Hydrogen bond

About: Hydrogen bond is a research topic. Over the lifetime, 57701 publications have been published within this topic receiving 1306326 citations.

The effect of cooperative hydrogen bonding on the OH stretching-band shift for water clusters studied by matrix-isolation infrared spectroscopy and density functional theory.

Abstract: Infrared spectra of the water clusters have been measured in the N2 + O2 matrix. The aggregation process of water in the matrix has been monitored by annealing the deposited samples up to 40 K and UV irradiation. The monomer, dimer, cyclic trimer and cyclic pentamer are found as water clusters in the matrix. For the hexamer, several structures such as chair, cage, prism, bag 1 and/or book 1 are likely to exist. By UV irradiation, the cyclic pentamer is predominantly formed from the monomer and dimer. On the other hand, by annealing the deposited sample, several hexamers are formed. The theoretical calculation for water clusters has revealed that the formation of one hydrogen bonding in a hydrogen-bonded chain cooperatively enhances or diminishes the strength of another hydrogen bond. Both proton donor (D) and acceptor (A) participating in a hydrogen-bonding pair DA are capable of forming hydrogen bonding with the other water molecules; D can additionally accept two protons and donate one proton, and A can additionally donate two protons and accept one proton. We have proposed the classification of hydrogen-bonding patterns considering the cooperativity, denoting as d′a′DAd″a″, where d and a are integers indicating the number of proton donors and acceptors to D (the single prime) and A (the double prime), respectively. Then, a magnitude given by MOH = −d′ + a′ + d″ − a″ has been introduced, which is very useful for connecting the hydrogen-bonding patterns to their OH wavenumbers. As a result, it is revealed that the OH stretching bands of water clusters are characterized by eight indicators (free and MOH = −2, −1, 0, 1, 2, 3 and 4). The classification proposed here is applicable to the OH band analysis for the hydrogen-bonded water and alcohols in a condensed phase.

Structures for polyinosinic acid and polyguanylic acid

Abstract: X-ray-diffraction analysis of oriented, partially crystalline fibres of polyinosinic acid has resulted in a new molecular model. This model consists of four identical polynucleotide chains related to one another by a fourfold rotation axis. The coaxial helices are righthanded (screw symmetry 23(2)) and have an axial translation per residue h=0.341nm and a rotation per residue t=31.3 degrees . Incorporated in the model are standard bond lengths, bond angles and C-2-endo furanose rings. The nucleotide conformation angles, determined by linked-atom least-squares methods, are orthodox and the fit with the X-ray intensities is good. Each hypoxanthine base is linked to two others by hydrogen bonds involving O-6 and N-1. Further stability may arise from intrachain hydrogen bonds between each ribose hydroxyl group and the phosphate oxygen O-3. If guanine were to be substituted for hypoxanthine in an isogeometrical molecular structure, additional hydrogen bonds could be made between every N-2 and N-7.

Heteroaromatic Modules for Self-Assembly Using Multiple Hydrogen Bonds

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.

A bond-order analysis of the mechanism for hydrated proton mobility in liquid water.

Abstract: Bond-order analysis is introduced to facilitate the study of cooperative many-molecule effects on proton mobility in liquid water, as simulated using the multistate empirical valence-bond methodology. We calculate the temperature dependence for proton mobility and the total effective bond orders in the first two solvation shells surrounding the H(5)O(2) (+) proton-transferring complex. We find that proton-hopping between adjacent water molecules proceeds via this intermediate, but couples to hydrogen-bond dynamics in larger water clusters than previously anticipated. A two-color classification of these hydrogen bonds leads to an extended mechanism for proton mobility.