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Investigations of the Hydrogen Bonds and Vibrational Spectra of Clathrate Ice XVI

ABSTRACT: Natural gas hydrates are ice-like crystalline materials formed from natural gas and clathrate ice under high pressure and low temperature. Ice XVI, the first S-II type clathrate ice produced in the lab, was simulated by first-principles density functional theory with the CASTEP code. A 34-molecule supercell was built to mimic the hydrogen-disordered structure. The vibrational spectra were calculated as a reference for inelastic neutron scattering (INS), infrared (IR) absorption, and Raman scattering experiments. Two kinds of H-bond vibration modes corresponding to two different bond strengths were found in our previous studies. In this paper, the statistics of distribution calculated by integrating these two kinds of modes was found to match the phonon density of states (PDOS) very well. We confirmed that the two basic types of H-bonds also appeared in clathrate ice XVI. The typical normal modes were analyzed to illustrate the dynamic process of lattice vibrations.

SUBMITTER: Wang Z

PROVIDER: S-EPMC6356410 | biostudies-literature | 2019 Jan

REPOSITORIES: biostudies-literature

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Project description:Infrared photodissociation analyses are supported by theoretical calculations that allow a trustworthy interpretation of experimental spectra of gaseous ions. B3LYP calculations are the most prominent method used to model IR spectra, as detailed in our bibliographic survey. However, this and other commonly used methods are known to provide inaccurate energy values and geometries, especially when it comes to long-range interactions, such as intramolecular H-bonds, which show increased anharmonicity. Therefore, we evaluated some of the most commonly used density functional theory methods (B3LYP, CAM-B3LYP, and M06-2X) and basis sets (6-31+G(d,p), 6-311++G(d,p), 6-311++G(3df,2pd), aug-cc-pVDZ, and aug-cc-pVTZ), including anharmonicity and dispersion corrections. The results were compared to MP2 calculations and to experimental high-frequency (2000-4000 cm-1) IR multiphotonic dissociation (IRMPD) spectra of two protonated model molecules containing intramolecular hydrogen bonds: biotin and tryptophan. M06-2X/6-31+G(d,p) was shown to be the most cost-effective level of theory, whereas CAM-B3LYP was the most efficient method to describe the van der Waals interactions. The use of the dispersion correction D3, proposed by Grimme, improved the description of O-H vibrations involved in H-bonding but worsened the description of N-H stretches. Anharmonic calculations were shown to be extremely expensive when compared to other approaches. The efficiencies of well-established scaling factors (SFs) in opposition to sample-dependent SFs were also discussed and the use of fitted SFs were shown to be the most cost-effective approach to predict IRMPD spectra. M06-2X/6-31+G(d,p) and CAM-B3LYP/aug-cc-pVDZ were also tested against the fingerprint region. Our results suggest that these methods can also be used for analysis in this lower frequency range and should be regarded as the methods of choice for cost-effective IRMPD simulations rather than the ubiquitous B3LYP method, especially when further molecular properties are needed.

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Investigations of the Hydrogen Bonds and Vibrational Spectra of Clathrate Ice XVI

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