Bn2DT3A, a Chelator for 68Ga Positron Emission Tomography: Hydroxide Coordination Increases Biological Stability of [68Ga][Ga(Bn2DT3A)(OH)].

The chelator Bn2DT3A was used to produce a novel 68Ga 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. Bn2DT3A complexes Ga3+ in a hexadentate manner, forming a mer-mer complex with log K([Ga(Bn2DT3A)]) = 18.25. Above pH 5, the hydroxide ion coordinates the Ga3+ ion following dissociation of a coordinated amine. Bn2DT3A radiolabeling displayed a pH-dependent speciation, with [68Ga][Ga(Bn2DT3A)(OH)]- being formed above pH 5 and efficiently radiolabeled at pH 7.4. Surprisingly, [68Ga][Ga(Bn2DT3A)(OH)]- was found to show an increased stability in vitro (for over 2 h in fetal bovine serum) compared to [68Ga][Ga(Bn2DT3A)]. The biodistribution of [68Ga][Ga(Bn2DT3A)(OH)]- in healthy rats showed rapid clearance and excretion via the kidneys, with no uptake seen in the lungs or bones.

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

With carbon dioxide (CO2) levels rising dramatically, climate change threatens marine environments. Due to increasing CO2 concentrations in the ocean, pH levels are expected to drop by 0.4 units by the end of the century. There is an urgent need to understand the impact of ocean acidification on chemical-ecological processes. To date, the extent and mechanisms by which the decreasing ocean pH influences chemical communication are unclear. Combining behaviour assays with computational chemistry, we explore the function of the predator related cue 2-phenylethylamine (PEA) for hermit crabs (Pagurus bernhardus) in current and end-of-the-century oceanic pH. Living in intertidal environments, hermit crabs face large pH fluctuations in their current habitat in addition to climate-change related ocean acidification. We demonstrate that the dietary predator cue PEA for mammals and sea lampreys is an attractant for hermit crabs, with the potency of the cue increasing with decreasing pH levels. In order to explain this increased potency, we assess changes to PEA's conformational and charge-related properties as one potential mechanistic pathway. Using quantum chemical calculations validated by NMR spectroscopy, we characterise the different protonation states of PEA in water. We show how protonation of PEA could affect receptor-ligand binding, using a possible model receptor for PEA (human TAAR1). Investigating potential mechanisms of pH-dependent effects on olfactory perception of PEA and the respective behavioural response, our study advances the understanding of how ocean acidification interferes with the sense of smell and thereby might impact essential ecological interactions in marine ecosystems.

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. Contrasting comparison strategies, which emphasize either the experimental or the theoretical input, are explored. Within the harmonic approximation, only a few composite computational approaches are able to achieve a satisfactory performance. Deuteration experiments suggest that the harmonic treatment itself is largely justified for the zero-point energy, likely and by design due to the systematic cancellation of important anharmonic contributions between the docking variants. Therefore, discrepancies between experiment and theory for the isomer abundance are tentatively assigned to electronic structure deficiencies, but uncertainties remain on the nuclear dynamics side. Attempts to include anharmonic contributions indicate that for systems of this size, a uniform treatment of anharmonicity with systematically improved performance is not yet in sight.

H2, HD, and D2 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 H2, HD, and D2 molecule confined inside the small cage of the structure II clathrate hydrate embedded in larger hydrate domains with up to 76 H2O molecules, treated as rigid. Our calculations use a pairwise-additive 6D intermolecular potential energy surface for H2 in the hydrate domain, based on an ab initio 6D H2-H2O pair potential for flexible H2 and rigid H2O. They extend to the first excited (v = 1) vibrational state of H2, along with two isotopologues, providing a direct computation of vibrational frequency shifts. We show that obtaining a converged v = 1 vibrational state of the caged molecule does not require converging the very large number of intermolecular translation-rotation states belonging to the v = 0 manifold up to the energy of the intramolecular stretch fundamental (≈4100 cm-1 for H2). Only a relatively modest-size basis for the intermolecular degrees of freedom is needed to accurately describe the vibrational averaging over the delocalized wave function of the quantum ground state of the system. For the caged H2, our computed fundamental translational excitations, rotational j = 0 → 1 transitions, and frequency shifts of the stretch fundamental are in excellent agreement with recent quantum 5D (rigid H2) results [A. Powers et al., J. Chem. Phys. 148, 144304 (2018)]. Our computed frequency shift of -43 cm-1 for H2 is only 14% away from the experimental value at 20 K.

Intramolecular stretching vibrational states and frequency shifts of (H2)2 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-H2)2 encapsulated in the large cage of structure II clathrate hydrate. The eight-dimensional (8D) quantum treatment assumes rotationless (j = 0) H2 moieties and a rigid clathrate structure but is otherwise fully coupled. The (H2)2-clathrate interaction is constructed in a pairwise-additive fashion, by combining the ab initio H2-H2O pair potential for flexible H2 and rigid H2O [D. Lauvergnat et al., J. Chem. Phys. 150, 154303 (2019)] and the six-dimensional (6D) H2-H2 potential energy surface [R. J. Hinde, J. Chem. Phys. 128, 154308 (2008)]. The calculations are performed by first solving for the eigenstates of a reduced-dimension 6D "intermolecular" Hamiltonian extracted from the full 8D Hamiltonian by taking the H2 moieties to be rigid. An 8D contracted product basis for the solution of the full problem is then constructed from a small number of the lowest-energy 6D intermolecular eigenstates and two discrete variable representations covering the H2-monomer internuclear distances. Converged results are obtained already by including just the two lowest intermolecular eigenstates in the final 8D basis of dimension 128. The two HH vibrational stretching fundamentals are computed for three hydrate domains having an increasing number of H2O molecules. For the largest domain, the two fundamentals are found to be site-split by ∼0.5 cm-1 and to be redshifted by about 24 cm-1 from the free-H2 monomer stretch frequency, in excellent agreement with the experimental value of 26 cm-1. A first-order perturbation theory treatment gives results that are nearly identical to those of the 8D quantum calculations.

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. In the case of water clathrates, all previous TR bound-state calculations of guest molecules consider that the caging water molecules are fixed at their equilibrium geometry. Only recently, a static investigation of the role of proton configurations was performed by Bacic and co-workers by sampling a very large number of different static structures of water clathrates. Here, we investigate the importance of the rotational degrees of freedom of the water cage on the TR levels of the guest molecule using an efficient adiabatic decoupling scheme. Our approach combines rigid body diffusion Monte Carlo calculations for the description of the rotational degree of freedom of water molecules surrounding the guest molecular hydrogen to an efficient Smolyak sparse-grid technique for the calculation of the TR levels. This approach allows us to take into account the highly anharmonic nature of the rotational water motions in a high-dimensional system. The clathrate-induced splittings of the j = 1 rotational levels are much more sensitive to the quantum hydrogen delocalisation than the translational transitions. This result is in good agreement with the previous static study of Bacic and co-workers.

23-Electron Octahedral Molybdenum Cluster Complex [{Mo6I8}Cl6].

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 (Bu4N)[{Mo6I8}Cl6], 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.

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 H2 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 H2 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 H2 and the water domains are treated as rigid. The 5D intermolecular potential energy surface (PES) of H2 inside a hydrate domain is assumed to be pairwise additive. The H2-H2O pair interaction, represented by the 5D (rigid monomer) PES that depends on the vibrational state of H2, v=0 or v=1, is derived from the high-quality ab initio full-dimensional (9D) PES of the H2-H2O complex [P. Valiron et al., J. Chem. Phys. 129, 134306 (2008)]. The H2 vibrational frequency shift calculated for the largest clathrate domain considered, which mimics the condensed-phase environment, is about 10% larger in magnitude than that obtained by taking into account only the small cage. The calculated splittings of the translational fundamental of H2 change very little with the domain size, unlike the H2 j = 1 rotational splittings that decrease significantly as the domain size increases. The changes in both the vibrational frequency shift and the j = 1 rotational splitting due to the condensed-phase effects arise predominantly from the H2O molecules in the first three complete hydration shells around H2.

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. From the measured bands, it was possible to identify a persistent hydrogen bonding OH-O motif in the predominant species. From the presence of another band, which can be attributed to an OH-π interaction, we were able to assert that the energy gap between the two types of dimers should be less than or close to 1 kJ/mol across the series. These values served as a first evaluation ruler for the 12 entries featured in the challenge. A tentative stricter evaluation of the challenge results is also carried out, combining theoretical and experimental results in order to define a smaller error bar. The process was carried out in a double-blind fashion, with both theory and experimental groups unaware of the results on the other side, with the exception of the 2,5-dimethylfuran system which was featured in an earlier publication.

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. Recent evidence also suggests that a range of chemically mediated behaviours and interactions in marine fish and invertebrates will be affected. Marine animals use chemical cues, for example, to detect predators, for settlement, homing and reproduction. But, while effects of high CO2 conditions on these behaviours are described across many species, little is known about the underlying mechanisms, particularly in invertebrates. Here, we investigate the direct influence of future oceanic pH conditions on the structure and function of three peptide signalling molecules with an interdisciplinary combination of methods. NMR spectroscopy and quantum chemical calculations were used to assess the direct molecular influence of pH on the peptide cues, and we tested the functionality of the cues in different pH conditions using behavioural bioassays with shore crabs (Carcinus maenas) as a model system. We found that peptide signalling cues are susceptible to protonation in future pH conditions, which will alter their overall charge. We also show that structure and electrostatic properties important for receptor binding differ significantly between the peptide forms present today and the protonated signalling peptides likely to be dominating in future oceans. The bioassays suggest an impaired functionality of the signalling peptides at low pH. Physiological changes due to high CO2 conditions were found to play a less significant role in influencing the investigated behaviour. From our results, we conclude that the change of charge, structure and consequently function of signalling molecules presents one possible mechanism to explain altered behaviour under future oceanic pH conditions.

Amine Catalysis for the Organocatalytic Diboration of Challenging Alkenes.

The generation of in situ sp2 -sp3 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. Here a new methodology based on the use of simple amines as catalyst is reported. This methodology provides a completely selective transformation overcoming current substrate scope and functional/protecting group limitations. Mechanistic studies have been included in this report.

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. In some cases, we use an efficient technique (fast-VSCF) assisted by the Voter-Chen potential in order to get an efficient reduction of the number of pair-couplings between modes. This allows us to efficiently reduce the computing time of 2D-PES without degrading the accuracy. We found that anharmonicity of the gold clusters is very small with maximum rms deviations of about 1 cm(-1), although for some particular modes anharmonicity reaches values slightly larger than 2 cm(-1). Silver clusters show slightly larger anharmonicity. In both cases, large differences between calculated and experimental vibrational frequencies (when available) stem more likely from the quality of the electronic structure method used than from vibrational anharmonicity. We show that noble gas embedding often affects the vibrational properties of these clusters more than anharmonicity, and discuss our results in the context of experimental studies.

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. We introduce an implementation of anharmonic z-polarized IR intensity calculation and explain the absence of antisymmetric O-H stretch in the experimental data for the adsorbed water molecule, while the symmetric O-H stretch is predicted to be visible.

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. First, we investigate the role of attractive and repulsive forces, and the frontier molecular orbitals. Second, we investigate the Au-Kr interaction in terms of reactivity and bonding character. We use a reactivity index derived from Fukui formalism, and criteria provided by the electron localization function (ELF), in order to classify the type of bonding. We carry out this study on the minimum energy structures of neutral gold clusters, as obtained using pseudo potential plane-wave density functional theory (DFT). A model is proposed that includes the effect of attractive electrostatic, van der Waals and repulsive forces, together with effects originating from orbital overlap. This satisfactorily explains minimum configurations of the noble gas-gold cluster systems, the site preference of the noble gas atoms, and changes in electronic properties.

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. The balance between both types of interactions is found when an imidazole is attached to a Au20 gold cluster. Thus, the present study has great significance in understanding and controlling the structures of weakly-bound molecular systems and materials, where hydrogen bonding and van der Waals interactions are competing. The applications are in the fields of the control of CO2 capture and scattering, catalysis and bio- and nanotechnologies.

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. We demonstrate a high-quality automated segmentation prediction of thoracic CT scans that correctly delineates the infected regions of the lungs. This segmentation automation can be used as a tool to speed up the contouring process, either to check manual contouring in place of a peer checking, when not possible or to give a rapid indication of infection to be referred for further treatment, thus saving time and resources. In contrast, manual contouring is a time-consuming process in which a professional would contour each patient one by one to be later checked by another professional. The proposed model uses approximately 49 k parameters while others average over 1,000 times more parameters. As our approach relies on a very compact model, shorter training times are observed, which make it possible to easily retrain the model using other data and potentially afford "personalised medicine" workflows. The model achieves similarity scores of Specificity (Sp) = 0.996 ± 0.001, Accuracy (Acc) = 0.994 ± 0.002 and Mean absolute error (MAE) = 0.0075 ± 0.0005.

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]. We study the effect of vibrational anharmonicity, polymorphism, noble gas embedding, and the use of various electronic-structure methods. We use a vibrational configuration-interaction approach (VCI) with a vibrational self-consistent field (VSCF) basis, in order to study the effect of vibrational anharmonicity for the density functional theory (DFT) global minimum energy structure. Our implementation of the VSCF/VCI method is based on the direct calculation of the potential energy surface (PES) using pseudo potential plane-wave DFT. An efficient reduction of the number of mode-mode couplings between vibrational modes (fast-VSCF/VCI) is used to speed up calculations. We show that the rather small anharmonicity does not account for the difference between harmonic and experimental frequencies and consequently for the large global scaling factor, reported by the authors of the experiment. Instead, the use of different electronic structure methods allows for a significant reduction of the scaling factor. We also show that krypton embedding does not significantly change the vibrational frequencies of the Au(7) cluster.

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. We also show that the accuracy of the presented approach with a suitable description of the periodic surface depends mainly on the accuracy of the high-level ab initio method used to describe the adsorbate molecule. Moreover, our technique potentially allows to predict adsorbate vibrational spectra with spectroscopic accuracy.

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. The efficiency of the present method is illustrated on the simulation of H2 caged in an sII clathrate hydrate including two kinds of cage modes. The transition energies are converged by increasing the number of normal modes of water molecules. Our results confirm the triplet splittings of both translational and rotational (j = 1) transitions of the H2 molecule. Furthermore, they show a slight increase of the translational transitions with respect to the ones in a rigid cage.

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)). For open-shell diatomic molecules, the SOS-MP2 (ε(MAD) =83 cm(-1)) and SCS-MP2 (ε(MAD) =81 cm(-1)) methods are of similar accuracy, while VOS-MP2 is slightly better (ε(MAD) =77 cm(-1)). Since the VOS-MP2 and SOS-MP2 methods tend to have smaller deviations from experiment, and they can be made computationally more economical than the SCS-MP2 or MP2 methods, we suggest that they should be the preferred ab initio method for computing vibrational frequencies in large molecules.