Adaptive time steps in trajectory surface hopping simulations

Trajectory surface hopping (TSH) simulations are often performed in combination with active-space multi-reference configuration interaction (MRCI) treatments. Technical problems may arise in such simulations if active and inactive orbitals strongly mix and switch in some particular regions. We propose to use adaptive time steps when such regions are encountered in TSH simulations. For this purpose, we present a computational protocol that is easy to implement and increases the computational effort only in the critical regions. We test this procedure through TSH simulations of a GFP chromophore model (OHBI) and a light-driven rotary molecular motor (F-NAIBP) on semiempirical MRCI potential energy surfaces, by comparing the results from simulations with adaptive time steps to analogous ones with constant time steps. For both test molecules, the number of successful trajectories without technical failures rises significantly, from 53% to 95% for OHBI and from 25% to 96% for F-NAIBP. The computed excited-state lifetime remains essentially the same for OHBI and increases somewhat for F-NAIBP, and there is almost no change in the computed quantum efficiency for internal rotation in F-NAIBP. We recommend the general use of adaptive time steps in TSH simulations with active-space CI methods because this will help to avoid technical problems, increase the overall efficiency and robustness of the simulations, and allow for a more complete sampling

Photodynamics of Schiff Base Salicylideneaniline: Trajectory Surface-Hopping Simulations

We report a computational study on the photochemistry of the prototypical aromatic Schiff base salicylideneaniline in the gas phase using static electronic structure calculations (TDDFT, OM2/MRCI) and surface-hopping dynamics simulations (OM2/MRCI). Upon photoexcitation of the most stable cis-enol tautomer into the bright S1 state, we find an ultrafast excited-state proton transfer that is complete within tens of femtoseconds, without any C═N double bond isomerization. The internal conversion of the resulting S1 cis-keto species is initiated by an out-of-plane motion around the C–C single bond, which guides the molecule toward a conical intersection that provides an efficient deactivation channel to the ground state. We propose that the ease of this C–C single bond rotation regulates fluorescence quenching and photocoloration in condensed-phase environments. In line with previous work, we find the S1 cis-keto conformer to be responsible for fluorescence, especially in rigid surroundings. The S0 cis-keto species is a transient photoproduct, while the stable S0 trans-keto photoproduct is responsible for photochromism. The trajectory calculations yield roughly equal amounts of the S0 cis-enol and trans-keto photoproducts. Methodologically, full-dimensional nonadiabatic dynamics simulations are found necessary to capture the preferences among competitive channels and to gain detailed mechanistic insight into Schiff base photochemistry

Semiempirical Quantum-Chemical Orthogonalization-Corrected Methods: Theory, Implementation, and Parameters

Semiempirical orthogonalization-corrected methods (OM1, OM2, and OM3) go beyond the standard MNDO model by explicitly including additional interactions into the Fock matrix in an approximate manner (Pauli repulsion, penetration effects, and core–valence interactions), which yields systematic improvements both for ground-state and excited-state properties. In this Article, we describe the underlying theoretical formalism of the OMx methods and their implementation in full detail, and we report all relevant OMx parameters for hydrogen, carbon, nitrogen, oxygen, and fluorine. For a standard set of mostly organic molecules commonly used in semiempirical method development, the OMx results are found to be superior to those from standard MNDO-type methods. Parametrized Grimme-type dispersion corrections can be added to OM2 and OM3 energies to provide a realistic treatment of noncovalent interaction energies, as demonstrated for the complexes in the S22 and S66×8 test sets

Developmental Splicing Deregulation in Leukodystrophies Related to EIF2B Mutations

Leukodystrophies (LD) are rare inherited disorders that primarily affect the white matter (WM) of the central nervous system. The large heterogeneity of LD results from the diversity of the genetically determined defects that interfere with glial cells functions. Astrocytes have been identified as the primary target of LD with cystic myelin breakdown including those related to mutations in the ubiquitous translation initiation factor eIF2B. EIF2B is involved in global protein synthesis and its regulation under normal and stress conditions. Little is known about how eIF2B mutations have a major effect on WM. We performed a transcriptomic analysis using fibroblasts of 10 eIF2B-mutated patients with a severe phenotype and 10 age matched patients with other types of LD in comparison to control fibroblasts. ANOVA was used to identify genes that were statistically significantly differentially expressed at basal state and after ER-stress. The pattern of differentially expressed genes between basal state and ER-stress did not differ significantly among each of the three conditions. However, 70 genes were specifically differentially expressed in eIF2B-mutated fibroblasts whatever the stress conditions tested compared to controls, 96% being under-expressed. Most of these genes were involved in mRNA regulation and mitochondrial metabolism. The 13 most representative genes, including genes belonging to the Heterogeneous Nuclear Ribonucleoprotein (HNRNP) family, described as regulators of splicing events and stability of mRNA, were dysregulated during the development of eIF2B-mutated brains. HNRNPH1, F and C mRNA were over-expressed in foetus but under-expressed in children and adult brains. The abnormal regulation of HNRNP expression in the brain of eIF2B-mutated patients was concomitant with splicing dysregulation of the main genes involved in glial maturation such as PLP1 for oligodendrocytes and GFAP in astrocytes. These findings demonstrate a developmental deregulation of splicing events in glial cells that is related to abnormal production of HNRNP, in eIF2B-mutated brains

Nonequilibrium H/D Isotope Effects from Trajectory-Based Nonadiabatic Dynamics

Ground-state equilibrium kinetic isotope effects can be treated well in the framework of transition state theory, whereas excited-state nonequilibrium isotope effects are theoretically less explored. In this article we show for the first time that trajectory-based nonadiabatic dynamics simulations are able to reproduce experimental values for nonequilibrium H/D isotope effects in excited-state processes. We use high-level electronic structure calculations (MS-CASPT2, DFT/MRCI, and TDDFT) and full-dimensional OM2/MRCI-based nonadiabatic dynamics simulations to study the ultrafast intramolecular excited-state proton transfer (ESIPT) and the subsequent deactivation of 7-(2-pyridyl)indole (7PyIn) and its deuterated analogue (7PyIn-D). We evaluate a total of 1367 surface-hopping trajectories to establish the differences in the dynamical behavior of 7PyIn and 7PyIn-D. The computed H/D isotope effects for ESIPT and excited-state decay are consistent with recent experimental results from femtosecond pump–probe resonance-enhanced multiphoton ionization spectroscopy. We also analyze the influence of temperature fluctuations in the initially prepared sample on the photodynamics of 7PyIn and 7PyIn-D

Nonadiabatic dynamics simulations of photoexcited urocanic acid

Urocanic acid (UA) is a UV filter found in human skin, which has been linked to photoimmunosuppression and the formation of skin cancer. Its UV-light-induced photoisomerization and radiationless deactivation mechanisms have been addressed previously by static calculations. In this paper, we present nonadiabatic trajectory-surface-hopping dynamics simulations of photoexcited UA using the semiempirical OM2/MRCI methodology and an adaptive-timestep algorithm. We have simulated almost 6000 trajectories, each for a simulation time of 1.6 ps, covering the entire conformational space of the E and Z isomers of both possible tautomers of the isolated neutral form of UA (overall 32 conformers). Initial conditions for the excited-state dynamics were obtained from 1 ns ground-state dynamics simulations. We find that UA has an ultrashort excited-state lifetime, which is due to ultrafast radiationless excited-state deactivation driven by E↔Z photoisomerization and excited-state intramolecular proton-transfer (ESIPT) processes. The computed S1 excited-state lifetimes for the E and Z isomers of the N1H and N3H tautomers range from 271 to 506 fs. The photoisomerization quantum yield is calculated to be 43% (32%) for the combined E (Z) isomers of both tautomers. The shorter lifetime and the lower photoisomerization quantum yield of the Z isomers can be rationalized by the larger number of available excited-state deactivation processes: the Z isomers can undergo ESIPT and photoisomerization, whereas the E isomers can only deactivate via the latter process. The intramolecular hydrogen bond that is present in many Z conformers can prevent successful photoisomerization to an E isomer. We find no evidence for an excitation-energy-dependent quantum yield for photoisomerization (EEDQY-PI) in isolated (E)-UA, which has previously been detected spectroscopically in aqueous solution. However, we do find an EEDQY-PI as well as a complementary excitation-energy-dependent quantum yield for ESIPT (EEDQY-ESIPT) for the N1H-Z isomers, which demonstrates the competition of the photoisomerization and ESIPT processes. The present comprehensive study lays the groundwork for future photodynamics simulations of UA in the aqueous phase

Ultrafast action chemistry in slow motion: atomistic description of the excitation and fluorescence processes in an archetypal fluorescent protein

We report quantum mechanical/molecular mechanical non-adiabatic molecular dynamics simulations on the electronically excited state of green fluorescent protein mutant S65T/H148D. We examine the driving force of the ultrafast (τ < 50 fs) excited-state proton transfer unleashed by absorption in the A band at 415 nm and propose an atomistic description of the two dynamical regimes experimentally observed [Stoner Ma et al., J. Am. Chem. Soc., 2008, 130, 1227]. These regimes are explained in terms of two sets of successive dynamical events: first the proton transfers quickly from the chromophore to the acceptor Asp148. Thereafter, on a slower time scale, there are geometrical changes in the cavity of the chromophore that involve the distance between the chromophore and Asp148, the planarity of the excited-state chromophore, and the distance between the chromophore and Tyr145. We find two different non-radiative relaxation channels that are operative for structures in the reactant region and that can explain the mismatch between the decay of the emission of A* and the rise of the emission of I*, as well as the temperature dependence of the non-radiative decay rate