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Bajaj N, Bhatt H, Murli C, Vishwakarma SR, Chitra R, Ravindran TR, Deo MN. Perceptible isotopic effect in 3D-framework of α-glycine at low temperatures. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2018; 204:495-507. [PMID: 29975911 DOI: 10.1016/j.saa.2018.06.087] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 06/22/2018] [Accepted: 06/23/2018] [Indexed: 06/08/2023]
Abstract
Glycine, the most fundamental amino acid, albeit studied for many decades, has kept researchers captivated with interesting structural variations relevant to important biological, astrophysical and technological applications. We report here a noticeable effect of deuteration on the three dimensional hydrogen bonding network of α-glycine using low temperature infrared absorption studies in a wide spectral range, corroborated with Raman scattering studies. These systematic studies in the range 300-4.2 K have demonstrated a relatively compact assembly of glycine molecules in the three dimensional bilayered structure of hydrogenated glycine (gly-h) at low temperatures. This is inferred from a remarkable temperature effect in the weak intra-bilayer hydrogen bond ~ along the b-axis, which strengthens upon cooling. A pronounced increase in the intensity of NH3 torsional and NH stretching modes has been observed. This is accompanied with a large rate of stiffening and softening respectively of these modes upon cooling and a change in slope across 210 K and 80 K. In contrast, the D---O hydrogen bond lengths in fully deuterated isotope (gly-d), as estimated using empirical correlation, show that the weak intra-bilayer hydrogen bond is not strengthened upon cooling down to 180 K, whereas the stronger intra-layer hydrogen bonds in the ac-plane become further strong. The ND3 torsional vibrations show no temperature effect. This implies a relatively stable two dimensional layered structure formed by strongly hydrogen bonded glycine sheets in the ac-plane. Below 180 K, similar qualitative trends have been obtained for the hydrogen bond lengths in the two isotopes. In addition, temperature induced variation of the characteristic "indicator" band of zwitterionic gly-h and gly-d has also been reported.
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Affiliation(s)
- Naini Bajaj
- High Pressure & Synchrotron Radiation Physics Division, Bhabha Atomic Research Centre, Mumbai, India; Homi Bhabha National Institute, Bhabha Atomic Research Centre, Mumbai, India
| | - Himal Bhatt
- High Pressure & Synchrotron Radiation Physics Division, Bhabha Atomic Research Centre, Mumbai, India.
| | - Chitra Murli
- High Pressure & Synchrotron Radiation Physics Division, Bhabha Atomic Research Centre, Mumbai, India; Homi Bhabha National Institute, Bhabha Atomic Research Centre, Mumbai, India
| | - S R Vishwakarma
- High Pressure & Synchrotron Radiation Physics Division, Bhabha Atomic Research Centre, Mumbai, India
| | - R Chitra
- Solid State Physics Division, Bhabha Atomic Research Centre, Mumbai, India
| | - T R Ravindran
- Materials Science Group, Indira Gandhi Centre for Atomic Research, Kalpakkam, India
| | - M N Deo
- High Pressure & Synchrotron Radiation Physics Division, Bhabha Atomic Research Centre, Mumbai, India; Homi Bhabha National Institute, Bhabha Atomic Research Centre, Mumbai, India.
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Remigio RD, Repisky M, Komorovsky S, Hrobarik P, Frediani L, Ruud K. Four-component relativistic density functional theory with the polarisable continuum model: application to EPR parameters and paramagnetic NMR shifts. Mol Phys 2016. [DOI: 10.1080/00268976.2016.1239846] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Roberto Di Remigio
- Department of Chemistry, Centre for Theoretical and Computational Chemistry, University of Tromsø– The Arctic University of Norway, Tromsø, Norway
| | - Michal Repisky
- Department of Chemistry, Centre for Theoretical and Computational Chemistry, University of Tromsø– The Arctic University of Norway, Tromsø, Norway
| | - Stanislav Komorovsky
- Department of Chemistry, Centre for Theoretical and Computational Chemistry, University of Tromsø– The Arctic University of Norway, Tromsø, Norway
| | - Peter Hrobarik
- Institut für Chemie, Technische Universität Berlin, Berlin, Germany
| | - Luca Frediani
- Department of Chemistry, Centre for Theoretical and Computational Chemistry, University of Tromsø– The Arctic University of Norway, Tromsø, Norway
| | - Kenneth Ruud
- Department of Chemistry, Centre for Theoretical and Computational Chemistry, University of Tromsø– The Arctic University of Norway, Tromsø, Norway
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Van Yperen-De Deyne A, De Meyer T, Pauwels E, Ghysels A, De Clerck K, Waroquier M, Van Speybroeck V, Hemelsoet K. Exploring the vibrational fingerprint of the electronic excitation energy via molecular dynamics. J Chem Phys 2015; 140:134105. [PMID: 24712778 DOI: 10.1063/1.4869937] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
A Fourier-based method is presented to relate changes of the molecular structure during a molecular dynamics simulation with fluctuations in the electronic excitation energy. The method implies sampling of the ground state potential energy surface. Subsequently, the power spectrum of the velocities is compared with the power spectrum of the excitation energy computed using time-dependent density functional theory. Peaks in both spectra are compared, and motions exhibiting a linear or quadratic behavior can be distinguished. The quadratically active motions are mainly responsible for the changes in the excitation energy and hence cause shifts between the dynamic and static values of the spectral property. Moreover, information about the potential energy surface of various excited states can be obtained. The procedure is illustrated with three case studies. The first electronic excitation is explored in detail and dominant vibrational motions responsible for changes in the excitation energy are identified for ethylene, biphenyl, and hexamethylbenzene. The proposed method is also extended to other low-energy excitations. Finally, the vibrational fingerprint of the excitation energy of a more complex molecule, in particular the azo dye ethyl orange in a water environment, is analyzed.
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Affiliation(s)
- Andy Van Yperen-De Deyne
- Center for Molecular Modeling (CMM), Ghent University, Technologiepark 903, 9052 Zwijnaarde, Belgium
| | - Thierry De Meyer
- Center for Molecular Modeling (CMM), Ghent University, Technologiepark 903, 9052 Zwijnaarde, Belgium
| | - Ewald Pauwels
- Center for Molecular Modeling (CMM), Ghent University, Technologiepark 903, 9052 Zwijnaarde, Belgium
| | - An Ghysels
- Center for Molecular Modeling (CMM), Ghent University, Technologiepark 903, 9052 Zwijnaarde, Belgium
| | - Karen De Clerck
- Department of Textiles, Ghent University, Technologiepark 907, 9052 Zwijnaarde, Belgium
| | - Michel Waroquier
- Center for Molecular Modeling (CMM), Ghent University, Technologiepark 903, 9052 Zwijnaarde, Belgium
| | - Veronique Van Speybroeck
- Center for Molecular Modeling (CMM), Ghent University, Technologiepark 903, 9052 Zwijnaarde, Belgium
| | - Karen Hemelsoet
- Center for Molecular Modeling (CMM), Ghent University, Technologiepark 903, 9052 Zwijnaarde, Belgium
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Pauwels E, De Cooman H, Waroquier M, Hole EO, Sagstuen E. Solved? The reductive radiation chemistry of alanine. Phys Chem Chem Phys 2014; 16:2475-82. [DOI: 10.1039/c3cp54441a] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Mathias G, Baer MD. Generalized Normal Coordinates for the Vibrational Analysis of Molecular Dynamics Simulations. J Chem Theory Comput 2011; 7:2028-39. [DOI: 10.1021/ct2001304] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Gerald Mathias
- Lehrstuhl für BioMolekulare Optik, Ludwig−Maximilians Universität München, Oettingenstrasse 67, 80538 München, Germany
| | - Marcel D. Baer
- Chemical and Materials Science Division, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99352, United States
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Rinkevicius Z, Murugan NA, Kongsted J, Aidas K, Steindal AH, Ågren H. Density Functional Theory/Molecular Mechanics Approach for Electronic g-Tensors of Solvated Molecules. J Phys Chem B 2011; 115:4350-8. [DOI: 10.1021/jp1108653] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Zilvinas Rinkevicius
- Department of Theoretical Chemistry and Biology, School of Biotechnology, Royal Institute of Technology, SE-106 91 Stockholm, Sweden
- Swedish e-Science Research Center (SeRC), Royal Institute of Technology, 10044 Stockholm, Sweden
| | - N. Arul Murugan
- Department of Theoretical Chemistry and Biology, School of Biotechnology, Royal Institute of Technology, SE-106 91 Stockholm, Sweden
| | - Jacob Kongsted
- Department of Physics and Chemistry, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
| | - Kęstutis Aidas
- Department of Theoretical Chemistry and Biology, School of Biotechnology, Royal Institute of Technology, SE-106 91 Stockholm, Sweden
| | - Arnfinn Hykkerud Steindal
- Centre of Theoretical and Computational Chemistry, Department of Chemistry, University of Tromsø, N-9037 Tromsø, Norway
| | - Hans Ågren
- Department of Theoretical Chemistry and Biology, School of Biotechnology, Royal Institute of Technology, SE-106 91 Stockholm, Sweden
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Pauwels E, Asher J, Kaupp M, Waroquier M. Cluster or periodic, static or dynamic—the challenge of calculating the g tensor of the solid-state glycine radical. Phys Chem Chem Phys 2011; 13:18638-46. [DOI: 10.1039/c1cp21452g] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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Bonhomme C, Gervais C, Coelho C, Pourpoint F, Azaïs T, Bonhomme-Coury L, Babonneau F, Jacob G, Ferrari M, Canet D, Yates JR, Pickard CJ, Joyce SA, Mauri F, Massiot D. New perspectives in the PAW/GIPAW approach: J(P-O-Si) coupling constants, antisymmetric parts of shift tensors and NQR predictions. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2010; 48 Suppl 1:S86-S102. [PMID: 20589728 DOI: 10.1002/mrc.2635] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
In 2001, Pickard and Mauri implemented the gauge including projected augmented wave (GIPAW) protocol for first-principles calculations of NMR parameters using periodic boundary conditions (chemical shift anisotropy and electric field gradient tensors). In this paper, three potentially interesting perspectives in connection with PAW/GIPAW in solid-state NMR and pure nuclear quadrupole resonance (NQR) are presented: (i) the calculation of J coupling tensors in inorganic solids; (ii) the calculation of the antisymmetric part of chemical shift tensors and (iii) the prediction of (14)N and (35)Cl pure NQR resonances including dynamics. We believe that these topics should open new insights in the combination of GIPAW, NMR/NQR crystallography, temperature effects and dynamics. Points (i), (ii) and (iii) will be illustrated by selected examples: (i) chemical shift tensors and heteronuclear (2)J(P-O-Si) coupling constants in the case of silicophosphates and calcium phosphates [Si(5)O(PO(4))(6), SiP(2)O(7) polymorphs and α-Ca(PO(3))(2)]; (ii) antisymmetric chemical shift tensors in cyclopropene derivatives, C(3)X(4) (X = H, Cl, F) and (iii) (14)N and (35)Cl NQR predictions in the case of RDX (C(3)H(6)N(6)O(6)), β-HMX (C(4)H(8)N(8)O(8)), α-NTO (C(2)H(2)N(4)O(3)) and AlOPCl(6). RDX, β-HMX and α-NTO are explosive compounds.
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Affiliation(s)
- Christian Bonhomme
- Laboratoire de Chimie de la Matière Condensée, Université Pierre et Marie Curie, Paris 06, CNRS UMR 7574, Collège de France, 75005 Paris, France.
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Přecechtělová J, Novák P, Munzarová ML, Kaupp M, Sklenář V. Phosphorus Chemical Shifts in a Nucleic Acid Backbone from Combined Molecular Dynamics and Density Functional Calculations. J Am Chem Soc 2010; 132:17139-48. [DOI: 10.1021/ja104564g] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Jana Přecechtělová
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, CZ-61137 Brno, Czech Republic, and Institut für Chemie, Technische Universität Berlin, Strasse des 17. Juni 135, D-10623 Berlin, Germany
| | - Petr Novák
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, CZ-61137 Brno, Czech Republic, and Institut für Chemie, Technische Universität Berlin, Strasse des 17. Juni 135, D-10623 Berlin, Germany
| | - Markéta L. Munzarová
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, CZ-61137 Brno, Czech Republic, and Institut für Chemie, Technische Universität Berlin, Strasse des 17. Juni 135, D-10623 Berlin, Germany
| | - Martin Kaupp
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, CZ-61137 Brno, Czech Republic, and Institut für Chemie, Technische Universität Berlin, Strasse des 17. Juni 135, D-10623 Berlin, Germany
| | - Vladimír Sklenář
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, CZ-61137 Brno, Czech Republic, and Institut für Chemie, Technische Universität Berlin, Strasse des 17. Juni 135, D-10623 Berlin, Germany
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Rakvin B, Maltar-Strmečki N, Kattnig D, Grampp G. ENDOR Study on the Dynamic Properties of the First Stable Paramagnetic Center in γ-Irradiated l-Alanine Crystals. J Phys Chem A 2010; 114:7500-5. [DOI: 10.1021/jp103883x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Boris Rakvin
- Ruđer Bošković Institute, P.O. Box 180, 10002, Zagreb, Croatia, Faculty of Veterinary Medicine, University of Zagreb, P.O. Box 466, 10002, Zagreb, Croatia, and Institute of Physical and Theoretical Chemistry, Graz University of Technology, Technikerstrasse 4/I, A-8010 Graz, Austria
| | - Nadica Maltar-Strmečki
- Ruđer Bošković Institute, P.O. Box 180, 10002, Zagreb, Croatia, Faculty of Veterinary Medicine, University of Zagreb, P.O. Box 466, 10002, Zagreb, Croatia, and Institute of Physical and Theoretical Chemistry, Graz University of Technology, Technikerstrasse 4/I, A-8010 Graz, Austria
| | - Daniel Kattnig
- Ruđer Bošković Institute, P.O. Box 180, 10002, Zagreb, Croatia, Faculty of Veterinary Medicine, University of Zagreb, P.O. Box 466, 10002, Zagreb, Croatia, and Institute of Physical and Theoretical Chemistry, Graz University of Technology, Technikerstrasse 4/I, A-8010 Graz, Austria
| | - Günter Grampp
- Ruđer Bošković Institute, P.O. Box 180, 10002, Zagreb, Croatia, Faculty of Veterinary Medicine, University of Zagreb, P.O. Box 466, 10002, Zagreb, Croatia, and Institute of Physical and Theoretical Chemistry, Graz University of Technology, Technikerstrasse 4/I, A-8010 Graz, Austria
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11
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Gervais C, Bonhomme-Coury L, Mauri F, Babonneau F, Bonhomme C. GIPAW (gauge including projected augmented wave) and local dynamics in 13C and 29Si solid state NMR: the study case of silsesquioxanes (RSiO1.5)8. Phys Chem Chem Phys 2009; 11:6953-61. [DOI: 10.1039/b907450c] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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12
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Verstraelen T, Van Houteghem M, Van Speybroeck V, Waroquier M. MD-TRACKS: A Productive Solution for the Advanced Analysis of Molecular Dynamics and Monte Carlo simulations. J Chem Inf Model 2008; 48:2414-24. [DOI: 10.1021/ci800233y] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Toon Verstraelen
- Center for Molecular Modeling, Ghent University, Proeftuinstraat 86, 9000 Ghent, Belgium
| | - Marc Van Houteghem
- Center for Molecular Modeling, Ghent University, Proeftuinstraat 86, 9000 Ghent, Belgium
| | | | - Michel Waroquier
- Center for Molecular Modeling, Ghent University, Proeftuinstraat 86, 9000 Ghent, Belgium
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