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Abstract: We studied the chemical modifications of open-cage fullerene [C.sub.60] derivatives encapsulating a small molecule such as [H.sub.2] and [H.sub.2]O. In these reactions, the entrapped molecules can be used as [...]

Abstract: Interest in the low carbonyl IR frequency of 2-hydroxy-N,N-bis(2-hydroxyethyl)acetamide (2) initially prompted our interest in the amide rotational barrier of this molecule and four related amides that present a [...]

The quantum nature of the proton can crucially affect the structural and physical properties of hydrogen compounds. For example, in the high-pressure phases (1,2) of [H.sub.2]O, quantum proton fluctuations lead to symmetrization of the hydrogen bond and reduce the boundary between asymmetric and symmetric structures in the phase diagram by 30 gigapascals (ref. 3). Here we show that an analogous quantum symmetrization occurs in the recently discovered (4) sulfur hydride superconductor with a superconducting transition temperature [T.sub.c] of 203 kelvin at 155 gigapascals--the highest [T.sub.c] reported for any superconductor so far. Superconductivity occurs via the formation of a compound with chemical formula [H.sub.3]S (sulfur trihydride) with sulfur atoms arranged on a body-centred cubic lattice (5-9). If the hydrogen atoms are treated as classical particles, then for pressures greater than about 175 gigapascals they are predicted to sit exactly halfway between two sulfur atoms in a structure with Im[bar.3]m symmetry. At lower pressures, the hydrogen atoms move to an off-centre position, forming a short H-S covalent bond and a longer H***S hydrogen bond in a structure with R3m symmetry (5-9). X-ray diffraction experiments confirm the [H.sub.3]S stoichiometry and the sulfur lattice sites, but were unable to discriminate between the two phases (10). Ab initio density-functional-theory calculations show that quantum nuclear motion lowers the symmetrization pressure by 72 gigapascals for [H.sub.3]S and by 60 gigapascals for [D.sub.3]S. Consequently, we predict that the Im[bar.3]m phase dominates the pressure range within which the high [T.sub.c] was measured. The observed pressure dependence of [T.sub.c] is accurately reproduced in our calculations for the Im[bar.3]m phase, but not for the R3m phase. Therefore, the quantum nature of the proton fundamentally changes the superconducting phase diagram of [H.sub.3]S., The recent discovery of high-temperature superconductivity in compressed hydrogen sulfide (4) has led to a number of theoretical studies aimed at understanding the phase diagram of the H-S system and [...]

Catalysis by neutral, organic, small molecules capable of binding and activating substrates solely via noncovalent interactions--particularly H-bonding--has emerged as an important approach in organocatalysis. The mechanisms by which such small molecule catalysts induce high enantioselectivity may be quite different from those used by catalysts that rely on covalent interactions with substrates. Attractive noncovalent interactions are weaker, less distance dependent, less directional, and more affected by entropy than covalent interactions. However, the conformational constraint required for high stereoinduction may be achieved, in principle, if multiple noncovalent attractive interactions are operating in concert. This perspective will outline some recent efforts to elucidate the cooperative mechanisms responsible for stereoinduction in highly enantioselective reactions promoted by noncovalent catalysts. enantioselectivity | H bonding | organocatalysis | transition state stabilization doi/ 10.1073/pnas.1006402107

Complementary to enantioselective transformations of planar functionalities, catalytic desymmetrization of meso compounds is another fundamentally important strategy for asymmetric synthesis. However, experimentally established stereochemical models on how a chiral catalyst discriminates between two enantiotopic functional groups in the desymmetrization of a meso substrate are particularly lacking. This article describes our endeavor to elucidate the chemical mechanism and characterization of the active conformation of the cinchona alkaloid-derived catalyst for a desymmetrization of meso cyclic anhydrides via asymmetric alcoholysis. First, our kinetic studies indicate that the cinchona alkaloid-catalyzed alcoholysis proceeds by a general base catalysis mechanism. Furthermore, the active conformer of the cinchona alkaloid-derived catalyst DHQD-PHN was clarified by catalyst conformation studies with a designed, rigid cinchona alkaloid derivative as a probe. These key mechanistic insights enabled us to construct a stereochemical model to rationalize how DHQD-PHN differentiates the two enantiotopic carbonyl groups in the transition state of the asymmetric alcoholysis of meso cydic anhydrides. This model not only is consistent with the sense of asymmetric induction of the asymmetric alcoholysis but also provides a rationale on how the catalyst tolerates a broad range of cyclic anhydrides. These mechanistic insights further guided us to develop a novel practical catalyst for the enantioselective alcoholysis of meso cyclic anhydrides. cinchona alkoloid | desymmetrization | organocatalysis | general base catalysis | hydrogen bonding doi/ 10.1073/pnas.104439107

Solvation of molecules in water is at the heart of a myriad of molecular phenomena and of crucial importance to understanding such diverse issues as chemical reactivity or biomolecular function. Complementing well-established approaches, it has been shown that laser spectroscopy in the THz frequency domain offers new insights into hydration from small solutes to proteins. Upon introducing spatially-resolved analyses of the absorption cross section by simulations, the sensitivity of THz spectroscopy is traced back to characteristic distance-dependent modulations of absorption intensities for bulk water. The prominent peak at [approximately equal to] 200 [cm.sup.-1] is dominated by first-shell dynamics, whereas a concerted motion involving the second solvation shell contributes most significantly to the absorption at about 80 [cm.sup.-1] [approximately equal to] 2.4 THz. The latter can be understood in terms of an umbrella-like motion of two hydrogen-bonded tetrahedra along the connecting hydrogen bond axis. Thus, a modification of the hydrogen bond network, e.g., due to the presence of a solute, is expected to affect vibrational motion and THz absorption intensity at least on a length scale that corresponds to two layers of solvating water molecules. This result provides a molecular mechanism explaining the experimentally determined sensitivity of absorption changes in the THz domain in terms of distinct, solute-induced dynamical properties in solvation shells of (bio)molecules--even in the absence of well-defined resonances. ab initio molecular dynamics | hydrogen-bonding | solvation | infrared spectroscopy | vibrational modes doi/10.1073/pnas.0914885107

The solvation of ions in aqueous media is a fundamental process in biology and chemistry. Here, we report direct time-domain observations of the hydrogen bond vibrational mode formed between a halide ion (chloride, bromide, or iodide) and the surrounding water molecules. The frequency of the hydrogen bond mode is sensitive to both the atomic weight and the concentration of the ion. The peak frequencies fair in the 125 to 175 wave-number range, a spectral region accessed through time-domain polarization-resolved coherent Raman scattering using a diffractive optic method. The polarized Raman response observed is discussed in terms of the structure of the anion's solvation shell and modeled through calculations on water chloride dusters. 10.1126/science.1183799

Resolving molecular determinants of mechanical stability of proteins is crucial in the rational design of advanced biomaterials for use in biomedical and nanotechnological applications. Here we present an interdisciplinary study combining bioinformatics screening, steered molecular dynamics simulations, protein engineering, and single-molecule force spectroscopy that explores the mechanical properties of a macro domain protein with mixed a + [beta] topology. The unique architecture is defined by a single seven-stranded [beta]-sheet in the core of the protein flanked by five [alpha]-helices. Unlike mechanically stable proteins studied thus far, the macro domain provides the distinct advantage of having the key load-bearing hydrogen bonds (H bonds) buried in the hydrophobic core protected from water attacks. This feature allows direct measurement of the force required to break apart the load-bearing H bonds under locally hydrophobic conditions. Steered molecular dynamics simulations predicted extremely high mechanical stability of the macro domain by using constant velocity and constant force methods. Single-molecule force spectroscopy experiments confirm the exceptional mechanical strength of the macro domain, measuring a rupture force as high as 570 pN. Furthermore, through selective deletion of shielding peptide segments, we examined the same key H bonds under hydrophilic environments in which the [beta]-strands are exposed to solvent and verify that the high mechanical stability of the macro domain results from excellent shielding of the load-bearing H bonds from competing water. Our study reveals that shielding water accessibility to the load-bearing strands is a critical molecular determinant for enhancing the mechanical stability of proteins. doi/10.1073/pnas.0905796107

The catalytic importance of enzyme active-site interactions is frequently assessed by mutating specific residues and measuring the resulting rate reductions. This approach has been used in bacterial ketosteroid isomerase to probe the energetic importance of active-site hydrogen bonds donated to the dienolate reaction intermediate. The conservative Tyr16Phe mutation impairs catalysis by [10.sup.5]-fold, far larger than the effects of hydrogen bond mutations in other enzymes. However, the less-conservative Tyr16Ser mutation, which also perturbs the Tyr16 hydrogen bond, results in a lesssevere 102-fold rate reduction. To understand the paradoxical effects of these mutations and clarify the energetic importance of the Tyr16 hydrogen bond, we have determined the 1.6-A resolution x-ray structure of the intermediate analogue, equilenin, bound to the Tyr16Ser mutant and measured the rate effects of mutating Tyr16 to Ser, Thr, Ala, and Gly. The nearly identical 200-fold rate reductions of these mutations, together with the 6.4-A distance observed between the Ser16 hydroxyl and equilenin oxygens in the x-ray structure, strongly suggest that the more moderate rate effect of this mutant is not due to maintenance of a hydrogen bond from Ser at position 16. These results, additional spectroscopic observations, and prior structural studies suggest that the Tyr16Phe mutation results in unfavorable interactions with the dienolate intermediate beyond loss of a hydrogen bond, thereby exaggerating the apparent energetic benefit of the Tyr16 hydrogen bond relative to the solution reaction. These results underscore the complex energetics of hydrogen bonding interactions and site-directed mutagenesis experiments. doi/10.10731pnas.0911168107

The crystal chemistry of sursassite, simplified formula [Mn.sup.2+.sub.2] [Al.sub.3] [Si.sub.3] [O.sub.11] [(OH).sub.3], from six different localities [(1) Falotta, Switzerland, (2) Woodstock, New Brunswick, Canada, (3) Kamisugai, Japan, (4) Kamogawa, Japan, (5) Molinello, Italy, and (6) Gambatesa, Italy] was studied using electron microprobe analysis (EMPA), Fourier transform infrared spectroscopy (FTIR), and single-crystal X-ray diffraction methods. The structure has two symmetry independent Mn sites. The Mnl site is seven coordinated by O and hosts, in addition to [Mn.sup.2+], up to 20% Ca, whereas Mn2 has octahedral coordination and is strongly selective for [Mn.sup.2+]. In the simplified formula, three smaller octahedral M sites are occupied by A1. However, M1 also accepts significant amounts of divalent cations, such as Cu, Mg, Fe, and Mn, whereas M2 is occupied exclusively by A1. The unit-cell parameters of sursassite area = 8.698-8.728, b = 5.789-5.807, c = 9.778-9.812 [Angstrom], [beta] = 108.879-109.060[degrees], V = 465.7-470.0 [[Angstrom].sup.3], the space group is [P2.sub.1/m]. Structure refinements converged to [R.sub.1] values of 2.15-6.62%. In agreement with bond-valence analyses, at least three OH groups, depending on the concentration of divalent cations at M1, are found at the O6, O7, and O11 positions. However, the bond-valence sum at O10 is always low, thus partial hydroxylation is assumed at O10 to maintain charge balance. Owing to the influence of divalent cations at M1 in sursassite the hydrogen-bond systems in sursassite and isostructural macfallite are different. The FTIR spectrum in the region of OH-stretching vibrations is characterized by three strong bands at 3511, 3262, and around 2950 [cm.sup.-1], the latter being broad. The band at 2950 [cm.sup.-1] is assigned to strong hydrogen bonds between O6 and O10 (O6 ... O10 = 2.66 [Angstrom]). Residual difference-Fourier peaks in the refinement of the Kamogawa and Molinello (specimen 1) crystals indicated less than 5% pumpellyite intergrowth. Keywords: Sursassite, hydrogen bond, infrared spectroscopy, crystal structure, macfallite, pumpellyite

The exchange of water hydroxyl hydrogen bonds between anions and water oxygens is observed directly with ultrafast 2D IR vibrational echo chemical exchange spectroscopy (CES). The OD hydroxyl stretch of dilute HOD in [H.sub.2]O in concentrated (5.5 M) aqueous solutions of sodium tetrafluoroborate (NaB[F.sub.4]) displays a spectrum with a broad water-like band (hydroxyl bound to water oxygen) and a resolved, blue shifted band (hydroxyl bound to B[F.sup.-.sub.4]). At short time (200 fs), the 2D IR vibrational echo spectrum has 4 peaks, 2 on the diagonal and 2 off-diagonal. The 2 diagonal peaks are the 0-1 transitions of the water-like band and the hydroxyl-anion band. Vibrational echo emissions at the 1-2 transition frequencies give rise to 2 off-diagonal peaks. On a picosecond time scale, additional off-diagonal peaks grow in. These new peaks arise from chemical exchange between water hydroxyls bound to anions and hydroxyls bound to water oxygens. The growth of the chemical exchange peaks yields the time dependence of anion--water hydroxyl hydrogen bond switching under thermal equilibrium conditions as [T.sub.aw] = 7 [+ or -] 1 ps. Pump-probe measurements of the orientational relaxation rates and vibrational lifetimes are used in the CES data analysis. The pump-probe measurements are shown to have the correct functional form for a system undergoing exchange. 2D IR spectroscopy | hydration of ions | hydrogen bond dynamics | ion hydrogen bonds chemical exchange | ionic solutions

Infrared/femtosecond multiphoton ionization spectroscopy (IR/fsMPI) and fluorescence-detected infrared (FDIR) spectrum are used for examining the structure of isolated 1H-pyrrolo[3,2-h]quinoline (PQ)/[water.sub.n] (n = 1.2) complexes. Findings reveal weaker hydrogen bonding in both 1:1 and 1:2 complexes of PQ with water.

The comparison of the emission spectra of five 1:1 complexes of 2-pyridone (2PY) with formic acid (FA), acetic acid (AA), propanoic acid (PA), formamide (FM) and acetamide (AM) is presented. Findings reveal that the methyl group belonging to the AA and AM moieties is responsible for the acceleration of the vibrational energy redistribution (IVR) in the 2PY moiety.

Dynamic hydrogen bonding has resulted in the appearance of additional signals in the [super 13]C CPMAS spectra of photodimerized [alpha]-trans-cinnamic acid. The joint approach of both X-ray analysis and solid-state NMR has disclosed the dynamic processes occurring in the topochemical reactions and has provided insights into the reaction mechanism of organic solid-state transformations.

An in silico study has examined the stabilities of hydrogen-bonded complexes between simple thiourea catalysts and three different electrophiles and has identified a novel, highly active N-tosyl urea catalyst for promoting the addition reactions to epoxide electrophiles. Studies have shown that relatively poor nucleophiles like sterically and electronically deactivated anilines, thiophenol and benzyl alcohol are regioselectively added to oxiranes under mild conditions.

The self-complementary molecules of calix[4]arenes substituted by four urea functions that spontaneously combine in apolar solvents in the presence of an ammonium salt to form dimeric capsules held together by a belt of hydrogen bonds is reported.

The synthesis of a series of atropisomeric iminothiazolines is carried out by using methoxy precursors. The reaction provides insight into stereodynamics of hydrogen bond between the proton of the OH group and the nitrogen of the imino group.

The study of geometrical structures and relative energies of dimers of boroglycine, [H.sub.2]N-C[H.sub.2]-B[(OH).sub.2] and [H.sub.3]C-NH-B[(OH).sub.2] is presented.

The synthesis and magnetostructural analysis of 2-(4,5,6,7-tetrafluorobenzidazol-2-yl)-4,4,5,5-tetramethyl-4,5-dihydro-1-H-imidazole-3-oxide-1-oxyl (F4BImNN) are described. Magnetic and calorimetric studies have shown that it has acted as a quasi one-dimensional (1D) organic ferromagnet whose FM coupled, hydrogen-bonded chains are antiferromagnetically coupled to give magnetic ordering below the critical temperature.

The dynamic supramolecular polymer that spontaneously self-assembles in a wide variety of solvents ranging in polarity from water to toluene is described. The presence of both hydrogen-bonding and hydrophobic groups has seen to that self-assembly has occurred in water, aprotic polar solvents and nonpolar solvents.

The rapid progress and discovery of diverse H-bond donor motifs as a small-molecule chiral catalyst used in enantioselective reactions is reviewed.

The photophysics and photochemistry of intramolecular and intermolecular hydrogen bonded-molecular systems was studied using ab initio electronic-structure calculations. The study was carried out by selecting molecular building blocks of indole-ammonia, pyridine-ammonia and indole-pyridine complexes as chromophores.

Molecular dynamics simulations are used for examining the complexes of HIV-1 reverse transcriptase (RT) with the substrate and the antiretrovirals AZT and d4t. Results suggest that the finger residues K65 and R72 form hydrogen bonds with the substituted nucleotides.

The unusual low-temperature hydrogen bonding, local structural transitions associated with stronger low-temperature hydrogen bonding, and striking multiphonon effects observed in copper pyrazine complexes is reported.

A 2-color IR spectroscopy is used to study ultrafast bulk melting of ice after laser-induced temperature jump in HDO:[D.sub.2]O system. The studies provide insight into experimental manipulation of H-bonded materials and hydrogen bonding in nature.

The calculation results for the strength of H-bond formed between a dipeptide and a proton acceptor molecule determined for wide range of different conformations of the dipeptide are presented.

Several pyrrolic and hydrogen-bonding ligands are incorporated into a benzene-based tripodal scaffold for the generation of a new series of receptors, which can be widely used for the molecular recognition of carbohydrates and monosaccharides. The study of the various geometric, functional and coordinative complementarity between the bonding groups and hydroxyls helps in analyzing the affinity of such products through a generalized binding receptor.

The technique of ultrafast two-dimensional infrared (2D-IR) vibrational echo chemical exchange spectroscopy is employed to analyze the hydrogen bond lifetimes and energetics of various solute or solvent complexes. The results show that the dissociation rates of the weak hydrogen bonds are strongly related to their formation enthalpies and can be easily described by an equation similar to the Arhenius equation.

Various related compounds of hexaphenylbenzene are examined, which usually engage in hydrogen bonding and hence give rise to numerous hydrogen-bonded molecular crystals. The results show that the number of hydrogen bonds and the percentage of volume accessible to the guests are found to be highest in such complexes, which demonstrates the importance of maintaining a consistent molecular shape while determining the properties.

The effect of loss of 5,10-methenyltetrahydrofolate polyglutamate (MTHF) on the protein-flavin adenine dinucleotide (FAD) interactions in Escherichia coli photolyase (EcPhr) is monitored to probe the protein-MTHF interactions in both EcPhr and Vibrio cholerae cryptochrome-1 (VcCry1) by using resonance Raman spectroscopy. It is found that there are differences in hydrogen bonding account for higher binding affinity of MTHF in VcCry1 compared to EcPhr.

Changes in the ultrafast dynamics and tetrahertz Raman spectrum of a homo-polypeptide associated with a secondary structure (alpha-helix to coil) transition due to changes in solvent-peptide hydrogen bonding are described. It was suggested that the fast motions of solvent molecules is referred to as the 'lubricant of life' and are expected to be significant in deciding the structure and activity of protein.

A protonated water/hydroxyl cluster inside the channel is assessed for the purpose of elucidating the mechanism of proton transport in the D-pathway of cytochrome c oxidase (CcO). Results reveal that a hydrogen-bonded network consisting of about 5 water molecules surrounded by three side chains.

A study was conducted to explore the unusual reactivity of Glu376, the base involved in substrate [alpha][H.sup.+] abstraction at the active center of medium-chain acyl-CoA dehydrogenase (MCAD) mutants, Gln and Gly. The results state that large isotope effects are attributed to the changes in state of several H-bonds that occur during the reaction process.

The protein-flavin interactions of the oxidized and anionic semiquinone states of the electron-transfer flavoprotein from the methylotropic bacteria W3A1 (wETF) in solution was investigated by using Nonresonance Raman spectroscopy. The results reveal that the presence of the hydrogen-bonding interaction at N(5) is apparent in the crystal structure of the oxidized protein persisting in the one-electron reduced state.

The hydrogen-bonding interaction at the N(5) atom of the flavin cofactors in the oxidized state was determined by studying the unique properties of the electron-transfer flavoprotein from the methylotrophic bacterial W3A1 (wETF). The findings reveal that the H-bonding interaction at the N(5) plays a key role in establishing the high midpoint potential for the first couple and the unusually high stability of the anionic semiquinone state in wETF.

The ab initio electron densities of pure water clusters and hydrated serine and tyrosine were generated to understand the molecular charge distribution of water molecule. The findings from the study helped to categorize types of water molecule with specific electronic characterizations based on H-bonds formed.

The synthesis and characterization of low-spin (2-methylimidazole)(octaethylporphyrinato)iron(III) chloride (perp-[Fe(OEP)[(2-MeHIm).sub.2]]Cl) is presented. A one-dimension hydrogen-bond is formed between chloride anions and uncoordinated imidazole nitrogen atoms and Mossbauer spectroscopy has verified the low-spin state of the species and confirmed that it is a type I low-spin species with ground state [([d.sub.xy]).sup.2][([d.sub.xz],[d.sub.yz]).sup.3].

Five novel arylsulfonates of Ni and Co are obtained hydrothermally and their structures are determined by X-ray single-crystal diffraction. Self-assembly interactions of all the five compounds have shown that one of them is a polymeric hydrogen-bonded supramolecular layered compound formed by self-assembly of tetraaquo-o-phenanthrolinenickel(II) cations and 1,5-NDS (naphthalenedisulfonate) anions, two are also 2D structures through O-H...O and [pi]-[pi] stacking interactions and only one presents a 3D structure through O-H...O hydrogen-bond layers and [pi]-[pi] parallel-displaced stacking interactions.

Ultraviolet resonance Raman spectroscopy is used to study the structure and hydrogen bonding state of the distal histidine (His42) in horseradish peroxidase (HRP) complexed with carbon monoxide (HRP-CO). The finding that His42 acts as a strong proton donor to carbon monoxide (CO) and decrease the CO bond order is consistent with role of HIs42 as a general acid to cleave the O-O bond of hydrogen peroxide, a specific oxidizing agent, in the catalytic cycle of HRP.

The first direct experimental evaluation of the hydrogen-bond affinity of the nicotinium pyridine nitrogen is described. The equilibrium constant of its association with a phenol is 1 order of magnitude greater than the association of the acetylcholine carbonyl oxygen.

The 1, 3-intramolecular hydrogen transfer in the HSCH(O) reversible reaction (S)CHOH and HSNO reversible reaction SNOH reactions are studied through density functional theory calculations. The reaction force together with structural and electronic properties is monitored along the reaction path to characterize the mechanism of hydrogen transfer.

The nuclear quadrupole coupling constants, chi's, of (super 2)H and (super 14)N in the hydrogen bond are appropriate parameters to characterize the properties of this bond. A single molecule of alpha-glycylglycine was studied and the nuclear quadrupole coupling constants of (super 2)H for the amide hydrogen bond was determined to be 217.51 kHz.

The nature of interactions of phenol with various molecules (Y = HF, HC1, H(sub 2)O, H(sub 2)S, NH(sub 3), PH(sub 3), MeOH, MeSH) is investigated using ab initio calculations. The conformational energetics was compared and their energy components were analyzed.

Accurate association constants of xanthosine and inosine dimers are determined by concentration dependent H NMR experiments, and a structural characterization of individual complexes formed in solution is performed through measurements under slow exchange conditions at very low temperatures. The influence of polar medium on the bonding properties is also estimated and the importance of the various effects is discussed.

The thermodynamics of the spin trapping of various cyclic nitrones with biologically relevant radicals such as methyl, mercapto, hydroperoxy, superoxide anion, and nitric oxide was investigated using computational methods. The study also predicted the favorable formation of certain adducts that exhibit intramolecular H-bonding interactions, nucleophilic addition, or H-atom transfer reactions.

An attempt was carried out to study the protonated 2,7-dimethoxy derivative of 1,8-bis(dimethylamino)naphthalene (DMAN) ((CH3O)2.DMAN) by X-ray diffraction. The calculations reproduced potential, yielding an ISR value displaying a very good agreement with the experimental one.

The physicochemical properties of the series of mono-/di-nuclear Cu(II) complexes with N(sub 3)(super -) and mu-O(sub 2)(super 2-) are analyzed and the hydrogen bonding effects of NH2 groups are examined. It was noticed that the thermal stability of the peroxo-copper species increased with increase in the number of the hydrogen-bonding interactions between the peroxide and amino groups.