1,721,142 research outputs found
Initial excited state relaxation of the isolated 11-cis protonated Schiff base of retinal: evidence for in-plane motion from ab initio quantum-chemical simulation of the resonance Raman spectrum
No full textThe intensity distribution in the resonance Raman (RR) spectrum of the 11-cis protonated Schiff base of retinal (PSB11) is modeled for the first time on the basis of ab initio quantum chemical calculations. To adequately represent the structure of PSB 11, 4-cis-y,η-dimethyl-C9H9 NH2+ is chosen as a model. The RR spectra of the model PSB11 and of several isotopomers are compared with the experimental spectra of PSB11 in solution. An excellent agreement is obtained in the structurally sensitive fingerprint region of the spectra (1100-1300 cm-1), where most of the observed details are quantitatively reproduced by the simulations. The 900-1100-cm-1 region of the RR spectrum of PSB11, which contains the signatures of the S0,S1 potential energy changes due to the protein environment, is also well reproduced. On the basis of the simulations, it is concluded that the activity observed at ca. 970 cm-1 in the spectrum of PSB11 in solution is due to in-plane modes, while a superposition of in-plane and out, of-plane motions is responsible for the increased RR activity in rhodopsin. The present analysis of RR activities along with the computed relaxation path structure provides support for the interpretation of the initial relaxation of photoexcited PSB11 in solution in terms of initial in-plane motion out of the Franck-Condon region followed by slow out-of-plane (i.e., cis → trans torsional) evolution along a flat energy plateau. Furthermore, the quality of the simulated spectra suggests that the quantum chemical method used in this work can be employed quantitatively to assist in the characterization of photoreaction intermediates in the visual cycle
Synthesis, physicochemical and vibrational spectral properties of 2–pyridone and 2–aminopyridine derivatives: An experimental and theoretical study
Full text linkA convenient and efficient one–pot three–component reaction of acetyl acetone, malononitrile and ammonium acetate was investigated for the synthesis of 3–cyano–4,6–dimethyl–2–pyridone (PI) and 2–amino–3–cyano–4,6–dimethylpyridine (PII). The products were achieved with high purity, high yields and short reaction time. The yields of the two products depend on the concentration of ammonium acetate, reaction time and the solvent used. The structures of the isolated products were confirmed by elemental analysis and spectral data, supported by quantum chemical (MP2) calculations, both in gas phase and solvents (water and ethanol), that were also employed to track the reaction mechanisms and model vibrational spectral properties for final characterization and interpretation of spectral data. A remarkable matching between theoretical predictions and experiments was attained both for the geometrical parameters, as compared to X-Ray data available in the literature, and for vibrational frequencies, leading to a correlation coefficient (R2) of 0.99. Molecular docking was further studied to predict the docking binding energy of the synthesized compounds with the target proteins
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Soft X-ray Spectroscopy Simulations with Multiconfigurational Wave Function Theory: Spectrum Completeness, Sub-eV Accuracy, and Quantitative Reproduction of Line Shapes
Full text linkMultireference methods are known for their ability to accurately treat states of very different nature in many molecular systems, facilitating high-quality simulations of a large variety of spectroscopic techniques. Here, we couple the multiconfigurational restricted active space self-consistent field RASSCF/RASPT2 method (of the CASSCF/CASPT2 methods family) to the displaced harmonic oscillator (DHO) model, to simulate soft X-ray spectroscopy. We applied such an RASSCF/RASPT2+DHO approach at the K-edges of various second-row elements for a set of small organic molecules that have been recently investigated at other levels of theory. X-ray absorption near-edge structure (XANES) and X-ray photoelectron spectroscopy (XPS) are simulated with a sub-eV accuracy and a correct description of the spectral line shapes. The method is extremely sensitive to the observed spectral shifts on a series of differently fluorinated ethylene systems, provides spectral fingerprints to distinguish between stable conformers of the glycine molecule, and accurately captures the vibrationally resolved carbon K-edge spectrum of formaldehyde. Differences with other theoretical methods are demonstrated, which show the advantages of employing a multireference/multiconfigurational approach. A protocol to systematically increase the number of core-excited states considered while maintaining a contained computational cost is presented. Insight is eventually provided for the effects caused by removing core-electrons from a given atom in terms of bond rearrangement and influence on the resulting spectral shapes within a unitary orbital-based framework for both XPS and XANES spectra
The short-chain acroleiniminium and pentadieniminium cations: towards a model for retinal photoisomerization. A CASSCF/PT2 study
No full textIn this communication we report the results obtained in a computational study of the Minimum Energy Paths (MEP) found in the first excited state S1 and in the ground state S0 of two short-chain protonated Schiff bases (PSB): the s-cis 1-iminium-2-propene cation H2C=CH-CH=NH2 + and the tZt 1-iminium- 2,4-pentadiene cation H2C=CH-CH=CH-CH=NH2 +. This computational study has been performed at an high ab-initio level where the geometries of the relevant points have been optimized at the CAS-SCF level and the energetics have been refined via single-point computations at the CAS-PT2 level. This communication provides the important information that the photochemistry of the two studied PSB is driven by the spectroscopic 1B ionic state which remains the lowest excited state along all the optimized MEP. Both PSB show a S1/S0 Conical Intersection which is reached through a low barrier (barrierless) relaxation path for the shorter (longer) system and has an almost 90°twisted double bond (the CH2=CH-double bond for the shorter and the central double bond for the longer PSB) which provides a route for fully efficient non-adiabatic cis- > trans isomerization. In both PSB the crossing involves also a charge transfer between the two twisted fragments and the isomerization reaction coordinates on S1 are dominated by a stretching planar mode in the initial part of the MEP.
Acroleiniminium; CASSCF/PT2; Pentadieniminium; Photoisomerization; Retina
Manipulating Core Excitations in Molecules by X-Ray Cavities
Full text linkCore excitations on different atoms are highly localized and therefore decoupled. By placing molecules in an x-ray cavity the core transitions become coupled via the exchange of cavity photons and form delocalized hybrid light-matter excitations known as core polaritons. We demonstrate these effects for the two inequivalent carbon atoms in 1,1-difluoroethylene. Polariton signatures in the x-ray absorption, two-photon absorption, and multidimensional four-wave mixing signals are predicted
Automatized protocol and interface to simulate QM/MM time-resolved transient absorption at TD-DFT level with COBRAMM
Full text linkWe present a series of new implementations that we recently introduced in COBRAMM, the open-source academic software developed in our group. The goal of these implementations is to offer an automatized workflow and interface to simulate time-resolved transient absorption (TA) spectra of medium-to-big chromophore embedded in a complex environment. Therefore, the excited states absorption and the stimulated emission are simulated along nonadiabatic dynamics performed with trajectory surface hopping. The possibility of treating systems from medium to big size is given by the use of time-dependent density functional theory (TD-DFT) and the presence of the environment is taken into account employing a hybrid quantum mechanics/molecular mechanics (QM/MM) scheme. The full implementation includes a series of auxiliary scripts to properly setup the QM/MM system, the calculation of the wavefunction overlap along the dynamics for the propagation, the evaluation of the transition dipole moment at linear response TD-DFT level, and scripts to setup, run and analyze the TA from an ensemble of trajectories. Altogether, we believe that our implementation will open the door to the easily simulate the time-resolved TA of systems so far computationally inaccessible
Quantum Chemical Modeling of the Photoinduced Activity of Multichromophoric Biosystems
Full text linkMultichromophoric biosystems represent a broad family with very diverse members, ranging from light-harvesting pigment-protein complexes to nucleic acids. The former are designed to capture, harvest, efficiently transport, and transform energy from sunlight for photosynthesis, while the latter should dissipate the absorbed radiation as quickly as possible to prevent photodamages and corruption of the carried genetic information. Because of the unique electronic and structural characteristics, the modeling of their photoinduced activity is a real challenge. Numerous approaches have been devised building on the theoretical development achieved for single chromophores and on model Hamiltonians that capture the essential features of the system. Still, a question remains: is a general strategy for the accurate modeling of multichromophoric systems possible? By using a quantum chemical point of view, here we review the advancements developed so far highlighting differences and similarities with the single chromophore treatment. Finally, we outline the important limitations and challenges that still need to be tackled to reach a complete and accurate picture of their photoinduced properties and dynamics
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