Proton affinities of deoxyribonucleosides via the ONIOM-ccCA methodology
Amanda G. Riojas
Department of Chemistry and Center for Advanced Scientific Computing and Modeling (CASCaM), University of North Texas, Denton, Texas 76203-5017
Search for more papers by this authorJoshua R. John
Department of Chemistry and Center for Advanced Scientific Computing and Modeling (CASCaM), University of North Texas, Denton, Texas 76203-5017
Search for more papers by this authorT. Gavin Williams
Department of Chemistry and Center for Advanced Scientific Computing and Modeling (CASCaM), University of North Texas, Denton, Texas 76203-5017
Search for more papers by this authorCorresponding Author
Angela K. Wilson
Department of Chemistry and Center for Advanced Scientific Computing and Modeling (CASCaM), University of North Texas, Denton, Texas 76203-5017
Department of Chemistry and Center for Advanced Scientific Computing and Modeling (CASCaM), University of North Texas, Denton, Texas 76203-5017Search for more papers by this authorAmanda G. Riojas
Department of Chemistry and Center for Advanced Scientific Computing and Modeling (CASCaM), University of North Texas, Denton, Texas 76203-5017
Search for more papers by this authorJoshua R. John
Department of Chemistry and Center for Advanced Scientific Computing and Modeling (CASCaM), University of North Texas, Denton, Texas 76203-5017
Search for more papers by this authorT. Gavin Williams
Department of Chemistry and Center for Advanced Scientific Computing and Modeling (CASCaM), University of North Texas, Denton, Texas 76203-5017
Search for more papers by this authorCorresponding Author
Angela K. Wilson
Department of Chemistry and Center for Advanced Scientific Computing and Modeling (CASCaM), University of North Texas, Denton, Texas 76203-5017
Department of Chemistry and Center for Advanced Scientific Computing and Modeling (CASCaM), University of North Texas, Denton, Texas 76203-5017Search for more papers by this authorAbstract
Utilizing the recently developed ONIOM-ccCA methodology, the proton affinities (PAs) of small biomolecules (∼15 nonhydrogen atoms) were determined. The ONIOM-ccCA method was used to predict the PAs of eight amine-containing molecules and these predictions were then compared with experiment. In these comparisons, a protocol for the determination of the model system size was established, and the low level method and basis set for the real system component of ONIOM-ccCA were considered. Several possible density functionals were investigated for description of the real system (low layer), including B3LYP, B97-1, B97-2, B98, BMK, M06, and M06-2X. The resulting proton affinities were compared both to experiment and to theoretical values that were calculated using the correlation consistent Composite Approach (ccCA). The impact of the choice of augmented correlation consistent basis sets in the ONIOM-ccCA low level calculation was also examined, and PAs calculated with augmented and non-augmented basis sets were compared to those extrapolated to the complete basis set (CBS) limit. ONIOM(ccCA:B3LYP/aug-cc-pVDZ) was then applied to deoxyribonucleosides to determine the PAs at possible sites of protonation. © 2012 Wiley Periodicals, Inc.
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