Browse
Submit Data
Databases
API
Help

Dataset Information

14 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Comparative Analysis of the Hydrogen Bond Vibrations of Ice XII.

ABSTRACT: It is difficult to theoretically study the vibrational spectrum of hydrogen-disordered ice XII compared with its hydrogen-ordered counterpart, ice XIV. We constructed a 24-molecule supercell of ice XII to mimic its real structure. We focused on hydrogen bond (HB) vibrational modes in the translation band using first-principles density functional theory (DFT). Our simulated results were in good agreement with inelastic neutron scattering experiments. We found that the optical vibrational modes of HBs are composed of three main components. These are cluster vibrations in the lowest-frequency region, four-bond HB vibrations in the highest-frequency region, and two-bond modes in between. Although the experimentally recorded curve of ice XII is smooth in the translation region, our results support the proposal that two types of intrinsic HB vibrational modes are common in the ice family.

SUBMITTER: Yuan XQ

PROVIDER: S-EPMC8792919 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Comparative Analysis of Hydrogen-Bonding Vibrations of Ice VI.

Project description:It is difficult to investigate the hydrogen-bonding dynamics of hydrogen-disordered ice VI. Here, we present a comparative method based on our previous study of its counterpart hydrogen-ordered phase, ice XV. The primitive cell of ice XV is a 10 molecule unit, and the vibrational normal modes were analyzed individually. We constructed an 80 molecule supercell of ice VI to mimic the periodic unit and performed first-principles density functional theory calculations. As the two vibrational spectra show almost identical features, we compared the molecular translation vibrations. Inspired by the phonon analysis of ice XV, we found that the vibrational modes in the translation band of ice VI are classifiable into three groups. The lowest-strength vibration modes represent vibrations between two sublattices that lack hydrogen bonding. The highest-strength vibration modes represent the vibration of four hydrogen bonds of one molecule. The middle-strength vibration modes mainly represent the molecular vibrations of only two hydrogen bonds. Although there are many overlapping stronger and middle modes, there are only two main peaks in the inelastic neutron scattering (INS) spectra. This work explains the origin of the two main peaks in the far-infrared region of ice VI and illustrates how to analyze a hydrogen-disordered ice structure.

| S-EPMC8190920 | biostudies-literature

Hydrogen-bond potential for ice VIII-X phase transition.

Project description:Repulsive force between the O-H bonding electrons and the O:H nonbonding pair within hydrogen bond (O-H:O) is an often overlooked interaction which dictates the extraordinary recoverability and sensitivity of water and ice. Here, we present a potential model for this hidden force opposing ice compression of ice VIII-X phase transition based on the density functional theory (DFT) and neutron scattering observations. We consider the H-O bond covalent force, the O:H nonbond dispersion force, and the hidden force to approach equilibrium under compression. Due to the charge polarization within the O:H-O bond, the curvatures of the H-O bond and the O:H nonbond potentials show opposite sign before transition, resulting in the asymmetric relaxation of H-O and O:H (O:H contraction and H-O elongation) and the H+ proton centralization towards phase X. When cross the VIII-X phase boundary, both H-O and O:H contract slightly. The potential model reproduces the VIII-X phase transition as observed in experiment. Development of the potential model may provide a choice for further calculations of water anomalies.

| S-EPMC5107924 | biostudies-literature

Spectroscopic Identification of Hydrogen Bond Vibrations and Quasi-Isostructural Polymorphism in N-Salicylideneaniline.

Project description:The ortho-hydroxy aryl Schiff base 2-[(E)-(phenylimino)methyl]phenol and its deutero-derivative have been studied by the inelastic incoherent neutron scattering (IINS), infrared (IR) and Raman experimental methods, as well as by Density Functional Theory (DFT) and Density-Functional Perturbation Theory (DFPT) simulations. The assignments of vibrational modes within the 3500-50 cm-1 spectral region made it possible to state that the strong hydrogen bond in the studied compound can be classified as the so-called quasi-aromatic bond. The isotopic substitution supplemented by the results of DFT calculations allowed us to identify vibrational bands associated with all five major hydrogen bond vibrations. Quasi-isostructural polymorphism of 2-[(E)-(phenylimino)methyl]phenol (SA) and 2-[(E)-(phenyl-D5-imino)methyl]phenol (SA-C6D5) has been studied by powder X-ray diffraction in the 20-320 K temperature range.

| S-EPMC8401763 | biostudies-literature

Ice Regelation: Hydrogen-bond extraordinary recoverability and water quasisolid-phase-boundary dispersivity.

Project description:Regelation, i.e., ice melts under compression and freezes again when the pressure is relieved, remains puzzling since its discovery in 1850's by Faraday. Here we show that hydrogen bond (O:H-O) cooperativity and its extraordinary recoverability resolve this anomaly. The H-O bond and the O:H nonbond possesses each a specific heat ηx(T/ΘDx) whose Debye temperature ΘDx is proportional to its characteristic phonon frequency ωx according to Einstein's relationship. A superposition of the ηx(T/ΘDx) curves for the H-O bond (x=H, ωH~3200 cm(-1)) and the O:H nonbond (x=L, ωL~200 cm(-1), ΘDL=198 K) yields two intersecting temperatures that define the liquid/quasisolid/solid phase boundaries. Compression shortens the O:H nonbond and stiffens its phonon but does the opposite to the H-O bond through O-O Coulomb repulsion, which closes up the intersection temperatures and hence depress the melting temperature of quasisolid ice. Reproduction of the Tm(P) profile clarifies that the H-O bond energy EH determines the Tm with derivative of EH=3.97 eV for bulk water and ice. Oxygen atom always finds bonding partners to retain its sp3-orbital hybridization once the O:H breaks, which ensures O:H-O bond recoverability to its original state once the pressure is relieved.

| S-EPMC4563362 | biostudies-literature

Computational Analysis of Exotic Molecular and Atomic Vibrations in Ice XV.

Project description:It is always difficult to assign the peaks of a vibrational spectrum in the far-infrared region. The two distinct peaks seen in many ice phases are still a mystery to date. The normal modes of ice XV were calculated using the CASTEP code based on first-principles density functional theory. On the basis of vibrational modes analysis, we divided the translational modes into three categories: four-bond vibrations, which have the highest energy levels; two-bond vibrations, which have medium levels of energy; and relative vibrations between two sublattices, which have the lowest energy. Whale et al. found that some intramolecular stretching modes include the isolated vibration of only one O-H bond, whereas the others do not vibrate in ice XV. We verified this phenomenon in this study and attributed it to local tetrahedral deformation. Analysis of normal modes, especially in the translation and stretching band of ice XV, clarified the physical insights of the vibrational spectrum and can be used with other ice phases.

| S-EPMC6749349 | biostudies-literature

The normal modes of lattice vibrations of ice XI.

Project description:The vibrational spectrum of ice XI at thermal wavelengths using the CASTEP code, a first-principles simulation method, is investigated. A dual-track approach is constructed to verify the validity for the computational phonon spectrum: collate the simulated spectrum with inelastic neutron scattering experiments and assign the photon scattering peaks according to the calculated normal vibration frequencies. The 33 optical normal vibrations at the Brillouin center are illustrated definitely from the ab initio outcomes. The depolarizing field effect of the hydrogen bond vibrations at frequencies of 229?cm(-1) and 310?cm(-1) is found to agree well with the LST relationship. It is a convincing evidence to manifest the LO-TO splitting of hydrogen bonds in ice crystal. We attribute the two hydrogen bond peaks to the depolarization effect and apply this viewpoint to ordinary ice phase, ice Ih, which is difficult to analyse their vibration modes due to proton disorder.

| S-EPMC4931684 | biostudies-literature

Computing Investigations of Molecular and Atomic Vibrations of Ice IX.

Project description:The normal modes of ice IX were investigated using the CASTEP code package, which is based on density functional theory. We found that the translational modes could be divided into three categories: four-bond vibrations, which possessed the highest energy; two-bond vibrations, which possessed the medium energy; and cluster vibrations with the lowest energy. The former two categories represent monomers vibrating against neighbors and present as two distinct peaks in many ice phases recorded in inelastic neutron-scattering experiments. It is typically difficult to assign the molecular vibration peaks in the far infrared region. The method we developed to analyze the normal modes, especially in the translation band of ice IX, provided physical insights into the vibrational spectrum of ice.

| S-EPMC6854819 | biostudies-literature

New insights into protein-DNA binding specificity from hydrogen bond based comparative study.

Project description:Knowledge of protein-DNA binding specificity has important implications in understanding DNA metabolism, transcriptional regulation and developing therapeutic drugs. Previous studies demonstrated hydrogen bonds between amino acid side chains and DNA bases play major roles in specific protein-DNA interactions. In this paper, we investigated the roles of individual DNA strands and protein secondary structure types in specific protein-DNA recognition based on side chain-base hydrogen bonds. By comparing the contribution of each DNA strand to the overall binding specificity between DNA-binding proteins with different degrees of binding specificity, we found that highly specific DNA-binding proteins show balanced hydrogen bonding with each of the two DNA strands while multi-specific DNA binding proteins are generally biased towards one strand. Protein-base pair hydrogen bonds, in which both bases of a base pair are involved in forming hydrogen bonds with amino acid side chains, are more prevalent in the highly specific protein-DNA complexes than those in the multi-specific group. Amino acids involved in side chain-base hydrogen bonds favor strand and coil secondary structure types in highly specific DNA-binding proteins while multi-specific DNA-binding proteins prefer helices.

| S-EPMC6868434 | biostudies-literature

Exotic Spectra and Lattice Vibrations of Ice X Using the DFT Method.

Project description:A typical vibrational spectrum in the ice phase has four separate bands: Translation, libration, bending, and stretching. Ice X, the final ice phase under high pressure, shows an exotic vibrational spectrum. Based on harmonic approximation, an ideal crystal of ice X has one peak, at 998 cm-1, for Raman scattering and two peaks, at 450 cm-1 and 1507 cm-1, for infrared absorption in this work. These three characteristic peaks are indicators of the phase transition between ice VII and VIII and ice X. Despite many experimental and theoretical works on ice X, only this study has clearly indicated these characteristic peaks in the region of the IR band. The phonon density of states shows quite different features than ice VIII, which could be verified by inelastic neutron scattering in the future. The dynamic processes of 15 vibrational normal modes are discussed and the typical hydrogen bonds are missing.

| S-EPMC6278396 | biostudies-literature

Structures, dynamics, and hydrogen-bond interactions of antifreeze proteins in TIP4P/Ice water and their dependence on force fields.

Project description:Tenebrio molitor antifreeze protein (TmAFP) was simulated with growing ice-water interfaces at a realistic melting temperature using TIP4P/Ice water model. To test compatibility of protein force fields (FFs) with TIP4P/Ice water, CHARMM, AMBER, and OPLS FFs were applied. CHARMM and AMBER FFs predict more ?-sheet structure and lower diffusivity of TmAFP at the ice-water interface than does OPLS FF, indicating that ?-sheet structure is important for the TmAFP-interface binding and antifreeze activity. In particular, CHARMM FF more clearly distinguishes the strengths of hydrogen bonds in the ice-binding and non-ice-binding sites of TmAFP than do other FFs, in agreement with experiments, implying that CHARMM FF can be a reasonable choice to simulate proteins with TIP4P/Ice water. Simulations of mutated TmAFPs show that for the same density of Thr residues, continuous arrangement of Thr with the distance of 0.4~0.6 nm induces the higher extent of antifreeze activity than does intermittent arrangement of Thr with larger distances. These findings suggest the choice of CHARMM FF for AFP-TIP4P/Ice simulations and help explain the relationship between Thr-residue arrangement and antifreeze activity.

| S-EPMC5991737 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data