Effect of the Hydration Shell on the Carbonyl Vibration in the Ala-Leu-Ala-Leu Peptide

The vibrational spectrum of the Ala-Leu-Ala-Leu peptide in solution, computed from first-principles simulations, shows a prominent band in the amide I region that is assigned to stretching of carbonyl groups. Close inspection reveals combined but slightly different contributions by the three carbonyl groups of the peptide. The shift in their exact vibrational signature is in agreement with the different probabilities of these groups to form hydrogen bonds with the solvent. The central carbonyl group has a hydrogen bond probability intermediate to the other two groups due to interchanges between different hydrogen-bonded states. Analysis of the interaction energies of individual water molecules with that group shows that shifts in its frequency are directly related to the interactions with the water molecules in the first hydration shell. The interaction strength is well correlated with the hydrogen bond distance and hydrogen bond angle, though there is no perfect match, allowing geometrical criteria for hydrogen bonds to be used as long as the sampling is sufficient to consider averages. The hydrogen bond state of a carbonyl group can therefore serve as an indicator of the solvent’s effect on the vibrational frequency.     

Effect of the type of hydrogen bonding on the reactivity of hydroxyl groups in the acetalization of poly(vinyl alcohol) with butanal

The parameters of hydrogen bonds formed during acetalization of poly(vinyl alcohol) with butanal are determined via computer-simulation methods. It is shown that alcohol groups involved in the formation of intermolecular hydrogen bonds are the least active in acetalization reactions. The kinetics of the acetalization reactions in 2,4-pentanediol-water-butanal and (vinyl alcohol)-water-butanal systems are studied at various concentrations of alcohols that model a change in the ratio of hydrogen bonds of various types and are realized in the aqueous solutions of poly(vinyl alcohol) and poly(vinyl butyral). The calculated rate constants are in agreement with the computer-simulation-based order of reactivity of alcohol groups involved in hydrogen bonds of various types. It is proposed that the reactivity of residual alcohol groups in a poly(vinyl butyral) macromolecule should increase when a certain conversion of the polymer is attained.     

Stiff, and sticky in the right places: the dramatic influence of preorganizing guest binding sites on the hydrogen bond-directed assembly of rotaxanes.

Structural rigidity and the preorganization of thread binding sites are shown to have a major influence on template efficiency in the synthesis of hydrogen bond-assembled rotaxanes. Preorganization is so effective, in fact, that with good hydrogen bond acceptors (amides) a "world record" yield of 97% for a [2]rotaxane is obtained. The truly remarkable feature of this efficient template, however, is that it allows even poor hydrogen bond acceptors (esters) to be used to prepare hydrogen bond-assembled rotaxanes, despite the presence of competing hydrogen bonding groups (anions) which bind the key intermediates at least 10000x more strongly than single, unorganized, ester groups! The structures of the rotaxanes are established unambiguously in solution by (1)H NMR spectroscopy and in the solid state by X-ray crystallography. As a series they provide unique experimental information regarding the nature of amide-ester hydrogen bonding interactions; in particular they suggest that in CDCl(3), amide-ester NH...O=C hydrogen bonds are approximately 1 kcal mol(-)(1) weaker than the corresponding amide-amide interactions.     

Study of the selective catalysis of metalloporphyrins for 2-methyl-butane oxidation with PhIO under mild conditions

Nine ironporphyrins and eight manganeseporphyrins were synthesized, and their selective catalysis for the oxidation of the secondary and tertiary carbon–hydrogen bonds of 2-methyl-butane with PhIO was studied. The proportion of the oxidation product of tertiary carbon–hydrogen bond to the one of secondary carbon–hydrogen bond was 3:1 when ironporphyrins were used as catalysts, and 2.3:1 when manganeseporphyrins were used as catalysts. The research showed that the substituting groups on the porphyrin rings influenced the catalytic selectivity of metalloporphyrins for the oxidation of the secondary and tertiary carbon–hydrogen bonds as well as the reaction yields. The electron-attracting groups on benzene rings of ironporphyrins increased the catalytic selectivity of ironporphyrins for the tertiary carbon–hydrogen bond oxidation and the reaction speeds, and the electron-releasing groups increased the catalytic selectivity for secondary carbon–hydrogen bond oxidation and reduced the reaction speeds. Both electron-attracting and -releasing groups on benzene rings of manganeseporphyrins enhanced the catalytic selectivity of manganeseporphyrins for the secondary carbon–hydrogen bond oxidation.     

Modulation of the relative reactivities of carbohydrate secondary hydroxyl groups. Modification of the hydrogen bond network

An approach towards the control of the relative regioselectivity of the secondary hydroxyl groups is presented. Original protecting groups, which are capable of specific intramolecular hydrogen bonds and are likely to modulate the partial charges of the oxygen atoms, have been developed. Qualitative NMR experiments confirmed the existence of the expected hydrogen bonds and shed light on the perturbation of the cooperative intramolecular hydrogen bond network. Further reactivity studies are presented and confirm the potential of protecting group-mediated regioselective functionalization of carbohydrates.     

Hydrogen bonding and the cryoprotective properties of glycerol/water mixtures

Molecular dynamics simulations and infrared spectroscopy were used to determine the hydrogen bond patterns of glycerol and its mixtures with water. The ability of glycerol/water mixtures to inhibit ice crystallization is linked to the concentration of glycerol and the hydrogen bonding patterns formed by these solutions. At low glycerol concentrations, sufficient amounts of bulk-like water exist, and at low temperature, these solutions demonstrate crystallization. As the glycerol concentration is increased, the bulk-like water pool is eventually depleted. Water in the first hydration shell becomes concentrated around the polar groups of glycerol, and the alkyl groups of glycerol self-associate. Glycerol-glycerol hydrogen bonds become the dominant interaction in the first hydration shell, and the percolation nature of the water network is disturbed. At glycerol concentrations beyond this point, glycerol/water mixtures remain glassy at low temperatures and the glycerol-water hydrogen bond favors a more linear arrangement. High glycerol concentration mixtures mimic the strong hydrogen bonding pattern seen in ice, yet crystallization does not occur. Hydrogen bond patterns are discussed in terms of hydrogen bond angle distributions and average hydrogen bond number. Shift in infrared frequency of related stretch and bend modes is also reviewed.     

The hydration of glucose: the local configurations in sugar-water hydrogen bonds

The hydration of a simple sugar is an essential model for understanding interactions between hydrophilic groups and interfacial water molecules. Here I perform first-principles molecular dynamics simulations on a glucose-water system and investigate how individual hydroxyl groups are locally hydrated. I demonstrate that the hydroxyl groups are less hydrated and more incompatible with a locally tetrahedral network of hydrogen bonds than previously thought. The results suggest that the hydroxyl groups form roughly two hydrogen bonds. Further, I find that the local hydration of the hydroxyl groups is sensitively affected by seemingly small variations in the local electronic structure and bond polarity of the groups. My findings offer insight into an atomic-level understanding of sugar-water interactions.     

Controlling the Formation of Ionic‐Liquid‐based Aqueous Biphasic Systems by Changing the Hydrogen‐Bonding Ability of Polyethylene Glycol End Groups

The formation of aqueous biphasic systems (ABS) when mixing aqueous solutions of polyethylene glycol (PEG) and an ionic liquid (IL) can be controlled by modifying the hydrogen‐bond‐donating/‐accepting ability of the polymer end groups. It is shown that the miscibility/immiscibility in these systems stems from both the solvation of the ether groups in the oxygen chain and the ability of the PEG terminal groups to preferably hydrogen bond with water or the anion of the salt. The removal of even one hydrogen bond in PEG can noticeably affect the phase behavior, especially in the region of the phase diagram in which all the ethylene oxide (EO) units of the polymeric chain are completely solvated. In this region, removing or weakening the hydrogen‐bond‐donating ability of PEG results in greater immiscibility, and thus, in a higher ability to form ABS, as a result of the much weaker interactions between the IL anion and the PEG end groups.     

Modeling of hydrogen and hydroxyl group migration on graphene

Density functional calculations of optimized geometries for the migration of single hydrogen and hydroxyl groups on graphene are performed. It is shown that the migration energy barrier for the hydroxyl group is three times larger than for hydrogen. The crucial role of supercell size for the values of the migration barriers is discussed. The paired migration of hydrogen and hydroxyl groups has also been examined. It could be concluded that hydroxyl group based magnetism is rather stable in contrast with unstable hydrogen based magnetism of functionalized graphene. The role of water in the migration of hydroxyl groups is also discussed, with the results of the calculations predicting that the presence of water weakens the covalent bonds and makes these groups more fluid. Increasing the number of water molecules associated with hydroxyl groups provides an increase of the migration energy.     

Neutron crystallographic and molecular dynamics studies of the structure of ammonia-cellulose I: rearrangement of hydrogen bonding during the treatment of cellulose with ammonia

The hydrogen bond arrangement in a complex of cellulose with ammonia has been studied using neutron crystallography in combination with molecular dynamics simulations. The O6 atom of the hydroxymethyl group is donor in a highly occupied hydrogen bond to an ammonia molecule. This rotating ammonia molecule is donor in partially occupied and transient hydrogen bonds to the O2, O3 and O6 atoms of the hydroxyl groups of other chains. The hydrogen atom bound to the O3 atom is disordered but it is almost always involved in some type of hydrogen bonding. It is donated in a hydrogen bond most of the time to the O5 atom on the same chain. However, it also rotates away from this O5 atom to be donated to an ammonia molecule part of the time. On the other hand the hydrogen atom bound to the O2 atom is free from hydrogen bonding most of the time. It is donated in a hydrogen bond to the O6 atom on a neighboring chain only with a relatively small probability. These results provide new insights into how hydrogen bonds are rearranged during the conversion of cellulose I to cellulose III_I by ammonia treatment.     

Shape of the proton potential in an intramolecular hydrogen-bonded system. Part II

The crystals of 5,5′-dibromo-3-diethylaminomethyl-2,2′-biphenol N-oxide were studied by X-ray and FT-IR spectroscopy. Within this molecule two short OHO intramolecular hydrogen bonds are formed. The NO?H⁺?O⁻ bond between the OH and the N-oxide groups is very strong, of 2.419(7) Å between the oxygen atoms. The proton potential of this hydrogen bond is flat, broad and has probably no barrier—consequently it could not be located from X-ray diffraction data. The other hydrogen bond formed between two hydroxyl groups appears asymmetrical from FT-IR spectra, and shows also relatively limited proton polarizability. The molecular conformation is non-planar, due to strong overcrowding effect between the oxygen atoms involved in the hydrogen bonds.     

Experimental Proof of the Bifunctional Mechanism for the Hydrogen Oxidation in Alkaline Media

Realization of the hydrogen economy relies on effective hydrogen production, storage, and utilization. The slow kinetics of hydrogen evolution and oxidation reaction (HER/HOR) in alkaline media limits many practical applications involving hydrogen generation and utilization, and how to overcome this fundamental limitation remains debatable. Here we present a kinetic study of the HOR on representative catalytic systems in alkaline media. Electrochemical measurements show that the HOR rate of Pt‐Ru/C and Ru/C systems is decoupled to their hydrogen binding energy (HBE), challenging the current prevailing HBE mechanism. The alternative bifunctional mechanism is verified by combined electrochemical and in situ spectroscopic data, which provide convincing evidence for the presence of hydroxy groups on surface Ru sites in the HOR potential region and its key role in promoting the rate‐determining Volmer step. The conclusion presents important references for design and selection of HOR catalysts.     

Study of the reactions of dimethyl hydrogen phosphonate with urethane and acetanilide

In this article, a new reactivity of dimethyl hydrogen phosphonate is described. It was established that the reaction between dimethyl hydrogen phosphonate and urethane encompasses two simultaneous processes: an exchange reaction between the methoxy groups of the phosphonate and urethane groups and alkylation of the urethane. The reaction of dimethyl hydrogen phosphonate with acetanilide represents an alkylation of the amido group. The structure of the resulting products was studied by means of ¹H, ³¹P, and ¹³C NMR spectroscopy. © 2000 John Wiley & Sons, Inc. Heteroatom Chem 11:205–208, 2000     

Semicarbazones and thiosemicarbazones of the heterocyclic series

IsatinΒ-thiosemicarbazone and its alkyl derivatives containing a hydrogen atom attached to N_(2′) exist primarily in the form of the syn isomer stabilized by intramolecular hydrogen bonding in solutions and in the crystalline state. The strength of this hydrogen bond increases when both hydrogen atoms in the primary thioamide group are replaced by alkyl groups.     

Hydrogen bond stabilization in 1,3-dimethylimidazolium methyl sulfate and 1-butyl-3-methylimidazolium hexafluorophosphate probed by high pressure: the role of charge-enhanced C-H...O interactions in the room-temperature ionic liquid

The hydrogen bonding structures of room-temperature ionic liquids 1,3-dimethylimidazolium methyl sulfate and 1-butyl-3-methylimidazolium hexafluorophosphate have been studied by infrared spectroscopy. High-pressure infrared spectral profiles and theoretical calculations allow us to make a vibrational assignment of these compounds. The imidazolium C-H bands of 1,3-dimethylimidazolium methyl sulfate display anomalous non-monotonic pressure-induced frequency shifts. This discontinuity in frequency shift is related to enhanced C-H...O hydrogen bonding. This behavior is in contrast with the trend of blue shifts in frequency for the methyl C-H stretching mode at ca. 2960 cm(-1). Our results indicated that the imidazolium C-H groups are more favorable sites for hydrogen bonding than the methyl C-H groups in the pure 1,3-dimethylimidazolium methyl sulfate. Nevertheless, both methyl C-H and imidazolium C-H groups are favorable sites for C-H...O hydrogen bonding in a dilute 1,3-dimethylimidazolium methyl sulfate/D(2)O mixture. Hydrogen bond-like C-H...F interactions were observed between PF(6)(-) and H atoms on the alkyl side chains and imidazolium ring for 1-butyl-3-methylimidazolium hexafluorophosphate.     

Investigation of the crystal structure of two amphiphilic diols

The crystal and molecular structures of (R)-4'-(2,3-dihydroxypropyloxy)-4-cyanobiphenyl, 1 and 4'-(cis-cis-3,5-dihydroxycyclohexyloxy)-4-cyanobiphenyl, 5 have been determined. The packing of compound 1 occurs in sheets, with a dense hydrogen bonding network within the layer of one sheet and to the next sheet, whereby the cyano groups are incorporated into the hydrogen bonding network. The hydrogen bonding scheme of compound 5 involves a water molecule; there is some disorder with regard to the hydrogen atoms bound to the water molecules.     

Influence of intrachain hydrogen bonding on the cyclization of a polystyrene chain

Cyclization of a polystyrene chain (M_n = 10,600; M_w/M_n = 1.09) both ends labeled with 4-(1-pyrenyl)butanoamide groups was studied in cyclohexane between 25 and 95°C. The amide groups (peptide bonds) at both ends can form an intrachain hydrogen bond between the amide hydrogen at one chain end and the carbonyl oxygen at the other. The presence of two sets of conformers, random coils, and chains cyclized through hydrogen bonding, complicates the data analysis. The pyrene excimer kinetics of this polymer is well described by a model composed of two monomers (hydrogen bonded and nonbonded chains) and one excimer, in equilibrium. The cyclization rate constant for hydrogen-bonded chains is larger than the one for nonhydrogen-bonded chains. The pyrene excimer binding energy (ca. 1.6 kcal/mol) is lower than the published value for nonhydrogen-bonded chains (～ 9 kcal/mol), suggesting that intrachain hydrogen bonding hinders the stabilization of the excimer. © 1994 John Wiley & Sons, Inc.     

取代基对有机金属铼化合物中分子内α-氢转移反应势垒的影响

使用B3LYP方法研究了有机铼化合物R³R⁵(NHR⁴)Re(＝CHR¹)(＝NR²)中分子内α-氢转移反应, 探讨了不同取代基对α-氢转移反应势垒的影响. 研究发现, 可以通过改变取代基来影响过渡金属Re有机化合物中的α-氢转移反应. R¹位置的取代基为Me或CMe₃时, 可以较大程度降低α-氢转移反应的势垒. R²为H时, α-氢转移反应势垒最低. R³和R⁵位置为SiH₃时的反应势垒最低. R⁴为CMe₃时, α-氢转移反应势垒最低. 研究结果还表明, 取代基对于反应势垒的影响有加和性.     

乙烯-乙烯醇共聚物氢键相互作用与链结构关系的变温溶液氢谱研究

用变温溶液核磁共振氢谱研究了不同组成的乙烯-乙烯醇共聚物在二甲亚砜溶液中的氢键相互作用.结果表明,乙烯醇单元中羟基的信号随温度升高而线性地向高场位移,且不同的三单元组中羟基信号的位移速率不同,表明羟基形成的氢键强度与链结构间存在相关性.