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

Molecular insights into the water dissociation and proton dynamics at the β-TaON (100)/water interface

Understanding the dynamic nature of the semiconductor-water interface is crucial for developing efficient photoelectrochemical water splitting catalysts, as it governs reactivity through charge and mass transport. In this study, we employ ab initio molecular dynamics simulations to investigate the structural and dynamical properties of water at the β-TaON (100) surface. We observed that a well-defined interface is established through the spontaneous dissociation of water and the reorganization of surface chemical bonds. This leads to the formation of a partially hydroxylated surface, accompanied by a strong network of hydrogen bonds at the TaON-water interface. Consequently, various proton transport routes, including the proton transfer through "low-barrier hydrogen bond" path, become active across the interface, dramatically increasing the overall rate of the proton hopping at the interface. Based on our findings, we propose that the observed high photocatalytic activity of TaON-based semiconductors could be attributed to the spontaneous water dissociation and the resulting high proton transfer rate at the interface.

Very Strong Hydrogen Bond in Nitrophthalic Cocrystals

This work presents the studies of a very strong hydrogen bond (VSHB) in biologically active phthalic acids. Research on VSHB comes topical due to its participation in many biological processes. The studies cover the modelling of intermolecular interactions and phthalic acids with 2,4,6-collidine and N,N-dimethyl-4-pyridinamine complexes with aim to obtain a VSHB. The four synthesized complexes were studied by experimental X-ray, IR, and Raman methods, as well as theoretical Car-Parrinello Molecular Dynamics (CP-MD) and Density Functional Theory (DFT) simulations. By variation of the steric repulsion and basicity of the complex' components, a very short intramolecular hydrogen bond was achieved. The potential energy curves calculated by the DFT method were characterized by a low barrier (0.7 and 0.9 kcal/mol) on proton transfer in the OHN intermolecular hydrogen bond for 3-nitrophthalic acid with either 2,4,6-collidine or N,N-dimethyl-4-pyridinamine cocrystals. Moreover, the CP-MD simulations exposed very strong bridging proton dynamics in the intermolecular hydrogen bonds. The accomplished crystallographic and spectroscopic studies indicate that the OHO intramolecular hydrogen bond in 4-nitrophthalic cocrystals is VSHB. The influence of a strong steric effect on the geometry of the studied cocrystals and the stretching vibration bands of the carboxyl and carboxylate groups was elaborated.

Electronic Fingerprint of the Protonated Imidazole Dimer Probed by X-ray Absorption Spectroscopy

Protons in low-barrier superstrong hydrogen bonds are typically delocalized between two electronegative atoms. Conventional methods to characterize such superstrong hydrogen bonds are vibrational spectroscopy and diffraction techniques. We introduce soft X-ray spectroscopy to uncover the electronic fingerprints for proton sharing in the protonated imidazole dimer, a prototypical building block enabling effective proton transport in biology and high-temperature fuel cells. Using nitrogen core excitations as a sensitive probe for the protonation status, we identify the X-ray signature of a shared proton in the solvated imidazole dimer in a combined experimental and theoretical approach. The degree of proton sharing is examined as a function of structural variations that modify the shape of the low-barrier potential in the superstrong hydrogen bond. We conclude by showing how the sensitivity to the quantum distribution of proton motion in the double-well potential is reflected in the spectral signature of the shared proton.

Structural Insight on Supramolecular Polyion Salts: Inositol Hexaphosphate Enclosed in Cationic Macrocyclic Clusters

Supramolecular macrocyclic forces have been used to trap phytate, myo-inositol-1,2,3,4,5,6-hexakisphosphate, a key bioanion with multiple roles in metabolic processes. Due to the complex chemistry of six multivalent phosphates surrounding the small, cyclic inositol framework, crystallographic information of simple phytate salts has been elusive. This report represents a combined crystallographic, theoretical, and solution binding investigation of a supramolecular macrocyclic complex of phytate. Together, the results provide significant insight to phytate's intramolecular and intermolecular interactions at the microenvironment level. The macrocycle-phytate aggregates consist of phytate anionic pairs, each partly sandwiched by two 24-membered, amide/amine-based cationic macrocycles. The phytate ion pairs hold the tetrameric macrocyclic array together by six strong intermolecular hydrogen bonds. Both phytates crystallize in 1a5e phosphate conformations (one axial (P2) and five equatorial phosphates). Solution NMR binding studies in 1 : 1 DMSO-d6  : D2 O indicate 2 : 1 macrocycle:phytate associations, suggesting that the sandwich-like nature of the complex holds together in solution. DFT studies indicate the likely occurrence of dynamic intramolecular interchange of phosphate protons, as well as important roles for the axial (P2) phosphate in both intramolecular and intermolecular hydrogen bonding interactions.

MOF-Based Solid-State Proton Conductors Obtained by Intertwining Protic Ionic Liquid Polymers with MIL-101

Solid-state proton conductors based on the use of metal-organic framework (MOF) materials as proton exchange membranes are being investigated as alternatives to the current state of the art. This study reports a new family of proton conductors based on MIL-101 and protic ionic liquid polymers (PILPs) containing different anions. By first installing protic ionic liquid (PIL) monomers inside the hierarchical pores of a highly stable MOF, MIL-101, then carrying out polymerization in situ, a series of PILP@MIL-101 composites was synthesized. The resulting PILP@MIL-101 composites not only maintain the nanoporous cavities and water stability of MIL-101, but the intertwined PILPs provide a number of opportunities for much-improved proton transport compared to MIL-101. The PILP@MIL-101 composite with HSO4 - anions shows superprotonic conductivity (6.3 × 10-2  S cm-1 ) at 85 °C and 98% relative humidity. The mechanism of proton conduction is proposed. In addition, the structures of the PIL monomers were determined by single crystal X-ray analysis, which reveals many strong hydrogen bonding interactions with O/NH···O distances below 2.6 Å.

Proton-Tunneling Dynamics along Low-Barrier Hydrogen Bonds: A Full-Dimensional Instanton Study of 6-Hydroxy-2-formylfulvene

Understanding the dynamics of proton transfer along low-barrier hydrogen bonds remains an outstanding challenge of great fundamental and practical interest, reflecting the central role of quantum effects in reactions of chemical and biological importance. Here, we combine ab initio calculations with the semiclassical ring-polymer instanton method to investigate tunneling processes on the ground electronic state of 6-hydroxy-2-formylfulvene (HFF), a prototypical neutral molecule supporting low-barrier hydrogen-bonding. The results emerging from a full-dimensional ab initio instanton analysis reveal that the tunneling path does not pass through the instantaneous transition-state geometry. Instead, the tunneling process involves a multidimensional reaction coordinate with concerted reorganization of the heavy-atom skeletal framework to substantially reduce the donor-acceptor distance and drive the ensuing intramolecular proton-transfer event. The predicted tunneling-induced splittings for HFF isotopologues are in good agreement with experimental findings, leading to percentage deviations of only 20-40%. Our full-dimensional results allow us to characterize vibrational contributions along the tunneling path, highlighting the intrinsically multidimensional nature of the attendant hydron-migration dynamics.

An N⋯H⋯N low-barrier hydrogen bond preorganizes the catalytic site of aspartate aminotransferase to facilitate the second half-reaction

Pyridoxal 5'-phosphate (PLP)-dependent enzymes have been extensively studied for their ability to fine-tune PLP cofactor electronics to promote a wide array of chemistries. Neutron crystallography offers a straightforward approach to studying the electronic states of PLP and the electrostatics of enzyme active sites, responsible for the reaction specificities, by enabling direct visualization of hydrogen atom positions. Here we report a room-temperature joint X-ray/neutron structure of aspartate aminotransferase (AAT) with pyridoxamine 5'-phosphate (PMP), the cofactor product of the first half reaction catalyzed by the enzyme. Between PMP NSB and catalytic Lys258 Nζ amino groups an equally shared deuterium is observed in an apparent low-barrier hydrogen bond (LBHB). Density functional theory calculations were performed to provide further evidence of this LBHB interaction. The structural arrangement and the juxtaposition of PMP and Lys258, facilitated by the LBHB, suggests active site preorganization for the incoming ketoacid substrate that initiates the second half-reaction.

Urea Disrupts the AOT Reverse Micelle Structure at Low Temperatures

Aside from its prominent role in the excretory system, urea is also a known protein denaturant. Here, we characterize urea as it behaves in confined spaces of AOT (sodium bis(2-ethylhexyl) sulfosuccinate) reverse micelles as a model of tight, confined spaces found at the subcellular level. Dynamic light scattering revealed that low temperatures (275 K) caused the smallest of the reverse micelle sizes, w₀ = 10, to destabilize and dramatically increase in apparent hydrodynamic diameter. We attribute this to urea embedded into the surfactant interface as confirmed by 2D ¹H-NOESY NMR spectroscopy. This increase in size in turn caused the hydrogen exchange between urea and water within the nanosized reverse micelles to increase as measured by 1D EXSY-NMR. A minimal enlarging effect and no increase in hydrogen exchange were observed when aqueous urea was introduced into w₀ = 15 or 20 reverse micelles, suggesting that this effect is unique to particularly small-diameter spaces (∼7 nm).

Structures of prokaryotic ubiquitin-like protein Pup in complex with depupylase Dop reveal the mechanism of catalytic phosphate formation

Pupylation is the post-translational modification of lysine side chains with prokaryotic ubiquitin-like protein (Pup) that targets proteins for proteasomal degradation in mycobacteria and other members of Actinobacteria. Pup ligase PafA and depupylase Dop are the two enzymes acting in this pathway. Although they share close structural and sequence homology indicative of a common evolutionary origin, they catalyze opposing reactions. Here, we report a series of high-resolution crystal structures of Dop in different functional states along the reaction pathway, including Pup-bound states in distinct conformations. In combination with biochemical analysis, the structures explain the role of the C-terminal residue of Pup in ATP hydrolysis, the process that generates the catalytic phosphate in the active site, and suggest a role for the Dop-loop as an allosteric sensor for Pup-binding and ATP cleavage.

Pupylation is a bacterial post-translational protein modification, where the small ubiquitin-like protein Pup is covalently attached to lysine side chains of target proteins, which is a reversible process and depupylation is catalysed by the depupylase enzyme, Dop. Here, the authors present crystal structures of Dop in different functional states, which together with biochemical experiments provide insights into the catalytic mechanism of this enzyme.

Dynamics of proton, ion, molecule, and crystal lattice in functional molecular assemblies

Dynamic molecular processes, such as short- or long-range proton (H⁺) and ion (M⁺) motions, and molecular rotations in electrical conducting and magnetic molecular assemblies enable the fabrication of electron-H⁺ (or M⁺) coupling systems, while crystal lattice dynamics and molecular conformation changes in hydrogen-bonded molecular crystals have been utilised in external stimuli responsive reversible gas-induced gate opening and molecular adsorption/desorption behavior. These dynamics of the polar structural units are responsible for the dielectric measurements. The H⁺ dynamics are formed from ferroelectrics and H⁺ conductors, while the dynamic M⁺ motions of Li⁺ and Na⁺ involve ionic conductors and coupling to the conduction electrons. In n-type organic semiconductors, the crystal lattices are modulated by replacing M⁺ cations, with cations such as Li⁺, Na⁺, K⁺, Rb⁺, and Cs⁺. The use of polar rotator or inversion structures such as alkyl amides, m-fluoroanilinium cations, and bowl-shaped trithiasumanene π-cores enables the formation of ferroelectric molecular assemblies. The host-guest molecular systems of ESIPT fluorescent chromic molecules showed interesting molecular sensing properties using various bases, where the dynamic transformation of the crystal lattice and the molecular conformational change were coupled to each other.

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.

Nanoconfinement Raises the Energy Barrier to Hydrogen Atom Exchange between Water and Glucose

In bulk aqueous environments, the exchange of protons between labile hydroxyl groups typically occurs easily and quickly. Nanoconfinement can dramatically change this normally facile process. Through exchange spectroscopy (EXSY) NMR measurements, we observe that nanoconfinement of glucose and water within AOT (sodium bis(2-ethylhexyl) sulfosuccinate) reverse micelles raises the energy barrier to labile hydrogen exchange, which suggests a disruption of the hydrogen bond network. Near room temperature, we measure barriers high enough to slow the process by as much as 2 orders of magnitude. Although exchange rates slow with decreasing temperatures in these nanoconfined environments, the barrier we measure below ∼285 K is 3-5 times lower than the barrier measured at room temperature, indicating a change in mechanism for the process. These findings suggest the possibility of hydrogen tunneling at a surprisingly high-temperature threshold. Furthermore, differences in exchange rates depend on the hydroxyl group position on the glucose pyranose ring and suggest a net orientation of glucose at the reverse micelle interface.

Direct detection of coupled proton and electron transfers in human manganese superoxide dismutase

Human manganese superoxide dismutase is a critical oxidoreductase found in the mitochondrial matrix. Concerted proton and electron transfers are used by the enzyme to rid the mitochondria of O₂^•−. The mechanisms of concerted transfer enzymes are typically unknown due to the difficulties in detecting the protonation states of specific residues and solvent molecules at particular redox states. Here, neutron diffraction of two redox-controlled manganese superoxide dismutase crystals reveal the all-atom structures of Mn³⁺ and Mn²⁺ enzyme forms. The structures deliver direct data on protonation changes between oxidation states of the metal. Observations include glutamine deprotonation, the involvement of tyrosine and histidine with altered pK_as, and four unusual strong-short hydrogen bonds, including a low barrier hydrogen bond. We report a concerted proton and electron transfer mechanism for human manganese superoxide dismutase from the direct visualization of active site protons in Mn³⁺ and Mn²⁺ redox states.

Human manganese superoxide dismutase (MnSOD) is an oxidoreductase that uses concerted proton and electron transfers to reduce the levels of superoxide radicals in mitochondria, but mechanistic insights into this process are limited. Here, the authors report neutron crystal structures of Mn³⁺SOD and Mn²⁺SOD, revealing changes in the protonation states of key residues in the enzyme active site during the redox cycle.

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.

Core level spectroscopies locate hydrogen in the proton transfer pathway - identifying quasi-symmetrical hydrogen bonds in the solid state

Short, strong hydrogen bonds (SSHBs) have been a source of interest and considerable speculation over recent years, culminating with those where hydrogen resides around the midpoint between the donor and acceptor atoms, leading to quasi-covalent nature. We demonstrate that X-ray photoelectron spectroscopy (XPS) and near-edge X-ray absorption fine structure (NEXAFS) spectroscopy provide deep insight into the electronic structure of the short OHN hydrogen bond of 3,5-pyridinedicarboxylic acid, revealing for the first time distinctive spectroscopic identifiers for these quasi-symmetrical hydrogen bonds. An intermediate nitrogen (core level) chemical shift occurs for the almost centrally located hydrogen compared to protonated (ionic) and non-ionic analogues, and it reveals the absence of two-site disorder. This type of bonding is also evident through broadening of the nitrogen 1s photoemission and 1s → 1π* peaks in XPS and NEXAFS, respectively, arising from the femtosecond lifetimes of hydrogen in the potential wells slightly offset to either side of the centre. The line-shape of the core level excitations are thus related to the population occupancies, reflecting the temperature-dependent shape of the hydrogen potential energy well. Both XPS and NEXAFS provide a distinctive identifier for these quasi-symmetrical hydrogen bonds, paving the way for detailed studies into their prevalence and potentially unique physical and chemical properties.

Simulations of Cellulose Synthesis Initiation and Termination in Bacteria

The processivity of cellulose synthesis in bacterial cellulose synthase (CESA) was investigated using molecular dynamics simulations and the hybrid quantum mechanics and molecular mechanics approach. Our results suggested that cellulose synthesis in bacterial CESA can be initiated with H₂O molecules. The chain length or degree of polymerization (DOP) of the product cellulose is related to the affinity of the cellulose chain to the transmembrane tunnel of the enzyme. This opens up the possibility of generating mutants that would produce cellulose chains with desired chain lengths that could have applications in the biofuel and textile fields that depend on the DOP of cellulose chains.

Role of Hydrogen in the Spin-Orbital-Entangled Quantum Liquid Candidate H_{3}LiIr_{2}O_{6}

Motivated by recent reports of H_{3}LiIr_{2}O_{6} as a spin-orbital-entangled quantum liquid, we investigate via a combination of density functional theory and nonperturbative exact diagonalization the microscopic nature of its magnetic interactions. We find that while the interlayer O─H─O bond geometry strongly affects the local magnetic couplings, these bonds are likely to remain symmetrical due to large zero-point fluctuations of the H positions. In this case, the estimated magnetic model lies close to the classical tricritical point between ferromagnetic, zigzag, and incommensurate spiral orders, what may contribute to the lack of magnetic ordering. However, we also find that substitution of H by D (deuterium) as well as disorder-induced inhomogeneities destabilizes the O─H or D─O bonds, modifying strongly the local magnetic couplings. These results suggest that the magnetic response in H_{3}LiIr_{2}O_{6} is likely sensitive to both the stoichiometry and the microstructure of the samples and emphasize the importance of a careful treatment of hydrogen for similar systems.

Sub-picomolar Inhibition of HIV-1 Protease with a Boronic Acid

Boronic acids have been typecast as moieties for covalent complexation and are employed only rarely as agents for non-covalent recognition. By exploiting the profuse ability of a boronic acid group to form hydrogen bonds, we have developed an inhibitor of HIV-1 protease with extraordinary affinity. Specifically, we find that replacing an aniline moiety in darunavir with a phenylboronic acid leads to 20-fold greater affinity for the protease. X-ray crystallography demonstrates that the boronic acid group participates in three hydrogen bonds, more than the amino group of darunavir or any other analog. Importantly, the boronic acid maintains its hydrogen bonds and its affinity for the drug-resistant D30N variant of HIV-1 protease. The BOH···OC hydrogen bonds between the boronic acid hydroxy group and Asp30 (or Asn30) of the protease are short ( rO···O = 2.2 Å), and density functional theory analysis reveals a high degree of covalency. These data highlight the utility of boronic acids as versatile functional groups in the design of small-molecule ligands.

Methylpiperidinium Iodides as Novel Antagonists for α7 Nicotinic Acetylcholine Receptors

The α7 nicotinic acetylcholine receptor (nAChR) is expressed in neuronal and non-neuronal cells and is involved in several physiopathological processes, and is thus an important drug target. We have designed and synthesized novel piperidine derivatives as α7 nAChR antagonists. Thus, we describe here a new series of 1-[2-(4-alkoxy-phenoxy-ethyl)]piperidines and 1-[2-(4-alkyloxy-phenoxy-ethyl)]-1-methylpiperidinium iodides (compounds 11a-11c and 12a-12c), and their actions on α7 nAChRs. The pharmacological activity of these compounds was studied in rat CA1 hippocampal interneurons by using the whole-cell voltage-clamp technique. Inhibition of the choline-induced current was less for 11a-11c than for the methylpiperidinium iodides 12a-12c and depended on the length of the aliphatic chain. Those compounds showing strong effects were studied further using molecular docking and molecular dynamics simulations. The strongest and non-voltage dependent antagonism was shown by 12a, which could establish cation–π interactions with the principal (+)-side and van der Waals interactions with the complementary (-)-side in the α7 nAChRs. Furthermore, compound 11a forms hydrogen bonds with residue Q115 of the complementary (-)-side through water molecules without forming cation–π interactions. Our findings have led to the establishment of a new family of antagonists that interact with the agonist binding cavity of the α7 nAChR, which represent a promising new class of compounds for the treatment of pathologies where these receptors need to be negatively modulated, including neuropsychiatric disorders as well as different types of cancer.

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.

Solid-State 17 O NMR Reveals Hydrogen-Bonding Energetics: Not All Low-Barrier Hydrogen Bonds Are Strong

While NMR and IR spectroscopic signatures and structural characteristics of low-barrier hydrogen bond (LBHB) formation are well documented in the literature, direct measurement of the LBHB energy is difficult. Here, we show that solid-state ¹⁷ O NMR spectroscopy can provide unique information about the energy required to break a LBHB. Our solid-state ¹⁷ O NMR data show that the HB enthalpy of the O⋅⋅⋅H⋅⋅⋅N LBHB formed in crystalline nicotinic acid is only 7.7±0.5 kcal mol^-1 , suggesting that not all LBHBs are particularly strong.

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.

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.

How Cellulose Elongates--A QM/MM Study of the Molecular Mechanism of Cellulose Polymerization in Bacterial CESA

The catalytic mechanism of bacterial cellulose synthase was investigated by using a hybrid quantum mechanics and molecular mechanics (QM/MM) approach. The Michaelis complex model was built based on the X-ray crystal structure of the cellulose synthase subunits BcsA and BcsB containing a uridine diphosphate molecule and a translocating glucan. Our study identified an SN2-type transition structure corresponding to the nucleophilic attack of the nonreducing end O4 on the anomeric carbon C1, the breaking of the glycosidic bond C1-O1, and the transfer of proton from the nonreducing end O4 to the general base D343. The activation barrier found for this SN2-type transition state is 68 kJ/mol. The rate constant of polymerization is estimated to be ∼8.0 s(-1) via transition state theory. A similar SN2-type transition structure was also identified for a second glucose molecule added to the growing polysaccharide chain, which aligned with the polymer 180° rotated compared to the initially added unit. This study provides detailed insights into how cellulose is extended by one glucose molecule at a time and how the individual glucose units align into cellobiose repeating units.

Monitoring ultrafast intramolecular proton transfer processes in an unsymmetric β-diketone

Electronic excitation of a UV-absorbing unsymmetric β-diketone discloses intramolecular proton transfer among electronic ground as well as excited states.

Probing keto–enol tautomerism using photoelectron spectroscopy

We theoretically investigate the mechanism of tautomerism in the gas-phase acetylacetone molecule.

Ultrafast proton shuttling in Psammocora cyan fluorescent protein

Cyan, green, yellow, and red fluorescent proteins (FPs) homologous to green fluorescent protein (GFP) are used extensively as model systems to study fundamental processes in photobiology, such as the capture of light energy by protein-embedded chromophores, color tuning by the protein matrix, energy conversion by Förster resonance energy transfer (FRET), and excited-state proton transfer (ESPT) reactions. Recently, a novel cyan fluorescent protein (CFP) termed psamFP488 was isolated from the genus Psammocora of reef building corals. Within the cyan color class, psamFP488 is unusual because it exhibits a significantly extended Stokes shift. Here, we applied ultrafast transient absorption and pump-dump-probe spectroscopy to investigate the mechanistic basis of psamFP488 fluorescence, complemented with fluorescence quantum yield and dynamic light scattering measurements. Transient absorption spectroscopy indicated that, upon excitation at 410 nm, the stimulated cyan emission rises in 170 fs. With pump-dump-probe spectroscopy, we observe a very short-lived (110 fs) ground-state intermediate that we assign to the deprotonated, anionic chromophore. In addition, a minor fraction (14%) decays with 3.5 ps to the ground state. Structural analysis of homologous proteins indicates that Glu-167 is likely positioned in sufficiently close vicinity to the chromophore to act as a proton acceptor. Our findings support a model where unusually fast ESPT from the neutral chromophore to Glu-167 with a time constant of 170 fs and resulting emission from the anionic chromophore forms the basis of the large psamFP488 Stokes shift. When dumped to the ground state, the proton on neutral Glu is very rapidly shuttled back to the anionic chromophore in 110 fs. Proton shuttling in excited and ground states is a factor of 20-4000 faster than in GFP, which probably results from a favorable hydrogen-bonding geometry between the chromophore phenolic oxygen and the glutamate acceptor, possibly involving a short hydrogen bond. At any time in the reaction, the proton is localized on either the chromophore or Glu-167, which implies that most likely no low-barrier hydrogen bond exists between these molecular groups. This work supports the notion that proton transfer in biological systems, be it in an electronic excited or ground state, can be an intrinsically fast process that occurs on a 100 fs time scale. PsamFP488 represents an attractive model system that poses an ultrafast proton transfer regime in discrete steps. It constitutes a valuable model system in addition to wild type GFP, where proton transfer is relatively slow, and the S65T/H148D GFP mutant, where the effects of low-barrier hydrogen bonds dominate.

Biophysical limits of protein-ligand binding

In classic work, Kuntz et al. (Proc. Nat. Acad. Sci. USA 1999, 96, 9997-10002) introduced the concept of ligand efficiency. Though that study focused primarily on drug-like molecules, it also showed that metal binding led to the greatest ligand efficiencies. Here, the physical limits of binding are examined across the wide variety of small molecules in the Binding MOAD database. The complexes with the greatest ligand efficiencies share the trait of being small, charged ligands bound in highly charged, well buried binding sites. The limit of ligand efficiency is -1.75 kcal/mol·atom for the protein-ligand complexes within Binding MOAD, and 95% of the set have efficiencies below a "soft limit" of -0.83 kcal/mol·atom. On the basis of buried molecular surface area, the hard limit of ligand efficiency is -117 cal/mol·Å(2), which is in surprising agreement with the limit of macromolecule-protein binding. Close examination of the most efficient systems reveals their incredibly high efficiency is dictated by tight contacts between the charged groups of the ligand and the pocket. In fact, a misfit of 0.24 Å in the average contacts inherently decreases the maximum possible efficiency by at least 0.1 kcal/mol·atom.

Field effects induce bathochromic shifts in xanthene dyes

There is ongoing interest in near-infrared (NIR) absorbing and emitting dyes for a variety of biomedical and materials applications. Simple and efficient synthetic procedures enable the judicious tuning of through-space polar (field) effects as well as low barrier hydrogen bonding to modulate the HOMO-LUMO gap in xanthene dyes. This affords unique NIR-absorbing xanthene chromophores.