Quantum-Classical Simulations Reveal the Photoisomerization Mechanism of a Prototypical First-Generation Molecular Motor.

Light-driven molecular rotary motors convert the energy of absorbed light into unidirectional rotational motion and are key components in the design of molecular machines. The archetypal class of light-driven rotary motors is chiral overcrowded alkenes, where the rotational movement is achieved through consecutive cis-trans photoisomerization reactions and thermal helix inversion steps. While the thermal steps have been rather well understood by now, our understanding of the photoisomerization reactions of overcrowded alkene-based motors still misses key points that would explain the striking differences in operation efficiency of the known systems.

Light-induced selectivity in an exemplary photodimerization reaction of varied azaanthracenes.

Currently, there is intense interest in light-driven chemical reactions, including photocatalytic processes, photopolymerization and photodimerization. The need for regiocontrol in such reactions is obvious, especially in cases where many products can potentially be formed. Here, the photodimerization involving various azaanthracenes is presented for the first time.

Theoretical Insights into Ultrafast Separation of Photogenerated Charges in a Push-Pull Polarized Molecular Triad.

Herein, we propose a purely-organic donor-acceptor (D-A) molecular triad, with a light-absorbing polarized molecular wire (PMW) used as a central linkage, as a proof of concept for the possible future applications of the D-PMW-A arrangement in molecular photovoltaics. This work builds upon our earlier study on the PMW unit itself, which proved to be highly promising for the ultrafast photogeneration of free charge carriers. Quantum-chemical calculations performed for the D-PMW-A triad at a semi-empirical level of theory reveal a large electric dipole moment of the system, and show strong charge-transfer (CT) character of its lowest-energy excited electronic states, including the , which favours efficient dissociation of an exciton initially formed upon the absorption of light.

Does the Composition of Gut Microbiota Affect Chronic Kidney Disease? Molecular Mechanisms Contributed to Decreasing Glomerular Filtration Rate.

Chronic kidney disease (CKD) is a very prevalent and insidious disease, particularly with initially poorly manifested symptoms that progressively culminate in the manifestation of an advanced stage of the condition. The gradual impairment of kidney function, particularly decreased filtration capacity, results in the retention of uremic toxins and affects numerous molecular mechanisms within the body. The dysbiotic intestinal microbiome plays a crucial role in the accumulation of protein-bound uremic toxins such as p-cresol (pC), indoxyl sulfate (IS), and p-cresyl sulfate (p-CS) through the ongoing fermentation process.

MLatom Software Ecosystem for Surface Hopping Dynamics in Python with Quantum Mechanical and Machine Learning Methods.

We present an open-source MLatom@XACS software ecosystem for on-the-fly surface hopping nonadiabatic dynamics based on the Landau-Zener-Belyaev-Lebedev algorithm. The dynamics can be performed via Python API with a wide range of quantum mechanical (QM) and machine learning (ML) methods, including ab initio QM (CASSCF and ADC(2)), semiempirical QM methods (e.g.

New insights into the photocyclization reaction of a popular diarylethene switch: a nonadiabatic molecular dynamics study.

Diarylethene (DAE) molecular switches have continued to attract the attention of researchers for over 20 years. Their remarkable photophysical properties endow them with countless applications in photonics and molecular technologies. However, despite extensive experimental and theoretical research, the mechanism of DAE photoswitching is not yet fully rationalized.

Photo-oxidation of methanol in complexes with pyrido[2,3-]pyrazine: a nonadiabatic molecular dynamics study.

Excited-state Proton-Coupled Electron Transfer (PCET) constitutes a key step in the photo-oxidation of small, electron-rich systems possessing acidic hydrogen atoms, such as water or alcohols, which can play a vital role in green hydrogen production. In this contribution, we employ quantum-chemical methods and on-the-fly nonadiabatic molecular dynamics simulations to study the mechanism and the photodynamics of PCET in 1 : 1 pyrido[2,3-]pyrazine complexes with methanol. We find the process to be ultrafast and efficient when the intramolecular hydrogen bond is formed with one of the β-positioned nitrogen atoms.

Interrelations between Linkage Isomers of an Efficient Square-planar Nickel(II) Nitrite Photoswitch in the Solid State.

An efficient nitrite nickel(II) photoswitch, with the 1-phenyl-2-hydroxyimino-3-[(2'-dimethylamino)ethyl]imino-1-propanone moiety used as the ancillary ligand, is reported. In the ground-state ('dark') crystal structure, the studied compound exists predominantly as the nitro-(η -N(O) ) isomer, however, traces of the exo- and endo-nitrito-(η -ONO) forms are detected both at 100 K (4-5 % each) and under ambient conditions (~9 % each). When excited with the 405-530 nm LED light, the nitro-to-nitrito isomerization takes place.

Loss of FAM111B protease mutated in hereditary fibrosing poikiloderma negatively regulates telomere length.

Hereditary fibrosing poikiloderma (HFP) is a rare human dominant negative disorder caused by mutations in the gene that encodes a nuclear trypsin-like serine protease. HFP patients present with symptoms including skin abnormalities, tendon contractures, myopathy and lung fibrosis. We characterized the cellular roles of human FAM111B using U2OS and MCF7 cell lines and report here that the protease interacts with components of the nuclear pore complex.

The radiative surface hopping (RSH) algorithm: Capturing fluorescence events in molecular systems within a semi-classical non-adiabatic molecular dynamics framework.

In this article, we present the radiative surface hopping algorithm, which enables modeling fluorescence within a semi-classical non-adiabatic molecular dynamics framework. The algorithm has been tested for the photodeactivation dynamics of trans-4-dimethylamino-4'-cyanostilbene (DCS). By treating on equal footing the radiative and non-radiative processes, our method allows us to attain a complete molecular movie of the excited-state deactivation.

Aluminum Enters Mammalian Cells and Destabilizes Chromosome Structure and Number.

Chromosome instability (CIN) consists of high rates of structural and numerical chromosome abnormalities and is a well-known hallmark of cancer. Aluminum is added to many industrial products of frequent use. Yet, it has no known physiological role and is a suspected human carcinogen.

Modern Theoretical Approaches to Modeling the Excited-State Intramolecular Proton Transfer: An Overview.

The excited-state intramolecular proton transfer (ESIPT) phenomenon is nowadays widely acknowledged to play a crucial role in many photobiological and photochemical processes. It is an extremely fast transformation, often taking place at sub-100 fs timescales. While its experimental characterization can be highly challenging, a rich manifold of theoretical approaches at different levels is nowadays available to support and guide experimental investigations.

Photo-cycloreversion mechanism in diarylethenes revisited: A multireference quantum-chemical study at the ODM2/MRCI level.

Photoswitchable diarylethenes (DAEs), over years of intense fundamental and applied research, have been established among the most commonly chosen molecular photoswitches, often employed as controlling units in molecular devices and smart materials. At the same time, providing reliable explanation for their photophysical behavior, especially the mechanism of the photo-cycloreversion transformation, turned out to be a highly challenging task. Herein, we investigate this mechanism in detail by means of multireference semi-empirical quantum chemistry calculations, allowing, for the first time, for a balanced treatment of the static and dynamic correlation effects, both playing a crucial role in DAE photochemistry.

Ultrafast nonradiative deactivation of photoexcited 8-oxo-hypoxanthine: a nonadiabatic molecular dynamics study.

In the scientific endeavor to understand the chemical origins of life, the photochemistry of the smallest life building blocks, nucleobases, has been a constant object of focus and intense research. Here, we report the results of the first theoretical study on the photo-properties of an 8-oxo-hypoxanthine molecule, the chromophore of 8-oxo-inosine, which is relevant to the recently proposed, prebiotically plausible synthetic routes to the formation of purine- and pyrimidine-nucleotides. With ab initio and semi-empirical OM2/MRCI quantum-chemistry calculations, we predict a strong photostability of the 8-oxo-hypoxanthine system and see the origin of this effect in ultrafast nonradiative relaxation through puckering of the 6-membered heterocyclic ring.

ZCWPW1 is recruited to recombination hotspots by PRDM9 and is essential for meiotic double strand break repair.

During meiosis, homologous chromosomes pair and recombine, enabling balanced segregation and generating genetic diversity. In many vertebrates, double-strand breaks (DSBs) initiate recombination within hotspots where PRDM9 binds, and deposits H3K4me3 and H3K36me3. However, no protein(s) recognising this unique combination of histone marks have been identified.

Multigene human artificial chromosome vector delivery with herpes simplex virus 1 amplicons.

Gene expression studies and gene therapy require efficient gene delivery into cells. Different technologies by viral and non-viral mechanisms have been used for gene delivery into cells. Small gene vectors transfer across the cell membrane with a relatively high efficiency, but not large genes or entire loci spanning several kilobases, which do not remain intact following introduction.

Long-term trends in HIV care entry: over 15 years of clinical experience from Poland.

Introduction: Delay in HIV diagnosis and consequently late care entry with low CD4 counts remain a major challenge for the control of the HIV/AIDS epidemic. The aim of this study was to analyse the evolution of characteristics of the HIV epidemic in Poland.

Methods: Cross-sectional data were collected for 3972 HIV-infected patients followed up in 14 of 17 Polish HIV treatment centres in the years 2000-2015.

Ehrenfest and classical path dynamics with decoherence and detailed balance.

We present a semiclassical approach for nonadiabatic molecular dynamics based on the Ehrenfest method with corrections for decoherence and detailed balance. Decoherence is described via a coherence penalty functional that drives dynamics away from regions in Hilbert space characterized by large values of coherences. Detailed balance is incorporated by modification of the off-diagonal matrix elements with a quantum correction factor used in semiclassical approximations to quantum time-correlation functions.

Lead and Cadmium Content in Grass Growing Near An Expressway.

The purpose of the study was to evaluate the effect of distance from a road on lead and cadmium content in grass species near an expressway and to assess bioaccumulation of these elements by morphological parts of the plants. The material for the research was the following grass species in their flowering stage: Dactylis glomerata, Arrenatherum elatius, and Alopecurus pratensis. Plant samples were collected along the international E30 road, the ring-road of Siedlce, in May 2015.

Real-Time Atomistic Dynamics of Energy Flow in an STM Setup: Revealing the Mechanism of Current-Induced Molecular Emission.

Detailed understanding of the current-induced fluorescence mechanism constitutes an exciting challenge as it can open the way to efficient coupling between an electric field and light at the nanoscale. At the same time, a number of published experimental studies give an unclear, contradictory picture of this phenomenon working principle. Here, for a system consisting of a silver tip and a porphyrin molecule, we perform for the first time fully atomistic, real-time nonadiabatic dynamics simulations to study the process of energy transfer and relaxation in an STM setup.

Strong Influence of Ti Adhesion Layer on Electron-Phonon Relaxation in Thin Gold Films: Ab Initio Nonadiabatic Molecular Dynamics.

Electron-phonon relaxation in thin metal films is an important consideration for many ultrasmall devices and ultrafast applications. Recent time-resolved experiments demonstrate a significant, more than a factor of five, increase in the electron-phonon coupling and acceleration in the electron-phonon relaxation rate when a narrow Ti adhesion layer is introduced between an Au film and a nonmetal substrate. Using nonadiabatic molecular dynamics combined with real-time time-dependent density functional theory, we identify the reasons that give rise to this strong effect.

Tailoring the Schiff base photoswitching - a non-adiabatic molecular dynamics study of substituent effect on excited state proton transfer.

Small molecular systems exhibiting Excited State Intramolecular Proton Transfer (ESIPT) attract considerable attention due to their possible role as ultrafast, efficient, and photostable molecular photoswitches. Here, by means of static potential energy profile scan and on-the-fly non-adiabatic dynamics simulations we study the photodeactivation process of a minimal-chromophore aromatic Schiff base, salicylidene methylamine (SMA), and its two derivatives 6-cyano-salicylidene methylamine (6-CN-SMA) and 3-hydroxy-salicylidene methylamine (3-OH-SMA). We show that the dominant character of the lowest excited singlet state - ππ* vs.

Ferroelectric Alignment of Organic Cations Inhibits Nonradiative Electron-Hole Recombination in Hybrid Perovskites: Ab Initio Nonadiabatic Molecular Dynamics.

Hybrid organic-inorganic perovskites show impressive potential for photovoltaic applications and currently give rise to one of the most vibrant research areas in the field. Until recently, the electrostatic interactions between their organic and inorganic components were considered mostly for stabilization of the fragile perovskite structure. We study the effect of local interactions of polar C-N bonds in the organic layer on the nonradiative electron-hole recombination in the recently reported room-temperature ferroelectric hybrid perovskite, (benzylammonium)PbCl.

Ferroelectric molecular field-switch based on double proton transfer process: Static and dynamical simulations.

In this work, we present a reversible ferroelectric molecular switch controlled by an external electric field. The studied (2Z)-1-(6-((Z)-2-hydroxy-2-phenylvinyl)pyridin-3-yl)-2-(pyridin-2(1H)-ylidene)ethanone (DSA) molecule is polarized by two uniaxial intramolecular hydrogen bonds. Two protons can be transferred along hydrogen bonds upon an electric field applied along the main molecular axis.