Showing papers on "Hydrogen bond published in 2000"
TL;DR: In this paper, the formation of low-barrier hydrogen bonds between ylides and different neutral molecules was studied, and the analysis of the protonation energies and the optimized geometries, interaction energies, and characteristics of the electron density of the complexes showed that these ylsides are very good HB acceptors, forming stable complexes even with weak HB donors.
Abstract: The hydrogen bond (HB) basicity of a series of ylides containing nitrogen, oxygen, or carbon as heavy atoms, as well as the influence of the formation of the HB complexes on their structure, has been studied. In addition, in this paper we propose the formation of some rather strong HBs (that could be considered low-barrier hydrogen bonds, LBHBs) between ylides and different neutral molecules. The ylides chosen for the study were H3N+−N-H, Me3N+−N-H, H2O+−N-H, Me2O+−N-H, H2O+−O-, Me2O+−O-, and Me3N+−C-H2. As HB donors, classical donors such as HF, HCN, and HCCH were used. The analysis of the protonation energies of the ylides and the optimized geometries, interaction energies, and characteristics of the electron density of the complexes shows that these ylides are very good HB acceptors, forming stable complexes even with weak HB donors. With strong donors, when the proton transfer did not take place, very strong HBs were formed with quite large interaction energies and very short HB distances which could ...
1,232 citations
TL;DR: In this article, the termini of low-molecular-weight telechelic polymers with strongly associating hydrogen bonding units are functionalized to obtain a new set of supramolecular materials.
Abstract: Functionalizing the termini of low-molecular-weight telechelic polymers with strongly associating hydrogen bonding units (see Figure) results in a new set of supramolecular materials, as reported here. These materials possess the unique combination of polymer-like properties at room temperature and monomer-like properties at elevated temperatures.
633 citations
TL;DR: In this article, the authors used molecular dynamics simulation to calculate different probability densities that govern the time evolution of the formation and rupture of hydrogen bonds, and provided analytical connections between these functions.
Abstract: This paper analyzes dynamic properties of hydrogen bonds in liquid water. We use molecular dynamics simulation to calculate different probability densities that govern the time evolution of the formation and rupture of hydrogen bonds. We provide analytical connections between these functions. Excellent agreement with our simulation results is observed. We prove transition state theory rate constant to be identical to the inverse of the associated mean first passage time (hydrogen bond lifetime). Hence, the analysis establishes its Arrhenius temperature dependence. We give the explicit relation between reactive flux correlation function for the relaxation dynamics of hydrogen bonds, and their first passage time probability densities. All the different observations in the existing literature, associated with various estimates of hydrogen bonding times in liquid water that are affected (or not affected) by particular bond criteria, as well as by different definitions of hydrogen bond lifetimes applied in sim...
609 citations
TL;DR: A family of oligomeric molecules with bent conformations is described, which exhibit dynamic exchange between single and double molecular helices in solution, through spiral sliding of the synthetic oligomer strands.
Abstract: Synthetic single-helical conformations are quite common, but the formation of double helices based on recognition between the two constituent strands is relatively rare. Known examples include duplex formation through base-pair-specific hydrogen bonding and stacking, as found in nucleic acids and their analogues, and polypeptides composed of amino acids with alternating L and D configurations. Some synthetic polymers and self-assembled fibres have double-helical winding induced by van der Waals interactions. A third mode of non-covalent interaction, coordination of organic ligands to metal ions, can give rise to double, triple and quadruple helices, although in this case the assembly is driven by the coordination geometry of the metal and the structure of the ligands, rather than by direct inter-strand complementarity. Here we describe a family of oligomeric molecules with bent conformations, which exhibit dynamic exchange between single and double molecular helices in solution, through spiral sliding of the synthetic oligomer strands. The bent conformations leading to the helical shape of the molecules result from intramolecular hydrogen bonding within 2'-pyridyl-2-pyridinecarboxamide units, with extensive intermolecular aromatic stacking stabilizing the double-stranded helices that form through dimerization.
602 citations
TL;DR: This work describes a general strategy for the design of functionalized monomer units and their association in either water or alkanes into non-covalently linked polymeric structures with controlled helicity and chain length.
Abstract: The double helix of DNA epitomizes this molecule's ability to self-assemble in aqueous solutions into a complex chiral structure using hydrogen bonding and hydrophobic interactions. Non-covalently interacting molecules in organic solvents are used to design systems that similarly form controlled architectures. Peripheral chiral centres in assemblies and chiral side chains attached to a polymer backbone, have been shown to induce chirality at the supramolecular level, and highly ordered structures stable in water are also known. However, it remains difficult to rationally exploit non-covalent interactions for the formation of chiral assemblies that are stable in water, where solvent molecules can compete effectively for hydrogen bonds. Here we describe a general strategy for the design of functionalized monomer units and their association in either water or alkanes into non-covalently linked polymeric structures with controlled helicity and chain length. The monomers consist of bifunctionalized ureidotriazine units connected by a spacer and carrying solubilizing chains at the periphery. This design allows for dimerization through self-complementary quadruple hydrogen bonding between the units and solvophobically induced stacking of the dimers into columnar polymeric architectures, whose structure and helicity can be adjusted by tuning the nature of the solubilizing side chains.
566 citations
TL;DR: It is shown, inter alia, that reproducible and transferable crystal synthesis strategies based on charge-assisted hydrogen bonds can be devised to build periodical supermolecules.
Abstract: The utilization of noncovalent interactions to construct molecular crystals is evaluated in the context of inorganic and organometallic crystal engineering. The attention is focused on hydrogen-bonding interactions involving metal complexes in which the metal atoms participate in the bonding either directly or as ancillary systems. The role of ionic charges is discussed. It is shown, inter alia, that reproducible and transferable crystal synthesis strategies based on charge-assisted hydrogen bonds can be devised to build periodical supermolecules.
488 citations
TL;DR: The dynamics of hydrogen-bond breaking is found to accelerate somewhat and that of hydrogen"-bond structural relaxation, which occurs at a longer time scale, is foundto slow down with increasing ion concentration for both NaCl and KCl solutions.
Abstract: We have performed a series of molecular dynamics simulations of aqueous NaCl and KCl solutions at different concentrations to investigate the effects of ion atmosphere on the dynamics of water-water hydrogen bonds at room temperature. The average number of hydrogen bonds per water molecule decreases with increase of ion concentration. The dynamics of hydrogen-bond breaking is found to accelerate somewhat and that of hydrogen-bond structural relaxation, which occurs at a longer time scale, is found to slow down with increasing ion concentration for both NaCl and KCl solutions.
485 citations
TL;DR: In this paper, high-level ab initio calculations were carried out to evaluate the interaction between the π face of benzene and hydrocarbon molecules (methane, ethane, ethanol, ethylene, and acetylene).
Abstract: High-level ab initio calculations were carried out to evaluate the interaction between the π face of benzene and hydrocarbon molecules (methane, ethane, ethylene, and acetylene). Intermolecular interaction energies were calculated from extrapolated MP2 interaction energies at the basis set limit and CCSD(T) correction terms. The calculated benzene−methane interaction energy (−1.45 kcal/mol) is considerably smaller than that of the hydrogen bond between waters. The benzene−methane complex prefers a geometry in which the C−H bond points toward the benzene ring. The potential energy surface is very flat near the minimum, which shows that the major source of the attraction is a long-range interaction. The HF interaction energy of the complex (0.85 kcal/mol) is repulsive. The large gain of the attraction energy (−2.30 kcal/mol) by electron correlation correction indicates that dispersion interaction is the major source of the attraction. Although the electrostatic energy (−0.25 kcal/mol) is small, a highly ori...
480 citations
TL;DR: In this article, the FT-IR spectra of I β cellulose were recorded on films made of hydrothermally treated Valonia microcrystals and a critical analysis of the spectra allowed to propose a detailed assignment for most of the bands at wavenumbers higher than 800 cm −1.
467 citations
TL;DR: Force spectroscopy using AFM promises to elucidate the dynamic mechanical properties of a wide variety of proteins at the single molecule level and provide an important complement to other structural and dynamic techniques (e.g., X-ray crystallography, NMR spectroscope, patch-clamp).
Abstract: Mechanical unfolding and refolding may regulate the molecular elasticity of modular proteins with mechanical functions. The development of the atomic force microscopy (AFM) has recently enabled the dynamic measurement of these processes at the single-molecule level. Protein engineering techniques allow the construction of homomeric polyproteins for the precise analysis of the mechanical unfolding of single domains. alpha-Helical domains are mechanically compliant, whereas beta-sandwich domains, particularly those that resist unfolding with backbone hydrogen bonds between strands perpendicular to the applied force, are more stable and appear frequently in proteins subject to mechanical forces. The mechanical stability of a domain seems to be determined by its hydrogen bonding pattern and is correlated with its kinetic stability rather than its thermodynamic stability. Force spectroscopy using AFM promises to elucidate the dynamic mechanical properties of a wide variety of proteins at the single molecule level and provide an important complement to other structural and dynamic techniques (e.g., X-ray crystallography, NMR spectroscopy, patch-clamp).
434 citations
TL;DR: In this article, a detailed study of the dimerization constant and lifetime of 2-ureido-4[1H]-pyrimidinone 1b was presented.
Abstract: 2-Ureido-4[1H]-pyrimidinones are known to dimerize via a strong quadruple hydrogen bond array. A detailed study of the dimerization constant and lifetime of the dimer is presented here. Excimer fluorescence of pyrene-labeled 2-ureido-4[1H]-pyrimidinone 1b was used to determine a dimerization constant Kdim of 6 × 107 M-1 in CHCl3, 1 × 107 M-1 in chloroform saturated with water, and 6 × 108 M-1 in toluene (all at 298 K). Under these conditions, the preexchange lifetime of the similar dimers of both 1d and 1e is 170 ms in CDCl3, 80 ms in wet CDCl3, and 1.7 s in toluene-d8, as determined by dynamic NMR spectroscopy. Association rate constants were calculated from the Kdim values and the preexchange lifetimes. The resulting values are significantly lower than the diffusion-controlled association rate constants calculated using the Stokes−Einstein and the Debeije equations. This difference is ascribed to a tautomeric equilibrium of the monomer between the dimerizing 4[1H]-pyrimidinone and nondimerizing 6[1H]-py...
15 Aug 2000
TL;DR: In this paper, it has been shown that homodromic hydrogen bonding networks, i.e., those exhibiting donor-acceptor (da) arrangements between all water molecules, are associated with the largest nonadditivities among other networks present in low lying minima of small water clusters.
Abstract: Clusters of water molecules are held together by hydrogen bonding networks. These networks are differentiated by the participation of the individual water molecules in the hydrogen bonds either as proton donors (d), proton acceptors (a) or their combinations. It has long been assumed that the stability of clusters is determined by the dominant two-body interactions between the water molecules. We have found that homodromic hydrogen bonding networks, i.e. those exhibiting donor–acceptor (da) arrangements between all water molecules, are associated with the largest non-additivities among other networks present in low lying minima of small water clusters. This finding offers a novel explanation for the stability of homodromic rings that are the global minima for the clusters trimer through pentamer. Among the non-additive terms, three-body terms are mainly responsible for determining the relative stabilities between the various trimer through pentamer isomers. This suggests that purely two-body pairwise additive potentials will result in errors exceeding 20% for clusters larger than the pentamer. Among all higher order components, the three-body term was found to be the most important.
TL;DR: In this article, the authors investigated the possible sources of the discrepancy between theory and experiment regarding hydrogen bond lengths in adenine−thymine (AT) and guanine−cytosine (GC) base pairs at various levels (BP86, PW91, and BLYP) in combination with different Slater-type orbital (STO) basis sets.
Abstract: Up till now, there has been a significant disagreement between theory and experiment regarding hydrogen bond lengths in Watson−Crick base pairs. To investigate the possible sources of this discrepancy, we have studied numerous model systems for adenine−thymine (AT) and guanine−cytosine (GC) base pairs at various levels (i.e., BP86, PW91, and BLYP) of nonlocal density functional theory (DFT) in combination with different Slater-type orbital (STO) basis sets. Best agreement with available gas-phase experimental A−T and G−C bond enthalpies (−12.1 and −21.0 kcal/mol) is obtained at the BP86/TZ2P level, which (for 298 K) yields −11.8 and −23.8 kcal/mol. However, the computed hydrogen bond lengths show again the notorious discrepancy with experimental values. The origin of this discrepancy is not the use of the plain nucleic bases as models for nucleotides: the disagreement with experiment remains no matter if we use hydrogen, methyl, deoxyribose, or 5‘-deoxyribose monophosphate as the substituents at N9 and N...
TL;DR: In this paper, the trans hydrogen bond 3hJNC was shown to be mediated by a closed shell, noncovalent interaction between the donor hydrogen atom and the acceptor oxygen atom.
Abstract: The trans hydrogen bond 3hJNC‘ coupling observed between peptide groups in proteins is shown to be mediated by a closed shell, noncovalent interaction between the donor hydrogen atom and the acceptor oxygen atom. The magnitude of 3hJNC‘ is shown to be an exponential function of the mutual penetration of the nonbonding van der Waals shells of the isolated donor and acceptor fragments. Our results also show that the magnitude of JFF, the through-space coupling between two nonbonded fluorine nuclei in organic molecules and in a protein, exhibits a similar exponential dependence upon penetration of nonbonding monomer charge densities. These results support the idea that the existence of electron-coupled nuclear spin−spin coupling requires neither a covalent bond nor an attractive electrostatic bond between the coupled nuclei. By relating the results of calculations using Bader's theory of Atoms in Molecules, (Bader, R. F. W. Atoms in Molecules−A Quantum Theory; Clarendon Press: Oxford, 1990) to these couplin...
TL;DR: In this article, a linear correlation between C−H···O bond energies and gas-phase anion proton affinities was reported and used to estimate values of De = −4.0 ± 0.5
Abstract: Although the existence of Cα−H···OC hydrogen bonds in protein structures recently has been established, little is known about their strength and, therefore, the relative importance of these interactions. We have discovered that similar interactions occur in N,N-dimethylformamide dimers. High level ab initio calculations (MP2/aug-cc-pTZV) yield electronic association energies (De) and association enthalpies (ΔH298) for four dimer geometries. These data provide a lower limit of De = −2.1 kcal mol-1 for the Cα−H···OC hydrogen bond. A linear correlation between C−H···O bond energies and gas-phase proton affinities is reported. The gas-phase anion proton affinity of a peptide Cα−H hydrogen was calculated (355 kcal mol-1) and used to estimate values of De = −4.0 ± 0.5 kcal mol-1 and ΔH298 = −3.0 ± 0.5 kcal mol-1 for the Cα−H···OC hydrogen bond. The magnitude of this interaction, roughly one-half the strength of the N−H···OC hydrogen bond, suggests that Cα−H···OC hydrogen bonding interactions represent a hithert...
TL;DR: In this article, high-level ab initio calculations were carried out to evaluate the interaction between the π face of benzene and ammonia as a model of NH/π interaction, and the intermolecular interaction energy was calculated from the extrapolated MP2 interaction energy at the basis set limit and a CCSD(T) correction term.
Abstract: High-level ab initio calculations were carried out to evaluate the interaction between the π face of benzene and ammonia as a model of NH/π interaction. The intermolecular interaction energy was calculated from the extrapolated MP2 interaction energy at the basis set limit and a CCSD(T) correction term. The calculated interaction energy (−2.22 kcal/mol) is considerably smaller than that of the hydrogen bond between waters. The monodentate complex is slightly more stable than the bidentate and tridentate complexes. The potential energy surface is very flat near the minimum, which shows that the major source of the attraction is a long-range interaction. The HF interaction energy of the monodentate complex (0.13 kcal/mol) is repulsive. The large gain in the attraction by electron correlation correction (−2.36 kcal/mol) indicates that the dispersion interaction is significantly important for the attraction. The electrostatic energy (−1.01 kcal/mol) is also important for the attraction. The benzene−water (OH/...
TL;DR: In this article, the proton transport mechanisms in systems containing water and in cubic perovskite-type oxides are analyzed in detail in terms of chemical interactions, which allow for high rates of proton transfer and structural reorganization.
TL;DR: In this paper, the topological properties of the charge density ρ ( r b ) at the (3, − 1) bond critical points (BCPs) where the gradient of ρ( r ) vanishes were investigated.
TL;DR: In this paper, the effects of confinement in nanotubes on the hydrogen bond structure of liquid water are studied by molecular dynamics simulation and the results indicate that the averaged number of hydrogen bonds decreases when compared with bulk water and it is roughly independent of the tube radius excepting for very narrow tubes, which suffer a dramatic destruction of the H-bond network.
TL;DR: It is concluded that partitioning into the lipid membrane is the rate-limiting step for the interaction of a substrate with P-glycoprotein and that dissociation of the P- glycoprotein-substrate complex is determined by the number and strength of the hydrogen bonds formed between the substrate and the transporter.
TL;DR: In this paper, the supramolecular chemistry and crystal structures of five bis(imidazolium 2,6-pyridinedicarboxylate)M(II) trihydrate complexes, where M = Mn2+, Co2+, Ni2+, Cu2+, or Zn2+ (1−5), are reported.
Abstract: The supramolecular chemistry and crystal structures of five bis(imidazolium 2,6-pyridinedicarboxylate)M(II) trihydrate complexes, where M = Mn2+, Co2+, Ni2+, Cu2+, or Zn2+ (1−5, respectively), are reported. These complexes serve as supramolecular building blocks that self-assemble when crystallized to generate a single, well-defined, predictable structure in the solid state. 2,6-Pyridinedicarboxylate anions and imidazolium cations form strong ionic hydrogen bonds that dominate crystal packing in compounds 1−5 by forming two-dimensional networks, or layers of molecules. This layer motif serves as a platform with which to control and predict molecular packing by design for engineering the structures of crystals. Moreover, compounds 1−5 create a robust organic host lattice that accommodates five different transition metals without significantly altering molecular packing. Growth of crystals from solutions that contain two or more different metal complexes produces mixed crystals in which mixtures of the diff...
TL;DR: In this article, the AIM approach, by analyzing the topological properties of the charge density with the determination of critical points, provides another way of looking for bonds, as discussed in several examples.
TL;DR: Although the occupancy and residence times of the majority of sites are rather bulk-like, the residence time distribution is shifted toward the longer components, relative to bulk, in a simulation of sperm whale myoglobin.
TL;DR: An Fourier transform infrared spectroscopic study of the thermal behavior of beta-lactoglobulin (beta-lg) in salt-free D(2)O solutions and low ionic strength at different pDs reveals differences between fine-stranded and particulate gels.
Abstract: In order to reveal at a molecular level differences between fine-stranded and particulate gels, we present an Fourier transform infrared spectroscopic study of the thermal behavior of beta-lactoglobulin (beta-lg) in salt-free D(2)O solutions and low ionic strength at different pDs. Differences are found in the denaturation mechanism, in the unfolded state of the protein, in the aggregate formation, and in the strength of the intermolecular interactions. For fine-stranded gels (pD 2.8 and 7.8), heating induces the dissociation of the dimers into monomers. The protein undergoes extensive structural modifications before aggregation begins. Aggregation is characterized by the appearance of a new band attributed to intermolecular beta-sheets which is located in the 1613-1619 cm(-1) range. For particulate gels (pD 4.4 and 5.4), the protein structure is almost preserved up to 75-80 degrees C with no splitting of the dimers. The band characteristic of aggregation originates from the component initially located at 1623 cm(-1), suggesting that at the beginning of aggregation, globular beta-lg in the dimeric form associate to constitute oligomers with higher molecular mass. Aggregation may result in the association of globular slightly denatured dimers, leading to the formation of spherical particles rather than linear strands. The aggregation band is always located in the 1620-1623 cm(-1) range for particulate gels showing that hydrogen bonds are weaker for these aggregates than for fine-stranded ones. This has been related to a more extensive protein unfolding for fine-stranded gels that allows a closer alignment of the polypeptide chains, and then to the formation of much stronger hydrogen bonds. Small differences are also found in protein organization and in intermolecular hydrogen bond strength vs pD within the same type of gel. Protein conformation and protein-protein interactions in the gel state may be responsible of the specific macroscopic properties of each gel network. A coarse representation of the different modes of gelation is described.
TL;DR: In this paper, the UV-visible spectra of 2-hydroxy Schiff bases are investigated in different solvents, acidic and basic media, and the structure of compound (2) was examined crystallographically.
TL;DR: A review of several classes of organic compounds capable of multiple hydrogen-bond recognition is presented in this paper with a focus on the factors that contribute to complex stability, including the properties of the donor and acceptor groups.
Abstract: Hydrogen bonding is a directional and moderately strong intermolecular force. Compounds that present multiple hydrogen-bond donor and acceptor groups have proven to be extremely important in creating new self-assembled structures. A review of several classes of organic compounds capable of multiple hydrogen-bond recognition is presented with a focus on the factors that contribute to complex stability.
TL;DR: The biological results obtained revealed that the acetylhydrazones and semicarbazones afforded good protection against convulsions while the oxamoylHydrazones were significantly less active, suggesting that terminal electron-donating groups enhanced the hydrogen bonding capabilities and anticonvulsant properties of these molecules.
TL;DR: In this paper, thermally stable poly(benzimidazole) (PBI) and strong acids were synthesized, and the PBI/H 3 PO 4 polymers were shown to be stable up to 500°C and 10 −5 S cm −1 at 160°C.
TL;DR: In this article, a correlation between the magnitude of the redshift (Δν = 20 to 2500 cm−1 ) and the length of the H-bond (rH···B = 0.28 to 0.12 nm) was found.
Abstract: A correlation is found between the magnitude of the redshift (Δν=20 to 2500 cm−1
relative to the free
molecule) of the stretching mode of H-bonded A–H groups in an A–H···B complex, and the length of the H-bond (rH···B=0.28 to 0.12 nm). The correlation is based on both new spectral data for narrow decoupled H-bands in cold isotopically diluted carbohydrate crystals with known H-bond distances and on literature spectral and structural data from a total of 36 systems. Once established, additional data for H-bonded crystals (hydrates,
acid salts of carboxylic acids) and for gas phase dimer systems also fit this correlation quite well.
Hydrogen bond enthalpies in the range of −ΔH=10–80 kJ mol−1 correlate with the inverse third power of the H-bond length. Literature experimental data on −ΔH and rH···B
of ten gas phase dimers confirm this relationship.