Membrane Stabilization of Helical Previtamin D Conformers as Possible Enhancement of Vitamin D Photoproduction

Photoinduced vitamin D formation occurs 10-15-fold faster in phospholipid bilayers (PLB) than in isotropic solution. It has been hypothesized that amphipatic interactions of the PLB with the rotationally flexible previtamin D (Pre) stabilize its helical conformers, enhancing thermal intramolecular [1,7]-hydrogen transfer, forming vitamin D. To test this hypothesis, we carried out molecular dynamics (MD) simulations of Pre in a PLB composed of dipalmitoylphosphatidylcholine (DPPC). We designed a classical force field capable of accurately describing the equilibrium composition of Pre conformers. Using adaptive biasing force MD simulations, we determined the free energy of Pre conformers in isotropic environments (hexane and gas-phase) and in the anisotropic environment of a DPPC PLB. We find a total increase of 25.5% of the population of both helical conformers (+20.5% g+Zg+ and +5% g-Zg-) in DPPC compared to hexane. In view of ab initio simulations, showing that hydrogen transfer occurs in both helical conformers, our study strongly suggests the validity of the initial hypothesis. Regarding the amphipatic interactions of Pre with the PLB, we find that, similar to cholesterol (Chol) and 7-dehydrocholesterol (7-DHC), Pre entertains hydrogen bonds mainly to the carbonyl groups of DPPC and, to a lesser extent, with phosphate oxygen atoms and rarely to water molecules at the interface. We further report order parameters of the Pre/DPPC system, which are slightly smaller than those for Chol/DPPC and 7-DHC/DPPC, but larger than for pure DPPC. This indicates a loss in membrane viscosity upon photochemical ring-opening of 7-DHC to form Pre.

Coherent x-ray spontaneous emission spectroscopy of conical intersections

Conical intersections are known to play a vital role in many photochemical processes. The breakdown of the Born-Oppenheimer approximation in the vicinity of a conical intersection causes exciting phenomena, such as the ultrafast radiationless decay of excited states. The passage of a molecule through a conical intersection creates a coherent superposition of electronic states via nonadiabatic couplings. Detecting this coherent superposition may serve as a direct probe of the conical intersection. In this paper, we theoretically demonstrate the use of coherent spontaneous emission in samples with long-range order for probing the occurrence of a conical intersection in a molecule. Our simulations show that the spectrum contains clear signatures of the created coherent superposition of electronic states. We investigate the bandwidth requirements for the x-ray probes, which influence the observation of coherent superposition generated by the conical intersection.

Exact-Factorization-Based Surface Hopping without Velocity Adjustment

While surface hopping has emerged as a powerful method for simulating non-adiabatic dynamics in large molecules, the ad hoc nature of the necessary velocity adjustments and decoherence corrections in the algorithm somewhat reduces its reliability. Here we propose a new scheme that eliminates these aspects by combining the nuclear equation from the quantum-trajectory surface-hopping approach with the electronic equation derived from the exact-factorization approach. The resulting method, denoted QTSH-XF, yields a surface-hopping method on firmer ground than previous and is shown to successfully capture dynamics in Tully models and in a linear vibronic coupling model of the photoexcited uracil cation.

Raman Spectroscopy of Conical Intersections Using Entangled Photons

Ultrafast Raman spectroscopy with attosecond pulses in the extreme ultraviolet and X-ray regime has been proposed theoretically for tracking the non-adiabatic dynamics of molecules in great detail. The large bandwidth of these pulses, which span several electronvolts within a couple of femtoseconds, provides a unique tool for tracking non-adiabatic phenomena. However, spectroscopy with classical light is limited by the time-bandwidth product of the probe laser pulse. In this work, we theoretically investigate an ultrafast Raman spectroscopy scheme that utilizes pairs of entangled photons. Our model simulations demonstrate that the dynamics in the vicinity of a conical intersection can be resolved with unprecedented resolution in the time and frequency domain.

TURBOMOLE: Today and Tomorrow

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.

Calcifediol: Mechanisms of Action

Due to its essential role in calcium and phosphate homeostasis, the secosteroid hormone calcitriol has received growing attention over the last few years. Calcitriol, like other steroid hormones, may function through both genomic and non-genomic mechanisms. In the traditional function, the interaction between the biologically active form of vitamin D and the vitamin D receptor (VDR) affects the transcription of thousands of genes by binding to repeated sequences present in their promoter region, named vitamin D-responsive elements (VDREs). Non-transcriptional effects, on the other hand, occur quickly and are unaffected by inhibitors of transcription and protein synthesis. Recently, calcifediol, the immediate precursor metabolite of calcitriol, has also been shown to bind to the VDR with weaker affinity than calcitriol, thus exerting gene-regulatory properties. Moreover, calcifediol may also trigger rapid non-genomic responses through its interaction with specific membrane vitamin D receptors. Membrane-associated VDR (mVDR) and protein disulfide isomerase family A member 3 (Pdia3) are the best-studied candidates for mediating these rapid responses to vitamin D metabolites. This paper provides an overview of the calcifediol-related mechanisms of action, which may help to better understand the vitamin D endocrine system and to identify new therapeutic targets that could be important for treating diseases closely associated with vitamin D deficiency.

Ab Initio Simulation of the Ultrafast Circular Dichroism Spectrum of Provitamin D Ring-Opening

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.

Sample preparation techniques for extraction of vitamin D metabolites from non-conventional biological sample matrices prior to LC-MS/MS analysis

The determination of vitamin D metabolites as status marker or for diagnostic purposes is almost entirely conducted from blood serum or plasma. Other biological matrices, however, have also interested researchers, for two main reasons: (1) alternative matrices may allow non-invasive sampling, permit easier sample transfer and require less demanding storage conditions; and (2) the levels of vitamin D metabolites in other body compartments may further aid the understanding of vitamin D metabolism and function. Thus, the development of reliable and efficient sample preparation protocols for sample matrices other than serum/plasma, which will remove potential interferences and selectively extract the targeted metabolites, is of great importance. This review summarizes sample preparation methods for measurement of vitamin D metabolites using liquid chromatography-(tandem)mass spectrometry in more than ten different human tissues, including hair, saliva, adipose tissue, brain and others.

Vitamin D as therapeutic modulator in cerebrovascular diseases: a mechanistic perspectives

Vitamin D deficiency has been linked to several major chronic diseases, such as cardiovascular and neurodegenerative diseases, diabetes, and cancer, linked to oxidative stress, inflammation, and aging. Vitamin D deficiency appears to be particularly harmful to the cardiovascular system, as it can cause endothelial dysfunctioning and vascular abnormalities through the modulation of various downstream mechanisms. As a result, new research indicates that therapeutic approaches targeting vitamin D inadequacies or its significant downstream effects, such as impaired autophagy, abnormal pro-inflammatory and pro-oxidant reactions, may delay the onset and severity of major cerebrovascular disorders such as stroke and neurologic malformations. Vitamin D modulates the various molecular pathways, i.e., Nitric Oxide, PI3K-Akt Pathway, cAMP pathway, NF-kB Pathway, Sirtuin 1, Nrf2, FOXO, in cerebrovascular disorder. The current review shows evidence for vitamin D's mitigating or slowing the progression of these cerebrovascular disorders, which are significant causes of disability and death worldwide.

Safety Assessment of Vitamin D and Its Photo-Isomers in UV-Irradiated Baker's Yeast

Vitamin D deficiency due to, e.g., nutritional and life style reasons is a health concern that is gaining increasing attention over the last two decades. Vitamin D₃, the most common isoform of vitamin D, is only available in food derived from animal sources. However, mushrooms and yeast are rich in ergosterol. This compound can be converted into vitamin D₂ by UV-light, and therefore act as a precursor for vitamin D. Vitamin D₂ from UV-irradiated mushrooms has become an alternative source of vitamin D, especially for persons pursuing a vegan diet. UV-irradiated baker’s yeast (Saccharomyces cerevisiae) for the production of fortified yeast-leavened bread and baked goods was approved as a Novel Food Ingredient in the European Union, according to Regulation (EC) No. 258/97. The Scientific Opinion provided by the European Food Safety Authority Panel on Dietetic Products, Nutrition, and Allergies has assessed this Novel Food Ingredient as safe under the intended nutritional use. However, recent findings on the formation of side products during UV-irradiation, e.g., the photoproducts tachysterol and lumisterol which are compounds with no adequate risk assessment performed, have only been marginally considered for this EFSA opinion. Furthermore, proceedings in analytics can provide additional insights, which might open up new perspectives, also regarding the bioavailability and potential health benefits of vitamin D-fortified mushrooms and yeast. Therefore, this review is intended to give an overview on the current status of UV irradiation in mushrooms and yeast in general and provide a detailed assessment on the potential health effects of UV-irradiated baker’s yeast.

An efficient implementation of spin-orbit coupling within the framework of semiempirical orthogonalization-corrected methods for ultrafast intersystem crossing dynamics

We implement spin-orbit coupling (SOC) within the framework of semiempirical orthogonalization-corrected methods (OMx). The excited-state wavefunction is generated from configuration interaction with single excitations (CIS). The SOC Hamiltonian in terms of the one-electron Breit-Pauli operator with effective nuclear charges is adopted in this work. Benchmark calculations show that SOCs evaluated using the OMx/CIS method agree very well with those obtained from time-dependent density functional theory. As a particularly attractive application, we incorporate SOCs between singlet and triplet states into Tully's fewest switches surface hopping algorithm to enable excited-state nonadiabatic dynamics simulations, treating internal conversion and intersystem crossing on an equal footing. This semiempirical dynamics simulation approach is applied to investigate ultrafast intersystem crossing processes in core-substituted naphthalenediimides.

Probing the Formation and Conformational Relaxation of Previtamin D3 and Analogues in Solution and in Lipid Bilayers

The photosynthesis of vitamin D₃ in mammalian skin results from UV-B irradiation of provitamin D₃ (7-dehydrocholesterol, DHC) at ca. 290 nm. Upon return to the ground state, the hexatriene product, previtamin D₃, undergoes a conformational equilibration between helical gZg and more planar tZg and tZt forms. The helical gZg forms provide a pathway for the formation of vitamin D₃ via a [1,7]-sigmatropic hydrogen shift. Steady state photolysis and UV transient absorption spectroscopy are combined to explore the conformational relaxation of previtamin D₃ formed from DHC in isotropic solution and confined to lipid bilayers chosen to model the biological cell membrane. The results are compared with measurements for two analogues: previtamin D₂ formed from ergosterol (provitamin D₂) and previtamin D₃ acetate formed from DHC acetate. The resulting spectral dynamics are interpreted in the context of simulations of optical excitation energy and oscillator strength as a function of conformation. In solution, the relaxation dynamics and steady state product distributions of the three compounds are nearly identical, favoring tZg forms. When confined to lipid bilayers, the heterogeneity and packing forces alter the conformational distributions and enhance the population of a gZg conformer capable of vitamin D formation.

Elucidating an Atmospheric Brown Carbon Species-Toward Supplanting Chemical Intuition with Exhaustive Enumeration and Machine Learning

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.

First principles theoretical spectroscopy of methylene blue: Between limitations of time-dependent density functional theory approximations and its realistic description in the solvent

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.

Vitamin D, sport and health: a still unresolved clinical issue

Vitamin D metabolites have a pleiotropic role in human physiology, both in static and dynamic conditions, and a lot of vitamin D-related biological effects could influence physical and sport performances in athletes. Probably due to different factors (e.g., drugs, doping, nutrition, ultraviolet B radiation exposure), in athletes a very high prevalence of vitamin D inadequacy (i.e., deficiency or insufficiency) has been observed. Vitamin D inadequacy in athletes could be associated with specific health risks and to alterations of functional capacities, potentially influencing the fine adjustment of physical performances during training and sport competitions. When risk factors for vitamin D inadequacy exist, a preventive vitamin D supplementation is indicated, and if a vitamin D inadequacy is diagnosed, its supplementation is recommended. Unfortunately, on these issues many concerns remain unresolved. Indeed, it is not clear if athletes should be classified as a special population at increased risk for vitamin D inadequacy; moreover, in comparison to the non-athletic population, it is still not clear if athletes should have different reference ranges and different optimal target levels for serum vitamin D, if they have additional health risks, and if they need different type of supplementations (doses) for prevention and/or replacement therapy. Moreover, in athletes also the abuse of vitamin D supplements for ergogenic purposes raise different ethical and safety concerns. In this review, the main physio-pathological, functional and clinical issues that relate vitamin D to the world of athletes are described.

TURBOMOLE: Modular program suite for ab initio quantum-chemical and condensed-matter simulations

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.

Azologization and repurposing of a hetero-stilbene-based kinase inhibitor: towards the design of photoswitchable sirtuin inhibitors

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.

Multistate hybrid time-dependent density functional theory with surface hopping accurately captures ultrafast thymine photodeactivation

We report an efficient analytical implementation of first-order nonadiabatic derivative couplings between arbitrary Born–Oppenheimer states in the hybrid time-dependent density functional theory (TDDFT) framework using atom-centered basis functions.

Calculation of vibrationally resolved absorption spectra of acenes and pyrene

Absorption spectra of polycyclic aromatic hydrocarbons have been simulated by using a real-time generating function method that combines adiabatic electronic excitation energies with vibrational energies of the excited states.

Tuning the photoreactivity of Z-hexatriene photoswitches by substituents - a non-adiabatic molecular dynamics study

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.

First-Principles Prediction of Wavelength-Dependent Product Quantum Yields

We present a method to predict wavelength-dependent product quantum yields (PQYs) for photochemical reactions and applied it to Z/E-isomerization and several ring-closing reactions of Z-2,5-dimethyl-1,3,5-hexatriene and truncated previtamin D. Using branching ratios from surface hopping molecular dynamics, individual trajectories are correlated with the absorption spectra of their initial structures. The wavelength-dependent PQYs are computed by dividing the average spectrum of the initial structures of the product-forming trajectories by the average spectrum of all initial structures. Accurate absorption spectra are calculated using the correlated ADC(2) method with an implicit solvent. Calculations reproduce the experimentally found trend of increasing six-ring formation and decreasing Z/E-isomerization on the red side of the spectrum. Over all seven reactions studied, the mean absolute error (MAE) between experimental and calculated PQYs (MAE) amounts to 8.1%, and the largest MAE is 18.6%. For four reactions, predicted values agree quantitatively with experiments within 5.6%.

Nitrogen-Containing, Light-Absorbing Oligomers Produced in Aerosol Particles Exposed to Methylglyoxal, Photolysis, and Cloud Cycling

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 ∼80% (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.