DOE PAGES title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: An Isosymmetric High-Pressure Phase Transition in α-Glycylglycine: A Combined Experimental and Theoretical Study

Abstract

We investigated the effects of hydrostatic pressure on α-glycylglycine (α-digly) using a combined experimental and theoretical approach. The results of powder X-ray diffraction show a change in compressibility of the axes above 6.7 GPa, but also indicate that the structure remains in the same monoclinic space group, suggesting an isosymmetric phase transition. A noticeable change in the Raman spectra between 6 and 7.5 GPa further supports the observed phase transition. First-principles-based calculations combined with the crystal structure prediction code USPEX predict a number of possible polymorphs at high pressure. An orthorhombic structure with a bent peptide backbone is the lowest enthalpy polymorph above 6.4 GPa; however, it is not consistent with experimental observations. A second monoclinic structure isosymmetric to α-digly, α'-digly, is predicted to become more stable above 11.4 GPa. The partial atomic charges in α'-digly differ from α-digly, and the molecule is bent, possibly indicating different reactivity of α'-digly. The similarity in the lattice parameters predicted from calculations and the axial changes observed experimentally support that the α'-digly phase is likely observed at high pressure. Here, a possible explanation for the isosymmetric phase transition is discussed in terms of relaxing strained hydrogen bonding interactions. Such combined experimental and modelingmore » efforts provide atomic-level insight into how pressure-driven conformational changes alter hydrogen-bonding networks in complicated molecular crystals.« less

Authors:
ORCiD logo [1];  [1]; ORCiD logo [1]; ORCiD logo [2];  [1]; ORCiD logo [1]
  1. Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)
  2. Univ. of Hawaii at Manoa, Argonne, IL (United States)
Publication Date:
Research Org.:
Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)
Sponsoring Org.:
USDOE National Nuclear Security Administration (NNSA); USDOE Office of Science (SC), Basic Energy Sciences (BES). Scientific User Facilities Division
OSTI Identifier:
1592022
Report Number(s):
LLNL-JRNL-772911
Journal ID: ISSN 1520-6106; 964101; TRN: US2100704
Grant/Contract Number:  
AC52-07NA27344; EAR-1634415; FG02-94ER14466; AC02-06CH11357; EAR-160685
Resource Type:
Accepted Manuscript
Journal Name:
Journal of Physical Chemistry. B, Condensed Matter, Materials, Surfaces, Interfaces and Biophysical Chemistry
Additional Journal Information:
Journal Volume: 124; Journal Issue: 1; Journal ID: ISSN 1520-6106
Publisher:
American Chemical Society
Country of Publication:
United States
Language:
English
Subject:
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY

Citation Formats

Clarke, Samantha M., Steele, Brad A., Kroonblawd, Matthew P., Zhang, Dongzhou, Kuo, I-Feng W., and Stavrou, Elissaios. An Isosymmetric High-Pressure Phase Transition in α-Glycylglycine: A Combined Experimental and Theoretical Study. United States: N. p., 2019. Web. doi:10.1021/acs.jpcb.9b07313.
Clarke, Samantha M., Steele, Brad A., Kroonblawd, Matthew P., Zhang, Dongzhou, Kuo, I-Feng W., & Stavrou, Elissaios. An Isosymmetric High-Pressure Phase Transition in α-Glycylglycine: A Combined Experimental and Theoretical Study. United States. https://doi.org/10.1021/acs.jpcb.9b07313
Clarke, Samantha M., Steele, Brad A., Kroonblawd, Matthew P., Zhang, Dongzhou, Kuo, I-Feng W., and Stavrou, Elissaios. Tue . "An Isosymmetric High-Pressure Phase Transition in α-Glycylglycine: A Combined Experimental and Theoretical Study". United States. https://doi.org/10.1021/acs.jpcb.9b07313. https://www.osti.gov/servlets/purl/1592022.
@article{osti_1592022,
title = {An Isosymmetric High-Pressure Phase Transition in α-Glycylglycine: A Combined Experimental and Theoretical Study},
author = {Clarke, Samantha M. and Steele, Brad A. and Kroonblawd, Matthew P. and Zhang, Dongzhou and Kuo, I-Feng W. and Stavrou, Elissaios},
abstractNote = {We investigated the effects of hydrostatic pressure on α-glycylglycine (α-digly) using a combined experimental and theoretical approach. The results of powder X-ray diffraction show a change in compressibility of the axes above 6.7 GPa, but also indicate that the structure remains in the same monoclinic space group, suggesting an isosymmetric phase transition. A noticeable change in the Raman spectra between 6 and 7.5 GPa further supports the observed phase transition. First-principles-based calculations combined with the crystal structure prediction code USPEX predict a number of possible polymorphs at high pressure. An orthorhombic structure with a bent peptide backbone is the lowest enthalpy polymorph above 6.4 GPa; however, it is not consistent with experimental observations. A second monoclinic structure isosymmetric to α-digly, α'-digly, is predicted to become more stable above 11.4 GPa. The partial atomic charges in α'-digly differ from α-digly, and the molecule is bent, possibly indicating different reactivity of α'-digly. The similarity in the lattice parameters predicted from calculations and the axial changes observed experimentally support that the α'-digly phase is likely observed at high pressure. Here, a possible explanation for the isosymmetric phase transition is discussed in terms of relaxing strained hydrogen bonding interactions. Such combined experimental and modeling efforts provide atomic-level insight into how pressure-driven conformational changes alter hydrogen-bonding networks in complicated molecular crystals.},
doi = {10.1021/acs.jpcb.9b07313},
journal = {Journal of Physical Chemistry. B, Condensed Matter, Materials, Surfaces, Interfaces and Biophysical Chemistry},
number = 1,
volume = 124,
place = {United States},
year = {2019},
month = {12}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record

Citation Metrics:
Cited by: 1 work
Citation information provided by
Web of Science

Save / Share:

Works referenced in this record:

High-pressure studies of pharmaceutical compounds and energetic materials
journal, January 2006

  • Fabbiani, Francesca P. A.; Pulham, Colin R.
  • Chemical Society Reviews, Vol. 35, Issue 10
  • DOI: 10.1039/b517780b

High pressure and the origin of life
journal, October 2002

  • Hazen, Robert M.; Boctor, Nabil; Brandes, Jay A.
  • Journal of Physics: Condensed Matter, Vol. 14, Issue 44
  • DOI: 10.1088/0953-8984/14/44/504

Origins of life and biochemistry under high-pressure conditions
journal, January 2006

  • Daniel, Isabelle; Oger, Philippe; Winter, Roland
  • Chemical Society Reviews, Vol. 35, Issue 10
  • DOI: 10.1039/b517766a

Pressure Effects on the Abiotic Polymerization of Glycine
journal, March 2007

  • Ohara, Shohei; Kakegawa, Takeshi; Nakazawa, Hiromoto
  • Origins of Life and Evolution of Biospheres, Vol. 37, Issue 3
  • DOI: 10.1007/s11084-007-9067-4

Peptide Synthesis in Early Earth Hydrothermal Systems
journal, March 2009

  • Lemke, Kono H.; Rosenbauer, Robert J.; Bird, Dennis K.
  • Astrobiology, Vol. 9, Issue 2
  • DOI: 10.1089/ast.2008.0166

Spontaneous Polymerization of Glycine under Hydrothermal Conditions
journal, May 2019


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
  • DOI: 10.1038/nchem.827

Glycine oligomerization up to triglycine by shock experiments simulating comet impacts
journal, January 2014


Stability of Amino Acids and Their Oligomerization Under High-Pressure Conditions: Implications for Prebiotic Chemistry
journal, October 2011

  • Otake, Tsubasa; Taniguchi, Takashi; Furukawa, Yoshihiro
  • Astrobiology, Vol. 11, Issue 8
  • DOI: 10.1089/ast.2011.0637

Synthesis of functionalized nitrogen-containing polycyclic aromatic hydrocarbons and other prebiotic compounds in impacting glycine solutions
journal, January 2019

  • Kroonblawd, Matthew P.; Lindsey, Rebecca K.; Goldman, Nir
  • Chemical Science, Vol. 10, Issue 24
  • DOI: 10.1039/C9SC00155G

High-pressure crystallographic study of L -cysteine, the route to a new polymorph
journal, August 2004

  • Moggach, S.; Parsons, S.; Allan, D. R.
  • Acta Crystallographica Section A Foundations of Crystallography, Vol. 60, Issue a1
  • DOI: 10.1107/S0108767304095029

High-pressure polymorphism in L -cysteine: the crystal structures of L -cysteine-III and L -cysteine-IV
journal, March 2006

  • Moggach, Stephen A.; Allan, David R.; Clark, Stewart J.
  • Acta Crystallographica Section B Structural Science, Vol. 62, Issue 2
  • DOI: 10.1107/S0108768105038802

High-pressure polymorphism in amino acids
journal, April 2008

  • Moggach, Stephen A.; Parsons, Simon; Wood, Peter A.
  • Crystallography Reviews, Vol. 14, Issue 2
  • DOI: 10.1080/08893110802037945

Effect of High Pressure on Crystalline Glycine: A New High-Pressure Polymorph
journal, May 2004


X-ray diffraction and Raman study of DL -alanine at high pressure: revision of phase transitions
journal, July 2012

  • Tumanov, Nikolay A.; Boldyreva, Elena V.
  • Acta Crystallographica Section B Structural Science, Vol. 68, Issue 4
  • DOI: 10.1107/S0108768112028972

Effect of hydrostatic pressure on the γ-polymorph of glycine. 1. A polymorphic transition into a new δ-form
journal, January 2005

  • Boldyreva, Elena V.; Ivashevskaya, Svetlana N.; Sowa, Heidrun
  • Zeitschrift für Kristallographie - Crystalline Materials, Vol. 220, Issue 1
  • DOI: 10.1524/zkri.220.1.50.58886

Effect of pressure on the crystal structure of α-glycylglycine to 4.7 GPa; application of Hirshfeld surfaces to analyse contacts on increasing pressure
journal, March 2006

  • Moggach, Stephen A.; Allan, David R.; Parsons, Simon
  • Acta Crystallographica Section B Structural Science, Vol. 62, Issue 2
  • DOI: 10.1107/S0108768105042072

Effect of pressure on the crystal structure of L -serine-I and the crystal structure of L -serine-II at 5.4 GPa
journal, January 2005

  • Moggach, Stephen A.; Allan, David R.; Morrison, Carole A.
  • Acta Crystallographica Section B Structural Science, Vol. 61, Issue 1
  • DOI: 10.1107/S0108768104031787

α-Glycine under high pressures: a Raman scattering study
journal, November 2003


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
  • DOI: 10.1021/cg049716m

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
  • DOI: 10.1021/acs.jctc.7b01266

The Crystal Structure of the Natural Amino Acids and Belated Compounds
journal, January 1931


The Crystal Structure of β-Glycylglycine
journal, August 1949

  • Hughes, Edward W.; Moore, Walter J.
  • Journal of the American Chemical Society, Vol. 71, Issue 8
  • DOI: 10.1021/ja01176a005

Deformation electron density of α-glycylglycine at 82 K. I. The neutron diffraction study
journal, December 1977

  • Kvick, Å.; Al-Karaghouli, A. R.; Koetzle, T. F.
  • Acta Crystallographica Section B Structural Crystallography and Crystal Chemistry, Vol. 33, Issue 12
  • DOI: 10.1107/S0567740877012102

Raman spectra and normal vibrations of dipeptides. I. Glycylglycine
journal, May 1983

  • Lagant, P.; Vergoten, G.; Loucheux-Lefebvre, M. H.
  • Biopolymers, Vol. 22, Issue 5
  • DOI: 10.1002/bip.360220503

Stability of peptides in high-temperature aqueous solutions
journal, September 1992


The Hydrogen Bond in the Solid State
journal, January 2002


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
  • DOI: 10.1088/0022-3727/42/7/075413

Toward an internally consistent pressure scale
journal, May 2007

  • Fei, Y.; Ricolleau, A.; Frank, M.
  • Proceedings of the National Academy of Sciences, Vol. 104, Issue 22
  • DOI: 10.1073/pnas.0609013104

Ruby under pressure
journal, June 2008


Advanced flat top laser heating system for high pressure research at GSECARS: application to the melting behavior of germanium
journal, September 2008


High Pressure Single Crystal Diffraction at PX^2
journal, January 2017

  • Zhang, Dongzhou; Dera, Przemyslaw K.; Eng, Peter J.
  • Journal of Visualized Experiments, Issue 119
  • DOI: 10.3791/54660

DIOPTAS : a program for reduction of two-dimensional X-ray diffraction data and data exploration
journal, May 2015


GSAS-II : the genesis of a modern open-source all purpose crystallography software package
journal, March 2013


EosFit7c and a Fortran module (library) for equation of state calculations
journal, January 2014

  • Angel, Ross J.; Alvaro, Matteo; Gonzalez-Platas, Javier
  • Zeitschrift für Kristallographie - Crystalline Materials, Vol. 229, Issue 5
  • DOI: 10.1515/zkri-2013-1711

Inhomogeneous Electron Gas
journal, November 1964


Self-Consistent Equations Including Exchange and Correlation Effects
journal, November 1965


Efficiency of ab-initio total energy calculations for metals and semiconductors using a plane-wave basis set
journal, July 1996


Projector augmented-wave method
journal, December 1994


From ultrasoft pseudopotentials to the projector augmented-wave method
journal, January 1999


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
  • DOI: 10.1103/PhysRevLett.77.3865

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
  • DOI: 10.1002/jcc.20495

Benchmark Databases for Nonbonded Interactions and Their Use To Test Density Functional Theory
journal, March 2005

  • Zhao, Yan; Truhlar, Donald G.
  • Journal of Chemical Theory and Computation, Vol. 1, Issue 3
  • DOI: 10.1021/ct049851d

Density functional theory with dispersion corrections for supramolecular structures, aggregates, and complexes of (bio)organic molecules
journal, January 2007

  • Grimme, Stefan; Antony, Jens; Schwabe, Tobias
  • Org. Biomol. Chem., Vol. 5, Issue 5
  • DOI: 10.1039/B615319B

Vibrational and thermal properties of β-HMX and TATB from dispersion corrected density functional theory
conference, January 2017

  • Landerville, Aaron C.; Oleynik, Ivan I.
  • SHOCK COMPRESSION OF CONDENSED MATTER - 2015: Proceedings of the Conference of the American Physical Society Topical Group on Shock Compression of Condensed Matter, AIP Conference Proceedings
  • DOI: 10.1063/1.4971541

Equations of state for energetic materials from density functional theory with van der Waals, thermal, and zero-point energy corrections
journal, December 2010

  • Landerville, A. C.; Conroy, M. W.; Budzevich, M. M.
  • Applied Physics Letters, Vol. 97, Issue 25
  • DOI: 10.1063/1.3526754

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
  • DOI: 10.1063/1.478401

Predicting the binding energies of H-bonded complexes: A comparative DFT study
journal, January 1999

  • Tuma, Christian; Daniel Boese, A.; Handy, Nicholas C.
  • Physical Chemistry Chemical Physics, Vol. 1, Issue 17
  • DOI: 10.1039/a904357h

On the accuracy of density-functional theory exchange-correlation functionals for H bonds in small water clusters: Benchmarks approaching the complete basis set limit
journal, November 2007

  • Santra, Biswajit; Michaelides, Angelos; Scheffler, Matthias
  • The Journal of Chemical Physics, Vol. 127, Issue 18
  • DOI: 10.1063/1.2790009

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
  • DOI: 10.1021/jp0377073

Evaluation of the Density Functional Approximation on the Computation of Hydrogen Bond Interactions
journal, October 1995

  • Novoa, Juan J.; Sosa, Carlos
  • The Journal of Physical Chemistry, Vol. 99, Issue 43
  • DOI: 10.1021/j100043a023

Towards an assessment of the accuracy of density functional theory for first principles simulations of water
journal, January 2004

  • Grossman, Jeffrey C.; Schwegler, Eric; Draeger, Erik W.
  • The Journal of Chemical Physics, Vol. 120, Issue 1
  • DOI: 10.1063/1.1630560

Molecular Dynamics Simulation of Liquid Water:  Hybrid Density Functionals
journal, March 2006

  • Todorova, Teodora; Seitsonen, Ari P.; Hutter, Jürg
  • The Journal of Physical Chemistry B, Vol. 110, Issue 8
  • DOI: 10.1021/jp055127v

USPEX—Evolutionary crystal structure prediction
journal, December 2006

  • Glass, Colin W.; Oganov, Artem R.; Hansen, Nikolaus
  • Computer Physics Communications, Vol. 175, Issue 11-12
  • DOI: 10.1016/j.cpc.2006.07.020

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
  • DOI: 10.1016/j.cpc.2010.06.007

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
  • DOI: 10.1063/1.2210932

New phenomena in minerals at high pressures
journal, September 1996


Ground state vibrations of N-glycylglycine hydrochloride: an ab initio study
journal, January 1994


Isosymmetric structural phase transitions: phenomenology and examples
journal, October 1995

  • Christy, A. G.
  • Acta Crystallographica Section B Structural Science, Vol. 51, Issue 5, p. 753-757
  • DOI: 10.1107/S0108768195001728

Symmetry systematics of pressure—induced phase transitions
journal, May 1994


Modeling Polymorphic Molecular Crystals with Electronic Structure Theory
journal, March 2016


Towards crystal structure prediction of complex organic compounds – a report on the fifth blind test
journal, November 2011

  • Bardwell, David A.; Adjiman, Claire S.; Arnautova, Yelena A.
  • Acta Crystallographica Section B Structural Science, Vol. 67, Issue 6
  • DOI: 10.1107/S0108768111042868

Report on the sixth blind test of organic crystal structure prediction methods
journal, August 2016

  • Reilly, Anthony M.; Cooper, Richard I.; Adjiman, Claire S.
  • Acta Crystallographica Section B Structural Science, Crystal Engineering and Materials, Vol. 72, Issue 4
  • DOI: 10.1107/S2052520616007447

Electronic Population Analysis on LCAO–MO Molecular Wave Functions. I
journal, October 1955

  • Mulliken, R. S.
  • The Journal of Chemical Physics, Vol. 23, Issue 10
  • DOI: 10.1063/1.1740588

Electrostatic decoupling of periodic images of plane‐wave‐expanded densities and derived atomic point charges
journal, November 1995

  • Blöchl, P. E.
  • The Journal of Chemical Physics, Vol. 103, Issue 17
  • DOI: 10.1063/1.470314

Water Molecule Dipole in the Gas and in the Liquid Phase
journal, April 1999