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Cycloheptatrienyl (tropyl) molecules are representative non-alternant hydrocarbons that offer interesting chemistry because of their unique structures and properties. However, there have been a limited number of polycyclic aromatic tropyl cations and radicals reported in the literature. Herein, we report the synthesis of a series of azahomocorannulene derivatives, where the key reactions are a 1,3-dipolar cycloaddition of polycyclic aromatic azomethine ylides with dibenzotropone and a subsequent palladium-catalyzed cyclization. X-ray diffraction analysis revealed that the obtained azahomocorannulenyl cation and radical adopt planar structures and exhibit unique packing structures. Their electronic and optical properties were investigated experimentally and theoretically to reveal their aromatic character.
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Over the past 3.5 billion years of evolution, enzymes have adopted a myriad of conformations to suit life on earth. However, torsional angles of proteins have settled into limited zones of energetically favorable dihedrals observed in Ramachandran plots. Areas outside said zones are believed to be disallowed to all amino acids, except glycine, due to steric hindrance. Triosephosphate isomerase (TIM), a homodimer with a catalytic rate approaching the diffusion limit, contains an active site lysine residue (K13) with dihedrals within the fourth quadrant (Φ = +51/Ψ = -143). Both the amino acid and the dihedral angles are conserved across all species of TIM and known crystal structures regardless of ligand. Only crystal structures of the engineered monomeric version (1MSS) show accepted ß-sheet dihedral values of Φ = -135/Ψ = +170 but experiments show a 1000-fold loss in activity. Based on these results, we hypothesized that adopting the unfavorable torsion angle for K13 contributes to catalysis. Using both, computational and experimental approaches, four residues that interact with K13 (N11, M14, E97, and Q64) were mutated to alanine. In silico molecular dynamics (MD) simulations were performed using 2JK2 unliganded human TIM as a starting structure. Ramachandran plots, containing K13 dihedral values reveal full or partial loss of disallowed zone angles. N11A showed no detectable catalytic activity and lost the unfavorable K13 dihedral angles across four separate force fields during simulation while all other mutants plus wild type retained activity and retained the conserved K13 dihedral angles.
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Proteínas , Triose-Fosfato Isomerase , Humanos , Triose-Fosfato Isomerase/genética , Triose-Fosfato Isomerase/química , Conformação Proteica , Proteínas/química , Ligantes , AminoácidosRESUMO
Brown carbon (BrC) is involved in atmospheric light absorption and climate forcing and can cause adverse health effects. Understanding the formation mechanisms and molecular structure of BrC is of key importance in developing strategies to control its environment and health impact. Structure determination of BrC is challenging, due to the lack of experiments providing molecular fingerprints and the sheer number of molecular candidates with identical mass. Suggestions based on chemical intuition are prone to errors due to the inherent bias. We present an unbiased algorithm, using graph-based molecule generation and machine learning, which can identify all molecular structures of compounds involved in biomass burning and the composition of BrC. We apply this algorithm to C12H12O7, a light-absorbing "test case" molecule identified in chamber experiments on the aqueous photo-oxidation of syringol, a prevalent marker in wood smoke. Of the 260 million molecular graphs, the algorithm leaves only 36,518 (0.01%) as viable candidates matching the spectrum. Although no unique molecular structure is obtained from only a chemical formula and a UV/vis absorption spectrum, we discuss further reduction strategies and their efficacy. With additional data, the method can potentially more rapidly identify isomers extracted from lab and field aerosol particles without introducing human bias.
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Carbono , Intuição , Aerossóis , Biomassa , Humanos , Aprendizado de MáquinaRESUMO
Methylene blue [3,7-Bis(di-methylamino) phenothiazin-5-ium chloride] is a phenothiazine dye with applications as a sensitizer for photodynamic therapy, photoantimicrobials, and dye-sensitized solar cells. Time-dependent density functional theory (TDDFT), based on (semi)local and global hybrid exchange-correlation functionals, fails to correctly describe its spectral features due to known limitations for describing optical excitations of π-conjugated systems. Here, we use TDDFT with a non-empirical optimally tuned range-separated hybrid functional to explore the optical excitations of gas phase and solvated methylene blue. We compute solvated configurations using molecular dynamics and an iterative procedure to account for explicit solute polarization. We rationalize and validate that by extrapolating the optimized range separation parameter to an infinite amount of solvating molecules, the optical gap of methylene blue is well described. Moreover, this method allows us to resolve contributions from solvent-solute intermolecular interactions and dielectric screening. We validate our results by comparing them to first-principles calculations based on the GW+Bethe-Salpeter equation approach and experiment. Vibronic calculations using TDDFT and the generating function method account for the spectra's subbands and bring the computed transition energies to within 0.15 eV of the experimental data. This methodology is expected to perform equivalently well for describing solvated spectra of π-conjugated systems.
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TURBOMOLE is a collaborative, multi-national software development project aiming to provide highly efficient and stable computational tools for quantum chemical simulations of molecules, clusters, periodic systems, and solutions. The TURBOMOLE software suite is optimized for widely available, inexpensive, and resource-efficient hardware such as multi-core workstations and small computer clusters. TURBOMOLE specializes in electronic structure methods with outstanding accuracy-cost ratio, such as density functional theory including local hybrids and the random phase approximation (RPA), GW-Bethe-Salpeter methods, second-order Møller-Plesset theory, and explicitly correlated coupled-cluster methods. TURBOMOLE is based on Gaussian basis sets and has been pivotal for the development of many fast and low-scaling algorithms in the past three decades, such as integral-direct methods, fast multipole methods, the resolution-of-the-identity approximation, imaginary frequency integration, Laplace transform, and pair natural orbital methods. This review focuses on recent additions to TURBOMOLE's functionality, including excited-state methods, RPA and Green's function methods, relativistic approaches, high-order molecular properties, solvation effects, and periodic systems. A variety of illustrative applications along with accuracy and timing data are discussed. Moreover, available interfaces to users as well as other software are summarized. TURBOMOLE's current licensing, distribution, and support model are discussed, and an overview of TURBOMOLE's development workflow is provided. Challenges such as communication and outreach, software infrastructure, and funding are highlighted.
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The absorption spectra of naphthalene, anthracene, pentacene and pyrene in the ultraviolet-visible (UV-Vis) range have been simulated by using an efficient real-time generating function method that combines calculated adiabatic electronic excitation energies with vibrational energies of the excited states. The vertical electronic excitation energies have been calculated at the density functional theory level using the PBE0 functional and at the second-order approximate coupled-cluster level (CC2). The absorption spectra have been calculated at the PBE0 level for the studied molecules and at the CC2 level for naphthalene. The transition probabilities between vibrationally resolved states were calculated by using the real-time generating function method employing the full Duschinsky formalism. The absorption spectrum for naphthalene calculated at the PBE0 and CC2 levels agrees well with the experimental one after the simulated spectra have been blue-shifted by 0.48 eV and 0.12 eV at the PBE0 and CC2 level, respectively. The absorption spectra for anthracene, pentacene and pyrene simulated at the PBE0 level agree well with the experimental ones when they are shifted by 0.49 eV, 0.57 eV and 0.46 eV, respectively. The strongest transitions of the main vibrational bands have been assigned.
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The use of light as an external trigger to change ligand shape and as a result its bioactivity, allows the probing of pharmacologically relevant systems with spatiotemporal resolution. A hetero-stilbene lead resulting from the screening of a compound that was originally designed as kinase inhibitor served as a starting point for the design of photoswitchable sirtuin inhibitors. Because the original stilbenoid structure exerted unfavourable photochemical characteristics it was remodelled to its heteroarylic diazeno analogue. By this intramolecular azologization, the shape of the molecule was left unaltered, whereas the photoswitching ability was improved. As anticipated, the highly analogous compound showed similar activity in its thermodynamically stable stretched-out (E)-form. Irradiation of this isomer triggers isomerisation to the long-lived (Z)-configuration with a bent geometry causing a considerably shorter end-to-end distance. The resulting affinity shifts are intended to enable real-time photomodulation of sirtuins in vitro.
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Aqueous methylglyoxal chemistry has often been implicated as an important source of oligomers in atmospheric aerosol. Here we report on chemical analysis of brown carbon aerosol particles collected from cloud cycling/photolysis chamber experiments, where gaseous methylglyoxal and methylamine interacted with glycine, ammonium, or methylammonium sulfate seed particles. Eighteen N-containing oligomers were identified in the particulate phase by liquid chromatography/diode array detection/electrospray ionization high-resolution quadrupole time-of-flight mass spectrometry. Chemical formulas were determined and, for 6 major oligomer products, MS2 fragmentation spectra were used to propose tentative structures and mechanisms. Electronic absorption spectra were calculated for six tentative product structures by an ab initio second order algebraic-diagrammatic-construction/density functional theory approach. For five structures, matching calculated and measured absorption spectra suggest that they are dominant light-absorbing species at their chromatographic retention times. Detected oligomers incorporated methylglyoxal and amines, as expected, but also pyruvic acid, hydroxyacetone, and significant quantities of acetaldehyde. The finding that â¼80% (by mass) of detected oligomers contained acetaldehyde, a methylglyoxal photolysis product, suggests that daytime methylglyoxal oligomer formation is dominated by radical addition mechanisms involving CH3CO*. These mechanisms are evidently responsible for enhanced browning observed during photolytic cloud events.
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Nitrogênio , Aldeído Pirúvico , Aerossóis , Cromatografia Gasosa-Espectrometria de Massas , FotóliseRESUMO
To understand how substituents can be used to increase the quantum yield of photochemical electrocyclic ring-closing of the Z-hexa-1,3,5-triene (HT) photoswitch forming cyclohexadiene (CHD), we investigate the S1 photo dynamics of HT and its derivatives 2,5-dimethyl-HT (DMHT), 2-isopropyl-5-methyl-HT (2,5-IMHT), 1-isopropyl-4-methyl-HT (1,4-IMHT), and 2,5-diisopropyl-HT (DIHT) using time-dependent density functional theory surface hopping dynamics. We report detailed photoproduct distributions, formation mechanisms, branching ratios, and wavelength-dependent product quantum yields. Most products have been confirmed experimentally and include all-trans HT derivatives, cyclopropanes, cyclobutenes, cyclopentene, cyclohexadienes, and bicyclic compounds. Regarding CHD formation, we find that for the 2,5-substituted derivatives DMHT, 2,5-IMHT, and DIHT, the branching ratios increase with increasing size of the substituents. In contrast the branching ratios of the E/Z-isomerization decrease with increasing size of the substituents. Due to steric interactions, increasing the size of the substituents increases the amount of gZg rotamers in the ground state, which are prone to CHD formation and have lower E/Z-isomerization probability. Furthermore, we find [1,4], [1,5], and [1,6]-sigmatropic hydrogen shift reactions occurring at large percentages (5% to 15%); for sterical reasons these reactions stem from tZg conformers. DIHT shows the lowest percentage of side product formation among the 2,5-substituted molecules and highest CHD branching ratio; its CHD quantum yield can be increased up to more than 64%, by excitation of DIHT on the red tail of its absorption spectrum, whereas the Z/E-isomerization is reduced below 5% and side reactions practically vanish. This makes DIHT the best candidate for applications in molecular switches.
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To investigate the role of tachysterol in the photophysical/photochemical regulation of vitamin D photosynthesis, we studied its electronic absorption properties and excited state dynamics using time-dependent density functional theory (TDDFT), second-order approximate coupled cluster theory (CC2), and non-adiabatic surface hopping molecular dynamics in the gas phase. In excellent agreement with experiments, the simulated electronic spectrum shows a broad absorption band with a remarkably higher extinction coefficient than the other vitamin D photoisomers provitamin D, lumisterol, and previtamin D. The broad band arises from the spectral overlap of four different ground state rotamers. After photoexcitation, the first excited singlet state (S1) decays with a lifetime of 882 fs. The S1 dynamics is characterized by a strong twisting of the central double bond. In 96% of all trajectories this is followed by unreactive relaxation to the ground state near a conical intersection. The double-bond twisting in the chemically unreactive trajectories induces a strong interconversion between the different rotamers. In 2.3% of the trajectories we observed [1,5]-sigmatropic hydrogen shift forming the partly deconjugated toxisterol D1. 1.4% previtamin D formation is observed via hula-twist double bond isomerization. In both reaction channels, we find a strong dependence between photoreactivity and dihedral angle conformation: hydrogen shift only occurs in cEc and cEt rotamers and double bond isomerization occurs mainly in cEc rotamers. Hence, our study confirms the previously formed hypothesis that cEc rotamers are more prone to previtamin D formation than other isomers. In addition, we also observe the formation of a cyclobutene-toxisterol in the hot ground state in 3 trajectories (0.7%). Due to its large extinction coefficient and mostly unreactive behavior, tachysterol acts mainly as a Sun shield suppressing previtamin D formation. Tachysterol shows stronger toxisterol formation than previtamin D and can thus be seen as the major degradation route of vitamin D. Absorption of low energy ultraviolet light by the cEc rotamer can lead to previtamin D formation. In addition, the cyclobutene-toxisterol, which possibly reacts thermally to previtamin D, is also preferably formed at long wavelengths. These two mechanisms are consistent with the wavelength dependent photochemistry found in experiments. Our study reinforces a recent hypothesis that tachysterol constitutes a source of previtamin D when only low energy ultraviolet light is available, as it is the case in winter or in the morning and evening hours of the day.
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Colecalciferol/análogos & derivados , Fotossíntese , Vitamina D/biossíntese , Colecalciferol/metabolismo , Simulação de Dinâmica Molecular , Processos FotoquímicosRESUMO
We have reinvestigated the excited state dynamics of cyclohexa-1,3-diene (CHD) with time-resolved photoelectron spectroscopy and fewest switches surface hopping molecular dynamics based on linear response time-dependent density functional theory after excitation to the lowest lying ππ* (1B) state. The combination of both theory and experiment revealed several new results: First, the dynamics progress on one single excited state surface. After an incubation time of 35 ± 10 fs on the excited state, the dynamics proceed to the ground state in an additional 60 ± 10 fs, either via a conrotatory ring-opening to hexatriene or back to the CHD ground state. Moreover, ring-opening predominantly occurs when the wavepacket crosses the region of strong nonadiabatic coupling with a positive velocity in the bond alternation coordinate. After 100 fs, trajectories remaining in the excited state must return to the CHD ground state. This extra time delay induces a revival of the photoelectron signal and is an experimental confirmation of the previously formulated model of two parallel reaction channels with distinct time constants. Finally, our simulations suggest that after the initially formed cis-Z-cis HT rotamer the trans-Z-trans isomer is formed, before the thermodynamical equilibrium of three possible rotamers is reached after 1 ps.
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Due to its favorable computational efficiency, time-dependent (TD) density functional theory (DFT) enables the prediction of electronic spectra in a high-throughput manner across chemical space. Its predictions, however, can be quite inaccurate. We resolve this issue with machine learning models trained on deviations of reference second-order approximate coupled-cluster (CC2) singles and doubles spectra from TDDFT counterparts, or even from DFT gap. We applied this approach to low-lying singlet-singlet vertical electronic spectra of over 20 000 synthetically feasible small organic molecules with up to eight CONF atoms. The prediction errors decay monotonously as a function of training set size. For a training set of 10 000 molecules, CC2 excitation energies can be reproduced to within ±0.1 eV for the remaining molecules. Analysis of our spectral database via chromophore counting suggests that even higher accuracies can be achieved. Based on the evidence collected, we discuss open challenges associated with data-driven modeling of high-lying spectra and transition intensities.
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Nanodiscs are binary discoidal complexes of a phospholipid bilayer circumscribed by belt-like helical scaffold proteins. Using coarse-grained and all-atom molecular dynamics simulations, we explore the stability, size, and structure of nanodiscs formed between the N-terminal domain of apolipoprotein E3 (apoE3-NT) and variable number of 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) molecules. We study both parallel and antiparallel double-belt configurations, consisting of four proteins per nanodisc. Our simulations predict nanodiscs containing between 240 and 420 DMPC molecules to be stable. The antiparallel configurations exhibit an average of 1.6 times more amino acid interactions between protein chains and 2 times more ionic contacts, compared to the parallel configuration. With one exception, DMPC order parameters are consistently larger in the antiparallel configuration than in the parallel one. In most cases, the root mean square deviation of the positions of the protein backbone atoms is smaller in the antiparallel configuration. We further report nanodisc size, thickness, radius of gyration, and solvent accessible surface area. Combining all investigated parameters, we hypothesize the antiparallel protein configuration leading to more stable and more rigid nanodiscs than the parallel one.
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Bicamadas Lipídicas , Simulação de Dinâmica Molecular , Apolipoproteína E3 , Bicamadas Lipídicas/química , Dimiristoilfosfatidilcolina/química , Fosfolipídeos/química , ProteínasRESUMO
Adiabatic nuclear potential energy surfaces (PESs) defined via the Born-Oppenheimer (BO) approximation are a fundamental concept underlying chemical reactivity theory. For a wide range of excited-state phenomena such as radiationless decay, energy and charge transfer, and photochemical reactions, the BO approximation breaks down due to strong couplings between two or more BO PESs. Non-adiabatic molecular dynamics (NAMD) is the method of choice to model these processes. We review new developments in quantum-classical dynamics, analytical derivative methods, and time-dependent density functional theory (TDDFT) which have lead to a dramatic expansion of the scope of ab initio NAMD simulations for molecular systems in recent years. We focus on atom-centered Gaussian basis sets allowing highly efficient simulations for molecules and clusters, especially in conjunction with hybrid density functionals. Using analytical derivative techniques, forces and derivative couplings can be obtained with machine precision in a given basis set, which is crucial for accurate and stable dynamics. We illustrate the performance of surface-hopping TDDFT for photochemical reactions of the lowest singlet excited states of cyclohexadiene, several vitamin D derivatives, and a bicyclic cyclobutene. With few exceptions, the calculated quantum yields and excited state lifetimes agree qualitatively with experiment. For systems with â¼50 atoms, the present Turbomole implementation allows NAMD simulations with 0.2-0.4 ns total simulation time using hybrid density functionals and polarized double zeta valence basis sets on medium-size compute clusters. We close by discussing open problems and future directions.
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We present a method to simulate ultrafast pump-probe time-resolved circular dichroism (TRCD) spectra based on time-dependent density functional theory trajectory surface hopping. The method is applied to simulate the TRCD spectrum along the photoinduced ring-opening of provitamin D. Simulations reveal that the initial decay of the signal is due to excited state relaxation, forming the rotationally flexible previtamin D. We further show that oscillations in the experimental TRCD spectrum arise from isomerizations between previtamin D rotamers with different chirality, which are associated with the helical conformation of the triene unit. We give a detailed description of the formation dynamics of different rotamers, playing a key role in the natural regulation vitamin D photosynthesis. Going beyond the sole extraction of decay rates, simulations greatly increase the amount of information that can be retrieved from ultrafast TRCD, making it a sensitive tool to unravel details in the sub-picosecond dynamics of photoinduced chirality changes.
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We present a method to simulate ultrafast pump-probe time-resolved circular dichroism (TRCD) spectra based on time-dependent density functional theory trajectory surface hopping. The method is applied to simulate the TRCD spectrum along the photoinduced ring-opening of provitamin D. Simulations reveal that the initial decay of the signal is due to excited state relaxation, forming the rotationally flexible previtamin D. We further show that oscillations in the experimental TRCD spectrum arise from isomerizations between previtamin D rotamers with different chirality, which are associated with the helical conformation of the triene unit. We give a detailed description of the formation dynamics of different rotamers, playing a key role in the natural regulation of vitamin D photosynthesis. Going beyond the sole extraction of decay rates, simulations greatly increase the amount of information that can be retrieved from ultrafast TRCD, making it a sensitive tool to unravel details in the subpicosecond dynamics of photoinduced chirality changes.
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Nanodiscs are binary discoidal complexes of a phospholipid bilayer circumscribed by belt-like helical scaffold proteins. Using coarse-grained and all-atom molecular dynamics simulations, we explore the stability, size, and structure of nanodiscs formed between the N-terminal domain of apolipoprotein E3 (apoE3-NT) and variable number of 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) molecules. We study both parallel and antiparallel double-belt configurations, consisting of four proteins per nanodisc. Our simulations predict nanodiscs containing between 240 and 420 DMPC molecules to be stable. The antiparallel configurations exhibit an average of 1.6 times more amino acid interactions between protein chains and 2 times more ionic contacts, compared to the parallel configuration. With one exception, DMPC order parameters are consistently larger in the antiparallel configuration than in the parallel one. In most cases, the root mean square deviation of the positions of the protein backbone atoms is smaller in the antiparallel configuration. We further report nanodisc size, thickness, radius of gyration, and solvent accessible surface area. Combining all investigated parameters, we hypothesize the antiparallel protein configuration leading to more stable and more rigid nanodiscs than the parallel one.
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TURBOMOLE is a highly optimized software suite for large-scale quantum-chemical and materials science simulations of molecules, clusters, extended systems, and periodic solids. TURBOMOLE uses Gaussian basis sets and has been designed with robust and fast quantum-chemical applications in mind, ranging from homogeneous and heterogeneous catalysis to inorganic and organic chemistry and various types of spectroscopy, light-matter interactions, and biochemistry. This Perspective briefly surveys TURBOMOLE's functionality and highlights recent developments that have taken place between 2020 and 2023, comprising new electronic structure methods for molecules and solids, previously unavailable molecular properties, embedding, and molecular dynamics approaches. Select features under development are reviewed to illustrate the continuous growth of the program suite, including nuclear electronic orbital methods, Hartree-Fock-based adiabatic connection models, simplified time-dependent density functional theory, relativistic effects and magnetic properties, and multiscale modeling of optical properties.
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Simulating vibrationally resolved electronic spectra of anharmonic systems, especially those involving double-well potential energy surfaces, often requires expensive quantum dynamics methods. Here, we explore the applicability and limitations of the recently proposed single-Hessian thawed Gaussian approximation for the simulation of spectra of systems with double-well potentials, including 1,2,4,5-tetrafluorobenzene, ammonia, phosphine, and arsine. This semiclassical wavepacket approach is shown to be more robust and to provide more accurate spectra than the conventional harmonic approximation. Specifically, we identify two cases in which the Gaussian wavepacket method is especially useful due to the breakdown of the harmonic approximation: (i) when the nuclear wavepacket is initially at the top of the potential barrier but delocalized over both wells, e.g., along a low-frequency mode, and (ii) when the wavepacket has enough energy to classically go over the low potential energy barrier connecting the two wells. The method is efficient and requires only a single classical ab initio molecular dynamics trajectory, in addition to the data required to compute the harmonic spectra. We also present an improved algorithm for computing the wavepacket autocorrelation function, which guarantees that the evaluated correlation function is continuous for arbitrary size of the time step.
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We investigate the photodynamics of vitamin D derivatives by a fully analytical implementation of the linear response time-dependent density functional theory surface hopping method (LR-TDDFT-SH). Our study elucidates the dynamics of the processes involved in vitamin D formation at the molecular level and with femtosecond resolution. We explain the major experimental findings and provide new insights that cannot directly be obtained from experiments: firstly, we investigate the dynamics of the photoinduced ring-opening of provitamin D (Pro) and cyclohexadiene (CHD) and the subsequent rotational isomerization. In agreement with recent experiments and CC2 calculations, only the bright S(1) state is involved in the ring-opening reaction. Our calculations confirm the experimentally reported 5 : 1 ratio between the excited state lifetimes of Pro and CHD. The longer lifetimes of Pro are attributed to steric constraints of the steroid skeleton and to temperature effects, both emerging directly from our simulations. For CHD and Pro, we present an explanation of the biexponential decay recently reported by Sension and coworkers [Tang et al., J. Phys. Chem., 2011, 134, 104503]: our calculations suggest that the fast and slow components arise from a reactive and an unreactive reaction pathway, respectively. Secondly, we assess the wavelength dependent photochemistry of previtamin D (Pre). Using replica exchange molecular dynamics we sample the Pre conformers present at thermal equilibrium. Based on this ensemble we explain the conformation dependent absorption and the essential features of Pre photochemistry. Consistent with the experiments, we find ring-closure to occur mostly after excitation of the cZc conformers and at lower energies, whereas Z/E isomerization of the central double bond preferably occurs after excitation at higher energies. For the isomerization we provide the first theoretical evidence of the proposed hula-twist mechanism. Our results show that LR-TDDFT-SH is a highly valuable tool for studying the photochemistry of moderately large systems, even though challenges remain in the vicinity of conical intersections.