Understanding how photoinduced charge redistribution directs competing reaction pathways is crucial to the rational design of excited-state intramolecular proton transfer (ESIPT) materials. Here, we employ extended multistate complete active space second-order perturbation theory (XMS-CASPT2) calculations and electrostatic potential (ESP) analysis to uncover the reaction mechanism of 3-mercaptopyran-4-one (3MP), a model of a thiol-based S-H···O intramolecular hydrogen-bond system. Photoexcitation of the bright S2(1ππ*) state triggers electron density redistribution from S to O, strengthening the O···H-S bond and driving subsequent proton transfer. After S2→S1 internal conversion, the electronic character dictates the reaction pathways: population of S1(1nOπ*) reduces the O electron density, weakens the hydrogen bond, induces H out-of-plane motion, and enables efficient intersystem crossing to the triplet state due to large spin-orbit coupling. On the other hand, internal conversion to S1(1ππ*) maintains the 1ππ* character of the S2 state and thus initiates the proton transfer to yield the enol tautomer, which exhibits weak fluorescence and promotes the reactions hereafter. Our findings establish a direct connection between electron density redistribution and reaction pathways, offering new mechanistic insights for designing advanced photofunctional materials.

We present a practical formulation of harmonic-oscillator-referenced ring-polymer molecular dynamics (RPMD) for the calculation of linear and nonlinear real-time correlation functions under quantum statistical conditions. The method is formulated as a direct extension of standard RPMD but incorporates three coordinated modifications aimed at observables for which a direct ring-polymer average is either inconvenient or strongly contaminated by internal-mode artifacts. First, the imaginary-time distribution is built from an exact harmonic oscillator reference rather than the primitive free particle Trotter factorization so that the exact harmonic canonical variance is already recovered at a finite bead number. Second, the real-time dynamics is centroid-anchored, ensuring that the slow collective mode evolves on the physical timescale while the internal modes remain statistically organized by the reference quadratic form. Third, nonlinear observables are reconstructed from the anchored linear correlation and sampled static moments through a Gaussian moment reconstruction. In the present work, this reconstruction is used primarily for canonical/Wigner-type correlation functions, while a Kubo mixed-moment reconstruction is retained as a special harmonic benchmark. The resulting scheme preserves the familiar ring-polymer workflow, is straightforward to incorporate into existing RPMD implementations, and provides a practical route to higher moments such as x(0)x(t)3 and related mixed correlations. We present the working formulation, implementation strategy, and benchmark structure for harmonic, mildly anharmonic, and strongly anharmonic quartic model systems.

The Paper I [H. Wang, J. Chem. Phys. 165, ■ (2026)] introduced harmonic-oscillator-referenced ring-polymer molecular dynamics (HO-RPMD) as a practical framework for approximately computing linear and nonlinear real-time quantum correlation functions. The present study develops the corresponding theoretical foundation in greater detail. The method is organized around three coordinated ingredients: exact harmonic-reference sampling in imaginary time, centroid-anchored real-time propagation, and Gaussian reconstruction of nonlinear observables from an anchored linear kernel together with sampled static information. We show that these elements are structurally linked. Once the quantum Boltzmann operator is represented by a harmonic reference kernel rather than by the primitive free-particle Trotter factorization, the centroid component of the real-time dynamical generator cannot generally be left unchanged without shifting the harmonic oscillation frequency. Likewise, beyond linear centroid observables, a direct nonlinear ring-polymer correlation function is no longer naturally protected from contamination by the internal fluctuation modes, and an explicit reconstruction step is therefore needed. We formulate these points at the operator, path integral, normal mode, and observable reconstruction levels and derive the finite-P reference distribution, the centroid-anchoring condition, and the Gaussian reconstruction logic. The resulting theory clarifies the relation of HO-RPMD to standard RPMD, centroid molecular dynamics, symmetrized/Wigner-type correlation-function formulations, and Gaussian moment-reconstruction ideas. It also makes clear that, beyond the harmonic limit, the natural practical nonlinear target of the present framework is the canonical hybrid correlation function, while nonlinear Kubo quantities remain primarily useful as harmonic benchmarks.

Photo-cross-linking reactions have been widely used for exploring the network of dynamic protein-protein interaction, and photolysis of cross-linker plays an extremely important role in the formation of the reactive intermediate and subsequent linking reaction. However, the detailed mechanism of the relevant reactions has been rarely reported up to date. In this work, 2-N-methylpyrrole-5-formylamino-tetrazole (MPFT) was chosen as a representative of the photo-cross-linkers developed recently. Structures and properties of MPFT in the three lowest-lying electronic states have been determined at the level of multistate complete active space second-order perturbation theory (MS-CASPT2). Meanwhile, the direct ab initio quantum trajectory mean-field (QTMF) method has been used to simulate nonadiabatic dynamics initiated from the first excited singlet state of MPFT. The combination of the MS-CASPT2 calculation and the QTMF simulation not only provided new insights into the mechanism of the MPFT photolysis but also revealed that the singlet excited-state nitrile imine is likely to be the reactive intermediate that is responsible for the cross-linking reaction with the site of target protein. Our conclusions obtained from MS-CASPT2 calculations and QTMF dynamical simulations are supported by the experimental findings.

The potential of chiral organic molecules exhibiting circularly polarized luminescence (CPL) for practical applications hinges on the luminescence efficiency and dissymmetry factor (glum). However, surpassing the molecular limitations of dissymmetry factors remains a significant challenge, primarily due to the different parity selection rules governing the electric and magnetic dipole moments in chiral molecules. In this study, we tackle this inherent constraint by designing a triplet sensitization photon upconversion system using nontoxic CuInS2 quantum dots (QDs) photosensitizer. We demonstrate a 43-fold amplification of CPL in QD-sensitized triplet fusion process compared to the direct photoexcitation. Notably, a high green-to-blue upconversion quantum efficiency of 12.7 ± 0.19% (normalized to 100%) was achieved. The dissymmetry factors of QD-sensitized upconversion CPL outperform previous reports based on molecular photosensitizers. The observed large glum, according to our modeling and first-principles calculations, originates from the unique structural rearrangement of the chiral emitter during the ultrafast triplet energy transfer process. Our work provides a new strategy and mechanistic insights for CPL amplification through triplet sensitization.

A central goal of chemical mechanism research is to provide a comprehensive interpretation of chemical reaction pathways to clarify the evolution patterns of reactions. In this work, we present an unprecedented comprehensive monitoring of the elementary reaction pathways of the SN1 solvolysis on an in situ real-time single-molecule electrical detection platform. Through precise control of oriented external electric fields, we capture two short-lived protonated intermediates at the single-molecule level and elucidate their roles in the reaction. Both temperature- and isotope-dependent experiments, in combination with theoretical simulations, reveal crucial roles for the hydrogen-bonded acetic-acid-mediated triple-proton-transfer and the proton tunneling effect in the interconversion of these two intermediates. This work highlights the precise manipulation of chemical reactions by electrostatic fields and opens up a universal route to discover unknown intermediates or novel phenomena in the processes of material transformation and life activities.

It has been established experimentally that aromatic thioketones possess several inherently unique photophysical properties, some of which are highly sensitive even to common hydrocarbon solvents. However, the deeper reasons and the underlying mechanisms remain unclear up to date. In this study, the multistate complete active space second-order perturbation theory (MS-CASPT2) has been utilized to investigate the five lowest-lying electronic states (S0, T1, S1, T2, and S2) of 4H-1-benzopyran-4-thione (BPT) in acetonitrile and hydrocarbons. The results show that the S1, T1, and T2 states of BPT are close in energy so that the T2-state-mediated S1 → T2 → T1 and T1 → T2 → S1 transitions could occur in tens of picoseconds, which exhibits little dependence on the formation of the BPT-solvent complexes and on the bulk-solvent effect. This explains why thermally activated delayed fluorescence from the S1 state has been observed for many aromatic thioketones in both inert media and hydrocarbons. Meanwhile, our calculations show that the intracomplex noncovalent interactions could be automatically adjusted by the redistribution of π-electrons in the flexible aromatic rings. This allows the S2 → S1 internal conversion to occur efficiently in the vicinity of the two-state conical intersection, which results in the remarkable changes in the S2-state lifetimes and fluorescence quantum yields of many aromatic thioketones from inert media to hydrocarbon solvents. The aforementioned inherent photophysical properties could be qualitatively understood by a simple model of frontier molecular orbitals. This model could be used to understand photophysical properties of other aromatic compounds (such as aldehydes, ketones, amines, and carboxylic acids) in different solvents.

Benzo[b]thiophene rings are common synthons for the development of novel drugs and materials, and thus, the discovery of facile ways for their functionalization is of value. In this work, a new method for the C3-chlorination of C2-substituted benzothiophene derivatives is described. The chlorine source is sodium hypochlorite pentahydrate (NaOCl5H(2)O), and optimal transformations occur in aqueous acetonitrile at 65-75 degrees C to provide the corresponding C3-halogenated products in variable yields (30-65%). The reaction occurs in the presence of vinyl and alkyl groups, while the presence of alcohols leads to competing oxidation reactions at the heterobenzylic position. The presence of a carbonyl group at the C2-position inhibited the halogenation reaction, while the use of benzofuran led to a highly exothermic reaction, presumably via the formation of a peroxide intermediate. Reactions carried out at lower temperatures led to side reactions associated with competing oxidative processes. To gain a better understanding of the mechanism of the reaction, DFT calculations were carried out, where the heteroatom enables the formation of a hypochlorous acidium ion that serves to generate a C2-C3 chloronium ion intermediate in a step-wise manner, which in turn leads to the formation of an S-stabilized C2-carbocation that undergoes re-aromatization to the corresponding C3-chlorinated products. To probe potential synthetic applications, a model C3-chloro derivative was coupled with phenylboronic acid using standard Suzuki-Miyaura coupling conditions.

Tree tensor network states (TTNS) decompose the system wavefunction to the product of low-rank tensors based on the tree topology, serving as the foundation of the multi-layer multi-configuration time-dependent Hartree method. In this work, we present an algorithm that automatically constructs the optimal and exact tree tensor network operators (TTNO) for any sum-of-product symbolic quantum operator. The construction is based on the minimum vertex cover of a bipartite graph. With the optimal TTNO, we simulate open quantum systems, such as spin relaxation dynamics in the spin-boson model and charge transport in molecular junctions. In these simulations, the environment is treated as discrete modes and its wavefunction is evolved on equal footing with the system. We employ the Cole-Davidson spectral density to model the glassy phonon environment and incorporate temperature effects via thermo-field dynamics. Our results show that the computational cost scales linearly with the number of discretized modes, demonstrating the efficiency of our approach.

Oligonucleotides can be chemically modified for a variety of applications that include their use as biomaterials, in therapeutics, or as tools to understand biochemical processes, among others. This work focuses on the functionalization of oligonucleotides of RNA and DNA (12- or 14-nucleotides long) with methylbenzothiophene (BT), at the C2′-O-position, which led to unique structural features. Circular dichroism (CD) analyses showed that positioning the BT units on one strand led to significant thermal destabilization, while duplexes where each strand contained 4-BT rings formed a distinct arrangement with cooperativity/interactions among the modifications (evidenced from the appearance of a band with positive ellipticity at 235 nm). Interestingly, the structural arrays displayed increased duplex stabilization (>10 °C higher than the canonical analogue) as a function of [Na+] with an unexpected structural rearrangement at temperatures above 50 °C. Density functional theory–polarizable continuum model (DFT-PCM) calculations were carried out, and the analyses were in agreement with induced structural changes as a function of salt content. A model was proposed where the hydrophobic surface allows for an internal nucleobase rearrangement into a more thermodynamically stable structure, before undergoing full denaturation, with increased heat. While this behavior is not common, B- to Z-form duplex transitions can occur and are dependent on parameters that were probed in this work, i.e., temperature, nature of modification, or ionic content. To take advantage of this phenomenon, we probed the ability of the modified duplexes to be recognized by Zα (an RNA binding protein that targets Z-form RNA) via electrophoretic analysis and CD. Interestingly, the protein did not bind to canonical duplexes of DNA or RNA; however, it recognized the modified duplexes, in a [monovalent/divalent salt] dependent manner. Overall, the findings describe methodology to attain unique structural motifs of modified duplexes of DNA or RNA, and control their behavior as a function of salt concentration. While their affinity to RNA binding proteins, and the corresponding mechanism of action, requires further exploration, the tunable properties can be of potential use to study this, and other, types of modifications. The novel arrays that formed, under the conditions described herein, provide a useful way to explore the structure and behavior of modified oligonucleotides, in general.

A fundamental goal of photochemistry is to understand how structural features of a chromophore can make specific bonds within a molecule prone to cleavage by light, or photolabile. The meta effect is an example of a regiochemical explanation for photolability, in which electron donating groups on an aromatic ring cause photolability selectively at the meta position. Here, we show, using a chromophore containing one ring with a meta-methoxy group and one ring with a para-methoxy group, that two stereoisomers of the same compounds can react with light differently, based simply on the three-dimensional positioning of a meta anisyl ring. The result is that the stereoisomers of the compound with the same configuration at both stereogenic centers are photolabile while the stereoisomers with opposite configuration do not react with light. Furthermore, time-dependent density functional theory (TD-DFT) calculations show distinct excitation pathways for each stereoisomer.

Whether chemical bonding can regulate the excited-state and optoelectronic properties of donor-acceptor dyads has been largely elusive. In this work, we used electronic structure and nonadiabatic dynamics methods to explore the excited-state properties of covalently bonded zinc phthalocyanine (ZnPc)-fullerene (C60 ) dyads with a 6-6 (or 5-6) bonding configuration in which ZnPc is bonded to two carbon atoms shared by the two hexagonal rings (or a pentagonal and a hexagonal ring) in C60 . In both cases, the locally excited (LE) states on ZnPc are spectroscopically bright. However, their different chemical bonding differentiates the electronic interactions between ZnPc and C60 . In the 5-6 bonding configuration, the LE states on ZnPc are much higher in energy than the LE states on C60 . Thus, the excitation energy transfer from ZnPc to C60 is thermodynamically favorable. On the other hand, in the 6-6 bonding configuration, such a process is inhibited because the LE states on ZnPc are the lowest ones. More detailed mechanisms are elucidated from nonadiabatic dynamics simulations. In the 6-6 bonding configuration, no excitation energy transfer was observed. In contrast, in the 5-6 bonding configuration, several LE and charge-transfer (CT) excitons were shown to participate in the energy-transfer process. Further analysis reveals that the photoinduced energy transfer is mediated by a CT exciton, such that electron- and hole-transfer processes take place in a concerted but asynchronous manner in the excitation energy transfer. It is also found that high-level electronic structure methods including exciton effects are indispensable to accurately describe photoinduced energy- and electron-transfer processes. Furthermore, this work opens up new avenues for regulating the excited-state properties of molecular donor-acceptor dyads by means of chemical bonding.

The multiconfiguration time-dependent Hartree (MCTDH) method and its generalization, the multilayer MCTDH (ML-MCTDH), result in equations of motion (EOMs) that are singular when there are virtual orbitals-the unoccupied single-particle functions-in the wave function expansion. For decades this singularity had been numerically removed by regularizing the reduced density matrix. In this Perspective we discuss our recent proposal to regularize the coefficient tensor instead, which has significant impact on both the efficiency and correctness of the EOMs in MCTDH and ML-MCTDH for challenging problems. We further demonstrate that when the system becomes large such that it is necessary to use ML-MCTDH with many layers, it is much more important to employ this new regularization scheme. We illustrate this point by studying a spin-boson model with a large bath that contains up to 100 000 modes. We show that even in the weak coupling regime the new regularization scheme is required to quickly rotate the virtual orbitals into the correct directions in Hilbert space. We argue that this situation can be common for applying a time-dependent tensor network approach to any large enough system.

Inosine is an important RNA modification, furthermore RNA oxidation has gained interest due, in part, to its potential role in the development/progression of disease as well as on its impact on RNA structure and function. In this report we established the base pairing abilities of purine nucleobases G, I, A, as well as their corresponding, 8-oxo-7,8-dihydropurine (common products of oxidation at the C8-position of purines), and 8-bromopurine (as probes to explore conformational changes), derivatives, namely 8-oxoG, 8-oxoI, 8-oxoA, 8-BrG, and 8-BrI. Dodecamers of RNA were obtained using standard phosphoramidite chemistry via solid-phase synthesis, and used as models to establish the impact that each of these nucleobases have on the thermal stability of duplexes, when base pairing to canonical and noncanonical nucleobases. Thermal stabilities were obtained from thermal denaturation transition (T-m) measurements, via circular dichroism (CD). The results were then rationalized using models of base pairs between two monomers, via density functional theory (DFT), that allowed us to better understand potential contributions from H-bonding patterns arising from distinct conformations. Overall, some of the important results indicate that: (a) an anti-I:syn-A base pair provides thermal stability, due to the absence of the exocyclic amine; (b) 8-oxoG base pairs like U, and does not induce destabilization within the duplex when compared to the pyrimidine ring; (c) a U:G wobble-pair is only stabilized by G; and (d) 8-oxoA displays an inherited base pairing promiscuity in this sequence context. Gaining a better understanding of how this oxidatively generated lesions potentially base pair with other nucleobases will be useful to predict various biological outcomes, as well as in the design of biomaterials and/or nucleotide derivatives with biological potential.

RETURN TO ISSUEViewpointNEXTMemorial Viewpoint for William L. HaseHans LischkaHans LischkaDepartment of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409-1061, United StatesMore by Hans Lischkahttp://orcid.org/0000-0002-5656-3975, John TullyJohn TullyDepartment of Chemistry, Yale University New Haven, Connecticut 06511-8499, United StatesMore by John Tully, Haobin WangHaobin WangDepartment of Chemistry, University of Colorado—Denver, Denver, Colorado 80217-3364, United StatesMore by Haobin Wanghttp://orcid.org/0000-0002-3532-7770, and George L. BarnesGeorge L. BarnesDepartment of Chemistry and Biochemistry, Siena College, Loudonville, New York 12211, United StatesMore by George L. Barneshttp://orcid.org/0000-0001-9211-2736Cite this: J. Phys. Chem. A 2020, 124, 21, 4183–4184Publication Date (Web):May 28, 2020Publication History Published online28 May 2020Published inissue 28 May 2020https://doi.org/10.1021/acs.jpca.0c03827Copyright © 2020 American Chemical SocietyRIGHTS & PERMISSIONSArticle Views1372Altmetric-Citations-LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit PDF (497 KB) Get e-AlertsSUBJECTS:Dissociation,Direct dynamics,Kinetics,Computer simulations Get e-Alerts

A trisulfur-radical-anion (S3̇-)-triggered C(sp2)-H amination of α,β-unsaturated carbonyl derivatives with simple amines has been demonstrated. This protocol provides convenient access to a variety of synthetically valuable N-unprotected and secondary β-enaminones with absolute Z selectivity and tertiary β-enaminones with E selectivity. Mechanistic probe and electronic structure theory calculations suggest that S3̇- initiates the nucleophilic attacks via a thiirane intermediate.

Extending our previous work, quantum dynamic simulations are performed to study low temperature heat transport in a spin-boson model where a two-level subsystem is coupled to two independent harmonic baths. Multilayer multiconfiguration time-dependent Hartree theory is used to numerically evaluate the thermal flux, for which the bath is represented by hundreds to thousands of modes. The simulation results are compared with the approximate Redfield theory approach, and the physics is analyzed versus different physical parameters.

Compartmentalization by liquid-liquid phase separation is implicated in transcription. It remains unclear whether and how transcriptional condensates accelerate the search of transcriptional regulatory factors for their target sites. Furthermore, the molecular mechanisms by which regulatory factors nucleate on chromatin to assemble transcriptional condensates remain incompletely understood. The CBX-PRC1 complexes compartmentalize key developmental regulators for repression through phase-separated condensates driven by the chromobox 2 (CBX2) protein. Here, by using live-cell single-molecule imaging, we show that CBX2 nucleates on chromatin independently of H3K27me3 and CBX-PRC1. The interactions between CBX2 and DNA are essential for nucleating CBX-PRC1 on chromatin to assemble condensates. The assembled condensates shorten 3D diffusion time and reduce trials for finding specific sites through revisiting the same or adjacent sites repetitively, thereby accelerating CBX2 in searching for target sites. Overall, our data suggest a generic mechanism by which transcriptional regulatory factors nucleate to assemble condensates that accelerate their target-search process.