Dynamic Electron Correlation Effects On The Ground State Potential Energy Surface Of A Retinal Chromophore Model

The ground state potential energy surface of the retinal chromophore of visual pigments (e.g., bovine rhodopsin) features a low-lying conical intersection surrounded by regions with variable charge transfer and diradical electronic structures. This implies that dynamic electron correlation may have a large effect on the shape of the force fields driving its reactivity. To investigate this effect, we focus on mapping the potential energy for three paths located along the ground state CASSCF potential energy surface of the penta-2,4-dieniminium cation taken as a minimal model of the retinal chromophore. The first path spans the bond length alternation coordinate and intercepts a conical intersection point. The other two are minimum energy paths along two distinct but kinetically competitive thermal isomerization coordinates. We show that the effect of introducing the missing dynamic electron correlation variationally (with MRCISD) and perturbatively (with the CASPT2, NEVPT2, and XMCQDPT2 methods) leads, invariably, to a stabilization of the regions with charge transfer character and to a significant reshaping of the reference CASSCF potential energy surface and suggesting a change in the dominating isomerization mechanism. The possible impact of such a correction on the photoisomerization of the retinal chromophore is discussed

Toward An Understanding Of The Retinal Chromophore In Rhodopsin Mimics

Recently, a rhodopsin protein mimic was constructed by combining mutants of the cellular retinoic acid binding protein II (CRABPII) with an all-trans retinal chromophore. Here, we present a combine computational quantum mechanics/molecular mechanics (QM/MM) and experimental ultrafast kinetic study of CRABPII. We employ the QM/MM models to study the absorption (lambda(a)(max)), fluorescence (lambda(f)(max)), and reactivity of a CRABPII triple mutant incorporating the all-trans protonated chromophore (PSB-KLE-CRABPII). We also study the spectroscopy of the same mutant incorporating the unprotonated chromophore and of another double mutant incorporating the neutral unbound retinal molecule held inside the pocket. Finally, for PSB-KLE-CRABPII, stationary fluorescence spectroscopy and ultrafast transient absorption spectroscopy resolved two different evolving excited state populations which were computationally assigned to distinct locally excited and charge-transfer species. This last species is shown to evolve along reaction paths describing a facile isomerization of the biologically relevant 11-cis and 13-cis double bonds. This work represents a first exploratory attempt to model and study these artificial protein systems. It also indicates directions for improving the QM/MM models so that they could be more effectively used to assist the bottom-up design of genetically encodable probes and actuators employing the retinal chromophore

Pickup ions at Dione and Enceladus: Cassini Plasma Spectrometer simulations

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/95406/1/jgra16800.pd

Chemical kinetics in an atmospheric pressure helium plasma containing humidity

Atmospheric pressure plasmas are sources of biologically active oxygen and nitrogen species, which makes them potentially suitable for the use as biomedical devices. Here, experiments and simulations are combined to investigate the formation of the key reactive oxygen species, atomic oxygen (O) and hydroxyl radicals (OH), in a radio-frequency driven atmospheric pressure plasma jet operated in humidified helium. Vacuum ultra-violet high-resolution Fourier-transform absorption spectroscopy and ultra-violet broad-band absorption spectroscopy are used to measure absolute densities of O and OH. These densities increase with increasing H 2 O content in the feed gas, and approach saturation values at higher admixtures on the order of 3 × 10 14 cm −3 for OH and 3 × 10 13 cm −3 for O. Experimental results are used to benchmark densities obtained from zero-dimensional plasma chemical kinetics simulations, which reveal the dominant formation pathways. At low humidity content, O is formed from OH + by proton transfer to H 2 O, which also initiates the formation of large cluster ions. At higher humidity content, O is created by reactions between OH radicals, and lost by recombination with OH. OH is produced mainly from H 2 O + by proton transfer to H 2 O and by electron impact dissociation of H 2 O. It is lost by reactions with other OH molecules to form either H 2 O + O or H 2 O 2 . Formation pathways change as a function of humidity content and position in the plasma channel. The understanding of the chemical kinetics of O and OH gained in this work will help in the development of plasma tailoring strategies to optimise their densities in applications

An Analysis of Artificial Rhodopsin Mimics Using Multiconfigurational Ab Initio Computations

Rhodopsin proteins are found in a wide range of organisms and perform a variety of functions. Vertebrate rhodopsins signal the G-protein transducin in the first step of the visual process while microbial rhodopsins can act as ion pumps or trigger phototaxis. In all varieties it is the retinyl chromophore that endows function to the protein by undergoing a light-initiated isomerization. Using bottom-up engineering, the retinyl chromophore has previously been incorporated into protein frameworks based on Cellular Retinoic Acid Binding Protein II (CRABPII). Two of these “rhodopsin mimics” are studied in this work. A quantum mechanics / molecular mechanics protocol based on ab initio multiconfigurational quantum chemistry was constructed to model the spectral and dynamic features of rhodopsin mimics. The accuracy of the models is established by showing that computations reproduce the observed absorption maxima of both mutants. The mechanism of spectral tuning is investigated in mutants incorporating a variety of forms of retinyl chromophore, including both the protonated and deprotonated all-trans Schiff base chromophore and non-covalently bound retinal. Exploration of the excited state potential energy surface reveal two minima from which fluorescence can occur in the R132K:R111L:L121E (KLE) mutant of CRABPII, findings which were supported by ultrafast transient absorption spectra that resolved two different evolving S1 populations. The KLE mutant is compared to solvated protonated all-trans retinal Schiff base (PSBAT) and both systems are found to be highly similar in terms of calculated absorption maxima and possible photoreactivity, as ascertained from relaxed scans performed on the KLE mutant

An Analysis of Artificial Rhodopsin Mimics Using Multiconfigurational Ab Initio Computations

Rhodopsin proteins are found in a wide range of organisms and perform a variety of functions. Vertebrate rhodopsins signal the G-protein transducin in the first step of the visual process while microbial rhodopsins can act as ion pumps or trigger phototaxis. In all varieties it is the retinyl chromophore that endows function to the protein by undergoing a light-initiated isomerization. Using bottom-up engineering, the retinyl chromophore has previously been incorporated into protein frameworks based on Cellular Retinoic Acid Binding Protein II (CRABPII). Two of these “rhodopsin mimics” are studied in this work. A quantum mechanics / molecular mechanics protocol based on ab initio multiconfigurational quantum chemistry was constructed to model the spectral and dynamic features of rhodopsin mimics. The accuracy of the models is established by showing that computations reproduce the observed absorption maxima of both mutants. The mechanism of spectral tuning is investigated in mutants incorporating a variety of forms of retinyl chromophore, including both the protonated and deprotonated all-trans Schiff base chromophore and non-covalently bound retinal. Exploration of the excited state potential energy surface reveal two minima from which fluorescence can occur in the R132K:R111L:L121E (KLE) mutant of CRABPII, findings which were supported by ultrafast transient absorption spectra that resolved two different evolving S1 populations. The KLE mutant is compared to solvated protonated all-trans retinal Schiff base (PSBAT) and both systems are found to be highly similar in terms of calculated absorption maxima and possible photoreactivity, as ascertained from relaxed scans performed on the KLE mutant

Carbon suboxide in comet Halley?

OBSERVATIONAL data acquired during the recent appearance of comet Halley pose a puzzle about the nature and distribution of elemental carbon and carbonaceous material in its nucleus and coma. The nucleus is darker even than coal (albedo <4%), suggesting that its volatile ices contain a few per cent of carbonaceous material in the form of graphitic or amorphous carbon. The very high abundance of light elements in the coma dust, particularly H, C, N and O, suggests the presence of a significant organic component. The emission feature near 3.4 μm also implies the presence of organic material in the dust. But the parent species for the primary carbon-containing material that have been identified so far (such as CO, CO_2 and CH_4) are not present in sufficient quantities to account for all of it. Here we propose that an additional contribution from carbon suboxide (C_3O_2) in the coma dust and the nucleus material is consistent with the observational data. A production rate in the coma for C_3O_2 of about 0.03–0.04 times that of water would provide the distributed source of elemental carbon and CO within 10^4 km of the nucleus that is required to explain the data from the Giotto spacecraft and from ground-based observations

Dynamic Electron Correlation Effects on the Ground State Potential Energy Surface of a Retinal Chromophore Model

The ground state potential energy surface of the retinal chromophore of visual pigments (e.g., bovine rhodopsin) features a low-lying conical intersection surrounded by regions with variable charge-transfer and diradical electronic structures. This implies that dynamic electron correlation may have a large effect on the shape of the force fields driving its reactivity. To investigate this effect, we focus on mapping the potential energy for three paths located along the ground state CASSCF potential energy surface of the penta-2,4-dieniminium cation taken as a minimal model of the retinal chromophore. The first path spans the bond length alternation coordinate and intercepts a conical intersection point. The other two are minimum energy paths along two distinct but kinetically competitive thermal isomerization coordinates. We show that the effect of introducing the missing dynamic electron correlation variationally (with MRCISD) and perturbatively (with the CASPT2, NEVPT2, and XMCQDPT2 methods) leads, invariably, to a stabilization of the regions with charge transfer character and to a significant reshaping of the reference CASSCF potential energy surface and suggesting a change in the dominating isomerization mechanism. The possible impact of such a correction on the photoisomerization of the retinal chromophore is discussed

Dynamic Electron Correlation Effects on the Ground State Potential Energy Surface of a Retinal Chromophore Model

The ground state potential energy surface of the retinal chromophore of visual pigments (e.g., bovine rhodopsin) features a low-lying conical intersection surrounded by regions with variable charge-transfer and diradical electronic structures. This implies that dynamic electron correlation may have a large effect on the shape of the force fields driving its reactivity. To investigate this effect, we focus on mapping the potential energy for three paths located along the ground state CASSCF potential energy surface of the penta-2,4-dieniminium cation taken as a minimal model of the retinal chromophore. The first path spans the bond length alternation coordinate and intercepts a conical intersection point. The other two are minimum energy paths along two distinct but kinetically competitive thermal isomerization coordinates. We show that the effect of introducing the missing dynamic electron correlation variationally (with MRCISD) and perturbatively (with the CASPT2, NEVPT2, and XMCQDPT2 methods) leads, invariably, to a stabilization of the regions with charge transfer character and to a significant reshaping of the reference CASSCF potential energy surface and suggesting a change in the dominating isomerization mechanism. The possible impact of such a correction on the photoisomerization of the retinal chromophore is discussed