Hydrogen Bond Model Research Articles

The Content of Different Hydrogen Bond Models and Crystal Structure of Eucalyptus Fibers during Beating

Different hydrogen bond and crystalline cellulose structure models of eucalyptus fibers were studied by Fourier transform infrared spectrometer (FTIR), X-ray diffraction (XRD), and Cross-Polarization Magic Angle Spinning Carbon-13 Nuclear Magnetic Resonance (CP/MAS 13C NMR). It was shown that when the beating time was increased from 5 to 15 min., the content of inter-molecular hydrogen bonds, O(6)H···O3′, increased by 11.2% as measured by FTIR. However, the content of the inter-molecular hydrogen bonds decreased quickly as the beating time was increased from 15 to 25 min. Meanwhile, the contents of the intra-molecular hydrogen bond, O(2)H···O(6) and O(3)H···O(5), changed from 8.25% to 8.18% and from 39.33% to 31.27%, respectively, when the beating time increased from 5 to 15 min. The content of the intra-molecular hydrogen bonds increased quickly with the further increase in the beating time. It was shown by XRD that there was a little difference in the average width of crystallite size in the (002) lattice plane when the beaten time was between 5 to 25 min. Non-linear fitting of the cellulose C4 region of the 13C CP/MAS NMR showed that the average lateral fibril aggregate dimensions and the content of different cellulose polymorphs changed during beating.

Refined Transition-State Models for Proline-Catalyzed Asymmetric Michael Reactions under Basic and Base-Free Conditions

The stereocontrolling transition state (TS) models for C-C bond formation relying on hydrogen bonding have generally been successful in proline-catalyzed aldol, Mannich, α-amination, and α-aminoxylation reactions. However, the suitability of the hydrogen-bonding model in protic and aprotic conditions as well as under basic and base-free conditions has not been well established for Michael reactions. Through a comprehensive density functional theory investigation, we herein analyze different TS models for the stereocontrolling C-C bond formation, both in the presence and absence of a base in an aprotic solvent (THF). A refined stereocontrolling TS for the Michael reaction between cyclohexanone and nitrostyrene is proposed. The new TS devoid of hydrogen bonding between the nitro group of nitrostyrene and carboxylic acid of proline, under base-free conditions, is found to be more preferred over the conventional hydrogen-bonding model besides being able to reproduce the experimentally observed stereochemical outcome. A DBU-bound TS is identified as more suitable for rationalizing the origin of asymmetric induction under basic reaction conditions. In both cases, the most preferred approach of nitrostyrene is identified as occurring from the face anti to the carboxylic acid of proline-enamine. The predicted enantio- and diastereoselectivities are in very good agreement with the experimental observations.

Role of Surface Hydrogen Bonds in Determining the Friction Behaviors of Hydrogenated Diamond-like Carbon Films

Friction behaviors of hydrogenated diamond-like carbon (H-DLC) films are investigated on a ball-on-disk type tribometer in dry N2 and dry vacuum. The result shows that the friction behaviors of the H-DLC films are very sensitive to the testing environment, the H-DLC films exhibit a very low friction coefficient of 0.016 in dry N2, and similarly in an inert gas the friction coefficient increases to about 0.063 in dry vacuum. Combining the testing conditions, friction results, SEM and XPS investigation, it is concluded that the friction behaviors of the hydrogenated DLC films are associated with surface hydrogen of the H-DLC films and are dictated by whether or not hydrogen bonds are formed between the transfer films/H-DLC films at the sliding interface. A hydrogen-induced hydrogen bond model is proposed to interpret the friction behaviors of hydrogenated DLC films in different environments.

A statistical model of hydrogen bond networks in liquid alcohols

We here present a statistical model of hydrogen bond induced network structures in liquid alcohols. The model generalises the Andersson-Schulz-Flory chain model to allow also for branched structures. Two bonding probabilities are assigned to each hydroxyl group oxygen, where the first is the probability of a lone pair accepting an H-bond and the second is the probability that given this bond also the second lone pair is bonded. The average hydroxyl group cluster size, cluster size distribution, and the number of branches and leaves in the tree-like network clusters are directly determined from these probabilities. The applicability of the model is tested by comparison to cluster size distributions and bonding probabilities obtained from Monte Carlo simulations of the monoalcohols methanol, propanol, butanol, and propylene glycol monomethyl ether, the di-alcohol propylene glycol, and the tri-alcohol glycerol. We find that the tree model can reproduce the cluster size distributions and the bonding probabilities for both mono- and poly-alcohols, showing the branched nature of the OH-clusters in these liquids. Thus, this statistical model is a useful tool to better understand the structure of network forming hydrogen bonded liquids. The model can be applied to experimental data, allowing the topology of the clusters to be determined from such studies.

Reentrant volume phase transition of cross-linked poly(N-isopropylacrylamide) gels in mixed solvents of water/methanol

The reentrant volume phase transition of cross-linked poly(N-isopropylacrylamide) gels in mixed water/methanol solvents is shown to be induced by the competition between polymer–water hydrogen bonds and polymer–methanol hydrogen bonds by means of the theoretical analysis of the experimental data. On the basis of a statistical-mechanical model for the competitive hydrogen bonds with cooperativity in forming sequences of hydrogen bonds on a polymer chain, the swelling ratio Q, the degree of hydration θw, the degree of methanol binding θm, the total coverage of polymer chains by the bound solvent molecules, the excess (selective) adsorption ΔξE of methanol, the spinodal region, are theoretically calculated as functions of temperature and the volume fraction ξ of methanol outside the gel. The results are compared with the experimental data. At room temperature T = 26.1 °C, the gel exhibits a discontinuous collapse (Q ≈ 0.15) at ξ ≈ 0.18 by the cooperative dehydration of the polymer chains. For higher ξ, the gel approaches the swollen state (Q ≈ 1.5), while in other temperature regions the coverage changes continuously.

On the potential application of DFT methods in predicting the interaction-induced electric properties of molecular complexes. Molecular H-bonded chains as a case of study

A detailed analysis of the selected DFT functionals for the calculations of interaction-induced dipole moment, polarizability and first-order hyperpolarizability has been carried out. The hydrogen-bonded model chains consisting of HF, H2CO and H3N molecules have been chosen as a case study. The calculations of the components of the static electric properties using the diffuse Dunning’s basis set (aug-cc-pVDZ) have been performed employing different types of density functionals (B3LYP, LC-BLYP, PBE0, M06-2X and CAM-B3LYP). Obtained results have been compared with those gained at the CCSD(T) level of theory. The counterpoise correction scheme, namely site-site function counterpoise, has been applied in order to eliminate basis set superposition error. The performed tests allow to conclude that the DFT functionals can provide a useful tool for prediction of the interaction-induced electric properties, however a caution has to be urged to their decomposition to the two- and many-body terms. Figure Hydrogen-bonded model chains consisting of HF, H2CO and H3N molecules

Vibrational spectroscopy of water in hydrated lipid multi-bilayers. I. Infrared spectra and ultrafast pump-probe observables.

The vibrational spectroscopy of hydration water in dilauroylphosphatidylcholine lipid multi-bilayers is investigated using molecular dynamics simulations and a mixed quantum/classical model for the OD stretch spectroscopy of dilute HDO in H(2)O. FTIR absorption spectra, and isotropic and anisotropic pump-probe decay curves have been measured experimentally as a function of the hydration level of the lipid multi-bilayer, and our goal is to make connection with these experiments. To this end, we use third-order response functions, which allow us to include non-Gaussian frequency fluctuations, non-Condon effects, molecular rotations, and a fluctuating vibrational lifetime, all of which we believe are important for this system. We calculate the response functions using existing transition frequency and dipole maps. From the experiments it appears that there are two distinct vibrational lifetimes corresponding to HDO molecules in different molecular environments. In order to obtain these lifetimes, we consider a simple two-population model for hydration water hydrogen bonds. Assuming a different lifetime for each population, we then calculate the isotropic pump-probe decay, fitting to experiment to obtain the two lifetimes for each hydration level. With these lifetimes in hand, we then calculate FTIR spectra and pump-probe anisotropy decay as a function of hydration. This approach, therefore, permits a consistent calculation of all observables within a unified computational scheme. Our theoretical results are all in qualitative agreement with experiment. The vibrational lifetime of lipid-associated OD groups is found to be systematically shorter than that of the water-associated population, and the lifetimes of each population increase with decreasing hydration, in agreement with previous analysis. Our theoretical FTIR absorption spectra successfully reproduce the experimentally observed red-shift with decreasing lipid hydration, and we confirm a previous interpretation that this shift results from the hydrogen bonding of water to the lipid phosphate group. From the pump-probe anisotropy decay, we confirm that the reorientational motions of water molecules slow significantly as hydration decreases, with water bound in the lipid carbonyl region undergoing the slowest rotations.

Characterization of the adsorption of oligonucleotides on mercaptopropionic acid-coated CdSe/ZnS quantum dots using fluorescence resonance energy transfer

Semiconductor quantum dots (QDs) coated with thioalkyl acid ligands are often used as probes and reporters for nucleic acid sensing, or protein sensing using aptamers, and are also potential vectors for gene delivery. In such applications, the interactions that potentially lead to the adsorption of oligonucleotides onto the surface of colloidal QDs are an important consideration. To explore such interactions, fluorescence resonance energy transfer (FRET) between QDs and oligonucleotides labeled with a fluorescent dye was used to identify and characterize a set of conditions that favor strong adsorption on 3-mercaptopropionic acid (MPA)-coated CdSe/ZnS QDs. Adsorption curves and competitive binding experiments were used to determine that the order of affinity for nucleobase adsorption was dC>dA⩾dG≫dT. The length of the oligonucleotide sequence was also important, with an 80-mer sequence adsorbing more strongly than its 20-mer analog. Adsorption decreased with increasing pH and corresponded to the ionization of the carboxylic acid groups of the MPA ligands. Increased ionic strength partially offsets ligand ionization and increased the extent of adsorption. The interaction between QDs and oligonucleotides was labile, with increases in adsorption at lower concentrations of oligonucleotide and with an increasing number of oligonucleotides per QD. The results were consistent with a hydrogen-bonding model for adsorption, where neutral thioalkyl acid ligands interact favorably with nucleobases and ionized ligands resist adsorption.

Preferential Adsorption and Co-nonsolvency of Thermoresponsive Polymers in Mixed Solvents of Water/Methanol

If two good solvents become poor for a polymer when mixed, the solvent pair is called a co-nonsolvent pair for the polymer. The sharp depression of the LCST by the co-nonsolvency in solutions of poly(N-isopropylacrylamide) in the mixed solvent of water and methanol is shown to be caused by the competitive hydrogen bonding of water and methanol molecules onto the polymer chains. On the basis of a new statistical-mechanical model for competitive hydrogen bonds, the degree of hydration θ(w) and of methanol binding θ(m), excess degree ΔθE of solvent binding, preferential adsorption coefficients Γ, LCST spinodal lines, and cloud-point depression ΔTcl are theoretically calculated and compared with the experimental results. The optimal composition xm(M) of methanol at which LCST takes the minimum value is studied as a function of the polymer molecular weight M. In the high molecular weight limit, it takes xm ≃ 0.35. The solution recovers a uniform state in the region of higher methanol composition. Such a peculiar phase separation is caused by the dehydration of the polymer chains by the mixed methanol molecules in a cooperative way.

Hydrogen bond cooperativity in polyols: A DFT and AIM study

Density functional theory calculations, and atoms in molecules analyses are performed to investigate both the strength and the cooperative enhancement of intramolecular O H⋯O H hydrogen bonding interactions occurring in polyols. The relative strength of the O H⋯O H interaction is evaluated in two basic model systems: 1,3-propanediol, and 1,8-napthalenediol. The backbone of the former model is aliphatic, whereas that of the latter is aromatic. The cooperative enhancement of the O H⋯O H interaction is evaluated by extending symmetrically the polyol chain of each model system on both sides of the interaction in the basic unit. Specifically, we considered polyols with an odd number of H bonds running from one to eleven depending on the size of the polyol. The polyols are chosen so that there is a carbon atom located in between adjacent hydroxyl groups. Pertinent geometrical, and topological parameters are used as primary indicators of H bond strength, and consequently for cooperativity assessment. Also, the Lippincott and Schroeder hydrogen bond model, LS-HB, is used to estimate intramolecular hydrogen bonding energies.

Effects of Water Contamination on the Supercooled Dynamics of a Hydrogen-Bonded Model Glass Former

Broad-band dielectric spectroscopy is a commonly used tool in the study of glass-forming liquids. The high sensitivity of the technique together with the wide range of probed time scales makes it a powerful method for investigating the relaxation spectra of liquids. One particularly important class of glass-forming liquids that is often studied using this technique consists of liquids dominated by hydrogen (H) bond interactions. When investigating such liquids, particular caution has to be taken during sample preparation due to their often highly hygroscopic nature. Water can easily be absorbed from the atmosphere, and dielectric spectroscopy is a very sensitive probe of such contamination due to the large dipole moment of water. Our knowledge concerning the effects of small quantities of water on the dielectric properties of these commonly investigated liquids is limited. We here demonstrate the effects due to the presence of small amounts of water on the dielectric response of a typical H-bonded model glass former, tripropylene glycol. We show how the relaxation processes present in the pure liquid are affected by addition of water, and we find that a characteristic water induced relaxation response is observed for water contents as low as 0.15 wt%. We stress the importance of careful purification of hygroscopic liquids before experiments and quantify what the effects are if such procedures are not undertaken.

RNA Internal Loops with Tandem AG Pairs: The Structure of the 5′GAGU/3′UGAG Loop Can Be Dramatically Different from Others, Including 5′AAGU/3′UGAA

Thermodynamic stabilities of 2 × 2 nucleotide tandem AG internal loops in RNA range from −1.3 to +3.4 kcal/mol at 37 °C and are not predicted well with a hydrogen-bonding model. To provide structural information to facilitate development of more sophisticated models for the sequence dependence of stability, we report the NMR solution structures of five RNA duplexes: (rGACGAGCGUCA)2, (rGACUAGAGUCA)2, (rGACAAGUGUCA)2, (rGGUAGGCCA)2, and (rGACGAGUGUCA)2. The structures of these duplexes are compared to that of the previously solved (rGGCAGGCC)2 (Wu, M., SantaLucia, J., Jr., and Turner, D. H. (1997) Biochemistry 36, 4449−4460). For loops bounded by Watson−Crick pairs, the AG and Watson−Crick pairs are all head-to-head imino-paired (cis Watson−Crick/Watson−Crick). The structures suggest that the sequence-dependent stability may reflect non-hydrogen-bonding interactions. Of the two loops bounded by G-U pairs, only the 5′UAGG/3′GGAU loop adopts canonical UG wobble pairing (cis Watson−Crick/Watson−Crick), with AG pairs that are only weakly imino-paired. Strikingly, the 5′GAGU/3′UGAG loop has two distinct duplex conformations, the major of which has both guanosine residues (G4 and G6 in (rGACGAGUGUCA)2) in a syn glycosidic bond conformation and forming a sheared GG pair (G4-G6*, GG trans Watson−Crick/Hoogsteen), both uracils (U7 and U7*) flipped out of the helix, and an AA pair (A5-A5*) in a dynamic or stacked conformation. These structures provide benchmarks for computational investigations into interactions responsible for the unexpected differences in loop free energies and structure.

Hydrogen bond models and theories: The dual hydrogen bond model and its consequences

The H-bond can be reinterpreted starting from the dual H-bond model, for which any D–H···:A bond is not a bond donated by D–H to :A but rather consists of two bonds formed by the central proton with two adjacent acceptors. Analogously, the H-bond energy, E HB, is not the D–H···:A dissociation energy but the smaller of two bond-dissociation energies, D 0(D–H) and D 0(H–A), by which −D: and :A are competitively bound to the proton. If one is stronger, the other is weaker, and weak the overall H-bond will be. Strong bonds occur when Δ D 0 = D 0(D–H) − D 0(H–A) = 0 or, in terms of affinity for the proton ( pa), when Δ pa = pa(D −) − pa(A) = 0. H-bond properties are then function of two variables, pa(D −) and pa(A), or better of their linear combinations, Σ pa = pa(D −) + pa(A) and Δ pa = pa(D −) − pa(A), having respective meanings of mean donor/acceptor electronegativity and of energy difference, Δ rE , between tautomeric D–H···:A and −D:···H–A + forms. Two cases are studied. The case: ‘Σ pa variable for Δ pa = 0’ leads to quantitative relationships between D/A electronegativity and maximum energy, E HB,MAX, achievable for each D/A electronegativity class, EC(D,A). The case: ‘Δ pa variable for Σ pa = constant’ leads to formulate three different but inter-consistent H-bond theories which are separately discussed. The last one, which is called ‘p K a equalization principle’ and where Δ pa values are empirically estimated from the acid–base dissociation constants in water as Δp K a = p K AH(D–H) − p K BH+(A–H +), is shown to be a powerful method of large applicability for predicting the H-bond strengths from thermodynamic parameters.

Protein Backbone Dynamics Simulations Using Coarse-Grained Bonded Potentials and Simplified Hydrogen Bonds.

A new set of bonded potentials is introduced to model the flexibility of coarse-grained polypeptide chains. Based on a statistical analysis of known structures, the bonded potentials are sequence-dependent, and the secondary-structure propensity of each amino acid is partially reflected in the Si-Bi-Bi+1-Bi+2 pseudotorsion angle, where Si and Bi denote the side-chain and backbone beads, respectively. To stabilize the secondary structures during simulations, the bonded force field must be balanced by a simplified model of the protein hydrogen bonds, based on dipole-dipole interactions. Tested on eight polypeptides with sequence lengths ranging from 17 to 98, using 200-ns molecular dynamics simulations, the coarse-grained model yields trajectories with RMSDs ranging from 3 to 8 Å from the experimental conformations. The less-structured regions of the simulated proteins exhibit the largest-amplitude movements.

Equation-of-state modeling of mixtures with ionic liquids

A non-electrolyte equation-of-state model was used to describe the phase behavior of binary systems containing alkyl-methyimidazolium bis(trifluoromethyl-sulfonyl)imide ionic liquids. A methodology is suggested for modeling this phase behavior by using the Non-Random Hydrogen-Bonding (NRHB) model. According to this methodology, the scaling constants of the ionic liquid are calculated using limited available experimental data on liquid densities and Hansen's solubility parameters, while all electrostatic interactions (polar, hydrogen bonding and ionic) are treated as strong specific interactions. Using the aforementioned methodology, the model is applied to describe the vapor-liquid and the liquid-liquid equilibria in mixtures of ionic liquids with various polar or quadrupolar solvents at low and high pressures. In all cases, one temperature-independent binary interaction parameter was used. Accurate correlations were obtained for the majority of the systems, both, for vapor-liquid and liquid-liquid equilibria.

Diastereomers of the pentacoordinate chiral phosphorus compounds in solution: absolute configurations and predominant conformations

The absolute structural information about four sets of diastereomers of pentacoordinate spirophosphoranes, derived separately from L (or D)-phenylglycine and L (or D)-phenylalanine, has been obtained by using vibrational circular dichroism (VCD) spectroscopic measurements and density functional theory (DFT) for the first time. Each compound contains a stereogenic centre at the phosphorus center and two at the amino acid ligands. Geometric searches at the B3LYP/6-311++G** level have been performed for all possible low energy conformers whose vibrational absorption (VA) and VCD spectra have also been simulated. The good agreement between the experimental VA and VCD spectra in the dimethyl sulfoxide (DMSO) solution and the simulated ones allows us to assign the absolute configurations and predominant conformations of these pentacoordinate phosphorus compounds with high confidence. Solvent effects have been examined by using both the experimental measurements and theoretical calculations. The implicit continuous polarization model and the explicit solute-solvent intermolecular hydrogen-bonding model have been considered to understand the effects of DMSO on the spectra observed. The influence of basis sets and different functionals on the VA and VCD spectra of this type of coordination compounds has also been investigated.

Effect of hydrogen bond networks on the nucleation mechanism of protein folding

We have recently developed a kinetic model for the nucleation mechanism of protein folding (NMPF) in terms of ternary nucleation by using the first passage time analysis. A protein was considered as a random heteropolymer consisting of hydrophobic, hydrophilic (some of which are negatively or positively ionizable), and neutral beads. The main idea of the NMPF model consisted of averaging the dihedral potential in which a selected residue is involved over all possible configurations of all neighboring residues along the protein chain. The combination of the average dihedral, effective pairwise (due to Lennard-Jones-type and electrostatic interactions), and confining (due to the polymer connectivity constraint) potentials gives rise to an overall potential around the cluster that, as a function of the distance from the cluster center, has a double-well shape. This allows one to evaluate the protein folding time. In the original NMPF model hydrogen bonding was not taken into account explicitly. To improve the NMPF model and make it more realistic, in this paper we modify our (previously developed) probabilistic hydrogen bond model and combine it with the former. Thus, a contribution due to the disruption of hydrogen bond networks around the interacting particles (cluster of native residues and residue in the protein unfolded part) appears in the overall potential field around a cluster. The modified model is applied to the folding of the same model proteins that were examined in the original model: a short protein consisting of 124 residues (roughly mimicking bovine pancreatic ribonuclease) and a long one consisting of 2500 residues (as a representative of large proteins with superlong polypeptide chains), at pH=8.3 , 7.3, and 6.3. The hydrogen bond contribution now plays a dominant role in the total potential field around the cluster (except for very short distances thereto where the repulsive energy tends to infinity). It is by an order of magnitude stronger for hydrophobic residues than for hydrophilic ones. The range of "residue-cluster" distances, at which the hydrogen bond effect exists, is twice as long for hydrophobic residues as for hydrophilic ones.

Why Hypothetical Protein KPN00728 of Klebsiella pneumoniae Should Be Classified as Chain C of Succinate Dehydrogenase?

Twenty percent of genes that encode for hypothetical proteins from Klebsiella pneumoniae MGH78578 were identified, leading to KPN00728 and KPN00729 after bioinformatics analysis. Both open reading frames showed high sequence homology to Succinate dehydrogenase Chain C (SdhC) and D (SdhD) from Escherichia coli. Recently, KPN00729 was assigned as SdhD. KPN00728 thus remains of particular interest as no annotated genes from the complete genome sequence encode for SdhC. We discovered KPN00728 has a missing region with conserved residues important for ubiquinone (UQ) and heme group binding. Structure and function prediction of KPN00728 coupled with secondary structure analysis and transmembrane topology showed KPN00728 adopts SDH-(subunit C)-like structure. To further probe its functionality, UQ was docked on the built model (consisting KPN00728 and KPN00729) and formation of hydrogen bonds between UQ and Ser27, Arg31 (KPN00728) and Tyr84 (KPN00729) further reinforces and supports that KPN00728 is indeed SDH. This is the first report on the structural and function prediction of KPN00728 of K. pneumoniae MGH78578 as SdhC.

Some improvements in DNA interaction calculations

Calculations are made on specific DNA-type complexes using refined expressions for electrostatic and polarization energies. Dispersion and repulsive terms are included in the evaluation of the total interaction energy. It is shown that the expansion of the electrostatic potential to include multipole moments up to octopole is necessary to achieve convergence of first-order energies. Polarization energies are not as sensitive to this expansion. The calculations also support the usefulness of the hard sphere model for DNA hydrogen bonds and indicate how stacking interactions are influenced by second-order energies.

Investigating the Hydrogen-Bonding Model of Urea Denaturation

The direct binding mechanism for urea-based denaturation of proteins was tested with a thermoresponsive polymer, poly(N-isopropylacrylamide) (PNIPAM). Thermodynamic measurements of the polymer's hydrophobic collapse were complemented by Fourier transform infrared (FTIR) spectroscopy, Stokes radius measurements, and methylated urea experiments. It was found that the lower critical solution temperature (LCST) of PNIPAM decreased as urea was added to the solution. Therefore, urea actually facilitated the hydrophobic collapse of the macromolecule. Moreover, these thermodynamic measurements were strongly correlated with amide I band data which indicated that the decrease in the LCST was coupled to the direct hydrogen bonding of urea to the amide moieties of the polymer. In addition, the hydrogen bonding was found to be highly cooperative, which is consistent with a cross-linking (bivalent binding) mechanism. Cross-linking was confirmed by Stokes radius measurements below the polymer's LCST using gel filtration chromatography. Finally, phase transition measurements with methylurea, dimethylurea, and tetramethylurea indicated that these substituted compounds caused the LCST of PNIPAM to rise with increasing methyl group content. No evidence could be found for the direct binding of any of these methylated ureas to the polymer amide moieties by FTIR. These results are inconsistent with a direct hydrogen-bonding mechanism for the urea-induced denaturation of proteins.