Characterization of interactions of metal‐containing nanoparticles with biomolecules by CE: An update (2012–2016)

The methodological developments and applications of CE related to studying biotransformations of metal‐based nanoscale particles of impending medicinal use are overviewed. This is an update to a previous review article (Aleksenko, S. S., Shmykov, A. Y., Oszwałdowski, S., Timerbaev, A. R., Metallomics 2012, 4 , 1141–1148) and it covers the research papers published within the last five years. As was anticipated in that review, CE can now be seen as a customary technique in the analysis of biomolecular interactions that exert an impact on the mechanism of action of nanoparticles, comprising metabolism, delivery, cell processing, and targeting. Different ways by which the CE method is applied for such monitoring, including conjugation mode, sample preparation, separation, and detection, are critically assessed. Special emphasis is put on examinations using inductively coupled plasma MS detection recent advent of which to the area made CE a versatile speciation tool for biomedical studies of nanomaterials containing metals.     

Rhorix: An interface between quantum chemical topology and the 3D graphics program blender

Chemical research is assisted by the creation of visual representations that map concepts (such as atoms and bonds) to 3D objects. These concepts are rooted in chemical theory that predates routine solution of the Schrödinger equation for systems of interesting size. The method of Quantum Chemical Topology (QCT) provides an alternative, parameter‐free means to understand chemical phenomena directly from quantum mechanical principles. Representation of the topological elements of QCT has lagged behind the best tools available. Here, we describe a general abstraction (and corresponding file format) that permits the definition of mappings between topological objects and their 3D representations. Possible mappings are discussed and a canonical example is suggested, which has been implemented as a Python “Add‐On” named Rhorix for the state‐of‐the‐art 3D modeling program Blender. This allows chemists to use modern drawing tools and artists to access QCT data in a familiar context. A number of examples are discussed. © 2017 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.     

Applicability of medium-size basis sets in calculations of molecular dynamic polarisabilities

Static and dynamic average polarisabilities and polarisability anisotropies of seven linear non-polar and polar molecules are calculated within the CCS, CC2, and CC3 approximations using a range of medium-sized basis sets: the polarised LPol-n (n = ds, dl, fs, fl), the aug-pc-n (n = 1, 2), the def2-SVPD, and -TZVPD basis sets. Reference values are obtained using a hierarchy of Dunning's (d-)aug-cc-pVXZ (X = D, T, Q, 5) basis sets. The results are discussed together with the available CCSD values in terms of basis set and correlation method errors, and their ratio. Detailed analysis shows that already the def2-SVPD basis set can be used in CCS polarisability calculations. When affordable, the slightly larger aug-pc-1 basis set is recommended, as it leads to significant reduction of basis set error. The def2-TZVPD, LPol-ds, and aug-pc-2 basis sets are optimal choice within the CC2 approximation, with the latter allowing to approach the CC2 basis set limit. The LPol-ds, -dl, and def2-TZVPD sets outperform the aug-cc-pVTZ set in average polarisability CCSD calculations, with the def2-TZVPD being competitive to other reduced-size sets also in determination of polarisability anisotropy. The aug-pc-2 basis is a particularly attractive choice for CCSD, giving the accuracy of aug-cc-pVQZ at a significantly reduced computational cost. The polarisability anisotropy is shown to be more computationally demanding than the average polarisability, in particular with respect to the accuracy of the correlation method and an accurate evaluation of this property requires at least the CCSD model.     

Helicity Control in the Preparation of Chiral Co-crystals from Tryptamine and Achiral Carboxylic Acids by Pseudo-seeding

Abstract

Chiral crystals of tryptamine and achiral carboxylic acids such as p-chlorobenzoic acid, cinnamic acid, p-chlorocinnarnic acid and p-methylcinnamic acid were prepared by crystallization from the solutions of both components. All the crystals belonged to typical chiral space group P2₁2₁2₁. The crystal chirality is generated through the formation of a unidirectional twofold helix between the two components through quaternary ammonium salt interaction and hydrogen bonding in the lattice. This kind of spontaneous crystallization necessarily gives crystals of both clockwise and counterclockwise helicites. Here, pseudo-seeding based on utilizing these crystals as seed crystals was examined, resulting in successful helicity control in crystallization from solutions of tryptamine and different carboxylic acids.     

Theoretical Study on the Hydrogen Bonding Interactions in Complexes of 5‐Hydroxytryptamine with Water

The energies, geometries and harmonic vibrational frequencies of 1:1 5‐hydroxytryptamine‐water (5‐HT‐H₂O) complexes are studied at the MP2/6‐311++G(d,p) level. Natural bond orbital (NBO), quantum theory of atoms in molecules (QTAIM) analyses and the localized molecular orbital energy decomposition analysis (LMO‐EDA) were performed to explore the nature of the hydrogen‐bonding interactions in these complexes. Various types of hydrogen bonds (H‐bonds) are formed in these 5‐HT‐H₂O complexes. The intermolecular C4H5^5‐HT···O^w H‐bond in HTW3 is strengthened due to the cooperativity, whereas no such cooperativity is found in the other 5‐HT‐H₂O complexes. H‐bond in which nitrogen atom of amino in 5‐HT acted as proton donors was stronger than other H‐bonds. Our researches show that the hydrogen bonding interaction plays a vital role on the relative stabilities of 5‐HT‐H₂O complexes.     

Electrochemical Recognition of Chiral Molecules with Poly(4‐bromoaniline) Modified Gold Electrode

A poly(4‐bromoaniline) (PBA) film is electrochemically synthesized on a gold electrode for the recognition of amino acids enantiomers. Scanning electron microscopy measurements show that the porous PBA films are made up of nano‐ribbons. At the PBA modified Au electrode differential pulse voltammograms of L ‐ and D ‐glutamic acids not only have very different current densities, but also produce different waveforms, providing an intuitive way to differentiate the two chiral molecules. Similar results are obtained in analyzing L ‐ and D ‐aspartic acids. Control experiments suggest that the observed sensing behavior arises from synergistic interactions between Au and the PBA film, where polymerization at the meta‐position creates a steric structure needed for differentiating chiral molecules.     

Electrophoretic separation of gold nanoparticles according to bifunctional molecules‐induced charge and size

Gold nanospheres modified with bifunctional molecules have been separated and characterized by using agarose gel electrophoresis as well as optical spectroscopy and electron microscopy. The electrophoretic mobility of a gold nanosphere capped with 11‐mercaptoundecanoic acid (MUA) has been found to depend on the number of MUA molecules per gold nanosphere, indicating that it increases with the surface charge of the nanoparticle. The extinction spectrum of gold nanospheres capped with MUA at an MUA molecules per gold nanosphere value of 1000 and connected via 1,6‐hexanedithiol (HDT) decreases by 33% in magnitude and shifts to the red as largely as 22 nm with the increase of the molar ratio of HDT to MUA (R_HM). Gold nanospheres capped with MUA and connected via HDT have been separated successfully using gel electrophoresis and characterized by measuring reflectance spectra of discrete electrophoretic bands directly in the gel and by monitoring transmission electron microscope images of gold nanoparticles collected from the discrete bands. Electrophoretic mobility has been found to decrease substantially with the increment of HDT to MUA, indicating that the size of aggregated gold nanoparticles increases with the concentration of HDT.     

An Interwoven Metal‐Organic Framework Combining Mechanically Interlocked Linkers and Interpenetrated Networks

New dibenzo[24]crown‐8 ether derivatives were prepared that contain appendages with thioether donors that can coordinate to a metal ion. These macrocycles were then combined with 1,2‐bis(pyridinium) ethane axles to create two types of [2]rotaxane ligands; those with the four thioether donors on the crown ether and those with six donor groups, four from the crown ether and two more attached to the stoppering groups of the dumbbell. The crown ethers and both types of [2]rotaxane ligands were allowed to react with Ag^I ions to form metal‐organic rotaxane framework (MORF) style coordination polymers. The interlocked hexadentate ligand forms the first example of a new type of lattice containing interwoven frameworks resulting from both interpenetration of frameworks due to the presence of an interlocked ligand and more classical interpenetration of independent frameworks.