Stable and accurate atomistic simulations of flexible molecules using conformationally generalisable machine learned potentials.

Computational simulation methods based on machine learned potentials (MLPs) promise to revolutionise shape prediction of flexible molecules in solution, but their widespread adoption has been limited by the way in which training data is generated. Here, we present an approach which allows the key conformational degrees of freedom to be properly represented in reference molecular datasets. MLPs trained on these datasets using a global descriptor scheme are generalisable in conformational space, providing quantum chemical accuracy for all conformers. These MLPs are capable of propagating long, stable molecular dynamics trajectories, an attribute that has remained a challenge. We deploy the MLPs in obtaining converged conformational free energy surfaces for flexible molecules via well-tempered metadynamics simulations; this approach provides a hitherto inaccessible route to accurately computing the structural, dynamical and thermodynamical properties of a wide variety of flexible molecular systems. It is further demonstrated that MLPs must be trained on reference datasets with complete coverage of conformational space, including in barrier regions, to achieve stable molecular dynamics trajectories.

A neural network potential based on pairwise resolved atomic forces and energies.

Molecular simulations have become a key tool in molecular and materials design. Machine learning (ML)-based potential energy functions offer the prospect of simulating complex molecular systems efficiently at quantum chemical accuracy. In previous work, we have introduced the ML-based PairF-Net approach to neural network potentials, that adopts a pairwise interatomic scheme to predicting forces within a molecular system. Here, we further develop the PairF-Net model to intrinsically incorporate energy conservation and couple the model to a molecular mechanical (MM) environment within the OpenMM package. The updated PairF-Net model yields energy and force predictions and dynamical distributions in good agreement with the rMD17 dataset of ten small organic molecules in the gas-phase. We further show that these in vacuo ML models of small molecules can be applied to force predictions in aqueous solution via hybrid ML/MM simulations. We present a new benchmark dataset for these ten molecules in solution, obtained from QM/MM simulations, which we denote as rMD17-aq (https://zenodo.org/records/10048644); and assess the ability of PairF-Net to reproduce the molecular energy, atomic forces and dynamical distributions of these solution conformations via ML/MM simulations.

A ring of rotaxanes: studies of a large paramagnetic assembly in solution.

Here we report the synthesis and structural characterization of four [7]rotaxanes formed by coordinating hybrid inorganic-organic [2]rotaxanes to a central {Ni12} core. X-ray single crystal diffraction demonstrate that [7]rotaxanes are formed, with a range of conformations in the crystal. Small angle X-ray scattering supported by molecular dynamic simulations demonstrates that the large molecules are stable in solution and also show that the conformers present in solution are not those found in the crystal. Pulsed EPR spectroscopy show that phase memory times for the {Cr7Ni} rings, which have been proposed as qubits, are reduced but not dramatically by the presence of the {Ni12} cage.

Adduct Ions as Diagnostic Probes of Metallosupramolecular Complexes Using Ion Mobility Mass Spectrometry.

Following electrospray ionization, it is common for analytes to enter the gas phase accompanied by a charge-carrying ion, and in most cases, this addition is required to enable detection in the mass spectrometer. These small charge carriers may not be influential in solution but can markedly tune the analyte properties in the gas phase. Therefore, measuring their relative influence on the target molecule can assist our understanding of the structure and stability of the analyte. As the formed adducts are usually distinguishable by their mass, differences in the behavior of the analyte resulting from these added species (e.g., structure, stability, and conformational dynamics) can be easily extracted. Here, we use ion mobility mass spectrometry, supported by density functional theory, to investigate how charge carriers (H+, Na+, K+, and Cs+) as well as water influence the disassembly, stability, and conformational landscape of the homometallic ring [Cr8F8(O2CtBu)16] and the heterometallic rotaxanes [NH2RR'][Cr7MF8(O2CtBu)16], where M = MnII, FeII, CoII, NiII, CuII, ZnII, and CdII. The results yield new insights on their disassembly mechanisms and support previously reported trends in cavity size and transition metal properties, demonstrating the potential of adduct ion studies for characterizing metallosupramolecular complexes in general.

Disassembly Mechanisms and Energetics of Polymetallic Rings and Rotaxanes.

Understanding the fundamental reactivity of polymetallic complexes is challenging due to the complexity of their structures with many possible bond breaking and forming processes. Here, we apply ion mobility mass spectrometry coupled with density functional theory to investigate the disassembly mechanisms and energetics of a family of heterometallic rings and rotaxanes with the general formula [NH2RR'][Cr7MF8(O2CtBu)16] with M = MnII, FeII, CoII, NiII, CuII, ZnII, CdII. Our results show that their stability can be tuned both by altering the d-metal composition in the macrocycle and by the end groups of the secondary ammonium cation [NH2RR']+. Ion mobility probes the conformational landscape of the disassembly process from intact complex to structurally distinct isobaric fragments, providing unique insights to how a given divalent metal tunes the structural dynamics.

Disproportionation of the Uranyl(V) Coordination Complexes in Aqueous Solution through Outer-Sphere Electron Transfer.

Among the linear actinyl(VI/V) cations, the uranyl(V) species are particularly intriguing because they are unstable and exhibit a unique behavior to undergo H+ promoted disproportionation in aqueous solution and form stable uranyl(VI) and U(IV) complexes. This study uses density functional theory (DFT) combined with the conductor-like polarizable continuum model approach to investigate [UO2]2+/+ to [UIVO2] reduction free energies (RFEs) and explores the stability of uranyl(V) complexes in aqueous solution through computing disproportionation free energies (DFEs) for an outer-sphere electron transfer process. In addition to the aqua complex (U1), another three commonly encountered ligands such as chloride (U2), acetate (U3), and carbonate (U4) in aqueous environmental conditions are taken into account. For the U1 complex, the computed 1e- (V/IV) and 2e- (VI/IV) RFEs are in good agreement with experiments. The computed DFEs reveal that the presence of H+ is imperative for the disproportionation to take place. Although the presence of the alkali cations favors the disproportionation to some extent, they cannot fully make the reaction thermodynamically feasible. For the anionic complexes, the high negative charge does not allow for the formation of a cation-cation encounter complex due to Coulombic repulsion. Furthermore, an additional factor is the ligand exchange reaction which is also an energy-demanding step. Therefore, the current study examined the Kern-Orlemann mechanism and our results validate the mechanism based on DFT computed DFEs and propose that for the anionic complexes, an outer-sphere electron transfer is highly probable and our computed protonation free energies further support this claim.

Gold(i) bridged dimeric and trimeric heterometallic {Cr7Ni}-based qubit systems and their characterization.

Gold(i) bridged dimeric and trimeric structures of a ground state spin S = 1/2 heterometallic {Cr7Ni} wheel have been prepared and studied by continuous wave (CW) and pulsed wave EPR spectrometry. The {Cr7Ni} relaxation time constants (T1 and Tm) show rates matching well with previous observations. Four pulse Double Electron Resonance (DEER) studies suggest presence of more than one conformations. Small Angle X-ray Scattering (SAXS) in conjunction with Molecular Dynamic (MD) Simulations were performed to look at the possible conformations in solution. In line with DEER results, simulation data further indicated more flexible molecular geometry in solution than the one in solid state.

Conformational Flexibility of Hybrid [3]- and [4]-Rotaxanes.

The synthesis, structures, and properties of [4]- and [3]-rotaxane complexes are reported where [2]-rotaxanes, formed from heterometallic {Cr7Ni} rings, are bound to a fluoride-centered {CrNi2} triangle. The compounds have been characterized by single-crystal X-ray diffraction and have the formulas [CrNi2(F)(O2CtBu)6]{(BH)[Cr7NiF8(O2CtBu)16]}3 (3) and [CrNi2(F)(O2CtBu)6(THF)]{(BH)[Cr7NiF8(O2CtBu)16]}2 (4), where B = py-CH2CH2NHCH2C6H4SCH3. The [4]-rotaxane 3 is an isosceles triangle of three [2]-rotaxanes bound to the central triangle while the [3]-rotaxane 4 contains only two [2]-rotaxanes bound to the central triangle. Studies of the behavior of 3 and 4 in solution by small-angle X-ray scattering and atomistic molecular dynamic simulations show that the structure of 3 is similar to that found in the crystal but that 4 has a different conformation to the crystal. Continuous wave and pulsed electron paramagnetic resonance spectroscopy was used to study the structures present and demonstrate that in frozen solutions (at 5 K) 4 forms more extended molecules than 3 and with a wider range of conformations.

Uranyl-Bound Tetra-Dentate Non-Innocent Ligands: Prediction of Structure and Redox Behaviour Using Density Functional Theory.

Computational methods have been applied to understand the reduction potentials of [UO2 -salmnt-L] complexes (L=pyridine, DMSO, DMF and TPPO), and their redox behavior is compared with previous experiments in dichloromethane solution. Since the experimental results were inconclusive regarding the influence of the uranyl-bound tetra-dentate 'salmnt' ligand, here we will show that salmnt acts as a redox-active ligand and exhibits non-innocent behavior to interfere with the otherwise expected one-electron metal (U) reduction. We have employed two approaches to determine the uranyl (VI/V) reduction potentials, using a direct study of one-electron reduction processes and an estimation of the overall reduction using isodesmic reactions. Hybrid density functional theory (DFT) methods were combined with the Conductor-like Polarizable Continuum Model (CPCM) to account for solvation effects. The computationally predicted one-electron reduction potentials for the range of [UO2 -salmnt-L] complexes are in excellent agreement with shoulder peaks (∼1.4 eV) observed in the cyclic voltammetry experiments and clearly correlate with ligand reduction. Highly conjugated pi-bonds stabilize the ligand based delocalized orbital relative to the localized U f-orbitals, and as a consequence, the ligand traps the incoming electron. A second reduction step results in metal U(VI) to U(V) reduction, in good agreement with the experimentally assigned uranyl (VI/V) reduction potentials.

Density functional theory (DFT) calculations of VI/V reduction potentials of uranyl coordination complexes in non-aqueous solutions.

Of particular interest within the +6 uranium complexes is the linear uranyl(vi) cation and it forms numerous coordination complexes in solution and exhibits incongruent redox behavior depending on coordinating ligands. In this study, to determine the reduction potentials of uranyl complexes in non-aqueous solutions, a hybrid density functional theory (DFT) approach was used in which two different DFT functionals, B3LYP and M06, were applied. Bulk solvent effects were invoked through the conductor-like polarizable continuum model. The solute cavities were described with the united-atom Kohn-Sham (UAKS) cavity definition. Inside the cavity the dielectric constant matches the value of a vacuum and outside the cavity the dielectric constant value is the same as that of the solvent of interest, for example, dimethyl sulfoxide (DMSO), dimethylformamide (DMF), dichloromethane (DCM), acetonitrile and pyridine. With the help of the Nernst equation the calculated reduction potentials with respect to the ferrocene (Fc) reference electrode are converted into reduction free energies (RFEs). Uranyl complexes of organic ligands which range from mono- to hexa-dentate coordination modes were investigated in non-aqueous solutions of DMSO, DMF, DCM, acetonitrile and pyridine solutions. The effect of the spin-orbit correction and the reference electrode correction on the RFEs and various methods such as the direct method and the isodesmic reaction model were explored. Overall, our computational determination of RFEs of uranyl complexes in various non-aqueous solutions demonstrates that the RFEs can be obtained within ∼0.2 eV of experimental values.

Hydrophilic 2,9-bis-triazolyl-1,10-phenanthroline ligands enable selective Am(iii) separation: a step further towards sustainable nuclear energy.

The first hydrophilic, 1,10-phenanthroline derived ligands consisting of only C, H, O and N atoms for the selective extraction of Am(iii) from spent nuclear fuel are reported herein. One of these 2,9-bis-triazolyl-1,10-phenanthroline (BTrzPhen) ligands combined with a non-selective extracting agent, was found to exhibit process-suitable selectivity for Am(iii) over Eu(iii) and Cm(iii), providing a clear step forward.

Exploring electronic effects on the partitioning of actinides(iii) from lanthanides(iii) using functionalised bis-triazinyl phenanthroline ligands.

The first examples of 4,7-disubstituted 2,9-bis(5,5,8,8-tetramethyl-5,6,7,8-tetrahydro-1,2,4-benzo-triazin-3-yl)-1,10-phenanthroline (CyMe4-BTPhen) ligands are reported herein. Evaluating the kinetics, selectivity and stoichiometry of actinide(iii) and lanthanide(iii) radiotracer extractions has provided a mechanistic insight into the extraction process. For the first time, it has been demonstrated that metal ion extraction kinetics can be modulated by backbone functionalisation and a promising new CHON compliant candidate ligand with enhanced metal ion extraction kinetics has been identified. The effects of 4,7-functionalisation on the equilibrium metal ion distribution ratios are far more pronounced than those of 5,6-functionalisation. The complexation of Cm(iii) with two of the functionalised ligands was investigated by TRLFS and, at equilibrium, species of 1 : 2 [M : L] stoichiometry were observed exclusively. A direct correlation between the ELUMO-EHOMO energy gap and metal ion extraction potential is reported, with DFT studies reaffirming experimental findings.

Disparate impact of oxidative host defenses determines the fate of Salmonella during systemic infection in mice.

Reactive oxygen and nitrogen species function in host defense via mechanisms that remain controversial. Pathogens might encounter varying levels of these species, but bulk measurements cannot resolve such heterogeneity. We used single-cell approaches to determine the impact of oxidative and nitrosative stresses on individual Salmonella during early infection in mouse spleen. Salmonella encounter and respond to both stresses, but the levels and impact vary widely. Neutrophils and inflammatory monocytes kill Salmonella by generating overwhelming oxidative stress through NADPH oxidase and myeloperoxidase. This controls Salmonella within inflammatory lesions but does not prevent their spread to more permissive resident red pulp macrophages, which generate only sublethal oxidative bursts. Regional host expression of inducible nitric oxide synthase exposes some Salmonella to nitrosative stress, triggering effective local Salmonella detoxification through nitric oxide denitrosylase. Thus, reactive oxygen and nitrogen species influence dramatically different outcomes of disparate Salmonella-host cell encounters, which together determine overall disease progression.

The Development of a Classical Force Field To Determine the Selectivity of an Aqueous Fe(3+)-EDA Complex for TcO4(-) and SO4(2.).

A classical force field has been developed in order to investigate the selective exchange of oxyanions (TcO4(-) vs SO4(2-)) with other ligands (H2O, Cl(-)) to an aqueous Fe(3+)-ethylenediamine (EDA) complex. Potentials of mean force for a range of exchange reactions were generated using umbrella sampling and classical molecular dynamics simulations in order to calculate the affinity of each oxyanion for the Fe(3+)-EDA complex in aqueous solution. In order to accurately introduce a degree of specificity for the interaction of Fe(3+) with each ligand type, force field parameters were tuned to match the results of density functional theory calculations. Preferential exchange of H2O, Cl(-), and SO4(2-) for TcO4(-) via an interchange mechanism is observed, in agreement with experimental observations. Both the relative solvation entropies and enthalpies of the anions were found to be critically important factors governing the magnitude of the observed selectivities. These results have important implications for the design and modeling of functionalized materials for the remediation of land contaminated with radioactive (99)Tc.

Parallel exploitation of diverse host nutrients enhances Salmonella virulence.

Pathogen access to host nutrients in infected tissues is fundamental for pathogen growth and virulence, disease progression, and infection control. However, our understanding of this crucial process is still rather limited because of experimental and conceptual challenges. Here, we used proteomics, microbial genetics, competitive infections, and computational approaches to obtain a comprehensive overview of Salmonella nutrition and growth in a mouse typhoid fever model. The data revealed that Salmonella accessed an unexpectedly diverse set of at least 31 different host nutrients in infected tissues but the individual nutrients were available in only scarce amounts. Salmonella adapted to this situation by expressing versatile catabolic pathways to simultaneously exploit multiple host nutrients. A genome-scale computational model of Salmonella in vivo metabolism based on these data was fully consistent with independent large-scale experimental data on Salmonella enzyme quantities, and correctly predicted 92% of 738 reported experimental mutant virulence phenotypes, suggesting that our analysis provided a comprehensive overview of host nutrient supply, Salmonella metabolism, and Salmonella growth during infection. Comparison of metabolic networks of other pathogens suggested that complex host/pathogen nutritional interfaces are a common feature underlying many infectious diseases.

Atomistic simulations of calcium uranyl(VI) carbonate adsorption on calcite and stepped-calcite surfaces.

Adsorption of actinyl ions onto mineral surfaces is one of the main mechanisms that control the migration of these ions in environmental systems. Here, we present computational classical molecular dynamics (MD) simulations to investigate the behavior of U(VI) in contact with different calcite surfaces. The calcium-uranyl-carbonate [Ca(2)UO(2)(CO(3))(3)] species is shown to display both inner- and outer-sphere adsorption to the flat {101̅4} and the stepped {314̅8} and {31̅2̅16} planes of calcite. Free energy calculations, using the umbrella sampling method, are employed to simulate adsorption paths of the same uranyl species on the different calcite surfaces under aqueous condition. Outer-sphere adsorption is found to dominate over inner-sphere adsorption because of the high free energy barrier of removing a uranyl-carbonate interaction and replacing it with a new uranyl-surface interaction. An important binding mode is proposed involving a single vicinal water monolayer between the surface and the sorbed complex. From the free energy profiles of the different calcite surfaces, the uranyl complex was also found to adsorb preferentially on the acute-stepped {314̅8} face of calcite, in agreement with experiment.

Investigation of ligand exchange reactions in aqueous uranyl carbonate complexes using computational approaches.

Carbonate anion exchange reactions with water in the uranyl-carbonate and calcium-uranyl-carbonate aqueous systems have been investigated using computational methods. Classical molecular dynamics (MD) simulations with the umbrella sampling technique were employed to determine potentials of mean force for the exchange reactions of water and carbonate. The presence of calcium counter-ions is predicted to increase the stability of the uranyl-carbonate species in accordance with previous experimental observations. However, the free energy barrier to carbonate exchange with water is found to be comparable both in the presence and absence of calcium cations. Possible implications of these results for uranyl adsorption on mineral surfaces are discussed. Density functional theory (DFT) calculations were also used to confirm the trends observed in classical molecular dynamics simulations and to corroborate the validity of the potential parameters employed in the MD scheme.

RcsB is required for inducible acid resistance in Escherichia coli and acts at gadE-dependent and -independent promoters.

RcsB interacts with GadE to mediate acid resistance in stationary-phase Escherichia coli K-12. We show here that RcsB is also required for inducible acid resistance in exponential phase and that it acts on promoters that are not GadE regulated. It is also required for acid resistance in E. coli O157:H7.

Low temperature CVD growth of PbS films on plastic substrates.

The low temperature growth of crystalline PbS films has been achieved on plastic substrates by CVD using a xanthate. The possible mechanism involved in this low temperature deposition has been probed by density functional theory calculations.

Novel aspects of the acid response network of E. coli K-12 are revealed by a study of transcriptional dynamics.

Understanding gene regulation and its adaptive significance requires not only a detailed knowledge of individual molecular interactions that give rise to changes in gene expression but also an overview of complete genetic networks and the ways in which components within them interact. Increasingly, such studies are being done using luminescent or fluorescent reporter proteins that enable monitoring of gene expression dynamics in real time, particularly during changes in expression. We show here that such an approach is valid for dissecting the responses of the AR2 or GAD network of Escherichia coli K-12 to changes in pH, which is one of the most complex networks known in E. coli. In addition to confirming several regulatory interactions that have been revealed by previous studies, this approach has identified new components in this system that lead to complex dynamics of gene expression following a drop in pH, including an auto-regulatory loop involving the YdeO activator protein and novel roles for the PhoP protein.