Static Electronic Structure Calculations Research Articles

Calculating absorption and fluorescence spectra for chromophores in solution with ensemble Franck-Condon methods.

Accurately modeling absorption and fluorescence spectra for molecules in solution poses a challenge due to the need to incorporate both vibronic and environmental effects, as well as the necessity of accurate excited state electronic structure calculations. Nuclear ensemble approaches capture explicit environmental effects, Franck-Condon methods capture vibronic effects, and recently introduced ensemble-Franck-Condon approaches combine the advantages of both methods. In this study, we present and analyze simulated absorption and fluorescence spectra generated with combined ensemble-Franck-Condon approaches for three chromophore-solvent systems and compare them to standard ensemble and Franck-Condon spectra, as well as to the experiment. Employing configurations obtained from ground and excited state abinitio molecular dynamics, three combined ensemble-Franck-Condon approaches are directly compared to each other to assess the accuracy and relative computational time. We find that the approach employing an average finite-temperature Franck-Condon line shape generates spectra nearly identical to the direct summation of an ensemble of Franck-Condon spectra at one-fourth of the computational cost. We analyze how the spectral simulation method, as well as the level of electronic structure theory, affects spectral line shapes and associated Stokes shifts for 7-nitrobenz-2-oxa-1,3-diazol-4-yl and Nile red in dimethyl sulfoxide and 7-methoxy coumarin-4-acetic acid in methanol. For the first time, our studies show the capability of combined ensemble-Franck-Condon methods for both absorption and fluorescence spectroscopy and provide a powerful tool for simulating linear optical spectra.

Selective phosphate removal with manganese oxide composite anion exchange membranes in membrane capacitive deionization

The discharge of excessive phosphorous into water bodies can lead to serious eutrophication threatening aquatic ecosystem. Membrane capacitive deionization (MCDI) is an effective platform for deionizing aqueous streams; however, conventional MCDI is unable to selectively remove targeted ions from a liquid mixture. In this work, we fabricated manganese oxide composite anion exchange membranes (AEMs) for MCDI to enhance phosphate removal selectivity from sodium chloride-sodium dihydrogen phosphate (10:1 M ratio) aqueous mixtures. We systematically investigated several critical factors, such as constant current or voltage operation, applied voltage amount, process stream pH, and manganese oxide (Mn2O3) content in the AEM, on phosphate removal efficiency and phosphate selectivity. A trade-off was observed between phosphate removal and selectivity when increasing the cell voltage. Under the best conditions, a MCDI unit with a 20 wt% Mn2O3 composite AEM and a bipolar membrane facilitated high phosphate removal efficiency of ≥ 31.8 % and a phosphate over chloride selectivity of 1.1 while showing stability for at least 30 cycles. To help understand how Mn2O3 composite AEM boosts phosphate selectivity, static electronic structure calculations were performed, and they revelated that hydrogen phosphate absorption on Mn2O3 composite AEM was 314 kcal/mol more exothermic than that on pristine AEM while chloride adsorption on Mn2O3 composite AEM was 2.2 kcal/mol less exothermic than that on a pristine AEM. Overall, this work presents an effective strategy for selectively removing phosphate from model wastewater solutions and the mechanistic understanding that governs ion selectivity in composite ion-exchange membranes used in MCDI.

Theoretical Investigation on the Reversible Photoswitch Mechanism of Benzylidene-Oxazolone System.

The design and application of molecular photoswitches have attracted much attention. Herein, we performed a detailed computational study on the photoswitch benzylidene-oxazolone system based on static electronic structure calculations and on-the-fly excited-state dynamic simulations. For the Z and E isomer, we located six and four minimum energy conical intersections (MECIs) between the first excited state (S1) and the ground state (S0), respectively. Among them, the relaxation pathway driven by ring-puckering motion is the most competitive channel with the photoisomeization process, leading to the low photoisomerization quantum yield. In the dynamic simulations, about 88 % and 66 % trajectories decay from S1 to S0 for Z and E isomer, respectively, within the total simulation time of ~2 ps. The photoisomeization quantum yields obtained in our study (0.20 for Z→E and 0.12 for E→Z) agree well with the experimental measured values (0.25 and 0.11), even though the number of trajectories is limited to 50. Our study sheds light on the complexity of the benzylidene-oxazolone system 's deactivation process and the competitive mechanisms among different reaction channels, which provides theoretical guidance for further design and development of benzylidene-oxazolone based molecular photoswitches.

Mechanistic Insights into the Excited-State Intramolecular Proton Transfer (ESIPT) Process of 2-(2-Aminophenyl)naphthalene.

The 2-(2-aminophenyl)naphthalene molecule attracted much attention due to excited-state intramolecular proton transfer (ESIPT) from an amino NH2 group to a carbon atom of an adjacent aromatic ring. The ESIPT mechanisms of 2-(2-aminophenyl)naphthalene are still unclear. Herein, the decay pathways of this molecule in vacuum were investigated by combining static electronic structure calculations and nonadiabatic dynamics simulations. The calculations indicated the existence of two stable structures (S0-1 and S0-2) in the S0 and S1 states. For the S0-1 isomer, upon excitation to the Franck-Condon point, the system relaxed to the S1 minimum quickly, and then there exist four decay pathways (two ESIPT ones and two decay channels with C atom pyramidalization). In the ESIPT decay pathways, the system encounters the S1S0-PT-1 or S1S0-PT-2 conical intersection, which funnels the system rapidly to the S0 state. In the other two pathways, the system de-excited from the S1 to the S0 state via the S1S0-1 or S1S0-2 conical intersection. For the S0-2 structure, the decay pathways were similar to those of S0-1. The dynamics simulations showed that 75 and 69% of trajectories experienced the two ESIPT conical intersections for the S0-1 and S0-2 structures, respectively. Our simulations showed that the lifetime of the S1 state of S0-1 (S0-2) is estimated to be 358 (400) fs. Notably, we not only found the detailed reaction mechanism of the system but also found that the different ground-state configurations of this system have little effect on the reaction mechanism in vacuum.

Photochemical Mechanisms of Hydroxyquinoline Benzimidazole: Insights from Electronic Structure Calculations and Nonadiabatic Dynamics Simulations.

Excited-state intramolecular double proton transfer (ESIDPT) has received much attention because of its widespread existence in the life reactions of living organisms, and materials with this property are significant for their special luminescent properties. In this work, the complete active space self-consistent field (CASSCF) and OM2/multireference configuration interaction (OM2/MRCI) methods have been employed to study the static electronic structure calculations of the photochemistry and the possibility of ESIDPT process of hydroxyquinoline benzimidazole (HQB) molecule, along with the nonadiabatic dynamics simulations. The computational results show that the HQB molecule is relaxed to the S1-ENOL minimum after being excited to the Franck-Condon point in the S1 state. Subsequently, during the nonadiabatic deactivation process, the OH···N proton transfer and the twisting of benzimidazole occur before arriving at the single proton transfer conical intersection S1S0-KETO. Finally, the system can either return to the initial ground-state structure S0-ENOL or to the single proton transfer ground-state structure S0-KETO, both of which have almost the same probability. The dynamics simulations also show that no double proton transfer occurs. The excited-state lifetime of HQB is fitted to 1.1 ps, and only 64% of the dynamic trajectories return to the ground state within the 2.0 ps simulation time. We hope the detailed reaction mechanism of the HQB molecule will provide new insights into similar systems.

Accurate Computation of Aqueous pKas of Biologically Relevant Organic Acids: Overcoming the Challenges Posed by Multiple Conformers, Tautomeric Equilibria, and Disparate Functional Groups with the Fully Black-Box pK-Yay Method.

The use of static electronic structure calculations to compute solution-phase pKas offers a great advantage in that a macroscopic bulk property could be computed via microscopic computations involving very few molecules. There are various sources of errors in the quantum chemical calculations though. Overcoming these errors to accurately compute pKas of a plethora of acids is an active area of research in physical chemistry pursued by both computational as well as experimental chemists. We recently developed the pK-Yay method in our attempt to accurately compute aqueous pKas of strong and weak acids. The method is fully black-box, computationally inexpensive, and is very easy for even a nonexpert to use. However, the method was thus far tested on very few molecules (only 16 in all). Herein, in order to assess the future applicability of pK-Yay, we study the effect of multiple conformers, the presence of tautomers under equilibrium, and the impact of a wide variety of functional groups (derivatives of acetic acid with substituents at various positions, dicarboxylic acids, aromatic carboxylic acids, amines and amides, phenols and thiols, and fluorine bearing organic acids). Starting with more than 1000 conformers and tautomers, this study establishes that overall errors of ∼ 1.0 pKa units are routinely obtained for a majority of the molecules. Larger errors are noted in cases where multiple charges, intramolecular hydrogen bonding, and several ionizable functional groups are simultaneously present. An important conclusion to emerge from this work is that, the computed pKas are insensitive (difference <0.5) to whether we consider multiple conformers/tautomers or only choose the most stable conformer/tautomer. Further, pK-Yay captures the stereoelectronic effects arising due to differing axial vs equatorial pattern, and is useful to predict the dominant acid-base equilibrium in a system featuring several equilibria. Overall, pK-Yay may be employed in several chemical applications featuring organic molecules and biomonomers.

Mass-selected ion-molecule cluster beam apparatus for ultrafast photofragmentation studies.

We describe an apparatus for investigating the excited-state dissociation dynamics of mass-selected ion-molecule clusters by mass-resolving and detecting photofragment-ions and neutrals, in coincidence, using an ultrafast laser operating at high repetition rates. The apparatus comprises a source that generates ion-molecule clusters, a time-of-flight spectrometer, and a mass filter that selects the desired anions, and a linear-plus-quadratic reflectron mass spectrometer that discriminates the fragment anions after the femtosecond laser excites the clusters. The fragment neutrals and anions are then captured by two channeltron detectors. The apparatus performance is tested by measuring the photofragments: I-, CF3I-, and neutrals from photoexcitation of the ion-molecule cluster CF3I·I- using femtosecond UV laser pulses with a wavelength of 266nm. The experimental results are compared with our ground state and excited state electronic structure calculations as well as the existing results and calculations, with particular attention to the generation mechanism of the anion fragments and dissociation channels of the ion-molecule cluster CF3I·I- in the charge-transfer excited state.

Intrinsic vs Reaction-Driven Fluxionality in Transition-Metal Oxide Clusters: What Does Probing the Dynamics of M3O6– (M = Mo and W) Reacting with H2O Teach Us?

Fluxionality is an important concept in cluster science, with far reaching implications in the area of catalysis. The interplay between intrinsic structural fluxionality and reaction-driven fluxionality though is underexplored in the literature and is a topic of contemporary interest in physical chemistry. In this work, we present an easy-to-use computational protocol combining ab initio molecular dynamics simulations with static electronic structure computations to ascertain the role of intrinsic structural fluxionality in the course of fluxionality occurring due to a chemical reaction. The reactions of structurally well-defined M3O6- (M = Mo and W) with water─which were originally used in the literature to illustrate the significance of reaction-driven fluxionality in transition-metal oxide (TMO) clusters, were chosen for this study. Besides probing the nature of fluxionality, this work provides the timescale for the key proton-hop step in the fluxionality pathway and further attests to the significance of hydrogen bonding in both stabilizing the key intermediates as well as driving forward the reactions of M3O6- (M = Mo and W) with water. The approach presented in this work becomes valuable given that the use of molecular dynamics alone may not help us in accessing some metastable states whose formation involves an appreciable energy barrier. Similarly, merely obtaining a slice of the potential energy surface via static electronic structure calculations will not be helpful in probing the different types of fluxionality. Hence, there is the need for a combined approach to study fluxionality in structurally well-defined TMO clusters. Our protocol may also serve as a starting point in the analysis of much more complicated fluxional chemistry happening on surfaces wherein the recently developed "ensemble of metastable states" approach to catalysis is deemed to be particularly promising.

Symmetric Post-Transition State Bifurcation Reactions with Berry Pseudomagnetic Fields

We investigate how the Berry force (i.e., the pseudomagnetic force operating on nuclei as induced by electronic degeneracy and spin-orbit coupling (SOC)) might modify a post-transition state bifurcation (PTSB) reaction path and affect product selectivity for situations when multiple products share the same transition state. To estimate the magnitude of this effect, Langevin dynamics are performed on a model system with a valley-ridge inflection (VRI) point in the presence of a magnetic field (that mimics the Berry curvature). We also develop an analytic model for such selectivity that depends on key parameters such as the surface topology, the magnitude of the Berry force, and the nuclear friction. Within this dynamical model, static electronic structure calculations (at the level of generalized Hartree-Fock with spin-orbit coupling (GHF+SOC) theory) suggest that electronic spin induced Berry force effects may indeed lead to noticeable changes in methoxy radical isomerization.

Non-adiabatic dynamics simulations of the S1 excited-state relaxation of diacetyl phenylenediamine.

The small molecule built around the benzene ring, diacetyl phenylenediamine (DAPA), has attracted much attention due to its synthesis accessibility, large Stokes shift, etc. However, its meta structure m-DAPA does not fluoresce. In a previous investigation, it was found that such a property is due to the fact that it undergoes an energy-reasonable double proton transfer conical intersection during the deactivation of the S1 excited-state, then returns to the ground state by a nonradiative relaxation process eventually. However, our static electronic structure calculations and non-adiabatic dynamics analysis results indicate that only one reasonable non-adiabatic deactivation channel exists: after being excited to the S1 state, m-DAPA undergoes an ultrafast and barrierless ESIPT process and reaches the single-proton-transfer conical intersection. Subsequently, the system either returns to the keto-form S0 state minimum with proton reversion or returns to the single-proton-transfer S0 minimum after undergoing a slight twist of the acetyl group. The dynamics results show that the S1 excited-state lifetime of m-DAPA is 139 fs. In other words, we propose an efficient single-proton-transfer non-adiabatic deactivation channel of m-DAPA that is different from previous work, which can provide important mechanistic information of similar fluorescent materials.

Free and internal energies for the adsorption of short alkanes into the zeolite SSZ-13 from ab initio molecular dynamics simulations.

Electronic structure calculations have become a valuable tool in understanding chemical reactions of hydrocarbons in zeolite pores. However, commonly applied approaches to calculate free energies based on static electronic structure calculations significantly overestimate the entropic penalty for molecular adsorption into zeolite pores. Here, we use ab initio molecular dynamics (AIMD) simulations to model the adsorption of methane, ethane, and propane to purely siliceous and protonated SSZ-13. In our analyses we focus on the internal and Helmholtz free energies of adsorption of each molecule and compare our results to various approaches for the calculation of free energies based on static calculations. We find that only an approach that retains two thirds of the translational entropy of the adsorbate upon adsorption compares favorably with AIMD simulations. However, comparison to experimental measurements of Gibbs free energies of adsorption reported in the literature implies that we might not have captured the full complexity of alkane adsorption in our model. We expect that results in this work will help to develop a better understanding of alkane adsorption in zeolites, and that the provided data will serve as a benchmark for free energy calculations of alkane adsorption in zeolites in the future.

Unraveling the Mechanistic Pathway for the Dual Fluorescence in Green Fluorescent Protein (GFP) Chromophore Analogue: A Detailed Theoretical Investigation.

The photophysical properties of the para-sulfonamide (p-TsABDI) analogue of the green fluorescent protein (GFP) chromophore with both proton donating and accepting sites have been exploited in polar solvents to understand the origin of the unusual dual fluorescence nature of the chromophore. In the polar solvents, the compound undergoes structural rearrangement upon photoexcitation, leading to the ultrafast excited-state intermolecular proton transfer (ESIPT) phenomenon at the S1 surface. In this work, we employed both the static electronic structure calculations and on-the-fly molecular dynamics simulation to unravel the underlying reason for this peculiar behavior of the p-TsABDI analogue in polar solvents. To represent this adequately and provide extensive information on the ESIPT mechanism mediated by the solvent molecules, we considered explicit solvent molecules using the integral equation formalism variant of polarizable continuum (IEFPCM) model. From the static calculation analysis, we can conclude that the dual emissive behavior of the compound is ascribed to the proton transfer (PT) phenomena in the excited-state. However, based on the static calculation exclusively, it is hard to ascertain the mechanistic pathway of the PT phenomena. Hence, to investigate the dynamics and reaction mechanism for the ESIPT process, we performed the on-the-fly dynamics simulation for p-TsABDI in solvent clusters. Dynamics simulation results reveal that, based on the time lag between all the proton transfer processes, the ESIPT mechanism occurs in a stepwise manner from the benzylidene moiety of the chromophore to its imidazolinone moiety. However, the nonexistence of crossings between the S1- and S0-states confirms the PT characteristics of the reactions.

Ultrafast charge transfer in a nonfullerene all-small-molecule organic solar cell: a nonadiabatic dynamics simulation with optimally tuned range-separated functional.

Herein, we have employed linear-response time dependent density functional theory (LR-TDDFT)-based nonadiabatic dynamics simulations to investigate the ultrafast charge transfer in a nonfullerene all-small-molecule donor-acceptor (D-A) system formed by a porphyrin small-molecule donor ZnP and a recently developed nonfullerene small-molecule acceptor 6TIC, during which the optimally tuned range-separated hybrid (OT-RSH) functional was adopted. In combination with static electronic structure calculations, several important conclusions were drawn. Firstly, the ZnP and 6TIC are more likely combined together non-covalently in parallel rather than in perpendicular to form ZnP-6TIC due to the much larger adsorption energies, i.e. -44.6 kcal mol-1vs. -25.2 kcal mol-1. Secondly, the excited state properties obtained by OT-RSH functionals seem more consistent with the experimental results compared to their untuned versions. Specifically, the energy of the lowest charge transfer (CT) state was predicted to be smaller than the lowest lying local excitation (LE) states using the OT-RSH functional-based LR-TDDFT calculations, which is beneficial for the charge transfer process that might be crucial for the high power conversion efficiency (PCE) achieved experimentally. In contrast, the untuned RS functionals all predict higher CT state energies, which is contradictory to the high PCE obtained in the experiment. Moreover, strong hybridization upon excitation between these states was revealed, which might be one of the reasons responsible for the high PCE observed in the experiment. Finally, ultrafast excited state relaxation can be completed within 500 fs due to the small energy gaps and the strong nonadiabatic couplings between these states, which is accompanied by ultrafast photoinduced electron transfer from ZnP to 6TIC and photoinduced hole transfer the other way around. The efficient charge transfer processes and the involvement of two charge generation channels might be another cause resulting in the excellent photovoltaic performance of ZnP-6TIC based OSCs. Our present work not only provides solid evidence for elucidating the underlying mechanism observed in previous experiments, but also suggests that the combination of OT-RSH functionals and LR-TDDFT-based nonadiabatic dynamics simulations might be a powerful tool for investigating the excited state dynamics of organic D-A systems, which is crucial for the theoretical design of novel OSCs with better performances in the future.

Ultrafast exciton delocalization and localization dynamics of a perylene bisimide quadruple π-stack: a nonadiabatic dynamics simulation.

Unraveling the photogenerated exciton dynamics of π-stacked molecular aggregates is of great importance for both fundamental studies and industrial applications. Among various π-stacked molecular aggregates, perylene tetracarboxylic acid bisimide (PBI) based aggregates are regarded as one of the prototypes due to their inherent high fluorescence quantum yield and excellent photostability and flexibility in controlling intermolecular forces via chemical modifications. However, the exciton dynamics of these PBI based aggregates remain elusive up to now. In this work, we have first employed LR-TDDFT-based nonadiabatic dynamics simulations and static electronic structure calculations to investigate the ultrafast exciton dynamics of a newly synthesized perylene bisimide quadruple (PBQ) π-stack. Upon photoexcitation, the S6 to S10 states are the most likely populated excited states, which can be regarded as a combination of local excited (LE) excitons and charge transfer (CT) excitons of those four PBI chromophores. Then, the excited PBQ π-stack relaxes ultrafast to the lowest lying excited S1 state within 500 fs, which is accompanied by the complicated exciton conversion as well as exciton localization/delocalization dynamics. In short, the initially populated hybrid LE and CT excitons convert to the LE excitons of B/C and A/D, in which the LE excitons of B/C contribute the most (∼0.44) while the LE excitons of A/D also have minor contributions (0.21), indicating the formation of the localized excimer state. We use the notations A/B/C/D here to represent the four PBI fragments of PBQ π-stacks along the direction perpendicular to the PBI molecular plane. Additionally, using a recently defined root mean square deviation (RMSD) of electron and hole spatial distributions along three Cartesian coordinates, we could investigate the exciton localization/delocalization dynamics in a quantitative way. Our simulation results indicate that the photoinduced electrons and holes of the PBQ π-stack exhibit an ultrafast localization(∼10 fs)-delocalization(∼60 fs)-localization(∼200 fs) dynamics, during which both LE and CT excitons play crucial roles. Our present work is not only consistent with previous experimental studies, but also provides more detailed insights into the relevant processes, which might be useful for the future design of PBI based optoelectronic devices with improved performances.

Excited-state photochemistry dynamics of 2-(1-naphthyl) phenol: electronic structure calculations and non-adiabatic dynamics simulations.

The excited-state proton transfer processes and the formation mechanism of quinone methide of (1-naphthyl)phenol were investigated by combining static electronic structure calculations and non-adiabatic dynamics simulations in vacuum. The results indicated the existence of two minimum energy structures (S0-ENOL-1 and S0-ENOL-2) in the ground and excited states, which correspond to two ESIPT pathways. Upon excitation of S0-ENOL-1 to the bright S1 state, the system relaxes to the S1 minimum quickly in the enol region, for which two decay pathways have been described. The first is a barrierless ESIPT-1 process that generates keto species. Afterwards, the system encounters a keto conical intersection, which funnels the system to the ground state. The generated keto species, in the S0 state, either regenerated the starting material via ground-state proton transfer or yielded the keto product at the end of the simulations. In the other pathway, the system de-excites from the S1 state to the S0 state via one enol-type conical intersection. The dynamics simulations showed that 58.8% of trajectories experience keto-type conical intersection and the rest undergo enol-type conical intersection. Besides the ESIPT-1 process, a new-type ESIPT (ESIPT-2), which was not observed experimentally, was found with the irradiation of S0-ENOL-2. The ESIPT-2 process occurs after overcoming a small barrier (0.9 kcal mol-1) and yields a distinct quinone methide. Our simulation results also showed that the S1 lifetime of S0-ENOL-1 (S0-ENOL-2) would be 437 (617) fs in the gas phase. These results provide detailed and important mechanistic insights into the systems in which ESPT to carbon atoms occurs.

"On-The-Fly" Non-Adiabatic Dynamics Simulations on Photoinduced Ring-Closing Reaction of a Nucleoside-Based Diarylethene Photoswitch.

Nucleoside-based diarylethenes are emerging as an especial class of photochromic compounds that have potential applications in regulating biological systems using noninvasive light with high spatio-temporal resolution. However, relevant microscopic photochromic mechanisms at atomic level of these novel diarylethenes remain to be explored. Herein, we have employed static electronic structure calculations (MS-CASPT2//M06-2X, MS-CASPT2//SA-CASSCF) in combination with non-adiabatic dynamics simulations to explore the related photoinduced ring-closing reaction of a typical nucleoside-based diarylethene photoswitch, namely, PS-IV. Upon excitation with UV light, the open form PS-IV can be excited to a spectroscopically bright S1 state. After that, the molecule relaxes to the conical intersection region within 150 fs according to the barrierless relaxed scan of the C1–C6 bond, which is followed by an immediate deactivation to the ground state. The conical intersection structure is very similar to the ground state transition state structure which connects the open and closed forms of PS-IV, and therefore plays a crucial role in the photochromism of PS-IV. Besides, after analyzing the hopping structures, we conclude that the ring closing reaction cannot complete in the S1 state alone since all the C1–C6 distances of the hopping structures are larger than 2.00 Å. Once hopping to the ground state, the molecules either return to the original open form of PS-IV or produce the closed form of PS-IV within 100 fs, and the ring closing quantum yield is estimated to be 56%. Our present work not only elucidates the ultrafast photoinduced pericyclic reaction of the nucleoside-based diarylethene PS-IV, but can also be helpful for the future design of novel nucleoside-based diarylethenes with better performance.

Position of the Benzene Ring Substituent Regulates the Excited-State Deactivation Process of the Benzyluracil Systems.

A systematic theoretical study of the regulating effect of the substituent position on the photoinduced deactivation process of the benzyluracil systems has been performed based on the high-level static electronic structure calculations and on-the-fly full-dimensional excited-state dynamics simulations. Similarities and differences coexist for the two systems by comparative studies on the photoinduced deactivation process of the 5-benzyluracil (5-BU) and 6-benzyluracil (6-BU) systems. They both obey an S2 → S1 → S0 two-step decay pattern, and the decay coordinates of the S2 → S1 and S1 → S0 processes are mainly driven by the elongation of the bridging bond and the out-of-plane ring deformation motion, respectively. However, the puckering motion occurring at the C2 atom in the uracil fragment dominates the decay pathway of the 5-BU system. On the contrary, the puckering motion at the C5 atom in the benzene fragment mainly drives the decay coordinate of the 6-BU system. Therefore, the substituent position could play significant roles in the deactivation process of the benzyluracil systems. Moreover, the S1 → S0 decay process of the 6-BU system consists of five pathways, possessing a more complex deactivation picture than the 5-BU system. The fitted time scale of the puckering motion is compatible with the experimentally observed lifetimes. This work provides a fundamental understanding of the photophysical and photochemical properties of the benzyluracil systems and can give rational suggestions to further design or regulate the bionic molecular systems.

Tracking of the molecular geometrical changes in the primary event of photoinduced ring-opening reactions of a spiropyran model in gas phase

Spiropyran (SP) is one of the photochromic molecules that have been extensively studied because of their huge commercial applications. When exposed to the UV light, SP undergoes a molecular arrangement to generate an open-form merocyanine (MC), which can revert to the closed-form photochemically or thermally. A sequential mechanism of the photoisomerisation involved in the photochromic process still remains controversial. The current work aimed at providing a detailed and comprehensive picture of the ring-opening process of the spiropyran by the combination of the CASPT2/CASSCF static electronic structure calculations and on-the-fly surface hopping dynamic simulations. Four different reaction pathways were observed in our results. The internal conversion process (IC) driven by C–O bond rapture can generate both the ring-opening and closed products on the S0 state, while generating only closed forms when driven by a hydrogen-out-of-plane (HOOP) mode. In addition, the ring-opening process of the spiropyran can also occur on the excited state. The C–N bond dissociation was not observed in our simulations results. The current investigation shed light on the complex mechanism of the SP-MC ring-opening process, which would provide helpful information for further design or improvement of SP-MC-based photochromic devices.

Photochemical and photophysical properties of cis-stilbene molecule by electronic structure calculations and nonadiabatic surface-hopping dynamics simulations

We combined the electronic structure calculations and OM2(orthogonalization model 2)/MRCI nonadiabatic surface-hopping dynamics simulations to scrutinize the photoisomerization mechanisms of cis-stilbene. The static electronic structure calculations showed that the irradiation of cis-stilbene populates the bright S1 state and we obtained three S1/S0 conical intersections (CIs) and proposed two nonadiabatic decay channels that efficiently de-excited to the ground state. In the first pathway, once excited to the S1 state, the cis-stilbene proceeds along S1 potential energy surface. Then, the molecule encounters S1S0-C CI, from which the system decays to S0 state. The other pathway involves the S1S0-D CI from where the S1 system hops to the ground state. In our simulations, we acquired cis, trans and DHP (4a,4b-dihydrophenanthrene) products and the ratio is estimated as 42:48:7. The present work show that the combination of electronic structure calculations and OM2/MRCI nonadiabatic dynamics can give detailed photochemical and photophysical information of stilbene systems.

Computational Structure-Activity Relationship (SAR) of Berberine Analogs in Double-Stranded and G-Quadruplex DNA Binding Reveals Both Position and Target Dependence

Berberine, a natural product alkaloid, and its analogs have a wide range of medicinal properties, including antibacterial and anticancer effects. Previous studies showed that berberine and its analogs intercalate into DNA, thereby inhibiting DNA replication. Berberine has also been studied as a photosensitizer and was shown to generate reactive singlet oxygen in situ, and this has applications in photodynamic therapy. Various groups have synthesized berberine analogs that have comparable or improved biological activity; however, an exhaustive structure-activity relationship of the free energy of binding of berberine analogs with substitution at C-8, C-12, and C-13 to DNA have not been previously reported. High throughput virtual screening (HTVS) allows for efficient analysis of compound libraries to identify lead compounds as possible pharmaceutical agents. Here, we employed HTVS towards a library of alkyl or aryl berberine analogs on C-8, C-12, and C-13 to probe binding to double-stranded and G-quadruplex DNA. Predicted free energies of binding to double-stranded DNA and G-quadruplex DNA were generated via molecular docking. The excited state electronic structure calculations were conducted via time-dependent density functional theory to probe the potential photosensitizing activity of each compound, and the potential G-quadruplex stabilizing abilities of key berberine analogs were probed through molecular dynamics simulations on a 4.0 nanosecond timescale. We determined that the nature of the substituent, the position of the substituent, and the nucleic acid target affect the free energy of binding of berberine analogs to DNA and G-quadruplex DNA, however berberine analogs did not result in net stabilization of G-quadruplex DNA.