Coherent exciton-vibrational dynamics and energy transfer in conjugated organics

Coherence, signifying concurrent electron-vibrational dynamics in complex natural and man-made systems, is currently a subject of intense study. Understanding this phenomenon is important when designing carrier transport in optoelectronic materials. Here, excited state dynamics simulations reveal a ubiquitous pattern in the evolution of photoexcitations for a broad range of molecular systems. Symmetries of the wavefunctions define a specific form of the non-adiabatic coupling that drives quantum transitions between excited states, leading to a collective asymmetric vibrational excitation coupled to the electronic system. This promotes periodic oscillatory evolution of the wavefunctions, preserving specific phase and amplitude relations across the ensemble of trajectories. The simple model proposed here explains the appearance of coherent exciton-vibrational dynamics due to non-adiabatic transitions, which is universal across multiple molecular systems. The observed relationships between electronic wavefunctions and the resulting functionalities allows us to understand, and potentially manipulate, excited state dynamics and energy transfer in molecular materials.Fil: Nelson, Tammie R.. Los Alamos National Laboratory; Estados UnidosFil: Ondarse Alvarez, Dianelys. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Nacional de Quilmes; ArgentinaFil: Oldani, Andres Nicolas. Universidad Nacional de Quilmes; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Rodríguez Hernández, Beatriz. Universidad Nacional de Quilmes; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Alfonso Hernandez, Laura. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Nacional de Quilmes; ArgentinaFil: Galindo, Johan F.. Universidad Nacional de Colombia; ColombiaFil: Kleiman, Valeria D.. University of Florida; Estados UnidosFil: Fernández Alberti, Sebastián. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Nacional de Quilmes; ArgentinaFil: Roitberg, Adrián. University of Florida; Estados UnidosFil: Tretiak, Sergei. Los Alamos National Laboratory; Estados Unido

Variations in the Electrostatic Landscape of Class II Human Leukocyte Antigen Molecule Induced by Modifications in the Myelin Basic Protein Peptide: A Theoretical Approach

The receptor-ligand interactions involved in the formation of the complex between Class II Major Histocompatibility Complex molecules and antigenic peptides, which are essential for establishing an adaptive immunological response, were analyzed in the Class II Human Leukocyte Antigen (HLA) - Myelin Basic Protein (MBP) peptide complex (HLA-DRβ1*1501-MBP) using a multipolar molecular electrostatic potential approach. The Human Leukocyte Antigen - peptide complex system was divided into four pockets together with their respective peptide fragment and the corresponding occupying amino acid was replaced by each of the remaining 19 amino acids. Partial atomic charges were calculated by a quantum chemistry approach at the Hatree Fock/3-21*G level, to study the behavior of monopole, dipole and quadrupole electrostatic multipolar moments. Two types of electrostatic behavior were distinguished in the pockets' amino acids: “anchoring” located in Pocket 1 and 4, and “recognition” located in Pocket 4 and 7. According to variations in the electrostatic landscape, pockets were ordered as: Pocket 1>Pocket 9≫Pocket 4≈Pocket 7 which is in agreement with the binding ability reported for Class II Major Histocompatibility Complex pockets. In the same way, amino acids occupying the polymorphic positions β13R, β26F, β28D, β9W, β74A, β47F and β57D were shown to be key for this Receptor-Ligand interaction. The results show that the multipolar molecular electrostatic potential approach is appropriate for characterizing receptor-ligand interactions in the MHC–antigenic peptide complex, which could have potential implications for synthetic vaccine design

QM/MM molecular dynamics study of the galactopyranose → galactofuranose reaction catalysed by Trypanosoma cruzi UDP-galactopyranose mutase.

The enzyme UDP-Galactopyranose Mutase (UGM) catalyses the conversion of galactopyranose into galactofuranose. It is known to be critical for the survival and proliferation of several pathogenic agents, both prokaryotic and eukaryotic. Among them is Trypanosoma cruzi, the parasite responsible for Chagas' disease. Since the enzyme is not present in mammals, it appears as a promising target for the design of drugs to treat this illness. A precise knowledge of the mechanism of the catalysed reaction would be crucial to assist in such design. In this article we present a detailed study of all the putative steps of the mechanism. The study is based on QM/MM free energy calculations along properly selected reaction coordinates, and on the analysis of the main structural changes and interactions taking place at every step. The results are discussed in connection with the experimental evidence and previous theoretical studies

Electronic Excited State Specific IR Spectra for Phenylene Ethynylene Dendrimer Building Blocks

Dendrimers are excellent candidates for applications in molecular devices and light harvesting where creating an energy gradient is crucial. Poly­(phenylene ethynylene) (PPE) molecules are building blocks for dendrimers that also display the necessary characteristics for efficient energy transfer, including differential spatial localization associated with different excited states. In this work we calculated the ground state (S₀) as well as the excited IR spectra for the S₁ and S₂ states of ortho- and meta- substituted PPE (<i>o</i>-PPE and <i>m</i>-PPE). To compute IR spectra, a conformational space exploration was performed using ground-state classical molecular dynamics followed by direct adiabatic and non-adiabatic excited state molecular dynamics. IR spectra were computed from the autocorrelation function of the dipole moment in each state. We identified a band at 2150 cm^–1 that is characteristic of S₁ in <i>m</i>-PPE. We show that in <i>m</i>-PPE, S₁ and S₂ have transition densities localized over different regions of the molecule, while in <i>o</i>-PPE the states are spread over the entire molecule. We find that the coupling between vibrations associated to the CC triple bonds plays an important role in the non-adiabatic electronic energy transfer. These results are a guide to the experimental characterization of the specific electronic excited states vibrations of these molecules

Revisiting the Dielectric Constant Effect on the Nucleophile and Leaving Group of Prototypical Backside S_N2 Reactions: A Reaction Force and Atomic Contribution Analysis

The solvent effect on the nucleophile and leaving group atoms of the prototypical F^– + CH₃Cl → CH₃F + Cl^– backside bimolecular nucleophilic substitution reaction (S_N2) is analyzed employing the reaction force and the atomic contributions methods on the intrinsic reaction coordinate (IRC). Solvent effects were accounted for using the polarizable continuum solvent model. Calculations were performed employing 11 dielectric constants, ε, ranging from 1.0 to 78.5, to cover a wide spectrum of solvents. The reaction force data reveal that the solvent mainly influences the region of the IRC preceding the energy barrier, where the structural rearrangement to reach the transition state occurs. A detailed analysis of the atomic role in the reaction as a function of ε reveals that the nucleophile and the carbon atom are the ones that contribute the most to the energy barrier. In addition, we investigated the effect of the choice of nucleophile and leaving group on the Δ<i>E</i>₀ and Δ<i>E</i>^‡ of Y^– + CH₃X → YCH₃ + X^– (X, Y = F, Cl, Br, I) in aqueous solution. Our analysis allowed us to find relationships between the atomic contributions to the activation energy and leaving group ability and nucleophilicity

Descriptores moleculares de origen cuántico y grafo-teórico para caracterizar la estructura secundaria del ARN a partir de sus nucleótidos

IP 1101-05-13613En este proyecto hemos desarrollado un modelo que permite codificar y comparar tRNAs de diferente procedencia biológica. Para ello hemos propuesto descomponer cada estructura secundaria de los tRNAs consideramos en una serie de fragmentos que incluyen los primeros vecinos de cada nucleótido. Estos fragmentos han sido previamente estudios desde el punto de vista de su estructura electrónica mediante cálculos cuánticos

Detailed mechanism for the reaction catalysed by <i>Tc</i>UGM.

<p>The mechanism includes the intermediates detected by experiments as well as those whose existence was inferred from theoretical considerations. Red color is used to denote the bonds being broken (solid line) or formed (dashed line), as well as the atoms involved. The distances between these atoms are labelled because they are used to define the reaction coordinates.</p

values for key residues at every step of the reaction mechanism shown in Fig. 2.

<p> values for key residues at every step of the reaction mechanism shown in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0109559#pone-0109559-g002" target="_blank">Fig. 2</a>.</p