Encoder-decoder convolutional neural network for simple CT segmentation of COVID-19 infected lungs.

This work presents the application of an Encoder-Decoder convolutional neural network (ED-CNN) model to automatically segment COVID-19 computerised tomography (CT) data. By doing so we are producing an alternative model to current literature, which is easy to follow and reproduce, making it more accessible for real-world applications as little training would be required to use this. Our simple approach achieves results comparable to those of previously published studies, which use more complex deep-learning networks.

, a Chelator for Ga Positron Emission Tomography: Hydroxide Coordination Increases Biological Stability of [Ga][Ga(BnDT3A)(OH)].

The chelator was used to produce a novel Ga complex for positron emission tomography (PET). Unusually, this system is stabilized by a coordinated hydroxide in aqueous solutions above pH 5, which confers sufficient stability for it to be used for PET. complexes Ga in a hexadentate manner, forming a complex with log ([Ga()]) = 18.

Smolyak Algorithm Adapted to a System-Bath Separation: Application to an Encapsulated Molecule with Large-Amplitude Motions.

A Smolyak algorithm adapted to system-bath separation is proposed for rigorous quantum simulations. This technique combines a sparse grid method with the system-bath concept in a specific configuration without limitations on the form of the Hamiltonian, thus achieving a highly efficient convergence of the excitation transitions for the "system" part. Our approach provides a general way to overcome the perennial convergence problem for the standard Smolyak algorithm and enables the simulation of floppy molecules with more than a hundred degrees of freedom.

Ocean Acidification Amplifies the Olfactory Response to 2-Phenylethylamine: Altered Cue Reception as a Mechanistic Pathway?

With carbon dioxide (CO) levels rising dramatically, climate change threatens marine environments. Due to increasing CO concentrations in the ocean, pH levels are expected to drop by 0.4 units by the end of the century.

The first microsolvation step for furans: New experiments and benchmarking strategies.

The site-specific first microsolvation step of furan and some of its derivatives with methanol is explored to benchmark the ability of quantum-chemical methods to describe the structure, energetics, and vibrational spectrum at low temperature. Infrared and microwave spectra in supersonic jet expansions are used to quantify the docking preference and some relevant quantum states of the model complexes. Microwave spectroscopy strictly rules out in-plane docking of methanol as opposed to the top coordination of the aromatic ring.

Intramolecular stretching vibrational states and frequency shifts of (H) confined inside the large cage of clathrate hydrate from an eight-dimensional quantum treatment using small basis sets.

We report the results of calculations pertaining to the HH intramolecular stretching fundamentals of (p-H) encapsulated in the large cage of structure II clathrate hydrate. The eight-dimensional (8D) quantum treatment assumes rotationless (j = 0) H moieties and a rigid clathrate structure but is otherwise fully coupled. The (H)-clathrate interaction is constructed in a pairwise-additive fashion, by combining the ab initio H-HO pair potential for flexible H and rigid HO [D.

Short- and Medium-Term Exposure to Ocean Acidification Reduces Olfactory Sensitivity in Gilthead Seabream.

The effects of ocean acidification on fish are only partially understood. Studies on olfaction are mostly limited to behavioral alterations of coral reef fish; studies on temperate species and/or with economic importance are scarce. The current study evaluated the effects of short- and medium-term exposure to ocean acidification on the olfactory system of gilthead seabream (), and attempted to explain observed differences in sensitivity by changes in the protonation state of amino acid odorants.

H, HD, and D in the small cage of structure II clathrate hydrate: Vibrational frequency shifts from fully coupled quantum six-dimensional calculations of the vibration-translation-rotation eigenstates.

We report the first fully coupled quantum six-dimensional (6D) bound-state calculations of the vibration-translation-rotation eigenstates of a flexible H, HD, and D molecule confined inside the small cage of the structure II clathrate hydrate embedded in larger hydrate domains with up to 76 HO molecules, treated as rigid. Our calculations use a pairwise-additive 6D intermolecular potential energy surface for H in the hydrate domain, based on an ab initio 6D H-HO pair potential for flexible H and rigid HO. They extend to the first excited (v = 1) vibrational state of H, along with two isotopologues, providing a direct computation of vibrational frequency shifts.

The inhibitory subunit of cardiac troponin (cTnI) is modified by arginine methylation in the human heart.

Background: The inhibitory subunit of cardiac troponin (cTnI) is a gold standard cardiac biomarker and also an essential protein in cardiomyocyte excitation-contraction coupling. The interactions of cTnI with other proteins are fine-tuned by post-translational modification of cTnI. Mutations in cTnI can lead to hypertrophic cardiomyopathy.

Does cage quantum delocalisation influence the translation-rotational bound states of molecular hydrogen in clathrate hydrate?

In this study, we examine the effect of a flexible description of the clathrate hydrate framework on the translation-rotation (TR) eigenstates of guest molecules such as molecular hydrogen. Traditionally, the water cage structure is assumed to be rigid, thus ignoring the quantum nature of hydrogen nuclei in the water framework. However, it has been shown that protons in a water molecule possess a marked delocalised character in many situations, ranging from water clusters to proton transfer in the bulk.

The effect of the condensed-phase environment on the vibrational frequency shift of a hydrogen molecule inside clathrate hydrates.

We report a theoretical study of the frequency shift (redshift) of the stretching fundamental transition of an H molecule confined inside the small dodecahedral cage of the structure II clathrate hydrate and its dependence on the condensed-phase environment. In order to determine how much the hydrate water molecules beyond the confining small cage contribute to the vibrational frequency shift, quantum five-dimensional (5D) calculations of the coupled translation-rotation eigenstates are performed for H in the v=0 and v=1 vibrational states inside spherical clathrate hydrate domains of increasing radius and a growing number of water molecules, ranging from 20 for the isolated small cage to over 1900. In these calculations, both H and the water domains are treated as rigid.

Influence of Solvent Representation on Nuclear Shielding Calculations of Protonation States of Small Biological Molecules.

In this study, we assess the influence of solvation on the accuracy and reliability of isotropic nuclear magnetic shielding calculations for amino acids in comparison to experimental data. We focus particularly on the performance of solvation methods for different protonation states, as biological molecules occur almost exclusively in aqueous solution and are subject to protonation with pH. We identify significant shortcomings of current implicit solvent models and present a hybrid solvation approach that improves agreement with experimental data by taking into account the presence of direct interactions between amino acid protonation state and water molecules.

The furan microsolvation blind challenge for quantum chemical methods: First steps.

Herein we present the results of a blind challenge to quantum chemical methods in the calculation of dimerization preferences in the low temperature gas phase. The target of study was the first step of the microsolvation of furan, 2-methylfuran and 2,5-dimethylfuran with methanol. The dimers were investigated through IR spectroscopy of a supersonic jet expansion.

23-Electron Octahedral Molybdenum Cluster Complex [{MoI}Cl].

Photoactive transition metal compounds that are prone to reversible redox reactions are important for myriad applications, including catalysis, optoelectronics, and sensing. This article describes chemical and electrochemical methods to prepare cluster complex (BuN)[{MoI}Cl], a rare example of a 23 e cluster complex within the family of octahedral clusters of Mo, W, and Re. The low temperature and room temperature crystal structures; electronic structure; and the magnetic, optical, and electrochemical properties of this complex are described.

Amine Catalysis for the Organocatalytic Diboration of Challenging Alkenes.

The generation of in situ sp -sp diboron adducts has revolutionised the synthesis of organoboranes. Organocatalytic diboration reactions have represented a milestone in terms of unpredictable reactivity of these adducts. However, current methodologies have limitations in terms of substrate scope, selectivity and functional group tolerance.

Octahedral molybdenum cluster complexes with aromatic sulfonate ligands.

This article describes the synthesis, structures and systematic study of the spectroscopic and redox properties of a series of octahedral molybdenum metal cluster complexes with aromatic sulfonate ligands (BuN)[{MoX}(OTs)] and (BuN)[{MoX}(PhSO)] (where X is Cl, Br or I; OTs is p-toluenesulfonate and PhSO is benzenesulfonate). All the complexes demonstrated photoluminescence in the red region and an ability to generate singlet oxygen. Notably, the highest quantum yields (>0.

Ocean acidification affects marine chemical communication by changing structure and function of peptide signalling molecules.

Ocean acidification is a global challenge that faces marine organisms in the near future with a predicted rapid drop in pH of up to 0.4 units by the end of this century. Effects of the change in ocean carbon chemistry and pH on the development, growth and fitness of marine animals are well documented.

Structurally optimised BODIPY derivatives for imaging of mitochondrial dysfunction in cancer and heart cells.

The structural features required for mitochondrial uptake of BODIPY-based optical imaging agents have been explored. The first derivatives of this class of dyes shown to have mitochondrial membrane potential-dependent uptake in both cancer and heart cells have been developed.

Vibrational anharmonicity of small gold and silver clusters using the VSCF method.

We study the vibrational spectra of small neutral gold (Au2-Au10) and silver (Ag2-Au5) clusters using the vibrational self-consistent field method (VSCF) in order to account for anharmonicity. We report harmonic, VSCF, and correlation-corrected VSCF calculations obtained using a vibrational configuration interaction approach (VSCF/VCI). Our implementation of the method is based on an efficient calculation of the potential energy surfaces (PES), using periodic density functional theory (DFT) with a plane-wave pseudopotential basis.

Vibrational Signature of a Single Water Molecule Adsorbed on Pt(111): Toward a Reliable Anharmonic Description.

In this study, we present a thorough benchmarking of our direct anharmonic vibrational variation-perturbation approach for adsorbed molecules on surfaces. We then use our method to describe the vibrational structure of a water molecule adsorbed on a Pt(111) surface and compare our results with the available experimental data. By using an explicitly correlated hybrid method to describe the molecule-surface interaction, we improve on the initial periodic PBE/DZP potential energy landscape and obtain vibrational frequencies that are of near-experimental accuracy.

The nature and role of the gold-krypton interactions in small neutral gold clusters.

We investigate the nature and role of krypton embedding in small neutral gold clusters. For some of these clusters, we observe a particular site-dependent character of the Kr binding that does not completely follow the criterion of binding at low-coordinated sites, widely accepted for interaction of a noble gas with closed-shell metal systems such as metal surfaces. We aim at understanding the effect of low dimensionality and open-shell electronic structure of the odd-numbered clusters on the noble gas-metal cluster interaction.

Carbon dioxide interaction with isolated imidazole or attached on gold clusters and surface: competition between σ H-bond and π stacking interaction.

Using first principle methodologies, we investigate the subtle competition between σ H-bond and π stacking interaction between CO2 and imidazole either isolated, adsorbed on a gold cluster or adsorbed on a gold surface. These computations are performed using MP2 as well as dispersion corrected density functional theory (DFT) techniques. Our results show that the CO2 interaction goes from π-type stacking into σ-type when CO2 interacts with isolated imidazole and Au clusters or surface.

A fragment method for systematic improvement of anharmonic adsorbate vibrational frequencies: acetylene on Cu(001).

We suggest a novel method for systematic improvement of anharmonic adsorbate frequencies based on a fragment approach. The calculations are carried out by considering the adsorbed molecule separately and computing an energy correction using high-level ab initio method in addition to a standard calculation of the whole adsorbed system using quantum mechanical techniques with periodic boundary conditions. We demonstrate its reliability for a C2H2 molecule chemisorbed on a Cu(001) surface.

Towards an understanding of the vibrational spectrum of the neutral Au7 cluster.

We present a detailed theoretical study of the vibrational spectrum of the neutral Au(7) cluster, aimed at understanding its reported experimental spectrum [P. Gruene et al., Science, 2008, 321, 674].

Assessing spin-component-scaled second-order Møller-plesset theory using anharmonic frequencies.

Four common parametrisations of spin-component-scaled second-order Møller-Plesset (MP2) theory are benchmarked by calculating the anharmonic vibrational frequencies of a test suite consisting of eighteen diatomic and five small molecules. Of the four methods, the scaled opposite-spin MP2 (SOS-MP2), the variable-scaling opposite-spin MP2 (VOS-MP2) and the spin-component-scaled MP2 (SCS-MP2) methods perform statistically better than standard MP2 theory, while the spin-component scaled for nucleic bases MP2 (SCSN-MP2) performs worse. Vibrations of closed-shell diatomic molecules are slightly more accurately described by the SOS-MP2 method of Head-Gordon (ε(MAD) =51 cm(-1) ) than the SCS-MP2 method of Grimme (ε(MAD) =61 cm(-1)) or the size-consistent parametrisation of VOS-MP2 (ε(MAD) =54 cm(-1)).