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Stare J, Mavri J, Grdadolnik J, Zidar J, Maksić ZB, Vianello R. Hydrogen Bond Dynamics of Histamine Monocation in Aqueous Solution: Car–Parrinello Molecular Dynamics and Vibrational Spectroscopy Study. J Phys Chem B 2011; 115:5999-6010. [DOI: 10.1021/jp111175e] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Jernej Stare
- National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia
| | - Janez Mavri
- National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia
- EN→FIST Centre of Excellence, Dunajska 156, SI-1000 Ljubljana, Slovenia
| | - Jože Grdadolnik
- National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia
- EN→FIST Centre of Excellence, Dunajska 156, SI-1000 Ljubljana, Slovenia
| | - Jernej Zidar
- National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia
- EN→FIST Centre of Excellence, Dunajska 156, SI-1000 Ljubljana, Slovenia
| | | | - Robert Vianello
- National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia
- Ruđer Bošković Institute, Bijenička cesta 54, HR-10000 Zagreb, Croatia
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Pirc G, Stare J, Mavri J. Car-Parrinello simulation of hydrogen bond dynamics in sodium hydrogen bissulfate. J Chem Phys 2010; 132:224506. [PMID: 20550407 DOI: 10.1063/1.3429251] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
We studied proton dynamics of a short hydrogen bond of the crystalline sodium hydrogen bissulfate, a hydrogen-bonded ferroelectric system. Our approach was based on the established Car-Parrinello molecular dynamics (CPMD) methodology, followed by an a posteriori quantization of the OH stretching motion. The latter approach is based on snapshot structures taken from CPMD trajectory, calculation of proton potentials, and solving of the vibrational Schrodinger equation for each of the snapshot potentials. The so obtained contour of the OH stretching band has the center of gravity at about 1540 cm(-1) and a half width of about 700 cm(-1), which is in qualitative agreement with the experimental infrared spectrum. The corresponding values for the deuterated form are 1092 and 600 cm(-1), respectively. The hydrogen probability densities obtained by solving the vibrational Schrodinger equation allow for the evaluation of potential of mean force along the proton transfer coordinate. We demonstrate that for the present system the free energy profile is of the single-well type and features a broad and shallow minimum near the center of the hydrogen bond, allowing for frequent and barrierless proton (or deuteron) jumps. All the calculated time-averaged geometric parameters were in reasonable agreement with the experimental neutron diffraction data. As the present methodology for quantization of proton motion is applicable to a variety of hydrogen-bonded systems, it is promising for potential use in computational enzymology.
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Affiliation(s)
- Gordana Pirc
- National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia
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Piccoli PMB, Koetzle TF, Schultz AJ, Zhurova EA, Stare J, Pinkerton AA, Eckert J, Hadzi D. Variable Temperature Neutron Diffraction and X-Ray Charge Density Studies of Tetraacetylethane. J Phys Chem A 2008; 112:6667-77. [DOI: 10.1021/jp800204r] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Paula M. B. Piccoli
- Intense Pulsed Neutron Source, Argonne National Laboratory, Argonne, Illinois 60439, Department of Chemistry, University of Toledo, Toledo, Ohio 43606, National Institute of Chemistry (KI), Hajdrihova 19, SI-1000, Ljubljana, Slovenia, and Materials Research Laboratory, University of California, Santa Barbara, California 93106
| | - Thomas F. Koetzle
- Intense Pulsed Neutron Source, Argonne National Laboratory, Argonne, Illinois 60439, Department of Chemistry, University of Toledo, Toledo, Ohio 43606, National Institute of Chemistry (KI), Hajdrihova 19, SI-1000, Ljubljana, Slovenia, and Materials Research Laboratory, University of California, Santa Barbara, California 93106
| | - Arthur J. Schultz
- Intense Pulsed Neutron Source, Argonne National Laboratory, Argonne, Illinois 60439, Department of Chemistry, University of Toledo, Toledo, Ohio 43606, National Institute of Chemistry (KI), Hajdrihova 19, SI-1000, Ljubljana, Slovenia, and Materials Research Laboratory, University of California, Santa Barbara, California 93106
| | - Elizabeth A. Zhurova
- Intense Pulsed Neutron Source, Argonne National Laboratory, Argonne, Illinois 60439, Department of Chemistry, University of Toledo, Toledo, Ohio 43606, National Institute of Chemistry (KI), Hajdrihova 19, SI-1000, Ljubljana, Slovenia, and Materials Research Laboratory, University of California, Santa Barbara, California 93106
| | - Jernej Stare
- Intense Pulsed Neutron Source, Argonne National Laboratory, Argonne, Illinois 60439, Department of Chemistry, University of Toledo, Toledo, Ohio 43606, National Institute of Chemistry (KI), Hajdrihova 19, SI-1000, Ljubljana, Slovenia, and Materials Research Laboratory, University of California, Santa Barbara, California 93106
| | - A. Alan Pinkerton
- Intense Pulsed Neutron Source, Argonne National Laboratory, Argonne, Illinois 60439, Department of Chemistry, University of Toledo, Toledo, Ohio 43606, National Institute of Chemistry (KI), Hajdrihova 19, SI-1000, Ljubljana, Slovenia, and Materials Research Laboratory, University of California, Santa Barbara, California 93106
| | - Juergen Eckert
- Intense Pulsed Neutron Source, Argonne National Laboratory, Argonne, Illinois 60439, Department of Chemistry, University of Toledo, Toledo, Ohio 43606, National Institute of Chemistry (KI), Hajdrihova 19, SI-1000, Ljubljana, Slovenia, and Materials Research Laboratory, University of California, Santa Barbara, California 93106
| | - Dusan Hadzi
- Intense Pulsed Neutron Source, Argonne National Laboratory, Argonne, Illinois 60439, Department of Chemistry, University of Toledo, Toledo, Ohio 43606, National Institute of Chemistry (KI), Hajdrihova 19, SI-1000, Ljubljana, Slovenia, and Materials Research Laboratory, University of California, Santa Barbara, California 93106
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