Editor-in-Chief : V.K. Rastogi
|Asian Journal of Physics||Vol 32, Nos 1 & 2 (2023) 101-126|
The performance of the X3LYP, M052X and M062X DFT methods in the study of the vibrational spectra of the biomolecule 5-Aminoorotic acid*
M Alcolea Palafox1, Kaushal Rani2,7, W Kiefer3, S P Singh4, M J Alam5, J K Vats6 and V K Rastogi7
1Departamento de Química-Física I, Facultad de Ciencias Químicas,
Universidad Complutense, Ciudad Universitaria, Madrid-28040, Spain.
2Department of Physics, Meerut College, Meerut-250 005, India
3Institut für Physikalische Chemie, Universität Würzburg, Am Hubland, D-97074 Würzburg, Germany
4Department of Physics, Govt Degree College, Mainpuri-205 001, India
5Department of Physics, Aligarh Muslim University, Aligarh-202 002, India
6Department of Physics, J P University, Chapra- 841 301, India
7Indian Spectroscopy Society, KC- 68/1, Old Kavinagar, Ghaziabad-201 002, India
A DFT study of the biomolecule of 5-aminoorotic acid (HAOA) has been carried out with the M052X and M062X methods using the Gaussian 09 program package for the first time. The performance of these methods was tested in the geometry structure and vibrational wavenumbers of HAOA in the isolated state. A comparison with the previous results with the DFT/B3LYP method was made. New and better IR and Raman spectra were included, and lattice modes were assigned. The total atomic charges and several calculated thermodynamic parameters were also compared and discussed. HOMO and LUMO orbital energy analysis were carried out. MEP has been plotted and several general conclusions on the use of these DFT methods were underlined. © Anita Publications. All rights reserved.
Keywords: Orotic acid, 5-aminoorotic acid, DFT/ B3LYP method, MEP, HOMO and LUMO.
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- Nath M, Vats M, Roy P, Tri-and diorganotin (IV) complexes of biologically important orotic acid: synthesis, spectroscopic studies, in vitro anti-cancer, DNA fragmentation, enzyme assays and in vivo anti-inflammatory activities, Eur J Med Chem, 59(2013)310–321.
- (a) Wysokiński R, Helios K, Lapinski L, Nowak M J, Michalska D, Matrix isolation infrared spectroscopic and quantum chemical studies on the rotational isomers of orotic acid (6-carboxyuracil), Vib Spectrosc, 64 (2013)108–118.
(b) Li X, Shi Q, Sun D, Bi W, Cao R, Synthesis and characterization of a series of lanthanide complexes constructed from orotic acid, Eur J Inorg Chem, 2004(2004)2747–2753.
- Schroeder P E, Patel D, Hasinoff B B, The dihydroorotase inhibitor 5-aminoorotic acid inhibits the metabolism in the rat of the cardioprotective drug dexrazoxane and its one-ring open metabolites. Drug Metab Dispos, 36(2008)1780–1785.
- Ortiz S, Palafox M A, Rastogi V K, Tomer R, Solid state simulation of tetramer form of 5-aminoorotic acid: The vibrational spectra and molecular structure study by using MP2 and DFT calculations, Spectrochim Acta, A97 (2012)948–962.
- Kostova I, Peica N, Kiefer W, Theoretical and spectroscopic studies of 5-aminoorotic acid and its new lanthanide (III) complexes, J Raman Spectrosc, 38(2007)205–216.
- Kostova I, Peica N, Kiefer W, Theoretical and spectroscopic studies of lanthanum (III) complex of 5-aminoorotic acid, Chem Phys, 327(2006)494–505.
- Kostova I, Rastogi V K, Kiefer W, Kostovski A, New cerium (III) and neodymium (III) complexes as cytotoxic agents, Appl Organomet Chem, 20(2006)483–493.
- Kostova I, Rastogi V K, Kiefer W, Kostovski A, New lanthanum (III) complex–synthesis, characterization, and cytotoxic activity, Archiv Pharmazie, 339(2006)598–607.
- El Kolli M, Coulibaly A, Chevalier J, Barbe J, Cremieux A, Antibacterial activity of 5-aminoorotic acid derivatives, Curr Microbiol, 36(1998)245–247.
- Seminario J M, Politzer P (Eds), Modern Density Functional Theory: a tool for chemistry, Vol 2, (Elsevier, Amsterdam), 1995.
- Palafox M A, Iza N, Tautomerism of the natural thymidine nucleoside and the antiviral analogue D4T. Structure and influence of an aqueous environment using MP2 and DFT methods, Phys Chem Chem Phys, 12(2010)881–893.
- Brovarets’ O O, Hovorun D M, Prototropic tautomerism and basic molecular principles of hypoxanthine mutagenicity: An exhaustive quantum-chemical analysis, J Biomol Struct Dyn, 31(2013)913–936.
- Danilov V I, Anisimov V M, Kurita N, Hovorun D M, MP2 and DFT studies of the DNA rare base pairs: the molecular mechanism of the spontaneous substitution mutations conditioned by tautomerism of bases, Chem Phys Lett, 412(2005)285–293.
- Alcolea Palafox M, Nielsen O F, Lang K, Garg P, Rastogi V K, Geometry and vibrational spectra of 5-substituted uracils, Asian Chem Lett, 8(2004)81–93.
- (a) Palafox M Alcolea, Rastogi V K, Quantum chemical predictions of the vibrational spectra of polyatomic molecules.The uracil molecule and two derivatives, Spectrochim Acta, A58(2002)411–440.
(b) Kattan D, Palafox M A, Rathor S K, VK Rastogi V K, A DFT analysis of the molecular structure, vibrational spectra and other molecular properties of 5-nitrouracil and comparison with uracil, J Mol Struct, 1106(2016)300–315.
(c) Palafox M Alcolea, Rastogi V K, 6-Aminouracil: Geometries and spectra in the isolated state and in the solid state simulation. A comparison with 5-aminouracil, J Mol Struct, 1108(2016)482–495.
(d) Rani K, Prakash J, Singh S P, Vats J K, Palafox M A, Rastogi V K, Molecular structure and vibrational spectra of 2-thiouracil: A comparison with uracil, Asian J Phys, 26(2017)365–373.
(e) Palafox M Alcolea, Rastogi V K, Singh S P, Effect of the sulphur atom on geometry and spectra of the biomolecule 2-thiouracil and in the WC base pair 2-thiouridine-adenosine. Influence of water in the first hydration shell, J Biomol Struct Dyn, 36(2018)1225–1254.
(f) Palafox M A, Rastogi V K, Singh S P, FT-IR and FT-Raman spectra of 5-chlorocytosine: Solid state simulation and tautomerism. Effect of the chlorine substitution in the Watson-Crick base pair 5-chlorodeoxycytidine, Spectrochim Acta, 188A(2018)418–435.
(g) Palafox M Alcolea, Benial A M F, Rastogi V K, Biomolecules of 2-Thiouracil, 4-Thiouracil and 2,4-Dithiouracil: A DFT Study of the Hydration, Molecular Docking and Effect in DNA:RNA Microhelixes, Int J Mol Sci, 20(2019)3477; doi:10.3390/ijms20143477.
(h) Palafox M Alcolea, Kiefer W, Rani K, Lal B, Vata J K, Singh S P and Rastogi V K, DFT Study on tautomerism of cytosine and its 5-haloderivatives: A Review, Asian J Phys, 30(2021)521–536.
(i) Palafox M A, Kattan, Velasco M L P, Isasi J, Posada-Moreno P, Rani K, Singh S P, Rastogi V K, Base pairs with 4-amino-3-nitrobenzonitrile: comparison with the natural WC pairs. Dimer and tetramer forms, Infrared and Raman spectra, and several proposed antiviral modified nucleosides, J Biomol Struct Dyn, (2022); doi.org/10.1080/07391102.2022.2069864.
- Rastogi V K, Palafox M Alcolea, Vibrational spectra, tautomerism and thermodynamics of anticarcinogenic drug: 5-Fluorouracil, Spectrochim Acta, A79(2011)970–977.
- Palafox M Alcolea, Iza N, Gil M, The hydration effect on the uracil frequencies: an experimental and quantum chemical study, J Molec Struct (Theochem), 585(2002)69–92.
- Becke A D, Perspective on Density functional thermochemistry. III. The role of exact exchange, J Chem Phys, 98 (1993)5648–5652.
- Lee C, Yang W, Parr R G, Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density, Phys Rev, B37(1988)785–789.
- Szafran M, Ostrowska K, Katrusiak A, Dega-Szafran Z, Spectral and structural studies of dimethylphenyl betaine hydrate, Spectrochim Acta, A128(2014)844–851.
- Arjunan V, Devi L, Subbalakshmi R, Rani T, Mohan S, Synthesis, vibrational, NMR, quantum chemical and structure-activity relation studies of 2-hydroxy-4-methoxyacetophenone, Spectrochim Acta, A130(2014)164–177.
- Arjunan V, Raj A, Anitha R, Mohan S, A new look into the quantum chemical and spectroscopic investigations of 5-chloro-1-methyl-4-nitroimidazole, Spectrochim Acta, A125(2014)160–174.
- (a) Arjunan V, Thillai Govindaraja, S, Jose S P, Mohan S, DFT simulation, quantum chemical electronic structure, spectroscopic and structure–activity investigations of 2-benzothiazole acetonitrile, Spectrochim Acta, A128(2014) 22–36.
(b) Arjunan V, Thillai Govindaraja S, Ravindran P, Mohan S, Exploring the structure–activity relations of N-carbethoxyphthalimide by combining FTIR, FT-Raman and NMR spectroscopy with DFT electronic structure method, Spectrochim Acta, A120(2014)473–488.
- Palafox M A, Tardajos G, Guerrero-Martínez A, Rastogi V K, Ojha S P, Kiefer W, FT-IR, FT-Raman spectra, density functional computations of the vibrational spectra and molecular geometry of biomolecule 5-aminouracil, Chem Phys, 340(2007)17–31.
- Palafox M A, Scaling factors for the prediction of vibrational spectra. I. Benzene molecule, Int J Quantum Chem, 77(2000)661–684.
- Rastogi V K, Palafox M A, Mittal L, Peica N, Kiefer W, Lang K, Ojha S P, FTIR and FT-Raman spectra and density functional computations of the vibrational spectra, molecular geometry and atomic charges of the biomolecule: 5-bromouracil, J Raman Spectrosc, 38(2007)1227–2141.
- Ponomareva A G, Yurenko Y P, Zhurakivsky R O, van Mourik T, Hovorun D M, Ponomareva A G, Yurenko Y P, Zhurakivsky R O, van Mourik T, Hovorun D M, Complete conformational space of the potential HIV-1 reverse transcriptase inhibitors d4U and d4C. A quantum chemical study, Phys Chem Chem Phys, 14(2012)6787–6795.
- Shishkin O V, Pelmenschikov A, Hovorun D M, Leszczynski J, Molecular structure of free canonical 2′-deoxyribonucleosides: a density functional study, J Molec Struct, 526(2000)329–341.
- Shishkin O V, Gorg L, Zhikol O A, Leszczynski J, Conformational analysis of canonical 2-deoxyribonucleotides. 1. Pyrimidine nucleotides, J Biomol Struct Dyn, 21(2004)537–553.
- Shishkin O V, Gorg L, Zhikol O A, Leszczynski J, Conformational analysis of canonical 2-deoxyribonucleotides. 2. Purine nucleotides, J Biomol Struct Dyn, 22(2004)227–243.
- Palamarchuk G V, Shishkin O V, Gorb L, Leszczynski J, Dependence of deformability of geometries and characteristics of intramolecular hydrogen bonds in canonical 2′-deoxyribonucleotides on DNA conformations, J Biomol Struct Dyn, 26(2009)653–661.
- Brovarets’ O O, Hovorun D M, Can tautomerization of the A• T Watson–Crick base pair via double proton transfer provoke point mutations during DNA replication? A comprehensive QM and QTAIM analysis, J Biomol Struct Dyn, 32(2014)127–154.
- Palafox M A, Molecular structure differences between the antiviral Nucleoside Analogue 5-iodo-2′-deoxyuridine and the natural nucleoside 2′-deoxythymidine using MP2 and DFT methods: Conformational analysis, crystal simulations, DNA pairs and possible behavior, J Biomol Struct Dyn, 32(2014)831–851.
- Palafox M A, Posada-Moreno P, Villarino-Marín A L, Martinez-Rincon C, Ortuño-Soriano I, Zaragoza-García I, DFT calculation of four new potential agents muscarinic of bispyridinium type: structure, synthesis, biological activity, hydration, and relations with the potents W84 and DUO-3O, J Comput-Aided Molec Design, 25(2011) 145–161.
- Hoffmann M, Rychlewski J, Density functional theory (DFT) and drug design, Rev Mod Quant Chem, 2(2002) 1767–1803.
- Zhao Y, Schultz N E, Truhlar D G, Design of density functionals by combining the method of constraint satisfaction with parametrization for thermochemistry, thermochemical kinetics, and noncovalent interactions, J Chem Theor Comput, 2(2006)364–382.
- Zhao Y, Truhlar D G, A new local density functional for main-group thermochemistry, transition metal bonding, thermochemical kinetics, and noncovalent interactions, J Chem Phys, 125(2006)194101; doi.org/10.1063/1.2370993.
- Zhao Y, Truhlar D G, Applications and validations of the Minnesota density functional, Chem Phys Lett, 502 (2011)1–13.
- van Mourik T, Assessment of density functionals for intramolecular dispersion-rich interactions, J Chem Theor Comput, 4(2008)1610–1619.
- Gaussian 09, Revision D.01, Frisch M J, Trucks G W, Schlegel H B, Scuseria G E, Robb M A, Cheeseman J R, Scalmani G, Barone V, Mennucci B, Petersson G A, Nakatsuji H, Caricato M, Li X, Hratchian H P, Izmaylov A F, Bloino J, Zheng G, Sonnenberg J L, Hada M, Ehara M, Toyota K, Fukuda R, Hasegawa J, Ishida M, Nakajima T, Honda Y, Kitao O, Nakai H, Vreven T, Montgomery J A (Jr), Peralta J E, Ogliaro F, Bearpark M, Heyd J J, Brothers E, Kudin K N, Staroverov V N, Kobayashi R, Normand J, Raghavachari K, Rendell A, Burant J C, Iyengar S S, Tomasi J, Cossi M, Rega N, Millam N J, Klene M, Knox J E, Cross J B, Bakken V, Adamo C, Jaramillo J, Gomperts R, Stratmann R E, Yazyev O, Austin A J, Cammi R, Pomelli C, Ochterski J W, Martin R L, Morokuma K, Zakrzewski V G, Voth G A, Salvador P, Dannenberg J J, Dapprich S, Daniels A D, Farkas Ö, Foresman J B, Ortiz J V, Cioslowski J, Fox D J, Gaussian, Inc., Wallingford CT, 2009.
- Carpenter J E, Weinhold F, Analysis of the geometry of the hydroxymethyl radical by the “different hybrids for different spins” natural bond orbital procedure. J Mol Struct (Theochem), 169(1988)41–62.
- Reed A E, Curtiss L A, Weinhold F, Intermolecular interactions from a natural bond orbital, donor-acceptor viewpoint Chem Rev, 88(1988)899–926.
- Palafox M Alcolea, Recent Research Developments in Physical Chemistry, India: Transworld Research Network, 2(1998)213–232.
- (a) Palafox M Alcolea, Iza N, Gil M, Rastogi V K, Perspectives in Engineering Optics, (Anita Publications, Delhi, India). 2002, p 356.
(b) Palafox M A, Tardajos G, Kim J J, Nielsen O F, Lodhi Rajive, Rastogi V K, Predicting wavenumbers of vibrational spectra, its use in spectroscopy, Asian J Phys,15(2006)281–285.
- Bekiroglu S, Kristiansson O, Hydrogen-bonded neutral and anionic lamellar networks: Crystal structures of bis (O, O′, O″-hydroorotato) disilver (i) dihydrate, potassium hydroorotate and rubidium hydroorotate. Ab initio calculations on orotic acid and the hydroorotate anion, J Chem Soc Dalton Trans, 7(2002)1330–1335.
- Palafox M Alcolea, Gil M, Núñez J L, Rastogi V K, Mittal L, Sharma R, Scaling factors for the prediction of vibrational spectra. II. The aniline molecule and several derivatives, Int J Quant Chem, 103(2005)394–421.
- Palafox M A, Núñez J L, Gil M, Theoretical quantum chemical study of benzoic acid: geometrical parameters and vibrational wavenumbers, Int J Quant Chem, 89(2002)1-24.
- Cuellar A, Palafox M Alcolea, Rastogi V K, Kiefer W, Schlücker S, Rathor S K, FT-IR and FT-Raman spectra of 5-fluoroorotic acid with solid state simulation by DFT methods, Spectrochim Acta, A132(2014)430–445.
- Weiner P K, Langridge R, Blane J M, Schaefer R, Kollman P A, Electrostatic potential molecular surfaces, Proc Natl Acad Sci, 79(1982)3754–3758.
- Sapse A M, Molecular orbital calculations for biological systems, (Oxford University Press), 1998.
- Alam M J, Ahmad S, Quantum chemical and spectroscopic investigations of 3-methyladenine, Spectrochim Acta, A128(2014)653–664.
- Alam M J, Ahmad S, Molecular structure, anharmonic vibrational analysis and electronic spectra of o-, m-, p-iodonitrobenzene using DFT calculations, J Mol Struct, 1059(2014)239–254.
- Arivazhagan M, Kumar J S, Vibrational assignment, HOMO–LUMO, first-hyperpolarizability and Mulliken’s charge analysis of 2, 7-dinitrofluorene, Indian J Pure Appl Phys, 50(2012)363–373.