towards the acceptor atom. The Gatti and Bader source function (S) is introduced to the analysis of strong HBs. The source function is found to be a sensitive measure for the nature of a hydrogen bond, and comparison with low-barrier and single-well hydrogen bonding systems (e.g., benzoylacetone and nitromalonamide) shows that the low-barrier hydrogen bond (LBHB) state is characterized by an enormously increased hydrogen atom source contribution to the bond critical point in the HB. In this context, HB2 can be characterized as intermediate between localized HBs and delocalized LBHBs.

Symmetry of N-H-N hydrogen bonds in 1,8-bis(dimethylamino)naphthalene.H+ and 2,7-dimethoxy-1,8-bis(dimethylamino)naphthalene.H+

In solution, are the hydrogen bonds in monoprotonated N,N,N',N'-tetramethyl-1,8-naphthalenediamines single- or double-well? To answer this question, isotopic perturbation of equilibrium is applied to a mixture of -d(0), -d(3), -d(6), -d(9), and -d(12) isotopologs. The N-methyls of the 2,7-dimethoxy analogue show intrinsic isotope shifts from the geminal CD(3) and from only one distant CD(3), an unusual stereochemical effect transmitted across the hydrogen bond. The (13)C NMR splittings and intensities at the various ring carbons of both ions are consistent with perturbation isotope shifts, intrinsic shifts, or a combination of both. The perturbation shifts mean that the protons reside in a double-minimum potential and that each ion is a pair of rapidly interconverting tautomers. The significance of this result for the role of low-barrier hydrogen bonds in enzyme-catalyzed reactions is discussed.

A QM/MM study of the racemization of vinylglycolate catalyzed by mandelate racemase enzyme

The experimentally postulated mechanism for the interconversion between (S)-vinylglycolate and (R)-vinylglycolate catalyzed by mandelate racemase enzyme consists of a two-step quite symmetric process through a dianionic enolic intermediate that is formed after the abstraction of the alpha-proton of vinylglycolate by a basic enzymatic residue and is then reprotonated by another residue. The challenging problem behind this reaction is how the enzyme manages to stabilize such an intermediate, that is, how it lowers enough the high pK(a) of the alpha-proton for the reaction to take place. The QM/MM simulations performed in this paper indicate that catalysis is based on the stabilization of the negative charge developed on the substrate along the reaction. We have identified three different reaction mechanisms starting from different quasi-degenerate structures of the substrate-enzyme complex. In two of them the stabilizing role is done by means of a catalytic proton transfer that avoids the formation of a dianionic intermediate, and they involve six steps instead of the two experimentally proposed. On the contrary, the third mechanism passes through a dianionic species stabilized by the concerted approach of a protonated enzymatic residue during the proton abstraction. The potential energy barriers theoretically found along these mechanisms are qualitatively in good agreement with the experimental free energy barriers determined for racemization of vinylglycolate and mandelate. The theoretical study of the effect of the mutation of Glu317 by Gln317 in the kinetics of the reaction reveals the important role in the catalysis of the hydrogen bond formed by Glu317 in the native enzyme, as only one of the mechanisms, the slower one, is able to produce the racemization in the active site of the mutant. However, we have found that this hydrogen bond is not an LBHB within our model.

Ab initio studies of

Ab initio calculations of the [1,5]-H shift in (3Z)-penta-1,3-diene and other substituted pentadienes and heteroanalogues using the hybrid density functional Becke3LYP with the 6-31G basis set are presented. Electron-donating substituents, such as methoxy in (3Z)-3-methoxypenta-1,3-diene 1, or heteroatoms such as a nitrogen atom in (Z)-ethylidenevinylamine 2, (1Z)-buta-1,3-dienylamine 3, (2Z)-but-2-enylideneamine 4, (Z)-allylidenemethylamine 5, and methylene-(Z)-propenylamine 6 are introduced. The electron-withdrawing fluoride is substituted for the hydrogen atoms in (3Z)-3-fluoropenta-1,3-diene 7, (3Z)-2,4-difluoropenta-1,3-diene 8, (3Z)-1,1',2,3,4,5,5'-heptafluoropenta- 1,3-diene 10, (1E,3E)-1,3,5-trifluoropenta-1,3-diene 11, and (1Z,3E)-1,3,5- trifluoropenta-1,3-diene 13. A detailed analysis of the geometries, energies, and electronic characteristics of the sigmatropic transposition compared to those of the unsubstituted case provides insights into substituent effects of this prototype of pericyclic reaction. The inductive and mesomeric effects of heteroatoms or heterosubstituents are of a great importance and in a continuous balance in the energetics of the transformation. Sterics can also play an important role due to the geometrical constraints of the reaction. As a general trend, decreasing the electron density of the phi system destabilizes the aromatic transition structure and increases the activation energy, and vice versa.

On the electronic nature of low-barrier hydrogen bonds in enzymatic reactions

The electronic nature of low-barrier hydrogen bonds (LBHBs) in enzymatic reactions is discussed based on combined low temperature neutron and x-ray diffraction experiments and on high level ab initio calculations by using the model substrate benzoylacetone. This molecule has a LBHB, as the intramolecular hydrogen bond is described by a double-well potential with a small barrier for hydrogen transfer. From an "atoms in molecules" analysis of the electron density, it is found that the hydrogen atom is stabilized by covalent bonds to both oxygens. Large atomic partial charges on the hydrogen-bonded atoms are found experimentally and theoretically. Therefore, the hydrogen bond gains stabilization from both covalency and from the normal electrostatic interactions found for long, weak hydrogen bonds. Based on comparisons with other systems having short-strong hydrogen bonds or LBHBs, it is proposed that all short-strong and LBHB systems possess similar electronic features of the hydrogen-bonded region, namely polar covalent bonds between the hydrogen atom and both heteroatoms in question.