2,848 research outputs found
Closed-shell properties of O with {\em ab initio} coupled-cluster theory
We present an \emph{ab initio} calculation of spectroscopic factors for
neutron and proton removal from O using the coupled-cluster method and a
state-of-the-art chiral nucleon-nucleon interaction at
next-to-next-to-next-to-leading order. In order to account for the coupling to
the scattering continuum we use a Berggren single-particle basis that treats
bound, resonant, and continuum states on an equal footing. We report neutron
removal spectroscopic factors for the O states ,
, and , and proton removal spectroscopic factors for the
N states and . Our calculations support the accumulated
experimental evidence that O is a closed-shell nucleus.Comment: 5 pages, 2 figures, 1 tabl
Hybrid RHF/MP2 geometry optimizations with the Effective Fragment Molecular Orbital Method
The frozen domain effective fragment molecular orbital method is extended to
allow for the treatment of a single fragment at the MP2 level of theory. The
approach is applied to the conversion of chorismate to prephenate by chorismate
mutase, where the substrate is treated at the MP2 level of theory while the
rest of the system is treated at the RHF level. MP2 geometry optimization is
found to lower the barrier by up to 3.5 kcal/mol compared to RHF optimzations
and ONIOM energy refinement and leads to a smoother convergence with respect to
the basis set for the reaction profile. For double zeta basis sets the increase
in CPU time relative to RHF is roughly a factor of two.Comment: 11 pages, 3 figure
Interface of the polarizable continuum model of solvation with semi-empirical methods in the GAMESS program
An interface between semi-empirical methods and the polarized continuum model
(PCM) of solvation successfully implemented into GAMESS following the approach
by Chudinov et al (Chem. Phys. 1992, 160, 41). The interface includes energy
gradients and is parallelized. For large molecules such as ubiquitin a
reasonable speedup (up to a factor of six) is observed for up to 16 cores. The
SCF convergence is greatly improved by PCM for proteins compared to the gas
phase
Comment on: "Estimating the Hartree-Fock limit from finite basis set calculations" [Jensen F (2005) Theor Chem Acc 113:267]
We demonstrate that a minor modification of the extrapolation proposed by
Jensen [(2005): Theor Chem Acc 113:267] yields very reliable estimates of the
Hartree-Fock limit in conjunction with correlation consistent basis sets.
Specifically, a two-point extrapolation of the form
yields HF limits
with an RMS error of 0.1 millihartree using aug-cc-pVQZ and
aug-cc-pV5Z basis sets, and of 0.01 millihartree using aug-cc-pV5Z and
aug-cc-pV6Z basis sets.Comment: Theoretical Chemistry Accounts, in pres
The Optimal Route of Administration of the Glycoprotein IIb/IIIa Receptor Antagonist Abciximab During Percutaneous Coronary Intervention; Intravenous Versus Intracoronary
The use of the glycoprotein (GP) IIb/IIIa receptor antagonist Abciximab has over the years become an important part of the anticoagulant regimen in patients with acute coronary syndrome undergoing percutaneous coronary intervention. Abciximab is a potent inhibitor of platelet aggregation and thrombus formation, but other mechanisms, such as suppression of the inflammatory pathways, have also been proposed to contribute to the benefits of Abciximab
Protein structure validation and refinement using amide proton chemical shifts derived from quantum mechanics
We present the ProCS method for the rapid and accurate prediction of protein
backbone amide proton chemical shifts - sensitive probes of the geometry of key
hydrogen bonds that determine protein structure. ProCS is parameterized against
quantum mechanical (QM) calculations and reproduces high level QM results
obtained for a small protein with an RMSD of 0.25 ppm (r = 0.94). ProCS is
interfaced with the PHAISTOS protein simulation program and is used to infer
statistical protein ensembles that reflect experimentally measured amide proton
chemical shift values. Such chemical shift-based structural refinements,
starting from high-resolution X-ray structures of Protein G, ubiquitin, and SMN
Tudor Domain, result in average chemical shifts, hydrogen bond geometries, and
trans-hydrogen bond (h3JNC') spin-spin coupling constants that are in excellent
agreement with experiment. We show that the structural sensitivity of the
QM-based amide proton chemical shift predictions is needed to refine protein
structures to this agreement. The ProCS method thus offers a powerful new tool
for refining the structures of hydrogen bonding networks to high accuracy with
many potential applications such as protein flexibility in ligand binding.Comment: PLOS ONE accepted, Nov 201
Effective Interaction Techniques for the Gamow Shell Model
We apply a contour deformation technique in momentum space to the newly
developed Gamow shell model, and study the drip-line nuclei 5He, 6He and 7He. A
major problem in Gamow shell-model studies of nuclear many-body systems is the
increasing dimensionality of many-body configurations due to the large number
of resonant and complex continuum states necessary to reproduce bound and
resonant state energies. We address this problem using two different effective
operator approaches generalized to the complex momentum plane. These are the
Lee-Suzuki similarity transformation method for complex interactions and the
multi-reference perturbation theory method. The combination of these two
approaches results in a large truncation of the relevant configurations
compared with direct diagonalization. This offers interesting perspectives for
studies of weakly bound systems.Comment: 18 pages, 17 figs, Revtex
Towards a barrier height benchmark set for biologically relevant systems
We have collected computed barrier heights and reaction energies (and associated model structures) for five enzymes from studies published by Himo and co-workers. Using this data, obtained at the B3LYP/6- 311+G(2d,2p)[LANL2DZ]//B3LYP/6-31G(d,p) level of theory, we then benchmark PM6, PM7, PM7-TS, and DFTB3 and discuss the influence of system size, bulk solvation, and geometry re-optimization on the error. The mean absolute differences (MADs) observed for these five enzyme model systems are similar to those observed for PM6 and PM7 for smaller systems (10–15 kcal/mol), while DFTB results in a MAD that is significantly lower (6 kcal/mol). The MADs for PMx and DFTB3 are each dominated by large errors for a single system and if the system is disregarded the MADs fall to 4–5 kcal/mol. Overall, results for the condensed phase are neither more or less accurate relative to B3LYP than those in the gas phase. With the exception of PM7-TS, the MAD for small and large structural models are very similar, with a maximum deviation of 3 kcal/mol for PM6. Geometry optimization with PM6 shows that for one system this method predicts a different mechanism compared to B3LYP/6-31G(d,p). For the remaining systems, geometry optimization of the large structural model increases the MAD relative to single points, by 2.5 and 1.8 kcal/mol for barriers and reaction energies. For the small structural model, the corresponding MADs decrease by 0.4 and 1.2 kcal/mol, respectively. However, despite these small changes, significant changes in the structures are observed for some systems, such as proton transfer and hydrogen bonding rearrangements. The paper represents the first step in the process of creating a benchmark set of barriers computed for systems that are relatively large and representative of enzymatic reactions, a considerable challenge for any one research group but possible through a concerted effort by the community. We end by outlining steps needed to expand and improve the data set and how other researchers can contribute to the process
spectra in elementary cellular automata and fractal signals
We systematically compute the power spectra of the one-dimensional elementary
cellular automata introduced by Wolfram. On the one hand our analysis reveals
that one automaton displays spectra though considered as trivial, and on
the other hand that various automata classified as chaotic/complex display no
spectra. We model the results generalizing the recently investigated
Sierpinski signal to a class of fractal signals that are tailored to produce
spectra. From the widespread occurrence of (elementary) cellular
automata patterns in chemistry, physics and computer sciences, there are
various candidates to show spectra similar to our results.Comment: 4 pages (3 figs included
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