A number of tautomeric geometries of 3-acetyl tetramic acid and 3-acetyl tetronic acid were examined using the AM1 and PM3 methods. The results are compared with experimental data and with studies using MNDO and older methods, with the conclusion that both AM1 and PM3 provide satisfactory models of the behaviour of these species.
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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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