Publications by authors named "Ruud K"

We report a light-promoted hydroselenation of alkenes with high -Markovnikov selectivity. Blue light activates an aryl diselenide to generate a seleno radical with subsequent addition into an alkene to form a β-seleno carbon radical. Hydrogen atom transfer (HAT) from the selenol to the carbon radical generates the linear selenide with high selectivity in preference to the branched isomer.

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Diverse ranges of chiral nitrogen-containing heterocycles serve as a molecular toolbox for modulating a wide array of biological processes, but enantioenriched production of smaller chiral heterocycles is a bottleneck. There is a lack of general approaches for the stereoselective preparation of chiral 4-membered monocyclic C2-substituted azetidines, where many routes to different substitution types are possible, but no simple and common approach exists. To bridge this gap, inexpensive and widely available chiral -butanesulfinamides are harnessed for chiral induction with 1,3-bis-electrophilic 3-chloropropanal, providing a three-step approach to C2-substituted azetidines with aryl, vinyl, allyl, branched alkyl, and linear alkyl substituents.

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We inspect the origin of the inverted singlet-triplet gap (INVEST) and slow change in the reverse intersystem crossing (rISC) rate with temperature, as recently observed. A Wigner phase space study reveals that, though INVEST is found at equilibrium geometry, variation in the exchange interaction and the doubles-excitation for other geometries in the harmonic region leads to non-INVEST behavior. This highlights the importance of nuclear degrees of freedom for the INVEST phenomenon, and in this case, geometric puckering of the studied molecule determines INVEST and the associated rISC dynamics.

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We present an accidental mechanism for efficient intersystem crossing (ISC) between singlet and triplet states with low spin-orbit coupling (SOC) in molecules having donor-acceptor (D-A) moieties separated by a Sigma bond. Our study shows that SOC between the lowest singlet excited state and the higher-lying triplet states, together with nuclear motion-driven coupling of this triplet state with lower-lying triplet states during the free rotation about a Sigma bond, is one of the possible ways to achieve the experimentally observed ISC rate for a class of D-A type photoredox catalysts. This mechanism is found to be the dominant contributor to the ISC process with the corresponding rate reaching a maximum at a dihedral angle in the range of 72°-78° between the D-A moieties of 10-(naphthalen-1-yl)-3,7-diphenyl-10-phenoxazine and other molecules included in the study.

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Cyclic peptides show a wide range of biological activities, among others as antibacterial agents. These peptides are often large and flexible with multiple chiral centers. The determination of the stereochemistry of molecules with multiple chiral centers is a challenging and important task in drug development.

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We present a composite framework for calculating the rates of non-radiative deactivation processes, namely internal conversion (IC) and intersystem crossing (ISC), on an equal footing by explicitly computing the non-adiabatic coupling (NAC) and spin-orbit coupling (SOC) constants, respectively. The stationary-state approach uses a time-dependent generating function based on Fermi's golden rule. We validate the applicability of the framework by computing the rate of IC for azulene, obtaining comparable rates to experimental and previous theoretical results.

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We describe the technology and validation of a new whole room indirect calorimeter (WRIC) methodology to quantify volume of methane (VCH) released from the human body over 24 h concurrently with the assessment of energy expenditure and substrate utilization. The new system extends the assessment of energy metabolism by adding CH, a downstream product of microbiome fermentation that could contribute to energy balance. Our new system consists of an established WRIC combined with the addition of off-axis integrated-cavity output spectroscopy (OA-ICOS) to measure CH concentration ([CH]).

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Objective: The aim of this study was to test proportional-integral-derivative (PID) control of air inflow rate in a whole-room indirect calorimeter to improve accuracy in measuring oxygen (O ) consumption ( ) and carbon dioxide (CO ) production ( ).

Methods: A precision gas blender infused nitrogen (N ) and CO into the calorimeter over 24 hours based on static and dynamic infusion profiles mimicking and patterns during resting and non-resting conditions. Constant (60 L/min) versus time-variant flow set by a PID controller based on the CO concentration was compared based on errors between measured versus expected values for respiratory exchange ratio, and metabolic rate.

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X-ray absorption spectroscopy (XAS) has gained popularity in recent years as it probes matter with high spatial and elemental sensitivities. However, the theoretical modeling of XAS is a challenging task since XAS spectra feature a fine structure due to scalar (SC) and spin-orbit (SO) relativistic effects, in particular near L and M absorption edges. While full four-component (4c) calculations of XAS are nowadays feasible, there is still interest in developing approximate relativistic methods that enable XAS calculations at the two-component (2c) level while maintaining the accuracy of the parent 4c approach.

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Modeling human breast tissue architecture is essential to study the pathophysiological conditions of the breast. We report that normal mammary epithelial cells grown in human breast extracellular matrix (ECM) hydrogel formed acini structurally similar to those of human and pig mammary tissues. Type I, II, III and V collagens were commonly identified in human, pig, and mouse breast ECM.

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We highlight the important roles the direct spin-orbit (DSO) coupling, the spin-vibronic (SV) coupling, and the dielectric constant of the medium play on the reverse intersystem crossing (RISC) mechanism of TXO-TPA and TXO-PhCz molecules. To understand this complex phenomenon, we have calculated the RISC rate constant, k, using a time-dependent correlation function-based method within the framework of second-order perturbation theory. Our computed k in two different solvents, toluene and chloroform, suggests that in addition to the DSO, a dielectric medium-dependent SV mechanism may also have a significant impact on the net enhancement of the rate of RISC from the lowest triplet state to the first excited singlet state.

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Antibiotic resistance among bacteria puts immense strain on public health. The discovery of new antibiotics that work through unique mechanisms is one important pillar toward combating this threat of resistance. A functionalized amino dihydropyrimidine was reported to exhibit antibacterial activity via the inhibition of dihydrofolate reductase, an underexploited antibacterial target.

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Zero-point vibrational (ZPV) corrections to the nuclear spin-spin coupling constants have been calculated using four-component Dirac-Kohn-Sham DFT for HX (where X = O, S, Se, Te, Po), XH (where X = N, P, As, Sb, Bi), and XH (where X = C, Si, Ge, Sn, and Pb) molecules and for HC≡CPbH. The main goal was to study the influence of relativistic effects on the ZPV corrections and thus results calculated at relativistic and nonrelativistic approaches have been compared. The effects of relativity become notable for the ZPV corrections to the spin-spin coupling constants for compounds with lighter elements (selenium and germanium) than for the spin-spin coupling constants themselves.

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Article Synopsis
  • * Chiroptical spectroscopies, like vibrational circular dichroism (VCD), help determine the stereochemistry of these molecules, but require advanced computational methods for accurate analysis.
  • * The presented computational protocol involves three main steps: conformational sampling, energy ranking of conformers, and VCD spectra generation, providing a robust method for studying cyclic oligopeptides relevant to antibiotic development.
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Background: Acute kidney injury (AKI) survivors are at heightened risk for poor short- and long-term health outcomes. Even among those who recover after an AKI episode, the risk for chronic kidney disease is 4- to 6-fold higher than in patients without AKI, underscoring the importance of identifying methods to improve AKI survivorship.

Objective: The purpose of this report was to describe the development and feasibility of a novel multidisciplinary approach to caring for AKI survivors at care transitions (ACT).

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We present a benchmark study of density functional approximation (DFA) performances in predicting the two-photon-absorption strengths in π-conjugated molecules containing electron-donating/-accepting moieties. A set of 48 organic molecules is chosen for this purpose, for which the two-photon-absorption (2PA) parameters are evaluated using different DFAs, including BLYP, PBE, B3LYP, PBE0, CAM-B3LYP, LC-BLYP, and optimally tuned LC-BLYP. Minnesota functionals and ωB97X-D are also used, applying the two-state approximation, for a subset of molecules.

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The simulation of X-ray absorption spectra requires both scalar and spin-orbit (SO) relativistic effects to be taken into account, particularly near L- and M-edges where the SO splitting of core p and d orbitals dominates. Four-component Dirac-Coulomb Hamiltonian-based linear damped response time-dependent density functional theory (4c-DR-TDDFT) calculates spectra directly for a selected frequency region while including the relativistic effects variationally, making the method well suited for X-ray applications. In this work, we show that accurate X-ray absorption spectra near L- and M-edges of closed-shell transition metal and actinide compounds with different central atoms, ligands, and oxidation states can be obtained by means of 4c-DR-TDDFT.

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We investigate the effect of relativity on harmonic vibrational frequencies. Density functional theory (DFT) calculations using the four-component Dirac-Coulomb Hamiltonian have been performed for 15 hydrides (HX, X = O, S, Se, Te, Po; XH, X = N, P, As, Sb, Bi; and XH, X = C, Si, Ge, Sn, Pb) as well as for HC≡CPbH. The vibrational frequencies have been calculated using finite differences of the molecular energy with respect to geometrical distortions of the nuclei.

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Tissue extracellular matrix (ECM) is a structurally and compositionally unique microenvironment within which native cells can perform their natural biological activities. Cells grown on artificial substrata differ biologically and phenotypically from those grown within their native tissue microenvironment. Studies examining human tissue ECM structures and the biology of human tissue cells in their corresponding tissue ECM are lacking.

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Article Synopsis
  • - The study reveals that spin-vibronic coupling is the primary mechanism driving vibrational coherence transfer (VCT) from the singlet (S) state to the triplet (T) state in the [Pt(POH)] complex.
  • - Findings indicate that direct spin-orbit coupling contributes minimally to intersystem crossing, but incorporating spin-vibronic effects significantly enhances VCT rates, making transitions between states feasible.
  • - The results show that the time for S to T transitions via VCT (1.084 ps) is much quicker compared to other transitions in different solvents, marking a new instance of VCT operating solely through spin-vibronic interactions, potentially influencing future photocatalysis developments.
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We present a fully analytic approach to calculate infrared (IR) and Raman spectra of molecules embedded in complex molecular environments modeled using the fragment-based polarizable embedding (PE) model. We provide the theory for the calculation of analytic second-order geometric derivatives of molecular energies and first-order geometric derivatives of electric dipole moments and dipole-dipole polarizabilities within the PE model. The derivatives are implemented using a general open-ended response theory framework, thus allowing for an extension to higher-order derivatives.

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The interpretation of the ultrafast photophysics of transition metal complexes following photo-absorption is quite involved as the heavy metal center leads to a complicated and entangled singlet-triplet manifold. This opens up multiple pathways for deactivation, often with competitive rates. As a result, intersystem crossing (ISC) and phosphorescence are commonly observed in transition metal complexes.

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Background: Breast cancer cells invading the connective tissues outside the mammary lobule or duct immerse in a reservoir of extracellular matrix (ECM) that is structurally and biochemically distinct from that of their site of origin. The ECM is a spatial network of matrix proteins, which not only provide physical support but also serve as bioactive ligands to the cells. It becomes evident that the dimensional, mechanical, structural, and biochemical properties of ECM are all essential mediators of many cellular functions.

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The properties of molecules depend on their chemical structure, and thus, structure-property relations help design molecules with desired properties. Few-state models are often used to interpret experimental observations of non-linear optical properties. Not only the magnitude but also the relative orientation of the transition dipole moment vectors is needed for few-state models of the non-linear optical properties.

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The Dalton Project provides a uniform platform access to the underlying full-fledged quantum chemistry codes Dalton and LSDalton as well as the PyFraME package for automatized fragmentation and parameterization of complex molecular environments. The platform is written in Python and defines a means for library communication and interaction. Intermediate data such as integrals are exposed to the platform and made accessible to the user in the form of NumPy arrays, and the resulting data are extracted, analyzed, and visualized.

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