Closed-shell properties of 24^{24}O with {\em ab initio} coupled-cluster theory

We present an \emph{ab initio} calculation of spectroscopic factors for neutron and proton removal from $^{24}$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 $^{23}$O states $J^{\pi} = 1/2^+$, $5/2^+$, $3/2^-$ and $1/2^-$, and proton removal spectroscopic factors for the $^{23}$N states $1/2^-$ and $3/2^-$. Our calculations support the accumulated experimental evidence that $^{24}$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 $E_{HF,L}=E_{HF,\infty}+A(L+1)\exp(-9\sqrt{L})$ yields HF limits $E_{HF,\infty}$ 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

1/fα1/f^\alpha 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 $1/f$ spectra though considered as trivial, and on the other hand that various automata classified as chaotic/complex display no $1/f$ spectra. We model the results generalizing the recently investigated Sierpinski signal to a class of fractal signals that are tailored to produce $1/f^{\alpha}$ 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

Frequency-Dependent Current Noise through Quantum-Dot Spin Valves

We study frequency-dependent current noise through a single-level quantum dot connected to ferromagnetic leads with non-collinear magnetization. We propose to use the frequency-dependent Fano factor as a tool to detect single-spin dynamics in the quantum dot. Spin precession due to an external magnetic and/or a many-body exchange field affects the Fano factor of the system in two ways. First, the tendency towards spin-selective bunching of the transmitted electrons is suppressed, which gives rise to a reduction of the low-frequency noise. Second, the noise spectrum displays a resonance at the Larmor frequency, whose lineshape depends on the relative angle of the leads' magnetizations.Comment: 12 pages, 15 figure