Equilibrium twist angles and rotational barriers for the three isomeric phenylpyrroles were calculated by means of MNDO and AMI. In each case MNDO incorrectly predicts the perpendicular conformation as the most stable one. In agreement with experimental evidence AMI predicts only slight deviations from planarity and very low 0°-barriers (1-phenylpyrrole: 0 = 28°, E = F6 kJ mol"; 2-phenylpyrrole...

An exploratory semiempirical Hamiltonian (PM3BP) is developed to model hydrogen bonding in nucleic acid base pairs. The PM3BP Hamiltonian is a novel reparametrization of the PM3 Hamiltonian designed to reproduce experimental base pair dimer enthalpies and high-level density-functional results. The parametrization utilized a suite of integrated nonlinear optimization algorithms interfaced with a...

The increasing role of quantum chemical calculations in drug and materials design has led to a demand for methods that can describe the electronic structures of large and complex systems. Semiempirical methods based on the neglect of diatomic differential overlap (NDDO) approximation (e.g., the MNDO [1, 2], MNDO/d [3], AM1 [4], AM1* [5], and PMx [6–8] methods) are important representatives of s...

The semiempirical Hamiltonians MNDO, AM1, PM3, RM1, PDDG/MNDO, PDDG/PM3, and SCC-DFTB, when used as part of a hybrid QM/MM scheme for the simulation of biological molecules, were compared on their abilities to reproduce experimental ensemble averages at or near room temperatures for the model system alanine dipeptide in water. Free energy surfaces in the (phi, psi) dihedral angle space, (3)J(H(...

Modified Neglect of Differential Overlap (MNDO) and MNDO/d based semiempirical methods are widely employed to explore structure and thermochemistry of molecular systems. In this work, the AM1/d method has been parametrized for systems containing platinum. The proposed scheme delivers excellent performance for binding energies of Pt complexes with ethylene and large pi conjugated hydrocarbons. T...

In the present work diazepam (Dz) drug was investigated using thermal analyses (TA) measurements (TG/DTG) in comparison with EI mass spectral (MS) fragmentation at 70 and 20 eV. Semi-empirical MO calculations, MNDO procedure, have been carried out on diazepam both as neutral molecule and the corresponding positively charged molecular ion. These include molecular geometry, bond order, charge dis...

The numerical accuracy of linear scaling semiempirical methods LocalSCF and MOZYME is analyzed in comparison to conventional matrix diagonalization with respect to a variety of molecular properties including conformational energy, dipole moment, atomic charges, and bond orders. Major semiempirical MNDO, AM1, PM3, and PM5 Hamiltonians were considered in the study. As the numerical tests demonstr...

Few groups of substituted 1-aminoisoquinoline, 4-aminoand 2,4-diaminoquinazoline derivatives have been examined in order to find general relationships between the basicity and a kind of substituent. pKa Values have been determined for these compounds and correlated with the original Hammett σm and σp constants. They clearly showed that the steric effects of the bulky substituents neighbouring t...

Version 9 of the Amber simulation programs includes a new semi-empirical hybrid QM/MM functionality. This includes support for implicit solvent (generalized Born) and for periodic explicit solvent simulations using a newly developed QM/MM implementation of the particle mesh Ewald (PME) method. The code provides sufficiently accurate gradients to run constant energy QM/MM MD simulations for many...