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We present a comprehensive study on the conformational behavior of diversely substituted 4-fluorotetrahydrothiopyran derivatives. Through quantum chemical simulations including DFT as well as NBO and NPA analysis, we elucidate the pivotal role of electrostatic interactions, occasionally complemented by hyperconjugative interactions, in stabilizing axial fluorine conformers. Less polar conformers were occasionally obtained, attributed to the interplay of electrostatic and hyperconjugative interactions. Experimental validation through NMR spectroscopy aligns with the computational analysis, thus providing a coherent understanding of the structural dynamics of these compounds., (© 2024 The Author(s). Chemistry - A European Journal published by Wiley-VCH GmbH.)

Photoisomerization of azobenzenes from their stable E isomer to the metastable Z state is the basis of numerous applications of these molecules. However, this reaction typically requires ultraviolet light, which limits applicability. In this study, we introduce disequilibration by sensitization under confinement (DESC), a supramolecular approach to induce the E -to- Z isomerization by using light of a desired color, including red. DESC relies on a combination of a macrocyclic host and a photosensitizer, which act together to selectively bind and sensitize E -azobenzenes for isomerization. The Z isomer lacks strong affinity for and is expelled from the host, which can then convert additional E- azobenzenes to the Z state. In this way, the host-photosensitizer complex converts photon energy into chemical energy in the form of out-of-equilibrium photostationary states, including ones that cannot be accessed through direct photoexcitation.

Telomere biology disorders (TBDs) are a spectrum of diseases that arise from mutations in genes responsible for maintaining telomere integrity. Human telomerase reverse transcriptase (hTERT) adds nucleotides to chromosome ends and is frequently mutated in individuals with TBDs. Previous studies have provided insight into how relative changes in hTERT activity can lead to pathological outcomes. However, the underlying mechanisms describing how disease-associated variants alter the physicochemical steps of nucleotide insertion remain poorly understood. To address this, we applied single-turnover kinetics and computer simulations to the Tribolium castaneum TERT (tcTERT) model system and characterized the nucleotide insertion mechanisms of six disease-associated variants. Each variant had distinct consequences on tcTERT's nucleotide insertion mechanism, including changes in nucleotide binding affinity, rates of catalysis, or ribonucleotide selectivity. Our computer simulations provide insight into how each variant disrupts active site organization, such as suboptimal positioning of active site residues, destabilization of the DNA 3' terminus, or changes in nucleotide sugar pucker. Collectively, this work provides a holistic characterization of the nucleotide insertion mechanisms for multiple disease-associated TERT variants and identifies additional functions of key active site residues during nucleotide insertion.

COVID19 has aptly revealed that airborne viruses such as SARS-CoV-2 with the ability to rapidly mutate combined with high rates of transmission and fatality can cause a deadly worldwide pandemic in a matter of weeks (Plato et al., 2021). Apart from vaccines and post-infection treatment options, strategies for preparedness will be vital in responding to the current and future pandemics. Therefore, there is wide interest in approaches that allow predictions of increase in infections ('surges') before they occur. We describe here real-time genomic surveillance particularly based on mutation analysis, of viral proteins as a methodology for a priori determination of surge in number of infection cases. The full results are available for SARS-CoV-2 at http://pandemics.okstate.edu/covid19/, and are updated daily as new virus sequences become available. This approach is generic and will also be applicable to other pathogens., Competing Interests: FN, EL, CM, VB, HW No competing interests declared, SH Reviewing editor, eLife, PA Founder and owner of Arium BioLabs LLC, (© 2023, Najar et al.)

Rhodopsins form a family of photoreceptor proteins which utilize the retinal chromophore for light energy conversion. Upon light absorption the retinal chromophore undergoes a photoisomerization. This reaction involves a non-radiative relaxation through a conical intersection between the singlet excited state and the ground state. In this work we studied the possible involvement of triplet states in the photoisomerization of retinaloids using the extended multistate (XMS) version of CASPT2. To this end, truncated models of three retinaloids were considered: protonated Schiff base, deprotonated Schiff base and the aldehyde form. The optimized geometries of the reactant, the product and the conical intersection were connected by a linear interpolation of internal coordinates to describe the isomerization. The energetic position of the low-lying singlet and triplet states as well as their spin-orbit coupling matrix elements (SOCME) were calculated along the isomerization profile. The SOCME values peaked in vicinity of the conical intersection for all the retinaloids. Furthermore, the magnitude of SOCME is invariant to the number of double bonds in the model. The SOCME for the protonated Schiff base is negligible (1.5 cm -1 ) which renders the involvement of the triplet state as improbable. However, the largest SOCME value of 30 cm -1 was found for the aldehyde form, followed by 15 cm -1 for the deprotonated Schiff base.

Many organisms sense light using rhodopsins, photoreceptive proteins containing a retinal chromophore. Here we report the discovery, structure and biophysical characterization of bestrhodopsins, a microbial rhodopsin subfamily from marine unicellular algae, in which one rhodopsin domain of eight transmembrane helices or, more often, two such domains in tandem, are C-terminally fused to a bestrophin channel. Cryo-EM analysis of a rhodopsin-rhodopsin-bestrophin fusion revealed that it forms a pentameric megacomplex (~700 kDa) with five rhodopsin pseudodimers surrounding the channel in the center. Bestrhodopsins are metastable and undergo photoconversion between red- and green-absorbing or green- and UVA-absorbing forms in the different variants. The retinal chromophore, in a unique binding pocket, photoisomerizes from all-trans to 11-cis form. Heterologously expressed bestrhodopsin behaves as a light-modulated anion channel., (© 2022. The Author(s), under exclusive licence to Springer Nature America, Inc.)

Proteorhodopsin (PR) is a photoactive proton pump found in marine bacteria. There are two phenotypes of PR exhibiting an environmental adaptation to the ocean's depth which tunes their maximum absorption: blue-absorbing proteorhodopsin (BPR) and green-absorbing proteorhodopsin (GPR). This blue/green color-shift is controlled by a glutamine to leucine substitution at position 105 which accounts for a 20 nm shift. Typically, spectral tuning in rhodopsins is rationalized by the external point charge model but the Q105L mutation is charge neutral. To study this tuning mechanism, we employed the hybrid QM/MM method with sampling from molecular dynamics. Our results reveal that the positive partial charge of glutamine near the C 14 -C 15 bond of retinal shortens the effective conjugation length of the chromophore compared to the leucine residue. The derived mechanism can be applied to explain the color regulation in other retinal proteins and can serve as a guideline for rational design of spectral shifts., (© 2022 The Authors. Chemistry - A European Journal published by Wiley-VCH GmbH.)

This perspective article highlights the challenges in the theoretical description of photoreceptor proteins using multiscale modeling, as discussed at the CECAM workshop in Tel Aviv, Israel. The participants have identified grand challenges and discussed the development of new tools to address them. Recent progress in understanding representative proteins such as green fluorescent protein, photoactive yellow protein, phytochrome, and rhodopsin is presented, along with methodological developments., (© 2021 American Society for Photobiology.)

MOLCAS/OpenMolcas is an ab initio electronic structure program providing a large set of computational methods from Hartree-Fock and density functional theory to various implementations of multiconfigurational theory. This article provides a comprehensive overview of the main features of the code, specifically reviewing the use of the code in previously reported chemical applications as well as more recent applications including the calculation of magnetic properties from optimized density matrix renormalization group wave functions.

In the version of this Article originally published, in Fig. 5, the chemical formula Br•CC 6 H 11 should have read Br•CH 3 C 6 H 11 .

In this work, the electronic structure and spectroscopic properties of lumiflavin are calculated using various quantum chemical methods. The excitation energies for ten singlet and triplet states as well as the analysis of the electron density difference are assessed using various wave function-based methods and density functionals. The relative order of singlet and triplet excited states is established on the basis of the coupled cluster method CC2. We find that at least seven singlet excited states are required to assign all peaks in the UV/Vis spectrum. In addition, we have studied the solvatochromic effect on the excitation energies and found differential effects except for the first bright excited state. Vibrational frequencies as well as IR, Raman and resonance Raman intensities are simulated and compared to their experimental counterparts. We have assigned peaks, assessed the effect of anharmonicity, and confirmed the previous assignments in case of the most intense transitions. Finally, we have studied the NMR shieldings and established the effect of the solvent polarity. The present study provides data for lumiflavin in the gas phase and in implicit solvent model that can be used as a reference for the protein-embedded flavin simulations and assignment of experimental spectra., (© 2018 The American Society of Photobiology.)

The primary photochemical reaction of the green-absorbing proteorhodopsin is studied by means of a hybrid quantum mechanics/molecular mechanics (QM/MM) approach. The simulations are based on a homology model derived from the blue-absorbing proteorhodopsin crystal structure. The geometry of retinal and the surrounding sidechains in the protein binding pocket were optimized using the QM/MM method. Starting from this geometry the isomerization was studied with a relaxed scan along the C13[double bond, length as m-dash]C14 dihedral. It revealed an "aborted bicycle pedal" mechanism of isomerization that was originally proposed by Warshel for bovine rhodopsin and bacteriorhodopsin. However, the isomerization involved the concerted rotation about C13[double bond, length as m-dash]C14 and C15[double bond, length as m-dash]N, with the latter being highly twisted but not isomerized. Further, the simulation showed an increased steric interaction between the hydrogen at the C14 of the isomerizing bond and the hydroxyl group at the neighbouring tyrosine 200. In addition, we have simulated a nonadiabatic trajectory which showed the timing of the isomerization. In the first 20 fs upon excitation the order of the conjugated double and single bonds is inverted, consecutively the C13[double bond, length as m-dash]C14 rotation is activated for 200 fs until the S1-S0 transition is detected. However, the isomerization is reverted due to the specific interaction with the tyrosine as observed along the relaxed scan calculation. Our simulations indicate that the retinal - tyrosine 200 interaction plays an important role in the outcome of the photoisomerization.

Femtosecond transient absorption measurements powered by 40 fs laser pulses reveal that ultrafast isomerization takes place upon S 1 excitation of both CH 2 I 2 and CHBr 3 in the gas phase. The photochemical conversion process is direct and intramolecular, i.e., it proceeds without caging media that have long been implicated in the photo-induced isomerization of polyhalogenated alkanes in condensed phases. Using multistate complete active space second order perturbation theory (MS-CASPT2) calculations, we investigate the structure of the photochemical reaction paths connecting the photoexcited species to their corresponding isomeric forms. Unconstrained minimum energy paths computed starting from the S 1 Franck-Condon points lead to S 1 /S 0 conical intersections, which directly connect the parent CHBr 3 and CH 2 I 2 molecules to their isomeric forms. Changes in the chemical bonding picture along the S 1 /S 0 isomerization reaction path are described using multireference average coupled pair functional (MRACPF) calculations in conjunction with natural resonance theory (NRT) analysis. These calculations reveal a complex interplay between covalent, radical, ylidic, and ion-pair dominant resonance structures throughout the nonadiabatic photochemical isomerization processes described in this work.

'Roaming' is a new and unusual class of reaction mechanism that has recently been discovered in unimolecular dissociation reactions of isolated molecules in the gas phase. It is characterized by frustrated bond cleavage, after which the two incipient fragments 'roam' on a flat region of the potential energy surface before reacting with one another. Here, we provide evidence that supports roaming in the liquid phase. We are now able to explain previous solution-phase experiments by comparing them with new ultrafast transient absorption data showing the photoisomerization of gas-phase CHBr3. We see that, upon S0-S1 excitation, gas-phase CHBr3 isomerizes within 100 fs into the BrHCBr-Br species, which is identical to what has been observed in solution. Similar sub-100 fs isomerization is now also observed for BBr3 and PBr3 in solution upon S1 excitation. Quantum chemical simulations of XBr3 (X = B, P or CH) suggest that photochemical reactivity in all three cases studied is governed by S1/S0 conical intersections and can best be described as occurring through roaming-mediated pathways.