RM1 Semiempirical Model: Chemistry, Pharmaceutical Research, Molecular Biology and Materials Science

In this review, we show improvements to the semiempirical quantum chemical method RM1 and present a wide range of its applications as reported by researchers of various areas, such as theoretical, organic, physical, analytical, and inorganic chemistry, as well as their interfaces with medicinal chemistry, biology, and materials science. Success of RM1 is seemingly due to its ability to predict structural, energetic, electronic and wave function dependent properties of the investigated systems, coupled with its low computational demand required to perform calculations when compared to ab initio and density functional methods. Moreover, RM1 is widely available in several computational chemistry softwares, such as MOPAC, GAMESS, Amber, Spartan, HyperChem, and AMPAC. This review describes various case studies that perhaps can be of interest to researchers who might need a more solid basis from which to expand the frontier of applicability of RM1 to even more complex problems on larger systems.

Keywords:
RM1; Recife model 1; semiempirical methods; computational chemistry; quantum chemistry

Authorship

Nathalia B.D. Lima

Departamento de Química Fundamental, Centro de Ciências Exatas e da Natureza (CCEN), Universidade Federal de Pernambuco, 50590-470 Recife-PE, BrazilUniversidade Federal de PernambucoBrazilRecife, PE, BrazilDepartamento de Química Fundamental, Centro de Ciências Exatas e da Natureza (CCEN), Universidade Federal de Pernambuco, 50590-470 Recife-PE, Brazil

Alfredo Mayall Simas obtained his PhD in Chemistry in 1982 from Queen’s University at Kingston, Canada and is a full professor of Chemistry at the Federal University of Pernambuco, Recife, Brazil, where he has been lecturing and doing research since 1985. He has been also participating in scientific taskforces and advisory committees of funding agencies of the Brazilian Government. His research group developed the various Sparkle models for lanthanoid complexes, and, in 2006, published the RM1 model which was later extended to the 15 lanthanoids. Professor Simas published 130 articles in prestigious journals and supervised several undergraduate and graduate students.

http://orcid.org/0000-0002-1550-5859

Gerd B. Rocha

Departamento de Química, Centro de Ciências Exatas e da Natureza (CCEN), Universidade Federal da Paraíba, 58051-970 João Pessoa-PB, BrazilUniversidade Federal da ParaíbaBrazilJoão Pessoa, PB, BrazilDepartamento de Química, Centro de Ciências Exatas e da Natureza (CCEN), Universidade Federal da Paraíba, 58051-970 João Pessoa-PB, Brazil

Dr Nathalia Bezerra de Lima is a researcher at the Federal University of Pernambuco, Recife, Pernambuco, Brazil. She obtained her doctor’s degree in 2015 and is currently working in the interface of Theoretical Inorganic Chemistry with Materials Science and Engineering. Her research interests are theoretical inorganic chemistry; lanthanoid chemistry; and construction materials. The scientific independence of Nathalia began in her graduate studies when she published her first article as a corresponding author. In 2018, Nathalia was laureated with the prestigious award “For Women in Science” by L’Oréal-UNESCO in conjunction with the Brazilian Academy of Sciences.

Ricardo O. Freire

Departamento de Química, Universidade Federal de Sergipe, 49000-100 São Cristóvão-SE, BrazilUniversidade Federal de SergipeBrazilSão Cristóvão, SE, BrazilDepartamento de Química, Universidade Federal de Sergipe, 49000-100 São Cristóvão-SE, Brazil

Gerd Bruno Rocha is an Associate Professor at the Federal University of Paraíba (UFPB), João Pessoa, Brazil, since 2006. He received his doctorate in Physical Chemistry from the Federal University of Pernambuco (UFPE), Recife, Brazil, in 2002. Gerd published about 60 scientific articles and has experience in Theoretical Chemistry, acting on the following subjects: development of semiempirical quantum chemistry methods; lanthanoid complexes; GPU programming; high performance computing; linear scaling methods; molecular simulations of bio and chemical systems; and the electronic structure of biomolecules and biomolecular processes. Additional information about his scientific activities and research group can be found at http://www.quantum-chem.pro.br/.

Alfredo M. Simas ^**e-mail: simas@ufpe.br

Ricardo Freire is an Associate Professor at the Federal University of Sergipe (UFS), Aracaju, SE, Brazil. He received his doctorate from the Federal University of Pernambuco (UFPE) in 2007. Ricardo Freire has more than 90 publications in international journals and an H-index of 29. He is currently working on the development and implementation of semiempirical methods and leads the LUMPAC project, which consists of: development of the LUMPAC software; development of theoretical methods for the calculation of spectroscopic properties of lanthanoid systems; application of these theoretical tools to the study of luminescent systems.

http://orcid.org/0000-0003-3653-6328

*e-mail: simas@ufpe.br

Alfredo Mayall Simas obtained his PhD in Chemistry in 1982 from Queen’s University at Kingston, Canada and is a full professor of Chemistry at the Federal University of Pernambuco, Recife, Brazil, where he has been lecturing and doing research since 1985. He has been also participating in scientific taskforces and advisory committees of funding agencies of the Brazilian Government. His research group developed the various Sparkle models for lanthanoid complexes, and, in 2006, published the RM1 model which was later extended to the 15 lanthanoids. Professor Simas published 130 articles in prestigious journals and supervised several undergraduate and graduate students.

Dr Nathalia Bezerra de Lima is a researcher at the Federal University of Pernambuco, Recife, Pernambuco, Brazil. She obtained her doctor’s degree in 2015 and is currently working in the interface of Theoretical Inorganic Chemistry with Materials Science and Engineering. Her research interests are theoretical inorganic chemistry; lanthanoid chemistry; and construction materials. The scientific independence of Nathalia began in her graduate studies when she published her first article as a corresponding author. In 2018, Nathalia was laureated with the prestigious award “For Women in Science” by L’Oréal-UNESCO in conjunction with the Brazilian Academy of Sciences.

Gerd Bruno Rocha is an Associate Professor at the Federal University of Paraíba (UFPB), João Pessoa, Brazil, since 2006. He received his doctorate in Physical Chemistry from the Federal University of Pernambuco (UFPE), Recife, Brazil, in 2002. Gerd published about 60 scientific articles and has experience in Theoretical Chemistry, acting on the following subjects: development of semiempirical quantum chemistry methods; lanthanoid complexes; GPU programming; high performance computing; linear scaling methods; molecular simulations of bio and chemical systems; and the electronic structure of biomolecules and biomolecular processes. Additional information about his scientific activities and research group can be found at http://www.quantum-chem.pro.br/.

Ricardo Freire is an Associate Professor at the Federal University of Sergipe (UFS), Aracaju, SE, Brazil. He received his doctorate from the Federal University of Pernambuco (UFPE) in 2007. Ricardo Freire has more than 90 publications in international journals and an H-index of 29. He is currently working on the development and implementation of semiempirical methods and leads the LUMPAC project, which consists of: development of the LUMPAC software; development of theoretical methods for the calculation of spectroscopic properties of lanthanoid systems; application of these theoretical tools to the study of luminescent systems.

SCIMAGO INSTITUTIONS RANKINGS

Figures | Tables | Formulas

Figures (4)
Tables (1)
Formulas (2)

Thumbnail

Table 1
Different atom-types for hydrogen, nitrogen and oxygen considered in the parameterization of COSMO by Anisimov and Cavasotto⁴¹41 Anisimov, V. M.; Cavasotto, C. N.; J. Phys. Chem. B 2011, 115, 7896.

Thumbnail

(1)

Thumbnail

(2)

Table 1 Different atom-types for hydrogen, nitrogen and oxygen considered in the parameterization of COSMO by Anisimov and Cavasotto⁴¹41 Anisimov, V. M.; Cavasotto, C. N.; J. Phys. Chem. B 2011, 115, 7896.

Atom	Hydrogen	Nitrogen	Oxygen
Type 1	polar	nitro-group	hydroxyl
Type 2	nonpolar	cyano-group	deprotonated hydroxyl
Type 3	-	amine	carbonyl
Type 4	-	protonated	ether
Type 5	-	generic	noncarbon connected sp2
Type 6	-	-	protonated oxygen
Type 7	-	-	generic

(1)

G_{i}^{MULTI} = E_{i}^{MP 2} + {ZPE}_{i}^{B 3 LYP} + G_{i}^{RM 1, local}

(2)

G_{i}^{MULTI} = E_{i}^{MP 2} + {ZPE}_{i}^{IEF - MST // B 3 LYP} + Δ G_{hyd, i}^{IEF - MST} + G_{i}^{MST - RM 1, local}

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RM1 Semiempirical Model: Chemistry, Pharmaceutical Research, Molecular Biology and Materials Science

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[1] *e-mail: simas@ufpe.br