Hydrogen Bonding in Carbohydrates

The effects of a hydrogen bond acceptor and hydrogen bond donor on carbon dioxide absorption via natural deep eutectic solvents were studied in this work. Naturally occurring non-toxic deep eutectic solvent constituents were considered; choline chloride, b-alanine, and betaine were selected as hydrogen bond acceptors; lactic acid, malic acid, and fructose were selected as hydrogen bond donors. Experimental gas absorption data were collected via experimental methods that uses gravimetric principles. Carbon dioxide capture data for an isolated hydrogen bond donor and hydrogen bond acceptor, as well as natural deep eutectic solvents, were collected. In addition to experimental data, a theoretical study using Density Functional Theory was carried out to analyze the properties of these fluids from the nanoscopic viewpoint and their relationship with the macroscopic behavior of the system, and its ability for carbon dioxide absorption. The combined experimental and theoretical reported approach work leads to valuable discussions on what is the effect of each hydrogen bond donor or acceptor, as well as how they influence the strength and stability of the carbon dioxide absorption in deep eutectic solvents. Theoretical calculations explained the experimental findings, and combined results showed the superiority of the hydrogen bond acceptor role in the gas absorption process, with deep eutectic solvents. Specifically, the cases in which choline chloride was used as hydrogen bond acceptor showed the highest absorption performance. Furthermore, it was observed that when malic acid was used as a hydrogen bond donor, it led to low carbon dioxide solubility performance in comparison to other studied deep eutectic solvents. The cases in which lactic acid was used as a hydrogen bond donor showed great absorption performance. In light of this work, more targeted, specific, deep eutectic solvents can be designed for effective and alternative carbon dioxide capture and management.

The binding of galactose-specific lectins from Erythrina indica (EIL), Erythrina arborescens (EAL), Ricinus communis (agglutinin; RCA-I), Abrus precatorius (agglutinin; APA), and Bandeiraea simplicifolia (lectin I; BSL-I) to fluoro-, deoxy-, and thiogalactoses were studied in order to determine the strength of hydrogen bonds between the hydroxyl groups of galactose and the binding sites of the proteins. The results have allowed insight into the nature of the donor/acceptor groups in the lectins that are involved in hydrogen bonding with the sugar. The data indicate that the C-2 hydroxyl group of galactose is involved in weak interactions as a hydrogen-bond acceptor with uncharged groups of EIL and EAL. With RCA-I, the C-2 hydroxyl group forms two weak hydrogen bonds in the capacity of a hydrogen-bond acceptor and a donor. On the other hand, there is a strong hydrogen bond between the C-2 hydroxyl group of galactose, which acts as a donor, and a charged group on BSL-I. The C-2 hydroxyl group of the sugar is also a hydrogen-bond donor to APA. The lectins are involved in strong hydrogen bonds through charged groups with the C-3 and C-4 hydroxyl groups of galactose, with the latter serving as hydrogen-bond donors. The C-6 hydroxyl group of the sugar is weakly hydrogen bonded with neutral groups of EIL, EAL, and APA. With BSL-I, however, a strong hydrogen bond is formed at this position with a charged group of the lectin. The C-6 hydroxyl groups is a hydrogen-bond acceptor for EIL and EAL, a hydrogen-bond donor for APA and BSL-I, and appears not to be involved in binding to RCA-I. The data with the thiosugars indicate the involvement of the C-1 hydroxyl group of galactose in binding to EIL, EAL, and BSL-I, but not to RCA-I and APA. We have also performed a similar analysis of the binding data of fluoro- and deoxysugars to concanavalin A [Poretz, R. D. and Goldstein, I. J. (1970) Biochemistry 9, 2890-2896]. This has allowed comparison of the donor/acceptor properties and free energies of hydrogen bonding of the hydroxyl groups of methyl alpha-D-mannopyranoside to concanavalin A with the results in the present study. On the basis of this analysis, new assignments are suggested for amino acid residues of concanavalin A [corrected] that may be involved in hydrogen bonding to the sugar.

Investigating the effect of systematically modifying the molar ratio of hydrogen bond donor and acceptor on solvation characteristics of deep eutectic solvents formed using choline chloride salt and polyalcohols

Water deviates from tetrahedral symmetry on different scales, creating "defects" that are important for its dynamics. In this Account, I trace the manifestations of these distortions from the isolated molecule through gas-phase clusters to the liquid phase. Unlike the common depiction, an isolated water molecule has a nonsymmetric charge distribution: although its positive charge is localized at the hydrogens, the negative charge is smeared between the lone-pair sites. This creates a "negativity track" along which a positive charge may slide. Consequently, the most facile motion within the water dimer is a reorientation of the hydrogen-bond (HB) accepting molecule (known as an "acceptor switch"), such that the donor hydrogen switches from one lone pair to the other. Liquid water exhibits asymmetry between donor and acceptor HBs. Molecular dynamics simulations show that the water oxygens accepting HBs from the central molecule are spatially localized, whereas water hydrogens donating HBs to it are distributed along the negativity track. This asymmetry is manifested in a wider acceptor- versus donor-HB distribution. There is a higher probability for a water molecule to accept one (trigonal symmetry) or three HBs than to donate one or three HBs. A simple model can explain semiquantitatively how these distributions evolve by distorting perfectly tetrahedral water. Just two reactions are required: the dissociation of a HB between a double-donor donating to a double-acceptor, D(2)···A(2), followed by a switching reaction in which a HB donor rotates its hydrogen between two double-acceptor molecules. The preponderance of D(2)···A(2) dissociation events is in line with HB "anticooperativity", whereas positive cooperativity is exhibited by conditional HB distributions: a molecule with more acceptor bonds tends to have more donor bonds and vice versa. Quantum mechanically, such an effect arises from intermolecular charge transfer, but it is observed even for fixed-charge water models. Possibly, in the liquid state this is partly a collective effect, for example, a more ordered hydration shell that enhances the probability for both acceptor and donor HBs. The activation energy for liquid water self-diffusion is considerably larger than its HB strength, pointing to the involvement of collective dynamics. The remarkable agreement between the temperature dependence of the water self-diffusion coefficient and its Debye relaxation time suggests that both share the same mechanism, likely consisting of coupled rotation and translation with collective rearrangement of the environment. The auto-correlation function of a hydrogen-bonded water molecule pair is depicted quantitatively by the solution of the diffusion equation for reversible geminate recombination, up to long times where the ubiquitous t(-3/2) power law prevails. From the model, one obtains the HB dissociation and formation rate coefficients and their temperature dependence. Both have a similar activation enthalpy, suggesting rapid formation of HBs with alternate partners, perhaps by the HB switching reaction involving the trigonal site. A detailed picture of how small fluctuations evolve into large-scale molecular motions in water remains elusive. Nonetheless, our results demonstrate how the plasticity of water can be traced to its asymmetric charge distribution, with duality between tetrahedral and trigonal ligation states.

Neighbouring groups can be strategically located to polarise HO.OH intramolecular hydrogen bonds in an intended direction. A group with a unique hydrogen-bond donor or acceptor character, located at hydrogen-bonding distance to a particular OH group, has been used to initiate the hydrogen-bond network and to polarise a HO.OH hydrogen bond in a predicted direction. This enhanced the donor character of a particular OH group and made it a cooperative hydrogen-bond centre. We have proved that a five-membered-ring intramolecular hydrogen bond established between an amide NH group and a hydroxy group (1,2-e,a), which is additionally located in a 1,3-cis-diaxial relationship to a second hydroxy group, can be used to select a unique direction on the six-membered-ring intramolecular hydrogen bond between the two axial OH groups, so that one of them behaves as an efficient cooperative donor. Talose derivative 3 was designed and synthesised to prove this hydrogen-bonding network by NMR spectroscopy, and the mannopyranoside derivatives 1 and 2 were used as models to demonstrate the presence in solution of the 1,2-(e,a)/five-membered-ring intramolecular hydrogen bond. Once a well-defined hydrogen-bond is formed between the OH and the amido groups of a pyranose ring, these hydrogen-bonding groups no longer act as independent hydrogen-bonding centres, but as hydrogen-bonding arrays. This introduces a new perspective on the properties of carbohydrate OH groups and it is important for the de novo design of molecular recognition processes, at least in nonpolar media. Carbohydrates 1-3 have shown to be efficient phosphate binders in nonpolar solvents owing to the presence of cooperative hydroxy centres in the molecule.

Article Crystal structure of 2,2′-biimidazolium bis(dihydrogen phosphate), [C6H8N4][H2PO4]2 was published on March 1, 2010 in the journal Zeitschrift für Kristallographie - New Crystal Structures (volume 225, issue 1).

In this study, we have determined the structure of a medicinally important molecule saligenin (2-hydroxybenzyl alcohol) using UV, IR and microwave absorption spectroscopy in a supersonic jet combined with ab initio calculations. The structure of the only observed conformer of saligenin corresponds to the global minimum on the conformational surface. The observed structure is stabilized by an intramolecular strong O-H···O hydrogen bonding as well as a very weak O-H···π interaction. The hydrogen bond is formed through phenolic OH as the hydrogen bond donor and benzylic OH as the hydrogen bond acceptor while the O-H···π interaction is through benzylic O-H as the hydrogen bond donor and phenyl group as the hydrogen bond acceptor. It has been observed that the benzylic OH stretching frequency in saligenin is more red-shifted compared to that in benzyl alcohol as the strong O-H···O interaction present in saligenin acts on the benzylic O-H group. In fact, there is a subtle interplay among the strong O-H···O hydrogen bond, weak O-H···π interaction, and steric effects arising from the ortho substitution of the OH group in benzyl alcohol. This fine-tuning of multiple interactions very often governs the specific structures of biomolecules and materials.

Partitioning behavior of rutin in novel liquid–liquid biphasic systems formed by choline chloride/ maltose natural deep eutectic solvents and n-propanol

Amides are important atmospheric organic–nitrogen compounds. Hydrogen bonded complexes of methanol (MeOH) with amides (formamide, N-methylformamide, N,N-dimethylformamide, acetamide, N-methylacetamide and N,N-dimethylacetamide) have been investigated. The carbonyl oxygen of the amides behaves as a hydrogen bond acceptor and the NH group of the amides acts as a hydrogen bond donor. The dominant hydrogen bonding interaction occurs between the carbonyl oxygen and the OH group of methanol as well as the interaction between the NH group of amides and the oxygen of methanol. However, the hydrogen bonds between the CH group and the carbonyl oxygen or the oxygen of methanol are also important for the overall stability of the complexes. Comparable red shifts of the C=O, NH- and OH-stretching transitions were found in these MeOH–amide complexes with considerable intensity enhancement. Topological analysis shows that the electron density at the bond critical points of the complexes fall in the range of hydrogen bonding criteria, and the Laplacian of charge density of the O–H∙∙∙O hydrogen bond slightly exceeds the upper value of the Laplacian criteria. The energy decomposition analysis further suggests that the hydrogen bonding interaction energies can be mainly attributed to the electrostatic, exchange and dispersion components.

Recognition of poly(C) DNA and RNA sequences in mammalian cells is achieved by a subfamily of the KH (hnRNP K homology) domain-containing proteins known as poly(C)-binding proteins (PCBPs). To reveal the molecular basis of poly(C) sequence recognition, we have determined the crystal structure, at 1.7-A resolution, of PCBP2 KH1 in complex with a 7-nucleotide DNA sequence (5'-AACCCTA-3') corresponding to one repeat of the human C-rich strand telomeric DNA. The protein-DNA interaction is mediated by the combination of several stabilizing forces including hydrogen bonding, electrostatic interactions, van der Waals contacts, and shape complementarities. Specific recognition of the three cytosine residues is realized by a dense network of hydrogen bonds involving the side chains of two conserved lysines and one glutamic acid. The co-crystal structure also reveals a protein-protein dimerization interface of PCBP2 KH1 located on the opposite side of the protein from the DNA binding groove. Numerous stabilizing protein-protein interactions, including hydrophobic contacts, stacking of aromatic side chains, and a large number of hydrogen bonds, indicate that the protein-protein interaction interface is most likely genuine. Interaction of PCBP2 KH1 with the C-rich strand of human telomeric DNA suggests that PCBPs may participate in mechanisms involved in the regulation of telomere/telomerase functions.

Aqueous hydroxyl group as the vibrational probe to access the hydrophobicity of amide derivatives

C22H20MnN3O5, monoclinic, P121/c1 (no. 14), a = 6.5219(5) A, b = 17.793(1) A, c = 17.344(1) A, 1 = 100.664(1)°, V = 1977.8 A, Z = 4, Rgt(F) = 0.042, wRref(F) = 0.119, T = 296 K. Source of material To 20mL ethanol solution containingH2salen (0.568 g, 2mmol), Mn(OAc)3 · 2H2O (0.536 g, 2 mmol) was added slowly as solid under continuous stirring at room temperature for 2 h. Nicotinic acid (0.123 g, 1 mmol) in 5mLwater was added and the resulting mixture stirred for another 4 h.A dark brown solutionwas formed and filtrated. The filtration was left for slow evaporation. Black block-shaped crystals were obtained after 2 weeks. Discussion The chemistry ofMn complexes is of continuous interest because of their functions in biological systems, in which considerable attention has been paid to salen-type complexes [1,2]. In the title structure, the complex [Mn(salen)(nicotinato-N)(H2O)] shows a pseudo-octahedral coordination environment. The metal center Mn is coordinated by an equatorial tetradentate salen ligand and axial nicotinato N atom and a water molecule, resulting in a fac-MnN3O3 group (figure, top). The bond lengths in the title complex show the usual pattern of unequal equatorial Mn—O (1.880(2) A and 1.881(2) A) and Mn—N (1.977(2) A and 1.992(2) A) distances, which are comparable with other Mn(salen) complexes [3-5]. The elongation of axial bonds, d(Mn—Owater) = 2.246(2)A and d(Mn—Nnicotinato) = 2.353(2)A, indicates a clear evidence of Jahn-Teller distortion for high spin Mn. The trans angles are ranging from .O2–Mn1–N1 = 173.70(9)° to.O3–Mn1–N3=178.85(8)° and cis angles ranging from .N2–Mn1–N1 = 82.27(9)° to .O2–Mn1–O1 = 93.77(8)°, which suggest the larger extent distortion on basal plane than the axial position. The manganese atom is 0.035 A out of the plane defined by N1, N2, O1 and O2. A close-packed hydrogen-bonded network is formed. Water of eachmolecule acts as hydrogen bonds donors, and the oxygen atoms of nicotinato from the symmetric motifs (symmetry codes: x,+2–y,–+2+z and 2–x,+2+y,+2–z) act as hydrogen bond acceptors. So, a cyclic tetrameric motif is created with the d(H···O) = 1.88A and d(O···O) = 2.69A (figure, bottom).Eachmolecule shares two hydrogen bonds with four neighbors with theMn···Mn distances of 9.01A and 15.96A, producing a 2D network by four hydrogen bonds. Moreover, the structural packing is maintained by the C–H···& interactions, which are weaker interactions in nature but further stabilize the network. It is very interesting that the neighboring molecules interacting both byO–H···O andC–H···& interactions. Thus the cyclic C–H···& interaction rings are formed. Twokinds of non-polarC–H···& ring exist in themiddle of the polar hydrogen bond ring, which are also in the middle of the C–H···& ring. There also exist two types of C–H···Oweak hydrogen bonds. Z. Kristallogr. NCS 222 (2007) 241-242 / DOI 10.1524/ncrs.2007.0101 241 © by Oldenbourg Wissenschaftsverlag, Munchen Crystal: black block, size 0.18 × 0.23 × 0.33 mm Wavelength: Mo K0 radiation (0.71073 A) %: 7.09 cm−1 Diffractometer, scan mode: Bruker SMART CCD, #/) 2'max: 50.2° N(hkl)measured, N(hkl)unique: 9918, 3521 Criterion for Iobs, N(hkl)gt: Iobs > 2 ((Iobs), 2807 N(param)refined: 258 Programs: SHELXS-97 [7], SHELXL-97 [8], SHELXTL [9] Table 1. Data collection and handling.

The dynamics of proton transfer (PT) through hydrogen bonds in a two-dimensional water layer confined between two graphene sheets at room temperature are investigated through ab initio and quantum-classical simulations. The excess proton is found to be mostly solvated as an Eigen cation where the hydronium ion donates three hydrogen bonds to the neighboring water molecules. In the solvation shell of the hydronium ion, the three coordinated water molecules with two donor hydrogen bonds are found to be properly presolvated to accept a proton. Although no hydrogen bond needs to be broken for transfer of a proton to such presolvated water molecules from the hydronium ion, the PT rate is still found to be not as fast as it is for one-dimensional chains. Here, the PT is slowed down as the probability of finding a water with two donor hydrogen bonds in the solvation shell of the hydronium ion is found to be only 25%-30%. The hydroxide ion is found to be solvated mainly as a complex anion where it accepts four H-bonds through its oxygen atom and the hydrogen atom of the hydroxide ion remains free all the time. Here, the presolvation of the hydroxide ion to accept a proton requires that one of its hydrogen bonds is broken and the proton comes from a neighboring water molecule with two acceptor and one donor hydrogen bonds. The coordination number reduction by breaking of a hydrogen bond is a slow process, and also the population of water molecules with two acceptor and one donor hydrogen bonds is only 20%-25% of the total number of water molecules. All these factors together tend to slow down the hydroxide ion migration rate in two-dimensional water layers compared to that in three-dimensional bulk water.

The role of hydrogen bonding in rigid-rod polymers: the crystal structure of a polybenzobisimidazole model compound

L-cysteine S-sulfate, Cys-SSO3H, and their derivatives play essential roles in biological chemistry and pharmaceutical synthesis, yet their intrinsic molecular properties have not been studied to date. In this contribution, the deprotonated anion [cysS-SO3]− was introduced in the gas phase by electrospray and characterized by size-selected, cryogenic, negative ion photoelectron spectroscopy. The electron affinity of the [cysS-SO3]• radical was determined to be 4.95 ± 0.10 eV. In combination with theoretical calculations, it was found that the most stable structure of [cysS-SO3]− (S1) is stabilized via three intramolecular hydrogen bonds (HBs); i.e., one O−H⋯⋯N between the –COOH and –NH2 groups, and two N−H⋯⋯O HBs between –NH2 and –SO3, in which the amino group serves as both HB acceptor and donor. In addition, a nearly iso-energetic conformer (S2) with the formation of an O−H⋯⋯N−H⋯⋯O−S chain-type binding motif competes with S1 in the source. The most reactive site of the molecule susceptible for electrophilic attacks is the linkage S atom. Theoretically predicted infrared spectra indicate that O−H and N−H stretching modes are the fingerprint region (2800 to 3600 cm−1) to distinguish different isomers. The obtained information lays out a foundation to better understand the transformation and structure–reactivity correlation of Cys-SSO3H in biologic settings.