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A comprehensive theoretical investigation on the structure and dynamics of the UO22+ion in aqueous solution using double-ζ HF level quantum mechanical charge field molecular dynamics is presented. The quantum mechanical region includes two full layers of hydration and is embedded in a large box of explicitly treated water to achieve a realistic environment. A number of different functions, including segmential, radial, and angular distribution functions, are employed together with tilt- and Θ-angle distribution functions to describe the complex structural properties of this ion. These data were compared to recent experimental data obtained from LAXS and EXAFS and results of various theoretical calculations. Some properties were explained with the aid of charge distribution plots for the solute. The solvent dynamics around the ion were investigated using distance plots and mean ligand residence times and the results compared to experimental and theoretical data of related ions. [ABSTRACT FROM AUTHOR]

A quantum mechanical charge field (QMCF) molecular dynamics (MD) study of Pb(II) in an aqueous medium was carried out in order to gain insight into its solvation behavior, for both structural and dynamic aspects. Applying the advanced methodology and different basis sets, some new aspects concerning the solvation of Pb(II) have been revealed. One of the most interesting outcomes of the current simulation is the variation of first shell coordination number from 7 to 9 in the Pb(H2O)n2+complex with Pb(H2O)82+as a major species. Moreover, a far more dynamic and labile hydration shell was found compared to previous QM/MM MD simulation with only the first hydration shell treated by quantum mechanics, which reported a very rigid first hydration shell with a fixed coordination number of 9. The current simulation results are in much better agreement with the properties reported from the recent thermodynamic studies than the previous QM/MM MD study. [ABSTRACT FROM AUTHOR]

The structural properties of the hydrated Sn2+ion have been investigated using ab initio quantum mechanical charge field molecular dynamics (QMCF MD) simulations at double-ξ HF quantum mechanical level. The results from the work significantly extend previous study using QM/MM MD simulation and are in good agreement with X-Ray and EXAFS diffraction experiments. The data indicate a set of characteristics for the first hydration shell uncommon among metal ions. Although frequent ligand exchange prevents the formation of a well defined structure, more detailed analyses reveal an asymmetric distribution of ligands around Sn(II). An average of eight water molecules coordinate with the Sn2+ion and are distributed at proximal and distal positions that are distinguishable from the second hydration shell and manifest dissimilar degrees of lability. [ABSTRACT FROM AUTHOR]

Quantum mechanical/molecular mechanical (QM/MM) and quantum mechanical charge field (QMCF) molecular (MD) simulations have been performed to describe structural and dynamical properties of Na(I) and K(I) in water and to compare the two approaches. The first and second hydration shells were treated by ab initio quantum mechanics at the restricted Hartree−Fock (RHF) level. The structural data are in good agreement with previously published experimental and theoretical results. A considerable number of water exchange reactions were observed within the first shell during the simulation time of 12 ps. The number of exchange events in both shells is higher in the case of K(I) than Na(I) reflecting the weaker ion−ligand bond strength of K(I). Comparison of the “conventional” QM/MM framework with the QMCF method clearly indicates the latter to be advantageous, as ambiguities arising from the coupling of the subregions occurring in the QM/MM MD simulations did not evolve when the QMCF ansatz was applied. [ABSTRACT FROM AUTHOR]

To assess the novel quantum mechanical charge field (QMCF) molecular dynamics (MD) approach, two simulations of hydrated Al(III) have been carried out, as this system proved to be a well-suited test case for hybrid ab initio/molecular mechanics simulations. Two different population analysis schemes according to Mulliken and Löwdin have been applied to evaluate the atomic charges in the QM region. It is shown that the QMCF MD approach yields a substantially improved description of the system and that, due to the fact that solute−solvent potentials can be renounced, the QMCF MD framework is a more convenient approach to investigate solvated systems compared to conventional ab initio QM/MM MD approaches. [ABSTRACT FROM AUTHOR]

The structural and dynamical properties of the cis-(O−Zn−O angle 90°) and trans-(O−Zn−O angle 180°) isomers of the model diaquotriamminezinc(II) complex in aqueous solution have been evaluated using the hybrid quantum mechanical/molecular mechanical molecular dynamics simulation approach at ab initio Hartree−Fock level. In both complexes, the first hydration shell contains five ligands (two water and three ammonia molecules) arranged in a trigonal bipyramidal geometry. In the metastable cis-isomer two different bond lengths of 2.34 and 2.13 Å are observed for the Zn−Oaxand Zn−Oeqbonds, respectively. The trans-isomer shows the maximum of the Zn−O distance at 2.26 Å. The Zn−N bond distances in both cases are ∼2.12 Å. A geometrical transformation of the cis-isomer into the trans-isomer was observed after 11.5 ps of simulation, and the trans-isomer then remained stable throughout the whole simulation time of 30 ps. A comparative study for both isomers has been performed in terms of radial distribution functions, coordination number distributions, angular distribution functions, tilt and angle distributions, ligands' mean residence time, ion−ligand stretching frequencies, and the vibrational and librational motions of water ligands. The results are compared with the data for the previously studied zinc−monoamine and −diamine complexes. [ABSTRACT FROM AUTHOR]

In the context of our detailed study of the chemical behavior of aquo− and ammine−Zn(II) complexes, ab initio quantum mechanical/molecular mechanical (QM/MM) molecular dynamics (MD) simulations were performed at the Hartree−Fock (HF) level for the zinc(II)−diamine complexes in aqueous solution. The initial structures of cis and trans isomers of the tetraaquodiamminezinc(II) complex were found to transform into the triaquodiamminezinc(II) complex by releasing one water ligand after ∼6 and ∼22 ps of simulation time, respectively. The structural and dynamical properties of these three zinc complexes, i.e., cis-Zn(NH3)2(H2O)42, trans-Zn(NH3)2(H2O)42, and Zn(NH3)2(H2O)32, were analyzed in terms of radial distribution functions (RDF), coordination number distributions (CND), angular distribution functions (ADF), tilt and angle distributions, ligands' mean residence times (MRTs), and ion−ligand stretching frequencies. One considerably elongated Zn−O bond of 2.43 Å was observed in the case of the cis isomer for one of the water ligands located in the trans position to an ammonia ligand. In the trans isomer the average Zn−O bond length was observed to be 2.23 Å, while in the triaquodiamminezinc(II) complex two distinct Zn−O bonds, namely 2.12 Å for the ligands in the trigonal plane and 2.26 Å for axial water molecules, were observed. As both of the octahedral isomers are transformed into the pentacoordinated structure within the picosecond range, they might be regarded as “metastable species or intermediates”, while the triaquodiamminezinc(II) complex is the most stable species of the zinc(II)−diamine complex in aqueous solution. [ABSTRACT FROM AUTHOR]

An ab initio quantum mechanical/molecular mechanical (QM/MM) molecular dynamics (MD) simulation at double-ζ restricted Hartree−Fock (RHF) level was performed at an elevated temperature of 363 K (90 °C) to study the temperature effects on the structural and dynamical properties of a Zn(II)−water complex in aqueous solution. The first hydration shell, consisting of 6 water molecules at a mean Zn−O distance of 2.16 Å, was found to remain stable also at 90 °C with respect to exchange processes. The flexible second shell contains, in average, ∼27 water ligands. To fully characterize the hydration structure, several other parameters such as radial and angular distribution functions (RDF and ADF) and tilt- and θ-angle distributions were evaluated and compared to data obtained at 298 K (25 °C). Temperature effects on the dynamics of the Zn(II)−water complex were studied in terms of water reorientations, mean ligand residence times (MRTs), and number of ligand exchange processes. To get further insight into the solute dynamics, additional data, in particular, librational and vibrational motions of water ligands and Zn−O stretching frequencies, were calculated. The second shell is considerably influenced by the elevated temperature, as the ligands' mean residence time is shortened to 4 ps from the value of 10.5 observed at room temperature. The values of the QM/MM MD simulation were also compared to the results of a classical molecular dynamics (CMD) simulation with two- plus three-body potential performed at 90 °C, revealing that an accurate description of the second shell and the dynamics of the Zn(II) hydrate needs the inclusion of quantum mechanics in the description. [ABSTRACT FROM AUTHOR]

Bacteria harboring glycerol/diol dehydratase (GDH) encoded by the genes pdu CDE metabolize glycerol and release acrolein during growth. Acrolein has antimicrobial activity, and exposure of human cells to acrolein gives rise to toxic and mutagenic responses. These biological responses are related to acrolein's high reactivity as a chemical electrophile that can covalently bind to cellular nucleophiles including DNA and proteins. Various food microbes and gut commensals transform glycerol to acrolein, but there is no direct evidence available for bacterial glycerol metabolism giving rise to DNA adducts. Moreover, it is unknown whether pathogens, such as Salmonella Typhymurium, catalyze this transformation. We assessed, therefore, acrolein formation by four GDH-competent strains of S. Typhymurium grown under either aerobic or anaerobic conditions in the presence of 50 mM glycerol. On the basis of analytical derivatization with a heterocyclic amine, all wild-type strains were observed to produce acrolein, but to different extents, and acrolein production was not detected in fermentations of a pdu C-deficient mutant strain. Furthermore, we found that, in the presence of calf thymus DNA, acrolein-DNA adducts were formed as a result of bacterial glycerol metabolism by two strains of Limosilactobacillus reuteri , but not a pdu CDE mutant strain. The quantification of the resulting adducts with increasing levels of glycerol up to 600 mM led to the production of up to 1.5 mM acrolein and 3600 acrolein-DNA adducts per 10 8 nucleosides in a model system. These results suggest that GDH-competent food microbes, gut commensals, and pathogens alike have the capacity to produce acrolein from glycerol. Further, the acrolein production can lead to DNA adduct formation, but requires high glycerol concentrations that are not available in the human gut.

The molecule 2-decyl-7-phenyl-[1]benzothieno[3,2- b ][1]benzothiophene is an organic semiconductor, with outstanding properties in terms of molecular packing and its use in organic electronics. The asymmetric shape of the molecule causes a double layer crystal structure at room temperature. In this work we report its thin film growth by physical vapor deposition starting from the monolayer regime up to thick films. The films are studied in terms of their morphology, crystallographic properties, and thermal stability by atomic force microscopy and X-ray diffraction methods. It is found that the bulk molecular packing of the bilayer is formed at the initial thin film growth stage. After a thickness of one double layer, a transition into a new polymorph is observed which is of metastable character. The new phase represents a single layer phase; the crystal structure could be solved by a combination of X-ray diffraction and molecular dynamics simulations. The observed thin film growth is outstanding in terms of surface crystallization: the formation of a metastable phase is not associated with the initial thin film growth, since the first growth stage represents rather the bulk crystal structure of this molecule. Its formation is associated with cross-nucleation of one polymorph by another, which explains why a metastable phase can be formed on top of a thermodynamically more stable phase., Competing Interests: The authors declare no competing financial interest., (© 2021 The Authors. Published by American Chemical Society.)

The formation of unknown polymorphs due to the crystallization at a substrate surface is frequently observed. This phenomenon is much less studied for epitaxially grown molecular crystals since the unambiguous proof of a new polymorph is a challenging task. The existence of multiple epitaxial alignments of the crystallites together with the simultaneous presence of different polymorphs does not allow simple phase identification. We present grazing incidence X-ray diffraction studies on conjugated molecules like perylenetetracarboxylic dianhydride (PTCDA), pentacene, dibenzopentacene ( trans -DBPen), and dicyanovinylquater-thiophene (DCV4T-Et2) grown by physical vapor deposition on single crystalline surfaces like Ag(111), Cu(111), and graphene. A new method for indexing the observed Bragg peaks allows the determination of the crystallographic unit cells so that the type of crystallographic phase can be clearly identified. This approach even works when several polymorphs are simultaneously present within a single sample as shown for DCV4T-Et2 on Ag(111). Additionally, epitaxial relationships between the epitaxially grown crystallites and the single crystalline surfaces are determined. In a subsequent step, the experimental data are used for the crystal structure solution of an unknown polymorph, as shown for the example trans -DBPen grown on Cu(111)., Competing Interests: The authors declare no competing financial interest., (© 2020 American Chemical Society.)

The aim of this study was to elucidate the influence of each material component-the support, the spacer, and the surface chemistry-on the overall material performance of an affinity type purification media for the capture of immunoglobulin G (IgG). Material properties were investigated in terms of an experimental evaluation using affinity chromatography as well as computer modeling. The biomimetic triazine-based A2P affinity ligand was chosen as a fixed point, while spacer and support were varied. The investigated spacers were 1-2-diaminoethane (2LP), 1,3-propanedithiol (SS3), 3,6-dioxo-1,8-octanedithiol (DES), and a 1,4-substituted [1,2,3]-triazole spacer (TRZ). The support media considered were the agarose (AG) resins, PuraBead, the polyvinylether, Fractoprep, the polymethacrylate, Fractogel, and the porous silica, Fractosil. All materials were tested with pure IgG standard solution, with a mock feed solution as well as real cell culture supernatant. The interaction between IgG and A2P linked through the investigated spacers to AG was studied using molecular dynamics. The effect of a modification of the support chemical structure or of the protein-ligand binding site on the material performances was studied through target oriented simulations. Dynamic binding experiments (DBC) revealed that the performances of materials containing 2LP spacers were significantly decreased in the presence of Pluronic F68. The simulations indicated that this is probably determined by the establishment of intermolecular interactions between the 2LP charged amino group and the ether oxygen of Pluronic F68. The spacer giving the highest IgG dynamic binding capacity when Pluronic F68 was present in the feed was TRZ. The simulations showed that, among the investigated spacers, TRZ is the only one that prevents the adsorption of A2P on the support surface, thus suggesting that the mobility and lack of interaction of the ligand with the support is an important property for an affinity material. Both experiments and calculations agree that the chemistry of the support surface can have a significant impact on IgG binding, either affecting the IgG DBC, as found experimentally for materials having similar ligand densities and spacer arms but different supports, or competing with the affinity ligand when hydrophobic groups are added to the model surface, as was computationally predicted.

Fast analysis of bioaerosols in clean room environments is necessary in order to prevent contamination of pharmaceutical products, minimize machine downtimes, or both. The detection and identification of microbes will be carried out in several steps: After impaction of the aerosol on a surface, the particles are presorted with glancing light illumination and fluorescence imaging in order to distinguish between abiotic and biotic particles. Since only the biotic particles are of interest, the analysis time can be minimized due to reduction of the data set. The biotic particles are then analyzed further with Raman spectroscopy and identified with a support vector machine.