Spin-flip Time-dependent Density Functional Theory Research Articles

Quantum-Chemistry Study of the Photophysical Properties of 4-Thiouracil and Comparisons with 2-Thiouracil.

DNA in living beings is constantly damaged by exogenous and endogenous agents. However, in some cases, DNA photodamage can have interesting applications, as it happens in photodynamic therapy. In this work, the current knowledge on the photophysics of 4-thiouracil has been extended by further quantum-chemistry studies to improve the agreement between theory and experiments, to better understand the differences with 2-thiouracil, and, last but not least, to verify its usefulness as a photosensitizer for photodynamic therapy. This study has been carried out by determining the most favorable deactivation paths of UV-vis photoexcited 4-thiouracil by means of the photochemical reaction path approach and an efficient combination of the complete-active-space second-order perturbation theory//complete-active-space self-consistent field (CASPT2//CASSCF), (CASPT2//CASPT2), time-dependent density functional theory (TDDFT), and spin-flip TDDFT (SF-TDDFT) methodologies. By comparing the data computed herein for both 4-thiouracil and 2-thiouracil, a rationale is provided on the relatively higher yields of intersystem crossing, triplet lifetime and singlet oxygen production of 4-thiouracil, and the relatively higher yield of phosphorescence of 2-thiouracil.

Survey of T1 and T2 Energies of Intramolecular Singlet Fission Chromophores

Singlet fission is a desired process in photovoltaics since it enhances photoelectric conversion efficiency. Intramolecular singlet fission is of special interest as the fission efficiency can be improved through tuning configurations between chromophore units that are covalently connected. However, intramolecular singlet fission chromophores feature a large tetraradical character, and may tend to dissatisfy the ET2>2ET1 criterion for all singlet fission chromophores, intramolecular or not. We performed spin-flip time-dependent density functional theory calculations for a collection of representative intramolecular singlet fission chromophores to show that this is indeed the case.

Singlet fission initiating organic photosensitizations

The feasibility of singlet fission (SF) in organic photosensitizers is investigated through spin-flip long-range corrected time-dependent density functional theory. This study focuses on four major organic photosensitizer molecules: benzophenone, boron-dipyrromethene, methylene blue, and rose bengal. Calculations demonstrate that all these molecules possess moderate pi-stacking energies and closely-lying singlet (S) and quintet (triplet–triplet, TT) excitations, satisfying the essential conditions for SF: (1) Near-degenerate low-lying S and (TT) excitations with a significant S–T energy gap, and (2) Moderate pi-stacking energy of chromophores, slightly higher than solvation energy, enabling dissociation for triplet-state chromophore generation. Moreover, based on the El-Sayed rule, intersystem crossing is found to simultaneously proceed at very slow rates in all these photosensitizers. This is attributed to the fact that the lowest singlet excitation of the monomers partly involves npi ^* transitions alongside the main pi pi ^* transitions. The proposed mechanisms are strongly substantiated by comparisons with experimental studies.

Roles of Singlet Fission in the Photosensitization of Silicon Phthalocyanine.

The roles of singlet fission in the triplet generation of silicon phthalocyanine (SiPc), a compound analogous to the IRDye700DX photosensitizer used in near-infrared photoimmunotherapy, are investigated by considering the energetical relation between the excitations of this compound. These excitations are obtained through spin-flip long-range corrected time-dependent density functional theory calculations. To initiate singlet fission, chromophores must meet two conditions: (1) near-degenerate low-lying singlet and quintet (triplet-triplet) excitations with a considerable energy gap of the lowest singlet and triplet excited states and (2) moderate π-stacking energy of chromophores, which is higher than but not far from the solvation energy, to facilitate the dissociation and generation of triplet-state chromophores. The present calculations demonstrate that SiPc satisfies both of these conditions after the formation of π-stacking irrespective of the presence of an axial ligand(s), suggesting that singlet fission plays a crucial role in the triplet generation process, although intersystem crossing occurs simultaneously at a very slow rate.

Excited State Properties of Point Defects in Semiconductors and Insulators Investigated with Time-Dependent Density Functional Theory.

We present a formulation of spin-conserving and spin-flip hybrid time-dependent density functional theory (TDDFT), including the calculation of analytical forces, which allows for efficient calculations of excited state properties of solid-state systems with hundreds to thousands of atoms. We discuss an implementation on both GPU- and CPU-based architectures along with several acceleration techniques. We then apply our formulation to the study of several point defects in semiconductors and insulators, specifically the negatively charged nitrogen-vacancy and neutral silicon-vacancy centers in diamond, the neutral divacancy center in 4H silicon carbide, and the neutral oxygen-vacancy center in magnesium oxide. Our results highlight the importance of taking into account structural relaxations in excited states in order to interpret and predict optical absorption and emission mechanisms in spin defects.

Solvent Effects and pH Dependence of the X-ray Absorption Spectra of Proline from Electrostatic Embedding Quantum Mechanics/Molecular Mechanics and Mixed-Reference Spin-Flip Time-dependent Density-Functional Theory.

The accurate description of solvent effects on X-ray absorption spectra (XAS) is fundamental for comparing the simulated spectra with experiments in solution. Currently, few protocols exist that can efficiently reproduce the effects of the solute/solvent interactions on XAS. Here, we develop an efficient and accurate theoretical protocol for simulating the solvent effects on XAS. The protocol combines electrostatic embedding QM/MM based on electrostatic potential fitted operators for describing the solute/solvent interactions and mixed-reference spin-flip time-dependent density functional theory (MRSF-TDDFT) for simulating accurate XAS spectra. To demonstrate the capabilities of our protocol, we compute the X-ray absorption of neutral proline in the gas phase and ionic proline in water in all relevant K-edges, showing excellent agreement with experiments. We show that states represented by core to π* transitions are almost unaffected by the interaction with water, whereas the core to σ* transitions are more impacted by the fluctuation of proline structure and the electrostatic interaction with the solvent. Finally, we reconstruct the pH-dependent XAS of proline in solution, determining that the N K-edge can be used to distinguish its three protonation states.

Doubly Tuned Exchange-Correlation Functionals for Mixed-Reference Spin-Flip Time-Dependent Density Functional Theory.

It is demonstrated that significant accuracy improvements in MRSF-TDDFT can be achieved by introducing two different exchange-correlation (XC) functionals for the reference Kohn-Sham DFT and the response part of the calculations, respectively. Accordingly, two new XC functionals of doubly tuned Coulomb attenuated method-vertical excitation energy (DTCAM-VEE) and DTCAM-AEE were developed on the basis of the "adaptive exact exchange (AEE)" concept in the framework of the Coulomb-attenuating XC functionals. The values by DTCAM-VEE are in excellent agreement with those of Thiel's set [mean absolute errors (MAEs) and the interquartile range (IQR) values of 0.218 and 0.327 eV, respectively]. On the other hand, DTCAM-AEE faithfully reproduced the qualitative aspects of conical intersections (CIs) of trans-butadiene and thymine and the nonadiabatic molecular dynamics (NAMD) simulations on thymine. The latter functional also remarkably exhibited the exact 1/R asymptotic behavior of the charge-transfer state of an ethylene-tetrafluoroethylene dimer and the accurate potential energy surfaces (PESs) along the two torsional angles of retinal protonated Schiff base model with six double bonds (rPSB6). Overall, DTCAM-AEE generally performs well, as its MAE (0.237) and IQR (0.41 eV) are much improved as compared to BH&HLYP. The current idea can also be applied to other XC functionals as well as other variants of linear response theories, opening a new way of developing XC functionals.

Mixed-Reference Spin-Flip Time-Dependent Density Functional Theory: Multireference Advantages with the Practicality of Linear Response Theory.

The density functional theory (DFT) and linear response (LR) time-dependent (TD)-DFT are of the utmost importance for routine computations. However, the single reference formulation of DFT suffers in the description of open-shell singlet systems such as diradicals and bond-breaking. LR-TDDFT, on the other hand, finds difficulties in the modeling of conical intersections, doubly excited states, and core-level excitations. In this Perspective, we demonstrate that many of these limitations can be overcome by recently developed mixed-reference (MR) spin-flip (SF)-TDDFT, providing an alternative yet accurate route for such challenging situations. Empowered by the practicality of the LR formalism, it is anticipated that MRSF-TDDFT can become one of the major workhorses for general routine tasks.

Ultrafast Photocontrolled Rotation in a Molecular Motor Investigated by Machine Learning-Based Nonadiabatic Dynamics Simulations.

The thermal helix inversion (THI) of the overcrowded alkene-based molecular motors determines the speed of the unidirectional rotation due to the high reaction barrier in the ground state, in comparison with the ultrafast photoreaction process. Recently, a phosphine-based motor has achieved all-photochemical rotation experimentally, promising to be controlled without a thermal step. However, the mechanism of this photochemical reaction has not yet been fully revealed. The comprehensive computational studies on photoisomerization still resort to nonadiabatic molecular dynamics (NAMD) simulations based on electronic structure calculations, which remains a high computational cost for large systems such as molecular motors. Machine learning (ML) has become an accelerating tool in NAMD simulations recently, where excited-state potential energy surfaces (PESs) are constructed analytically with high accuracy, providing an efficient approach for simulations in photochemistry. Herein the reaction pathway is explored by a spin-flip time-dependent density functional theory (SF-TDDFT) approach in combination with ML-based NAMD simulations. According to our computational simulations, we notice that one of the key factors of fulfilling all-photochemical rotation in the phosphine-based motor is that the excitation energies of four isomers are similar. Additionally, a shortcut photoinduced transformation between unstable isomers replaces the THI step, which shares the conical intersection (CI) with photoisomerization. In this study, we provide a practical approach to speed up the NAMD simulations in photochemical reactions for a large system that could be extended to other complex systems.

High-efficient luminescence induced by the restriction of benzothiazole group torsion for the HBT-H-H molecule in the aggregate state

The aggregation-induced emission (AIE) effect has been demonstrated to have great potential application in different areas, from organic electronics to biomedical research and physical process monitoring. In general, molecules with AIE characteristic exhibit fluorescence enhancement in the aggregated state by restricting intramolecular motion consumption. The combination of AIE and excited-state intramolecular proton transfer (ESIPT) is meaningful for promoting luminescence. Recently, HBT-H-H molecule, as a derivative of 2-(2-Hydroxyphenyl)benzothiazole (HBT), has drawn extensive attention from researchers. The molecule possesses the intramolecular hydrogen bonding structure which has the potential for ESIPT. Moreover, the fluorescence quantum yield of HBT-H-H in the aggregation state is 35 times higher than that in Toluene. However, the interplay between excited state dynamics and the AIE effect for this molecule is not clear. Especially, how does AIE effect beat non-radiative transition channel by affecting motions of molecular structure. Herein, we investigated the excited state dynamics of HBT-H-H molecule by the spin-flip time-dependent density functional theory and QM/MM method. We found that the molecule relaxes to the conical intersection region through the twisting motion of the benzothiazole group in Toluene solvent. While the AIE effect effectively inhibits this process by preventing the torsion of benzothiazole group, which induces the emission enhancement. The interplay between the excited-state dynamics and AIE effect for the HBT-H-H molecule delineated in this work not only benefits the deep understanding of molecular behavior to the aggregate level, but also provides a guide for the synthesis of AIE materials with favorable performance.

Turn on the luminescence channel by the suppression of conical intersection process for the sulfur-containing hydrogen-bonded molecules

The sulfur-containing hydrogen bonds exhibit notable potential in gene and protein engineering. As an important research direction of sulfur-containing hydrogen bonding dynamics, the excited-state intramolecular proton transfer (ESIPT) reaction of the thiol proton has garnered significant interest. Recently, Chou et al. synthesized a series of sulfur-containing H-bonded molecules, inclusive of 3-thiolflavone (3 TF), its trifluoromethyl derivative (3FTF), and its diethylamino derivative (3NTF), thereby inaugurating a new chapter in the ESIPT reaction of the thiol proton. Nevertheless, many open issues cannot be answered solely by experimental means and call for a detailed theoretical investigation, especially the relationship between the molecular excited-state properties and different luminescence properties of the three molecules. Herein, we validate that the molecules undergo the ESIPT reaction of the thiol proton and identify the time scale through the time-dependent density functional theory (TDDFT) calculation. Moreover, employing the spin-flip TDDFT approach, the analysis of the non-radiative transition process reveals that difference in Gibbs free energy of activation (ΔG⧧) for the transition from Frank-Condon point to minimum energy conical intersection (MECI) point primarily accounts for the different luminescence properties of the three molecules. Besides, we also reveal the reason for the abnormal blue-shifted fluorescence of the 3NTF in the aggregated state by the ONIOM (TDDFT: UFF) strategy. These findings are favorable to understanding the luminescence mechanism of sulfur-containing H-bonded molecules and provide a reference for the synthesis and design of the luminescent materials based on the molecules with thiol proton transfer properties.

Unveiling controlling factors of the S0/S1 minimum-energy conical intersection (3): Frozen orbital analysis based on the spin-flip theory.

Conical intersections (CIs), which indicate the crossing of two or more adiabatic electronic states, are crucial in the mechanisms of photophysical, photochemical, and photobiological processes. Although various geometries and energy levels have been reported using quantum chemical calculations, the systematic interpretation of the minimum energy CI (MECI) geometries is unclear. A previous study [Nakai et al., J. Phys. Chem. A 122, 8905 (2018)] performed frozen orbital analysis (FZOA) based on time-dependent density functional theory (TDDFT) at the MECI formed between the ground and first electronic excited states (S0/S1 MECI), thereby inductively clarifying two controlling factors. However, one of the factors that the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO) energy gap became close to the HOMO-LUMO Coulomb integral was not valid in the case of spin-flip TDDFT (SF-TDDFT), which is frequently used as a means of the geometry optimization of MECI [Inamori et al., J. Chem. Phys. 152, 144108 (2020)]. This study revisited the controlling factors using FZOA for the SF-TDDFT method. Based on spin-adopted configurations within a minimum active space, the S0-S1 excitation energy is approximately represented by the HOMO and LUMO energy gap ΔεHL, a contribution from Coulomb integrals JHL″ and that from the HOMO-LUMO exchange integral KHL″. Furthermore, numerical applications of the revised formula at the SF-TDDFT method confirmed the control factors of S0/S1 MECI.

Carbon Condensation via [4 + 2] Cycloaddition of Highly Unsaturated Carbon Chains.

We present computational studies of reaction pathways for alkyne/polyyne dimerization that represent plausible early steps in mechanisms for carbon condensation. A previous computational study of the ring coalescence and annealing model of C60 formation revealed that a 1,4-didehydrobenzocyclobutadiene intermediate (p-benzyne derivative) has little to no barrier to undergoing an unproductive retro-Bergman cyclization, which brings into question the relevance of that reaction pathway. The current study investigates an alternative model, which proceeds through an initial [4 + 2] cycloaddition instead of a [2 + 2] cycloaddition. In this pathway, the problematic intermediate is avoided, with the reaction proceeding via a (potentially) more kinetically stable tetradehydronaphthalene derivative. The computational studies of the [2 + 2] and [4 + 2] model systems, with increasing alkyne substitutions, reveal that the para-benzyne diradical of the [4 + 2] pathway has a significantly greater barrier to ring opening than the analogous intermediates of the [2 + 2] pathway and that alkyne substitution has little effect on this important barrier. These studies employ spin-flip, time-dependent density functional theory (SF-TDDFT) to provide suitable treatment of open-shell diradical intermediates.

Dihydropyrene/Cyclophanediene Photoswitching Mechanism Revisited with Spin-Flip Time-Dependent Density Functional Theory: Nature of the Photoisomerization Funnel at Stake!

The complex photoisomerization mechanism of the dihydropyrene (DHP) photochromic system is revisited using spin-flip time-dependent density functional theory (SF-TD-DFT). The photoinduced ring-opening reaction of DHP into its cyclophanediene isomer involves multiple coupled electronic states of different character. A balanced treatment of both static and dynamic electron correlations is required to determine both the photophysical and photochemical paths in this system. The present results provide a refinement of the mechanistic picture provided in a previous complete active space self-consistent field plus second-order perturbation theory (CASPT2//CASSCF) study based on geometry optimizations at the CASSCF level. In particular, the nature of the conical intersection playing the central role of the photochemical funnel is different. While at the CASSCF level, the crossing with the ground state involves a covalent doubly excited state leading to a three-electron/three-center bond conical intersection, SF-TD-DFT predicts a crossing between the ground state and a zwitterionic state. These results are supported by multi-state CASPT2 calculations. This study illustrates the importance of optimizing conical intersections at a sufficiently correlated level of theory to describe a photochemical path involving crossings between covalent and ionic states.

Noncollinear and Spin-Flip TDDFT in Multicollinear Approach

Time-dependent density functional theory (TDDFT) is one of the most important tools for investigating the excited states of electrons. The TDDFT calculation for spin-conserving excitation, where collinear functionals are sufficient, has obtained great success and has become routine. However, TDDFT for noncollinear and spin-flip excitations, where noncollinear functionals are needed, is less widespread and still a challenge nowadays. This challenge lies in the severe numerical instabilities that root in the second-order derivatives of commonly used noncollinear functionals. To be free from this problem radically, noncollinear functionals with numerical stable derivatives are desired, and our recently developed approach, called the multicollinear approach, provides an option. In this work, the multicollinear approach is implemented in noncollinear and spin-flip TDDFT, and prototypical tests are given.

Noncollinear density functional theory

An approach to generalize any kind of collinear functional in density functional theory to noncollinear functionals is proposed. This approach satisfies the correct collinear limit for any kind of functional, guaranteeing that the exact collinear functional after generalization is still exact for collinear spins. Besides, it has well-defined and numerically stable functional derivatives, a desired feature for noncollinear and spin-flip time-dependent density functional theory. Furthermore, it provides local torque, hinting at its applications in spin dynamics.

Prototropically Controlled Dynamics of Cytosine Photodecay

The effect of the existence of several prototropic tautomers of cytosine on its UV/vis spectra and the excited state decay dynamics is studied by spectral and nonadiabatic molecular dynamics (NAMD) simulations in connection with the mixed-reference spin-flip time-dependent density functional theory (MRSF-TDDFT) method. Simulated UV/vis spectra provide a strong indication that the H3N keto-amino cytosine tautomer (the least anticipated species) may be present under experimental conditions. The NAMD simulations yield a wide range of excited state decay constants for various tautomers of cytosine, ranging from ∼1.3 ps for the biologically relevant H1N keto-amino tautomer to ∼0.1 ps for the keto-imino tautomer. The slowness of the H1N decay dynamics follows from the presence of a barrier on the excited state energy surface separating the Franck-Condon structure from the major decay funnel, the conical intersection seam. It is suggested that the experimentally observed photodecay dynamics may result from a combination of the decay processes of various tautomers (H3N in particular) present simultaneously under the experimental conditions.

Photochemistry of Thymine in Solution and DNA Revealed by an Electrostatic Embedding QM/MM Combined with Mixed-Reference Spin-Flip TDDFT

The photochemistry of nucleobases, important for their role as building blocks of DNA, is largely affected by the electrostatic environment in which they are soaked. For example, despite the numerous studies of thymine in solution and DNA, there is still a debate on the photochemical deactivation pathways after UV absorption. Many theoretical models are oversimplified due to the lack of computationally accurate and efficient electronic structure methodologies that capture excited state electron correlation effects when nucleobases are embedded in large electrostatic media. Here, we combine mixed-reference spin-flip time-dependent density functional theory (MRSF-TDDFT) with electrostatic embedding QM/MM using electrostatic potential fittingfitted (ESPF) atomic charges, as a strategy to accurately and efficiently describe the electronic structure of chromophores polarized by an electrostatic medium. In particular, we develop analytic expressions for the energy and gradient of MRSF/MM based on the ESPF coupling using atom-centered grids and total charge conservation. We apply this methodology to the study of solvation effects on thymine photochemistry in water and thymine dimers in DNA. In the former, the combination of trajectory surface hopping (TSH) nonadiabatic molecular dynamics (NAMD) with MRSF/MM remarkably revealed accelerated deactivation decay pathways, which is consistent with the experimental decay time of ∼400 fs. The enhanced hopping rate can be explained by the preferential stabilization of corresponding conical interactions due to their increased dipole moments. Structurally, it is a consequence of characteristic methyl puckered geometries near the conical intersection region. For the thymine dimer in B-DNA, we found new photochemical pathways through conical intersections that could explain the formation of cyclobutadiene dimers and 6-4 photoproducts.

All Visible Light Photoswitch Based on the Dimethyldihydropyrene Unit Operating in Aqueous Solutions with High Quantum Yields.

Molecular systems and devices whose properties can be modulated using light as an external stimulus are the subject of numerous research studies in the fields of materials and life sciences. In this context, the use of photochromic compounds that reversibly switch upon light irradiation is particularly attractive. However, for many envisioned applications, and in particular for biological purposes, illumination with harmful UV light must be avoided and these photoactivable systems must operate in aqueous media. In this context, we have designed a benzo[e]-fused dimethyldihydropyrene compound bearing a methyl-pyridinium electroacceptor group that meets these requirements. This compound (closed state) is able to reversibly isomerize under aerobic conditions into its corresponding cyclophanediene form (open isomer) through the opening of its central carbon-carbon bond. Both the photo-opening and the reverse photoclosing processes are triggered by visible light illumination and proceed with high quantum yields (respectively 14.5% yield at λ = 680 nm and quantitative quantum yield at λ = 470 nm, in water). This system has been investigated by nuclear magnetic resonance and absorption spectroscopy, and the efficient photoswitching behavior was rationalized by spin-flip time-dependent density functional theory calculations. In addition, it is demonstrated that the isomerization from the open to the closed form can be electrocatalytically triggered.

Singlet fission initiating triplet generations of BODIPY derivatives through pi -stacking: a theoretical study

The role of singlet fission (SF) in the triplet-state generation mechanism of 1,3,5,7-tetramethyl-boron-dipyrromethene derivatives is revealed by exploring the cause for the solvent dependence of the generation rate. Comparing the adsorption energy calculations of solvent molecules, i.e., cyclohexane, chloroform and acetonitrile molecules, to the derivatives with the pi -stacking energies of these derivatives surprisingly show that the hierarchy of the solvation energies and pi -stacking energies strongly correlates with the experimentally-suggested solvent dependence of the triplet-state generation of these derivatives for five and more adsorbing solvent molecules. Following this finding, the excitation spectra of these derivatives in acetonitrile solvent are explored using the proprietary spin-flip long-range corrected time-dependent density functional theory. It is, consequently, confirmed that the pi -stacking activates the second lowest singlet excitation to trigger the spin-allowed transition to the singlet doubly-excited tetraradical (TT)_1 state, which generates the long-lived quintet (TT)_1 state causing the SF. However, it is also found that the pi -stacking also get a slow intersystem crossing active around the intersections of the lowest singlet excitations with the lowest triplet T_1 excitations in parallel with the SF due to the charge transfer characters of the lowest singlet excitations. These results suggest that SF initiates the triplet-state generations through near-degenerate low-lying singlet and (TT) excitations with a considerable singlet-triplet energy gap after the pi -stacking of chromophores stronger than but not far from the solvation. Since these derivatives are organic photosensitizers, this study proposes that SF should be taken into consideration in developing novel heavy atom-free organic photosensitizers, which will contribute to a variety of research fields such as medical care, photobiology, energy science, and synthetic chemistry.