Electronic Couplings versus Thermal Fluctuations in the Internal Conversion of Perylene Diimides: The Battle to Localize the Exciton.

Energy transfer processes among units of light-harvesting homo-oligomers impact the efficiency of these materials as components in organic optoelectronic devices such as solar cells. Perylene diimide (PDI), a prototypical dye, features exceptional light absorption and highly tunable optical and electronic properties. These properties can be modulated by varying the number of PDI units and linkers between them. Herein, atomistic nonadiabatic excited state molecular dynamics is used to explore the energy transfer during the internal conversion of acetylene and diacetylene bridged dimeric and trimeric PDIs. Our simulations reveal a significant impact of the bridge type on the transient exciton localization/delocalization between units of PDI dimers. After electronic relaxation, larger exciton delocalization occurs in the PDI dimer connected by the diacetylene bridge with respect to the one connected by the shorter acetylene bridge. These changes can be rationalized by the Frenkel exciton model. We outline a technique for deriving parameters for this model using inputs provided by nonadiabatic dynamics simulations. Frenkel exciton description reveals an interplay between the relative strengths of the diagonal and off-diagonal disorders. Moreover, atomistic simulations and the Frenkel exciton model of the PDI trimer systems corroborate in detail the localization properties of the exciton on the molecular units during the internal conversion to the lowest-energy excited state when the units become effectively decoupled. Overall, atomistic nonadiabatic simulations in combination with the Frenkel exciton model can serve as a predictive framework for analyzing and predicting desired exciton traps in PDI-based oligomers designed for organic electronics and photonic devices.

Impact of the core on the inter-branch exciton exchange in dendrimers.

Organic dendrimers with π conjugated systems are capable of capturing solar energy as a renewable source for human use. Nonetheless, further study regarding the relationship between the structure and the energy transfer mechanism in these types of molecules is still necessary. In this work, nonadiabatic excited state molecular dynamics (NEXMD) were carried out to study the intra- and inter-branch exciton migration in two tetra-branched dendrimers, C(dSSB)4 and Ad(BuSSB)4, which differ in their respective carbon and adamantane core. Both systems undergo a ladder decay mechanism between excited states, with back-and-forth transitions between S1 and S2. Despite presenting very similar absorption-emission spectra, differences in the photoinduced energy relaxation are observed. The size of the core impacts the inter-branch energy exchange and transient exciton localization/delocalization, which ultimately condition the relative energy relaxation rates, being faster in Ad(BuSSB)4 with respect to C(dSSB)4. Nevertheless, the photoinduced processes lead to a progressive final exciton-self-trapping in one of the branches of both dendrimers, which is a desirable feature in organic photovoltaic applications. Our results can inspire the design of more efficient dendrimers with the desired magnitude of inter-branch exciton exchange and localization/delocalization according to changes in their core.

Vibrational Funnels for Energy Transfer in Organic Chromophores.

Photoinduced intramolecular energy transfers in multichromophoric molecules involve nonadiabatic vibronic channels that act as energy transfer funnels. They commonly take place through specific directions of motion dictated by the nonadiabatic coupling vectors. Vibrational funnels may support persistent coherences between electronic states and sometimes delineate the presence of minor alternative energy transfer pathways. The ultimate confirmation of their role on the interchromophoric energy transfer can be achieved by performing nonadiabatic excited-state molecular dynamics simulations by selectively freezing the nuclear motions in question. Our results point out this strategy as a useful tool to identify and evaluate the impact of these vibrational funnels on the energy transfer processes and guide the in silico design of materials with tunable properties and enhanced functionalities. Our work encourages applications of this methodology to different chemical and biochemical processes such as reactive scattering and protein conformational changes, to name a few.

Exciton-vibrational dynamics induces efficient self-trapping in a substituted nanoring.

Cycloparaphenylenes, being the smallest segments of carbon nanotubes, have emerged as prototypes of the simplest carbon nanohoops. Their unique structure-dynamics-optical properties relationships have motivated a wide variety of synthesis of new related nanohoop species. Studies of how chemical changes, introduced in these new materials, lead to systems with new structural, dynamics and optical properties, expand their functionalities for optoelectronics applications. Herein, we study the effect that conjugation extension of a cycloparaphenylene through the introduction of a satellite tetraphenyl substitution has on its structural and dynamical properties. Our non-adiabatic excited state molecular dynamics simulations suggest that this substitution accelerates the electronic relaxation from the high-energy band to the lowest excited state. This is partially due to efficient conjugation achieved between specific phenyl units as introduced by the tetraphenyl substitution. We observe a particular exciton redistribution during relaxation, in which the tetraphenyl substitution plays a significant role. As a result, an efficient inter-band energy transfer takes place. Besides, the observed phonon-exciton interplay induces a significant exciton self-trapping. Our results encourage and guide the future studies of new phenyl substitutions in carbon nanorings with desired optoelectronic properties.

Infinitene: Computational Insights from Nonadiabatic Excited State Dynamics.

Progress in organic synthesis opens exploration of a rich diversity of molecules with interesting new structural topologies. This is the case of a recently synthesized helically twisted figure-eight molecule coined infinitene. The molecule belongs to a numerous family of looped polyarenes, where the degree of π-conjugation is controlled by high strain energies and steric hindrances. A particular balance of these ingredients leads to unusual optoelectronic properties potentially suitable for a range of applications in nanoelectronics and photonics. Due to its recent discovery, the photophysical properties of infinitene remain unexplored. In this Letter, atomistic nonadiabatic excited state molecular dynamics modeling unveils unique features of intramolecular electronic and vibrational energy relaxation and redistribution that take place after molecular photoexcitation. Our results detail relationships between optical and electronic properties providing useful knowledge for future molecular designs related to infinitene.

Impact of protein conformational diversity on AlphaFold predictions.

MOTIVATION: After the outstanding breakthrough of AlphaFold in predicting protein 3D models, new questions appeared and remain unanswered. The ensemble nature of proteins, for example, challenges the structural prediction methods because the models should represent a set of conformers instead of single structures. The evolutionary and structural features captured by effective deep learning techniques may unveil the information to generate several diverse conformations from a single sequence. Here, we address the performance of AlphaFold2 predictions obtained through ColabFold under this ensemble paradigm. RESULTS: Using a curated collection of apo-holo pairs of conformers, we found that AlphaFold2 predicts the holo form of a protein in ∼70% of the cases, being unable to reproduce the observed conformational diversity with the same error for both conformers. More importantly, we found that AlphaFold2's performance worsens with the increasing conformational diversity of the studied protein. This impairment is related to the heterogeneity in the degree of conformational diversity found between different members of the homologous family of the protein under study. Finally, we found that main-chain flexibility associated with apo-holo pairs of conformers negatively correlates with the predicted local model quality score plDDT, indicating that plDDT values in a single 3D model could be used to infer local conformational changes linked to ligand binding transitions. AVAILABILITY AND IMPLEMENTATION: Data and code used in this manuscript are publicly available at https://gitlab.com/sbgunq/publications/af2confdiv-oct2021. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Vibronic Photoexcitation Dynamics of Perylene Diimide: Computational Insights.

Perylene diimide (PDI) represents a prototype material for organic optoelectronic devices because of its strong optical absorbance, chemical stability, efficient energy transfer, and optical and chemical tunability. Herein, we analyze in detail the vibronic relaxation of its photoexcitation using nonadiabatic excited-state molecular dynamics simulations. We find that after the absorption of a photon, which excites the electron to the second excited state, S2, induced vibronic dynamics features persistent modulations in the spatial localization of electronic and vibrational excitations. These energy exchanges are dictated by strong vibronic couplings that overcome structural disorders and thermal fluctuations. Specifically, the electronic wavefunction periodically swaps between localizations on the right and left sides of the molecule. Within 1 ps of such dynamics, a nonradiative transition to the lowest electronic state, S1, takes place, resulting in a complete delocalization of the wavefunction. The observed vibronic dynamics emerges following the electronic energy deposition in the direction that excites a combination of two dominant vibrational normal modes. This behavior is maintained even with a chemical substitution that breaks the symmetry of the molecule. We believe that our findings elucidate the nature of the complex dynamics of the optically excited states and, therefore, contribute to the development of tunable functionalities of PDIs and their derivatives.

Analysis of changes of cavity volumes in predefined directions of protein motions and cavity flexibility.

Dynamics of protein cavities associated with protein fluctuations and conformational plasticity is essential for their biological function. NMR ensembles, molecular dynamics (MD) simulations, and normal mode analysis (NMA) provide appropriate frameworks to explore functionally relevant protein dynamics and cavity changes relationships. Within this context, we have recently developed analysis of null areas (ANA), an efficient method to calculate cavity volumes. ANA is based on a combination of algorithms that guarantees its robustness against numerical differentiations. This is a unique feature with respect to other methods. Herein, we present an updated and improved version that expands it use to quantify changes in cavity features, like volume and flexibility, due to protein structural distortions performed on predefined biologically relevant directions, for example, directions of largest contribution to protein fluctuations (principal component analysis [PCA modes]) obtained by MD simulations or ensembles of NMR structures, collective NMA modes or any other direction of motion associated with specific conformational changes. A web page has been developed where its facilities are explained in detail. First, we show that ANA can be useful to explore gradual changes of cavity volume and flexibility associated with protein ligand binding. Secondly, we perform a comparison study of the extent of variability between protein backbone structural distortions, and changes in cavity volumes and flexibilities evaluated for an ensemble of NMR active and inactive conformers of the epidermal growth factor receptor structures. Finally, we compare changes in size and flexibility between sets of NMR structures for different homologous chains of dynein.

Intrinsically Disordered Region Modulates Ligand Binding in Glutaredoxin 1 from Trypanosoma Brucei.

Glutaredoxins are small proteins that share a common well-conserved thioredoxin-fold and participate in a wide variety of biological processes. Among them, class II Grx are redox-inactive proteins involved in iron-sulfur (Fe-S) metabolism. In the present work, we report different structural and dynamics aspects of 1CGrx1 from the pathogenic parasite Trypanosoma brucei that differentiate it from other orthologues by the presence of a parasite-specific unstructured N-terminal extension whose role has not been fully elucidated yet. Previous nuclear magnetic resonance (NMR) studies revealed significant differences with respect to the mutant lacking the disordered tail. Herein, we have performed atomistic molecular dynamics simulations that, complementary to NMR studies, confirm the intrinsically disordered nature of the N-terminal extension. Moreover, we confirm the main role of these residues in modulating the conformational dynamics of the glutathione-binding pocket. We observe that the N-terminal extension modifies the ligand cavity stiffening it by specific interactions that ultimately modulate its intrinsic flexibility, which may modify its role in the storage and/or transfer of preformed iron-sulfur clusters. These unique structural and dynamics aspects of Trypanosoma brucei 1CGrx1 differentiate it from other orthologues and could have functional relevance. In this way, our results encourage the study of other similar protein folding families with intrinsically disordered regions whose functional roles are still unrevealed and the screening of potential 1CGrx1 inhibitors as antitrypanosomal drug candidates.

Mesoporous thin films on graphene FETs: nanofiltered, amplified and extended field-effect sensing.

The ionic screening and the response of non-specific molecules are great challenges of biosensors based on field-effect transistors (FETs). In this work, we report the construction of graphene based transistors modified with mesoporous silica thin films (MTF-GFETs) and the unique (bio)sensing properties that arise from their synergy. The developed method allows the preparation of mesoporous thin films free of fissures, with an easily tunable thickness, and prepared on graphene-surfaces, preserving their electronic properties. The MTF-GFETs show good sensing capacity to small probes that diffuse inside the mesopores and reach the graphene semiconductor channel such as H+, OH-, dopamine and H2O2. Interestingly, MTF-GFETs display a greater electrostatic gating response in terms of amplitude and sensing range compared to bare-GFETs for charged macromolecules that infiltrate the pores. For example, for polyelectrolytes and proteins of low MW, the amplitude increases almost 100% and the sensing range extends more than one order of magnitude. Moreover, these devices show a size-excluded electrostatic gating response given by the pore size. These features are even displayed at physiological ionic strength. Finally, a developed thermodynamic model evidences that the amplification and extended field-effect properties arise from the decrease of free ions inside the MTFs due to the entropy loss of confining ions in the mesopores. Our results demonstrate that the synergistic coupling of mesoporous films with FETs leads to nanofiltered, amplified and extended field-effect sensing (NAExFES).

Back-and-Forth Energy Transfer during Electronic Relaxation in a Chlorin-Perylene Dyad.

Donor-acceptor dyads represent a practical approach to tuning the photophysical properties of linear conjugated polymers in materials chemistry. Depending on the absorption wavelength, the acceptor and donor roles can be interchanged, and as such, the directionality of the energy transfer can be controlled. Herein, nonadiabatic excited state molecular dynamics simulations have been performed in an arylethylene-linked perylene-chlorin dyad. After an initial photoexcitation at the Soret band of chlorin, we observe an ultrafast sequential electronic relaxation to the lowest excited state. This process is accomplished through an efficient round-trip chlorin-to-perylene-to-chlorin energy transfer. It is characterized by successive intermittent localized and delocalized vibronic dynamics. Nonradiative relaxation takes place mainly through energy transfer events with perylene acting as a "heat sink" through which the nonradiative relaxation is efficiently funneled, and the excess energy is dispersed in a larger space of vibrational degrees of freedom. Thus, our findings suggest the use of donor-acceptor dyads as a useful strategy when one needs to deactivate an electronic excitation.

Excitation Energy Transfer between bodipy Dyes in a Symmetric Molecular Excitonic Seesaw.

We examine the redistribution of energy between electronic and vibrational degrees of freedom that takes place between a π-conjugated oligomer, a phenylene-butadiynylene, and two identical boron-dipyrromethene (bodipy) end-caps using femtosecond transient absorption spectroscopy, single-molecule spectroscopy, and nonadiabatic excited-state molecular dynamics (NEXMD) modeling techniques. The molecular structure represents an excitonic seesaw in that the excitation energy on the oligomer backbone can migrate to either one end-cap or the other, but not to both. The NEXMD simulations closely reproduce the characteristic time scale for redistribution of electronic and vibrational energy of 2.2 ps and uncover the vibrational modes contributing to the intramolecular relaxation. The calculations indicate that the dihedral angle between the bodipy dye and the oligomer change upon excitation of the oligomer. Single-molecule experiments reveal a difference in photoluminescence lifetime of the bodipy dyes depending on whether they are excited by direct absorption or by redistribution of energy from the backbone. This difference in lifetime may be attributed to the difference in dihedral angle. The simulations also suggest that a strong coupling can occur between the two end-caps, giving rise to a reversible shuttling of excitation energy between them. Strong coupling should lead to a pronounced loss in polarization memory of the fluorescence since the oligomer backbone tends to be slightly distorted and the two bodipy transition dipoles have different orientations. A sensitive single-molecule technique is presented to test for such coupling. However, although redistribution of electronic and vibrational energy between the end-caps can occur, it appears to be unidirectional and irreversible, suggesting that an additional localization mechanism is at play which is, as yet, not fully accounted for in the simulations.

Nonadiabatic Excited-State Molecular Dynamics Methodologies: Comparison and Convergence.

Direct atomistic simulation of nonadiabatic molecular dynamics is a challenging goal that allows important insights into fundamental physical phenomena. A variety of frameworks, ranging from fully quantum treatment of nuclei to semiclassical and mixed quantum-classical approaches, were developed. These algorithms are then coupled to specific electronic structure techniques. Such diversity and lack of standardized implementation make it difficult to compare the performance of different methodologies when treating realistic systems. Here, we compare three popular methods for large chromophores: Ehrenfest, surface hopping, and multiconfigurational Ehrenfest with ab initio multiple cloning (MCE-AIMC). These approaches are implemented in the NEXMD software, which features a common computational chemistry model. The resulting comparisons reveal the method performance for population relaxation and coherent vibronic dynamics. Finally, we study the numerical convergence of MCE-AIMC algorithms by considering the number of trajectories, cloning thresholds, and Gaussian wavepacket width. Our results provide helpful reference data for selecting an optimal methodology for simulating excited-state molecular dynamics.

Exciton Spatial Dynamics and Self-Trapping in Carbon Nanocages.

Three-dimensional cage-shaped molecules formed from chainlike structures hold potential as unique optoelectronic materials and host compounds. Their optical, structural, and dynamical features are tunable by changes in shape and size. We perform a comparison of these properties for three sizes of strained conjugated [n.n.n]carbon nanocages composed of three paraphenylene chains (bridges) of length n = 4, 5, or 6. The exciton intramolecular redistribution occurring during nonradiative relaxation has been explored using nonadiabatic excited-state molecular dynamics. Our results provide atomistic insight into the conformational features associated with the observed red- and blue-shift trends in the absorption and fluorescence spectra, respectively, with increasing nanocage size. Their internal conversion processes involve intramolecular energy transfer that leads to exciton self-trapping on a few phenylene units at the center of a single bridge. The dependence of these dynamical features on the size of the nanocage can be used to tune their host-guest chemical properties and their use for organic electronics and catenane-like applications.

Experimental and theoretical study of energy transfer in a chromophore triad: What makes modeling dynamics successful?

Simulation of electronic dynamics in realistically large molecular systems is a demanding task that has not yet achieved the same level of quantitative prediction already realized for its static counterpart. This is particularly true for processes occurring beyond the Born-Oppenheimer regime. Non-adiabatic molecular dynamics (NAMD) simulations suffer from two convoluted sources of error: numerical algorithms for dynamics and electronic structure calculations. While the former has gained increasing attention, particularly addressing the validity of ad hoc methodologies, the effect of the latter remains relatively unexplored. Indeed, the required accuracy for electronic structure calculations to reach quantitative agreement with experiment in dynamics may be even more strict than that required for static simulations. Here, we address this issue by modeling the electronic energy transfer in a donor-acceptor-donor (D-A-D) molecular light harvesting system using fewest switches surface hopping NAMD simulations. In the studied system, time-resolved experimental measurements deliver complete information on spectra and energy transfer rates. Subsequent modeling shows that the calculated electronic transition energies are "sufficiently good" to reproduce experimental spectra but produce over an order of magnitude error in simulated dynamical rates. We further perform simulations using artificially shifted energy gaps to investigate the complex relationship between transition energies and modeled dynamics to understand factors affecting non-radiative relaxation and energy transfer rates.

Exploring Conformational Space with Thermal Fluctuations Obtained by Normal-Mode Analysis.

Proteins in their native states can be represented as ensembles of conformers in dynamical equilibrium. Thermal fluctuations are responsible for transitions between these conformers. Normal-modes analysis (NMA) using elastic network models (ENMs) provides an efficient procedure to explore global dynamics of proteins commonly associated with conformational transitions. In the present work, we present an iterative approach to explore protein conformational spaces by introducing structural distortions according to their equilibrium dynamics at room temperature. The approach can be used either to perform unbiased explorations of conformational space or to explore guided pathways connecting two different conformations, e.g., apo and holo forms. In order to test its performance, four proteins with different magnitudes of structural distortions upon ligand binding have been tested. In all cases, the conformational selection model has been confirmed and the conformational space between apo and holo forms has been encompassed. Different strategies have been tested that impact on the efficiency either to achieve a desired conformational change or to achieve a balanced exploration of the protein conformational multiplicity.

Network analysis of dynamically important residues in protein structures mediating ligand-binding conformational changes.

According to the generalized conformational selection model, ligand binding involves the co-existence of at least two conformers with different ligand-affinities in a dynamical equilibrium. Conformational transitions between them should be guaranteed by intramolecular vibrational dynamics associated to each conformation. These motions are, therefore, related to the biological function of a protein. Positions whose mutations are found to alter these vibrations the most can be defined as key positions, that is, dynamically important residues that mediate the ligand-binding conformational change. In a previous study, we have shown that these positions are evolutionarily conserved. They correspond to buried aliphatic residues mostly localized in regular structured regions of the protein like ß-sheets and α-helices. In the present paper, we perform a network analysis of these key positions for a large dataset of paired protein structures in the ligand-free and ligand-bound form. We observe that networks of interactions between these key positions present larger and more integrated networks with faster transmission of the information. Besides, networks of residues result that are robust to conformational changes. Our results reveal that the conformational diversity of proteins seems to be guaranteed by a network of strongly interconnected key positions rather than individual residues.

Chemical Stability of Mesoporous Oxide Thin Film Electrodes under Electrochemical Cycling: from Dissolution to Stabilization.

Mesoporous oxide thin films (MOTF) present very high surface areas and highly controlled monodisperse pores in the nanometer range. These features spurred their possible applications in separation membranes and permselective electrodes. However, their performance in real applications is limited by their reactivity. Here, we perform a basic study of the stability of MOTF toward dissolution in aqueous media using a variety of characterization techniques. In particular, we focus in their stability behavior under the influence of ionic strength, adsorption of electrochemical probes, and applied electrode potential. Mesoporous silica thin films present a limited chemical stability after electrochemical cycling, particularly under high ionic strength, due to their high specific surface area and the interactions between the electrochemical probes and the surface. In contrast, TiO2 or Si0.9Zr0.1O2 matrices present higher stability; thus, they are an adequate alternative to produce accessible, sensitive, and robust permselective electrodes or membranes that perform under a wide variety of conditions.

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.

Dynamics fingerprints of active conformers of epidermal growth factor receptor kinase.

Epidermal growth factor receptor (EGFR) is a prototypical cell-surface receptor that plays a key role in the regulation of cellular signaling, proliferation and differentiation. Mutations of its kinase domain have been associated with the development of a variety of cancers and, therefore, it has been the target of drug design. Single amino acid substitutions (SASs) in this domain have been proven to alter the equilibrium of pre-existing conformer populations. Despite the advances in structural descriptions of its so-called active and inactive conformations, the associated dynamics aspects that characterize them have not been thoroughly studied yet. As the dynamic behaviors and molecular motions of proteins are important for a complete understanding of their structure-function relationships we present a novel procedure, using (or based on) normal mode analysis, to identify the collective dynamics shared among different conformers in EGFR kinase. The method allows the comparison of patterns of low-frequency vibrational modes defining representative directions of motions. Our procedure is able to emphasize the main similarities and differences between the collective dynamics of different conformers. In the case of EGFR kinase, two representative directions of motions have been found as dynamics fingerprints of the active conformers. Protein motion along both directions reveals to have a significant impact on the cavity volume of the main pocket of the active site. Otherwise, the inactive conformers exhibit a more heterogeneous distribution of collective motions. © 2018 Wiley Periodicals, Inc.