Effects of pressure on the structure and lattice dynamics of α-glycine: a combined experimental and theoretical study
Abstract
α-Glycine is studied up to 50 GPa using synchrotron angle-dispersive X-ray powder diffraction (XRD), Raman spectroscopy, and quantum chemistry calculations performed at multiples levels of theory. Results from both XRD and Raman experiments reveal an extended pressure stability of the α phase up to 50 GPa and the room temperature (RT) equation of state (EOS) was determined up to this pressure. Additionally, this extended stability is corroborated by density functional theory (DFT) based calculations using the USPEX evolutionary structural search algorithm. Two calculated EOSs, as determined by DFT at T = 0 K and semiempirical density functional tight-binding (DFTB) at RT, and the calculated Raman modes frequencies show a good agreement with the corresponding experimental results. In conclusion, our work provides a definitive phase diagram and EOS for α-glycine up to 50 GPa, which informs prebiotic synthesis scenarios that can involve pressures well in excess of 10 GPa.
- Authors:
-
- Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Univ. of Nevada, Las Vegas, NV (United States)
- Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)
- Univ. of Chicago, IL (United States)
- Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
- Publication Date:
- Research Org.:
- Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
- Sponsoring Org.:
- USDOE National Nuclear Security Administration (NNSA); USDOE Office of Science (SC), Basic Energy Sciences (BES). Scientific User Facilities Division; USDOE Laboratory Directed Research and Development (LDRD) Program
- OSTI Identifier:
- 1548346
- Alternate Identifier(s):
- OSTI ID: 1493494; OSTI ID: 1656493
- Report Number(s):
- LLNL-JRNL-763707
Journal ID: ISSN 1466-8033; CRECF4; 953584
- Grant/Contract Number:
- AC52-07NA27344; FG02-94ER14466; AC02-06CH11357; AC02-05CH11231; 18-LW-036
- Resource Type:
- Accepted Manuscript
- Journal Name:
- CrystEngComm
- Additional Journal Information:
- Journal Volume: 21; Journal Issue: 30; Journal ID: ISSN 1466-8033
- Publisher:
- Royal Society of Chemistry
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 36 MATERIALS SCIENCE; 37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY
Citation Formats
Hinton, Jasmine K., Clarke, Samantha M., Steele, Brad A., Kuo, I-Feng W., Greenberg, Eran, Prakapenka, Vitali B., Kunz, Martin, Kroonblawd, Matthew P., and Stavrou, Elissaios. Effects of pressure on the structure and lattice dynamics of α-glycine: a combined experimental and theoretical study. United States: N. p., 2019.
Web. doi:10.1039/C8CE02123F.
Hinton, Jasmine K., Clarke, Samantha M., Steele, Brad A., Kuo, I-Feng W., Greenberg, Eran, Prakapenka, Vitali B., Kunz, Martin, Kroonblawd, Matthew P., & Stavrou, Elissaios. Effects of pressure on the structure and lattice dynamics of α-glycine: a combined experimental and theoretical study. United States. https://doi.org/10.1039/C8CE02123F
Hinton, Jasmine K., Clarke, Samantha M., Steele, Brad A., Kuo, I-Feng W., Greenberg, Eran, Prakapenka, Vitali B., Kunz, Martin, Kroonblawd, Matthew P., and Stavrou, Elissaios. Mon .
"Effects of pressure on the structure and lattice dynamics of α-glycine: a combined experimental and theoretical study". United States. https://doi.org/10.1039/C8CE02123F. https://www.osti.gov/servlets/purl/1548346.
@article{osti_1548346,
title = {Effects of pressure on the structure and lattice dynamics of α-glycine: a combined experimental and theoretical study},
author = {Hinton, Jasmine K. and Clarke, Samantha M. and Steele, Brad A. and Kuo, I-Feng W. and Greenberg, Eran and Prakapenka, Vitali B. and Kunz, Martin and Kroonblawd, Matthew P. and Stavrou, Elissaios},
abstractNote = {α-Glycine is studied up to 50 GPa using synchrotron angle-dispersive X-ray powder diffraction (XRD), Raman spectroscopy, and quantum chemistry calculations performed at multiples levels of theory. Results from both XRD and Raman experiments reveal an extended pressure stability of the α phase up to 50 GPa and the room temperature (RT) equation of state (EOS) was determined up to this pressure. Additionally, this extended stability is corroborated by density functional theory (DFT) based calculations using the USPEX evolutionary structural search algorithm. Two calculated EOSs, as determined by DFT at T = 0 K and semiempirical density functional tight-binding (DFTB) at RT, and the calculated Raman modes frequencies show a good agreement with the corresponding experimental results. In conclusion, our work provides a definitive phase diagram and EOS for α-glycine up to 50 GPa, which informs prebiotic synthesis scenarios that can involve pressures well in excess of 10 GPa.},
doi = {10.1039/C8CE02123F},
journal = {CrystEngComm},
number = 30,
volume = 21,
place = {United States},
year = {2019},
month = {1}
}
Web of Science
Works referenced in this record:
Generalized Gradient Approximation Made Simple
journal, October 1996
- Perdew, John P.; Burke, Kieron; Ernzerhof, Matthias
- Physical Review Letters, Vol. 77, Issue 18, p. 3865-3868
Elongation of Oligopeptides in a Simulated Submarine Hydrothermal System
journal, February 1999
- Imai, E.
- Science, Vol. 283, Issue 5403
Glycine oligomerization up to triglycine by shock experiments simulating comet impacts
journal, January 2014
- Sugahara, Haruna; Mimura, Koichi
- GEOCHEMICAL JOURNAL, Vol. 48, Issue 1
Projector augmented-wave method
journal, December 1994
- Blöchl, P. E.
- Physical Review B, Vol. 50, Issue 24, p. 17953-17979
Behavior of intermolecular interactions in α-glycine under high pressure
journal, January 2018
- Shinozaki, Ayako; Komatsu, Kazuki; Kagi, Hiroyuki
- The Journal of Chemical Physics, Vol. 148, Issue 4
Density-functional tight-binding for beginners
journal, November 2009
- Koskinen, Pekka; Mäkinen, Ville
- Computational Materials Science, Vol. 47, Issue 1
DFTB+, a Sparse Matrix-Based Implementation of the DFTB Method †
journal, July 2007
- Aradi, B.; Hourahine, B.; Frauenheim, Th.
- The Journal of Physical Chemistry A, Vol. 111, Issue 26
What a difference a decade makes: progress in ab initio studies of the hydrogen bond
journal, October 2001
- Del Bene, Janet E.; Jordan, Meredith J. T.
- Journal of Molecular Structure: THEOCHEM, Vol. 573, Issue 1-3
From ultrasoft pseudopotentials to the projector augmented-wave method
journal, January 1999
- Kresse, G.; Joubert, D.
- Physical Review B, Vol. 59, Issue 3, p. 1758-1775
Finite Elastic Strain of Cubic Crystals
journal, June 1947
- Birch, Francis
- Physical Review, Vol. 71, Issue 11
GSAS-II : the genesis of a modern open-source all purpose crystallography software package
journal, March 2013
- Toby, Brian H.; Von Dreele, Robert B.
- Journal of Applied Crystallography, Vol. 46, Issue 2
On the Accuracy of DFT for Describing Hydrogen Bonds: Dependence on the Bond Directionality
journal, July 2004
- Ireta, Joel; Neugebauer, Jörg; Scheffler, Matthias
- The Journal of Physical Chemistry A, Vol. 108, Issue 26
Fast Parallel Algorithms for Short-Range Molecular Dynamics
journal, March 1995
- Plimpton, Steve
- Journal of Computational Physics, Vol. 117, Issue 1
Shock synthesis of amino acids from impacting cometary and icy planet surface analogues
journal, September 2013
- Martins, Zita; Price, Mark C.; Goldman, Nir
- Nature Geoscience, Vol. 6, Issue 12
Generating Converged Accurate Free Energy Surfaces for Chemical Reactions with a Force-Matched Semiempirical Model
journal, March 2018
- Kroonblawd, Matthew P.; Pietrucci, Fabio; Saitta, Antonino Marco
- Journal of Chemical Theory and Computation, Vol. 14, Issue 4
Self-consistent-charge density-functional tight-binding method for simulations of complex materials properties
journal, September 1998
- Elstner, M.; Porezag, D.; Jungnickel, G.
- Physical Review B, Vol. 58, Issue 11, p. 7260-7268
Structure and Conformational Behavior of Biopolymers by Density Functional Calculations Employing Periodic Boundary Conditions. I. The Case of Polyglycine, Polyalanine, and Poly-α-aminoisobutyric Acid in Vacuo
journal, April 2001
- Improta, Roberto; Barone, Vincenzo; Kudin, Konstantin N.
- Journal of the American Chemical Society, Vol. 123, Issue 14
The Structure of Glycine Dihydrate: Implications for the Crystallization of Glycine from Solution and Its Structure in Outer Space
journal, January 2017
- Xu, Wenqian; Zhu, Qiang; Hu, Chunhua Tony
- Angewandte Chemie International Edition, Vol. 56, Issue 8
Effect of High Pressure on the Crystal Structures of Polymorphs of Glycine
journal, July 2005
- Dawson, Alice; Allan, David R.; Belmonte, Scott A.
- Crystal Growth & Design, Vol. 5, Issue 4
Pathways for the formation and evolution of peptides in prebiotic environments
journal, January 2012
- Danger, Grégoire; Plasson, Raphaël; Pascal, Robert
- Chemical Society Reviews, Vol. 41, Issue 16
DIOPTAS : a program for reduction of two-dimensional X-ray diffraction data and data exploration
journal, May 2015
- Prescher, Clemens; Prakapenka, Vitali B.
- High Pressure Research, Vol. 35, Issue 3
Finite strain isotherm and velocities for single-crystal and polycrystalline NaCl at high pressures and 300°K
journal, January 1978
- Birch, Francis
- Journal of Geophysical Research, Vol. 83, Issue B3, p. 1257-1268
USPEX—Evolutionary crystal structure prediction
journal, December 2006
- Glass, Colin W.; Oganov, Artem R.; Hansen, Nikolaus
- Computer Physics Communications, Vol. 175, Issue 11-12
A unified formulation of the constant temperature molecular dynamics methods
journal, July 1984
- Nosé, Shuichi
- The Journal of Chemical Physics, Vol. 81, Issue 1
Density Functional Theory and Biomolecules: A Study of Glycine, Alanine, and Their Oligopeptides
journal, June 1998
- Kaschner, R.; Hohl, D.
- The Journal of Physical Chemistry A, Vol. 102, Issue 26
From Interstellar Amino Acids to Prebiotic Catalytic Peptides: A Review
journal, April 2007
- Brack, André
- Chemistry & Biodiversity, Vol. 4, Issue 4
Effect of High Pressure on Crystalline Glycine: A New High-Pressure Polymorph
journal, May 2004
- Boldyreva, E. V.; Ivashevskaya, S. N.; Sowa, H.
- Doklady Physical Chemistry, Vol. 396, Issue 1-3
How to predict very large and complex crystal structures
journal, September 2010
- Lyakhov, Andriy O.; Oganov, Artem R.; Valle, Mario
- Computer Physics Communications, Vol. 181, Issue 9
Self-Consistent Equations Including Exchange and Correlation Effects
journal, November 1965
- Kohn, W.; Sham, L. J.
- Physical Review, Vol. 140, Issue 4A, p. A1133-A1138
The Crystal Structure of Glycine
journal, May 1939
- Albrecht, Gustav.; Corey, Robert B.
- Journal of the American Chemical Society, Vol. 61, Issue 5
Density Functional Theory Vibrational Frequencies of Amides and Amide Dimers
journal, August 2002
- Watson, Tim M.; Hirst, Jonathan D.
- The Journal of Physical Chemistry A, Vol. 106, Issue 34
Thermal properties of molecular crystals through dispersion-corrected quasi-harmonic ab initio calculations: the case of urea
journal, January 2016
- Erba, Alessandro; Maul, Jefferson; Civalleri, Bartolomeo
- Chemical Communications, Vol. 52, Issue 9
Synthesis of glycine-containing complexes in impacts of comets on early Earth
journal, September 2010
- Goldman, Nir; Reed, Evan J.; Fried, Laurence E.
- Nature Chemistry, Vol. 2, Issue 11
Vibrational spectra and intermolecular potential of the α-form crystal of glycine
journal, January 1977
- Machida, Katsunosuke; Kagayama, Akira; Saito, Yutaka
- Spectrochimica Acta Part A: Molecular Spectroscopy, Vol. 33, Issue 5
Efficiency of ab-initio total energy calculations for metals and semiconductors using a plane-wave basis set
journal, July 1996
- Kresse, G.; Furthmüller, J.
- Computational Materials Science, Vol. 6, Issue 1, p. 15-50
Collective vibrational spectra of α- and γ-glycine studied by terahertz and Raman spectroscopy
journal, September 2005
- Shi, Yulei; Wang, Li
- Journal of Physics D: Applied Physics, Vol. 38, Issue 19
Extended Lagrangian Born–Oppenheimer molecular dynamics with dissipation
journal, June 2009
- Niklasson, Anders M. N.; Steneteg, Peter; Odell, Anders
- The Journal of Chemical Physics, Vol. 130, Issue 21
Pressure-induced oligomerization of alanine at 25 °C
journal, January 2015
- Fujimoto, Chikako; Shinozaki, Ayako; Mimura, Koichi
- Chemical Communications, Vol. 51, Issue 69
Special points for Brillouin-zone integrations
journal, June 1976
- Monkhorst, Hendrik J.; Pack, James D.
- Physical Review B, Vol. 13, Issue 12, p. 5188-5192
Advanced flat top laser heating system for high pressure research at GSECARS: application to the melting behavior of germanium
journal, September 2008
- Prakapenka, V. B.; Kubo, A.; Kuznetsov, A.
- High Pressure Research, Vol. 28, Issue 3
Probing the different spatial scales of Kel F-800 polymeric glass under pressure
journal, February 2013
- Stavrou, Elissaios; Ahart, Muhtar; Mahmood, Mohammad F.
- Scientific Reports, Vol. 3, Issue 1
Proton transfer in the ground and lowest excited states of malonaldehyde: A comparative density functional and post‐Hartree–Fock study
journal, December 1996
- Barone, Vincenzo; Adamo, Carlo
- The Journal of Chemical Physics, Vol. 105, Issue 24
Extended Born-Oppenheimer Molecular Dynamics
journal, March 2008
- Niklasson, Anders M. N.
- Physical Review Letters, Vol. 100, Issue 12
Assessment of the Perdew–Burke–Ernzerhof exchange-correlation functional
journal, March 1999
- Ernzerhof, Matthias; Scuseria, Gustavo E.
- The Journal of Chemical Physics, Vol. 110, Issue 11
Inhomogeneous Electron Gas
journal, November 1964
- Hohenberg, P.; Kohn, W.
- Physical Review, Vol. 136, Issue 3B, p. B864-B871
On the Raman spectra of solid natural α-glycine and solid 15N-substituted α-glycine
journal, June 1976
- Stenback, Hans
- Journal of Raman Spectroscopy, Vol. 5, Issue 1
Time-Reversible Born-Oppenheimer Molecular Dynamics
journal, September 2006
- Niklasson, Anders M. N.; Tymczak, C. J.; Challacombe, Matt
- Physical Review Letters, Vol. 97, Issue 12
Hydrostatic limits of 11 pressure transmitting media
journal, March 2009
- Klotz, S.; Chervin, J-C.; Munsch, P.
- Journal of Physics D: Applied Physics, Vol. 42, Issue 7, Article No. 075413
Construction of tight-binding-like potentials on the basis of density-functional theory: Application to carbon
journal, May 1995
- Porezag, D.; Frauenheim, Th.; Köhler, Th.
- Physical Review B, Vol. 51, Issue 19
Lagrangian formulation with dissipation of Born-Oppenheimer molecular dynamics using the density-functional tight-binding method
journal, July 2011
- Zheng, Guishan; Niklasson, Anders M. N.; Karplus, Martin
- The Journal of Chemical Physics, Vol. 135, Issue 4
Peptide Synthesis in Aqueous Environments: The Role of Extreme Conditions on Peptide Bond Formation and Peptide Hydrolysis
journal, September 2009
- Schreiner, Eduard; Nair, Nisanth N.; Marx, Dominik
- Journal of the American Chemical Society, Vol. 131, Issue 38
Canonical dynamics: Equilibrium phase-space distributions
journal, March 1985
- Hoover, William G.
- Physical Review A, Vol. 31, Issue 3
The Pyrite-Type High-Pressure Form of Silica
journal, August 2005
- Kuwayama, Y.
- Science, Vol. 309, Issue 5736
Semiempirical GGA-type density functional constructed with a long-range dispersion correction
journal, January 2006
- Grimme, Stefan
- Journal of Computational Chemistry, Vol. 27, Issue 15, p. 1787-1799
α-Glycine under high pressures: a Raman scattering study
journal, November 2003
- Murli, Chitra; Sharma, Surinder M.; Karmakar, S.
- Physica B: Condensed Matter, Vol. 339, Issue 1
The crystal structure of γ-glycine
journal, January 1961
- Iitaka, Y.
- Acta Crystallographica, Vol. 14, Issue 1
A beamline for high-pressure studies at the Advanced Light Source with a superconducting bending magnet as the source
journal, August 2005
- Kunz, Martin; MacDowell, Alastair A.; Caldwell, Wendel A.
- Journal of Synchrotron Radiation, Vol. 12, Issue 5
POWDER CELL – a program for the representation and manipulation of crystal structures and calculation of the resulting X-ray powder patterns
journal, June 1996
- Kraus, W.; Nolze, G.
- Journal of Applied Crystallography, Vol. 29, Issue 3, p. 301-303
Crystal structure prediction using ab initio evolutionary techniques: Principles and applications
journal, June 2006
- Oganov, Artem R.; Glass, Colin W.
- The Journal of Chemical Physics, Vol. 124, Issue 24
Stability of peptides in high-temperature aqueous solutions
journal, September 1992
- Shock, Everett L.
- Geochimica et Cosmochimica Acta, Vol. 56, Issue 9
Powder pattern indexing with the dichotomy method
journal, September 2004
- Boultif, Ali; Louër, Daniel
- Journal of Applied Crystallography, Vol. 37, Issue 5
The Structure of Glycine Dihydrate: Implications for the Crystallization of Glycine from Solution and Its Structure in Outer Space
journal, January 2017
- Xu, Wenqian; Zhu, Qiang; Hu, Chunhua Tony
- Angewandte Chemie, Vol. 129, Issue 8
Amorphization-induced surface electronic states modulation of cobaltous oxide nanosheets for lithium-sulfur batteries
journal, May 2021
- Li, Ruilong; Rao, Dewei; Zhou, Jianbin
- Nature Communications, Vol. 12, Issue 1
Reducing Dzyaloshinskii-Moriya interaction and field-free spin-orbit torque switching in synthetic antiferromagnets
journal, May 2021
- Chen, Ruyi; Cui, Qirui; Liao, Liyang
- Nature Communications, Vol. 12, Issue 1
High-resolution X-ray luminescence extension imaging
journal, February 2021
- Ou, Xiangyu; Qin, Xian; Huang, Bolong
- Nature, Vol. 590, Issue 7846
Electronic structure of AlFeN films exhibiting crystallographic orientation change from c- to a-axis with Fe concentrations and annealing effect
journal, February 2020
- Tatemizo, Nobuyuki; Imada, Saki; Okahara, Kizuna
- Scientific Reports, Vol. 10, Issue 1
The crystal structure of γ-glycine
journal, March 1958
- Iitaka, Y.
- Acta Crystallographica, Vol. 11, Issue 3
Extended Lagrangian Born–Oppenheimer molecular dynamics with dissipation
text, January 2009
- Niklasson, A. M. N.; Steneteg, P.; Odell, A.
- American Institute of Physics
From Interstellar Amino Acids to Prebiotic Catalytic Peptides: A Review
journal, June 2007
- Brack, Andre
- ChemInform, Vol. 38, Issue 26
Works referencing / citing this record:
High-pressure polymorphism in l -threonine between ambient pressure and 22 GPa
journal, January 2019
- Giordano, Nico; Beavers, Christine M.; Kamenev, Konstantin V.
- CrystEngComm, Vol. 21, Issue 30