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Stoppleman JP, McDaniel JG, Cicerone MT. Excitations follow (or lead?) density scaling in propylene carbonate. J Chem Phys 2022; 157:204506. [DOI: 10.1063/5.0123444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Structural excitations that enable interbasin (IB) barrier crossings on a potential energy landscape are thought to play a facilitating role in the relaxation of liquids. Here, we show that the population of these excitations exhibits the same density scaling observed for α relaxation in propylene carbonate, even though they are heavily influenced by intramolecular modes. We also find that IB crossing modes exhibit a Gr[Formula: see text]neisen parameter ( γ G) that is approximately equivalent to the density scaling parameter γ TS. These observations suggest that the well-documented relationship between γ G and γ TS may be a direct result of the pressure dependence of the frequency of unstable (relaxation) modes associated with IB motion.
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Affiliation(s)
- John P. Stoppleman
- Department of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, USA,
| | - Jesse G. McDaniel
- Department of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, USA,
| | - Marcus T. Cicerone
- Department of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, USA,
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2
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Torii H. Intermolecular charge fluxes and far-infrared spectral intensities of liquid formamide. Phys Chem Chem Phys 2018; 20:3029-3039. [DOI: 10.1039/c7cp02644g] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Intermolecular charge fluxes induced by hydrogen-bond length modulations occurring upon molecular librations lead to intensity enhancement of the far-infrared spectrum.
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Affiliation(s)
- Hajime Torii
- Department of Chemistry
- Faculty of Education, and Department of Optoelectronics and Nanostructure Science
- Graduate School of Science and Technology
- Shizuoka University
- Shizuoka 422-8529
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3
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Mukherjee K, Das A, Choudhury S, Barman A, Biswas R. Dielectric Relaxations of (Acetamide + Electrolyte) Deep Eutectic Solvents in the Frequency Window, 0.2 ≤ ν/GHz ≤ 50: Anion and Cation Dependence. J Phys Chem B 2015; 119:8063-71. [DOI: 10.1021/acs.jpcb.5b01502] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Kallol Mukherjee
- Chemical, Biological
and Macromolecular Sciences (CBMS), and ‡Condensed Matter
Physics and Material Sciences (CMPMS), S. N. Bose National Centre for Basic Sciences, JD Block, Sector III, Salt Lake, Kolkata 700098, India
| | - Anuradha Das
- Chemical, Biological
and Macromolecular Sciences (CBMS), and ‡Condensed Matter
Physics and Material Sciences (CMPMS), S. N. Bose National Centre for Basic Sciences, JD Block, Sector III, Salt Lake, Kolkata 700098, India
| | - Samiran Choudhury
- Chemical, Biological
and Macromolecular Sciences (CBMS), and ‡Condensed Matter
Physics and Material Sciences (CMPMS), S. N. Bose National Centre for Basic Sciences, JD Block, Sector III, Salt Lake, Kolkata 700098, India
| | - Anjan Barman
- Chemical, Biological
and Macromolecular Sciences (CBMS), and ‡Condensed Matter
Physics and Material Sciences (CMPMS), S. N. Bose National Centre for Basic Sciences, JD Block, Sector III, Salt Lake, Kolkata 700098, India
| | - Ranjit Biswas
- Chemical, Biological
and Macromolecular Sciences (CBMS), and ‡Condensed Matter
Physics and Material Sciences (CMPMS), S. N. Bose National Centre for Basic Sciences, JD Block, Sector III, Salt Lake, Kolkata 700098, India
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4
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Processing of protease under sub- and supercritical conditions for activity and stability enhancement. Biochem Eng J 2014. [DOI: 10.1016/j.bej.2014.06.021] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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5
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Treatment of immobilized α-amylase under supercritical CO2 conditions: Can activity be enhanced after consecutive enzymatic reactions? ACTA ACUST UNITED AC 2013. [DOI: 10.1016/j.molcatb.2013.03.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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6
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7
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High pressure stabilization of collagen structure. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2009; 1794:1151-8. [DOI: 10.1016/j.bbapap.2009.04.005] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2008] [Revised: 03/31/2009] [Accepted: 04/06/2009] [Indexed: 11/20/2022]
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8
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Kashyap HK, Pradhan T, Biswas R. Limiting ionic conductivity and solvation dynamics in formamide. J Chem Phys 2006; 125:174506. [PMID: 17100453 DOI: 10.1063/1.2387947] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
A self-consistent microscopic theory has been used to calculate the limiting ionic conductivity of unipositive rigid ions in formamide at different temperatures. The calculated results are found to be in good agreement with the experimental data. The above theory can also predict successfully the experimentally observed temperature dependence of total ionic conductivity of a given uniunivalent electrolyte in formamide. The effects of dynamic polar solvent response on ionic conductivity have been investigated by studying the time dependent progress of solvation of a polarity probe dissolved in formamide. The intermolecular vibration (libration) band that is often detected in the range of 100-200 cm(-1) in formamide is found to play an important role in determining both the conductivity and the ultrafast polar solvent response in formamide. The time dependent decay of polar solvation energy in formamide has been studied at three different temperatures, namely, at 283.15, 298.15, and 328.15 K. While the predicted decay at 298.15 K is in good agreement with the available experimental data, the calculated results at the other two temperatures should be tested against experiments.
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Affiliation(s)
- Hemant K Kashyap
- S. N. Bose National Centre for Basic Sciences, JD Block, Sector III, Salt Lake, Kolkata 700 098, India
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9
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McCarthy AN, Grigera JR. Effect of pressure on the conformation of proteins. A molecular dynamics simulation of lysozyme. J Mol Graph Model 2006; 24:254-61. [PMID: 16243554 DOI: 10.1016/j.jmgm.2005.09.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2005] [Revised: 09/18/2005] [Accepted: 09/20/2005] [Indexed: 11/22/2022]
Abstract
The effect of pressure on the structure and mobility of lysozyme was studied by molecular dynamics computer simulation at 1 and 3 kbar (1 atm = 1.01325 bar = 101.325 kPa). The results have good agreement with the available experimental data, allowing the analysis of other features of the effect of pressure on the protein solution. The studies of mobility show that although the general mobility is restricted under pressure this is not true for some particular residues. From the analysis of secondary structure along the trajectories it is observed that the conformation under pressure is more stable, suggesting that pressure acts as a 'conformer selector' on the protein. The difference in solvent-accessed surface (SAS) with pressure shows a clear inversion of the hydrophilic/hydrophobic SAS ratio, which consequently shows that the hydrophobic interaction is considerably weaker under high hydrostatic pressure conditions.
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Affiliation(s)
- Andrés N McCarthy
- Instituto de Física de Líquidos y Sistemas Biológicos (IFLYSIB), CONICET-UNLP-CIC, La Plata, Argentina
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10
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Boonyaratanakornkit BB, Park CB, Clark DS. Pressure effects on intra- and intermolecular interactions within proteins. BIOCHIMICA ET BIOPHYSICA ACTA 2002; 1595:235-49. [PMID: 11983399 DOI: 10.1016/s0167-4838(01)00347-8] [Citation(s) in RCA: 275] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The effects of pressure on protein structure and function can vary dramatically depending on the magnitude of the pressure, the reaction mechanism (in the case of enzymes), and the overall balance of forces responsible for maintaining the protein's structure. Interactions between the protein and solvent are also critical in determining the response of a protein to pressure. Pressure has long been recognized as a potential denaturant of proteins, often promoting the disruption of multimeric proteins, but recently examples of pressure-induced stabilization have also been reported. These global effects can be explained in terms of pressure effects on individual molecular interactions within proteins, including hydrophobic, electrostatic, and van der Waals interactions, which can now be studied in greater detail than ever before. However, many uncertainties remain, and thorough descriptions of how proteins respond to pressure remain elusive. This review summarizes basic concepts and new findings related to pressure effects on intra- and intermolecular interactions within proteins and protein complexes, and discusses their implications for protein structure-function relationships under pressure.
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11
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Shirota H, Castner EW. Ultrafast dynamics in aqueous polyacrylamide solutions. J Am Chem Soc 2001; 123:12877-85. [PMID: 11749546 DOI: 10.1021/ja010290z] [Citation(s) in RCA: 77] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We have investigated the ultrafast dynamics of aqueous polyacrylamide ([-CH(2)CH(CONH(2))-](n), or PAAm) solutions using femtosecond optical heterodyne-detected Raman-induced Kerr effect spectroscopy (OHD-RIKES). The observed aqueous PAAm dynamics are nearly identical for both M(w) = 1500 and 10 000. Aqueous propionamide (CH(3)CH(2)CONH(2), or PrAm) solutions were also studied, because PrAm is an exact model for the PAAm constitutional repeat unit (CRU). The longest time scale dynamics observed for both aqueous PAAm and PrAm solutions occur in the 4-10 ps range. Over the range of concentrations from 0 to 40 wt %, the picosecond reorientation time constants for the aqueous PAAm and PrAm solutions scale linearly with the solution concentration, despite the fact that the solution shear viscosities vary exponentially from 1 to 264 cP. For a given value of solution concentration in weight percent, constant ratios of measured reorientation time constants for PAAm to PrAm are obtained. This ratio of PAAm to PrAm reorientation time constants is equal to the ratio of the volume for the PAAm constitutional repeat unit (-CH(2)CHCONH(2)-) to the molecular volume of PrAm. For these reasons, we assign the polymer reorientation dynamics to motions of the entire constitutional repeat unit, not only side group motions. Simple molecular dynamics simulations of H[-CH(2)CH(CONH(2))-](7)H in a periodic box with 180 water molecules support this assignment. Amide-amide and amide-water hydrogen-bonding interactions lead to strongly oscillatory femtosecond dynamics in the Kerr transients, peaking at 80, 410, and 750 fs.
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Affiliation(s)
- H Shirota
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 610 Taylor Road, Piscataway, NJ 08854-8087, USA.
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Hansen MJ, Wendt MA, Farrar TC. Temperature Dependence of the Deuterium Quadrupole Coupling Constants and the Correlation Times for Neat Formamide. J Phys Chem A 2000. [DOI: 10.1021/jp000004q] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Mary J. Hansen
- Department of Chemistry, University of WisconsinMadison, 1101 University Avenue, Madison, Wisconsin 53706
| | - Mark A. Wendt
- Department of Chemistry, University of WisconsinMadison, 1101 University Avenue, Madison, Wisconsin 53706
| | - Thomas C. Farrar
- Department of Chemistry, University of WisconsinMadison, 1101 University Avenue, Madison, Wisconsin 53706
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13
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Loughnane BJ, Scodinu A, Farrer RA, Fourkas JT, Mohanty U. Exponential intermolecular dynamics in optical Kerr effect spectroscopy of small-molecule liquids. J Chem Phys 1999. [DOI: 10.1063/1.479544] [Citation(s) in RCA: 122] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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14
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Weemaes C, de Cordt S, Goossens K, Ludikhuyze L, Hendrickx M, Heremans K, Tobback P. High pressure, thermal, and combined pressure–temperature stabilities of α-amylases fromBacillus species. Biotechnol Bioeng 1996; 50:49-56. [DOI: 10.1002/(sici)1097-0290(19960405)50:1<49::aid-bit6>3.0.co;2-1] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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15
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Goossens K, Smeller L, Frank J, Heremans K. Pressure-tuning the conformation of bovine pancreatic trypsin inhibitor studied by Fourier-transform infrared spectroscopy. EUROPEAN JOURNAL OF BIOCHEMISTRY 1996; 236:254-62. [PMID: 8617273 DOI: 10.1111/j.1432-1033.1996.00254.x] [Citation(s) in RCA: 66] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
A hydrostatic pressure of 1.5 GPa induces changes in the secondary structure of bovine pancreatic trypsin inhibitor (BPTI) as revealed by the analysis of the amide I' band with Fourier-transform infrared (FTIR) spectroscopy in the diamond anvil cell. The features of the secondary structure remain distinct at high pressure suggesting that the protein does not unfold. The fitted percentages of the secondary structure elements during compression and decompression strongly suggest that the pressure-induced changes are reversible. The pressure-induced changes in the tyrosine side chain band are also reversible. The results demonstrate that the infrared technique explores different aspects of the behaviour of proteins in comparison with two published molecular dynamics studies performed up to 1 GPa [Kitchen, D.B., Reed, L.H. & Levy, R.M.(1992) Biochemistry 31, 10083-10093] and 500 MPa [Brunne, R.M. & van Gunsteren, W.F.(1993) FEBS Lett. 323, 215-217]. A possible explanation for the difference is the time scale of the experiments.
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Affiliation(s)
- K Goossens
- Department of Chemistry, Katholieke Universiteit Leuven, Belgium
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17
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Abstract
Many biochemists would regard pressure as a physical parameter mainly of theoretical interest and of rather limited value in experimental biochemistry. The goal of this overview is to show that pressure is a powerful tool for the study of proteins and modulation of enzymatic activity.
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Affiliation(s)
- V V Mozhaev
- Institut National de la Santé et de la Recherche Médicale, INSERM U 128, Montpellier, France
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