Biomedical subjects

Amir Karton

Publications and source records attributed to Amir Karton.

8 recordsLinked to original sources

PubMed2006

W4 theory for computational thermochemistry: In pursuit of confident sub-kJ/mol predictions.

In an attempt to improve on our earlier W3 theory [A. D. Boese et al., J. Chem. Phys. 120, 4129 (2004)] we consider such refinements as more accurate estimates for the contribution of connected quadruple excitations (T4), inclusion of connected quintuple excitations (T5), diagonal Born-Oppenheimer corrections (DBOC), and improved basis set extrapolation procedures. Revised experimental data for validation purposes were obtained from the latest version of the Active Thermochemical Tables thermochemical network. The recent CCSDT(Q) method offers a cost-effective way of estimating T4, but is insufficient by itself if the molecule exhibits some nondynamical correlation. The latter considerably slows down basis set convergence for T4, and anomalous basis set convergence in highly polar systems makes two-point extrapolation procedures unusable. However, we found that the CCSDTQ-CCSDT(Q) difference converges quite rapidly with the basis set, and that the formula 1.10[CCSDT(Q)cc-pVTZ+CCSDTQcc-pVDZ-CCSDT(Q)cc-pVDZ] offers a very reliable as well as fairly cost-effective estimate of the basis set limit T4 contribution. The T5 contribution converges very rapidly with the basis set, and even a simple double-zeta basis set appears to be adequate. The largest T5 contribution found in the present work is on the order of 0.5 kcal/mol (for ozone). DBOCs are significant at the 0.1 kcal/mol level in hydride systems. Post-CCSD(T) contributions to the core-valence correlation energy are only significant at that level in systems with severe nondynamical correlation effects. Based on the accumulated experience, a new computational thermochemistry protocol for first- and second-row main-group systems, to be known as W4 theory, is proposed. Its computational cost is not insurmountably higher than that of the earlier W3 theory, while performance is markedly superior. Our W4 atomization energies for a number of key species are in excellent agreement (better than 0.1 kcal/mol on average, 95% confidence intervals narrower than 1 kJ/mol) with the latest experimental data obtained from Active Thermochemical Tables. Lower-cost variants are proposed: the sequence W1-->W2.2-->W3.2-->W4lite-->W4 is proposed as a converging hierarchy of computational thermochemistry methods. A simple a priori estimate for the importance of post-CCSD(T) correlation contributions (and hence a pessimistic estimate for the error in a W2-type calculation) is proposed.

Journal Article↗

PubMed2006

The lowest singlet-triplet excitation energy of BN: A converged coupled cluster perspective.

The notoriously small X 3Pi-a 1Sigma+ excitation energy of the BN diatomic has been calculated using high-order coupled cluster methods. Convergence has been established in both the one-particle basis set and the coupled cluster expansion. Explicit inclusion of connected quadruple excitations T4 is required for even semiquantitative agreement with the limit value, while connected quintuple excitations T5 still have an effect of about 60 cm(-1). Still higher excitations only account for about 10 cm(-1). Inclusion of inner-shell correlation further reduces Te by about 60 cm(-1) at the CCSDT, and 85 cm(-1) at the CCSDTQ level. Our best estimate, Te = 183+/-40 cm(-1), is in excellent agreement with earlier calculations and experiment, albeit with a smaller (and conservative) uncertainty. The dissociation energy of BN(X 3Pi) is De = 105.74+/-0.16 kcal/mol and D0 = 103.57+/-0.16 kcal/mol.

Journal Article↗

PubMed2006

Selective sp3 C-H activation of ketones at the beta position by Ir(I). Origin of regioselectivity and water effect.

The reaction of the cationic (PNP)Ir(I)(cyclooctene) complex (1) (PNP = 2,6-bis-(di-tert-butylphosphinomethyl)pyridine) with 2-butanone or 3-pentanone results in the selective, quantitative activation of a beta C-H bond, yielding O,C-chelated complexes. Calculations show that the selectivity is both kinetically (because of steric reasons in the rate determingin step (RDS)) and thermodynamically controlled, the latter as a result of carbonyl oxygen coordination in the product. The RDS is formation of the eta2-C,H intermediates from the complexed ketone intermediates. Water has a strong influence on the regioselectivity, and in its presence, reaction of 1 with 2-butanone gives also the alpha terminal C-H activation product. Computational studies suggest that water can stabilize the terminal alpha C-H activation product by hydrogen bonding, forming a six-membered ring with the ketone, as experimentally observed in the X-ray structure of the acetonyl hydride aqua complex.

Journal Article↗

PubMed2006

Benchmark study of DFT functionals for late-transition-metal reactions.

The performance of a wide variety of DFT exchange-correlation functionals for a number of late-transition-metal reaction profiles has been considered. Benchmark ab-initio reference data for the prototype reactions Pd + H2, Pd + CH4, Pd + C2H6 (both C-C and C-H activation), and Pd + CH3Cl are presented, while ab-initio data of lesser quality were obtained for the catalytic hydrogenation of acetone and for the low-oxidation-state and high-oxidation-state mechanisms of the Heck reaction. "Kinetics" functionals such as mPW1K, PWB6K, BB1K, and BMK clearly perform more poorly for late-transition-metal reactions than for main-group reactions, as well as compared to general-purpose functionals. There is no single "best functional" for late-transition-metal reactions, but rather a cluster of several functionals (PBE0, B1B95, PW6B95, and TPSS25B95) that perform about equally well; if main-group thermochemical performance is additionally considered, then B1B95 and PW6B95 emerge as the best performers. TPSS25B95 and TPSS33B95 offer attractive performance compromises if weak interactions and main-group barrier heights, respectively, are also important. In the ab-initio calculations, basis set superposition errors (BSSE) can be greatly reduced by ensuring that the metal spd shell has sufficient radial flexibility in the high-exponent range. Optimal HF percentages in hybrid functionals depend on the class of systems considered, increasing from anions to neutrals to cations to main-group barrier heights; transition-metal barrier heights represent an intermediate situation. The use of meta-GGA correlation functionals appears to be quite beneficial.

Journal Article↗

PubMed2005

Platinum stilbazoles: ring-walking coupled with aryl-halide bond activation.

The reaction between tetrakis(triethylphosphine)platinum(0) and 4-[trans-2-(4-bromophenyl)vinyl]pyridine (1) is examined. Initially, the metal center coordinates to the bridging double bond of 1. Complexes 2 and 3 were fully characterized, and their X-ray crystallography structures are presented. Upon heating, either in solution or in the solid state, complex 2 undergoes C-Br oxidative addition to give complex 3. Kinetic studies revealed that this conversion is unimolecular and does not involve dissociation of the metal center from the double bond. Density functional studies show that a plausible mechanism involves the metal center "walking" around the pi-system from the bridging C=C double bond to the C-Br bond.

Journal Article↗

PubMed2005

NLO properties of metallabenzene-based chromophores: a time-dependent density functional study.

The static and dynamic first hyperpolarizabilities for a series of substituted metallabenzene-based nonlinear optical (NLO) chromophores were determined by time-dependent density functional theory (TDDFT). The electronic excitation contributions to the first hyperpolarizability are rationalized in terms of the two-level model. The effects on the hyperpolarizabilities of (a) the metal center (Os, Ir, Pt); (b) the ligand environment (PH3, CO, Cl); (c) various donor and acceptor substituents (NH2, OH, Me, H, Cl, Br, I, COOMe, COOH, CN, NO2); and (d) the length of pi-conjugation were studied. Our calculations predict that metallabenzenes have significant second-order NLO susceptibilities, ranging from = 1.0 x 10(-29) to 5.6 x 10(-28) esu and from mu = 3.0 x 10(-47) to 1.1 x 10(-44) esu, that can be tuned by changing the metal center and/or ligand environment.

Journal Article↗

PubMed2004

Stable room-temperature molecular negative differential resistance based on molecule-electrode interface chemistry.

We show reproducible, stable negative differential resistance (NDR) at room temperature in molecule-controlled, solvent-free devices, based on reversible changes in molecule-electrode interface properties. The active component is the cyclic disulfide end of a series of molecules adsorbed onto mercury. As this active component is reduced, the Hg-molecule contact is broken, and an insulating barrier at the molecule-electrode interface is formed. Therefore, the alignment of the molecular energy levels, relative to the Fermi levels of the electrodes, is changed. This effect results in a decrease in the current with voltage increase as the reduction process progresses, leading to the so-called NDR behavior. The effect is reproducible and repeatable over more than 50 scans without any reduction in the current. The stability of the system, which is in the "solid state" except for the Hg, is due to the molecular design where long alkyl chains keep the molecules aligned with respect to the Hg electrode, even when they are not bound to it any longer.

Journal Article↗

PubMed2004

Real-time 2D NMR identification of analytes undergoing continuous chromatographic separation.

We have recently proposed and demonstrated an approach that enables the acquisition of multidimensional nuclear magnetic resonance (NMR) spectra within a single scan. A promising application opened up by this new accelerated form of data acquisition concerns the possibility of monitoring in real time the chemical nature of analytes subject to a continuous flow. The present paper illustrates such potential, with the real-time acquisition of a series of 2D 1H NMR spectra arising from a mixture of compounds subject to a continuous liquid chromatography (LC) separation. This real-time 2D NMR identification of chemicals eluted minutes apart under usual LC-NMR conditions differs from the way in which LC-2D NMR has hitherto been carried out, which relies on stopped-flow modes of operations whereby fractions are first collected and then subject to individual, aliquot-by-aliquot analyses. The real-time LC-2D NMR experiment hereby introduced can be implemented in a straightforward manner using modern commercial LC-NMR hardware, thus opening up immediate possibilities in high-throughput characterizations of complex molecules.

Chromatography, Liquid↗