Model Systems for Dynamics of π-Conjugated Biomolecules in Excited States

2017 ◽  
pp. 1697-1739 ◽  
Author(s):  
Mario Barbatti ◽  
Matthias Ruckenbauer ◽  
Jaroslaw J. Szymczak ◽  
Bernhard Sellner ◽  
Mario Vazdar ◽  
...  
Keyword(s):  
Excited States ◽  
Model Systems

scholarly journals Role of Chiral Configuration in the Photoinduced Interaction of D- and L-Tryptophan with Optical Isomers of Ketoprofen in Linked Systems

2021 ◽  
Vol 22 (12) ◽  
pp. 6198
Author(s):  
Aleksandra A. Ageeva ◽  
Ilya M. Magin ◽  
Alexander B. Doktorov ◽  
Victor F. Plyusnin ◽  
Polina S. Kuznetsova ◽  
...  
Keyword(s):  
Amino Acid ◽  
Excited States ◽  
Resonance Energy Transfer ◽  
Resonance Energy ◽  
Dipole Interaction ◽  
The Body ◽  
Model Systems ◽  
Optical Isomers ◽  
Amino Acid Properties ◽  
Parkinson’S Diseases

The study of the L- and D-amino acid properties in proteins and peptides has attracted considerable attention in recent years, as the replacement of even one L-amino acid by its D-analogue due to aging of the body is resulted in a number of pathological conditions, including Alzheimer’s and Parkinson’s diseases. A recent trend is using short model systems to study the peculiarities of proteins with D-amino acids. In this report, the comparison of the excited states quenching of L- and D-tryptophan (Trp) in a model donor–acceptor dyad with (R)- and (S)-ketoprofen (KP-Trp) was carried out by photochemically induced dynamic nuclear polarization (CIDNP) and fluorescence spectroscopy. Quenching of the Trp excited states, which occurs via two mechanisms: prevailing resonance energy transfer (RET) and electron transfer (ET), indeed demonstrates some peculiarities for all three studied configurations of the dyad: (R,S)-, (S,R)-, and (S,S)-. Thus, the ET efficiency is identical for (S,R)- and (R,S)-enantiomers, while RET differs by 1.6 times. For (S,S)-, the CIDNP coefficient is almost an order of magnitude greater than for (R,S)- and (S,R)-. To understand the source of this difference, hyperpolarization of (S,S)-and (R,S)- has been calculated using theory involving the electron dipole–dipole interaction in the secular equation.

The electronic structure of low-lying excited states of two model systems of retinal

1986 ◽  
Vol 30 (2) ◽  
pp. 289-302 ◽  
Author(s):  
Takayuki Shoda ◽  
Takeshi Noro ◽  
Tsutomu Nomura ◽  
Kimio Ohno
Keyword(s):  
Electronic Structure ◽  
Excited States ◽  
Model Systems

Modeling Diarylethene Excited States with Ab Initio Tools: From Model Systems to Large Multimers

2017 ◽  
pp. 321-341 ◽  
Author(s):  
Martial Boggio-Pasqua ◽  
Aurélie Perrier ◽  
Arnaud Fihey ◽  
Denis Jacquemin
Keyword(s):  
Ab Initio ◽  
Excited States ◽  
Model Systems

scholarly journals Cooperative changes in solvent exposure identify cryptic pockets, conformational switches, and allosteric coupling

2018 ◽  
Author(s):  
Justin R. Porter ◽  
Katelyn E. Moeder ◽  
Carrie A. Sibbald ◽  
Maxwell I. Zimmerman ◽  
Kathryn M. Hart ◽  
...  
Keyword(s):  
Excited States ◽  
Conformational Changes ◽  
Protein Structures ◽  
Experimental Tests ◽  
Model Systems ◽  
Allosteric Site ◽  
Solvent Exposure ◽  
Allosteric Coupling ◽  
Functional Sites ◽  
Conformational Switches

AbstractProteins are dynamic molecules that undergo conformational changes to a broad spectrum of different excited states. Unfortunately, the small populations of these states make it difficult to determine their structures or functional implications. Computer simulations are an increasingly powerful means to identify and characterize functionally-relevant excited states. However, this advance has uncovered a further challenge: it can be extremely difficult to identify the most salient features of large simulation datasets. We reasoned that many functionally-relevant conformational changes are likely to involve large, cooperative changes to the surfaces that are available to interact with potential binding partners. To examine this hypothesis, we introduce a method that returns a prioritized list of potentially functional conformational changes by segmenting protein structures into clusters of residues that undergo cooperative changes in their solvent exposure, along with the hierarchy of interactions between these groups. We term these groups exposons to distinguish them from other types of clusters that arise in this analysis and others. We demonstrate, using three different model systems, that this method identifies experimentally-validated and functionally-relevant conformational changes, including conformational switches, allosteric coupling, and cryptic pockets. Our results suggest that key functional sites are hubs in the network of exposons. As a further test of the predictive power of this approach, we apply it to discover cryptic allosteric sites in two different β-lactamase enzymes that are widespread sources of antibiotic resistance. Experimental tests confirm our predictions for both systems. Importantly, we provide the first evidence for a cryptic allosteric site in CTX-M-9 β-lactamase. Experimentally testing this prediction did not require any mutations, and revealed that this site exerts the most potent allosteric control over activity of any pockets found in β-lactamases to date. Discovery of a similar pocket that was previously overlooked in the well-studied TEM-1 β-lactamase demonstrates the utility of exposons.

scholarly journals Complex Excited State Polarizabilities in the ADC/ISR Framework

2020 ◽  
Author(s):  
Maximilian Scheurer ◽  
Thomas Fransson ◽  
Patrick Norman ◽  
Andreas Dreuw ◽  
Dirk R. Rehn
Keyword(s):  
Excited States ◽  
Model Systems ◽  
Coupled Cluster ◽  
Complex Frequency ◽  
State Representation ◽  
Third Order ◽  
Dispersion Coefficients ◽  
Coupled Cluster Theory ◽  
Small Model ◽  
Complex Polarizability

<div><div><div><p>We present the derivation and implementation of complex, frequency-dependent polarizabilities for excited states using the algebraic-diagrammatic construction for the polarization propagator (ADC) and its intermediate state representation (ISR). Based on the complex polarizability we evaluate C<sub>6</sub> dispersion coefficients for excited states. The methodology is implemented up to third order in perturbation theory in the Python-driven adcc toolkit for the development and application of ADC methods. We exemplify the approach using small model systems and compare it to results from coupled-cluster theory and from experiments.</p></div></div></div>

scholarly journals Near-field effects and energy transfer in hybrid metal-oxide nanostructures

2013 ◽  
Vol 4 ◽  
pp. 306-317 ◽  
Author(s):  
Ulrich Herr ◽  
Balati Kuerbanjiang ◽  
Cahit Benel ◽  
Giorgos Papageorgiou ◽  
Manuel Goncalves ◽  
...  
Keyword(s):  
Energy Transfer ◽  
Excited States ◽  
Field Enhancement ◽  
Metallic Nanostructures ◽  
Hybrid Nanostructures ◽  
Model Systems ◽  
Narrow Particle Size Distribution ◽  
Energy Technology ◽  
Organic Pigment ◽  
Transfer Processes

One of the big challenges of the 21st century is the utilization of nanotechnology for energy technology. Nanoscale structures may provide novel functionality, which has been demonstrated most convincingly by successful applications such as dye-sensitized solar cells introduced by M. Grätzel. Applications in energy technology are based on the transfer and conversion of energy. Following the example of photosynthesis, this requires a combination of light harvesting, transfer of energy to a reaction center, and conversion to other forms of energy by charge separation and transfer. This may be achieved by utilizing hybrid nanostructures, which combine metallic and nonmetallic components. Metallic nanostructures can interact strongly with light. Plasmonic excitations of such structures can cause local enhancement of the electrical field, which has been utilized in spectroscopy for many years. On the other hand, the excited states in metallic structures decay over very short lifetimes. Longer lifetimes of excited states occur in nonmetallic nanostructures, which makes them attractive for further energy transfer before recombination or relaxation sets in. Therefore, the combination of metallic nanostructures with nonmetallic materials is of great interest. We report investigations of hybrid nanostructured model systems that consist of a combination of metallic nanoantennas (fabricated by nanosphere lithography, NSL) and oxide nanoparticles. The oxide particles were doped with rare-earth (RE) ions, which show a large shift between absorption and emission wavelengths, allowing us to investigate the energy-transfer processes in detail. The main focus is on TiO2 nanoparticles doped with Eu3+, since the material is interesting for applications such as the generation of hydrogen by photocatalytic splitting of water molecules. We use high-resolution techniques such as confocal fluorescence microscopy for the investigation of energy-transfer processes. The experiments are supported by simulations of the electromagnetic field enhancement in the vicinity of well-defined nanoantennas. The results show that the presence of the nanoparticle layer can modify the field enhancement significantly. In addition, we find that the fluorescent intensities observed in the experiments are affected by agglomeration of the nanoparticles. In order to further elucidate the possible influence of agglomeration and quenching effects in the vicinity of the nanoantennas, we have used a commercial organic pigment containing Eu, which exhibits an extremely narrow particle size distribution and no significant agglomeration. We demonstrate that quenching of the Eu fluorescence can be suppressed by covering the nanoantennas with a 10 nm thick SiO x layer.

scholarly journals A General Approach for Multireference Ground and Excited States using Non-Orthogonal Configuration Interaction

2019 ◽  
Author(s):  
Hugh G. A. Burton ◽  
Alex Thom
Keyword(s):  
Excited State ◽  
Excited States ◽  
Configuration Interaction ◽  
System Size ◽  
Model Systems ◽  
Teller Distortion ◽  
Hartree Fock ◽  
Jahn Teller ◽  
Static Correlation ◽  
Small Model

A balanced description of ground and excited states is essential for the description of many chemical processes. However, few methods can handle cases where static correlation is present, and often these scale very unfavourably with system size. Recently, multiple Hartree-Fock (HF) solutions have been proposed as a basis for non-orthogonal configuration interaction (NOCI) to provide multireference ground and excited state energies, although applications across multiple geometries have been limited by the coalescence of HF solutions. Holomorphic HF (h-HF) theory allows solutions to be analytically continued beyond the Coulson-Fischer points at which they vanish but, until now, this has only been demonstrated for small model systems. In this work, we propose a general protocol for computing NOCI ground and excited state energies using multiple HF solutions. To do so, we outline an active space variation of SCF metadynamics that allows a chemically relevant set of HF states to be identified, and describe how these states can be routinely traced across all molecular geometries by exploiting the topology of h-HF solutions in the complex plane. Finally, we illustrate our approach using the dissociation of the fluorine dimer and the pseudo-Jahn-Teller distortion of cyclobutadiene, demonstrating its applicability for multireference ground and excited states. <br>

Model Systems for Dynamics of π-Conjugated Biomolecules in Excited States

2012 ◽  
pp. 1175-1213 ◽  
Author(s):  
Mario Barbatti ◽  
Matthias Ruckenbauer ◽  
Jaroslaw J Szymczak ◽  
Bernhard Sellner ◽  
Mario Vazdar ◽  
...  
Keyword(s):  
Excited States ◽  
Model Systems
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