New Insights to Understand the CoMFA Analysis within the Density Functional Theory Framework

Roya Momen; Alejandro Morales-Bayuelo*

Roya Momen and Alejandro Morales-Bayuelo*

Volume2-Issue11
Dates: Received: 2021-10-25 | Accepted: 2021-11-03 | Published: 2021-11-05
Pages: 1067-1073

Abstract

The Three-Dimensional Quantitative Structure-Activity Relationship (3D QSAR) models now have a wide range of applications; however, new methodologies are required due to the complexity in understanding their results. This research presents a generalized version of quantum similarity field and chemical reactivity descriptors within the density functional theory framework.

By taking reference compounds, this generalized methodology can be used to understand the biological activity of a molecular set. In this sense, this methodology allows to study of the CoMFA in quantum similarity and chemical reactivity. It is feasible to investigate steric and electrostatic effects on local substitutions using this method. They were considering that how these methodologies could be used when the receptor is known or unknown.

FullText HTML FullText PDF DOI: 10.37871/jbres1349

Certificate of Publication

Copyright

How to cite this article

Momen R, Morales-Bayuelo A. New Insights to Understand the CoMFA Analysis within the Density Functional Theory Framework. J Biomed Res Environ Sci. 2021 Nov 05; 2(11): 1067-1073. doi: 10.37871/jbres1349, Article ID: JBRES1349, Available at: https://www.jelsciences.com/articles/jbres1349.pdf

Subject area(s)

Material Science

University/Institute

Central South University

References

Morales-Bayuelo A, Matute R A, Caballero J. New Insights from the CoMSIA Analysis within the Framework of Density Functional Theory. J Mol Model. 2015;21:156. https://bit.ly/3GLDQLs
Carbó-Dorca R, Arnau M, Leyda L. How similar is a molecule to another? An electron density measure of similarity between two molecular structures. Int J Quant Chem. 1980;17:1185. https://bit.ly/3mLwbVy
Amat L, Carbó-Dorca R. Use of promolecular ASA density functions as a general algorithm to obtain starting MO in SCF calculations. Int J Quant Chem. 2002;87:59. https://bit.ly/31zkJUX
Gironés X, Carbó-Dorca R. Modelling toxicity using molecular quantum similarity measures. QSAR Comb Sci. 2006;25:579. https://bit.ly/3BKbNbz
Carbó-Dorca R, Gironés X. New insights to understand the CoMFA and CoMSIA analysis within the framework of Density Functional Theory. Toward a generalized methodology. Int J Quat Chem. 2005;101:8.
Bultinck P, Rafat M, Ponec R, Gheluwe B V, Carbó-Dorca R, Popelier P. Electron Delocalization and Aromaticity in Linear Polyacenes: Atoms in Molecules Multicenter Delocalization Index. J Phys Chem A. 2006;110:7642. https://bit.ly/3GTyePd
Morales-Bayuelo A, Vivas-Reyes R. Theoretical model for the polarization molecular and Hückel treatment of PhosphoCyclopentadiene in an external electric field: Hirschfeld study. J Math Chem. 2013;51:1835. https://bit.ly/3COQ4AI
Morales-Bayuelo A, Vivas-Reyes R. Topological model to quantify the global reactivity indexes as local in Diels–Alder reactions, using density function theory (DFT) and local quantum similarity (LQS). J Math Chem. 2013;51:125. https://bit.ly/3wgMeOa
Parr R G, Yang W. Density Functional Theory of Atoms and Compounds; Oxford University Press: New York. 1989. https://bit.ly/3qa6Hn2
Geerlings P, De Proft F, Langenaeker W. Conceptual Density Functional Theory. Chem Rev. 2003;103:1793. https://bit.ly/3k60eW4
Carbó-Dorca R. Tagged sets, convex sets and quantum similarity measures. J Math Chem. 1998;23:353.
Kumar A, Siddiqi MI. CoMFA based de novo design of pyrrolidine carboxamides as inhibitors of enoyl acyl carrier protein reductase from Mycobacterium tuberculosis. J Mol Model. 2008 Oct;14(10):923-35. doi: 10.1007/s00894-008-0326-8. Epub 2008 Jul 15. PMID: 18626672.
Carbó-Dorca R. SM and ASA density functions, diagonal vector spaces and quantum chemistry. Adv Molec Simil. 1998;2:43-72.
Carbó-Dorca R, Gironés X. Foundation of quantum similarity measures and their relationship to QSPR: density function structure, approximations, and application examples. Int J Quant Chem. 2005;101:8. https://bit.ly/3q6lwGX
Alejandro Morales-Bayuelo, Juan Torres, Ricardo Vivas-Reyes. Hückel treatment of pyrrole and pentalene as a function of cyclopentadienyl using Local Quantum Similarity Index (LQSI) and the Topo-Geometrical Superposition Approach (TGSA). J Theoret Comp Chem. 2012;11:223. https://bit.ly/3bK2TAg
Hirshfeld FL. Bonded-atom fragments for describing molecular charge densities. Theor Chim Acta. 1977;44:129. https://bit.ly/3k7rkfN
De Proft F, Van Alsenoy C, Peeters A, Langenaeker W, Geerlings P. Atomic charges, dipole moments, and Fukui functions using the Hirshfeld partitioning of the electron density. J Comput Chem. 2002;23:1198.
Randic M, Johnson M A, Maggiora G M. In Concepts and Applications of Molecular Similarity, Design of Compounds with Desired Properties. Eds., Wiley-Interscience. New York. 1990;77.
Morales-Bayuelo A, Matute RA, Caballero J. Understanding the comparative molecular field analysis (CoMFA) in terms of molecular quantum similarity and DFT-based reactivity descriptors. J Mol Model. 2015 Jun;21(6):156. doi: 10.1007/s00894-015-2690-5. Epub 2015 May 28. PMID: 26016942.
Ayers P W, Anderson J S M, Bartolotti L J. Perturbative perspectives on the chemical reaction prediction problem. Int. J Quant. Chem. 2005;101:520. https://bit.ly/3EJtmun
Harbola MK, Chattaraj PK, Parr RG. Aspects of the Softness and Hardness Concepts of Density‐Functional Theory. Isr J Chem. 1991;31:395. https://bit.ly/3wjZRvW
Pearson RG. Chemical Hardness; Applications from Compounds to Solids; Wiley-VHC, Verlag GMBH: Weinheim, Germany. 1997.
Yang W T, Parr R G. Hardness, softness, and the fukui function in the electronic theory of metals and catalysis. Proc Natl Acad Sci. 1985;82:6723.
Chattaraj PK, Sarkar U, Roy DR. Update 1 of: electrophilicity index. Chem rev. 2006;106:2065. https://bit.ly/3wiZAJJ
Ayers P, Parr R G. Variational principles for describing chemical reactions: the Fukui function and chemical hardness revisited. J Am Chem Soc. 2000;122:2010. https://bit.ly/3mMoRcr
Galván M, Pérez P, Contreras R, Fuentealba P. Condensed-to-atoms electronic Fukui functions within the framework of spin-polarized density-functional theory. Chem Phys Lett. 1999;30:405.
Mortier W J, Yang W. The use of global and local molecular parameters for the analysis of the gas-phase basicity of amines. J Am Chem Soc. 1986;108:5708.
Fuentealba P, Pérez P, Contreras R. On the condensed Fukui function. J Chem Phys. 2000;113:2544.
Oliveira M, Cenzi G, Nunes RR, Andrighetti, Valadão D MS, Reis C, Oliveira Simões CM, Nunes RJ, Júnior MC, Taranto AG, Sanchez BAM. Viana GHR Varotti FP 2013 Molecules. 2013;18:15276.
Carbó-Dorca R. Mathematical aspects of the LCAO MO first order density function (5): centroid shifting of MO shape functions basis set, properties and applications. J Math Chem. 2013;51:289.
Carbó-Dorca R. Diagonal coefficient representation of density functions and quantum similarity measures. J Math Chem. 2008;44:621.
Becke AD. Density-functional exchange-energy approximation with correct asymptotic behavior. Phys Rev A Gen Phys. 1988 Sep 15;38(6):3098-3100. doi: 10.1103/physreva.38.3098. PMID: 9900728.
GAUSSIAN 09, Revision C.01, Frisch M J, G. Trucks 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 HP, Izmaylov AF, Bloino J, Zheng G, Sonnenberg JL, Hada M, Ehara M, Toyota K, Fukuda R, Hasegawa J, Ishida M, Nakajima T, Honda Y, Kitao O, Nakai H, Vreven T, Montgomery JA Jr, Peralta JE, Ogliaro F, Bearpark M, Heyd JJ, Brothers E, Kudin KN, Staroverov V N, Keith T, Kobayashi R, Normand J, Raghavachari K, Rendell A, Burant JC, Iyengar SS, Tomasi J, Cossi M, Rega N, Millam JM, Klene M, Knox JE, Cross JB, Bakken V, Adamo C, Jaramillo J, Gomperts R, Stratmann RE, Yazyev O, Austin AJ, Cammi R, Pomelli C, Ochterski JW, Martin RL, Morokuma K. Zakrzewski V G, Voth GA, Salvador P, Dannenberg JJ, Dapprich S, Daniels AD, Farkas O, Foresman JB, Ortiz JV, Cioslowski J, and Fox DJ, Gaussian, Inc., Wallingford CT. 2010.
Carbó-Dorca R, Besalú E, Amat L, Fradera X. Quantum molecular similarity measures (QMSM) as a natural way leading towards a theoretical foundation of quantitative structure-properties relationships (QSPR). J Math Chem. 1995;18:237.
Besalú E, Gironés X, Amat L, Carbó-Dorca R. Molecular quantum similarity and the fundamentals of QSAR. Acc Chem Res. 2002 May;35(5):289-95. doi: 10.1021/ar010048x. PMID: 12020166.
Boon G, Langenaeker W, De Proft F, De Winter H, Tollenaere JP, Geerlings PJ. Systematic study of the quality of various quantum similarity descriptors. Use of the autocorrelation function and principal component analysis. Phys Chem A. 2001;105:8805.