QM/MM studies on the excited-state relaxation mechanism of a semisynthetic dTPT3 base

Photocyclization and Photoisomerization Mechanisms of an Indolylfulgide Derivative in Acetonitrile Solution by Using the QM (MS-CASPT2)/MM Method

The indolylfulgide systems have been extensively investigated due to their potential applications as photochromic materials. In this work, the photoinduced ring-closure/opening and isomerization reactions of a photochromic indolylfulgide in vacuum and acetonitrile solvent have been investigated by means of MS-CASPT2//CASSCF and QM(MS-CASPT2)//CASSCF/MM. The deactivation mechanisms of indolylfulgide have been proposed based on the optimized structures in the S0 and S1 states, S1/S0 conical intersections, and the calculated minimum-energy paths. After excitation into the first singlet excited-state, which is spectroscopically bright in the Franck-Condon point of the E, the photoprocesses proceed toward a nearby S1 minimum. Then, two possible nonadiabatic relaxation paths exist to repopulate the ground state. In the ring closure reaction, the S1 E isomer evolves directly into one S1/S0 conical intersection and decays to the ground state with bifurcation toward C or E. In the E → Z tautomerization pathway, the excited system can deactivate to the S0 state via a distinct conical intersection. The minimum-energy paths of the indolylfulgide revealed that the ring closure reaction in the solvent is more facile to take place than the E → Z isomerization after irradiation of the same E. Furthermore, for the ring opening reaction from the C side, there exists an energy barrier (11.1 kcal/mol) in the S1 state before arriving at the conical intersection. The computational results showed that the solvent has some influence on the system compared with that in the gas phase. The present work could contribute to comprehending the photoreactions of indolylfulgide and its derivatives in solution.

Investigation of the Nonradiative Photoprocesses of Unnatural DNA Base: 7-(2-Thienyl)-imidazo[4,5-b]pyridine (Ds)─A Computational Study

7-(2-Thienyl)-imidazo[4,5-b]pyridine (Ds) is an unnatural nucleic acid that forms a stable pair with pyrrole-2-carbaldehyde (Pa) in DNA. This Ds-Pa pair gets stabilized via van der Waals interaction and shape fitting. In our previous study [Ghosh, P. J. Phys. Chem. A 2021, 125, 5556-5561], we investigated the nonradiative photoprocesses of the unnatural DNA base Pa, and also there are some studies on its stability and reactivity in the ground state. But, to consider it as a good unnatural base pair, one has to understand its stability not only in the ground state but also in the excited states after absorbing ultraviolet (UV) radiation. Therefore, in this study, the excited-state photoprocesses of Ds on UV irradiation and its nonradiative decay channels have been investigated using state-of-the-art multireference methods, and this investigation finally leads the molecule to access the minimum energy crossing point (MECP) via a downhill pathway.

"On-the-Fly" Nonadiabatic Dynamics Simulation on the Ultrafast Photoisomerization of a Molecular Photoswitch Iminothioindoxyl: An RMS-CASPT2 Investigation

Iminothioindoxyl (ITI) is a new class of photoswitch that exhibits many excellent properties including well-separated absorption bands in the visible region for both conformers, ultrafast Z to E photoisomerization as well as the millisecond reisomerization at room temperature for the E isomer, and switchable ability in both solids and various solvents. However, the underlying ultrafast photoisomerization mechanism at the atomic level remains unclear. In this work, we have employed a combination of high-level RMS-CASPT2-based static electronic structure calculations and nonadiabatic dynamics simulations to investigate the ultrafast photoisomerization dynamics of ITI. Based on the minimum-energy structures, minimum-energy conical intersections, linear interpolation internal coordinate paths, and nonadiabatic dynamics simulations, the overall photoisomerization scenario of ITI upon excitation is established. Upon excitation around 416 nm, the molecule will be excited to the S2 state considering its close energy to the experimentally measured absorption maximum and larger oscillator strength, from which ultrafast decay of S2 to S1 state can take place efficiently with a time constant of 62 fs. However, the photoisomerization is not likely to complete in the S2 state since the dihedral associated with the Z to E isomerization changes little during the relaxation. Upon relaxing to the S1 state, the molecule will decay to the S0 state ultrafast with a time constant of 232 fs. In contrast, the decay of the S1 state is important for the isomerization considering that the dihedral related to the isomerization of the hopping structures is close to 90°. Therefore, the S1/S0 intersection region should be important for the isomerization of ITI. Arriving at the S0 state, the molecule can either go back to the original Z reactant or isomerize to the E products. At the end of the 500 fs simulation time, the E configuration accounts for nearly 37% of the final structures. Moreover, the photoisomerization mechanism is different from the isomerization mechanism in the ground state; i.e., instead of the inversion mechanism in the ground state, the photoisomerization prefers the rotation mechanism. Our results not only agree well with previous experimental studies but also provide some novel insights that could be helpful for future improvements in the performance of the ITI photoswitches.

PyDFT-QMMM: A modular, extensible software framework for DFT-based QM/MM molecular dynamics

PyDFT-QMMM is a Python-based package for performing hybrid quantum mechanics/molecular mechanics (QM/MM) simulations at the density functional level of theory. The program is designed to treat short-range and long-range interactions through user-specified combinations of electrostatic and mechanical embedding procedures within periodic simulation domains, providing necessary interfaces to external quantum chemistry and molecular dynamics software. To enable direct embedding of long-range electrostatics in periodic systems, we have derived and implemented force terms for our previously described QM/MM/PME approach [Pederson and McDaniel, J. Chem. Phys. 156, 174105 (2022)]. Communication with external software packages Psi4 and OpenMM is facilitated through Python application programming interfaces (APIs). The core library contains basic utilities for running QM/MM molecular dynamics simulations, and plug-in entry-points are provided for users to implement custom energy/force calculation and integration routines, within an extensible architecture. The user interacts with PyDFT-QMMM primarily through its Python API, allowing for complex workflow development with Python scripting, for example, interfacing with PLUMED for free energy simulations. We provide benchmarks of forces and energy conservation for the QM/MM/PME and alternative QM/MM electrostatic embedding approaches. We further demonstrate a simple example use case for water solute in a water solvent system, for which radial distribution functions are computed from 100 ps QM/MM simulations; in this example, we highlight how the solvation structure is sensitive to different basis-set choices due to under- or over-polarization of the QM water molecule's electron density.

Theoretical insights into the photophysics of an unnatural base Z: A MS-CASPT2 investigation

We have employed the highly accurate multistate complete active space second-order perturbation theory (MS-CASPT2) method to investigate the photoinduced excited state relaxation properties of one unnatural base, namely Z. Upon excitation to the S2 state of Z, the internal conversion to the S1 state would be dominant. From the S1 state, two intersystem crossing paths leading to the T2 and T1 states and one internal conversion path to the S0 state are possible. However, considering the large barrier to access the S1 /S0 conical intersection and the strong spin-orbit coupling between S1 and T2 states (>40 cm-1 ), the intersystem crossing to the triplet manifolds is predicted to be more preferred. Arriving at the T2 state, the internal conversion to the T1 state and the intersystem crossing back to the S1 state are both possible considering the S1 /T2 /T1 three-state intersection near the T2 minimum. Upon arrival at the T1 state, the deactivation to S0 can be efficient after overcoming a small barrier to access T1 /S0 crossing point, where the spin-orbit coupling (SOC) is as large as 39.7 cm-1 . Our present work not only provides in-depth insights into the photoinduced process of unnatural base Z, but can also help the future design of novel unnatural bases with better photostability.

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 E_α 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.

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.

Mechanistic photophysics and photochemistry of unnatural bases and sunscreen molecules: insights from electronic structure calculations

Photophysics and photochemistry are basic subjects in the study of light-matter interactions and are ubiquitous in diverse fields such as biology, energy, materials, and environment. A full understanding of mechanistic photophysics and photochemistry underpins many recent advances and applications. This contribution first provides a short discussion on the theoretical calculation methods we have used in relevant studies, then we introduce our latest progress on the mechanistic photophysics and photochemistry of two classes of molecular systems, namely unnatural bases and sunscreens. For unnatural bases, we disclose the intrinsic driving forces for the ultrafast population to reactive triplet states, impacts of the position and degree of chalcogen substitutions, and the effects of complex environments. For sunscreen molecules, we reveal the photoprotection mechanisms that dissipate excess photon energy to the surroundings by ultrafast internal conversion to the ground state. Finally, relevant theoretical challenges and outlooks are discussed.

Quantum Mechanics/Molecular Mechanics Studies on the Photophysical Mechanism of Methyl Salicylate

Methyl salicylate (MS) as a subunit of larger salicylates found in commercial sunscreens has been shown to exhibit keto-enol tautomerization and dual fluorescence emission via excited-state intramolecular proton transfer (ESIPT) after the absorption of ultraviolet (UV) radiation. However, its excited-state relaxation mechanism is unclear. Herein, we have employed the quantum mechanics(CASPT2//CASSCF)/molecular mechanics method to explore the ESIPT and excited-state relaxation mechanism of MS in the lowest three electronic states, that is, S₀, S₁, and T₁ states, in a methanol solution. Based on the optimized geometric and electronic structures, conical intersections and crossing points, and minimum-energy paths combined with the computed linearly interpolated Cartesian coordinate paths, the photophysical mechanism of MS has been proposed. The S₁ state is a spectroscopically bright ¹ππ* state in the Franck-Condon region. From the initially populated S₁ state, there exist three nonradiative relaxation paths to repopulate the S₀ state. In the first one, the S₁ system (i.e., ketoB form) first undergoes an ESIPT path to generate an S₁ tautomer (i.e., enol form) that exhibits a large Stokes shift in experiments. The generated S₁ enol tautomer further evolves toward the nearby S₁/S₀ conical intersection and then hops to the S₀ state, followed by the backward ground-state intramolecular proton transfer (GSIPT) to the initial ketoB form S₀ state. In the second one, the S₁ system first hops through the S₁ → T₁ intersystem crossing (ISC) to the T₁ state, which then further decays to the S₀ state via T₁ → S₀ ISC at the T₁/S₀ crossing point. In the third path, the T₁ system that stems from the S₁ → T₁ ISC process via the S₁/T₁ crossing point first takes place a T₁ ESIPT to generate a T₁ enol tautomer, which can further decay to the S₀ state via T₁-to-S₀ ISC. Finally, the GSIPT occurs to back the system to the initial ketoB form S₀ state. Our present work could contribute to understanding the photophysics of MS and its derivatives.

Theoretical studies on the photochemistry of 2-nitrofluorene in the gas phase and acetonitrile solution

The photophysical and photochemical mechanisms of 2-nitrofluorene (2-NF) in the gas phase and acetonitrile solution have been studied theoretically. Upon ∼330 nm irradiation to the first bright state (¹ππ*), the 2-NF system can decay to triplet excited states via rapid intersystem crossing (ISC) processes through different surface crossing points or to the ground state via an ultrafast internal conversion (IC) process through the S₁/S₀ conical intersection. The ¹nπ* dark state will serve as a bridge when the system leaves the Franck-Condon (FC) region and approaches to the S₁ minimum. The molecule maintains a planar geometry during the excited-state relaxation processes. The differences on excitation properties such as electronic configurations and spin-orbit coupling (SOC) interactions between those in the gas phase and acetonitrile solution cannot be neglected, indicating possible changes on the efficiency of the related ISC processes for the 2-NF system in solution. Once arrived at the T₁ state, it would further decay to the S₀ state or photodegrade into the Ar-O˙ and NO˙ free radicals. During the intramolecular rearrangement process, the twisting of the nitro group out of the aromatic-ring plane is regarded as a critical structural variation for the photodegradation of the 2-NF system. The free radicals finally form through oxaziridine-type intermediate and transition state structures. The present work provides important mechanistic insights to the photochemistry of nitro-substituted polyaromatic compounds.

QM/MM Studies on the Photophysical Mechanism of a Truncated Octocrylene Model

Methyl 2-cyano-3,3-diphenylacrylate (MCDPA) shares the same molecular skeleton with octocrylene (OCR) that is one of the most common molecules used in commercially available sunscreens. However, its excited-state relaxation mechanism is unclear. Herein, we have used the QM(CASPT2//CASSCF)/MM method to explore spectroscopic properties, geometric and electronic structures, relevant conical intersections and crossing points, and excited-state relaxation paths of MCDPA in methanol solution. We found that in the Franck-Condon (FC) region, the V(¹ππ*) state is energetically lower than the V'(¹ππ*) state only by 2.8 kcal/mol and is assigned to experimentally observed maximum absorption band. From these two initially populated singlet states, there exist three nonradiative relaxation paths to repopulate the S₀ state. In the first one, when the V(¹ππ*) state is populated in the FC region, the system diabatically evolves along the V(¹ππ*) state into its minimum where the internal conversion to S₀ occurs. In the second one, the V'(¹ππ*) state is populated in the FC region and the system adiabatically overcomes a barrier of ca. 3.0 kcal/mol to approach the V(¹ππ*) minimum eventually leading to a V(¹ππ*)-to-S₀ internal conversion. In the third one, the V'(¹ππ*) state first hops via the intersystem crossing to the T₂ state, which then decays through the internal conversion to the T₁ state. The T₁ state is finally converted to the S₀ state via the T₁/S₀ crossing point. Our present work contributes to understanding the photophysics of OCR and its variants.

Optimization of Replication, Transcription, and Translation in a Semi-Synthetic Organism

Previously, we reported the creation of a semi-synthetic organism (SSO) that stores and retrieves increased information by virtue of stably maintaining an unnatural base pair (UBP) in its DNA, transcribing the corresponding unnatural nucleotides into the codons and anticodons of mRNAs and tRNAs, and then using them to produce proteins containing noncanonical amino acids (ncAAs). Here we report a systematic extension of the effort to optimize the SSO by exploring a variety of deoxy- and ribonucleotide analogues. Importantly, this includes the first in vivo structure-activity relationship (SAR) analysis of unnatural ribonucleoside triphosphates. Similarities and differences between how DNA and RNA polymerases recognize the unnatural nucleotides were observed, and remarkably, we found that a wide variety of unnatural ribonucleotides can be efficiently transcribed into RNA and then productively and selectively paired at the ribosome to mediate the synthesis of proteins with ncAAs. The results extend previous studies, demonstrating that nucleotides bearing no significant structural or functional homology to the natural nucleotides can be efficiently and selectively paired during replication, to include each step of the entire process of information storage and retrieval. From a practical perspective, the results identify the most optimal UBP for replication and transcription, as well as the most optimal unnatural ribonucleoside triphosphates for transcription and translation. The optimized SSO is now, for the first time, able to efficiently produce proteins containing multiple, proximal ncAAs.

Progress Toward a Semi-Synthetic Organism with an Unrestricted Expanded Genetic Alphabet

We have developed a family of unnatural base pairs (UBPs), exemplified by the pair formed between dNaM and dTPT3, for which pairing is mediated not by complementary hydrogen bonding but by hydrophobic and packing forces. These UBPs enabled the creation of the first semisynthetic organisms (SSOs) that store increased genetic information and use it to produce proteins containing noncanonical amino acids. However, retention of the UBPs was poor in some sequence contexts. Here, to optimize the SSO, we synthesize two novel benzothiophene-based dNaM analogs, dPTMO and dMTMO, and characterize the corresponding UBPs, dPTMO-dTPT3 and dMTMO-dTPT3. We demonstrate that these UBPs perform similarly to, or slightly worse than, dNaM-dTPT3 in vitro. However, in the in vivo environment of an SSO, retention of dMTMO-dTPT3, and especially dPTMO-dTPT3, is significantly higher than that of dNaM-dTPT3. This more optimal in vivo retention results from better replication, as opposed to more efficient import of the requisite unnatural nucleoside triphosphates. Modeling studies suggest that the more optimal replication results from specific internucleobase interactions mediated by the thiophene sulfur atoms. Finally, we show that dMTMO and dPTMO efficiently template the transcription of RNA containing TPT3 and that their improved retention in DNA results in more efficient production of proteins with noncanonical amino acids. This is the first instance of using performance within the SSO as part of the UBP evaluation and optimization process. From a general perspective, the results demonstrate the importance of evaluating synthetic biology "parts" in their in vivo context and further demonstrate the ability of hydrophobic and packing interactions to replace the complementary hydrogen bonding that underlies the replication of natural base pairs. From a more practical perspective, the identification of dMTMO-dTPT3 and especially dPTMO-dTPT3 represents significant progress toward the development of SSOs with an unrestricted ability to store and retrieve increased information.

Photochemical and Photodynamical Properties of Sulfur-Substituted Nucleic Acid Bases

Sulfur-substituted nucleobases (a.k.a., thiobases) are among the world's leading prescriptions for chemotherapy and immunosuppression. Long-term treatment with azathioprine, 6-mercaptopurine and 6-thioguanine has been correlated with the photoinduced formation of carcinomas. Establishing an in-depth understanding of the photochemical properties of these prodrugs may provide a route to overcoming these carcinogenic side effects, or, alternatively, a basis for developing effective compounds for targeted phototherapy. In this review, a broad examination is undertaken, surveying the basic photochemical properties and excited-state dynamics of sulfur-substituted analogs of the canonical DNA and RNA nucleobases. A molecular-level understanding of how sulfur substitution so remarkably perturbs the photochemical properties of the nucleobases is presented by combining experimental results with quantum-chemical calculations. Structure-property relationships demonstrate the impact of site-specific sulfur substitution on the photochemical properties, particularly on the population of the reactive triplet state. The value of fundamental photochemical investigations for driving the development of ultraviolet-A chemotherapeutics is showcased. The most promising photodynamic agents identified thus far have been investigated in various carcinoma cell lines and shown to decrease cell proliferation upon exposure to ultraviolet-A radiation. Overarching principles have been elucidated for the impact that sulfur substitution of the carbonyl oxygen has on the photochemical properties of the nucleobases.