Suite Of Programs Research Articles

Kinetics of the Reactions of Chlorinated Very Short-Lived Substances (VSLSs) with Chlorine Atoms.

Chlorinated very short-lived substances (VSLSs), which are not controlled by the Montreal Protocol, are of current concern with regard to recovery of stratospheric ozone. Further study is needed on the temperature dependences of chlorinated VSLSs relevant to atmospheric conditions. Here, the kinetics of chlorinated VSLSs, such as chloroform (CHCl3), dichloromethane (CH2Cl2), dichloroethane (CH2ClCH2Cl), and trichloroethene (C2HCl3) reacting with chlorine atoms, were investigated between 180 and 400 K, expanding the range of temperatures relative to previous studies. RRKM/Master Equation and Canonical Variational Transition State Theory were utilized to calculate the rate coefficients using the MultiWell suite of programs. CCSD(T), QCISD(T), and M062X with aug-cc-pV(T+d)Z levels of theory were used to calculate the kinetic parameters. Arrhenius equations obtained from fits to the calculated rate coefficients are k1 = (2.66 ± 0.7) × 10-12 exp [(-927 ± 131)/T] cm3 molecule-1 s-1, k2 = (8.99 ± 0.3) × 10-12 exp [(-957 ± 19)/T] cm3 molecule-1 s-1, k3 = (1.51 ± 0.16) × 10-11 exp [(-714 ± 54)/T] cm3 molecule-1 s-1, and k4 = (9.17 ± 1.8) × 10-12 exp [(612 ± 101)/T] cm3 molecule-1 s-1 for the reactions of CHCl3, CH2Cl2, CH2ClCH2Cl, and C2HCl3 with Cl atoms, respectively. The rate coefficients for the reactions of chlorinated VSLSs with Cl atoms from this study are compared with the most recent recommended values from the NASA/JPL and IUPAC evaluations and with literature values. The reactivity trends of the reactions are discussed.

Seafloor and Ocean Crust Structure of the Kerguelen Plateau from Marine Geophysical and Satellite Altimetry Datasets

The volcanic Kerguelen Islands are formed on one of the world’s largest submarine plateaus. Located in the remote segment of the southern Indian Ocean close to Antarctica, the Kerguelen Plateau is notable for a complex tectonic origin and geologic formation related to the Cretaceous history of the continents. This is reflected in the varying age of the oceanic crust adjacent to the plateau and the highly heterogeneous bathymetry of the Kerguelen Plateau, with seafloor structure differing for the southern and northern segments. Remote sensing data derived from marine gravity and satellite radar altimetry surveys serve as an important source of information for mapping complex seafloor features. This study incorporates geospatial information from NOAA, EMAG2, WDMAM, ETOPO1, and EGM96 datasets to refine the extent and distribution of the extracted seafloor features. The cartographic joint analysis of topography, magnetic anomalies, tectonic and gravity grids is based on the integrated mapping performed using the Generic Mapping Tools (GMT) programming suite. Mapping of the submerged features (Broken Ridge, Crozet Islands, seafloor fabric, orientation, and frequency of magnetic anomalies) enables analysis of their correspondence with free-air gravity and magnetic anomalies, geodynamic setting, and seabed structure in the southwest Indian Ocean. The results show that integrating the datasets using advanced cartographic scripting language improves identification and visualization of the seabed objects. The results include 11 new maps of the region covering the Kerguelen Plateau and southwest Indian Ocean. This study contributes to increasing the knowledge of the seafloor structure in the French Southern and Antarctic Lands.

Phenomenological description of the acidity of the citric acid and its deprotonated species: informational-theoretical study.

In spite of the fact that molecular acidity is a fundamental physicochemical property of molecular systems, the vast majority of theoretical studies have focused attention on monoprotic acids and on the prediction of pKa's. Polyprotic acids, represent a challenge for electronic structure calculations since the multiple acidic sites result in a vast group of species with different conformations and reactivities. In this work, Information-theoretic (IT) concepts of localizability, order and uniformity are applied to the Citric Acid and its deprotonated species through the one-electron density functionals: Shannon entropy (S), Fisher information (I) and Disequilibrium (D), respectively. We pursue the goal of characterizing the acidity of the aforementioned species with the aim to associate the IT concepts to chemical features such as the polarizability of the protonated/deprotonated species, the liability of the acidic sites, atomic electrostatic potentials, covalent bonding. IT analyses looks very promising for future studies on the acidity of specific deprotonation-sites of polyprotic acids. Density functional theory (DFT) calculations were performed with Gaussian 09 program. A sensitivity analysis of the IT-measures was performed for the citric acid and the citrate using B3LYP, B3PW91, BPW91, M05-2X, M06-2X and PBEPBE functionals with the 6-311++g(3df,2p), 6-311++g(d,p), 6.311+g(d,p) and aug-cc-pVDZ basis sets. The rest of the analysis was performed with the M05-2X/6-311+G(d,p) level of theory. Additionally, aqueous media was considered by use of the SMD solvent model. The IT-measures were calculated using a suite of programs developed in our laboratory jointly with the DGRID software package.

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.

The VEGA web service: multipurpose online tools for molecular modelling and docking analyses.

The paper presents the VEGA Online web service, which includes a set of freely available tools deriving from the development of the VEGA suite of programs. In detail, the paper is focused on two tools: the VEGA Web Edition (WE) and the Score tool. The former is a versatile file format converter including relevant features for 2D/3D conversion, for surface mapping and for editing/preparing input files. The Score application allows rescoring docking poses and in particular includes the MLP Interactions Scores (MLPInS) for describing hydrophobic interactions. To the best of our knowledge, this web service is the only available resource by which one can calculate both the virtual log P of a given input molecule according to the MLP approach plus the corresponding MLP surface.

Friedel-Crafts Reaction of Vinyltrimethoxysilane with Styrene and Composite Materials on Their Base

Friedel-Crafts alkylation reaction of vinyltri-methoxysilane with styrene was performed in the pres-ence of anhydrous AlCl3. Alkoxy(4-vinylphenethyl)silane has been obtained. The synthesized products were identified by 1H, 13C, COSY NMR, and FTIR spectroscopy. Calculations using the quantum-chemical non-empirical density functional theory (DFT) method for the reaction between vinyltrimethoxysilane and styrene performed for ortho-, meta- and para-positions were discussed. For the theoretical modeling an online prediction program "Priroda 04: A quantum-chemical program suite" was used. Composite materials based on wood sawdust with various dispersion qualities and synthesized trimethoxysilylated styrene as a binding and reinforcing agent with degrees of silylation (5 %), in the presence of various organic/inorganic additives, fire retardants, and antioxidants, have been developed at different temperatures and pressures via hot press method or extrusion. The physico-mechanical properties of composites have been investigated.

Reactivity properties of the HOSO and HSO2 isomers in liquid medium: a sequential Monte Carlo/quantum mechanics study.

The rationalization of acid rain formation steps is fundamental for mitigating its effects. It is believed the hydroxysulfinyl radical is an intermediate species for the production of atmospheric sulfuric acid. Two stable configurations HOSO and HSO2 have been reported for such a radical in the gas phase. This work aims at studying these isomers in the aqueous medium. The electrical and reactivity quantities - electronic chemical potential ([Formula: see text]), chemical hardness ([Formula: see text]), and electrophilicity ([Formula: see text]) - are here calculated and compared. Considering first solvation shells (15H2O for HSO2 and 23H2O for HOSO), an increase of 25% in the dipole moment of HSO2 was obtained, while the dipole moment of HOSO decreases in 11%. Both solvated isomers grow softer ([Formula: see text] decreases) contrasted to the gas phase. HOSO and HSO2 are studied through a sequential Monte Carlo/quantum mechanics approach. Lennard-Jones plus the Coulomb potentials were used to represent intermolecular potential interaction in the frame of the DICE package. Molecular structure calculations were performed at CASPT2/aug - cc - pV(T + d)Z level of theory using the MOLPRO suite of programs.

Continuous development in macromolecular crystallography with CCP4.

The evolution of the Collaborative Computational Project No. 4 (CCP4) has been described in a new article by Agirre et al. [(2023). Acta Cryst. D79, 449-461] that should provide the definitive reference for the CCP4 suite of programs.

Hibridon: A program suite for time-independent non-reactive quantum scattering calculations

Hibridon is a program package to solve the close-coupled equations which occur in the time independent quantum treatment of inelastic atomic and molecular collisions. Gas-phase scattering, photodissociation, collisions of atoms and/or molecules with flat surfaces, and bound states of weakly-bound complexes can be treated. From calculation of the S matrix, integral and differential cross sections, stereodynamic (alignment and steric asymmetry) cross sections, as well as more specialized quantities, such as transport and tensor cross sections, and cross sections between hyperfine levels, and photodissociation amplitudes can be obtained. The program is capable of treating closed-shell systems where the nuclear motion takes place on a single Born-Oppenheimer potential as well as open-shell systems for which the nuclear motion can evolve on several coupled electronic (Born-Oppenheimer) potentials. Program summaryProgram Title: HibridonCPC Library link to program files:https://doi.org/10.17632/sk9zcvz8vs.1Developer's repository link:https://doi.org/10.5281/zenodo.7551616Licensing provisions: GPLv3Programming language: Fortran 90External routines/libraries: LAPACK, BLASNature of problem: Solution of the time-independent Schrödinger equation for the inelastic scattering of atoms and molecules, for the photodissociation of molecules, and for the ro-vibrational motion of weakly bound molecular complexes.Solution method: The scattering wavefunction is expanded in a set of internal states of the system, constructed as direct products of the internal states of one (or both) fragments and angular functions which describe the rotation of one collision partner about the other. The Schrödinger equation for the nuclear motion is solved by determining the expansion coefficients as a function of the interparticle separation starting from the short-range classically forbidden region outwards to the asymptotic region. The S matrix is given by the asymptotic behavior of the wavefunction. Integral and differential cross sections, as well as other scattering and photodissociation quantities are calculated from the S matrix.

Disentangling the confounding spectroscopy of C1 molecules: Without symmetry as a guide, everything is allowed

The spectra of C1 molecules are confounding in that each of the fundamental vibrational modes transform as the same irreducible representation (A) and hence each band consists of a seemingly random distribution of a-, b-, and c-type transitions. This is in contrast to higher symmetry molecules for which band types are readily deduced by simple symmetry rules. Herein, we present a method to simulate the convoluted rotational contours in the gas-phase spectra of C1 molecules by combining existing ab initio calculations with Colin Western’s pgopher rotational contour program. Specifically, ab initio calculations in the NWChem suite of programs were employed to predict the components of the dipole moment derivatives along the principal axes of the moments of inertia. This information was then input into pgopher to model the fundamental band contours as a sum of a-, b-, and c-type transitions. This method was applied to simulate the rotational contour spectra of a series of representative C1 molecules which were then compared against both ab initio stick spectra and experimentally measured broadband IR spectra from the Pacific Northwest National Laboratory infrared gas-phase database. In addition to providing further insight beyond what is revealed in a typical stick spectrum, the simulated contours showed good agreement with the measured spectra.

New experimental evidence for pervasive dynamics in proteins.

There is ample computational, but only sparse experimental data suggesting that pico-ns motions with 1 Å amplitude are pervasive in proteins in solution. Such motions, if present in reality, must deeply affect protein function and protein entropy. Several NMR relaxation experiments have provided insights into motions of proteins in solution, but they primarily report on azimuthal angle variations of vectors of covalently-linked atoms. As such, these measurements are not sensitive to distance fluctuations, and cannot but under-represent the dynamical properties of proteins. Here we analyze a novel NMR relaxation experiment to measure amide proton transverse relaxation rates in uniformly 15 N labeled proteins, and present results for protein domain GB1 at 283 and 303 K. These relaxation rates depend on fluctuations of dipolar interactions between 1 HN and many nearby protons on both the backbone and sidechains. Importantly, they also report on fluctuations in the distances between these protons. We obtained a large mismatch between rates computed from the crystal structure of GB1 and the experimental rates. But when the relaxation rates were calculated from a 200 ns molecular dynamics trajectory using a novel program suite, we obtained a substantial improvement in the correspondence of experimental and theoretical rates. As such, this work provides novel experimental evidence of widespread motions in proteins. Since the improvements are substantial, but not sufficient, this approach may also present a new benchmark to help improve the theoretical forcefields underlying the molecular dynamics calculations.

Hydrogen bonding guest-water interactions in pinacolone, tert-butyl amine, and tert-butylmethyl ether: a theoretical study on energetics, structure, and topological +

In guest-host interactions, guest molecules used for hydrogen bonding potential of clathrate hydrate cages are involved as "promoters" for hydrogen or methane storage. Among the promoter molecules, there are pinacolone and tert-butylmethyl ether containing oxygen atom, and tert-butyl amine among those containing nitrogen atom. The dimer and trimer interactions of these molecules with the water clusters were investigated. The cooperativity effect, which is a measure of the hydrogen bonding of these oxygen and nitrogen-containing complexes, was calculated and these complexes were analyzed. Moreover, molecular electrostatic potential (MEP) analysis was performed to determine intermolecular interactions. Clusters of several molecules may seem like a non-significant state of matter; however, in systematic studies with small clusters, important results can be obtained. Therefore, it is very useful to work with clusters to understand the properties of the dense phase, and this study aimed to examine the properties of structures, energies, infrared vibration frequencies, and topological parameters, which develop as a result of the interaction of structures in different clusters with water molecules. The MP2 level was performed using aug-cc-pVDZ basis set calculations for this study. Tight converting criteria were used in the optimization step. Harmonic vibrational modes were calculated at the MP2/aug-cc-pVDZ level. Each minima obtained from the MP2 level was subjected to single-point energy calculations using CCSD(T) levels with the aug-cc-pVDZ basis set by the Gaussian16 package program suite. Thetopological analyseswere performed withnon-covalent interaction (NCI). MEP surface of the complex was also composed by Gaussian program using the optimized geometry at a MP2/aug-cc-pvdz level.

Evaluating programs for young people with a family member with mental health challenges: protocol for a mixed methods, longitudinal, collaborative evaluation

BackgroundYoung people with a sibling or parent who experiences mental health challenges have their own support needs. Most programs designed for this population lack a strong evidence base, and the involvement of young people in the development and evaluation of programs designed to support them is unclear or lacking.MethodsThis paper describes a protocol for a mixed methods, longitudinal, collaborative evaluation of a suite of programs delivered by The Satellite Foundation, a not-for-profit organisation for young people (5–25 years) who have a family member with mental health challenges. Young people’s lived experience and knowledge will guide the research approach. Institutional ethics approval has been obtained. Over a three year period, approximately 150 young people will be surveyed online on various wellbeing outcome measures, prior to, six and twelve months following program participation with data analysed using multi-level modelling. Groups of young people will be interviewed after participating in different Satellite programs each year. An additional group of young people will be interviewed individually over time. Transcripts will be analysed using thematic analysis. Young people’s creative artworks on their experiences will be included as part of the evaluation data.DiscussionThis novel, collaborative evaluation will provide vital evidence on young people’s experiences and outcomes during their time with Satellite. Findings will be used to inform future program development and policy. The approach used here may guide other researchers engaging in collaborative evaluations with community organisations.

The Allied Health Expansion Program: Rethinking how to prepare a workforce to enable improved public health outcomes.

Improvements in global public health require universal health care supported by a health workforce with competencies appropriate for local population needs-the right capabilities, in the right place, and at the right time. Health inequities persist in Tasmania, and Australia more broadly, most notably for those people living in rural and remote areas. The article describes the curriculum design thinking approach being used to codesign and develop a connected system of education and training to target intergenerational change in the allied health (AH) workforce capacity in Tasmania, and beyond. A curriculum design thinking process is engaging AH participant groups (faculty, AH professionals, and leaders across health, education, aged and disability sectors) in a series of focus groups and workshops. The design process deals with four questions: What is? What if? What wows? and What works? It also involves Discover, Define, Develop and Deliver phases that continue to inform the development of the new suite of AH education programs. The British Design Council's Double Diamond model is used to organize and interpret stakeholder input. During the initial design thinking discover phase, stakeholders identified four overarching problems: rurality, workforce challenges, graduate skill set shortfalls, and clinical placements and supervision. These problems are described in terms of relevance to the contextual learning environment in which AH education innovation is occurring. The develop phase of design thinking continues to involve working collaboratively with stakeholders to codesign potential solutions. Solutions to date include AH advocacy, a transformative visionary curriculum, and an interprofessional community-based education model. In Tasmania, innovative educational innovations are catalyzing attention and investment in the effective preparation of AH professionals for practice to deliver improved public health outcomes. A suite of AH education that is deeply networked and engaged with Tasmanian communities is being developed to drive transformational public health outcomes. These programs are playing an important role in strengthening the supply of allied health professionals with the right capabilities for metropolitan, regional, rural, and remote Tasmania. They are situated in a broader AH education and training strategy that supports the ongoing development of the AH workforce to better meet the therapy needs of people in Tasmanian communities.

Ot2Rec: A semi-automatic, extensible, multi-software tomographic reconstruction workflow.

Electron cryo-tomography (cryo-ET) is an imaging technique that produces relatively high-resolution three-dimensional images. With the advancement in microscopic and computational technologies, data collection and processing on both the hardware and software facets have become ever faster and more automated. Nowadays, tens of tilt series (up to several terabytes in total) can be collected per day, in turn shifting the experimental bottleneck to data processing. Here we present Ot2Rec, a novel workflow for performing tomographic image processing, providing access to several state-of-the-art tools within a single “wrapper” user interface. The functionality of Ot2Rec covers most tasks within a common image processing pipeline, from the motion-correction of raw multi-frame micrographs to the estimation of the true defoci from which the contrast transfer function (CTF) of images is calculated, and from the alignment of tilted image stacks to the full reconstruction of the final 3D tomogram. Moreover, Ot2Rec can carry out several novel post-processing operations such as simulation of stack point-spread functions and CTF corrections by means of deconvolution. Ot2Rec also provides automated reporting of processing parameters and quality metrics for optimisation and performance evaluation of processing workflows. Ot2Rec has been developed with the central philosophy of metadata unification. We have unified the metadata structure across the suite, so that the components within the suite can be used in a user/developer defined order (for instance, MotionCor2 -> CTFFind4 -> IMOD) with data flowing seamlessly between any pair of components and with consideration of required prerequisites. Lastly, Ot2Rec is an open-source program suite (Apache License V2). The raw code and documentation can be found at https://github.com/rosalindfranklininstitute/Ot2Rec.

Molecular structure and spectroscopic properties of two radicals of C4H2N: a DFT study.

The cyano propargyl radical (CH2C3N and HC3HCN) is important reaction intermediate in both combustion flames and extraterrestrial environments such as cold molecular clouds and circumstellar envelopes of carbon stars. The acquisition of spectroscopic constants and anharmonic effect facilitates a more in-depth study of this radical. However, the data available in the literature do not allow the precise predictions for it in the interstellar medium. In this work, complete spectroscopic parameters as well as anharmonic constants of two radicals of C4H2N have been evaluated by different DFT methods. The calculated results show that it is reasonable to study the molecular spectroscopic properties of C4H2N by wB97XD/6-311++G theoretical level. On this basis, the sextic centrifugal distortion constants, anharmonic constants, vibration-rotation interaction constants, and so on are predicted for the study of high-precision rovibrational spectrum. In addition, the relationship between the anharmonic effect and vibration mode of CH2C3N and HC3HCN and their infrared spectroscopic characteristics are discussed. The calculation of the anharmonic force fields and spectroscopy properties was performed using B3LYP, B3PW91, CAM-B3LYP, and wB97XD methods combined with the 6-311++G and aug-ccpVTZ basis sets, respectively, by the Gaussian16 program suite. The IR spectra were performed with Multiwfn3.8.

Electro-optic properties of ZrO2 , HfO2 , and LiNbO3 ferroelectric phases: A comparative density functional study

We report the Pockels electro-optic properties of ${\mathrm{ZrO}}_{2}$ and ${\mathrm{HfO}}_{2}$ orthorhombic $Pbc{2}_{1}$ and rhombohedral $R3m$ ferroelectric phases, and we compare them to the well-known rhombohedral $R3c$ ${\mathrm{LiNbO}}_{3}$ Pockels material from density functional theory calculations using the crystal suite of programs. Specifically, three essential processes are explicitly investigated: The electronic, the ionic (or vibrational), and the piezoelectric contributions. Our calculations reveal that the ionic part coming from the low-frequency phonon modes contributes the most to the electro-optic coefficients of rhombohedral ${\mathrm{LiNbO}}_{3}$ and of orthorhombic ${\mathrm{ZrO}}_{2}$ and ${\mathrm{HfO}}_{2}$. Additionally, the low-frequency phonon modes exhibit zero contribution to the Pockels coefficients of ${\mathrm{ZrO}}_{2}$ and ${\mathrm{HfO}}_{2}$ rhombohedral $R3m$ phase.

SonicPy: a suite of programs for ultrasound pulse-echo data acquisition and analysis

ABSTRACT Sound speed and elastic constants measurements in solids and liquids are commonly performed using the ultrasound pulse-echo technique. Recent advances have expanded the use of this technique at numerous high pressure synchrotron beamlines and offline laboratories. However, the increased experimental throughput has revealed many limitations in existing software for handling the rapid measurement and the subsequent data-reduction. We report the development of a collection of computer programs for sound speed measurements using the ultrasound pulse-echo technique, compatible with stepped multi-frequency, as well as broadband-pulse, couplant-corrected methods. The programs provide a highly interactive graphical interface, enable efficient measurement, exploration and near real-time analysis of the ultrasound data, and contain features useful for working with samples under high pressure and/or high temperature. The included analysis programs can alleviate the time required for data reduction from hours to less than a minute, allowing users to make timely and informed decisions regarding the appropriate experimental parameters.

Curator – A data curation tool for clinical real-world evidence

ObjectiveThis research aims to establish an efficient, systematic, reproducible, and transparent solution for advanced curation of real-world data, which are highly complex and represent an invaluable source of information for academia and industry. Materials and methodsWe propose a novel software solution that splits the statistical analytical pipeline into two phases. The first phase is implemented through Curator, which performs data engineering and data modelling on deidentified real-world data to achieve advanced curation and provides selected information ready to be analyzed in the second phase by statistical packages. Curator is made of a suite of Python programs and uses MySQL as its database management system. Curator has been utilised with several UK primary and secondary care data sources. ResultsCurator has been used in 25 completed clinical and health economics research studies. Their output has been published in 2 NIHR-funded reports and 33 prestigious international peer-reviewed journals and presented at 38 global conferences. Curator has consistently reduced research time and costs by over 36% and made research more reproducible and transparent. DiscussionCurator fits in well with recent UK governmental guidelines that recognise health data curation as a complex standalone technical challenge. Curator has been used extensively on UK real-world data and can handle several linked datasets. However, for Curator to be accessed by a wider audience, it needs to become more user-friendly. ConclusionCurator has proven to be a cost-effective and trustworthy data curation tool, which should be developed further and made available to third parties.

Catalytic exploration of NHC-Ag(I)HMDS complexes for the hydroboration and hydrosilylation of carbonyl compounds.

The synthesis and full characterisation of two silver(I) amido complexes, stabilised by ancillary N-heterocyclic carbene (NHC) ligands is presented. The light stable complexes [Ag(IDipp)HMDS] 3 and [Ag(IAd)HMDS] 4 were explored as suitable pre-catalysts in the hydroboration and hydrosilylation of a range of carbonyl substrates, with complex 3 out-performing 4 and our previous phosphine-stabilised lead catalyst [Ag(PCy3)HMDS] 5. This study highlights that changing the stabilising Lewis donor in the silver(I)amide system has an influence on catalytic efficiency. Finally, to shed light on the catalytic differences of pre-catalysts 3-5, we used a suite of programs to examine the influence of steric bulk on the Lewis donor ligand including percent buried volume (%VBur), Solid-G and AtomAccess which revealed the most sterically protected Ag(I) metal centre correlated to the most effective pre-catalyst 3.