Structure and Thermodynamics of Mg:Phosphate Interactions in Water: A Simulation Study

The association of Mg²⁺ and H₂PO₄^? in water can give insights into Mg:phosphate interactions in general, which are very widespread, but for which experimental data is surprisingly sparse. It is studied through molecular dynamics simulations (>100 ns) by using the polarizable AMOEBA force field, and the association free energy is computed for the first time. Explicit consideration of outer‐sphere and two types of inner‐sphere association provides considerable insight into the dynamics and thermodynamics of ion pairing. After careful assessment of the computational approximations, the agreement with experimental values indicates that the methodology can be extended to other inorganic and biological Mg:phosphate interactions in solution.     

Natural and artificial light-harvesting systems utilizing the functions of carotenoids

Carotenoids are essential pigments in natural photosynthesis. They absorb in the blue–green region of the solar spectrum and transfer the absorbed energy to (bacterio-)chlorophylls, and so expand the wavelength range of light that is able to drive photosynthesis. This process is an example of singlet–singlet energy transfer and so carotenoids serve to enhance the overall efficiency of photosynthetic light reactions. Carotenoids also act to protect photosynthetic organisms from the harmful effects of excess exposure to light. In this case, triplet–triplet energy transfer from (bacterio-)chlorophyll to carotenoid plays a key role in this photoprotective reaction. In the light-harvesting pigment–protein complexes from purple photosynthetic bacteria and chlorophytes, carotenoids have an additional role, namely the structural stabilization of those complexes. In this article we review what is currently known about how carotenoids discharge these functions. The molecular architecture of photosynthetic systems will be outlined to provide a basis from which to describe the photochemistry of carotenoids, which underlies most of their important functions in photosynthesis. Then, the possibility to utilize the functions of carotenoids in artificial photosynthetic light-harvesting systems will be discussed. Some examples of the model systems are introduced.     

Inverse colloidal crystal membranes for hydrophobic interaction membrane chromatography

A collaborative study on the robustness and portability of a capillary electrophoresis‐mass spectrometry method for peptide mapping was performed by an international team, consisting of 13 independent laboratories from academia and industry. All participants used the same batch of samples, reagents and coated capillaries to run their assays, whereas they utilized the capillary electrophoresis‐mass spectrometry equipment available in their laboratories. The equipment used varied in model, type and instrument manufacturer. Furthermore, different types of sheath‐flow capillary electrophoresis–mass spectrometry interfaces were used. Migration time, peak height and peak area of ten representative target peptides of trypsin‐digested bovine serum albumin were determined by every laboratory on two consecutive days. The data were critically evaluated to identify outliers and final values for means, repeatability (precision within a laboratory) and reproducibility (precision between laboratories) were established. For relative migration time the repeatability was between 0.05 and 0.18% RSD and the reproducibility between 0.14 and 1.3% RSD. For relative peak area repeatability and reproducibility values obtained were 3–12 and 9–29% RSD, respectively. These results demonstrate that capillary electrophoresis‐mass spectrometry is robust enough to allow a method transfer across multiple laboratories and should promote a more widespread use of peptide mapping and other capillary electrophoresis‐mass spectrometry applications in biopharmaceutical analysis and related fields.     

Characterization of different substrates for Raman spectroscopic imaging of eukaryotic cells

For Raman spectroscopic analyses of the cells and other biological samples, the choice of the right substrate material is very important to avoid loss of information in characteristic spectral features because of competing background signals. In the current study, Raman spectroscopy is used to characterize several potential Raman substrates. Raman vibrational bands of the substrate material are discussed. The surface topography is analyzed by atomic force microscopy, and the root mean square surface roughness values are reported. Biocompatibility of the substrates is tested with Hep G2 cells evaluating cellular morphology as well as live/dead staining. Calcium fluoride, silicon, fused silica, borofloat glass, and silicon nitride membranes support cell growth and adherence. Silicon, borofloat glass, and fused silica give rise to Raman signals in the region of interest. Calcium fluoride substrate (UV grade) is suitable for Raman spectroscopic investigation of living cells. Nickel foil is suitable substrate for Raman spectroscopic investigation but cellular adherence and viability depend on the quality of the foil. Silicon nitride membranes coated with nickel chrome is a suitable Raman substrate in closed microfluidic systems. Copyright © 2016 John Wiley & Sons, Ltd.     

Surface plasmon polariton assisted optical pulling force

We demonstrate both analytically and numerically the existence of optical pulling forces acting on particles located near plasmonic interfaces. Two main factors contribute to the appearance of this negative recoil force. The interference between the incident and reflected waves induces a rotating dipole with an asymmetric scattering pattern, while the directional excitation of surface plasmon polaritons (SPPs) enhances the linear momentum of scattered light. The strongly asymmetric SPP excitation is determined by spin–orbit coupling of the rotating dipole and surface plasmon polariton. As a result of the total momentum conservation, the force acting on the particle points in a direction opposite to the incident wave propagation. We derive analytical expressions for the force acting on dipolar particles placed in the proximity of plasmonic surfaces. Analytical expressions for this pulling force are derived within the dipole approximation and are in excellent agreement with results of electromagnetic numerical calculations. The forces acting on larger particles are analyzed numerically, beyond the dipole approximation.

     

Nucleic acid reactivity: Challenges for next‐generation semiempirical quantum models

Semiempirical quantum models are routinely used to study mechanisms of RNA catalysis and phosphoryl transfer reactions using combined quantum mechanical (QM)/molecular mechanical methods. Herein, we provide a broad assessment of the performance of existing semiempirical quantum models to describe nucleic acid structure and reactivity to quantify their limitations and guide the development of next‐generation quantum models with improved accuracy. Neglect of diatomic differential overlap and self‐consistent density‐functional tight‐binding semiempirical models are evaluated against high‐level QM benchmark calculations for seven biologically important datasets. The datasets include: proton affinities, polarizabilities, nucleobase dimer interactions, dimethyl phosphate anion, nucleoside sugar and glycosidic torsion conformations, and RNA phosphoryl transfer model reactions. As an additional baseline, comparisons are made with several commonly used density‐functional models, including M062X and B3LYP (in some cases with dispersion corrections). The results show that, among the semiempirical models examined, the AM1/d‐PhoT model is the most robust at predicting proton affinities. AM1/d‐PhoT and DFTB3‐3ob/OPhyd reproduce the MP2 potential energy surfaces of 6 associative RNA phosphoryl transfer model reactions reasonably well. Further, a recently developed linear‐scaling “modified divide‐and‐conquer” model exhibits the most accurate results for binding energies of both hydrogen bonded and stacked nucleobase dimers. The semiempirical models considered here are shown to underestimate the isotropic polarizabilities of neutral molecules by approximately 30%. The semiempirical models also fail to adequately describe torsion profiles for the dimethyl phosphate anion, the nucleoside sugar ring puckers, and the rotations about the nucleoside glycosidic bond. The modeling of pentavalent phosphorus, particularly with thio substitutions often used experimentally as mechanistic probes, was problematic for all of the models considered. Analysis of the strengths and weakness of the models suggests that the creation of robust next‐generation models should emphasize the improvement of relative conformational energies and barriers, and nonbonded interactions. © 2015 Wiley Periodicals, Inc.     

QuickFF: A program for a quick and easy derivation of force fields for metal‐organic frameworks from ab initio input

QuickFF is a software package to derive accurate force fields for isolated and complex molecular systems in a quick and easy manner. Apart from its general applicability, the program has been designed to generate force fields for metal‐organic frameworks in an automated fashion. The force field parameters for the covalent interaction are derived from ab initio data. The mathematical expression of the covalent energy is kept simple to ensure robustness and to avoid fitting deficiencies as much as possible. The user needs to produce an equilibrium structure and a Hessian matrix for one or more building units. Afterward, a force field is generated for the system using a three‐step method implemented in QuickFF. The first two steps of the methodology are designed to minimize correlations among the force field parameters. In the last step, the parameters are refined by imposing the force field parameters to reproduce the ab initio Hessian matrix in Cartesian coordinate space as accurate as possible. The method is applied on a set of 1000 organic molecules to show the easiness of the software protocol. To illustrate its application to metal‐organic frameworks (MOFs), QuickFF is used to determine force fields for MIL‐53(Al) and MOF‐5. For both materials, accurate force fields were already generated in literature but they requested a lot of manual interventions. QuickFF is a tool that can easily be used by anyone with a basic knowledge of performing ab initio calculations. As a result, accurate force fields are generated with minimal effort. © 2015 Wiley Periodicals, Inc.     

Interaction potential models for bulk Zns,Zns nanoparticle,and Zns nanoparticle‐PMMA from first‐principles

An ab initio derived transferable polarizable force‐field has been developed for Zinc sulphide (ZnS) nanoparticle (NP) and ZnS NP‐PMMA nanocomposite. The structure and elastic constants of bulk ZnS using the new force‐field are within a few percent of experimental observables. The new force‐field show remarkable ability to reproduce structures and nucleation energies of nanoclusters (Zn₁S₁‐Zn₁₂S₁₂) as validated with that of the density functional theory calculations. A qualitative agreement of the radial distribution functions of Zn? O, in a ZnS nanocluster‐PMMA system, obtained using molecular mechanics molecular dynamics (MD) and ab initio MD (AIMD) simulations indicates that the ZnS–PMMA interaction through Zn? O bonding is explained satisfactorily by our force‐field. © 2015 Wiley Periodicals, Inc.