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

Abstract

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.

Structures and Properties of the Self-Assembling Diphenylalanine Peptide Nanotubes Containing Water Molecules: Modeling and Data Analysis

“…These methods are called neglect of differential overlap (NDO) methods. These methods were further improved and developed by Stewart et al [ 52 , 53 , 54 , 55 , 56 , 57 , 58 , 59 ], and they are based on the so called “neglect of diatomic differential overlap (NDDO)” approximation, with several modifications and with the choice of a wide number of parameters enables one to reproduce experimental quantities. NDDO retains all one-center differential overlap terms when Coulomb and exchange integrals are computed.…”

“…As a rule, non-covalent interactions in the PM3 method are less repulsive than in AM1. Recife Model 1 (RM1) is another semiempirical method that was parameterized to calculate dipole moments and enthalpies of formation, with errors smaller than those for AM1 and PM3 [ 58 , 59 ]. Energetic properties of organic compounds can be calculated in both forms: isolated, and in solvent medium.…”

“…To obtain the values of the energy, dipole moment, and polarization of the optimized D-FF and L-FF structures with and without water and individual extracted water clusters, the HyperChem package [ 38 ] was used with various quantum-mechanical semi-empirical AM1 (Austin Model 1, developed by Dewar M.J.S., et al [ 52 , 53 ]), PM3 (Parametrization Method No. 3, is a reparameterization of AM1, developed by Stewart J.J.P., et al [ 53 , 54 , 55 , 56 , 57 ]), RM1 (Recife Model 1, is a reparameterization of AM1, developed by Rocha G.B., et al [ 58 , 59 ]) methods (the restricted Hartree-Fock (RHF) approximation was used). For this purpose, the optimization of 21 water molecules embedded in D-FF and L-FF cavity with fixed unit cell parameters (corresponding to the experimental data [ 25 , 29 , 33 , 39 ]) was performed.…”

Molecular modeling and computational study of the chiral-dependent structures and properties of the self-assembling diphenylalanine peptide nanotubes, containing water molecules

“…As a rule, non-covalent interactions in the PM3 method are less repulsive than in AM1. RM1 is other semi-empirical method which was parameterized to calculate dipole moments and enthalpies of formation, with errors smaller than those for AM1 and PM3 [56,57]. Energetic properties of organic compounds can be calculated in both forms: isolated, and in solvent medium.…”

Potential Therapeutic Approaches to Alzheimer’s Disease By Bioinformatics, Cheminformatics And Predicted Adme-Tox Tools

“…Also, semi-empirical complex optimization can be considered a useful tool in AD drug design and analyses [ 100 ]. Moreover, this method was implemented in several computational chemistry softwares, such as MOPAC, GAMESS, Amber, Spartan, HyperChem, and AMPAC [ 100 ].…”