3 research outputs found
Can Path Integral Molecular Dynamics Make a Good Approximation for Vapor Pressure Isotope Effects Prediction for Organic Solvents? A Comparison to ONIOM QM/MM and QM Cluster Calculation
Isotopic
fractionation of volatile organic compounds (VOCs), which
are under strict measures of control because of their potential harm
to the environment and humans, has an important ecological aspect,
as the isotopic composition of compounds may depend on the conditions
in which such compounds are distributed in Nature. Therefore, detailed
knowledge on isotopic fractionation, not only experimental but also
based on theoretical models, is crucial to follow conditions and pathways
within which these contaminants are spread throughout the ecosystems.
In this work, we present carbon and, for the first time, bromine vapor
pressure isotope effect (VPIE) on the evaporation process from pure-phase
systemsî—¸dibromomethane and bromobenzene, the representatives
of aliphatic and aromatic brominated VOCs. We combine isotope effects
measurements with their theoretical prediction using three computational
techniques, namely path integral molecular dynamics, QM cluster, and
hybrid ONIOM models. While evaporation of both compounds resulted
in normal bromine VPIEs, the difference in the direction of carbon
isotopic fractionation is observed for the aliphatic and aromatic
compounds, where VPIEs are inverse and normal, respectively. Even
though theoretical models tested here turned out to be insufficient
for quantitative agreement with the experimental values, cluster electronic
structure calculations, as well as two-layer ONIOM computations, provided
better reproduction of experimental trends
The Contribution of Atom Accessibility to Site of Metabolism Models for Cytochromes P450
Three different types of atom accessibility descriptors
are investigated
in relation to site of metabolism predictions. To enable the integration
of local accessibility we have constructed 2DSASA, a method for the
calculation of the atomic solvent accessible surface area that is
independent of 3D coordinates. The method was implemented in the SMARTCyp
site of metabolism prediction models and improved the results by up
to 4 percentage points for nine cytochrome P450 isoforms. The final
models are made available at http://www.farma.ku.dk/smartcyp
The Contribution of Atom Accessibility to Site of Metabolism Models for Cytochromes P450
Three different types of atom accessibility descriptors
are investigated
in relation to site of metabolism predictions. To enable the integration
of local accessibility we have constructed 2DSASA, a method for the
calculation of the atomic solvent accessible surface area that is
independent of 3D coordinates. The method was implemented in the SMARTCyp
site of metabolism prediction models and improved the results by up
to 4 percentage points for nine cytochrome P450 isoforms. The final
models are made available at http://www.farma.ku.dk/smartcyp