OMx-D: semiempirical methods with orthogonalization and dispersion corrections. Implementation and biochemical application

The semiempirical methods of the OMx family (orthogonalization models OM1, OM2, and OM3) are known to describe biochemical systems more accurately than standard semiempirical approaches such as AM1. We investigate the benefits of augmenting these methods with an empirical dispersion term (OMx-D) taken from recent density functional work, without modifying the standard OMx parameters. Significant improvements are achieved for non-covalent interactions, with mean unsigned errors of 1.41 kcal/mol (OM2-D) and 1.31 kcal/mol (OM3-D) for the binding energy of the complexes in the JSCH-2005 data base. This supports the use of these augmented methods in quantum mechanical/molecular mechanical (QM/MM) studies of biomolecules, for example during system preparation and equilibration. As an illustrative application, we present QM and QM/MM calculations on the binding between antibody 34E4 and a hapten, where OM3-D performs better than the methods without dispersion terms (AM1, OM3)

Equilibrium Structures of Pyrazine, s-Triazine, and s-Tetrazine

In recent years, accurate equilibrium (re) structures have been determined for pyridine, pyridazine, and pyrimidine. Here, we report accurate re structures for the structurally related molecules pyrazine, s-triazine, and s-tetrazine, which were obtained using a composite approach based on explicitly correlated coupled-cluster theory (CCSD(T)-F12b) in conjunction with a large correlation-consistent basis set (cc-pCVQZ-F12) to take core–valence electron correlation into account. Additional terms were included to correct for the effects of iterative triple excitations (CCSDT), noniterative quadruple excitations (CCSDT(Q)), and scalar relativistic contributions (DKH2-CCSD(T)). The performance of this computational procedure was established through test calculations on selected small molecules. For s-triazine, accurate experimental ground-state rotational constants (B0) of the parent molecule and six D3h isotopologues from the literature were used to determine a semiexperimental re structure, which was found to be essentially identical with the best estimate from the current composite approach. The presently recommended equilibrium structural parameters of s-triazine are re(CH) = 108.17 pm, re(CN) = 133.19 pm, and θe(NCN) = 125.95°, with estimated uncertainties of ±0.10 pm and ±0.10°, respectively. The predicted equilibrium geometries for pyrazine and s-tetrazine are expected to be of the same accuracy. We recommend for pyrazine: re(CH) = 108.16 pm, re(CN) = 133.34 pm, re(CC) = 139.07 pm, θe(CNC) = 115.60°, and θe(HCC) = 120.75°; and for s-tetrazine: re(CH) = 107.95 pm, re(CN) = 133.39 pm, re(NN) = 132.01 pm, and θe(NCN) = 126.59°

Stabilization of a Two-Coordinate [GeCl]⁺ Cation by Simultaneous σ and π Donation from a Monodentate Carbodiphosphorane

Give me four: The synthesis, structure, and reactivity of [GeCl]+ and [SnCl]+ cations bearing a carbodiphosphorane as ancillary ligand are presented. In the Ge compound, simultaneous σ and π donation from the carbodiphosphorane to Ge is observed (see HOMO (left) and HOMO−1 (right); C black, H white, P orange, Cl green, Ge purple (not visible)), whereas only the σ dative component is present in the Sn analogue

Catalytic reaction between adsorbed oxygen and hydrogen on Rh(111)

Abstract unavailable

The rat race of getting funded

In this creative writing piece, Dr. Thiel explores an alternate approach for the grant review process, ultimately concluding that the current pipeline is not inappropriately rigorous

Thomas Gellhaus, MD

Dr. Thomas Gellhaus, the recently appointed Division Director for General Obstetrics and Gynecology, brings to the Department a wealth of clinical experience and passions for teaching, advocacy, and providing care to patients in the developing world

Marygrace Elson, MD, MME

Marygrace Elson, MD, MME, joins us as guest editor for this issue of Proceedings in Obstetrics and Gynecology, which is focused on topics related to education. Dr. Elson is the Vice-Chair for Education, Residency Program Director, and Clinical Professor, Dr. William C. Keettel Chair of Obstetrics and Gynecology in the Department of Obstetrics and Gynecology at the University of Iowa