Dutra J.D.L.,Federal University of Sergipe |
Filho M.A.M.,Federal University of Sergipe |
Rocha G.B.,Federal University of Paraiba |
Freire R.O.,Federal University of Sergipe |
And 2 more authors.
Journal of Chemical Theory and Computation | Year: 2013
The recently published Parametric Method number 7, PM7, is the first semiempirical method to be successfully tested by modeling crystal structures and heats of formation of solids. PM7 is thus also capable of producing results of useful accuracy for materials science and constitutes a great improvement over its predecessor, PM6. In this article, we present Sparkle model parameters to be used with PM7 that allow the prediction of geometries of metal complexes and materials which contain lanthanide trications. Accordingly, we considered the geometries of 224 high-quality crystallographic structures of complexes for the parametrization set and 395 more for the validation of the parametrization for the whole lanthanide series, from La(III) to Lu(III). The average unsigned error for Sparkle/PM7 for the distances between the metal ion and its coordinating atoms is 0.063 Å for all lanthanides, ranging from a minimum of 0.052 Å for Tb(III) to 0.088 Å for Ce(III), comparable to the equivalent errors in the distances predicted by PM7 for other metals. These distance deviations follow a gamma distribution within a 95% level of confidence, signifying that they appear to be random around a mean, confirming that Sparkle/PM7 is a well-tempered method. We conclude by carrying out a Sparkle/PM7 full geometry optimization of two spatial groups of the same thulium-containing metal organic framework, with unit cells accommodating 376 atoms, of which 16 are Tm(III) cations; the optimized geometries were in good agreement with the crystallographic ones. These results emphasize the capability of the use of the Sparkle model for the prediction of geometries of compounds containing lanthanide trications within the PM7 semiempirical model, as well as the usefulness of such semiempirical calculations for materials modeling. Sparkle/PM7 is available in the software package MOPAC2012, at no cost for academics and can be obtained from http://openmopac.net. © 2013 American Chemical Society.
Wick C.R.,The Interdisciplinary Center |
Hennemann M.,The Interdisciplinary Center |
Stewart J.J.P.,Stewart Computational Chemistry |
Clark T.,The Interdisciplinary Center |
Clark T.,University of Portsmouth
Journal of Molecular Modeling | Year: 2014
Proteins in the gas phase present an extreme (and unrealistic) challenge for self-consistent-field iteration schemes because their ionized groups are very strong electron donors or acceptors, depending on their formal charge. This means that gas-phase proteins have a very small band gap but that their frontier orbitals are localized compared to "normal" conjugated semiconductors. The frontier orbitals are thus likely to be separated in space so that they are close to, but not quite, orthogonal during the SCF iterations. We report full SCF calculations using the massively parallel EMPIRE code and linear scaling localized-molecular-orbital (LMO) calculations using Mopac2009. The LMO procedure can lead to artificially over-polarized wavefunctions in gas-phase proteins. The full SCF iteration procedure can be very slow to converge because many cycles are needed to overcome the over-polarization by inductive charge shifts. Example molecules have been constructed to demonstrate this behavior. The two approaches give identical results if solvent effects are included. © 2014 Springer-Verlag.
Stewart J.J.P.,Stewart Computational Chemistry
Journal of Molecular Modeling | Year: 2013
Modern semiempirical methods are of sufficient accuracy when used in the modeling of molecules of the same type as used as reference data in the parameterization. Outside that subset, however, there is an abundance of evidence that these methods are of very limited utility. In an attempt to expand the range of applicability, a new method called PM7 has been developed. PM7 was parameterized using experimental and high-level ab initio reference data, augmented by a new type of reference data intended to better define the structure of parameter space. The resulting method was tested by modeling crystal structures and heats of formation of solids. Two changes were made to the set of approximations: a modification was made to improve the description of noncovalent interactions, and two minor errors in the NDDO formalism were rectified. Average unsigned errors (AUEs) in geometry and ΔH f for PM7 were reduced relative to PM6; for simple gas-phase organic systems, the AUE in bond lengths decreased by about 5 % and the AUE in ΔH f decreased by about 10 %; for organic solids, the AUE in ΔH f dropped by 60 % and the reduction was 33.3 % for geometries. A two-step process (PM7-TS) for calculating the heights of activation barriers has been developed. Using PM7-TS, the AUE in the barrier heights for simple organic reactions was decreased from values of 12.6 kcal/mol-1 in PM6 and 10.8 kcal/mol-1 in PM7 to 3.8 kcal/mol-1. The origins of the errors in NDDO methods have been examined, and were found to be attributable to inadequate and inaccurate reference data. This conclusion provides insight into how these methods can be improved. © 2012 The Author(s).
High-throughput calculations of molecular properties in the MedeA environment: Accuracy of PM7 in predicting vibrational frequencies, ideal gas entropies, heat capacities, and gibbs free energies of organic molecules
Rozanska X.,Materials Design S.a.r.l. |
Stewart J.J.P.,Stewart Computational Chemistry |
Ungerer P.,Materials Design S.a.r.l. |
Leblanc B.,Materials Design S.a.r.l. |
And 3 more authors.
Journal of Chemical and Engineering Data | Year: 2014
The atomistic and molecular simulation environment MedeA (MedeA: Materials Exploration and Design Analysis, version 2.14.6; Material Design, Inc.: Angel Fire, NM, 1998-2014; http://www.materialsdesign.com) in its functionalities and graphical user interface has been enhanced to prepare and submit on the order of 1000 simulations on different structures, and to collect and help in the analysis of the results. We illustrate this with the determination of the accuracy of the semiempirical (SE) package MOPAC2012 (Stewart, J. J. P. MOPAC2012; Stewart Computational Chemistry: Colorado Springs, CO, USA, 2012; http://OpenMOPAC.net) with the PM7 method (Stewart, J. J. P. Optimization of parameters for semiempirical methods VI: more modifications to the NDDO approximations and reoptimization of parameters. J. Mol. Model. 2013, 19, 1-32) to compute frequencies of vibration and thermodynamic properties, specifically the zero point energies, ideal gas heat capacity at constant pressure, entropy, and Gibbs free energy, between 200 and 1000 K for 795 organic molecules. The results were compared with experimental data and density functional theory (DFT) values (using B3LYP/TZVP and BP86/TZVP DFT methods). This comparison showed that the PM7 frequencies of vibration above 2500 cm-1 are systematically underestimated. An a posteriori correction using a linear relationship rescaling of the frequencies permitted resetting to zero the average relative deviations with respect to experimental reference values. This frequency correction also removed the bias from the zero point energies, ideal gas heat capacity, and entropy average deviations from the PM7 results. The root-mean-square deviation (RMSD) of PM7 and the DFT heat capacities of 160 organic molecules were equivalent with respect to experimental values, being about 5 %, 2.5 %, and 3 % at 300 K, 600 K, and 1000 K, respectively. The RMSD of PM7, when compared to the DFT values, became 4 %, 2 %, and 1 % for the same temperatures when the analysis was extended to a set of 795 molecules. In the case of the ideal gas entropies, the RMSD of the PM7 relative to DFT values were between 5 % and 4 % between 300 K and 1000 K, respectively. The RMSD of the Gibbs free energies of PM7 were 15 kJ mol-1 and 30 kJ mol-1 at 300 K and 1000 K, respectively. The efficiency of this semiempirical approach was tested on a set of approximately 5800 molecules. This set was processed in about a day, thus demonstrating the scalability of the approach to big data sets. © 2014 American Chemical Society.
Agency: Department of Health and Human Services | Branch: | Program: SBIR | Phase: Phase II | Award Amount: 750.00K | Year: 2004
DESCRIPTION (provided by applicant): Software for full quantum mechanics modeling of biological macromolecules that is both fast and accurate is proposed. Cancer researchers could use this software to model protein and enzyme structure as well as enzym