Contrasting the excited state properties of different conformers of trans- and cis-2,2'-bipyridine oligomers in the gas phase.

In this article, we present conformation-dependent photophysical and excited state properties of trans- and cis- BPY oligomers. Oligomers up to tetramers for three conformers, namely, o-, m-, and p-, are constructed and optimized at the B3LYP-D3/def2-SVPD level. The photophysical and excited state properties are interpreted in terms of UV and CD spectra at the RI-ADC(2)/def2-TZVPD level. The UV spectra of oligomers of the m-conformer show high-intensity and red-shifted UV bands compared to o- and p-oligomers. The CD spectra of p-oligomers show intense CD bands compared to o- and p-oligomers in the case of trans-structures. In contrast, oligomers of each conformer of cis-structures show high-intensity CD bands. The excited states of (BPY)2 and (BPY)4 are also characterized by analysis of one-electron transition density matrix considering three descriptors: ωCT, dexc, and PRNTO. The ωCT values of dimers are in the range of 0.06-0.32, which indicates the excited states are mainly LE states, whereas, for (BPY)4, the ωCT values range from 0.17 to 0.53, indicating the possibility of partial CT in the excited states. These observations are also explained using the NTOs and e-h correlation plots.

Splitting probabilities as optimal controllers of rare reactive events.

The committor constitutes the primary quantity of interest within chemical kinetics as it is understood to encode the ideal reaction coordinate for a rare reactive event. We show the generative utility of the committor in that it can be used explicitly to produce a reactive trajectory ensemble that exhibits numerically exact statistics as that of the original transition path ensemble. This is done by relating a time-dependent analog of the committor that solves a generalized bridge problem to the splitting probability that solves a boundary value problem under a bistable assumption. By invoking stochastic optimal control and spectral theory, we derive a general form for the optimal controller of a bridge process that connects two metastable states expressed in terms of the splitting probability. This formalism offers an alternative perspective into the role of the committor and its gradients in that they encode force fields that guarantee reactivity, generating trajectories that are statistically identical to the way that a system would react autonomously.

Photon echoes using atomic frequency combs in Pr:YSO - experiment and semiclassical theory.

Photon echoes in rare-earth-doped crystals are studied to understand the challenges of making broadband quantum memories using the atomic frequency comb (AFC) protocol in systems with hyperfine structure. The hyperfine structure of Pr3+ poses an obstacle to this goal because frequencies associated with the hyperfine transitions change the simple picture of modulation at an externally imposed frequency. The current work focuses on the intermediate case where the hyperfine spacing is comparable to the comb spacing, a challenging regime that has recently been considered. Operating in this regime may facilitate storing quantum information over a larger spectral range in such systems. In this work, we prepare broadband AFCs using optical combs with tooth spacings ranging from 1 MHz to 16 MHz in fine steps, and measure transmission spectra and photon echoes for each. We predict the spectra and echoes theoretically using the optical combs as input to either a rate equation code or a density matrix code, which calculates the redistribution of populations. We then use the redistributed populations as input to a semiclassical theory using the frequency-dependent dielectric function. The two sets of predictions each give a good, but different account of the photon echoes.

Effect of Fluorine Substitution on Absorption and Emission Properties of Figure-eight-shaped [5]Helicene Dimer: A Computational Study at RI-MP2/RI-ADC(2) Level.

Chirality is a very important characteristic of optically active molecules and polyaromatics with helical structures, and plays a vital role in various applications in material science. In the present work, we show the effects of fluorine substitution at various positions in a figure-8-shaped [5]helicene dimer on the ground and excited state g-factors. Calculations for the ground and excited states are performed at the MP2 and ADC(2) levels of theory, respectively. The results reveal that fluorination has a large effect on the excited state structures. The values of the excited state dissymmetry factors for the molecules with fluorinations at both ends of the figure-8 systems are smaller than that of the parent system. On the other hand, fluorinations only in the stacked-phenyl region results in an increase in the value of g cpl ${\left| {g_{{\rm{cpl}}} } \right|}$ . The perfluorinated system shows the smallest g cpl ${\left| {g_{{\rm{cpl}}} } \right|}$ .

Conformational Effect on the Excitonic States of 2-Phenylpyridine Oligomers: Ab Initio Studies and Analysis.

In this work, we report the effect of different conformations of 2-phenylpyridine oligomers ((PhPy)n=1-5) on the excited state properties from the results obtained at the RI-ADC(2)/def2-TZVP level. Three different conformers, namely, A, B, and C, are considered for each oligomer. All the oligomers of conformer A have linear-type structures, whereas conformers B and C form helical structures at n = 5 and n = 3, respectively. The differences in the geometries of the three conformers are reflected in the UV and CD spectra. The UV spectra of conformer A show high-intensity peaks compared to the conformers B and C, for each oligomer. While the helical oligomers of conformers B and C show high-intensity CD bands, the intensities of CD bands for all of the oligomers of conformer A are weaker. Analysis of the properties of the first five excited states in (PhPy)5 is carried out using three descriptors, and the results reveal that these are partially charge transfer states.

Theoretical Investigation of the E/Z Photoisomerization Pathway in 1-(2-Pyrrolyl)-2-(2-thienyl)ethylene.

Molecular-level understanding of photochemistry in simple vinylene-linked systems such as ethylene and stilbene has been a major area of research. However, the effect of replacing the two benzene rings by five-membered heterocyclic rings, thiophene and pyrrole, is yet to be reported. In the present theoretical study, our aim is to illustrate photoinduced processes in a vinylene-linked thiophene-pyrrole system. Computational studies are carried out at the RI-MP2/RI-ADC(2)/cc-pVTZ level to explore different isomerization pathways. Minimum-energy conical intersection (MECI) structures are categorized into two types: closed-ring and twisted-pyramidalized structures. Relaxation through the former MECIs is accessible only from the cis isomers. However, the latter MECIs are inaccessible due to high energy barriers along the linear interpolation in internal coordinate paths.

Effect of Terminal Fluorination on Chiroptical Properties of Carbo[5-8]helicenes: A Systematic Computational Study at the RI-ADC(2) Level.

In this article, effects of di-, tetra-, and octafluorination on the structural and chiroptical properties of carbo[5-8]helicenes are reported. Three fluorinated derivatives are designed from each parent carbohelicene by substituting either one, two, or four hydrogens at each terminal ring with fluorine atoms. Excited states properties such as UV-vis and CD spectra of all the six fluorinated carbohelicenes are computed at the ADC(2)/def2-TZVP level, and the results are compared against the results of their respective parent carbohelicene. In addition, CPL properties are also computed at the same level of theory. In the case of carbo[5]helicene (5H), gCPL decreases with an increase in the degree of fluorination. A similar observation is made in carbo[6]helicene (6H) too, although the value for tetrafluorinated 6H is slightly larger than for difluorinated 6H. Di- and tetrafluorination in carbo[7]helicene (7H), and all types of considered fluorination in carbo[8]helicene (8H) produce improved gCPL results. Results for fluorescence rate constants are also shown. Results are analyzed in terms of the transition dipole moment vectors and the angles between those.

Variational deep learning of equilibrium transition path ensembles.

We present a time-dependent variational method to learn the mechanisms of equilibrium reactive processes and efficiently evaluate their rates within a transition path ensemble. This approach builds off of the variational path sampling methodology by approximating the time-dependent commitment probability within a neural network ansatz. The reaction mechanisms inferred through this approach are elucidated by a novel decomposition of the rate in terms of the components of a stochastic path action conditioned on a transition. This decomposition affords an ability to resolve the typical contribution of each reactive mode and their couplings to the rare event. The associated rate evaluation is variational and systematically improvable through the development of a cumulant expansion. We demonstrate this method in both over- and under-damped stochastic equations of motion, in low-dimensional model systems, and in the isomerization of a solvated alanine dipeptide. In all examples, we find that we can obtain quantitatively accurate estimates of the rates of the reactive events with minimal trajectory statistics and gain unique insights into transitions through the analysis of their commitment probability.

Improved Estimates of Host-Guest Interaction Energies for Endohedral Fullerenes Containing Rare Gas Atoms, Small Molecules, and Cations.

Endohedral fullerenes have evinced much interest from the fundamental and applications points of view. However, given the nature of the weak interaction between the guest species and the host cage in these confined systems, the interaction energy values obtained using various theoretical methods, and different basis sets vary over a wide range. For example, the reported interaction energy for the HF@C60 system ranges from -2.5 kcal/mol to -14.9 kcal/mol. In the present manuscript, we report reliable interaction energy values for different endohedral fullerenes (He@C60 , Ne@C60 , Ar@C60 , Kr@C60 , H2 @C60 , HF@C60 , H2 O@C60 , NH3 @C60 , CH4 @C60 , Li+ @C60 , Na+ @C60 , and K+ @C60 ) obtained using the domain-based local pair natural orbital coupled-cluster singles, doubles, and perturbative triples (DLPNO-CCSD(T)) method and the def2-TZVP basis set. We believe that these energy values could be considered as benchmark values, and the performance of other quantum chemical methods could be assessed accordingly. Local energy decomposition analysis within the DLPNO-CCSD(T) framework is used to estimate the electrostatic, exchange, and dispersion components of the interaction energy for some of the endohedral fullerenes.

Effects of Heterocyclic Ring Fusion and Chain Elongation on Chiroptical Properties of Polyaza[9]helicene: A Computational Study.

In the present work, the effect of lateral and helical extensions on the physical and chiroptical properties of azahelicenes is reported. Starting with the experimentally reported polyaza[9]helicene (9Ha), three derivatives, two with laterally fused electron-withdrawing rings and the third with larger helical length, are designed. For the excited-state properties such as UV-vis and CD spectra, performances of different DFT functionals are evaluated by comparing the energies and characters of the excited states against the ADC(2) results. CPL properties are calculated at DFT level. Among the three designed systems, pyrazine-based 9HaP shows an improved gCPL value compared to that for parent 9Ha. However, quinoxaline-based 9HaQ is found to be the worst CPL emitter with the lowest dissymmetry factor. The helically extended derivative, 11Ha, shows good CPL results, but gCPL remains smaller than that for the parent system. The CPL results are analyzed in terms of electric dipole transition moment (EDTM) and magnetic dipole transition moment (MDTM) vectors, and angles between these two vectors.

Modular nanoarray vaccine for SARS-CoV-2.

The current vaccine development strategies for the COVID-19 pandemic utilize whole inactive or attenuated viruses, virus-like particles, recombinant proteins, and antigen-coding DNA and mRNA with various delivery strategies. While highly effective, these vaccine development strategies are time-consuming and often do not provide reliable protection for immunocompromised individuals, young children, and pregnant women. Here, we propose a novel modular vaccine platform to address these shortcomings using chemically synthesized peptides identified based on the validated bioinformatic data about the target. The vaccine is based on the rational design of an immunogen containing two defined B-cell epitopes from the spike glycoprotein of SARS-CoV-2 and the universal T-helper epitope PADRE. The epitopes were conjugated to short DNA probes and combined with a complementary scaffold strand, resulting in sequence-specific self-assembly. The immunogens were then formulated by conjugation to gold nanoparticles by three methods or by co-crystallization with epsilon inulin. BALB/C mice were immunized with each formulation, and the IgG immune responses and virus neutralizing titers were compared. The results demonstrate that this assembly is immunogenic and generates neutralizing antibodies against wildtype SARS-CoV-2 and the Delta variant.

Moderately dilated ascending aorta-The right wrap?

External reinforcement of the dilated or thin-walled aorta has been tried for nearly half a century. A range of materials has been used as external support. This commentary assesses the evidence that exists regarding the efficacy of wrapping the aorta as well as compares the different options available with a particular focus on the usage of the autologous pericardium.

Aortic root enlargement: Short-term outcomes from a decade's worth of experience.

BACKGROUND: Patient prosthesis mismatch is a real problem observed in patients receiving aortic valves too small for their body surface area. This situation is entirely preventable with the apt use of root augmentation procedures. This study aims to evaluate and analyze short-term outcomes in patients who have undergone root enlargement procedures. METHODS: Fifty-five patients with ages ranging from 11 to 65 years (36.74 ± 13.27), who have undergone root enlargement procedures between January 2009 and January 2019 are recruited for this study. The group comprises 23 males (41.8%) and 32 females (58.2%). Admission and follow-up parameters recorded over a period of 1 year were used for analyzing outcomes. The mean iAVA (aortic valve area indexed to body surface area) of the group was 0.49 ± 0.06 cm2 /m2 . RESULTS: There was a significant increase in the indexed aortic valve area after root enlargement surgery from 0.49 ± 0.06 to 1.09 ± 0.19 cm2 /m2 . The difference was statistically significant (p < .05). St Jude Masters bileaflet prosthesis resulted in the highest iEOA (1.29 ± 0.18 cm2 /m2 ). TTK Chitra monoleaflet valve was the most commonly used valve in 61.81% of the cohort. At 1 year follow-up, there was a progressive decrease in left ventricle (LV) mass Index and mean gradients resulting in progressive improvement in the New York Heart Association functional class among patients. CONCLUSION: In experienced hands, root enlargement procedures result in good curative outcomes for patients through effective LV regression and symptom resolution on a short-term basis.

Current Advancements in the Molecular Mechanism of Plasma Treatment for Seed Germination and Plant Growth.

Low-temperature atmospheric pressure plasma has been used in various fields such as plasma medicine, agriculture, food safety and storage, and food manufacturing. In the field of plasma agriculture, plasma treatment improves seed germination, plant growth, and resistance to abiotic and biotic stresses, allows pesticide removal, and enhances biomass and yield. Currently, the complex molecular mechanisms of plasma treatment in plasma agriculture are fully unexplored, especially those related to seed germination and plant growth. Therefore, in this review, we have summarized the current progress in the application of the plasma treatment technique in plants, including plasma treatment methods, physical and chemical effects, and the molecular mechanism underlying the effects of low-temperature plasma treatment. Additionally, we have discussed the interactions between plasma and seed germination that occur through seed coat modification, reactive species, seed sterilization, heat, and UV radiation in correlation with molecular phenomena, including transcriptional and epigenetic regulation. This review aims to present the mechanisms underlying the effects of plasma treatment and to discuss the potential applications of plasma as a powerful tool, priming agent, elicitor or inducer, and disinfectant in the future.

Genome-Wide Mutagenesis of Hepatitis C Virus Reveals Ability of Genome To Overcome Detrimental Mutations.

To gain insight into the impact of mutations on the viability of the hepatitis C virus (HCV) genome, we created a set of full-genome mutant libraries, differing from the parent sequence as well as each other, by using a random mutagenesis approach; the proportion of mutations increased across these libraries with declining template amount or dATP concentration. The replication efficiencies of full-genome mutant libraries ranged between 71 and 329 focus-forming units (FFU) per 105 Huh7.5 cells. Mutant libraries with low proportions of mutations demonstrated low replication capabilities, whereas those with high proportions of mutations had their replication capabilities restored. Hepatoma cells transfected with selected mutant libraries, with low (4 mutations per 10,000 bp copied), moderate (33 mutations), and high (66 mutations) proportions of mutations, and their progeny were subjected to serial passage. Predominant virus variants (mutants) from these mutant libraries (Mutantl, Mutantm, and Mutanth, respectively) were evaluated for changes in growth kinetics and particle-to-FFU unit ratio, virus protein expression, and modulation of host cell protein synthesis. Mutantm and Mutantl variants produced >3.0-log-higher extracellular progeny per ml than the parent, and Mutanth produced progeny at a rate 1.0-log lower. More than 80% of the mutations were in a nonstructural part of the mutant genomes, the majority were nonsynonymous, and a moderate to large proportion were in the conserved regions. Our results suggest that the HCV genome has the ability to overcome lethal/deleterious mutations because of the high reproduction rate but highly selects for random, beneficial mutations.IMPORTANCE Hepatitis C virus (HCV) in vivo displays high genetic heterogeneity, which is partly due to the high reproduction and random substitutions during error-prone genome replication. It is difficult to introduce random substitutions in vitro because of limitations in inducing mutagenesis from the 5' end to the 3' end of the genome. Our study has overcome this limitation. We synthesized full-length genomes with few to several random mutations in the background of an HCV clone that can recapitulate all steps of the life cycle. Our study provides evidence of the capability of the HCV genome to overcome deleterious mutations and remain viable. Mutants that emerged from the libraries had diverse phenotype profiles compared to the parent, and putative adaptive mutations mapped to segments of the conserved nonstructural genome. We demonstrate the potential utility of our system for the study of sequence variation that ensures the survival and adaptation of HCV.

A year-long extended release nanoformulated cabotegravir prodrug.

Long-acting cabotegravir (CAB) extends antiretroviral drug administration from daily to monthly. However, dosing volumes, injection site reactions and health-care oversight are obstacles towards a broad usage. The creation of poloxamer-coated hydrophobic and lipophilic CAB prodrugs with controlled hydrolysis and tissue penetrance can overcome these obstacles. To such ends, fatty acid ester CAB nanocrystal prodrugs with 14, 18 and 22 added carbon chains were encased in biocompatible surfactants named NMCAB, NM2CAB and NM3CAB and tested for drug release, activation, cytotoxicity, antiretroviral activities, pharmacokinetics and biodistribution. Pharmacokinetics studies, performed in mice and rhesus macaques, with the lead 18-carbon ester chain NM2CAB, showed plasma CAB levels above the protein-adjusted 90% inhibitory concentration for up to a year. NM2CAB, compared with NMCAB and NM3CAB, demonstrated a prolonged drug release, plasma circulation time and tissue drug concentrations after a single 45 mg per kg body weight intramuscular injection. These prodrug modifications could substantially improve CAB's effectiveness.

Assessing Effects of Different π bridges on Properties of Random Benzodithiophene-thienothiophene Donor and Non-fullerene Acceptor Based Active Layer.

This report presents the effect of insertion of four different π bridges, furan, thienothiophene, thiophene, and thiazole, into a random benzodithiophene (BDT)-fluorinated-thienothiophene (TT-F) based donor. Starting from a structure of synthesized donor (D)-acceptor (A) random copolymer with 3:1 ratio, we have designed four D-π-A systems with four different π bridges. Structural, optoelectronic, and charge transport/transfer properties of these donors and donor/NDI (NDI = poly[N,N'-bis(2-hexyldecyl)-naphthalene-1,4,5,8-bis(dicarboximide)-2,6-diyl]-alt-5,5'-(2,2'-bithiophene)) blends are investigated using DFT and TD-DFT methodologies. Our results show that the thiazole based TzP1 oligomer has the deepest HOMO value resulting in the highest open circuit voltage among all systems. The maximum absorption wavelengths of π-linked systems are red-shifted compared to the parent molecule. Rates of charge transfer and charge recombination are the highest and smallest in case of the thiazole/NDI blend system. In addition, hole mobilities in thiophene, thienothiophene, and thiazole based systems are larger than in the parent system. The results indicate that the thiazole unit among the four π bridge units is the most suitable for active layer construction.

Insights into the Excited-State Processes in 1-Hydroxy-2-acetonaphthone at ADC(2) and CASSCF Levels.

1-Hydroxy-2-acetonaphthone (HAN) has been extensively studied both experimentally and computationally to ascertain the existence of the excited-state proton transfer process. However, the process of full photocycle including the nonradiative relaxation pathways is yet to be proposed. Therefore, in the present study, we aim at providing a comprehensive picture of the excited-state processes in HAN including the proton transfer and relaxation processes through electronic structure calculations at second-order algebraic diagrammatic construction (ADC(2)) and complete active space second-order perturbation theory (CASPT2)//complete active space self-consistent field (CASSCF) and dynamics simulations at ADC(2) levels. Our studies show that the proton transfer process in the S1 state is barrierless and produces a stable keto form, which is in accordance with previous experimental and computational studies. Adiabatic dynamics simulations at the ADC(2) level confirmed the ultrafast process with an average proton transfer time of 43 fs. The resultant keto conformer then undergoes torsional rotation, leading to a conical intersection that mediates the internal conversion process to the ground state. Our dynamics simulation predicted that this deactivation process occurs at a time scale beyond 600 fs of simulation time. We also explored nonradiative relaxation from the enol Franck-Condon region, and this process was found to be improbable from the static point of view at both the ADC(2) and CASPT2 levels of theory due to a high energy barrier along the torsional coordinate.

Assessing the Performance of DFT Functionals for Excited-State Properties of Pyridine-Thiophene Oligomers.

In this article, we have examined the accuracy of various density functional theory (DFT) functionals to reproduce the absorption and CD spectra of pyridine-thiophene oligomers. The performance of different levels of approximations in DFT functionals is discussed with reference to the ADC(2) results. Starting from a linear system, like monomer, calculations are carried out at ADC(2) and DFT levels till a helical system, like pentamer, is formed. For vertical excitation energies, results obtained with functionals, like CAM-B3LYP, ωB97XD, and M06-2X, are closer to the ADC(2) results. However, analysis of excited-state properties shows that the state ordering patterns or results regarding natural transition orbitals from these DFT functionals sometimes differ from the ADC(2) results. Global hybrid functionals like B3LYP and PBE0 produce excitation energies which are far away from the ADC(2) benchmark results. Similarly, pure functionals and their long-range corrected versions produce either redshifted or blueshifted energies. For the CD spectra, the above three mentioned functionals, CAM-B3LYP, ωB97XD, and M06-2X, again produce spectra closer to the benchmark spectra.

Solid-liquid coexistence of neon, argon, krypton, and xenon studied by simulations.

The noble elements constitute the simplest group of atoms. At low temperatures or high pressures, they freeze into the face-centered cubic (fcc) crystal structure (except helium). This paper investigates neon, argon, krypton, and xenon by molecular dynamics using the simplified atomic potentials recently proposed by Deiters and Sadus [J. Chem. Phys. 150, 134504 (2019)], which are parameterized using data from accurate ab initio quantum-mechanical calculations by the coupled-cluster approach at the single-double-triple level. We compute the fcc freezing lines and find good agreement with the empirical values. At low pressures, predictions are improved by including many-body corrections. Hidden scale invariance of the potential-energy function is established by showing that mean-squared displacement and the static structure factor are invariant along the lines of constant excess entropy (isomorphs). The isomorph theory of melting [Pedersen et al., Nat. Commun. 7, 12386 (2016)] is used to predict from simulations at a single state point the freezing line's shape, the entropy of melting, and the Lindemann parameter of the crystal at melting. Finally, our results suggest that the body-centered cubic crystal is the thermodynamically stable phase at high pressures.