Interfacing the Ab Initio Multiple Spawning Method with Electronic Structure Methods in GAMESS: Photodecay of trans-Azomethane

This work presents a nonadiabatic molecular dynamics study of the nonradiative decay of photoexcited trans-azomethane, using the ab initio multiple spawning (AIMS) program that has been interfaced with the General Atomic and Molecular Electronic Structure System (GAMESS) quantum chemistry package for on-the-fly electronic structure evaluation. The interface strategy is discussed, and the capabilities of the combined programs are demonstrated with a nonadiabatic molecular dynamics study of the nonradiative decay of photoexcited trans-azomethane. Energies, gradients, and nonadiabatic coupling matrix elements were obtained with the state-averaged complete active space self-consistent field method, as implemented in GAMESS. The influence of initial vibrational excitation on the outcome of the photoinduced isomerization is explored. Increased vibrational excitation in the CNNC torsional mode shortens the excited state lifetime. Depending on the degree of vibrational excitation, the excited state lifetime varies from ∼60–200 fs. These short lifetimes are in agreement with time-resolved photoionization mass spectroscopy experiments

Design and Implementation of Scientific Software Components to Enable Multiscale Modeling: The Effective Fragment Potential (QM/EFP) Method

The design and development of scientific software components to provide an interface to the effective fragment potential (EFP) methods are reported. Multiscale modeling of physical and chemical phenomena demands the merging of software packages developed by research groups in significantly different fields. Componentization offers an efficient way to realize new high performance scientific methods by combining the best models available in different software packages without a need for package readaptation after the initial componentization is complete. The EFP method is an efficient electronic structure theory based model potential that is suitable for predictive modeling of intermolecular interactions in large molecular systems, such as liquids, proteins, atmospheric aerosols, and nanoparticles, with an accuracy that is comparable to that of correlated ab initio methods. The developed components make the EFP functionality accessible for any scientific component-aware software package. The performance of the component is demonstrated on a protein interaction model, and its accuracy is compared with results obtained with coupled cluster methods

Effect of covalent links on the structure, spectra, and redox properties of myeloperoxidase - A density functional study.

The enzyme myeloperoxidase shows several unusual properties compared to other peroxidases, e.g. a red-shifted absorption spectrum and a peroxidase activity towards chloride. It has been suggested that this is caused by the unusual covalent links between the heme group and the surrounding protein, but whether it is caused by the two ester links to Glu-242 and Asp-94 or the sulfonium ion linkage to Met-243 is unclear. To investigate these suggestions, we have used density functional theory to study the structure, spectra, and reduction potential of 25 models of myeloperoxidase in the reduced (Fe(II)) and oxidized (Fe(III)) states, as well as in the compound I (formally Fe(V)O) and II (Fe(IV)O or Fe(IV)OH) states, using appropriate models of the linkages to the Asp, Glu, and Met residues (including the back-bone connection between Glu-242 and Met-243) in varying combinations. The calculated spectral shifts indicate that both the ester and sulfonium linkages play a role in the spectral shift. On the other hand, the sulfonium linkage seems to be mainly responsible for the high positive reduction potential for the both ferric/ferrous and compound I/II couples of myeloperoxidase

Structural and photoluminescence properties of excited state intramolecular proton transfer capable compounds - Potential emissive and electron transport materials

Electronic factors influencing the photoluminescence properties and rates of excited state intramolecular proton transfer (ESIPT) reaction of o-hydroxy derivatives of 2,5-diphenyl-1,3,4-oxadiazole have been studied. The potential of these molecules as emissive and electron transport materials in designing improved organic light emitting diodes (OLEDs) has been studied by analyzing possible reasons for the unusually high Stokes shifts and ESIPT reaction rates. Time-dependent density functional theory (TDDFT) methods have been used to calculate the ground and excited state properties of the phototautomers that are the ESIPT reaction products. We study the relative effect of electron-withdrawing substituents on the proton-acceptor moiety and predict that the lowest ESIPT rate (1.9 x 10(11) s(-1)) is achieved with a dimethylamino substituent and that the Stokes shifts are around 11 000 cm(-1) for all three derivatives

Effect of covalent links on the structure, spectra, and redox properties of myeloperoxidase - A density functional study. [Elektronisk resurs]

The enzyme myeloperoxidase shows several unusual properties compared to other peroxidases, e.g. a red-shifted absorption spectrum and a peroxidase activity towards chloride. It has been suggested that this is caused by the unusual covalent links between the heme group and the surrounding protein, but whether it is caused by the two ester links to Glu-242 and Asp-94 or the sulfonium ion linkage to Met-243 is unclear. To investigate these suggestions, we have used density functional theory to study the structure, spectra, and reduction potential of 25 models of myeloperoxidase in the reduced (Fe(II)) and oxidized (Fe(III)) states, as well as in the compound I (formally Fe(V)O) and II (Fe(IV)O or Fe(IV)OH) states, using appropriate models of the linkages to the Asp, Glu, and Met residues (including the back-bone connection between Glu-242 and Met-243) in varying combinations. The calculated spectral shifts indicate that both the ester and sulfonium linkages play a role in the spectral shift. On the other hand, the sulfonium linkage seems to be mainly responsible for the high positive reduction potential for the both ferric/ferrous and compound I/II couples of myeloperoxidase