Voltage Gated Ion Channels: Structure, Pharmacology and Photopharmacology

Voltage-gated ion channels are transmembrane proteins responsible for the generation and propagation of action potentials in excitable cells. In the past few years, crystal structures of ion channels have become accessible and, when combined with mutagenesis data, have aided in the discovery of drugs that can modulate ion conduction. However, many traditional drugs lack selectivity and come with adverse side effects. The emergence of photopharmacology has provided an orthogonal way of controlling the activity of compounds, enabling the regulation of ion conduction with light. In this review, we explore the central pore region of voltage-gated sodium and potassium channels, providing insights from both structural and pharmacological perspectives. We discuss the different binding modes of synthetic compounds that can physically occlude the pore and, therefore, block the ion conduction. Moreover, we examine recent advances in the photopharmacology of voltage-gated ion channels, introducing molecular approaches aimed at controlling their activity by using photosensitive drugs.

Membrane Permeation of Psychedelic Tryptamines by Dynamic Simulations

Renewed scientific interest in psychedelic compounds represents one of the most promising avenues for addressing the current burden of mental health disorders. Classic psychedelics are a group of compounds that exhibit structural similarities to the naturally occurring neurotransmitter serotonin (5-HT). Acting on the 5-HT type 2A receptors (HT2ARs), psychedelics induce enduring neurophysiological changes that parallel their therapeutic psychological and behavioral effects. Recent preclinical evidence suggests that the ability of psychedelics to exert their action is determined by their ability to permeate the neuronal membrane to target a pool of intracellular 5-HT2ARs. In this computational study, we employ classical molecular dynamics simulations and umbrella sampling techniques to investigate the permeation behavior of 12 selected tryptamines and to characterize the interactions that drive the process. We aim at elucidating the impact of N-alkylation, indole ring substitution and positional modifications, and protonation on their membrane permeability. Dimethylation of the primary amine group and the introduction of a methoxy group at position 5 exhibited an increase in permeability. Moreover, there is a significant influence of positional substitutions on the indole groups, and the protonation of the molecules substantially increases the energy barrier at the center of the bilayer, making the compounds highly impermeable. All the information extracted from the trends predicted by the simulations can be applied in future drug design projects to develop psychedelics with enhanced activity.

Large vibrationally induced parity violation effects in CHDBrI. Chem Commun (Camb) 2023;59:14579-14582. [PMID: 37990542 DOI: 10.1039/d3cc03787h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0]

The isotopically chiral molecular ion CHDBrI+ is identified as an exceptionally promising candidate for the detection of parity violation in vibrational transitions. The largest predicted parity-violating frequency shift reaches 1.8 Hz for the hydrogen wagging mode which has a sub-Hz natural line width and its vibrational frequency auspiciously lies in the available laser range. In stark contrast to this result, the parent neutral molecule is two orders of magnitude less sensitive to parity violation. The origin of this effect is analyzed and explained. Precision vibrational spectroscopy of CHDBrI+ is feasible as it is amenable to preparation at internally low temperatures and resistant to predissociation, promoting long interrogation times (Landau et al., J. Chem. Phys., 2023, 159, 114307). The intersection of these properties in this molecular ion places the first observation of parity violation in chiral molecules within reach.

Nature of Hops, Coordinates, and Detailed Balance for Nonadiabatic Simulations in the Condensed Phase

Photoinduced processes play a crucial role in a multitude of important molecular phenomena. Accurately modeling these processes in an environment other than a vacuum requires a detailed description of the electronic states involved as well as how energy flows are coupled to the surroundings. Nonadiabatic effects must also be included in order to describe the exchange of energy between electronic and nuclear degrees of freedom correctly. In this work, we revisit the ring-opening reaction 1,3-cylohexadiene (CHD) in a solvent environment. Using our newly developed Interface for Non-Adiabatic Quantum mechanics/molecular mechanics in Solvent (INAQS) we trace the evolution of the reaction via hybrid quantum mechanics/molecular mechanics (QM/MM) surface hopping with a focus on the solvent's participation in the nonadiabatic relaxation process and the long-time approach to equilibrium. We explicitly include the MM solvent contribution to the nonadiabatic coupling vector─enabling an accurate approach to equilibrium at long times─and find that in highly multidimensional systems gradients can have little or nothing to do with the nonadiabatic couplings.

Chiral molecule candidates for trapped ion spectroscopy by ab initio calculations: From state preparation to parity violation

Parity non-conservation (PNC) due to the weak interaction is predicted to give rise to enantiomer dependent vibrational constants in chiral molecules, but the phenomenon has so far eluded experimental observation. The enhanced sensitivity of molecules to physics beyond the Standard Model (BSM) has led to substantial advances in molecular precision spectroscopy, and these may be applied to PNC searches as well. Specifically, trapped molecular ion experiments leverage the universality of trapping charged particles to optimize the molecular ion species studied toward BSM searches, but in searches for PNC, only a few chiral molecular ion candidates have been proposed so far. Importantly, viable candidates need to be internally cold, and their internal state populations should be detectable with high quantum efficiency. To this end, we focus on molecular ions that can be created by near threshold resonant two-photon ionization and detected via state-selective photo-dissociation. Such candidates need to be stable in both charged and neutral chiral versions to be amenable to these methods. Here, we present a collection of suitable chiral molecular ion candidates we have found, including CHDBrI+ and CHCaBrI+, that fulfill these conditions according to our ab initio calculations. We find that organo-metallic species have low ionization energy as neutrals and relatively high dissociation thresholds. Finally, we compute the magnitude of the PNC values for vibrational transitions for some of these candidates. An experimental demonstration of state preparation and readout for these candidates will be an important milestone toward measuring PNC in chiral molecules for the first time.

Multiscale Simulations of the Covalent Inhibition of the SARS-CoV-2 Main Protease: Four Compounds and Three Reaction Mechanisms

We report the results of computational modeling of the reactions of the SARS-CoV-2 main protease (MPro) with four potential covalent inhibitors. Two of them, carmofur and nirmatrelvir, have shown experimentally the ability to inhibit MPro. Two other compounds, X77A and X77C, were designed computationally in this work. They were derived from the structure of X77, a non-covalent inhibitor forming a tight surface complex with MPro. We modified the X77 structure by introducing warheads capable of reacting with the catalytic cysteine residue in the MPro active site. The reaction mechanisms of the four molecules with MPro were investigated by quantum mechanics/molecular mechanics (QM/MM) simulations. The results show that all four compounds form covalent adducts with the catalytic cysteine Cys 145 of MPro. From the chemical perspective, the reactions of these four molecules with MPro follow three distinct mechanisms. The reactions are initiated by a nucleophilic attack of the thiolate group of the deprotonated cysteine residue from the catalytic dyad Cys145-His41 of MPro. In the case of carmofur and X77A, the covalent binding of the thiolate to the ligand is accompanied by the formation of the fluoro-uracil leaving group. The reaction with X77C follows the nucleophilic aromatic substitution SNAr mechanism. The reaction of MPro with nirmatrelvir (which has a reactive nitrile group) leads to the formation of a covalent thioimidate adduct with the thiolate of the Cys145 residue in the enzyme active site. Our results contribute to the ongoing search for efficient inhibitors of the SARS-CoV-2 enzymes.

Effect of stacking interactions on charge transfer states in photoswitches interacting with ion channels

The activity of ion channels can be reversibly photo-controlled via the binding of molecular photoswitches, often based on an azobenzene scaffold. Those azobenzene derivatives interact with aromatic residues of the protein via stacking interactions. In the present work, the effect of face-to-face and t-shaped stacking interactions on the excited state electronic structure of azobenzene and p-diaminoazobenzene integrated into the NaV1.4 channel is computationally investigated. The formation of a charge transfer state, caused by electron transfer from the protein to the photoswitches, is observed. This state is strongly red shifted when the interaction takes place in a face-to-face orientation and electron donating groups are present on the aromatic ring of the amino acids. The low-energy charge transfer state can interfere with the photoisomerization process after excitation to the bright state by leading to the formation of radical species.

M-Chem: a Modular Software Package for Molecular Simulation that Spans Scientific Domains

We present a new software package called M-Chem that is designed from scratch in C++ and parallelized on shared-memory multi-core architectures to facilitate efficient molecular simulations. Currently, M-Chem is a fast molecular dynamics (MD) engine that supports the evaluation of energies and forces from two-body to many-body all-atom potentials, reactive force fields, coarse-grained models, combined quantum mechanics molecular mechanics (QM/MM) models, and external force drivers from machine learning, augmented by algorithms that are focused on gains in computational simulation times. M-Chem also includes a range of standard simulation capabilities including thermostats, barostats, multi-timestepping, and periodic cells, as well as newer methods such as fast extended Lagrangians and high quality electrostatic potential generation. At present M-Chem is a developer friendly environment in which we encourage new software contributors from diverse fields to build their algorithms, models, and methods in our modular framework. The long-term objective of M-Chem is to create an interdisciplinary platform for computational methods with applications ranging from biomolecular simulations, reactive chemistry, to materials research.

INAQS, a Generic Interface for Nonadiabatic QM/MM Dynamics: Design, Implementation, and Validation for GROMACS/Q-CHEM simulations

The accurate description of large molecular systems in complex environments remains an ongoing challenge for the field of computational chemistry. This problem is even more pronounced for photoinduced processes, as multiple excited electronic states and their corresponding nonadiabatic couplings must be taken into account. Multiscale approaches such as hybrid quantum mechanics/molecular mechanics (QM/MM) offer a balanced compromise between accuracy and computational burden. Here, we introduce an open-source software package (INAQS) for nonadiabatic QM/MM simulations that bridges the sampling capabilities of the GROMACS MD package and the excited-state infrastructure of the Q-CHEM electronic structure software. The interface is simple and can be adapted easily to other MD codes. The code supports a variety of different trajectory-based molecular dynamics, ranging from Born-Oppenheimer to surface hopping dynamics. To illustrate the power of this combination, we simulate electronic absorption spectra, free-energy surfaces along a reaction coordinate, and the excited-state dynamics of 1,3-cyclohexadiene in solution.

How Reproducible Are QM/MM Simulations? Lessons from Computational Studies of the Covalent Inhibition of the SARS-CoV-2 Main Protease by Carmofur

This work explores the level of transparency in reporting the details of computational protocols that is required for practical reproducibility of quantum mechanics/molecular mechanics (QM/MM) simulations. Using the reaction of an essential SARS-CoV-2 enzyme (the main protease) with a covalent inhibitor (carmofur) as a test case of chemical reactions in biomolecules, we carried out QM/MM calculations to determine the structures and energies of the reactants, the product, and the transition state/intermediate using analogous QM/MM models implemented in two software packages, NWChem and Q-Chem. Our main benchmarking goal was to reproduce the key energetics computed with the two packages. Our results indicate that quantitative agreement (within the numerical thresholds used in calculations) is difficult to achieve. We show that rather minor details of QM/MM simulations must be reported in order to ensure the reproducibility of the results and offer suggestions toward developing practical guidelines for reporting the results of biosimulations.

Providing theoretical insight into the role of symmetry in the photoisomerization mechanism of a non-symmetric dithienylethene photoswitch

Dithienylethene (DTE) molecular photoswitches have shown to be excellent candidates in the design of efficient optoelectronic devices, due to their high photoisomerization quantum yield (QY), for which symmetry is suggested to play a crucial role. Here, we present a theoretical study on the photochemistry of a non-symmetric dithienylethene photoswitch, with a special emphasis on the effect of asymmetric substitution on the photocyclization and photoreversion mechanisms. We used the Spin-Flip Time Dependent Density Functional Theory (SF-TDDFT) method to locate and characterize the main structures (conical intersections and minima) of the ground state and the first two excited states, S₁ and S₂, along the ring-opening/closure reaction coordinate of the photocyclization and photoreversion processes, and to identify the important coordinates governing the radiationless decay pathways. Our results suggest that while the main features that characterize the photoisomerization of symmetric DTEs are also present for the photoisomerization of the non-symmetric DTE, the lower energy barrier on S₁ along the cycloreversion reaction speaks in favor of a more efficient and therefore a higher cycloreversion QY for the non-symmetric DTEs, making them a better candidate for molecular optoelectronic devices than their symmetric counterparts.

Intramolecular hydrogen transfer in DNA induced by site-selective resonant core excitation

We present experimental evidence for soft X-ray induced intramolecular hydrogen transfer in the protonated synthetic tri-oligonucleotide d($^{\mbox{\footnotesize{F}}}$UAG) in the gas-phase. The trinucleotide cations were stored in a cryogenic ion trap...

Sequential Voxel-Based Leaflet Segmentation of Complex Lipid Morphologies

As molecular dynamics simulations increase in complexity, new analysis tools are necessary to facilitate interpreting the results. Lipids, for instance, are known to form many complicated morphologies, because of their amphipathic nature, becoming more intricate as the particle count increases. A few lipids might form a micelle, where aggregation of tens of thousands could lead to vesicle formation. Millions of lipids comprise a cell and its organelle membranes, and are involved in processes such as neurotransmission and transfection. To study such phenomena, it is useful to have analysis tools that understand what is meant by emerging entities such as micelles and vesicles. Studying such systems at the particle level only becomes extremely tedious, counterintuitive, and computationally expensive. To address this issue, we developed a method to track all the individual lipid leaflets, allowing for easy and quick detection of topological changes at the mesoscale. By using a voxel-based approach and focusing on locality, we forego costly geometrical operations without losing important details and chronologically identify the lipid segments using the Jaccard index. Thus, we achieve a consistent sequential segmentation on a wide variety of (lipid) systems, including monolayers, bilayers, vesicles, inverted hexagonal phases, up to the membranes of a full mitochondrion. It also discriminates between adhesion and fusion of leaflets. We show that our method produces consistent results without the need for prefitting parameters, and segmentation of millions of particles can be achieved on a desktop machine.

The effect of adding pyridoxine to soybean lecithin-based extender on goat semen quality parameters after the freeze-thawing process

Background

Supplementing the semen extender with various antioxidants can increase the quality of semen.

Aims

The aim of the present study was to investigate the addition of pyridoxine (vitamin B₆), a phenolic compound with antioxidant properties, to soybean lecithin extender on motility and quality indices of goat sperm after freezing-thawing process.

Methods

Semen was collected at weekly intervals from four Mahabadi goats, mixed, and was divided into 7 subsamples. They were then diluted with the basal extender supplemented with 0, 2, 4, 6, 8, 10, and 12 mM pyridoxine. Following freeze-thawing process, quality parameters such as sperm motility characteristics, viability, plasma membrane integrity, and malondialdehyde content were determined.

Results

The results showed that pyridoxine at the level of 6 mM caused the highest total motility rate (P<0.05). Progressive sperm motility was highest at the 4, 6, and 8 mM pyridoxine (P<0.05). Although the control group showed the least progressive motility, it was not statistically significantly different from the 12 mM level. Among the pyridoxine levels, the 6 mM level recorded the best performance in term of plasma membrane integrity, sperm viability, and decreasing malondialdehyde concentration compared to the control group (P<0.05).

Conclusion

The findings indicated that soybean lecithin extender supplemented with 6 mM pyridoxine can improve motility and quality parameters such as viability, plasma membrane integrity, and reduce oxidative stress of goat sperm after thawing.

Software for the frontiers of quantum chemistry: An overview of developments in the Q-Chem 5 package

This article summarizes technical advances contained in the fifth major release of the Q-Chem quantum chemistry program package, covering developments since 2015. A comprehensive library of exchange-correlation functionals, along with a suite of correlated many-body methods, continues to be a hallmark of the Q-Chem software. The many-body methods include novel variants of both coupled-cluster and configuration-interaction approaches along with methods based on the algebraic diagrammatic construction and variational reduced density-matrix methods. Methods highlighted in Q-Chem 5 include a suite of tools for modeling core-level spectroscopy, methods for describing metastable resonances, methods for computing vibronic spectra, the nuclear-electronic orbital method, and several different energy decomposition analysis techniques. High-performance capabilities including multithreaded parallelism and support for calculations on graphics processing units are described. Q-Chem boasts a community of well over 100 active academic developers, and the continuing evolution of the software is supported by an "open teamware" model and an increasingly modular design.

Q-Force: Quantum Mechanically Augmented Molecular Force Fields

The quality of molecular dynamics simulations strongly depends on the accuracy of the underlying force fields (FFs) that determine all intra- and intermolecular interactions of the system. Commonly, transferable FF parameters are determined based on a representative set of small molecules. However, such an approach sacrifices accuracy in favor of generality. In this work, an open-source and automated toolkit named Q-Force is presented, which augments these transferable FFs with molecule-specific bonded parameters and atomic charges that are derived from quantum mechanical (QM) calculations. The molecular fragmentation procedure allows treatment of large molecules (>200 atoms) with a low computational cost. The generated Q-Force FFs can be used at the same computational cost as transferable FFs, but with improved accuracy: We demonstrate this for the vibrational properties on a set of small molecules and for the potential energy surface on a complex molecule (186 atoms) with photovoltaic applications. Overall, the accuracy, user-friendliness, and minimal computational overhead of the Q-Force protocol make it widely applicable for atomistic molecular dynamics simulations.

Site-selective soft X-ray absorption as a tool to study protonation and electronic structure of gas-phase DNA

The conformation and the electronic structure of gas-phase oligonucleotides depends strongly on the protonation site. 5'-d(FUAG) can either be protonated at the A-N1 or at the G-N7 position. We have stored protonated 5'-d(FUAG) cations in a cryogenic ion trap held at about 20 K. To identify the protonation site and the corresponding electronic structure, we have employed soft X-ray absorption spectroscopy at the nitrogen K-edge. The obtained spectra were interpreted by comparison to time-dependent density functional theory calculations using a short-range exchange correlation functional. Despite the fact that guanine has a significantly higher proton affinity than adenine, the agreement between experiment and theory is better for the A-N1 protonated system. Furthermore, an inverse site sensitivity is observed in which the yield of the nucleobase fragments that contain the absorption site appears substantially reduced, which could be explained by non-statistical fragmentation processes, localized on the photoabsorbing nucleobase.

Influence of the Environment on Shaping the Absorption of Monomeric Infrared Fluorescent Proteins

Infrared fluorescent proteins (iRFPs) are potential candidates for deep-tissue in vivo imaging. Here, we provide molecular-level insights into the role of the protein environment in the structural stability of the chromophore within the protein binding pocket through the flexible hydrogen-bonding network using molecular dynamics simulation. Furthermore, we present systematic excited-state analysis to characterize the nature of the first two excited states and the role of the environment in shaping the nature of the chromophore's excited states within the hybrid quantum mechanics/molecular mechanics framework. Our results reveal that the environment red-shifts the absorption of the chromophore by about 0.32 eV compared to the isolated counterpart, and besides the structural stability, the protein environment does not alter the nature of the excited state of the chromophore significantly. Our study contributes to the fundamental understanding of the excited-state processes of iRFPs in a complex environment and provides a design principle for developing iRFPs with desired spectral properties.

Theoretical investigation of a novel xylene-based light-driven unidirectional molecular motor

In this study, the working mechanism of the first light-driven rotary molecular motors used to control an eight-base-pair DNA hairpin has been investigated. In particular, this linker was reported to have promising photophysical properties under physiological conditions, which motivated our work at the quantum mechanical level. Cis-trans isomerization is triggered by photon absorption at wavelengths ranging 300 nm-400 nm, promoting the rotor to the first excited state, and it is mediated by an energy-accessible conical intersection from which the ground state is reached back. The interconversion between the resulting unstable isomer and its stable form occurs at physiological conditions in the ground state and is thermally activated. Here, we compare three theoretical frameworks, generally used in the quantum description of medium-size chemical systems: Linear-Response Time-Dependent Density Functional Theory (LR-TDDFT), Spin-Flip TDDFT (SF-TDDFT), and multistate complete active space second-order perturbation theory on state-averaged complete active space self consistent field wavefunctions (MS-CASPT2//SA-CASSCF). In particular, we show the importance of resorting to a multireference approach to study the rotational cycle of light-driven molecular motors due to the occurrence of geometries described by several configurations. We also assess the accuracy and computational cost of the SF-TDDFT method when compared to MS-CASPT2 and LR-TDDFT.

Binding of azobenzene and p-diaminoazobenzene to the human voltage-gated sodium channel Nav1.4

The activity of voltage-gated ion channels can be controlled by the binding of photoswitches inside their internal cavity and subsequent light irradiation. We investigated the binding of azobenzene and p-diaminoazobenzene to the human Na_v1.4 channel in the inactivated state by means of Gaussian accelerated molecular dynamics simulations and free-energy computations. Three stable binding pockets were identified for each of the two photoswitches. In all the cases, the binding is controlled by the balance between the favorable hydrophobic interactions of the ligands with the nonpolar residues of the protein and the unfavorable polar solvation energy. In addition, electrostatic interactions between the ligand and the polar aminoacids are also relevant for p-diaminoazobenzene due to the presence of the amino groups on the benzene moieties. These groups participate in hydrogen bonding in the most favorable binding pocket and in long-range electrostatic interactions in the other pockets. The thermodinamically preferred binding sites found for both photoswitches are close to the selectivity filter of the channel. Therefore, it is very likely that the binding of these ligands will induce alterations in the ion conduction through the channel.

Influence of the crystal packing in singlet fission: one step beyond the gas phase approximation

Singlet fission (SF), a multiexciton generation process, has been proposed as an alternative to enhance the performance of solar cells. The gas phase dimer model has shown its utility to study this process, but it does not always cover all the physics and the effect of the surrounding atoms has to be included in such cases. In this contribution, we explore the influence of crystal packing on the electronic couplings, and on the so-called exciton descriptors and electron–hole correlation plots. We have studied three tetracene dimers extracted from the crystal structure, as well as several dimers and trimers of the α and β polymorphs of 1,3-diphenylisobenzofuran (DPBF). These polymorphs show different SF yields. Our results highlight that the character of the excited states of tetracene depends on both the mutual disposition of molecules and inclusion of the environment. The latter does however not change significantly the interpretation of the SF mechanism in the studied systems. For DPBF, we establish how the excited state analysis is able to pinpoint differences between the polymorphs. We observe strongly bound correlated excitons in the β polymorph which might hinder the formation of the ¹TT state and, consequently, explain its low SF yield.

Singlet fission (SF), a multiexciton generation process, has been proposed as an alternative to enhance the performance of solar cells.

PySurf: A Framework for Database Accelerated Direct Dynamics

The greatest restriction to the theoretical study of the dynamics of photoinduced processes is computationally expensive electronic structure calculations. Machine learning algorithms have the potential to reduce the number of these computations significantly. Here, PySurf is introduced as an innovative code framework, which is specifically designed for rapid prototyping and development tasks for data science applications in computational chemistry. It comes with powerful Plugin and Workflow engines, which allows intuitive customization for individual tasks. Data is automatically stored through the database framework, which enables additional interpolation of properties in previously evaluated regions of the conformational space. To illustrate the potential of the framework, a code for nonadiabatic surface hopping simulations based on the Landau-Zener algorithm is presented here. Deriving gradients from the interpolated potential energy surfaces allows for full-dimensional nonadiabatic surface hopping simulations using only adiabatic energies (energy only). Simulations of a pyrazine model and ab initio-based calculations of the SO2 molecule show that energy-only calculations with PySurf are able to correctly predict the nonadiabatic dynamics of these prototype systems. The results reveal the degree of sophistication, which can be achieved by the database accelerated energy-only surface hopping simulations being competitive to commonly used semiclassical approaches.

Theoretical insights into the effect of size and substitution patterns of azobenzene derivatives on the DNA G-quadruplex

Introducing photoswitches into the DNA G-quadruplex provides excellent opportunities to control folding and unfolding of these assemblies, demonstrating their potential in the development of novel nanodevices with medical and nanotechnology applications. Using a quantum mechanics/molecular mechanics (QM/MM) scheme, we carried out a series of simulations to identify the effect of the size and substitution patterns of three azobenzene derivatives (AZ1, AZ2 and AZ3) on the excitation energies of the two lowest excited states of the smallest photoswitchable G-quadruplex reported to date. We demonstrated that the size and the substitution pattern do not affect the ultrafast cis-trans photoiomerization mechanism of the azobenzene derivatives significantly, in agreement with the experiment. However, molecular dynamics simulations revealed that while AZ2 and AZ3 G-quadruplexes are structurally stable during the simulations, the AZ1 G-quadruplex undergoes larger structural changes and shows two ground state populations that differ in the azobenzene backbone adopting two different conformations. AZ1, with para-para substitution pattern, provides more flexibility to the whole G-quadruplex structure compared to AZ2 and AZ3, and can thus facilitate the photoisomerization reaction between a nonpolymorphic, stacked, tetramolecular G-quadruplex and an unstructured state after trans-cis isomerization occurring in a longer time dynamics, in agreement with the experimental findings. The QM/MM simulations of the absorption spectra indicated that the thermal fluctuation plays a more crucial role in the main absorption band of the azobenzene derivatives than the inclusion of the G-quadruplex, implying that the influence of the G-quadruplex environment is minimal. We propose that the latter is attributed to the position of the azobenzene linkers in the G-quadruplexes, i.e. the edgewise loops containing the azobenzene moieties that are located above the G-quartets, not being fully embedded inside or involved in the stacked structure. Our theoretical findings provide support to a recent study of the photoresponsive formation of photoswitchable G-quadruplex motifs.

GronOR: Massively parallel and GPU-accelerated non-orthogonal configuration interaction for large molecular systems

GronOR is a program package for non-orthogonal configuration interaction calculations for an electronic wave function built in terms of anti-symmetrized products of multi-configuration molecular fragment wave functions. The two-electron integrals that have to be processed may be expressed in terms of atomic orbitals or in terms of an orbital basis determined from the molecular orbitals of the fragments. The code has been specifically designed for execution on distributed memory massively parallel and Graphics Processing Unit (GPU)-accelerated computer architectures, using an MPI+OpenACC/OpenMP programming approach. The task-based execution model used in the implementation allows for linear scaling with the number of nodes on the largest pre-exascale architectures available, provides hardware fault resiliency, and enables effective execution on systems with distinct central processing unit-only and GPU-accelerated partitions. The code interfaces with existing multi-configuration electronic structure codes that provide optimized molecular fragment orbitals, configuration interaction coefficients, and the required integrals. Algorithm and implementation details, parallel and accelerated performance benchmarks, and an analysis of the sensitivity of the accuracy of results and computational performance to thresholds used in the calculations are presented.

Order–disorder transition in supramolecular polymer combs/brushes with polymeric side chains

Three groups of supramolecular comb/brush polymers with polymeric side chains are developed, showing different mechanical properties and morphologies.

Structure and photophysics of indigoids for singlet fission: Cibalackrot

We report an investigation of structure and photophysics of thin layers of cibalackrot, a sturdy dye derived from indigo by double annulation at the central double bond. Evaporated layers contain up to three phases, two crystalline and one amorphous. Relative amounts of all three have been determined by a combination of X-ray diffraction and FT-IR reflectance spectroscopy. Initially, excited singlet state rapidly produces a high yield of a transient intermediate whose spectral properties are compatible with charge-transfer nature. This intermediate more slowly converts to a significant yield of triplet, which, however, does not exceed 100% and may well be produced by intersystem crossing rather than singlet fission. The yields were determined by transient absorption spectroscopy and corrected for effects of partial sample alignment by a simple generally applicable procedure. Formation of excimers was also observed. In order to obtain guidance for improving molecular packing by a minor structural modification, calculations by a simplified frontier orbital method were used to find all local maxima of singlet fission rate as a function of geometry of a molecular pair. The method was tested at 48 maxima by comparison with the ab initio Frenkel-Davydov exciton model.

Eliminating Fatigue in Surface-Bound Spiropyrans

This paper describes an experimental approach to eliminating the loss of reversibility that surface-bound spiropyrans exhibit when switched with light. Although such fatigue can be controlled in other contexts, on surfaces, the photochromic compounds are held in close proximity to each other and relatively few molecules modulate the properties of a device, leading to a loss of functionality after only a few switching cycles. The switching process was characterized by photoelectron spectroscopy and differences in tunneling currents in the spiropyran and merocyanine forms using eutectic Ga-In. Self-assembled monolayers comprising only the photochromic compounds degraded rapidly, while mixed monolayers with hexanethiol showed different behaviors depending on the relative humidity. Under dry conditions, no chemical degradation was observed and the switching process was reversible over at least 100 cycles. Under humid conditions, no degradation occurred, but the switching process became irreversible. The absence of degradation observed in mixed monolayers is ascribed to the lack of solvation, which increases the barrier to a key bond rotation past the available thermal energy. These results highlight important differences in the contexts in which photochromic compounds are utilized and demonstrate that they can be leveraged to extract device-relevant functionality from surface-bound switches by suppressing fatigue and irreversibility.

Supramolecular Mimic for Bottlebrush Polymers in Bulk

A series of poly(tetrahydrofuran)s with molecular weights above entanglement molecular weight M _e were synthesized, and one of their end-groups was functionalized with a supramolecular entity so that the corresponding polymers form a brushlike structure suitable for comparison with conventional irreversible bottlebrush polymers. To compare their relaxation mechanisms, linear rheology was employed and showed that a hierarchical relaxation, which is usually observed in bottlebrush polymers, occurs in these materials, too. The polymer chain segments close to the supramolecular backbone are highly immobilized due to strong association in the center of polymer brush and cannot relax via reptation mechanism, which is mainly responsible for linear entangled polymer relaxations. Therefore, disentanglement can take much longer through contour length fluctuations and arm retraction processes similar to covalent bottlebrush polymers and combs. The relaxed ends of polymers then act as solvent to let the remaining segments of the polymeric brush undergo Rouse-like motions (constraint release Rouse). At longer times, additional plateau appears, which can be attributed to the relaxation of the entire supramolecular bottlebrush polymer via hopping or reptative motions. With an increase of temperature, viscoelastic solid behavior turns into viscoelastic liquid due to reversible depolymerization of the supramolecular backbone of the bottlebrush polymer. The elastic modulus (G' in the order of kPa) was much less than the values found for the entanglement plateau modulus of linear poly(tetrahydrofuran) (in order of MPa). This low modulus value, which exists up to very low frequencies (high temperatures), makes them a good candidate for supersoft elastomers.

Binding of quinazolinones to c-KIT G-quadruplex; an interplay between hydrogen bonding and π-π stacking

Stabilization of G-quadruplex structures in the c-KIT promoter with the aid of ligands has become an area of great interest in potential cancer therapeutics. Understanding the binding process between ligands and G-quadruplex is essential for a discovery of selective ligands with high binding affinity to G-quadruplex. In the present work, binding mechanisms of 4-quinazolinones to c-KIT G-quadruplex were investigated theoretically by means of molecular dynamics (MD) simulations. To explore the binding affinity of ligands, binding free energy calculations were performed using the molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) method. We demonstrate that the key interactions in G-quadruplex-ligand complexes are π-π stacking and hydrogen bond interactions. However, neither of these two interactions alone determines the stability of the G-quadruplex-ligand complexes; rather, it is the result of an intricate interplay between the two. To further examine the nature of the binding, a free energy decomposition analysis at residue level was carried out. The results clearly demonstrate the crucial roles of two hot spot residues (DG4 and DG8) for the binding of ligands to c-KIT G-quadruplex, and highlight the importance of the planar aromatic moiety of ligands in G-quadruplex stabilization via π-π stacking interactions. Our study can assist in the design of new derivatives of 4-quinazolinone with high binding affinity for c-KIT G-quadruplex.

Algebraic diagrammatic construction for the polarisation propagator in combination with effective fragment potentials

The effective fragment potential (EFP) method for the efficient inclusion of solvation effects is combined with the algebraic diagrammatic construction (ADC) scheme for the second- and third-order polarisation propagator.

Highly Strained Organogold Complexes and Their Gold- or Rhodium-Catalyzed Isomerizations

The synthesis and characterization of (NHC)(tricyclo[4.1.0.0^2,7 ]hept-1-yl)gold(I) compounds is reported. Several of these organometallic compounds could be obtained by transmetalation from the organolithium precursor to the corresponding (NHC)gold(I) chlorides. These are by far the most strained stable organogold compounds reported so far. With these new compounds we were able to efficiently and selectively accomplish the first gold-catalyzed rearrangement of organogold compounds, even better yields were obtained by the first rhodium-catalyzed rearrangement of these organogold species. (E/Z)-Mixtures of (NHC)(cyclohex-2-en-1-ylidenemethyl)gold(I) were obtained, none of the other known rearrangement products of tricycloheptanes. Additional insight into the chemical and physical properties of the strained compounds was obtained by spectroscopic and computational studies.

Insights into Light-driven DNA Repair by Photolyases: Challenges and Opportunities for Electronic Structure Theory

Ultraviolet radiation causes two of the most abundant mutagenic and cytotoxic DNA lesions: cyclobutane pyrimidine dimers and 6-4 photoproducts. (6-4) Photolyases are light-activated enzymes that selectively bind to DNA and trigger repair of mutagenic 6-4 photoproducts via photoinduced electron transfer from flavin adenine dinucleotide anion (FADH^- ) to the lesion triggering repair. This review provides an overview of the sequential steps of the repair process, that is light absorption and resonance energy transfer, photoinduced electron transfer and electron-induced splitting mechanisms, with an emphasis on the role of theory and computation. In addition, theoretical calculations and physical properties that can be used to classify specific mechanism are discussed in an effort to trace the fundamental aspects of each individual step and assist the interpretation of experimental data. The current challenges and suggested future directions are outlined for each step, concluding with a view on the future.

Characterization of the Intermediate in and Identification of the Repair Mechanism of (6-4) Photolesions by Photolyases

Quantum mechanics/molecular mechanics calculations are employed to assign previously recorded experimental spectroscopic signatures of the intermediates occurring during the photo-induced repair of (6-4) photolesions by photolyases to specific molecular structures. Based on this close comparison of experiment and theory it is demonstrated that the acting repair mechanism involves proton transfer from the protonated His365 to the N3' nitrogen of the lesion, which proceeds simultaneously with intramolecular OH transfer along an oxetane-like transition state.

On the Nature of an Extended Stokes Shift in the mPlum Fluorescent Protein

Far-red fluorescent proteins (FPs) enable deep-tissue in vivo imaging. Combining FPs with large and small Stokes shifts enables single-excitation/dual-emission multicolor applications. Using a quantum mechanics/molecular mechanics (QM/MM) scheme, we carried out a series of simulations to identify the origin of an extended Stokes shift (0.2 eV) observed in mPlum, one of the most far-red-shifted FPs. We demonstrated that the red shift of emission is largely due to the excited-state relaxation of the chromophore itself. Rigid protein environment suppresses the relaxation; however, if the hydrogen-bond network around the chromophore is sufficiently flexible, it can rearrange upon electronic excitation, allowing the chromophore to relax. The reorganization of the hydrogen-bond network is driven by changes in bonding and charge distributions of the chromophore in the excited state. The ILE65 and GLU16 residues play the most important role. The MD simulations reveal two ground-state populations with the direct (Chro-ILE65···GLU16) and water-mediated (Chro-ILE65···Wat321···GLU16) hydrogen-bond patterns. In the excited state, both populations relax to a single emitting state with the water-mediated (Chro-ILE65···Wat321···GLU16) hydrogen-bond pattern, which provides a better match for the excited-state charge distribution (the acylimine's oxygen has a larger negative charge in S1 than in S0). The extended Stokes shift arises due to the conversion of the direct hydrogen-bond pattern to the water-mediated one accompanied by large structural relaxation of the electronically excited chromophore. This conclusion is supported by calculations for the GLU16LEU mutant, which has only one hydrogen-bond pattern. Consequently, no interconversion is possible, and the computed Stokes shift is small, in agreement with the experiment. Our theoretical findings provide support to a recent study of the Stokes shifts in mPlum and its mutants.

Dynamics of drops – Formation, growth, oscillation, detachment, and coalescence

Single drops or bubbles are frequently used for the characterization of liquid-fluid interfaces. Their advantage is the small volume and the various protocols of their formation. Thus, several important methods are based on single drops and bubbles, such as capillary pressure and profile analysis tensiometry. However, these methods are often applied under dynamic conditions, although their principles are defined under equilibrium conditions. Thus, specific attention has to be paid when these methods are used beyond certain limits. In many cases, computational fluid dynamics (CFD) simulations have allowed researchers, to extend these limits and to gain important information on the interfacial dynamics. Examples discussed here are the capillary pressure tensiometry used for short time and profile analysis tensiometry for long time dynamic interfacial tension measurements, the oscillating drop methods for measuring dilational visco-elasticity. For measuring the coalescence of two drops the liquid dynamics of the subsequently formed liquid bridges have to be considered. In this paper, a thorough review of important experimental and computational findings, related to the dynamics of drops, including its formation, growth, oscillation, detachment, and coalescence is presented. Emphasis is however on some selected important developments. In addition, the paper tries to predict the main directions of advancement in interfacial research for the near future.

A quantum chemical perspective on (6-4) photolesion repair by photolyases

(6-4)-Photolyases are fascinating enzymes which repair (6-4)-DNA photolesions utilizing light themselves. It is well known that upon initial photo-excitation of an antenna pigment an electron is transferred from an adjacent FADH(-) cofactor to the photolesion initiating repair, i.e. restoration of the original undamaged DNA bases. Concerning the molecular details of this amazing repair mechanism, the early steps of energy transfer and catalytic electron generation are well understood, the terminal repair mechanism, however, is still a matter of ongoing debate. In this perspective article, recent results of quantum chemical investigations are presented, and their meaning for the repair mechanism under natural conditions is outlined. Consequences of natural light conditions, temperature and thermal equilibration are highlighted when issues like the initial protonation state of the relevant histidines and the lesion, or the direction of electron transfer are discussed.

Combined QM/MM investigation on the light-driven electron-induced repair of the (6-4) thymine dimer catalyzed by DNA photolyase

The (6-4) photolyases are blue-light-activated enzymes that selectively bind to DNA and initiate splitting of mutagenic thymine (6-4) thymine photoproducts (T(6-4)T-PP) via photoinduced electron transfer from flavin adenine dinucleotide anion (FADH(-)) to the lesion triggering repair. In the present work, the repair mechanism after the initial electron transfer and the effect of the protein/DNA environment are investigated theoretically by means of hybrid quantum mechanical/molecular mechanical (QM/MM) simulations using X-ray structure of the enzyme-DNA complex. By comparison of three previously proposed repair mechanisms, we found that the lowest activation free energy is required for the pathway in which the key step governing the repair photocycle is electron transfer coupled with the proton transfer from the protonated histidine, His365, to the N3' nitrogen of the pyrimidone thymine. The transfer simultaneously occurs with concerted intramolecular OH transfer without formation of an oxetane or isolated water molecule intermediate. In contrast to previously suggested mechanisms, this newly identified pathway requires neither a subsequent two-photon process nor electronic excitation of the photolesion.

Quantum chemical study of the enzymatic repair of T(6-4)C/C(6-4)T UV-photolesions by DNA photolyases

Several strategies have evolved to repair one of the abundant UV radiation-induced damages caused to DNA, namely the mutagenic pyrimidine (6-4) pyrimidone photolesions. DNA (6-4)-photolyases are enzymes repairing these lesions by a photoinitiated electron transfer. An important aspect of a possible repair mechanism is its generality and transferability to different (6-4) lesions. Therefore, previously suggested mechanisms for the repair of the T(6-4)T lesion are here transferred to the T(6-4)C and C(6-4)T lesions and investigated theoretically using quantum chemical methods. Despite the different functional groups of the pyrimidine bases involved, a general valid molecular mechanism was identified, in which the initial step is an electron transfer coupled to a proton transfer from the protonated HIS365 to the N3(') nitrogen of the 3(') pyrimidine, followed by an intramolecular OH/NH2 transfer in one concerted step, which does not require an oxetane/azetidine or isolated water/ammonia intermediate.

Intermolecular Coulombic Decay in Biology: The Initial Electron Detachment from FADH(-) in DNA Photolyases

Intermolecular coulombic decay (ICD) is an efficient mechanism of low-energy electron generation in condensed phases and is discussed as their potential source in living cells, tissues, and materials. The first example of ICD as an operating mechanism in real biological systems, that is, in the DNA repair enzymes photolyases, is presented. Photolyase function involves light-induced electron detachment from a reduced flavin adenine dinucleotide (FADH(-)), followed by its transfer to the DNA-lesion triggering repair of covalently bound nucleobase dimers. Modern quantum chemical methods are employed to demonstrate that the transferred electron is efficiently generated via a resonant ICD process between the antenna pigment and the FADH(-) cofactors.