Hydrogen Bonding Interaction between Atmospheric Gaseous Amides and Methanol

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.

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

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).

A series of nine tripodal tetradentate ligands based on tris(pyridyl-2-methyl)amine TPA with hydrogen bond donors R in one, two and three of the pyridine 6-positions (R = NH2 amino, L(Am-1,2,3); NHCH2(t)Bu neopentylamino, L(Np-1,2,3); NHCO(t)Bu pivaloylamido, L(Piv-1,2,3)) and TPA are used to investigate the effect of different hydrogen bonding microenvironments on electrochemical properties of their LCuCl complexes. The hydrogen bond donors are rigidly preorganised and suitably oriented for intramolecular N-H...Cl-Cu hydrogen bonds. Cyclic voltammetry studies show that the reduction potential of the Cu(II)/Cu(I) couple as a function of the ligand follows the order TPA < L(Am-n) < or approximately L(Np-n) < L(Piv-n), and that the magnitude of the effect increases with the number of hydrogen bonding groups. These trends could be explained in terms of the steric and electronic effects exerted by these groups stabilising the Cu(I) oxidation state. In fact, the X-ray structure of the air-stable [(L(Piv-3))Cu(I)Cl] complex is reported and shows elongated Cu-N and Cu-Cl bonds, presumably due to the combination of steric and electron withdrawing effects exerted by the three pivaloylamido groups. We reasoned that the strength of hydrogen bonding in the Cu(I) and Cu(II) oxidation states could differ and therefore contribute also to the aforementioned redox changes; this hypothesis is tested using IR and NMR spectroscopy. IR studies of the [(L(Piv-1,2,3))Cu(I)Cl] and [(L(Piv-1,2,3))Cu(II)Cl]+ complexes in acetonitrile show that the intramolecular N-H...Cl-Cu hydrogen bonding weakens in the order L(Piv-1) > L(Piv-2) > L(Piv-3), and that it is stronger in the Cu(I) complexes. The 1H NMR spectra of the [(L(Piv1,2,3))Cu(I)Cl] complexes are in complete agreement with the IR data, and reveal that the stability of the Cu(I) complexes to oxidation in air increases in the order L(Piv-1) < L(Piv-2) << L(Piv-3). The hydrogen bonds in the Cu(I) complexes are stronger because of the higher electron density on the Cl ligand, when compared to the Cu(II) complexes. This is consistent with ab initio MP2 calculations performed on the complexes [(L(Piv-3))Cu(I)Cl] and [(L(Piv-3))Cu(II)Cl]+. Thus, the electron density of a metal-bound ligand acting as hydrogen bond acceptor is revealed as the major factor in determining the strength of the hydrogen bonds formed. From the IR data the energies of the N-H...Cl-Cu hydrogen bonds is estimated, as is the contribution of changes in hydrogen bond strength with the oxidation state of the copper centre and number of interactions to stabilising the Cu(I) state. Some of the implications of this result in dioxygen activation chemistry are discussed.

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

The transition structures (TSs) for the epoxidation of 2-propen-1-ol and 2-cyclobuten-1-ol with peroxyformic acid have been located with the B3LYP method using three basis sets (i.e., 6-31G*, 6-311G**, and 6-311+G**). Syn attacks on these alcohols by peroxy acid lead to syn TSs in which hydrogen bonding is operative. The allylic OH group always acts as hydrogen-bond donor while either the carbonyl oxygen or the peroxo oxygens of the peroxy acid can play the role of hydrogen-bond acceptors. In the case of propenol, the two syn TSs (O−C−CC dihedral angles: 135.0° and 16.0°, respectively) with the peroxo oxygens involved in hydrogen bonding have free enthalpies comparable with those of their counterparts (O−C−CC dihedral angles: 134.0° and 16.3°, respectively) with hydrogen bonding to carbonyl oxygen. Basis set extension as well as electrostatic solvation effects favor the former TSs over the latter ones. In the case of cyclobutenol the syn TS (O−C−CC dihedral angle = 124.2°) with hydrogen bonding to perox...

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.

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.

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.

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.

Thermo-rheological characterization of Malic Acid based Natural Deep Eutectic Solvents

The focus of the investigation is physicochemical properties (electrical conductivity, electrochemical window) and theoretical study of stability of the formed deep eutectic solvents (DESs). Quantum-chemical calculations have been performed to predict the formation of solvents with higher stability. The reported results reveal a complete description of fluid’s characteristics which of the components is the most effective donor for creation hydrogen bond with hydrogen bond acceptor. Two DESs have been synthesized by using of choline chloride as hydrogen bond acceptors (HBAs) and Urea and Lactic acid as hydrogen bond donors (HBDs). Also, DES have been synthesized by using of Lactic acid as hydrogen bond acceptors (HBAs) and Sodium Acetate as hydrogen bond donors (HBDs). The electrical conductivity of deep eutectic solvents was measured and the width of electrochemical window was evaluated using cycling voltammetry depending on water content in the solvent (0–25%).

ABSTRACTDeep eutectic solvents (DES) have gained a reputation as inexpensive and easy to handle ionic liquid analogues. This work employs molecular dynamics (MD) to simulate a variety of DES. The hydrogen bond acceptor (HBA) choline chloride was paired with the hydrogen bond donors (HBD) glycerol, 1,4-butanediol, and levulinic acid. Levulinic acid was also paired with the zwitterionic HBA betaine. In order to evaluate the reliability of data MD simulations can provide for DES, two force fields were compared: the Merck Molecular Force Field and the General Amber Force Field with two different sets of partial charges for the latter. The force fields were evaluated by comparing available experimental thermodynamic and transport properties against simulated values. Structural analysis was performed on the eutectic systems and compared to non-eutectic compositions. All force fields could be validated against certain experimental properties, but performance varied depending on the system and property in question. While extensive hydrogen bonding was found for all systems, details about the contribution of individual groups strongly varied among force fields. Interaction potentials revealed that HBA–HBA interactions weaken linearly with increasing HBD ratio, while HBD–HBD interactions grew disproportionally in magnitude, which might hint at the eutectic composition of a system.

The release of ubiquitin from attachment to other proteins and adducts is critical for ubiquitin biosynthesis, proteasomal degradation and other cellular processes. De-ubiquitination is accomplished in part by members of the UCH (ubiquitin C-terminal hydrolase) family of enzymes. We have determined the 2.25 A resolution crystal structure of the yeast UCH, Yuh1, in a complex with the inhibitor ubiquitin aldehyde (Ubal). The structure mimics the tetrahedral intermediate in the reaction pathway and explains the very high enzyme specificity. Comparison with a related, unliganded UCH structure indicates that ubiquitin binding is coupled to rearrangements which block the active-site cleft in the absence of authentic substrate. Remarkably, a 21-residue loop that becomes ordered upon binding Ubal lies directly over the active site. Efficiently processed substrates apparently pass through this loop, and constraints on the loop conformation probably function to control UCH specificity.

The influence of surfactant type on migration behavior and chemical selectivity in micellar electrokinetic chromatography (MEKC) is investigated through linear solvation energy relationships (LSER) and functional group selectivities. In LSER modeling, solutes' capacity factors are correlated with their structural descriptors such as size, dipolarity, and hydrogen-bonding abilities. Using the LSER methodology, useful information about the nature of solute interactions with different types of surfactant aggregates can be obtained since capacity factor in MEKC is directly related to solute distribution between the bulk aqueous solvent and micelles. High correlations were observed for different LSER models of migration behavior in MEKC for a group of 60 uncharged aromatic compounds of non-hydrogen bonding (NHB), hydrogen-bonding acceptor (HBA) bases, and hydrogen-bonding donor (HBD) acids. In two anionic, hydrocarbon micellar systems of sodium dodecyl sulfate (SDS) and sodium cholate (SC), retention is primarily influenced by the size of molecules and their hydrogen bond accepting basicity. Their dipolarity/polarizability and hydrogen bond donating acidity play minor roles. Capacity factors of solutes in SDS and SC systems increase with their size and decrease for stronger hydrogen bond acceptor bases. These results are similar to those observed for other systems where hydrophobic interactions play a major role, e.g., solute distribution in the 1-octanol-water solvent system or retention in reversed phase LC. In MEKC with an anionic fluorocarbon surfactant, lithium perfluorooctanesulfonate (LiPFOS), however, size and solute HBD acidity are the two predominant factors. The LSER results indicate that compounds find the SDS micellar environments slightly less cohesive (i.e., more apolar) than the SC micelles, while the LiPFOS micelles are the most cohesive among the three surfactant aggregates and 1-octanol provides the least cohesive environment. The fluorocarbon micelles of LiPFOS, on the other hand, are the strongest hydrogen bond donor acids, followed by SDS, SC, and 1-octanol, respectively. The SC micelles have the most hydrogen bond acceptor basic characteristics, followed by 1-octanol, SDS, and LiPFOS micelles. It can be concluded that selectivity differences between these surfactant types in MEKC is primarily due to hydrogen-bonding interactions rather than the dipolar interactions. Comparing the perfluorinated and the hydrocarbon surfactants, even solute size can play a role in selective migration patterns. In addition, information from polar and hydrophobic group selectivities confirm the LSER conclusions about the underlying interactions that control migration behavior and chemical selectivity in MEKC.(ABSTRACT TRUNCATED AT 400 WORDS)