State-of-the-Art Thermochemical and Kinetic Computations for Astrochemical Complex Organic Molecules: Formamide Formation in Cold Interstellar Clouds as a Case Study.

We describe an integrated computational strategy aimed at providing reliable thermochemical and kinetic information on the formation processes of astrochemical complex organic molecules. The approach involves state-of-the-art quantum-mechanical computations, second-order vibrational perturbation theory, and kinetic models based on capture and transition state theory together with the master equation approach. Notably, tunneling, quantum reflection, and leading anharmonic contributions are accounted for in our model.

Vitamin C: an experimental and theoretical study on the gas-phase structure and ion energetics of protonated ascorbic acid.

In order to investigate the gas-phase mechanisms of the acid catalyzed degradation of ascorbic acid (AA) to furan, we undertook a mass spectrometric (ESI/TQ/MS) and theoretical investigation at the B3LYP/6-31 + G(d,p) level of theory. The gaseous reactant species, the protonated AA, [C H O ]H , were generated by electrospray ionization of a 10  M H O/CH OH (1 : 1) AA solution. In order to structurally characterize the gaseous [C H O ]H ionic reactants, we estimated the proton affinity and the gas-phase basicity of AA by the extended Cooks's kinetic method and by computational methods at the B3LYP/6-31 + G(d,p) level of theory.

Toward a General Yet Effective Computational Approach for Diffusive Problems: Variable Diffusion Tensor and DVR Solution of the Smoluchowski Equation along a General One-Dimensional Coordinate.

A generalization to arbitrary large amplitude motions of a recent approach to the evaluation of diffusion tensors [ J. Comput. Chem.

Chain length, temperature and solvent effects on the structural properties of α-aminoisobutyric acid homooligopeptides.

Non-coded α-amino acids, originally exploited by nature, have been successfully reproduced by recent synthetic strategies to confer special structural and functional properties to small peptides. The most known and well-studied atypical residue is α-aminoisobutyric acid (Aib), which is contained in a fairly large number of peptides with known antibiotic effects. Here, we report on a molecular dynamics (MD) study of a series of homooligopeptides based on α-aminoisobutyric acid (Aib) with increasing length (Ac-(Aib)n-NMe, n = 5, 6, 7 and 10) and at various temperatures, employing a recent extension of the AMBER force field tailored for the Aib residue.

Optogenetic Control of Nodal Signaling Reveals a Temporal Pattern of Nodal Signaling Regulating Cell Fate Specification during Gastrulation.

During metazoan development, the temporal pattern of morphogen signaling is critical for organizing cell fates in space and time. Yet, tools for temporally controlling morphogen signaling within the embryo are still scarce. Here, we developed a photoactivatable Nodal receptor to determine how the temporal pattern of Nodal signaling affects cell fate specification during zebrafish gastrulation.

New insights into the vibrational and optical signatures of trans-stilbene via integrated experimental and quantum mechanical approaches.

The structure, spectroscopic parameters and optical properties of stilbene have been investigated by a computational protocol including suitable treatment of anharmonic contributions together with new experimental results. A full reproduction of the 500-3500 cm(-1) IR spectrum has been possible using the VPT2 approach and new insights are provided in the 6000 cm(-1) region where typical signatures have been characterized as a set of overtones and combination bands. Vibrational contributions to electronic transitions have been taken into account to simulate the optical (absorption and emission) properties of stilbene.

Cultivating Chlorella vulgaris and Scenedesmus quadricauda microalgae to degrade inorganic compounds and pesticides in water.

This work evaluates the possibility of cultivating Scenedesmus quadricauda and Chlorella vulgaris microalgae in wastewater from the hydroponic cultivation of tomatoes with the aim of purifying the water. S. quadricauda and C.

Simulation of Vacuum UV Absorption and Electronic Circular Dichroism Spectra of Methyl Oxirane: The Role of Vibrational Effects.

Vibrationally resolved one-photon absorption and electronic circular dichroism spectra of (R)-methyl oxirane were calculated with different electronic and vibronic models selecting, through an analysis of the convergence of the results, the best compromise between reliability and computational cost. Linear-response TD-DFT/CAM-B3LYP/SNST electronic computations in conjunction with the simple vertical gradient vibronic model were chosen and employed for systematic comparison with the available experimental data. Remarkable agreement between simulated and experimental spectra was achieved for both one-photon absorption and circular dichroism concerning peak positions, relative intensities, and general spectral shapes considering the computational efficiency of the chosen theoretical approach.

Vapochromic Behaviour of Polycarbonate Films Doped with a Luminescent Molecular Rotor.

We report on vapochromic films suitable for detecting volatile organic compounds (VOCs), based on polycarbonate (PC) doped with 4-(triphenylamino)phthalonitrile (), a fluorescent molecular rotor sensitive to solvent polarity and viscosity. PC films of variable thickness (from 20 up to 80 µm) and containing small amounts of (0.05 wt.

Vibronic Effects on Rates of Excitation Energy Transfer and Their Temperature Dependence.

Vibronic effects on rate constants governing excitation energy transfer between different electronic states have been studied within the adiabatic regime and the harmonic oscillator approximation, possibly including bulk solvent effects with the polarizable continuum model. A recent implementation in the Gaussian package has been extended for this purpose, with the possibility of taking into account frequency shifts and mode mixing effects between ground and excited electronic states. The potentialities of the new computational tool have been analyzed for a number of case studies, including excimers of naphthalene and zinc porphyrin complexes.

Tuning of dye optical properties by environmental effects: a QM/MM and experimental study.

The present work is aimed at a deeper investigation of two recently synthesized heteroaromatic fluorophores by means of a computational multilayer approach, integrating quantum mechanics (QM) and molecular mechanics (MM). In particular, dispersion of the title dyes in a polymer matrix is studied in connection with potential applications as photoactive species in luminescent solar concentrators (LSCs). Molecular dynamics simulations, based on accurate QM-derived force fields, reveal increased stiffness of these organic dyes when going from CHCl3 solution to the polymer matrix.

Neutral copper(I) complexes featuring phosphinesulfonate chelates.

The reaction of diphenylphosphinobenzenesulfonic acid with copper(i) oxide resulted in the formation of the new neutral dimeric copper(i) complex {Cu2(DPPBS)2·(MeOH)2}. X-ray diffraction studies revealed that the complex has a dimeric structure and a pyramidal trigonal geometry around the copper atom which contains coordinated methanol molecules at the copper centers. Cleavage of the dimer by reaction with various bipyrimidines enabled the preparation of the corresponding well-defined heterotopic mononuclear [Cu(P^O)(N^N)] and dinuclear {(P^O)Cu(N^N)Cu(P^O)} complexes.

Reliable vibrational wavenumbers for C=O and N-H stretchings of isolated and hydrogen-bonded nucleic acid bases.

The accurate prediction of vibrational wavenumbers for functional groups involved in hydrogen-bonded bridges remains an important challenge for computational spectroscopy. For the specific case of the C=O and N-H stretching modes of nucleobases and their oligomers, the paucity of experimental reference values needs to be compensated by reliable computational data, which require the use of approaches going beyond the standard harmonic oscillator model. Test computations performed for model systems (formamide, acetamide and their cyclic homodimers) in the framework of the second order vibrational perturbation theory (VPT2) confirmed that anharmonic corrections can be safely computed by global hybrid (GHF) or double hybrid (DHF) functionals, whereas the harmonic part is particularly challenging.

General formulation of vibronic spectroscopy in internal coordinates.

Our general platform integrating time-independent and time-dependent evaluations of vibronic effects at the harmonic level for different kinds of absorption and emission one-photon, conventional and chiral spectroscopies has been extended to support various sets of internal coordinates. Thanks to the implementation of analytical first and second derivatives of different internal coordinates with respect to cartesian ones, both vertical and adiabatic models are available, with the inclusion of mode mixing and, possibly, Herzberg-Teller contributions. Furthermore, all supported non-redundant sets of coordinates are built from a fully automatized algorithm using only a primitive redundant set derived from a bond order-based molecular topology.

Anharmonic Computations Meet Experiments (IR, Raman, Neutron Diffraction) for Explaining the Behavior of 1,3,5-Tribromo-2,4,6-trimethylbenzene.

In the present paper we first show the experimental Raman, infrared, and neutron INS spectra of tribromomesitylene (TBM) measured in the range 50-3200 cm(-1) using crystalline powders at 6 or 4 K. Then, the bond lengths and angles determined by neutron diffraction using a TBM single crystal at 14 K are compared to the computed ones at different levels of theory. Anharmonic computations were then performed on the relaxed structure using the VPT2 approach, and for the lowest normal modes, the HRAO model has led to a remarkable agreement for the assignment of the experimental signatures.

A markerless system based on smartphones and webcam for the measure of step length, width and duration on treadmill.

Background And Objective: A markerless low cost prototype has been developed for the determination of some spatio-temporal parameters of human gait: step-length, step-width and cadence have been considered. Only a smartphone and a high-definition webcam have been used.

Methods: The signals obtained by the accelerometer embedded in the smartphone are used to recognize the heel strike events, while the feet positions are calculated through image processing of the webcam stream.

Methods for Calculating Partition Functions of Molecules Involving Large Amplitude and/or Anharmonic Motions.

We present a method for calculating partition functions taking into account anharmonic contributions for systems involving both small-amplitude vibrations and hindered rotations. The Wang-Landau scheme is used in the first case, while two alternative schemes are used for hindered rotation based on imaginary time propagation and fitting of the exact energy levels as a function of quantum number. These two schemes are shown to be complementary in their ranges of applicability (in terms of the torsional rotational constant and the relevant potential).

Evaluation of gender-related differences in co-contraction activity of shank muscles during gait.

This study aims to investigate the possible differences between genders in co-contractions of tibialis anterior (TA) and gastrocnemius lateralis (GL), during walking at self-selected speed. To this purpose, the statistical gait analysis (SGA) was performed on seven female (F-group) and seven male (M-group) adults. SGA is a recently developed methodology for the characterization of gait, by averaging spatiotemporal and electromyographic parameters over hundreds of strides per subject.

Insights into structural and dynamical features of water at halloysite interfaces probed by DFT and classical molecular dynamics simulations.

Density functional theory calculations and classical molecular dynamics simulations have been used to investigate the structure and dynamics of water molecules on kaolinite surfaces and confined in the interlayer of a halloysite model of nanometric dimension. The first technique allowed us to accurately describe the structure of the tetrahedral-octahedral slab of kaolinite in vacuum and in interaction with water molecules and to assess the performance of two widely employed empirical force fields to model water/clay interfaces. Classical molecular dynamics simulations were used to study the hydrogen bond network structure and dynamics of water adsorbed on kaolinite surfaces and confined in the halloysite interlayer.

Temperature Dependence of Radiative and Nonradiative Rates from Time-Dependent Correlation Function Methods.

The temperature dependence of the rate constants in radiative and nonradiative decays from excited electronic states has been studied using a time-dependent correlation function approach in the framework of the adiabatic representation and the harmonic oscillator approximation. The present work analyzes the vibrational aspect of the processes, which gives rise to the temperature dependence, with the inclusion of mode-mixing, as well as of frequency change effects. The temperature dependence of the rate constants shows a contrasting nature, depending on whether the process has been addressed within the Franck-Condon approximation or beyond it.

Vibrationally resolved NEXAFS at C and N K-edges of pyridine, 2-fluoropyridine and 2,6-difluoropyridine: A combined experimental and theoretical assessment.

In the present work, the near edge X-ray absorption spectroscopy (NEXAFS) spectra at both C and N K-edges of pyridine, 2-fluoropyridine, and 2,6-difluoropyridine have been studied both experimentally and theoretically. From an electronic point of view, both transition potential density functional theory and time-dependent density functional theory approaches lead to reliable results provided that suitable basis sets and density functionals are employed. In this connection, the global hybrid B3LYP functional in conjunction with the EPR-III basis set appears particularly suitable after constant scaling of the band positions.

Virtual eyes for technology and cultural heritage: toward computational strategy for new and old indigo-based dyes.

A cost-effective, robust, and reliable computational strategy is applied to simulate peak positions and band-shapes of UV-vis spectra together with the dye colours perceived by human eyes. The features of our virtual multifrequency spectrometer (VMS) relevant to this topic are sketched with special focus on the selection of density functional, vibronic model, and solvent description. Furthermore, the new VMS-Draw graphical user interface (GUI) is employed for user-friendly pre- and post-processing of the computed data.