New Type of Phase Transformation in Gas Hydrate Forming System at High Pressures. Some Experimental and Computational Investigations of Clathrate Hydrates Formed in the SF<sub>6</sub>−H<sub>2</sub>O System

Ey, Aladko; Анчаров, А. И.; Sv, Goryainov; Kurnosov, AV; Eg, Larionov; Ay, Likhacheva; Ay, Manakov; Потемкин, В. А.; Ma, Sheromov; Ae, Teplykh; Vi, Voronin; Fv, Zhurko

doi:10.1021/jp061698r

Cited by 21 publications

(17 citation statements)

References 43 publications

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“…The conformational search of the peptides has been performed within MulgiGen algorithm using combined MM3/ MERA force field with continual account of solvent (Potemkin et al, 2002;Aladko et al, 2006). Calculation of surface has been made according to Connolly algorithm (Connolly, 1983(Connolly, , 1985.…”

Section: Methodsmentioning

confidence: 99%

Mutations in fd phage major coat protein modulate affinity of the displayed peptide

Kuzmicheva

Jayanna

Eroshkin

et al. 2009

Protein Engineering Design and Selection

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Multibillion-clone libraries of phages displaying guest peptides fused to the major coat protein pVIII (landscape libraries) are a rich source of probes for proteinaceous and non-proteinaceous targets. As opposed to the pIII-type fusion phages, which display peptides as independent structural domains, the guest peptides in the pVIII-fusion phages can be structurally and functionally influenced by contiguous subunits. To decipher the impact of the locale of a guest peptide on its affinity characteristics, we constructed a library of phages carrying beta-galactosidase-binding peptide ADTFAKSMQ at the N-terminus of the pVIII protein surrounded by random amino acids. It was found that mutagenesis of amino acids 12-19 (domain C) has polar effects on target binding affinity of the displayed peptide. The phages with highest affinity are characterized by: (i) a net electrostatic charge around -1 of domain C of the mutated phages at pH 7.0; (ii) a lower radius of cylinder coaxial to alpha-helix formed by domain C; (iii) a lower higher occupied molecular orbital (HOMO) of domain C leading to a decreased formation of hydrogen bonds and (iv) positively charged surface and torsion energy of domain C, which may require a conformational transition of N-terminal peptide ADTFAKSMQ for its binding with beta-galactosidase. Influence of the guest peptide on the diversity of mutations in the neighboring landscape area was also observed.

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Section: Methodsmentioning

confidence: 99%

Mutations in fd phage major coat protein modulate affinity of the displayed peptide

Kuzmicheva

Jayanna

Eroshkin

et al. 2009

Protein Engineering Design and Selection

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“…Manakov et al have found two new hydrates in the THF-water system above 0.25 and 0.49 GPa, respectively, and dissociation into THF and water at 3 GPa, 67 but there is to date no structural characterisation. Aladko et al 68 and Dyadin et al 69 have studied the dissociation curve of the SF 6 -water system using DTA and found evidence for two new hydrates. Using X-ray diffraction techniques, they showed that the first transition at 0.05 GPa is a change from CS-II to CS-I.…”

Section: Other Simple Molecular Hydratesmentioning

confidence: 99%

“…The second transition at 0.13 GPa is isostructural and involves population of the small cage with guest species, as shown by neutron diffraction studies at 0.9 GPa. 68,69 Based on Raman data they argued that no further structural transitions occur at higher pressures but found evidence for dissociation into ice and SF 6 at 4.4 GPa. 68,69 There has also been work on these hydrates at low temperatures (77 K).…”

Section: Other Simple Molecular Hydratesmentioning

confidence: 99%

High-pressure gas hydrates

Loveday

Nelmes

2008

Phys. Chem. Chem. Phys.

159

209

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It has long been known that crystalline hydrates are formed by many simple gases that do not interact strongly with water, and in most cases the gas molecules or atoms occupy 'cages' formed by a framework of water molecules. The majority of these gas hydrates adopt one of two cubic cage structures and are called clathrate hydrates. Notable exceptions are hydrogen and helium which form 'exotic' hydrates with structures based on ice structures, rather than clathrate hydrates, even at low pressures. Clathrate hydrates have been extensively studied because they occur widely in nature, have important industrial applications, and provide insight into water-guest hydrophobic interactions. Until recently, the expectation-based on calculations-had been that all clathrate hydrates were dissociated into ice and gas by the application of pressures of 1 GPa or so. However, over the past five years, studies have shown that this view is incorrect. Instead, all the systems so far studied undergo structural rearrangement to other, new types of hydrate structure that remain stable to much higher pressures than had been thought possible. In this paper we review work on gas hydrates at pressures above 0.5 GPa, identify common trends in transformations and structures, and note areas of uncertainty where further work is needed.

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“…[59] Under these conditions, a weak effect of the nature of guest molecule on compressibility (bulk modulus) of the gas hydrate appears to be reasonable. On the other hand, in the case of the high-pressure hydrate of SF 6 (CS-I) [60,61] and the hydrate of CCl 4 (CS-II) existing at atmospheric pressure, [62] guest molecules are in close contact with the atoms of the framework or with the guest molecules occupying neighboring cavities. In these cases, one may expect substantially smaller hydrate compressibilities in comparison with the values given above.…”

mentioning

confidence: 99%

“…In these cases, one may expect substantially smaller hydrate compressibilities in comparison with the values given above. Data available on the hydrate of SF 6 (CS-I) [60] show that the compression curve is not described by Equation (2); in this situation, the slope of the compression curve to the pressure axis rapidly decreases as the pressure increase.…”

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confidence: 99%

Compressibility of Gas Hydrates

Manakov¹,

Likhacheva²,

Потемкин³

et al. 2011

ChemPhysChem

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Experimental data on the pressure dependence of unit cell parameters for the gas hydrates of ethane (cubic structure I, pressure range 0-2 GPa), xenon (cubic structure I, pressure range 0-1.5 GPa) and the double hydrate of tetrahydrofuran+xenon (cubic structure II, pressure range 0-3 GPa) are presented. Approximation of the data using the cubic Birch-Murnaghan equation, P=1.5B(0)[(V(0)/V)(7/3)-(V(0)/V)(5/3)], gave the following results: for ethane hydrate V(0)=1781 Å(3) , B(0)=11.2 GPa; for xenon hydrate V(0)=1726 Å(3) , B(0)=9.3 GPa; for the double hydrate of tetrahydrofuran+xenon V(0)=5323 Å(3) , B(0)=8.8 GPa. In the last case, the approximation was performed within the pressure range 0-1.5 GPa; it is impossible to describe the results within a broader pressure range using the cubic Birch-Murnaghan equation. At the maximum pressure of the existence of the double hydrate of tetrahydrofuran+xenon (3.1 GPa), the unit cell volume was 86% of the unit cell volume at zero pressure. Analysis of the experimental data obtained by us and data available from the literature showed that 1) the bulk modulus of gas hydrates with classical polyhedral structures, in most cases, are close to each other and 2) the bulk modulus is mainly determined by the elasticity of the hydrogen-bonded water framework. Variable filling of the cavities with guest molecules also has a substantial effect on the bulk modulus. On the basis of the obtained results, we concluded that the bulk modulus of gas hydrates with classical polyhedral structures and existing at pressures up to 1.5 GPa was equal to (9±2) GPa. In cases when data on the equations of state for the hydrates were unavailable, the indicated values may be recommended as the most probable ones.

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New Type of Phase Transformation in Gas Hydrate Forming System at High Pressures. Some Experimental and Computational Investigations of Clathrate Hydrates Formed in the SF₆−H₂O System

Cited by 21 publications

References 43 publications

Mutations in fd phage major coat protein modulate affinity of the displayed peptide

Mutations in fd phage major coat protein modulate affinity of the displayed peptide

High-pressure gas hydrates

Compressibility of Gas Hydrates

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New Type of Phase Transformation in Gas Hydrate Forming System at High Pressures. Some Experimental and Computational Investigations of Clathrate Hydrates Formed in the SF6−H2O System

Cited by 21 publications

References 43 publications

Mutations in fd phage major coat protein modulate affinity of the displayed peptide

Mutations in fd phage major coat protein modulate affinity of the displayed peptide

High-pressure gas hydrates

Compressibility of Gas Hydrates

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Product

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New Type of Phase Transformation in Gas Hydrate Forming System at High Pressures. Some Experimental and Computational Investigations of Clathrate Hydrates Formed in the SF₆−H₂O System