Triplets Of Atoms Research Articles

On the relevance of query definition in the performance of 3D ligand-based virtual screening

Ligand-based virtual screening (LBVS) methods are widely used to explore the vast chemical space in the search of novel compounds resorting to a variety of properties encoded in 1D, 2D or 3D descriptors. The success of 3D-LBVS is affected by the overlay of molecular pairs, thus making selection of the template compound, search of accessible conformational space and choice of the query conformation to be potential factors that modulate the successful retrieval of actives. This study examines the impact of adopting different choices for the query conformation of the template, paying also attention to the influence exerted by the structural similarity between templates and actives. The analysis is performed using PharmScreen, a 3D LBVS tool that relies on similarity measurements of the hydrophobic/philic pattern of molecules, and Phase Shape, which is based on the alignment of atom triplets followed by refinement of the volume overlap. The study is performed for the original DUD-E+ database and a Morgan Fingerprint filtered version (denoted DUD-E+-Diverse; available in https://github.com/Pharmacelera/Query-models-to-3DLBVS), which was prepared to minimize the 2D resemblance between template and actives. Although in most cases the query conformation exhibits a mild influence on the overall performance, a critical analysis is made to disclose factors, such as the content of structural features between template and actives and the induction of conformational strain in the template, that underlie the drastic impact of the query definition in the recovery of actives for certain targets. The findings of this research also provide valuable guidance for assisting the selection of the query definition in 3D LBVS campaigns.Graphical

Enhancing Flavins Photochemical Activity in Hydrogen Atom Abstraction and Triplet Sensitization through Ring‐Contraction

AbstractThe isoalloxazine heterocycle of flavin cofactors reacts with various nucleophiles to form covalent adducts with important functions in enzymes. Molecular flavin models allow for the characterization of such adducts and the study of their properties. A fascinating set of reactions occurs when flavins react with hydroxide base, which leads to imidazolonequinoxalines, ring‐contracted flavins, with so far unexplored activity. We report a systematic study of the photophysical properties of this new chromophore by absorption and emission spectroscopy as well as cyclic voltammetry. Excited, ring‐contracted flavins are significantly stronger hydrogen atom abstractors when compared to the parent flavins, which allowed the direct trifluoromethylthiolation of aliphatic methine positions (bond dissociation energy (BDE) of 400.8 kJ mol−1). In an orthogonal activity, their increased triplet energy (E(S0←T1)=244 kJ mol−1) made sensitized reactions possible which exceeded the power of standard flavins. Combining both properties, ring‐contracted flavin catalysts enabled the one‐pot, five‐step transformation of α‐tropolone into trans‐3,4‐disubstituted cyclopentanones. We envision this new class of flavin‐derived chromophores to open up new modes of reactivity that are currently impossible with unmodified flavins.

Enhancing Flavins Photochemical Activity in Hydrogen Atom Abstraction and Triplet Sensitization through Ring-Contraction.

The isoalloxazine heterocycle of flavin cofactors reacts with various nucleophiles to form covalent adducts with important functions in enzymes. Molecular flavin models allow for the characterization of such adducts and the study of their properties. A fascinating set of reactions occurs when flavins react with hydroxide base, which leads to imidazolonequinoxalines, ring-contracted flavins, with so far unexplored activity. We report a systematic study of the photophysical properties of this new chromophore by absorption and emission spectroscopy as well as cyclic voltammetry. Excited, ring-contracted flavins are significantly stronger hydrogen atom abstractors when compared to the parent flavins, which allowed the direct trifluoromethylthiolation of aliphatic methine positions (bond dissociation energy (BDE) of 400.8 kJ mol-1). In an orthogonal activity, their increased triplet energy (E(S0←T1)=244 kJ mol-1) made sensitized reactions possible which exceeded the power of standard flavins. Combining both properties, ring-contracted flavin catalysts enabled the one-pot, five-step transformation of α-tropolone into trans-3,4-disubstituted cyclopentanones. We envision this new class of flavin-derived chromophores to open up new modes of reactivity that are currently impossible with unmodified flavins.

Electron Lone-Pairs Stereochemistry and Drastic van der Waals and Pressure Effects in AsF3 from First Principles

AsF3E as a representative of a molecular crystal has been chosen to find the precise localization of the lone pair (LP) E centroid 4s2 of As3+ and to enlighten the behavior of lone pair triplets of fluorine atoms. Starting from stereochemistry rationale, Density Functional (DFT) electronic structure calculations yielding the electron localization (ELF) mapping led to precise large crystal structure evolutions from basic X-rays data (V = 267.2Å3 at 193K), to (V = 230.5Å3) and under Van der Waals forces (DEW) V = 206.4Å3, and then under pressure P, all illustrated with ELF maps and band structures. Calibrated pressures up to 100 GPa exhibit the remarkable shrinking of all inter-atomic distances including As-E from 0.94Å down to 0.46Å, while the major three bonds As-F1, As-F2 and As-F3 are continuously expanding. The resulting picture of the application of pressure on AsF3 molecular structure leads to the progressive immersion of the 4s2 doublet within the electronic cloud with an original new status of As with its 4s2 E expressed as [AsE]3+. The expanded size becomes close to big LP-free K+, Ba2+ cations or LP characterized bismuth cation: [BiE]3+, which appear inserted in cubes or square anti-prisms with coordination number 8 (CN8) or in tricapped trigonal prisms with CN9.

Electron number density measurements in nanosecond repetitively pulsed discharges in water vapor at atmospheric pressure

This article reports on experiments in a nonequilibrium plasma produced by nanosecond repetitively pulsed (NRP) spark discharges in water vapor at 450 K and atmospheric pressure. The objective is to determine the electron number density in the post-discharge, with spatial and temporal resolution, to gain a better understanding of the discharge development and chemical kinetics. Electron number densities were measured in water vapor from the broadenings and shifts of the Hα and Hβ lines of the hydrogen Balmer series and of the atomic oxygen triplet at 777 nm. For an average reduced electric field of about 150 Td, high electron densities up to 3 × 1018 cm−3 are measured at the cathode, up to 5 × 1017 cm−3 at the anode, and up to 4 × 1016 cm−3 in the interelectrode gap. The high density near the electrodes is attributed to ionization enhancement and secondary electron emission due to the high electric field in the plasma sheath. In the middle of the inter-electrode gap, we show that the electron density mainly decays by electron attachment reactions. The dissociation fraction of water vapor is estimated to be around 2% in the middle of the gap.

Redox Modifications of Carbon Dots Shape Their Optoelectronics

Carbon dots (CDs) are 1–10 nm scaled complex nanostructures with a wide range of applications and show unconventional photophysical behavior upon excitation. In this article, we have unveiled some of the underlying mechanisms and excited state dynamics of CDs by perturbing their interface with oxidizing and reducing agents. With no substantial alteration in size of surface-treated oxidized (OCDs), reduced (RCDs), and untreated CDs (UCDs), we observe marked changes in their charge transport properties and diverse spectral signatures in singlet and triplet excited states. Fine tuning of the spectral behavior of nanomaterials is often treated as an outcome of quantum confinement of the excitons. Herein with different spectroscopic techniques along with conducting atomic force microscopy and triplet–triplet absorption, we elucidate that, not just confinement, the structural modification at the surface also dictates optoelectronic behavior by altering some properties such as energy band gap, quantum tunneling ...

A Simple Matrix Approach to Determination of the Helium Atom Energies

Calculation of He atomic energy levels using the first order perturbation theory taught in the Basic Quantum Mechanics course has led to relatively large errors. To improve its accuracy, several methods have been developed but most of them are too complicated to be understood by undergraduate students. The purposes of this study are to apply a simple matrix method in calculating some of the lowest energy levels of He atom (1s2, triplet 1s2s, and singlet 1s2s states) and to reduce errors obtained from calculations using the standard perturbation theory. The convergence of solutions as a function of the number of bases is also examined. The calculation is done analytically for 3 bases and computationally with the number of bases using MATHEMATICA. First, the 2-electron wave function of the Helium atom is written as the multiplication of two He+ ion wave functions, which are then expanded into finite dimension bases. These bases are used to calculate the elements of the Hamiltonian matrix, which are then substituted back to the energy eigenvalue equation to determine the energy values of the system. Based on the calculation results, the error obtained for the He ground state energy using 3 bases is 2.51 %, smaller than the errors of the standard perturbation theory (5.28 %). Despite the fact that the error is still relatively large from the analytical calculations for singlet-triplet 1s2s energy splitting of He atom, this error is successfully reduced significantly as more bases were used in the numerical calculations. In particular, for n = 25, the current calculation error for all states is much smaller than the errors obtained from calculations using standard perturbation theory. In conclusion, the analytical calculations for the energy eigenvalue equation for the 3 lowest states of the Helium atom using 3 bases have been carried out. It was also found in this study that increasing the number of bases in our numerical calculations has significantly reduced the errors obtained from the analytical calculations.

QSAR Studies of New Pyrido[3,4-b]indole Derivatives as Inhibitors of Colon and Pancreatic Cancer Cell Proliferation.

We have discovered a new class of pyrido[b]bindole derivatives that show potent and broad spectrum anticancer activity with IC50 values down to submicromolar levels. Structure-activity relationship data acquired with the compounds as antiproliferative agents against several cancer cell lines, i.e. human HCT116 colon cancer cell line, and HPAC, Mia-PaCa2 and Panc-1 pancreatic cancer cell lines, were subjected to two different QSAR modeling methods. A kernel-based partial least squares (KPLS) regression analysis with chemical 2D fingerprint descriptors, and a PHASE pharmacophore alignment with 3D-QSAR study. The KPLS method afforded successful predictive QSAR models for antiproliferative activity of the HCT116 colon cell line and on two of the pancreatic cancer cell lines HPAC and Mia-PaCa2, with the following statistics: R 2s of 0.99, 0.99 and 0.98, for training set coefficients of determination, and external test set predictive r 2s of 0.70, 0.58 and 0.70, respectively. The best 2D fingerprint descriptor for both the HCT116 and HPAC data out of the eight finger prints utilized was the atom triplet fingerprint; whereas the one that worked best for the Mia-PaCa2 data was the linear fingerprint descriptor. The PHASE pharmacophore based 3D-QSAR study afforded a four-point pharmacophore model comprising one hydrogen bond donor (D) and three ring (R) elements, which yielded a successful 3D-QSAR model only with the HCT116 cell line data with training set R 2 of 0.683, and an external test set predictive r 2 of 0.562. With the PHASE 3D-QSAR, the influence of electronic effects and hydrophobicity were visualized, and were in agreement with the observed SAR of substitutions, while the KPLS method the relative extent of contribution of each atom in a compound to the activity. These models will foster the lead optimization process for this potent series of anticancer pyrido [3,4-b]indole compounds.

Application of portable near-infrared spectrometer to Heliotron J plasma diagnostics.

A simple near-infrared (NIR) spectrometer with a wavelength range of 898-2130 nm has recently been applied to diagnose Heliotron J plasmas. It adopts a symmetrical crossed Czerny-Turner mount equipped with a thermoelectrically cooled 512 channel InGaAs linear sensor. Reciprocal linear dispersion was deduced to 96.37 nm/mm at the center of the detector. External filters can be inserted into the path of the collection optics to reject second-order spectra, as needed. Absolute intensity calibration was performed together with a visible spectrometer using a tungsten halogen lamp, and the effect of the transmittance fringe in the visible region of the applied long-pass filter on the NIR calibration was investigated. The intended application of the NIR spectrometer includes extending the wavelength region of a spectral monitor to less contaminated regions for Heliotron J plasma studies. In preliminary measurements, we observed the Paschen series for the hydrogen pellet injection plasma and two atomic helium lines, i.e., 2S-2P singlet and triplet lines, in helium gas puffing experiments. A continuum spectrum in this regime that is attributable to black-body radiation from hot spots on the plasma-facing components was identified. In addition, this may also be used to monitor background radiation in the YAG-Thomson scattering signals near 1064 nm.

Improved test time evaluation in an expansion tube

Traditionally, expansion tube test times have been experimentally evaluated using test section mounted impact pressure probes. This paper proposes two new methods which can be performed using a high-speed camera and a simple circular cylinder test model. The first is the use of a narrow bandpass optical filter to allow time-resolved radiative emission from an important species to be captured, and the second is using edge detection to track how the model shock standoff changes with time. Experimental results are presented for two test conditions using an air test gas and an optical filter aimed at capturing emission from the 777 nm atomic oxygen triplet. It is found that the oxygen emission is the most reliable experimental method, because it is shown to exhibit significant changes at the end of the test time. It is also proposed that, because the camera footage is spatially resolved, the radiative emission method can be used to examine the ‘effective’ test time in multiple regions of the flow. For one of the test conditions, it is found that the effective test time away from the stagnation region for the cylindrical test model is at most 45% of the total test time. For the other test condition, it is found that the effective test time of a 54 $$^\circ$$ wedge test model is at most a third of the total test time.

Ligand-based studies on cis-stilbene derivatives as cyclo-oxygenase inhibitors

In this work, we have developed predictive quantitative structure–activity relationship models using kernel-based partial least squares method on cis-stilbene derivatives having potency profile against cyclooxygenase-1 and 2. The models were built using two approaches: fingerprint-based and fingerprint descriptors based. The fingerprint models building with linear, atompairs and atom triplet yielded a similar test set prediction for cyclooxygenase-1 and cyclooxygenase-2. Atompairs fingerprint model performs better for cyclooxygenase-1 and cyclooxygenase-2 with Q 2 = 0.7884 and Q 2 = 0.7744, respectively. This reveals the importance of size in the anti-inflammatory activity of the molecule. In order to explore into the information content of fingerprints and descriptors, kernel-based partial least squares models were also built by combination between hashed fingerprints and independent descriptors. The results suggest that the combination fingerprint-descriptors improve the quality of information about the ligands. For us, the most important was the advantage of kernel-based partial least squares fingerprint models to be decomposed into atomic effects on the activity. So, using atompairs, which gave the best pure-fingerprint model, we can visualize the contributions of each atom to the model and deconstruct a molecule into atomic contributions as favorable and unfavorable structural characteristics. Through the use of model visualization, the study provided structural modifications of two inactive molecules to optimize their potency. The predicted structures, submitted to experimental tests, would be used as guide for the development of newer cis-stilbene derivatives with better anti-inflammatory activities.

Microscopic theory of the second- and third-order elastic constants of cobalt in a thermodynamic module

The total potential energy of a crystal is presented as an expansion by irreducible interactions in clusters containing pairs of atomic triplets and quadruplets. The potential energy of the clusters in the adiabatic approximation is a function of vectors \(\vec r_{ik}\) connecting the centers of atoms in the clusters. Arguments (basic functions) affecting the potential energy of clusters are found using the model with allowance for the exchange symmetry of atoms and the irreducibility of the considered energies of doublet, triplet, and quadruplet atoms and interactions. This allows us to present arguments of the potential energy in the form of summed integral numbers (latticed sums) multiplied by a fixed value of the crystal unit cell parameter, and to set the numerical values of the potential energy arguments as a function of vectors \(\vec r_{ik}\). A potential corresponding to the thermodynamic additivity concept of crystal energy is selected as the model potential of pairwise interaction. Secondand third-order moduli of the rigidity of Co crystals with A1, A2, and HCP structures are calculated using this model of multiatom interactions.

Density-functional approach to the three-body dispersion interaction based on the exchange dipole moment.

We implement and compute the density functional nonadditive three-body dispersion interaction using a combination of Tang-Karplus formalism and the exchange-dipole moment model of Becke and Johnson. The computation of the C9 dispersion coefficients is done in a non-empirical fashion. The obtained C9 values of a series of noble atom triplets agree well with highly accurate values in the literature. We also calculate the C9 values for a series of benzene trimers and find a good agreement with high-level ab initio values reported recently in the literature. For the question of damping of the three-body dispersion at short distances, we propose two damping schemes and optimize them based on the benzene trimers data, and the fitted analytic potentials of He3 and Ar3 trimers fitted to the results of high-level wavefunction theories available from the literature. Both damping schemes respond well to the optimization of two parameters.

High-Resolution Spectroscopy of the Hayabusa Reentry Using a Fabry–Perot Interferometer

Spectroscopic observations of the Hayabusa reentry are presented as obtained by an instrument combining Fabry–Perot interferometry and classical optical emission spectroscopy. The instrument was deployed onboard NASA’s DC-8 airborne laboratory as part of the Hayabusa Reentry Airborne Observation Campaign led by NASA, in close collaboration with Japan Aerospace Exploration Agency. The covered wavelength range in the low-resolution mode is from 738.4 to 852.1 nm with the aim to acquire simultaneously the neutral atomic oxygen triplets at 777 and 844 nm and the nitrogen lines at 746 and 821 nm. The high-resolution mode reaches a wavelength resolution of . The intention of this instrument was to measure the translational temperature of the neutral atoms in the plasma flow ahead of the Hayabusa capsule. Air plasma emissions were detected at high resolution, but not at high enough signal to noise to measure the linewidth with sufficient accuracy. As expected, the measurements demonstrate the absence of significant pressure broadening in the lines compared with plasma wind-tunnel conditions.

Excitations and benchmark ensemble density functional theory for two electrons.

A new method for extracting ensemble Kohn-Sham potentials from accurate excited state densities is applied to a variety of two-electron systems, exploring the behavior of exact ensemble density functional theory. The issue of separating the Hartree energy and the choice of degenerate eigenstates is explored. A new approximation, spin eigenstate Hartree-exchange, is derived. Exact conditions that are proven include the signs of the correlation energy components and the asymptotic behavior of the potential for small weights of the excited states. Many energy components are given as a function of the weights for two electrons in a one-dimensional flat box, in a box with a large barrier to create charge transfer excitations, in a three-dimensional harmonic well (Hooke's atom), and for the He atom singlet-triplet ensemble, singlet-triplet-singlet ensemble, and triplet bi-ensemble.

Modelling borosilicate glasses of nuclear interest with the help of RMC, WAXS, neutron diffraction and 11B NMR

In this study, the structures of four borosilicate glasses of nuclear interest were investigated by performing Reverse Monte Carlo (RMC) simulations with the help of experimental data from Wide Angle X-ray Scattering (WAXS), neutron diffraction and 11B Nuclear Magnetic Resonance (NMR). Three to six oxide glasses based on Si, B, Na, Ca, Al and Zr species were modelled. For each glass, the boron coordination calculated relied on the experimental value, enabling accurate four-fold boron proportions to be obtained. The local environment and medium range order of glasses were inferred from the atomistic configurations, with an emphasis on the six oxide glass. Both proportion variations in structural units centred on silica atoms and atomic triplet average angles XOY (X, Y=Si, B, Al, Zr) and OXO were also quantified. More generally, we showed that EPSR succeeds in modelling local and medium range order of borosilicate glasses, even with complex compositions.

Electron delocalization index based on bond order orbitals

A new index of electron delocalization in atomic rings is introduced and briefly discussed. The newly proposed delocalization descriptor is defined as an atom averaged measure of the effectiveness of forming linear combinations from two-center bond-order orbitals for a given sequence of bonded atomic triplets, and corresponds directly to electron population analysis; it allows one to get very compact and intuitive description of π-conjugation effects without additional parametrization and calibration to the reference molecular systems. The numerical results of illustrative calculations for several typical aromatic and homoaromatic compounds seem to validate the presented methodology and definitions.

Path-integral Mayer-sampling calculations of the quantum Boltzmann contribution to virial coefficients of helium-4

We present Mayer-sampling Monte Carlo calculations of the quantum Boltzmann contribution to the virial coefficients B(n), as defined by path integrals, for n = 2 to 4 and for temperatures from 2.6 K to 1000 K, using state-of-the-art ab initio potentials for interactions within pairs and triplets of helium-4 atoms. Effects of exchange are not included. The vapor-liquid critical temperature of the resulting fourth-order virial equation of state is 5.033(16) K, a value only 3% less than the critical temperature of helium-4: 5.19 K. We describe an approach for parsing the Boltzmann contribution into components that reduce the number of Mayer-sampling Monte Carlo steps required for components with large per-step time requirements. We estimate that in this manner the calculation of the Boltzmann contribution to B(3) at 2.6 K is completed at least 100 times faster than the previously reported approach.

BCL::EMAS — Enantioselective Molecular Asymmetry Descriptor for 3D-QSAR

Stereochemistry is an important determinant of a molecule’s biological activity. Stereoisomers can have different degrees of efficacy or even opposing effects when interacting with a target protein. Stereochemistry is a molecular property difficult to represent in 2D-QSAR as it is an inherently three-dimensional phenomenon. A major drawback of most proposed descriptors for 3D-QSAR that encode stereochemistry is that they require a heuristic for defining all stereocenters and rank-ordering its substituents. Here we propose a novel 3D-QSAR descriptor termed Enantioselective Molecular ASymmetry (EMAS) that is capable of distinguishing between enantiomers in the absence of such heuristics. The descriptor aims to measure the deviation from an overall symmetric shape of the molecule. A radial-distribution function (RDF) determines a signed volume of tetrahedrons of all triplets of atoms and the molecule center. The descriptor can be enriched with atom-centric properties such as partial charge. This descriptor showed good predictability when tested with a dataset of thirty-one steroids commonly used to benchmark stereochemistry descriptors (r2 = 0.89, q2 = 0.78). Additionally, EMAS improved enrichment of 4.38 versus 3.94 without EMAS in a simulated virtual high-throughput screening (vHTS) for inhibitors and substrates of cytochrome P450 (PUBCHEM AID891).

Polaron master equation theory of the quantum-dot Mollow triplet in a semiconductor cavity-QED system

We present a comprehensive theoretical study of the resonance fluorescence spectra of an coherently-driven quantum dot (QD) placed inside a high-$Q$ semiconductor cavity and interacting with an acoustic-phonon bath. We derive a quantum master equation (ME) in the polaron frame, which includes exciton-phonon and exciton-cavity coupling to all orders. This work details and extends the theory used in a recent paper [C. Roy and S. Hughes, Phys. Rev. Lett. 106, 247403 (2011)] to describe the QD Mollow triplet in the regime of semiconductor cavity QED. Here, we introduce two ME forms, Nakajima-Zwanzig and time convolutionless (TC), both to second order in the system--phonon-reservoir perturbation. In the polaron frame, these two ME forms are shown to yield equivalent population dynamics and fluorescence spectra for a continuous wave (cw) driving field. We also demonstrate that a Markov approximation is valid for computing the incoherent scattering processes, and we subsequently exploit the TC ME to explore the resonance fluorescence spectra of an exciton-driven QD. Both cavity-emitted and exciton-emitted spectra are studied, and these are found to have qualitatively different spectral features. Using a coherent driving field, the well-known characteristics of the atomic Mollow triplet are shown to be considerably modified with electron--acoustic-phonon scattering, and we highlight the key effects arising from both cavity coupling and electron-phonon coupling. Regimes of pronounced cavity feeding and anharmonic cavity QED are exemplified, and we find that the cavity coupling depends sensitively on the exciton-cavity detuning and the temperature of the phonon bath. We show how the full width at half maximum (linewidth) of the Mollow-triplet sidebands varies as a function of the square of the Rabi frequency of the cw pump. Phonon-mediated cavity coupling also contributes to the spectral broadening of the Mollow triplet, depending upon the exciton-cavity detuning and the strength of the exciton-cavity coupling rate. Finally, we calculate the fluorescence spectra for off-resonance cw driving and investigate the resulting Mollow-triplet linewidths.