Abstract
At present, physicochemical properties of amino acid molecular crystals are of the utmost interest. The compounds where molecules have different chirality are the focus of particular interest. This paper, presents a study on the structural and electronic properties of crystalline l- and dl-valine within the framework of density functional theory including van der Waals interactions. The results of this study showed that electronic properties of the two forms of valine are similar at zero pressure. Pressure leads to different responses in these crystals which is manifested as various deformations of molecules. The pressure effect on the infrared spectra and distribution of electron density of l- and dl-valine has been studied.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
References
Abraham BM, Ghule VD, Vaitheeswaran G (2018) A comparative study of the structure, stability, and energetic performance of 5,5′-bitetrazole-1,1′-diolate based energetic ionic salts: future high energy density materials. Phys Chem Chem Phys 20:29693–29707. https://doi.org/10.1039/C8CP06635C
Adamo C, Barone V (1999) Toward reliable density functional methods without adjustable parameters: the PBE0 model. J Chem Phys 110:6158. https://doi.org/10.1063/1.478522
Amalanathan M, Hubert Joe I, Rastogi VK (2011) Molecular structure, vibrational spectra and nonlinear optical properties of l-valine hydrobromide: DFT study. J Mol Struct 985:48–56. https://doi.org/10.1016/j.molstruc.2010.10.012
Bader RRW (1990) Atoms in molecules. Clarendon Press, Oxford
Barone V, Casarin M, Forrer D et al (2009) Role and effective treatment of dispersive forces in materials: polyethylene and graphite crystals as test cases. J Comput Chem 30:934–939. https://doi.org/10.1002/jcc.21112
Becke AD (2014) Perspective: 50 years of density-functional theory in chemical physics. J Chem Phys 140:18A301. https://doi.org/10.1063/1.4869598
Berland K, Cooper VR, Lee K et al (2015) van der Waals forces in density functional theory: a review of the vdW-DF method. Rep Prog Phys 78:66501. https://doi.org/10.1088/0034-4885/78/6/066501
Boldyreva EV, Ivashevskaya SN, Sowa H et al (2005) Effect of hydrostatic pressure on the γ-polymorph of glycine 1 A polymorphic transition into a new δ-form. Zeitschrift für Krist Cryst Mater. https://doi.org/10.1524/zkri.220.1.50.58886
Civalleri B (2008) B3LYP augmented with an empirical dispersion term (B3LYP-D*) as applied to molecular crystals. CrystEngComm 10:368–376. https://doi.org/10.1039/b715494a
da Silva JH, Lemos V, Freire PTC et al (2009) Stability of the crystal structure of l-valine under high pressure. Phys Status Solidi Basic Res 210:553–557. https://doi.org/10.1002/pssb.200880523
Dal Corso A (2016) Elastic constants of beryllium: a first-principles investigation. J Phys Condens Matter 28:075401. https://doi.org/10.1088/0953-8984/28/7/075401
Dalhus B, Görbitz CH (1996) Triclinic form of dl-valine. Acta Crystallogr Sect C Cryst Struct Commun 52:1759–1761. https://doi.org/10.1107/S0108270196002491
Dalhus B, Görbitz CH, Kofod P et al (1996) Crystal structures of hydrophobic amino acids. I. Redeterminations of l-methionine and l-valine at 120 K. Acta Chem Scand 50:544–548. https://doi.org/10.3891/acta.chem.scand.50-0544
Dion M, Rydberg H, Schröder E et al (2004) Van der Waals density functional for general geometries. Phys Rev Lett 92:246401–246411. https://doi.org/10.1103/PhysRevLett.92.246401
Dobson JF, Gould T (2012) Calculation of dispersion energies. J Phys Condens Matter 24:073201. https://doi.org/10.1088/0953-8984/24/7/073201
Dovesi R, Saunders VR, Roetti C, Orlando R, Zicovich-Wilson CM, Pascale F, Civalleri B, Doll K, Harrison NM, Bush IJ, D’Arco Ph, Llunell M, Caussa MNY (2014) CRYSTAL14 user’s manual. University of Torino, Torino
Fedorov IA (2019) Pressure effect on the band structure and topological properties of the electron density of pyrene: first-principles calculations. Chem Phys 518:8–14. https://doi.org/10.1016/j.chemphys.2018.11.007
Fedorov IA, Zhuravlev YN, Berveno VP (2013) Structural and electronic properties of perylene from first principles calculations. J Chem Phys 138:094509. https://doi.org/10.1063/1.4794046
Fedorov IA, Fedorova TP, Zhuravlev YN (2016a) Hydrostatic pressure effects on structural and electronic properties of ETN and PETN from first-principles calculations. J Phys Chem A 120:3710–3717. https://doi.org/10.1021/acs.jpca.6b03335
Fedorov IA, Zhuravlev YN, Klishin YA (2016b) Ab initio study of the effect of pressure on structural and electronic properties of crystalline dl-alanine. Russ Phys J 59:466–468. https://doi.org/10.1007/s11182-016-0795-7
Fletcher R (1980) Practical methods of optimization, vol 1. Wiley, New York
Foster ME, Sohlberg K (2010) Empirically corrected DFT and semi-empirical methods for non-bonding interactions. Phys Chem Chem Phys 12:307–322. https://doi.org/10.1039/b912859j
Gatti C, Casassa S (2014) TOPOND14 user’s manual. CNR-ISTM Milano, Milano
Gatti C, Saunders VR, Roetti C (1994) Crystal field effects on the topological properties of the electron density in molecular crystals: the case of urea. J Chem Phys 101:10686–10696. https://doi.org/10.1063/1.467882
Giannozzi P, Baroni S, Bonini N et al (2009) QUANTUM ESPRESSO: a modular and open-source software project for quantum simulations of materials. J Phys Condens Matter 21:395502. https://doi.org/10.1088/0953-8984/21/39/395502
Grimme S (2004) Accurate description of van der Waals complexes by density functional theory including empirical corrections. J Comput Chem 25:1463–1473. https://doi.org/10.1002/jcc.20078
Grimme S (2006) Semiempirical GGA-type density functional constructed with a long-range dispersion correction. J Comput Chem 27:1787–1799. https://doi.org/10.1002/jcc.20495
Grimme S, Antony J, Ehrlich S, Krieg H (2010) A consistent and accurate ab initio parameterization of density functional dispersion correction (DFT-D) for the 94 elements H-Pu. J Chem Phys 132:154104. https://doi.org/10.1063/1.3382344
Grimme S, Ehrlich S, Goerigk L (2011) Effect of the damping function in dispersion corrected density functional theory. J Comput Chem 32:1456–1465. https://doi.org/10.1002/jcc.21759
Guo HM, Liu HW, Wang YL et al (2004) Surface structures of dl-valine and l-alanine crystals observed by atomic force microscopy at a molecular resolution. Surf Sci 552:70–76. https://doi.org/10.1016/j.susc.2003.12.049
Hamada I (2014) van der Waals density functional made accurate. Phys Rev B 89:121103. https://doi.org/10.1103/PhysRevB.89.121103
Herlinger AW, Wenhold SL, Longd TV, Herlinger AW (1970) Infrared spectra of amino acids and their metal complexes. II. Geometrical isomerism in bis (amino acidato)copper(II) complexes. J Am Chem Soc 92:6674–6681. https://doi.org/10.1021/ja00725a015
Johnson ER, Becke AD (2005) A post-Hartree–Fock model of intermolecular interactions. J Chem Phys 123:024101. https://doi.org/10.1063/1.1949201
Johnson ER, Becke AD (2006) A post-Hartree–Fock model of intermolecular interactions: inclusion of higher-order corrections. J Chem Phys 124:174104. https://doi.org/10.1063/1.2190220
Kohn W, Meir Y, Makarov DE (1998) van der Waals energies in density functional theory. Phys Rev Lett 80:4153–4156. https://doi.org/10.1103/PhysRevLett.80.4153
Korabel’nikov DV, Zhuravlev YN (2019) The nature of the chemical bond in oxyanionic crystals based on QTAIM topological analysis of electron densities. RSC Adv 9:12020–12033. https://doi.org/10.1039/C9RA01403A
Lee K, Murray ÉD, Kong L et al (2010) Higher-accuracy van der Waals density functional. Phys Rev B Condens Matter Mater Phys 82:081101. https://doi.org/10.1103/PhysRevB.82.081101
Lima JA, Freire PTC, Lima RJC et al (2005) Raman scattering of l-valine crystals. J Raman Spectrosc 36:1076–1081. https://doi.org/10.1002/jrs.1410
Matta CF, Boyd RJ (2007) An introduction to the quantum theory of atoms in molecules. In: Matta CF, Boyd RJ (eds) The quantum theory of atoms in molecules. Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim, Germany, pp 1–34
Moitra S, Kar T (2010) Growth and characterization of l-valine—a nonlinear optical crystal. Cryst Res Technol 45:70–74. https://doi.org/10.1002/crat.200900447
Moitra S, Kumar Seth S, Kar T (2010) Synthesis, crystal structure, characterization and DFT studies of l-valine l-valinium hydrochloride. J Cryst Growth 312:1977–1982. https://doi.org/10.1016/j.jcrysgro.2010.03.016
Monkhorst H, Pack J (1976) Special points for Brillouin zone integrations. Phys Rev B 13:5188–5192. https://doi.org/10.1103/PhysRevB.13.5188
Murli C, Vasanthi R, Sharma SM (2006) Raman spectroscopic investigations of dl-serine and dl-valine under pressure. Chem Phys 331:77–84. https://doi.org/10.1016/j.chemphys.2006.09.030
Nakagawa I, Hooper RJ, Walter JL, Lane TJ (1965) Infrared absorption spectra of metal-amino acid complexes—III. Spectrochim Acta 21:1–14. https://doi.org/10.1016/0371-1951(65)80100-X
Perdew J, Burke K, Ernzerhof M (1996) Generalized gradient approximation made simple. Phys Rev Lett 77:3865–3868. https://doi.org/10.1103/PhysRevLett.77.3865
Rappe AM, Rabe KM, Kaxiras E, Joannopoulos JD (1990) Optimized pseudopotentials. Phys Rev B 41:1227–1230. https://doi.org/10.1103/PhysRevB.41.1227
Ravindran P, Fast L, Korzhavyi PA et al (1998) Density functional theory for calculation of elastic properties of orthorhombic crystals: application to TiSi2. J Appl Phys 84:4891–4904. https://doi.org/10.1063/1.368733
Rêgo FSC, Lima JA, Freire PTC et al (2016) Raman spectroscopic study of dl-valine under pressure up to 20 GPa. J Mol Struct 1109:220–225. https://doi.org/10.1016/j.molstruc.2015.12.026
Reshak AH, Lakshminarayana G, Kamarudin H et al (2012) Amino acid 2-aminopropanoic CH3CH(NH2)COOH crystals: materials for photo- and acoustoinduced optoelectronic applications. J Mater Sci Mater Electron 23:1922–1931. https://doi.org/10.1007/s10854-012-0890-7
Román-Pérez G, Soler JM (2009) Efficient implementation of a van der Waals density functional: application to double-wall carbon nanotubes. Phys Rev Lett 103:096102. https://doi.org/10.1103/PhysRevLett.103.096102
Sabatini R, Küçükbenli E, Kolb B et al (2012) Structural evolution of amino acid crystals under stress from a non-empirical density functional. J Phys Condens Matter 24:424209. https://doi.org/10.1088/0953-8984/24/42/424209
Sangeetha MK, Mariappan M, Madhurambal G, Mojumdar SC (2015) TG-DTA, XRD, SEM, EDX, UV, and FT-IR spectroscopic studies of l-valine thiourea mixed crystal. J Therm Anal Calorim 119:907–913. https://doi.org/10.1007/s10973-014-4123-6
Smith SJ, Montgomery JM, Vohra YK (2016) High-pressure high-temperature phase diagram of organic crystal paracetamol. J Phys Condens Matter 28:035101. https://doi.org/10.1088/0953-8984/28/3/035101
Thonhauser T, Cooper VR, Li S et al (2007) Van der Waals density functional: self-consistent potential and the nature of the van der Waals bond. Phys Rev B Condens Matter Mater Phys 76:125112. https://doi.org/10.1103/PhysRevB.76.125112
Torii K, Iitaka Y (1970) The crystal structure of l-valine. Acta Crystallogr Sect B Struct Crystallogr Cryst Chem 26:1317–1326. https://doi.org/10.1107/S0567740870004065
Tumanov NA, Boldyreva EV (2012) X-ray diffraction and Raman study of dl-alanine at high pressure: revision of phase transitions. Acta Crystallogr Sect B Struct Sci 68:412–423. https://doi.org/10.1107/S0108768112028972
Vijayan N (2006) Growth and characterization of nonlinear optical amino acid single crystal: l-alanine. Cryst Growth Des 6:2441–2445. https://doi.org/10.1021/cg049594y
Yedukondalu N, Vaitheeswaran G, Modak P, Verma AK (2019) Negative linear compressibility and structural phase transition in energetic silver azide under pressure: a first principles study. Solid State Commun 297:39–44. https://doi.org/10.1016/j.ssc.2019.05.006
Zakharov BA, Boldyreva EV (2019) High pressure: a complementary tool for probing solid-state processes. Cryst Eng Comm 21:10–22. https://doi.org/10.1039/C8CE01391H
URL
Quantum ESPRESSO. http://www.quantum-espresso.org. Accessed 1 Jun 2019
AK Grimme Research Web Site, Universität Bonn. https://www.chemie.uni-bonn.de/pctc/mulliken-center/grimme. Accessed 1 Jun 2019
thermo_pw is an extension of the main QE package which provides an alternative organization of the QE work-flow for the most common tasks. https://dalcorso.github.io/thermo_pw/. Accessed 1 Jun 2019
Acknowledgements
The authors gratefully acknowledge the Center for collective use “High Performance Parallel Computing” of the Kemerovo State University for providing the computational facilities. I. Fedorov acknowledges support from the Ministry of Science and Higher Education of the Russian Federation (Project No. FZSR-2020-0007). D. Korabel’nikov acknowledges support from the Ministry of Science and Higher Education of the Russian Federation (Project No. 15.3487.2017/PP). A. Prosekov acknowledges support from the grant of the President of the Russian Federation for leading scientific school (Grant No. NSh-2694.2020.4).
Author information
Authors and Affiliations
Corresponding authors
Ethics declarations
Conflict of interest
The authors declare no conflict of interest.
Research involving human participants and/or animals
This research did not involve human participants or animals.
Informed consent
Informed consent obtaining for this type of study is not required.
Additional information
Handling Editor: T. Langer.
Publisher's Note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Electronic supplementary material
Below is the link to the electronic supplementary material.
Rights and permissions
About this article
Cite this article
Fedorov, I., Korabel’nikov, D., Nguyen, C. et al. Physicochemical properties of l- and dl-valine: first-principles calculations. Amino Acids 52, 425–433 (2020). https://doi.org/10.1007/s00726-020-02818-3
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s00726-020-02818-3