1,721,230 research outputs found
Probing the Rhodopsin Cavity with Reduced Retinal Models at the CASPT2//CASSCF/AMBER Level of Theory
No full textWe show that the ab initio CASPT2//CASSCF strategy previously used to investigate the ground and excited states of the chromophore of the vision receptor rhodopsin (Rh) in vacuo can be successfully implemented in a QM/MM scheme allowing for CASPT2//CASSCF/AMBER geometry optimization and excited state property evaluation in proteins. Two receptor models (Rh-1 and Rh-2) incorporating different reduced chromophores are investigated. It is shown that Rh-2 features a chromophore equilibrium structure with the correct helicity and a λmax that is only 52 nm blue-shifted from the observed value. This result should open the way to a qualitatively correct ab initio QM/MM modeling of the early excited state transient species involved in the vision process. Copyright © 2003 American Chemical Society
From a one-mode to a multi-mode understanding of conical intersection mediated ultrafast organic photochemical reactions
Full text linkOver the last few decades, conical intersections (CoIns) have grown from theoretical curiosities into common mechanistic features of photochemical reactions, whose function is to funnel electronically excited molecules back to their ground state in regions where the potential energy surfaces (PESs) of two electronic states become degenerate. Analogous to transition states in thermal chemistry, CoIns appear as transient structures providing a kinetic bottleneck along a reaction coordinate. However, such a bottleneck is not associated with the probability of crossing an energy barrier but rather with an excited state decay probability along a full "line" of transient structures connected by non-reactive modes, the intersection space (IS). This article will review our understanding of the factors controlling CoIn mediated ultrafast photochemical reactions, taking a physical organic chemist approach by discussing a number of case studies for small organic molecules and photoactive proteins. Such discussion will be carried out by first introducing the "standard" one-mode model based on Landau-Zener (LZ) theory to describe a reactive excited state decay event intercepting, locally, a single CoIn along a single direction, and then by providing a modern perspective based on the effects of the phase matching of multiple modes on the same local event, thus redefining and expanding the description of the excited state reaction coordinate. The direct proportionality between the slope (or velocity) along one mode and decay probability at a single CoIn is a widely applied fundamental principle that follows from the LZ model, yet it fails to provide a complete understanding of photochemical reactions whose local reaction coordinate changes along the IS. We show that in these situations, in particular by focussing on rhodopsin double bond photoisomerization, it is mandatory to consider additional molecular modes and their phase relationship approaching the IS, hence providing a key mechanistic principle of ultrafast photochemistry based on the phase matching of those modes. We anticipate that this qualitative mechanistic principle should be considered in the rational design of any ultrafast excited state process, impacting various fields of research ranging from photobiology to light-driven molecular devices
Chemical Selectivity through Control of Excited–State Dynamics
No full text(Graph Presented) Trust is good, control is better: In thermal processes in which the interconversion of reactant conformers R1/2 is faster than the reaction itself, selectivity can be tailored by modulating the energy barriers of competing reaction paths. Ultrafast photoexcitation promotes separate conformers to different regions of the potential energy surface, where the wave packet may reach different conical intersections CI1/2, giving rise to product selectivity (P1/2). © 2008 Wiley-VCH Verlag GmbH & Co. KGaA
Designing Conical Intersections for Light-Driven Single Molecule Rotary Motors: From Precessional to Axial Motion
Full text linkIn the past, the design of light-driven single molecule rotary motors has been mainly guided by the modification of their ground-state conformational properties. Further progress in this field is thus likely to be achieved through a detailed understanding of light-induced dynamics of the system and the ways of modulating it by introducing chemical modifications. In the present theoretical work, the analysis of model organic chromophores and synthesized rotary motors is used for rationalizing the effect of electron-withdrawing heteroatoms (such as a cationic nitrogen) on the topography and branching plane of mechanistically relevant conical intersections. Such an analysis reveals how the character of rotary motion could be changed from a precessional motion to an axial rotational motion. These concepts are then used to design and build quantum chemical models of three distinct types of Schiff base rotary motors. One of these models, featuring the synthetically viable indanylidenepyrroline framework, has conical intersection structures consistent with an axial rotation not hindered by ground-state conformational barriers. It is expected that this type of motor should be capable of funneling the photon energy into specific rotary modes, thus achieving photoisomerization quantum efficiencies comparable to those seen in visual pigments. © 2014 American Chemical Society
Photochemical processes: potential energy surface topology and rationalization using VB arguments
No full textThe development of quantum chemical methods capable of treating excited and ground states of organic molecules in a balanced way has prompted many applications in the field of mechanistic organic photochemistry. In this paper, we review a few representative computational results which illustrate the currently emerging concept of a photochemical (and photophysical) reaction pathway. In particular, we focus on the shape (topology) of the potential energy surface along the excited state branch of the reaction path as well as on the shape and nature of the photochemical funnel where decay to the ground state occurs. The chemical effect of different topologies and their origin in terms of simple valence bond ideas are discussed. (C) 2001 Elsevier Science B.V. All rights reserved
How Does the Relocation of Internal Water Affect Resonance Raman Spectra of Rhodopsin? An Insight from CASSCF/Amber Calculations
Full text linkThe effect of relocation of the W2 crystallographic water in bovine rhodopsin has been investigated by comparing and analyzing simulated resonance Raman spectra of 1HZX- and 1U19-based quantum mechanics/molecular mechanics (CASSCF/MM) models. The main target is to explore the sensitivity of the simulated resonance Raman spectra to protein cavity change. In particular, we focus on a quantitative investigation of the changes in the vibrational activity of rhodopsin induced by modifications in the protein cavity structure and in the water position. Comparison of the simulated RR spectra of the Rh-1U19 and Rh-1HZX models with the measured spectrum of rhodopsin reveals that the Rh-1U19 model provides a slightly better rhodopsin model consistently with the simulations of the absorption maxima. On the other hand, and irrespective of the comparison with the experimental data, the analysis of two different computational models for the same protein and chromophore makes it possible to investigate and disentangle the relationship between structural features and change in the RR intensities in an unusually detailed way. © 2009 American Chemical Society
Basic Concepts of Electronic Excited States
No full textThis chapter is intended to identify some of the central concepts associated with excited state computation. So it is more like a “tutorial” rather than a review, with an emphasis on work carried out in the authors’ laboratories. The concepts we will discuss include gradients, conical intersections, and non-adiabatic dynamics, and are central to all the topics discussed in the specialist reviews that follow
A VB Model of Transition Structure Regions of the Potential Energy Surfaces for Forbidden and Allowed Cycloaddition Reactions
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