Yoelvis Orozco-Gonzalez

Bio: Yoelvis Orozco-Gonzalez is an academic researcher from Georgia State University. The author has contributed to research in topics: Excited state & Flavin group. The author has an hindex of 11, co-authored 23 publications receiving 269 citations. Previous affiliations of Yoelvis Orozco-Gonzalez include Bowling Green State University & University of São Paulo.

Toward Automatic Rhodopsin Modeling as a Tool for High-Throughput Computational Photobiology

Abstract: We report on a prototype protocol for the automatic and fast construction of congruous sets of QM/MM models of rhodopsin-like photoreceptors and of their mutants. In the present implementation the information required for the construction of each model is essentially a crystallographic structure or a comparative model complemented with information on the protonation state of ionizable side chains and distributions of external counterions. Starting with such information, a model formed by a fixed environment system, a flexible cavity system, and a chromophore system is automatically generated. The results of the predicted vertical excitation energy for 27 different rhodopsins including vertebrate, invertebrate, and microbial pigments indicate that such basic models could be employed for predicting trends in spectral changes and/or correlate the spectral changes with structural variations in large sets of proteins.

Fluorescence Enhancement of a Microbial Rhodopsin via Electronic Reprogramming

Abstract: The engineering of microbial rhodopsins with enhanced fluorescence is of great importance in the expanding field of optogenetics. Here we report the discovery of two mutants (W76S/Y179F and L83Q) of a sensory rhodopsin from the cyanobacterium Anabaena PCC7120 with opposite fluorescence behavior. In fact, while W76S/Y179F displays, with respect to the wild-type protein, a nearly 10-fold increase in red-light emission, the second is not emissive. Thus, the W76S/Y179F, L83Q pair offers an unprecedented opportunity for the investigation of fluorescence enhancement in microbial rhodopsins, which is pursued by combining transient absorption spectroscopy and multiconfigurational quantum chemistry. The results of such an investigation point to an isomerization-blocking electronic effect as the direct cause of instantaneous (subpicosecond) fluorescence enhancement.

Electronic spectra of flavin in different redox and protonation states: a computational perspective on the effect of the electrostatic environment

Abstract: Flavins are versatile molecules due to their ability to exist in multiple redox and protonation states At physiological conditions, they are usually encountered either as oxidized quinones, neutral semiquinones, anionic semiquinones, neutral hydroquinones, or anionic hydroquinones We compute the electronic near-UV/vis spectra for flavin in each of these five states Specifically, we compute vertical, adiabatic, and vibronic excitations for all excited states that have wavelengths longer than 300 nm We employ the calculations to assign the peaks in the corresponding experimental UV/vis spectra from literature We also compare the effect of polar and non-polar solvents on the spectra using a polarizable continuum model Finally, we construct “electrostatic spectral tuning maps” for prominent peaks in each of the five states These maps qualitatively describe how the flavin electronic spectra will be shifted by an anisotropic electrostatic environment such as a protein Understanding how flavin's UV/vis absorption spectrum is modulated by its environment can aid in experiments employing flavin as a probe of internal electrostatics of a protein and in engineering new color variants of flavoproteins

Theoretical study of the absorption and nonradiative deactivation of 1-nitronaphthalene in the low-lying singlet and triplet excited states including methanol and ethanol solvent effects.

Abstract: The photophysics of the 1-nitronaphthalene molecular system, after the absorption transition to the first singlet excited state, is theoretically studied for investigating the ultrafast multiplicity change to the triplet manifold. The consecutive transient absorption spectra experimentally observed in this molecular system are also studied. To identify the electronic states involved in the nonradiative decay, the minimum energy path of the first singlet excited state is obtained using the complete active space self-consistent field//configurational second-order perturbation approach. A near degeneracy region was found between the first singlet and the second triplet excited states with large spin-orbit coupling between them. The intersystem crossing rate was also evaluated. To support the proposed deactivation model the transient absorption spectra observed in the experiments were also considered. For this, computer simulations using sequential quantum mechanic-molecular mechanic methodology was used to consider the solvent effect in the ground and excited states for proper comparison with the experimental results. The absorption transitions from the second triplet excited state in the relaxed geometry permit to describe the transient absorption band experimentally observed around 200 fs after the absorption transition. This indicates that the T2 electronic state is populated through the intersystem crossing presented here. The two transient absorption bands experimentally observed between 2 and 45 ps after the absorption transition are described here as the T1→T3 and T1→T5 transitions, supporting that the intermediate triplet state (T2) decays by internal conversion to T1.

Impact of Electronic State Mixing on the Photoisomerization Time Scale of the Retinal Chromophore

Abstract: Spectral data show that the photoisomerization of retinal protonated Schiff base (rPSB) chromophores occurs on a 100 fs time scale or less in vertebrate rhodopsins, it is several times slower in microbial rhodopsins and it is between one and 2 orders of magnitude slower in solution. These time scale variations have been attributed to specific modifications of the topography of the first excited state potential energy surface of the chromophore. However, it is presently not clear which specific environment effects (e.g., electrostatic, electronic, or steric) are responsible for changing the surface topography. Here, we use QM/MM models and excited state trajectory computations to provide evidence for an increase in electronic mixing between the first and the second excited state of the chromophore when going from vertebrate rhodopsin to the solution environments. Ultimately, we argue that a correlation between the lifetime of the first excited state and electronic mixing between such state and its higher n...

Ab initio calculation of vibrational absorption and circular dichroism spectra using density functional force fields

Abstract: : The unpolarized absorption and circular dichroism spectra of the fundamental vibrational transitions of the chiral molecule, 4-methyl-2-oxetanone, are calculated ab initio. Harmonic force fields are obtained using Density Functional Theory (DFT), MP2, and SCF methodologies and a 5S4P2D/3S2P (TZ2P) basis set. DFT calculations use the Local Spin Density Approximation (LSDA), BLYP, and Becke3LYP (B3LYP) density functionals. Mid-IR spectra predicted using LSDA, BLYP, and B3LYP force fields are of significantly different quality, the B3LYP force field yielding spectra in clearly superior, and overall excellent, agreement with experiment. The MP2 force field yields spectra in slightly worse agreement with experiment than the B3LYP force field. The SCF force field yields spectra in poor agreement with experiment.The basis set dependence of B3LYP force fields is also explored: the 6-31G* and TZ2P basis sets give very similar results while the 3-21G basis set yields spectra in substantially worse agreements with experiment. jg

Spin-Vibronic Mechanism for Intersystem Crossing

Abstract: Intersystem crossing (ISC), formally forbidden within nonrelativistic quantum theory, is the mechanism by which a molecule changes its spin state. It plays an important role in the excited state decay dynamics of many molecular systems and not just those containing heavy elements. In the simplest case, ISC is driven by direct spin–orbit coupling between two states of different multiplicities. This coupling is usually assumed to remain unchanged by vibrational motion. It is also often presumed that spin-allowed radiationless transitions, i.e. internal conversion, and the nonadiabatic coupling that drives them, can be considered separately from ISC and spin–orbit coupling owing to the vastly different time scales upon which these processes are assumed to occur. However, these assumptions are too restrictive. Indeed, the strong mixing brought about by the simultaneous presence of nonadiabatic and spin–orbit coupling means that often the spin, electronic, and vibrational dynamics cannot be described independe...

All-optical electrophysiology in mammalian neurons using engineered microbial rhodopsins

Abstract: All-optical electrophysiology—spatially resolved simultaneous optical perturbation and measurement of membrane voltage—would open new vistas in neuroscience research. We evolved two archaerhodopsin-based voltage indicators, QuasAr1 and QuasAr2, which show improved brightness and voltage sensitivity, have microsecond response times and produce no photocurrent. We engineered a channelrhodopsin actuator, CheRiff, which shows high light sensitivity and rapid kinetics and is spectrally orthogonal to the QuasArs. A coexpression vector, Optopatch, enabled cross-talk–free genetically targeted all-optical electrophysiology. In cultured rat neurons, we combined Optopatch with patterned optical excitation to probe back-propagating action potentials (APs) in dendritic spines, synaptic transmission, subcellular microsecond-timescale details of AP propagation, and simultaneous firing of many neurons in a network. Optopatch measurements revealed homeostatic tuning of intrinsic excitability in human stem cell–derived neurons. In rat brain slices, Optopatch induced and reported APs and subthreshold events with high signal-to-noise ratios. The Optopatch platform enables high-throughput, spatially resolved electrophysiology without the use of conventional electrodes.

Modern quantum chemistry with [Open]Molcas

Abstract: MOLCAS/OpenMolcas is an ab initio electronic structure program providing a large set of computational methods from Hartree-Fock and density functional theory to various implementations of multiconfigurational theory. This article provides a comprehensive overview of the main features of the code, specifically reviewing the use of the code in previously reported chemical applications as well as more recent applications including the calculation of magnetic properties from optimized density matrix renormalization group wave functions.

Theory and Simulation of the Ultrafast Double-Bond Isomerization of Biological Chromophores.

Abstract: Ultrafast processes in light-absorbing proteins have been implicated in the primary step in the light-to-energy conversion and the initialization of photoresponsive biological functions. Theory and computations have played an instrumental role in understanding the molecular mechanism of such processes, as they provide a molecular-level insight of structural and electronic changes at ultrafast time scales that often are very difficult or impossible to obtain from experiments alone. Among theoretical strategies, the application of hybrid quantum mechanics and molecular mechanics (QM/MM) models is an important approach that has reached an evident degree of maturity, resulting in several important contributions to the field. This review presents an overview of state-of-the-art computational studies on subnanosecond events in rhodopsins, photoactive yellow proteins, phytochromes, and some other photoresponsive proteins where photoinduced double-bond isomerization occurs. The review also discusses current limit...