Prototropically Controlled Dynamics of Cytosine Photodecay

Photophysics of 5,6,7,8-tetrahydrobiopterin on a femtosecond time-scale

Pterins are naturally occurring compounds widespread in living organisms. 5,6,7,8-Tetrahydrobiopterin (H4Bip) is a cofactor of several key enzymes, including NO-synthases and phenylalanine hydroxylase, whereas tetrahydrocyanopterin is a photoreceptor molecule in cyanobacteria. In this regard, tetrahydropterins (H4pterins) photochemistry and photophysics have been attracting our attention. H4pterins photodegrade in presence of molecular oxygen yielding dihydropterins (H2pterins) and oxidized pterins. Meanwhile, the excited states dynamics of H4pterins on a femto- and picosecond time-scale remains unclear. To shed light on this area, we perform time-resolved spectroscopy of H4Bip using fluorescence up-conversion as well as transient absorption spectroscopy techniques along with TD-DFT non-adiabatic molecular dynamics. We show that the lowest H4Bip exited state has a lifetime of ca. 200 fs. Using the BHandHLYP functional and multireference spin-flip (MRSF) method we demonstrate that starting from the S4 state, H4Bip passes to the S1 state within 50 fs, and after 200 fs a conical intersection with the ground S0 state is achieved. As a whole, the excited state behavior of H4Bip is similar to DNA nucleobases, in particular guanine. These findings allow us to make some speculations about the biochemical role of H4pterins photophysics.

Expanding Horizons in Quantum Chemical Studies: The Versatile Power of MRSF-TDDFT

ConspectusWhile traditional quantum chemical theories have long been central to research, they encounter limitations when applied to complex situations. Two of the most widely used quantum chemical approaches, Density Functional Theory (DFT) and Time-Dependent Density Functional Theory (TDDFT), perform well in cases with relatively weak electron correlation, such as the ground-state minima of closed-shell systems (Franck-Condon region). However, their applicability diminishes in more demanding scenarios. These limitations arise from the reliance of DFT on a single-determinantal framework and the inability of TDDFT to capture double and higher excited configurations in its response space.The recently developed Multi-Reference Spin-Flip Time-Dependent Density Functional Theory (MRSF-TDDFT) successfully overcomes these challenges, pushing the boundaries of DFT methods. MRSF-TDDFT is exceptionally versatile, making it suitable for various applications, including bond-breaking and bond-forming reactions, open-shell singlet systems such as diradicals, and a more accurate depiction of transition states. It also provides the correct topology for conical intersections (CoIns) and incorporates double excitations into the response space for a more precise description of excited states. With the help of its formal framework, core-hole relaxation for accurate X-ray absorption prediction can be also done readily. Notably, MRSF-TDDFT achieves an equal footing description of ground and excited states, with its dual-reference framework ensuring a balanced treatment of both dynamic and nondynamic electron correlations for high accuracy.In predictive tasks, such as calculating adiabatic singlet-triplet gaps, MRSF-TDDFT achieves accuracy comparable to that of far more computationally expensive coupled-cluster methods. The missing doubly excited state of H2 observed in TDDFT is accurately captured by MRSF-TDDFT, which also reproduces the correct asymptotic bond-breaking potential energy surface. Furthermore, the CoIns of butadiene, missed by both TDDFT and Complete-Active Space Self-Consistent Field (CASSCF) methods, are successfully recovered by MRSF-TDDFT, achieving results consistent with high-level theories, an important aspect for successful study of photochemical processes. Additionally, the common issue of CASSCF overestimating bright states (ionic states) due to the missing dynamic correlation is effectively resolved by MRSF-TDDFT.Despite its numerous advancements, MRSF-TDDFT retains the computational efficiency of conventional TDDFT, making it a practical tool for routine calculations. In addition, it has been demonstrated that the prediction accuracy of MRSF-TDDFT can be further enhanced through the development of tailor-made exchange-correlation functionals, paving the way for the creation of new, specialized functionals. Consequently, with its remarkable versatility, high accuracy, and computational practicality, this innovative method significantly expands scientists' ability to explore complex molecular behaviors and design advanced materials, including applications in photobiology, organic LEDs, photovoltaics, and spintronics, to name a few.

Temperature Controlled Decay and Pendulum Dynamics of Green Fluorescent Protein (GFP) Chromophore

The excited-state dynamics of the GFP chromophore, HBDI- (anionic p-hydroxybenzylidene-2,3-dimethylimidazolinone), were investigated through a combination of theoretical nonadiabatic molecular dynamics (NAMD) simulations and femtosecond transient absorption spectroscopy (fs-TA). The NAMD simulations revealed that the primary dynamics in excited states involve the formation of a P-twisted intermediate (S1min,P), which undergoes pendulum-like oscillations with respect to ϕ = 90°. This motion serves as a reservoir for the excited-state population and the primary source of fluorescence. Rather than a direct channel from the major S1min,P, a coordinated pathway of S1min,P → S1min → S1min,I → S0 is responsible for the decay to the ground state, emphasizing the importance of planar intermediate (S1min) formation. The experimental fs-TA spectra confirmed these dynamics, revealing three distinct time scales (340-470 fs, 1.4 ps, and 8.3 ps), corresponding to the formation of S1min,P and its decay governed by the coordinated pathway. At low temperatures, the coordinated decay pathway is suppressed, leading to prolonged fluorescence lifetimes, consistent with low-temperature experimental results. This study presents a new model for the excited-state dynamics of GFP chromophore, suggesting that pendulum motion and the coordinated decay pathway play a crucial role in regulating fluorescence intensity.

OpenQP: A Quantum Chemical Platform Featuring MRSF-TDDFT with an Emphasis on Open-Source Ecosystem

The OpenQP (Open Quantum Platform) is a new open-source quantum chemistry library developed to tackle sustainability and interoperability challenges in the field of computational chemistry. OpenQP provides various popular quantum chemical theories as autonomous modules such as energy and gradient calculations of HF, DFT, TDDFT, SF-TDDFT, and MRSF-TDDFT, thereby allowing easy interconnection with third-party software. A scientifically notable feature is the innovative mixed-reference spin-flip time-dependent density functional theory (MRSF-TDDFT) and its customized exchange-correlation functionals such as the DTCAM series of VAEE, XI, XIV, AEE, and VEE, which significantly expand the applicability scope of DFT and TDDFT. OpenQP also supports parallel execution and is optimized with BLAS and LAPACK for high performance. Future enhancements such as extended Koopman's theorem (EKT)-MRSF-TDDFT and spin-orbit coupling (SOC)-MRSF-TDDFT will further expand OpenQP's capabilities. Additionally, a Python wrapper PyOQP is provided that performs tasks such as geometry optimization, conical intersection searches, and nonadiabatic coupling calculations, among others, by prototyping the modules of the OpenQP library in combination with third-party libraries. Overall, OpenQP aligns with modern trends in high-performance scientific software development by offering flexible prototyping and operation while retaining the performance benefits of compiled languages like Fortran and C. They enhance the sustainability and interoperability of quantum chemical software, making OpenQP a crucial platform for accelerating the development of advanced quantum theories like MRSF-TDDFT.

UMRSF-TDDFT: Unrestricted Mixed-Reference Spin-Flip-TDDFT

An unrestricted version of Mixed-Reference Spin-Flip Time-Dependent Density Functional Theory (UMRSF-TDDFT) was developed based on unrestricted Kohn-Sham orbitals (UKS) with a new molecular orbital (MO) reordering scheme. Additionally, a simple yet accurate method for estimating ⟨S2⟩ expectation values was devised. UMRSF-TDDFT was benchmarked against cases where DFT, TDDFT, and SF-TDDFT traditionally fail to provide accurate descriptions. In an application to the ground and excited states of a Be atom, UMRSF-TDDFT successfully recovers the degenerate states, with its energies slightly reduced compared to its RO counterpart, due to the additional variational flexibility of UKS. A clear difference between UMRSF and U-SF-TDDFT is evident in the bond breaking of the hydrogen fluoride system, as the latter misses an important configuration. In the case of the Jahn-Teller distortion of trimethylenemethane (TMM), the relative singlet energy compared to the triplet is lower by 0.1 and 0.2 eV for UMRSF and U-SF-TDDFT, respectively, than that of MRSF-TDDFT. The reduction in UMRSF energy is attributed to spatial orbital relaxations, whereas the reduction in U-SF-TDDFT energy results from spin contamination. Overall, the additional orbital relaxations afforded by unrestricted Kohn-Sham (UKS) orbitals in UMRSF-TDDFT lead to lower total system energies compared to their restricted open-shell counterparts. This enhancement adds a practical and accurate quantum chemical theory to the existing RO variant for addressing challenging systems where traditional quantum theories suffer.

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.

High-performance strategies for the recent MRSF-TDDFT in GAMESS

Multiple ERI (Electron Repulsion Integral) tensor contractions (METC) with several matrices are ubiquitous in quantum chemistry. In response theories, the contraction operation, rather than ERI computations, can be the major bottleneck, as its computational demands are proportional to the multiplicatively combined contributions of the number of excited states and the kernel pre-factors. This paper presents several high-performance strategies for METC. Optimal approaches involve either the data layout reformations of interim density and Fock matrices, the introduction of intermediate ERI quartet buffer, and loop-reordering optimization for a higher cache hit rate. The combined strategies remarkably improve the performance of the MRSF (mixed reference spin flip)-TDDFT (time-dependent density functional theory) by nearly 300%. The results of this study are not limited to the MRSF-TDDFT method and can be applied to other METC scenarios.