Comparative molecular dynamics simulations provided insights into the mechanisms of cold-adaption of alginate lyases from the PL7 family.

Alginate is an important polysaccharide that is abundant in the marine environments, including the Polar Regions, and bacterial alginate lyases play key roles in its degradation. Many reported alginate lyases show characteristics of cold-adapted enzymes, including relatively low temperature optimum of activities (Topt) and low thermal stabilities. However, the cold-adaption mechanisms of alginate lyases remain unclear. Here, we studied the cold-adaptation mechanisms of alginate lyases by comparing four members of the PL7 family from different environments: AlyC3 from the Arctic ocean (Psychromonas sp. C-3), AlyA1 from the temperate ocean (Zobellia galactanivorans), PA1167 from the human pathogen (Pseudomonas aeruginosa PAO1), and AlyQ from the tropic ocean (Persicobacter sp. CCB-QB2). Sequence comparison and comparative molecular dynamics (MD) simulations revealed two main strategies of cold adaptation. First, the Arctic AlyC3 and temperate AlyA1 increased the flexibility of the loops close to the catalytic center by introducing insertions at these loops. Second, the Arctic AlyC3 increased the electrostatic attractions with the negatively charged substrate by introducing a high portion of positively charged lysine at three of the insertions mentioned above. Furthermore, our study also revealed that the root mean square fluctuation (RMSF) increased greatly when the temperature was increased to Topt or higher, suggesting the RMSF increase temperature as a potential indicator of the cold adaptation level of the PL7 family. This study provided new insights into the cold-adaptation mechanisms of bacterial alginate lyases and the marine carbon cycling at low temperatures.

Multi-fidelity machine learning for predicting bandgaps of nonlinear optical crystals.

Nonlinear optical (NLO) materials are of great importance in modern optics and industry because of their intrinsic capability of wavelength conversion. Bandgap is a key property of NLO crystals. In recent years, machine learning (ML) has become a powerful tool to predict the bandgaps of compounds before synthesis. However, the shortage of available experimental data of NLO crystals poses a significant challenge for the exploration of new NLO materials using ML. In this work, we proposed a new multi-fidelity ML approach based on the multilevel descriptors developed by us (Z.-Y. Zhang, X. Liu, L. Shen, L. Chen and W.-H. Fang, J. Phys. Chem. C, 2021, 125, 25175-25188) and the gradient boosting regression tree algorithm. The calculated and experimental bandgaps of NLO crystals were collected as the low- and high-fidelity labels, respectively. The experimental values were predicted based on chemical compositions of crystals without prior knowledge about crystal structures. The multi-fidelity ML model overcame the performance of single-fidelity predictor. Furthermore, it was observed that less accurate predictions on the low-fidelity label may result in more accurate prediction on the high-fidelity label, at least in the present case. Using the multi-fidelity ML model with the best performance in this work, the mean absolute error on the test set of experimental bandgaps was 0.293 eV, which is smaller than that using the single-fidelity model (0.355 eV). It is far from perfect but accurate enough as an effective computational tool in the first step to discover novel NLO materials.

Construction of Highly Accurate Machine Learning Potential Energy Surfaces for Excited-State Dynamics Simulations Based on Low-Level Data Sets.

Machine learning is capable of effectively predicting the potential energies of molecules in the presence of high-quality data sets. Its application in the construction of ground- and excited-state potential energy surfaces is attractive to accelerate nonadiabatic molecular dynamics simulations of photochemical reactions. Because of the huge computational cost of excited-state electronic structure calculations, the construction of a high-quality data set becomes a bottleneck. In the present work, we first built two data sets. One was obtained from surface hopping dynamics simulations at the semiempirical OM2/MRCI level. Another was extracted from the dynamics trajectories at the CASSCF level, which was reported previously. The ground- and excited-state potential energy surfaces of ethylene-bridged azobenzene at the CASSCF computational level were constructed based on the former low-level data set. Although non-neural network machine learning methods can achieve good or modest performance during the training process, only neural network models provide reliable predictions on the latter external test data set. The BPNN and SchNet combined with the Δ-ML scheme and the force term in the loss functions are recommended for dynamics simulations. Then, we performed excited-state dynamics simulations of the photoisomerization of ethylene-bridged azobenzene on machine learning potential energy surfaces. Compared with the lifetimes of the first excited state (S1) estimated at different computational levels, our results on the E isomer are in good agreement with the high-level estimation. However, the overestimation of the Z isomer is unimproved. It suggests that smaller errors during the training process do not necessarily translate to more accurate predictions on high-level potential energies or better performance on nonadiabatic dynamics simulations, at least in the present case.

Excited-State Decay and Photolysis of O-Nitrophenol after Proton Transfer. II: A Theoretical Investigation in the Microsolvated Atmospheric Environment.

Changes in atmospheric humidity affect the number of water molecules surrounding o-nitrophenol (ONP), creating an anisotropic chemical environment. It, in turn, influences the photodynamic behaviors of ONP, differing from those observed in the gas phase and in solution. Recently, we explored the excited-state decay and the generation of the hydroxyl (OH) radical before proton transfer of ONP in the microsolvated environment using the MS-CASPT2//CASSCF approach. As is well known, ONP is capable of converting to its aci-nitro isomer (aciONP) via an excited-state intramolecular proton transfer (ESIPT) process. In the present work, the photoinduced dynamics of aciONP, which can lead to an OH radical and nitrous acid (HONO), was studied using the same computational model. Our calculations demonstrated that increasing the number of water molecules affects the molecular geometries, particularly the key bond lengths and dihedral angles of the HONO group, while also reducing the relative energies of minima and intersections. Moreover, we identified two distinct types of minimum structures: one that retains the intramolecular hydrogen bond and the other that breaks the hydrogen bond with the H atom flipping outward. The latter structure, compared with the former, has a different electronic-state character and facilitates intersystem crossing processes. Subsequently, two major excited-state decay paths were proposed: (PATH I) ESIPT → S1 → S1S0 → S0; (PATH II) ESIPT → S1 → S1-2 → S1T1 → T1 → S0T1 → S0. Furthermore, the T1 state has a relatively long lifetime, allowing for the formation of the OH radical and HONO, and the corresponding energy barriers decrease as the number of water molecules increases. These theoretical findings provide valuable insights into the photodynamics of aciONP in the microsolvated atmospheric environment.

Excited-State Decay and Photolysis of O-Nitrophenol before Proton Transfer. I: A Theoretical Investigation in the Microsolvated Atmospheric Environment.

As a potential source of the hydroxyl (OH) radical and nitrous acid (HONO), photolysis of o-nitrophenol (ONP) is of significant interest in both experimental and theoretical studies. In the atmospheric environment, the number of water molecules surrounding ONP changes with the humidity of the air, leading to an anisotropic chemical environment. This may have an impact on the photodynamics of ONP and provide a mechanism that differs from previously reported ones in the gas phase or in solution. Herein, the high-level MS-CASPT2//CASSCF method was performed to elucidate the excited-state decay and the generation of the OH radical for ONP before proton transfer in the microsolvated surrounding. We found that the varying number of water molecules affects the ground-state structures and alters the energy levels of nπ* and ππ* at the Franck-Condon (FC) region. Nevertheless, this is not the case for the excited-state minima, which exhibit very similar adiabatic excitation properties. In addition, the presence of water molecules also significantly influences the intersection structures since hydrogen bonds will hinder or alleviate the rotation or pyramidalization of the nitro (NO2) group. This will, in turn, change the excited-state relaxation mechanism of ONP. Finally, we speculated that the OH radical might be formed in the hot ground state of ONP in the microsolvated surrounding after exploring all possible electronic states.

Genomic and Metagenomic Insights into the Distribution of Nicotine-degrading Enzymes in Human Microbiota.

Introduction: Nicotine degradation is a new strategy to block nicotine-induced pathology. The potential of human microbiota to degrade nicotine has not been explored. Aims: This study aimed to uncover the genomic potentials of human microbiota to degrade nicotine. Methods: To address this issue, we performed a systematic annotation of Nicotine-Degrading Enzymes (NDEs) from genomes and metagenomes of human microbiota. A total of 26,295 genomes and 1,596 metagenomes for human microbiota were downloaded from public databases and five types of NDEs were annotated with a custom pipeline. We found 959 NdhB, 785 NdhL, 987 NicX, three NicA1, and three NicA2 homologs. Results: Genomic classification revealed that six phylum-level taxa, including Proteobacteria, Firmicutes, Firmicutes_A, Bacteroidota, Actinobacteriota, and Chloroflexota, can produce NDEs, with Proteobacteria encoding all five types of NDEs studied. Analysis of NicX prevalence revealed differences among body sites. NicX homologs were found in gut and oral samples with a high prevalence but not found in lung samples. NicX was found in samples from both smokers and non-smokers, though the prevalence might be different. Conclusion: This study represents the first systematic investigation of NDEs from the human microbiota, providing new insights into the physiology and ecological functions of human microbiota and shedding new light on the development of nicotine-degrading probiotics for the treatment of smoking-related diseases.

Phosphorus-Mediated Local Charge Distribution of N-Configuration Adsorption Sites with Enhanced Zincophilicity and Hydrophilicity for High-Energy-Density Zn-Ion Hybrid Supercapacitors.

Tailor-made carbonaceous-based cathodes with zincophilicity and hydrophilicity are highly desirable for Zn-ion storage applications, but it remains a great challenge to achieve both advantages in the synthesis. In this work, a template electrospinning strategy is developed to synthesize nitrogen and phosphorous co-doped hollow porous carbon nanofibers (N, P-HPCNFs), which deliver a high capacity of 230.7 mAh g-1 at 0.2 A g-1 , superior rate capability of 131.0 mAh g-1 at 20 A g-1 , and a maximum energy density of 196.10 Wh kg-1 at the power density of 155.53 W kg-1 . Density functional theory calculations (DFT) reveal that the introduced P dopants regulate the distribution of local charge density of carbon materials and therefore facilitate the adsorption of Zn ions due to the increased electronegativity of pyridinic-N. Ab initio molecular dynamics (AIMD) simulations indicate that the doped P species induce a series of polar sites and create a hydrophilic microenvironment, which decreases the impedance between the electrode and the electrolyte and therefore accelerates the reaction kinetics. The marriage of ex situ/in situ experimental analyses and theoretical simulations uncovers the origin of the enhanced zincophilicity and hydrophilicity of N, P-HPCNFs for energy storage, which accounts for the faster ion migration and electrochemical processes.

Understanding the Excited-State Relaxation Mechanisms of Xanthophyll Lutein by Multi-configurational Electronic Structure Calculations.

The contradictory behaviors in light harvesting and non-photochemical quenching make xanthophyll lutein the most attractive functional molecule in photosynthesis. Despite several theoretical simulations on the spectral properties and excited-state dynamics, the atomic-level photophysical mechanisms need to be further studied and established, especially for an accurate description of geometric and electronic structures of conical intersections for the lowest several electronic states of lutein. In the present work, semiempirical OM2/MRCI and multi-configurational restricted active space self-consistent field methods were performed to optimize the minima and conical intersections in and between the 1Ag-, 2Ag-, 1Bu+, and 1Bu- states. Meanwhile, the relative energies were refined by MS-CASPT2(10,8)/6-31G*, which can reproduce correct electronic state properties as those in the spectroscopic experiments. Based on the above calculation results, we proposed a possible excited-state relaxation mechanism for lutein from its initially populated 1Bu+ state. Once excited to the optically bright 1Bu+ state, the system will propagate along the key reaction coordinate, i.e., the stretching vibration of the conjugated carbon chain. During this period of time, the 1Bu- state will participate in and forms a resonance state between the 1Bu- and 1Bu+ states. Later, the system will rapidly hop to the 2Ag- state via the 1Bu+/2Ag- conical intersection. Finally, the lutein molecule will survive in the 2Ag- state for a relatively long time before it internally converts to the ground state directly or via a twisted S1/S0 conical intersection. Notably, though the photophysical picture may be very different in solvents and proteins, the current theoretical study proposed a promising calculation protocol and also provided many valuable mechanistic insights for lutein and similar carotenoids.

Quantum mechanics/molecular mechanics studies on the excited-state decay mechanisms of cytidine aza-analogues: 5-azacytidine and 2'-deoxy-5-azacytidine in aqueous solution.

The excited state properties and deactivation pathways of two DNA methylation inhibitors, i.e., 5-azacytidine (5ACyd) and 2'-deoxy-5-azacytidine (5AdCyd) in aqueous solution, are comprehensively explored with the QM(CASPT2//CASSCF)/MM protocol. We systematically map the feasible decay mechanisms based on the obtained excited-state decay paths involving all the identified minimum-energy structures, conical intersections, and crossing points driving the different internal conversion (IC) and intersystem crossing (ISC) routes in and between the 1ππ*, 1nπ*, 3ππ*, 3nπ*, and S0 states. Unlike the 1nπ* state below the 1ππ* state in 5ACyd, deoxyribose group substitution at the N1 position leads to the 1ππ* state becoming the S1 state in 5AdCyd. In 5ACyd and 5AdCyd, the initially populated 1ππ* state mainly deactivates to the S0 state through the direct 1ππ* → S0 IC or mediated by the 1nπ* state. The former nearly barrierless IC channel of 1ππ* → S0 occurs ultrafast via the nearby low-lying 1ππ*/S0 conical intersection. In the latter IC channel of 1ππ* → 1nπ* → S0, the initially photoexcited 1ππ* state first approaches the nearby S2/S1 conical section 1ππ*/1nπ* and then undergoes efficient IC to the 1nπ* state, followed by the further IC to the initial S0 state via the S1/S0 conical intersection 1nπ*/S0. The 1nπ*/S0 conical intersection is estimated to be located 6.0 and 4.9 kcal mol-1 above the 1nπ* state minimum in 5ACyd and 5AdCyd, respectively, at the QM(CASPT2)/MM level. In addition to the efficient singlet-mediated IC channels, the minor ISC routes would populate 1ππ* to T1(ππ*) through 1ππ* → T1 or 1ππ* → 1nπ* → T1. Relatively, the 1ππ* → 1nπ* → T1 route benefits from the spin-orbit coupling (SOC) of 1nπ*/3ππ* of 8.7 cm-1 in 5ACyd and 10.2 cm-1 in 5AdCyd, respectively. Subsequently, the T1 system will approach the nearby T1/S0 crossing point 3ππ*/S0 driving it back to the S0 state. Given the 3ππ*/S0 crossing point located above the T1 minimum and the small T1/S0 SOC, i.e., 8.4 kcal mol-1 and 2.1 cm-1 in 5ACyd and 6.8 kcal mol-1 and 1.9 cm-1 in 5AdCyd, respectively, the slow T1 → S0 would trap the system in the T1 state for a while. The present work could contribute to understanding the mechanistic photophysics and photochemistry of similar aza-nucleosides and their derivatives.

Quantum mechanics/molecular mechanics studies on mechanistic photophysics of cytosine aza-analogues: 2,4-diamino-1,3,5-triazine and 2-amino-1,3,5-triazine in aqueous solution.

The excited-state properties and photophysics of cytosine aza-analogues, i.e., 2,4-diamino-1,3,5-triazine (2,4-DT) and 2-amino-1,3,5-triazine (2-AT) in solution have been systematically explored using the QM(MS-CASPT2//CASSCF)/MM approach. The excited-state nonradiative relaxation mechanisms for the initially photoexcited S1(ππ*) state decay back to the S0 state are proposed in terms of the present computed minima, surface crossings (conical intersections and singlet-triplet crossings), and excited-state decay paths in the S1, S2, T1, T2, and S0 states. Upon photoexcitation to the bright S1(ππ*) state, 2,4-DT quickly relaxes to its S1 minimum and then overcomes a small energy barrier of 5.1 kcal mol-1 to approach a S1/S0 conical intersection, where the S1 system hops to the S0 state through S1 → S0 internal conversion (IC). In addition, at the S1 minimum, the system could partially undergo intersystem crossing (ISC) to the T1 state, followed by further ISC to the S0 state via the T1/S0 crossing point. In the T1 state, an energy barrier of 7.9 kcal mol-1 will trap 2,4-DT for a while. In parallel, for 2-AT, the system first relaxes to the S1 minimum and then S1 → S0 IC or S1 → T1 → S0 ISCs take place to the S0 state by surmounting a large barrier of 15.3 kcal mol-1 or 11.9 kcal mol-1, respectively, which heavily suppress electronic transition to the S0 state. Different from 2,4-DT, upon photoexcitation in the Franck-Condon region, 2-AT can quickly evolve in an essentially barrierless manner to nearby S2/S1 conical intersection, where the S2 and T1 states can be populated. Once it hops to the S2 state, the system will overcome a relatively small barrier (6.6 kcal mol-1vs. 15.3 kcal mol-1) through IC to the S0 state. Similarly, an energy barrier of 11.9 kcal mol-1 heavily suppresses the T1 state transformation to the S0 state. The present work manifests that the amination/deamination of the triazine rings can affect some degree of different vertical and adiabatic excitation energies and nonradiative decay pathways in solution. It not only rationalizes excited-state decay dynamics of 2,4-DT and 2-AT in aqueous solution but could also provide insights into the understanding of the photophysics of aza-nucleobases.

Improved Interfacial Ion Migration and Deposition through the Chain-Liquid Synergistic Effect by a Carboxylated Hydrogel Electrolyte for Stable Zinc Metal Anodes.

The large-scale applicability of Zn-metal anodes is severely impeded by the issues such as the dendrite growth, complicated hydrogen evolution, and uncontrollable passivation reaction. Herein, a negatively charged carboxylated double-network hydrogel electrolyte (Gelatin/Sodium alginate-acetate, denoted as Gel/SA-acetate) has been developed to stabilize the interfacial electrochemistry, which restructures a type of Zn2+ ion solvent sheath optimized via a chain-liquid synergistic effect. New hydrogen bonds are reconstructed with water molecules by the zincophilic functional groups, and directional migration of hydrated Zn2+ ions is therefore induced. Concomitantly, the robust chemical bonding of such hydrogel layers to the Zn slab exhibits a desirable anti-catalytic effect, thereby greatly diminishing the water activity and eliminating side reactions. Subsequently, a symmetric cell using the Gel/SA-acetate electrolyte demonstrates a reversible plating/stripping performance for 1580 h, and an asymmetric cell reaches a state-of-the-art runtime of 5600 h with a high average Coulombic efficiency of 99.9 %. The resultant zinc ion hybrid capacitors deliver exceptional properties including the capacity retention of 98.5 % over 15000 cycles, energy density of 236.8 Wh kg-1 , and high mechanical adaptability. This work is expected to pave a new avenue for the development of novel hydrogel electrolytes towards safe and stable Zn anodes.

Modulating Cation Migration and Deposition with Xylitol Additive and Oriented Reconstruction of Hydrogen Bonds for Stable Zinc Anodes.

Highly reversible plating/stripping in aqueous electrolytes is one of the critical processes determining the performance of Zn-ion batteries, but it is severely impeded by the parasitic side reaction and dendrite growth. Herein, a novel electrolyte engineering strategy is first proposed based on the usage of 100 mM xylitol additive, which inhibits hydrogen evolution reaction and accelerates cations migration by expelling active H2 O molecules and weakening electrostatic interaction through oriented reconstruction of hydrogen bonds. Concomitantly, xylitol molecules are preferentially adsorbed by Zn surface, which provides a shielding buffer layer to retard the sedimentation and suppress the planar diffusion of Zn2+ ions. Zn2+ transference number and cycling lifespan of Zn∥Zn cells have been significantly elevated, overwhelmingly larger than bare ZnSO4 . The cell coupled with a NaV3 O8 cathode still behaves much better than the additive-free device in terms of capacity retention.

Selectively Identifying Exposed-over-Unexposed C-C+ Pairs in Human Telomeric i-Motif Structures with Length-Dependent Polymorphism.

The i-motif structure (iM) has attracted much attention, because of its in vivo bioactivity and wide in vitro applications such as DNA-based switches. Herein, the length-dependent folding of cytosine-rich repeats of the human telomeric 5'-(CCCTAA)n-1CCC-3' (iM-n, where n = 2-8) was fully explored. We found that iM-4, iM-5, and iM-8 mainly form the intramolecular monomer iM structures, while a tetramolecular structure populates only for iM-3. However, iM-6 and iM-7 have the potential to fold as well into the dimeric iM structures besides the monomer ones. The natural hypericin (Hyp) was used as the polymorphism-selective probe to recognize the iM structures. Interestingly, only iM-3, iM-6, and iM-7 can efficiently switch on the Hyp fluorescence by specifically binding with the outmost C-C+ base pairs that are exposed directly to solution. However, other iM structures that fold in a way with a coverage of the outmost C-C+ pairs by loop sequences are totally unavailable for the Hyp binding. Theoretical modeling indicates that adaptive π-π and cation-π interactions contribute to the Hyp recognition toward the exposed C-C+ pairs. This specific iM recognition can be boosted by a photocatalytic DNAzyme construct. Our work provides a reliable fluorescence method to selectively explore the polymorphism of iM structures.

Quantum mechanics/molecular mechanics studies on excited state decay pathways of 5-azacytosine in aqueous solution.

In this work, we have used the QM(CASPT2//CASSCF)/MM approach to study the photophysical properties and relaxation mechanism of 5-azacytosine (5-AC) in aqueous solution. Based on the relevant minimum-energy structures and intersection structures, and excited-state decay paths in the S1, S2, T1, T2, and S0 states, several feasible excited-state nonradiative decay channels from the initially populated S2(ππ*) state are proposed. Two major channels are singlet-mediated nonradiative pathways, in which the S2 system will internally convert (IC) to the S0 state directly or mediated by the 1nπ* state via a 1ππ*/1nπ* conical intersection. The minor ones are related to intersystem crossing (ISC) processes. The system would populate to the T1 state via the S2 → S1 → T1 or S2 → T2 → T1 ISC process, followed by further decay to the S0 state via the transition from T1 to S0. However, due to small spin-orbit couplings (SOCs) at the singlet-triplet crossing points, the related ISC would be less efficient and probably take longer. The present work rationalizes the ultrafast excited-state decay dynamics of 5-AC in aqueous solution and its low quantum yields of triplets and fluorescence. It provides important mechanistic insights into understanding 5-AC's derivatives and analogues.

A theoretical insight into excited-state decay and proton transfer of p-nitrophenylphenol in the gas phase and methanol solution.

The excited-state decay (ESD) and proton transfer (EPT) of p-nitrophenylphenol (NO2-Bp-OH), especially in the triplet states, were not characterized with high-level theoretical methods to date. Herein, the MS-CASPT2//CASSCF and QM(MS-CASPT2//CASSCF)/MM methods were employed to gain an atomic-level understanding of the ESD and EPT of NO2-Bp-OH in the gas phase and its hydrogen-bonded complex in methanol. Our calculation results revealed that the S1 and S2 states of NO2-Bp-OH are of 1ππ* and 1nπ* characters at the Franck-Condon (FC) point, which correspond to the ICT-EPT and intramolecular charge-transfer (ICT) states in spectroscopic experiments. The former state has a charge-transfer property that could facilitate the EPT reaction, while the latter one might be unfavorable for EPT. The vertical excitation energies of these states are almost degenerate at the FC region and the electronic configurations of 1ππ* and 1nπ* will exchange from the S1 FC region to the S1 minimum, which means that the 1nπ* state will participate in ESD once NO2-Bp-OH departs from the S1 FC region. Besides, we found that three triplets lie below the first bright state and will play very important roles in intersystem crossing processes. In terms of several pivotal surface crossings and relevant linearly interpolated internal coordinate (LIIC) paths, three feasible but competing ESD channels that could effectively lead the system to the ground state or the lowest triplet state were put forward. Once arrived at the T1 state, the system has enough time and internal energy to undergo the EPT reaction. The methanol solvent has a certain effect on the relative energies and spin-orbit couplings, but does not qualitatively change the ESD processes of NO2-Bp-OH. By contrast, the solvent effects will remarkably stabilize the proton-transferred product by the hydrogen bond networks and assist to form the triplet anion. Our present work would pave the road to properly understand the mechanistic photochemistry of similar hydroxyaromatic compounds.

Combined QM (MS-CASPT2)/MM studies on photocyclization and photoisomerization of a fulgide derivative in toluene solution.

Photocyclization and photoisomerization of fulgides have been extensively studied experimentally and computationally due to their significant potential applications for example as photoswitches in memory devices. However, the reported excited-state decay mechanisms of fulgides do not include the effects of solvation explicitly to date. Herein, calculations using the high-level MS-CASPT2//CASSCF method were conducted to explore the photoinduced excited-state decay processes of the Eα conformer of a fulgide derivative in toluene with solvent effects treated by implicit PCM and explicit QM/MM models, respectively. Several minima and conical intersections were optimized successfully in and between the S0 and S1 states; then, two nonadiabatic excited-state decay channels that could efficiently drive the system to the ground state were proposed based on the excited-state ring-closure and isomerization paths. In addition, we also found that in the ring-closure path, the potential energy surface is essentially barrierless before approaching the conical intersection, while it needs to overcome a small energy barrier along the E → Z photoisomerization path for the nonadiabatic S1 → S0 internal conversion process. The present computational results could provide useful mechanistic insights into the photoinduced cyclization and isomerization reactions of fulgide and its derivatives.

Generalized Ab Initio Nonadiabatic Dynamics Simulation Methods from Molecular to Extended Systems.

Nonadiabatic dynamics simulation has become a powerful tool to describe nonadiabatic effects involved in photophysical processes and photochemical reactions. In the past decade, our group has developed generalized trajectory-based ab initio surface-hopping (GTSH) dynamics simulation methods, which can be used to describe a series of nonadiabatic processes, such as internal conversion, intersystem crossing, excitation energy transfer and charge transfer of molecular systems, and photoinduced nonadiabatic carrier dynamics of extended systems with and without spin-orbit couplings. In this contribution, we will first give a brief introduction to our recently developed methods and related numerical implementations at different computational levels. Later, we will present some of our latest applications in realistic systems, which cover organic molecules, biological proteins, organometallic compounds, periodic organic and inorganic materials, etc. Final discussion is given to challenges and outlooks of ab initio nonadiabatic dynamics simulations.

Comparative genomics reveals broad genetic diversity, extensive recombination and nascent ecological adaptation in Micrococcus luteus.

BACKGROUND: Micrococcus luteus is a group of actinobacteria that is widely used in biotechnology and is being thought as an emerging nosocomial pathogen. With one of the smallest genomes of free-living actinobacteria, it is found in a wide range of environments, but intraspecies genetic diversity and adaptation strategies to various environments remain unclear. Here, comparative genomics, phylogenomics, and genome-wide association studies were used to investigate the genomic diversity, evolutionary history, and the potential ecological differentiation of the species. RESULTS: High-quality genomes of 66 M. luteus strains were downloaded from the NCBI GenBank database and core and pan-genome analysis revealed a considerable intraspecies heterogeneity. Phylogenomic analysis, gene content comparison, and average nucleotide identity calculation consistently indicated that the species has diverged into three well-differentiated clades. Population structure analysis further suggested the existence of an unknown ancestor or the fourth, yet unsampled, clade. Reconstruction of gene gain/loss events along the evolutionary history revealed both early events that contributed to the inter-clade divergence and recent events leading to the intra-clade diversity. We also found convincing evidence that recombination has played a key role in the evolutionary process of the species, with upto two-thirds of the core genes having been affected by recombination. Furthermore, distribution of mammal-associated strains (including pathogens) on the phylogenetic tree suggested that the last common ancestor had a free-living lifestyle, and a few recently diverged lineages have developed a mammal-associated lifestyle separately. Consistently, genome-wide association analysis revealed that mammal-associated strains from different lineages shared genes functionally relevant to the host-associated lifestyle, indicating a recent ecological adaption to the new host-associated habitats. CONCLUSIONS: These results revealed high intraspecies genomic diversity of M. luteus and highlighted that gene gain/loss events and extensive recombination events played key roles in the genome evolution. Our study also indicated that, as a free-living species, some lineages have recently developed or are developing a mammal-associated lifestyle. This study provides insights into the mechanisms that drive the genome evolution and adaption to various environments of a bacterial species.

MS-CASPT2 studies on the mechanistic photophysics of tellurium-substituted guanine and cytosine.

Sulfur-substituted nucleobases are highly promising photosensitizers that are widely used in photodynamic therapy, and there are numerous studies exploring their unique photophysical behaviors. However, relevant photophysical investigations on selenium and tellurium substitutions are still rare. Herein, the high-level multistate complete-active-space second-order perturbation (MS-CASPT2) method was performed for the first time to explore the excited-state relaxation processes of tellurium-substituted guanine (TeG) and cytosine (TeC). Based on the electronic state properties in the Franck-Condon (FC) region, we found that the lowest five (S0, S1, S2, T1, and T2) and six (S0, S1, S2, T1, T2 and T3) states will participate in the nonadiabatic transition processes of TeG and TeC systems, respectively. In these electronic states, two kinds of minimum and intersection structures (i.e., planar and twisted structures) were obtained for both TeG and TeC systems. The linearly interpolated internal coordinate (LIIC) paths and spin-orbit coupling (SOC) constants revealed several possible planar and twisted excited-state decay channels, which could lead the systems to the lowest reactive triplet state of T1. Small energy barriers in the T1 state will trap the TeG and TeC systems for a while before they finally populate to the ground state. Although tellurium substitution would further redshift the absorption wavelength and enhance the intersystem crossing (ISC) rate to the T1 state compared with sulfur and selenium substitutions, the rapid ISC process of T1 → S0 may make it a less effective photosensitizer to sensitize the molecular oxygen. We believe our present work will provide important mechanistic insights into the photophysics of tellurium-substituted nucleobases.

Nonadiabatic dynamics simulation of photoinduced ring-opening reaction of 2(5H)-thiophenone with internal conversion and intersystem crossing.

In the present work, the quantum trajectory mean-field approach, which is able to overcome the overcoherence problem, was generalized to simulate internal conversion and intersystem crossing processes simultaneously. The photoinduced ring-opening and subsequent rearrangement reactions of isolated 2(5H)-thiophenone were studied based on geometry optimizations on critical structures and nonadiabatic dynamics simulations using this method. Upon 267 nm irradiation, the molecule is initially populated in the 1ππ* state. After a sudden rupture of one C-S bond within 100 fs in this state, the lowest two singlet excited states and the lowest two triplet excited states become quasi-degenerated, and then the intersystem crossing processes between singlet and triplet states accompanied by rearrangement reactions can be observed several times. Compared with our previous nonadiabatic simulations in the absence of intersystem crossing (ChemPhotoChem, 2019, 3, 897-906), some new nonadiabatic relaxation pathways involving triplet states and different ring-opening products were identified. The present work provides new mechanistic insights into the photoinduced ring-opening of thio-substituted heterocyclic molecules and reveals the importance of nonadiabatic dynamics simulation that is able to deal with multiple electronic states with different spin multiplicities.