Twenty years ago, the landmark AM1 was introduced, and has since had an increasingly wide following among chemists due to its consistently good results and time-tested reliability--being presently available in countless computational quantum chemistry programs. However, semiempirical molecular orbital models still are of limited accuracy and need to be improved if the full potential of new linear scaling techniques, such as MOZYME and LocalSCF, is to be realized. Accordingly, in this article we present RM1 (Recife Model 1): a reparameterization of AM1. As before, the properties used in the parameterization procedure were: heats of formation, dipole moments, ionization potentials and geometric variables (bond lengths and angles). Considering that the vast majority of molecules of importance to life can be assembled by using only six elements: C, H, N, O, P, and S, and that by adding the halogens we can now build most molecules of importance to pharmaceutical research, our training set consisted of 1736 molecules, representative of organic and biochemistry, containing C, H, N, O, P, S, F, Cl, Br, and I atoms. Unlike AM1, and similar to PM3, all RM1 parameters have been optimized. For enthalpies of formation, dipole moments, ionization potentials, and interatomic distances, the average errors in RM1, for the 1736 molecules, are less than those for AM1, PM3, and PM5. Indeed, the average errors in kcal x mol(-1) of the enthalpies of formation for AM1, PM3, and PM5 are 11.15, 7.98, and 6.03, whereas for RM1 this value is 5.77. The errors, in Debye, of the dipole moments for AM1, PM3, PM5, and RM1 are, respectively, 0.37, 0.38, 0.50, and 0.34. Likewise, the respective errors for the ionization potentials, in eV, are 0.60, 0.55, 0.48, and 0.45, and the respective errors, in angstroms, for the interatomic distances are 0.036, 0.029, 0.037, and 0.027. The RM1 average error in bond angles of 6.82 degrees is only slightly higher than the AM1 figure of 5.88 degrees, and both are much smaller than the PM3 and PM5 figures of 6.98 degrees and 9.83 degrees, respectively. Moreover, a known error in PM3 nitrogen charges is corrected in RM1. Therefore, RM1 represents an improvement over AM1 and its similar successor PM3, and is probably very competitive with PM5, which is a somewhat different model, and not fully disclosed. RM1 possesses the same analytical construct and the same number of parameters for each atom as AM1, and, therefore, can be easily implemented in any software that already has AM1, not requiring any change in any line of code, with the sole exception of the values of the parameters themselves.
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http://dx.doi.org/10.1002/jcc.20425 | DOI Listing |
J Comput Chem
December 2024
N.N. Semenov Federal Research Center for Chemical Physics RAS, Moscow, Russian Federation.
An impact of an electronic structure or force field method, gas-phase thermodynamic correction, and continuum solvation model on organic carbonate clusters (S) conformational and binding energies is explored. None of the tested force field (GFN-FF, GAFF, MMFF94) and standard semiempirical methods (PM3, AM1, RM1, PM6, PM6-D3, PM6-D3H4, PM7) can reproduce reference RI-SCS-MP2 conformational energies. Tight-binding GFNn-xTB methods provide more realistic conformational energies which are accurate enough to discard the least stable conformers.
View Article and Find Full Text PDFJ Mol Model
July 2024
Institute of Mathematical Problems of Biology, Keldysh Institute of Applied Mathematics, RAS, 142290, Pushchino, Moscow Region, Russia.
Context: The paper considers the features of the structure and dipole moments of several amino acids and their dipeptides which play an important role in the formation of the peptide nanotubes based on them. The influence of the features of their chirality (left L and right D) and the alpha-helix conformations of amino acids are taken into account. In particular, amino acids with aromatic rings, such as phenylalanine (Phe/F), and branched-chain amino acids (BCAAs)-leucine (Leu/L) and isoleucine (Ile/I)-as well as corresponding dipeptides (diphenylalanine (FF), dileucine (LL), and diisoleucine (II)) are considered.
View Article and Find Full Text PDFJ Chem Theory Comput
June 2024
Department of Biological Sciences, Chemistry, Bioengineering, and Computer Science and Engineering, Lehigh University, Bethlehem, Pennsylvania 18015, United States.
Quantum mechanical (QM) treatments, when combined with molecular mechanical (MM) force fields, can effectively handle enzyme-catalyzed reactions without significantly increasing the computational cost. In this context, we present CHARMM-GUI , a web-based cyberinfrastructure designed to streamline the preparation of various QM/MM simulation inputs with ligand modification. The development of has been achieved through integration with existing CHARMM-GUI modules, such as , , and .
View Article and Find Full Text PDFJ Chem Theory Comput
June 2024
College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, China.
We present an open-source MLatom@XACS software ecosystem for on-the-fly surface hopping nonadiabatic dynamics based on the Landau-Zener-Belyaev-Lebedev algorithm. The dynamics can be performed via Python API with a wide range of quantum mechanical (QM) and machine learning (ML) methods, including ab initio QM (CASSCF and ADC(2)), semiempirical QM methods (e.g.
View Article and Find Full Text PDFMolecules
December 2022
Department of Chemistry, Faculty of Chemistry and Chemical Engineering, Babeş-Bolyai University, 11 Arany Janos Street, 400028 Cluj-Napoca, Romania.
The nature of the blue color in the iodine-starch reaction is still a matter of debate. Some textbooks still invoke charge-transfer bands within a chain of neutral I molecules inside the hydrophobic channel defined by the interior of the amylose helical structure. However, the consensus is that the interior of the helix is not altogether hydrophobic-and that a mixture of I molecules and iodide anions reside there and are responsible for the intense charge-transfer bands that yield the blue color of the "iodine-starch complex".
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