Photoselective Chemistry

Jortner, Joshua; Levine, R. D.

doi:10.1002/9780470142677.ch1

Cited by 90 publications

(8 citation statements)

References 322 publications

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“…Specifically, here, we present techniques to probe: (a) the role of active site molecular vibrations and the mechanism by which these couple to facilitate H/D transfer, (b) the isotope dependence of such coupling, and (c) common vibrational characteristics between multiple productive trajectories. The methods discussed in this section are closely related to the approaches in refs − and are motivated by the idea of energy redistribution in chemical systems. − …”

Section: Methods To Quantitatively Gauge the Effect Of Active Site Vi...mentioning

confidence: 99%

Active Site Dynamical Effects in the Hydrogen Transfer Rate-limiting Step in the Catalysis of Linoleic Acid by Soybean Lipoxygenase-1 (SLO-1): Primary and Secondary Isotope Contributions

et al. 2015

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Using ab initio molecular dynamics (AIMD) simulations that facilitate the treatment of rare events, we probe the active site participation in the rate-determining hydrogen transfer step in the catalytic oxidation of linoleic acid by soybean lipoxygenase-1 (SLO-1). The role of two different active site components is probed. (a) On the hydrogen atom acceptor side of the active site, the hydrogen bonding propensity between the acceptor side hydroxyl group, which is bound to the iron cofactor, and the backbone carboxyl group of isoleucine (residue number 839) is studied toward its role in promoting the hydrogen transfer event. Primary and secondary (H/D) isotope effects are also probed and a definite correlation with subtle secondary H/D isotope effects is found. With increasing average nuclear kinetic energy, the increase in transfer probability is enhanced due to the presence of the hydrogen bond between the backbone carbonyl of I839 and the acceptor oxygen. Further increase in average nuclear kinetic energy reduces the strength of this secondary hydrogen bond which leads to a deterioration in hydrogen transfer rates and finally embrances an Arrhenius-like behavior. (b) On the hydrogen atom donor side, the coupling between vibrational modes predominantly localized on the donor-side linoleic acid group and the reactive mode is probed. There appears to be a qualitative difference in the coupling between modes that belong to linoleic acid and the hydrogen transfer mode, for hydrogen and deuterium transfer. For example, the donor side secondary hydrogen atom is much more labile (by nearly a factor of 5) during deuterium transfer as compared to the case for hydrogen transfer. This appears to indicate a greater coupling between the modes belonging to the linoleic acid scaffold and the deuterium transfer mode and also provides a new rationalization for the abnormal (nonclassical) secondary isotope effect results obtained by Knapp, Rickert, and Klinman in J. Am. Chem. Soc. , 2002 , 124 , 3865 . To substantiate our findings noted in point a above, we have suggested an I839 → A839 or I839 → V839 mutation. This will modify the bulkiness of hydrogen the bonding residue, allowing greater flexibility in the secondary hydrogen bond formation highlighted above and adversely affecting the reaction rate.

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Section: Methods To Quantitatively Gauge the Effect Of Active Site Vi...mentioning

confidence: 99%

Active Site Dynamical Effects in the Hydrogen Transfer Rate-limiting Step in the Catalysis of Linoleic Acid by Soybean Lipoxygenase-1 (SLO-1): Primary and Secondary Isotope Contributions

et al. 2015

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“…With a universal presence in all molecules and solids, van der Waals forces (vdW) are important interactions to consider in the study of matter. − Although weak in comparison to chemical bonds, their long-range nature and their collective effect play a decisive role in the structure of molecules and their interaction with surfaces. − Nevertheless, their description from first principles has proven to be challenging. Most of the common theoretical methods, such as the density functional theory (DFT), fail to describe them properly.…”

Section: Introductionmentioning

confidence: 99%

Effects of van der Waals Interactions in the Adsorption of Isooctane and Ethanol on Fe(100) Surfaces

et al. 2014

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van der Waals (vdW) forces play a fundamental role in the structure and behavior of diverse systems. Because of development of functionals that include nonlocal correlation, it is possible to study the effects of vdW interactions in systems of industrial and tribological interest. Here we simulated within the framework of density functional theory (DFT) the adsorption of isooctane (2,2,4-trimethylpentane) and ethanol on an Fe(100) surface, employing various exchange–correlation functionals to take vdW forces into account. In particular, this paper discusses the effect of vdW forces on the magnitude of adsorption energies, equilibrium geometries, and their role in the binding mechanism. According to our calculations, vdW interactions increase the adsorption energies and reduce the equilibrium distances. Nevertheless, they do not influence the spatial configuration of the adsorbed molecules. Their effect on the electronic density is a nonisotropic, delocalized accumulation of charge between the molecule and the slab. In conclusion, vdW forces are essential for the adsorption of isooctane and ethanol on a bcc Fe(100) surface.

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“…In the statistical limit, IVR involves the decay of a vibrational mode, i.e., a doorway state, to the vibronic quasicontinuum (7). IVR in the statistical limit was central in the description of high-order molecular multiphoton excitation and dissociation processes (89), laying foundations for photoselective laser chemistry (89). In the 1980s spectroscopic evidence emerged for the identification of the onset of the vibronic quasicontinuum in cold, isolated, large molecules (90,91).…”

Section: Radiationless Transitionsmentioning

confidence: 99%

REFLECTIONS ON PHYSICAL CHEMISTRY: Science and Scientists

Jortner

2006

Annu. Rev. Phys. Chem.

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Key Words physical chemistry in Israel, radiationless transitions, chemical and biological electron transfer, dynamics of finite systems, structure-dynamics-function relations ■ Abstract This is the story of a young person who grew up in Tel-Aviv during the period of the establishment of the State of Israel and was inspired to become a physical chemist by the cultural environment, by the excellent high-school education, and by having been trained by some outstanding scientists at the Hebrew University of Jerusalem and, subsequently, by the intellectual environment and high-quality scientific endeavor at the University of Chicago. Since serving as the first chairman of the Chemistry Department of the newly formed Tel-Aviv University he has been immersed in research, in the training of young scientists, and in intensive and extensive international scientific collaboration. Together with the members of his "scientific family" he has explored the phenomena of energy acquisition, storage and disposal and structure-dynamics-function relations in large molecules, condensed phase, clusters and biomolecules, and is looking forward to many future adventures in physical chemistry. "What to leave out and what to put in? That

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Photoselective Chemistry

Cited by 90 publications

References 322 publications

Active Site Dynamical Effects in the Hydrogen Transfer Rate-limiting Step in the Catalysis of Linoleic Acid by Soybean Lipoxygenase-1 (SLO-1): Primary and Secondary Isotope Contributions

Active Site Dynamical Effects in the Hydrogen Transfer Rate-limiting Step in the Catalysis of Linoleic Acid by Soybean Lipoxygenase-1 (SLO-1): Primary and Secondary Isotope Contributions

Effects of van der Waals Interactions in the Adsorption of Isooctane and Ethanol on Fe(100) Surfaces

REFLECTIONS ON PHYSICAL CHEMISTRY: Science and Scientists

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