Photoinduced Intra- and Intermolecular Energy Transfer in Chlorophyll a Dimer

Applying nonadiabatic excited-state molecular dynamics, we investigate excitation energy transfer and exciton localization dynamics in a chlorophyll a (Chla) dimer system at the interface of two monomers of light-harvesting complex II trimer. After its optical excitation at the red edge of the Soret (B) band, the Chla dimer experiences an ultrafast intra- and intermolecular nonradiative relaxation process to the lowest band (Qy). The energy relaxation is found to run faster in the Chla dimer than in the Chla monomer. Once the molecular system reaches the lowest Qy band composed of two lowest excited states S1 and S2, the concluding relaxation step involves the S2 → S1 population transfer, resulting in a relatively slower relaxation rate. The strength of thermal fluctuations exceeds intraband electronic coupling between the states belonging to a certain band (B, Qx, and Qy), producing localized states on individual chromophores. Therefore, time evolution of spatial electronic localization during internal conversion reveals transient trapping on one of the Chla monomers participating in the events of intermonomeric energy exchange. In the phase space domains where electronic states are strongly coupled, these states become nearly degenerate promoting Frenkel-exciton-like delocalization and interchromophore energy transfer. As energy relaxation occurs, redistribution of the transition density on two Chla monomers leads to nearly equal distribution of the exciton among the molecules. For a single Chla, our analysis of excitonic dynamics reveals wave function amplitude transfer from nitrogen and outer carbon atoms to inner carbon atoms during nonradiative relaxation.Fil: Zheng, Fulu. Nanyang Technological University; SingapurFil: Fernández Alberti, Sebastián. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Nacional de Quilmes; ArgentinaFil: Tretiak, Sergei. Los Alamos National Laboratory; Estados UnidosFil: Zhao, Yang. Nanyang Technological University; Singapu

Nonadiabatic excited-state molecular dynamics: treatment of electronic Decoherence

Within the fewest switches surface hopping (FSSH) formulation, a swarm of independent trajectories is propagated and the equations of motion for the quantum coefficients are evolved coherently along each independent nuclear trajectory. That is, the phase factors, or quantum amplitudes, are retained. At a region of strong coupling, a trajectory can branch into multiple wavepackets. Directly following a hop, the two wavepackets remain in a region of nonadiabatic coupling and continue exchanging population. After these wavepackets have sufficiently separated in phase space, they should begin to evolve independently from one another, the process known as decoherence. Decoherence is not accounted for in the standard surface hopping algorithm and leads to internal inconsistency. FSSH is designed to ensure that at any time, the fraction of classical trajectories evolving on each quantum state is equal to the average quantum probability for that state. However, in many systems this internal consistency requirement is violated. Treating decoherence is an inherent problem that can be addressed by implementing some form of decoherence correction to the standard FSSH algorithm. In this study, we have implemented two forms of the instantaneous decoherence procedure where coefficients are reinitialized following hops. We also test the energy-based decoherence correction (EDC) scheme proposed by Granucci et al. and a related version where the form of the decoherence time is taken from Truhlar's Coherent Switching with Decay of Mixing method. The sensitivity of the EDC results to changes in parameters is also evaluated. The application of these computationally inexpensive ad hoc methods is demonstrated in the simulation of nonradiative relaxation in two conjugated oligomer systems, specifically poly-phenylene vinylene and poly-phenylene ethynylene. We find that methods that have been used successfully for treating small systems do not necessarily translate to large polyatomic systems and their success depends on the particular system under study.Fil: Nelson, Tammie. Los Alamos National Laboratory; Estados UnidosFil: Fernández Alberti, Sebastián. Universidad Nacional de Quilmes; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Roitberg, Adrián. University of Florida; Estados UnidosFil: Tretiak, Sergei. Los Alamos National Laboratory; Estados Unido

Identification of unavoided crossings in nonadiabatic photoexcited dynamics involving multiple electronic states in polyatomic conjugated molecules

Radiationless transitions between electronic excited states in polyatomic molecules take place through unavoided crossings of the potential energy surfaces with substantial non-adiabatic coupling between the respective adiabatic states. While the extent in time of these couplings are large enough, these transitions can be reasonably well simulated through quantum transitions using trajectory surface hopping-like methods. In addition, complex molecular systems may have multiple trivial unavoided crossings between noninteracting states. In these cases, the non-adiabatic couplings are described as sharp peaks strongly localized in time. Therefore, their modeling is commonly subjected to the identification of regions close to the particular instantaneous nuclear configurations for which the energy surfaces actually cross each other. Here, we present a novel procedure to identify and treat these regions of unavoided crossings between non-interacting states using the so-called Min-Cost algorithm. The method differentiates between unavoided crossings between interacting states (simulated by quantum hops), and trivial unavoided crossings between non-interacting states (detected by tracking the states in time with Min-Cost procedure). We discuss its implementation within our recently developed non-adiabatic excited state molecular dynamics framework. Fragments of two- and four-ring linear polyphenylene ethynylene chromophore units at various separations have been used as a representative molecular system to test the algorithm. Our results enable us to distinguish and analyze the main features of these different types of radiationless transitions the molecular system undertakes during internal conversion.Fil: Fernández Alberti, Sebastián. Universidad Nacional de Quilmes; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Roitberg, Adrián. University of Florida; Estados UnidosFil: Nelson, Tammie. Los Alamos National Laboratory; Estados UnidosFil: Tretiak, Sergei. Los Alamos National Laboratory; Estados Unido

Pockets as structural descriptors of EGFR kinase conformations

Epidermal Growth Factor Receptor (EGFR), a tyrosine kinase receptor, is one of the main tumor markers in different types of cancers. The kinase native state is mainly composed of two populations of conformers: active and inactive. Several sequence variations in EGFR kinase region promote the differential enrichment of conformers with higher activity. Some structural characteristics have been proposed to differentiate kinase conformations, but these considerations could lead to ambiguous classifications. We present a structural characterisation of EGFR kinase conformers, focused on active site pocket comparisons, and the mapping of known pathological sequence variations. A structural based clustering of this pocket accurately discriminates active from inactive, well-characterised conformations. Furthermore, this main pocket contains, or is in close contact with, ≈65% of cancer-related variation positions. Although the relevance of protein dynamics to explain biological function has been extensively recognised, the usage of the ensemble of conformations in dynamic equilibrium to represent the functional state of proteins and the importance of pockets, cavities and/or tunnels was often neglected in previous studies. These functional structures and the equilibrium between them could be structurally analysed in wild type as well as in sequence variants. Our results indicate that biologically important pockets, as well as their shape and dynamics, are central to understanding protein function in wild-type, polymorphic or disease-related variations.Fil: Hasenahuer, Marcia Anahí. Universidad Nacional de Quilmes. Departamento de Ciencia y Tecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Barletta Roldan, Patricio German. Universidad Nacional de Quilmes. Departamento de Ciencia y Tecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Fernández Alberti, Sebastián. Universidad Nacional de Quilmes. Departamento de Ciencia y Tecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Parisi, Gustavo Daniel. Universidad Nacional de Quilmes. Departamento de Ciencia y Tecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Fornasari, Maria Silvina. Universidad Nacional de Quilmes. Departamento de Ciencia y Tecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentin

Nonadiabatic excited-state molecular dynamics: Numerical tests of convergence and parameters

Nonadiabatic molecular dynamics simulations, involving multiple Born-Oppenheimer potential energy surfaces, often require a large number of independent trajectories in order to achieve the desired convergence of the results, and simulation relies on different parameters that should be tested and compared. In addition to influencing the speed of the simulation, the chosen parameters combined with the frequently reduced number of trajectories can sometimes lead to unanticipated changes in the accuracy of the simulated dynamics. We have previously developed a nonadiabatic excited state molecular dynamics methodology employing Tullys fewest switches surface hopping algorithm. In this study, we seek to investigate the impact of the number of trajectories and the various parameters on the simulation of the photoinduced dynamics of distyrylbenzene (a small oligomer of polyphenylene vinylene) within our developed framework. Various user-defined parameters are analyzed: classical and quantum integration time steps, the value of the friction coefficient for Langevin dynamics, and the initial seed used for stochastic thermostat and hopping algorithms. Common approximations such as reduced number of nonadiabatic coupling terms and the classical path approximation are also investigated. Our analysis shows that, at least for the considered molecular system, a minimum of ∼400 independent trajectories should be calculated in order to achieve statistical averaging necessary for convergence of the calculated relaxation timescales.Fil: Nelson, Tammie. Los Alamos National Laboratory; Estados UnidosFil: Fernández Alberti, Sebastián. Universidad Nacional de Quilmes; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Chernyak, Vladimir. Wayne State University (wayne State University); Estados UnidosFil: Roitberg, Adrián. University of Florida; Estados UnidosFil: Tretiak, Sergei. Los Alamos National High Magnetic Field Laboratory; Estados Unido

Computational study of photoexcited dynamics in bichromophoric cross-shaped oligofluorene

The non-adiabatic excited state molecular dynamics (NA-ESMD) approach is applied to investigate photoexcited dynamics and relaxation pathways in a spiro-linked conjugated polyfluorene at room (T = 300 K) and low (T = 10 K) temperatures. This dimeric aggregate consists of two perpendicularly oriented weakly interacting α-polyfluorene oligomers. The negligible coupling between the monomer chains results in an initial absorption band composed of equal contributions of the two lowest excited electronic states, each localized on one of the two chains. After photoexcitation, an efficient ultrafast localization of the entire electronic population to the lowest excited state is observed on the time scale of about 100 fs. Both internal conversion between excited electronic states and vibronic energy relaxation on a single electronic state contribute to this process. Thus, photoexcited dynamics of the polyfluorene dimer follows two distinct pathways with substantial temperature dependence on their efficiency. One relaxation channel involves resonance electronic energy transfer between the monomer chains, whereas the second pathway concerns the relaxation of the electronic energy on the same chain that has been initially excited due to electron-phonon coupling. Despite the slower vibrational relaxation, a more efficient ultrafast electronic relaxation is observed at low temperature. Our numerical simulations analyze the effects of molecular geometry distortion during the electronic energy redistribution and suggest spectroscopic signatures reflecting complex electron-vibrational dynamics.Fil: Ondarse Alvarez, Dianelys. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Nacional de Quilmes; ArgentinaFil: Oldani, Andres Nicolas. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Nacional de Quilmes; ArgentinaFil: Tretiak, S.. Los Alamos National Laboratory. Los Alamos; Estados UnidosFil: Fernández Alberti, Sebastián. Universidad Nacional de Quilmes; Argentin

Ultrafast Non-Forster Intramolecular Donor Acceptor Excitation Energy Transfer

Ultrafast intramolecular electronic energy transfer in a conjugated donor-acceptor system is simulated using nonadiabatic excited-state molecular dynamics. After initial site-selective photoexcitation of the donor, transition density localization is monitored throughout the S-2 -> S-1 internal conversion process, revealing an efficient unidirectional donor acceptor energy-transfer process. Detailed analysis of the excited state trajectories uncovers several salient features of the energy-transfer dynamics. While a weak temperature dependence is observed during the entire electronic energy relaxation, an ultrafast initially temperature-independent process allows the molecular system to approach the S-2-S-1 potential energy crossing seam within the first ten femtoseconds. Efficient energy transfer occurs in the absence of spectral overlap between the donor and acceptor units and is assisted by a transient delocalization phenomenon of the excited-state wave function acquiring Frenkel-exciton character at the moment of quantum transition.This project has received funding from the Universidad Carlos III de Madrid, the European Union’s Seventh Framework Programme for research, technological development and demonstration under grant agreement n° 600371, el Ministerio de Economia y Competitividad (COFUND2014-51509), el Ministerio de Educación, cultura y Deporte (CEI-15-17) and Banco Santander. This work was partially supported by CONICET, UNQ, ANPCyT (PICT-2014-2662). We also acknowledge support of the Center for Integrated Nano-technology (CINT), a U.S. Department of Energy, Office of Basic Energy Sciences user facility, as well as additional funding from the Bavarian University Centre for Latin America (BAYLAT). The work in Mons is supported by BELSPO through the PAI P6/27 Functional Supramolecular Systems project and by the Belgian National Fund for Scientific Research FNRS/F.R.S. DB is a Research Director of FNRS

Fatty acid and retinol-binding protein: Unusual protein conformational and cavity changes dictated by ligand fluctuations

Lipid-binding proteins (LBPs) are soluble proteins responsible for the uptake, transport, and storage of a large variety of hydrophobic lipophilic molecules including fatty acids, steroids, and other lipids in the cellular environment. Among the LBPs, fatty acid binding proteins (FABPs) present preferential binding affinities for long-chain fatty acids. While most of FABPs in vertebrates and invertebrates present similar β-barrel structures with ligands accommodated in their central cavity, parasitic nematode worms exhibit additional unusual α-helix rich fatty acid- and retinol-binding proteins (FAR). Herein, we report the comparison of extended molecular dynamics (MD) simulations performed on the ligand-free and palmitic acid-bond states of the Necator americanus FAR-1 (Na-FAR-1) with respect to other classical β-barrel FABPs. Principal component analysis (PCA) has been used to identify the different conformations adopted by each system during MD simulations. The α-helix fold encompasses a complex internal ligand-binding cavity with a remarkable conformational plasticity that allows reversible switching between distinct states in the holo-Na-FAR-1. The cavity can change up to one-third of its size affected by conformational changes of the protein-ligand complex. Besides, the ligand inside the cavity is not fixed but experiences large conformational changes between bent and stretched conformations. These changes in the ligand conformation follow changes in the cavity size dictated by the transient protein conformation. On the contrary, protein-ligand complex in β-barrel FABPs fluctuates around a unique conformation. The significantly more flexible holo-Na-FAR-1 ligand-cavity explains its larger ligand multiplicity respect to β-barrel FABPs.Fil: Barletta Roldan, Patricio German. Universidad Nacional de Quilmes. Departamento de Ciencia y Tecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Franchini, Gisela Raquel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Investigaciones Bioquímicas de La Plata "Prof. Dr. Rodolfo R. Brenner". Universidad Nacional de la Plata. Facultad de Ciencias Médicas. Instituto de Investigaciones Bioquímicas de La Plata "Prof. Dr. Rodolfo R. Brenner"; ArgentinaFil: Córsico, Betina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Investigaciones Bioquímicas de La Plata "Prof. Dr. Rodolfo R. Brenner". Universidad Nacional de la Plata. Facultad de Ciencias Médicas. Instituto de Investigaciones Bioquímicas de La Plata "Prof. Dr. Rodolfo R. Brenner"; ArgentinaFil: Fernández Alberti, Sebastián. Universidad Nacional de Quilmes. Departamento de Ciencia y Tecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentin

Let Digons be Bygones: The Fate of Excitons in Curved π-Systems

We explore the diverse origins of unpolarized absorption and emission of molecular polygons consisting of π-conjugated oligomer chains held in a bent geometry by strain controlled at the vertex units. For this purpose, we make use of atomistic nonadiabatic excited-state molecular dynamics simulations of a bichromophore molecular polygon (digon) with bent chromophore chains. Both structural and photoexcited dynamics were found to affect polarization features. Bending strain induces exciton localization on individual chromophore units of the conjugated chains. The latter display different transition dipole moment orientations, a feature not present in the linear oligomer counterparts. In addition, bending makes exciton localization very sensitive to molecular distortions induced by thermal fluctuations. The excited-state dynamics reveals an ultrafast intramolecular energy redistribution that spreads the exciton equally among spatially separated chromophore fragments within the molecular system. As a result, digons become virtually unpolarized absorbers and emitters, in agreement with recent experimental studies on the single-molecule level.Fil: Ondarse Alvarez, Dianelys.Fil: Nelson, Tammie.Fil: Lupton, John M..Fil: Tretiak, Sergei.Fil: Fernandez-Alberti, Sebastian

Analysis of State-Specific Vibrations Coupled to the Unidirectional Energy Transfer in Conjugated Dendrimers

The nonadiabatic excited-state molecular dynamics (NA-ESMD) method and excited-state instantaneous normal modes (ES-INMs) analyses have been applied to describe the state-specific vibrations that participate in the unidirectional energy transfer between the coupled chromophores in a branched dendrimeric molecule. Our molecule is composed of two-, three-, and four-ring linear poly(phenyleneethynylene) (PPE) units linked through meta-substitutions. After an initial laser excitation, an ultrafast sequential S3 → S 2 → S1 electronic energy transfer from the shortest to longest segment takes place. During each Sn → Sn-1 (n = 3, 2) transition, ES-INM(Sn) and ES-INM(Sn-1) analyses have been performed on Sn and Sn-1 states, respectively. Our results reveal a unique vibrational mode localized on the Sn state that significantly matches with the corresponding nonadiabatic coupling vector dn,(n-1). This mode also corresponds to the highest frequency ES-INM(Sn) and it is seen mainly during the electronic transitions. Furthermore, its absence as a unique ES-INM(S n-1) reveals that state-specific vibrations play the main role in the efficiency of the unidirectional Sn → Sn-1 electronic and vibrational energy funneling in light-harvesting dendrimers.Fil: Soler, Miguel A.. Universidad Nacional de Quilmes; ArgentinaFil: Roitberg, Adrián E.. University of Florida; Estados UnidosFil: Nelson, Tammie. Los Alamos National High Magnetic Field Laboratory; Estados UnidosFil: Tretiak, Sergei. Los Alamos National High Magnetic Field Laboratory; Estados UnidosFil: Fernández Alberti, Sebastián. Universidad Nacional de Quilmes; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentin