Theory of adiabatic Hexaamminecobalt-Self-Exchange

We have reexamined the thermally induced Co(NH_3)_6^{2+/3+} [Co(II/III)] redox reaction using the first principles density-functional-theory method, semiclassical Marcus theory, and known charge transfer parameters. We confirm a previously suggested mechanism involving excited state (^2E_g) of Co(II) which becomes lower than the ground state (^4T_1g) in the transition state region. This lowers the transition state barrier considerably by about 6.9 kcal/mol and leads to a spin-allowed and adiabatic electron exchange process. Our calculations are consistent with previous experimental results regarding the spin-excitation energy (^3T_1g) of Co(III), and the fact that an optical absorption peak (^2E_g) of the Co(II) species could not be found experimentally. Our rate is of order 6 10^{-3} 1/Ms and hence 2 orders of magnitude faster than determined previously by experiments.Comment: 10 pages, 5 figures, 4 tables; submitted to J.Chem.Phy

Electronic correlations in organometallic complexes

We investigate an effective model for organometallic complexes (with potential uses in optoelectronic devices) via both exact diagonalisation and the configuration interaction singles (CIS) approximation. This model captures a number of important features of organometallic complexes, notably the sensitivity of the radiative decay rate to small chemical changes. We find that for large parameter ranges the CIS approximation accurately reproduces the low energy excitations and hence the photophysical properties of the exact solution. This suggests that electronic correlations do \emph{not} play an important role in these complexes. This explains why time-dependent density functional theory works surprisingly well in these complexes.Comment: 11 pages, 6 figure

Conformational Dependence of a Protein Kinase Phosphate Transfer Reaction

Atomic motions and energetics for a phosphate transfer reaction catalyzed by the cAMP-dependent protein kinase (PKA) are calculated by plane-wave density functional theory, starting from structures of proteins crystallized in both the reactant conformation (RC) and the transition-state conformation (TC). In the TC, we calculate that the reactants and products are nearly isoenergetic with a 0.2 eV barrier; while phosphate transfer is unfavorable by over 1.2 eV in the RC, with an even higher barrier. With the protein in the TC, the motions involved in reaction are small, with only P$_\gamma$ and the catalytic proton moving more than 0.5 \AA. Examination of the structures reveals that in the RC the active site cleft is not completely closed and there is insufficient space for the phosphorylated serine residue in the product state. Together, these observations imply that the phosphate transfer reaction occurs rapidly and reversibly in a particular conformation of the protein, and that the reaction can be gated by changes of a few tenths of an \AA in the catalytic site.Comment: revtex4, 7 pages, 4 figures, to be submitted to Scienc

A complete small molecule dataset from the protein data bank

AbstractA complete set of 6300 small molecule ligands was extracted from the protein data bank, and deposited online in PubChem as data source ‘SMID’. This set’s major improvement over prior methods is the inclusion of cyclic polypeptides and branched polysaccharides, including an unambiguous nomenclature, in addition to normal monomeric ligands. Only the best available example of each ligand structure is retained, and an additional dataset is maintained containing co-ordinates for all examples of each structure. Attempts are made to correct ambiguous atomic elements and other common errors, and a perception algorithm was used to determine bond order and aromaticity when no other information was available

Fat Pig (2010)

https://digitalcommons.oberlin.edu/productions_2010-2011/1001/thumbnail.jp

The Genesis of a Theorem

In this article we trace the genesis of a theorem that gives for the first time examples of Galois group $G_S$ of the maximal $p$-extension of $\mathbb{Q}$, unramified outside a finite set of primes not containing $p$, that are of cohomological dimension $2$. The pro-$p$-group $G_S$ is a fab pro-$p$-group which means that all its derived factors are finite