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Sentell Z, Spooner J, Weinberg N. Molecular Dynamics Calculations of Partial Molar Volumes of Amino Acids in Aqueous Solutions. CAN J CHEM 2022. [DOI: 10.1139/cjc-2021-0217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Partial molar volumes of amino acids in their zwitterionic and molecular forms have been calculated using molecular dynamics simulations of these systems in aqueous solutions. Calculations performed with the TIP4P, SPC (rigid and flexible), SPC/E, and polarizable water models show that the choice of water model can have a significant impact on the calculated volumes. The effect of treatment of long-range electrostatic interactions on the calculated results was also investigated. Volumes obtained in simulations with a properly chosen water model fit well the experimental data for both molecular and zwitterionic forms of amino acids.
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Affiliation(s)
- Zachary Sentell
- University of the Fraser Valley, 1011, Department of Chemistry, Abbotsford, Canada
| | - Jacob Spooner
- University of the Fraser Valley, 1011, Department of Chemistry, Abbotsford, Canada, V2S 7M8
| | - Noham Weinberg
- University of the Fraser Valley, 1011, Department of Chemistry, Abbotsford, Canada, V2S 7M8
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Spooner J, Wiebe H, Louwerse M, Reader B, Weinberg N. Theoretical analysis of high-pressure effects on conformational equilibria. CAN J CHEM 2018. [DOI: 10.1139/cjc-2017-0411] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Along with temperature, pressure is the most important physical parameter determining the thermodynamic properties and reactivity of chemical systems. In this work, we discuss the effects of high pressure on conformational properties of organic molecules and propose an approach toward calculation of conformational volume changes based on molecular dynamics simulations. The results agree well with the experimental data. Furthermore, we demonstrate that pressure can be used as an instrument for fine-tuning of molecular conformations and to propel a properly constructed molecular rotor possessing a suitable combination of energy and volume profiles.
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Affiliation(s)
- Jacob Spooner
- Department of Chemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | - Heather Wiebe
- Department of Chemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | - Miranda Louwerse
- Department of Chemistry, University of the Fraser Valley, Abbotsford, BC V2S 7M8, Canada
| | - Brandon Reader
- Department of Chemistry, University of the Fraser Valley, Abbotsford, BC V2S 7M8, Canada
| | - Noham Weinberg
- Department of Chemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
- Department of Chemistry, University of the Fraser Valley, Abbotsford, BC V2S 7M8, Canada
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Wiebe H, Louwerse M, Weinberg N. Theoretical volume profiles for conformational changes: Application to internal rotation of benzene ring in 1,12-dimethoxy-[12]-paracyclophane. J Chem Phys 2017; 146:104107. [DOI: 10.1063/1.4977732] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Affiliation(s)
- Heather Wiebe
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Miranda Louwerse
- Department of Chemistry, University of the Fraser Valley, Abbotsford, British Columbia V2S 7M8, Canada
| | - Noham Weinberg
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
- Department of Chemistry, University of the Fraser Valley, Abbotsford, British Columbia V2S 7M8, Canada
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Pagliai M, Cardini G, Cammi R. Vibrational Frequencies of Fullerenes C60 and C70 under Pressure Studied with a Quantum Chemical Model Including Spatial Confinement Effects. J Phys Chem A 2014; 118:5098-111. [DOI: 10.1021/jp504173k] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Marco Pagliai
- Dipartimento di Chimica “Ugo Schiff”, Università degli Studi di Firenze, via della Lastruccia 3, 50019 Sesto Fiorentino, Florence, Italy
| | - Gianni Cardini
- Dipartimento di
Chimica “Ugo Schiff”, Università degli Studi di Firenze, via della Lastruccia 3, 50019 Sesto Fiorentino, Florence, Italy
| | - Roberto Cammi
- Dipartimento di Chimica, Università degli Studi di Parma, Parco Area delle
Scienze 17/A, 43124 Parma, Italy
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