Saturation transfer difference 1D-TOCSY experiments to map the topography of oligosaccharides recognized by a monoclonal antibody directed against the cell-wall polysaccharide of group A streptococcus

A new saturation transfer difference 1D-TOCSY NMR experiment that allows the investigation of complex ligands interacting with proteins and its application in the mapping of which portions of oligosaccharide ligands (epitope) interact with a complementary antibody are described. The interaction between trisaccharide and hexasaccharide ligands, corresponding to fragments of the cell-wall polysaccharide of Streptococcus Group A, and a monoclonal antibody directed against the polysaccharide is investigated at the molecular level. The polysaccharide consists of alternating alpha-(1-->2) and alpha-(1-->3) linked L-rhamnopyranose (Rha) residues with branching N-acetyl-D-glucopyranosylamine (GlcNAc) residues linked beta-(1-->3) to alternate rhamnopyranose rings. The epitope is proven to consist not only of the immunodominant GlcNAc sugar but also of an entire branched trisaccharide repeating unit. The experimental NMR data serve to check and validate the computed models of the oligosaccharide-antibody complexes.     

Inclusion of the ligand field contribution in a polarizable molecular mechanics: SIBFA-LF

To account for the distortion of the coordination sphere that takes place in complexes containing open-shell metal cations such as Cu(II), we implemented, in sum of interactions between fragments ab initio computed (SIBFA) molecular mechanics, an additional contribution to take into account the ligand field splitting of the metal d orbitals. This term, based on the angular overlap model, has been parameterized for Cu(II) coordinated to oxygen and nitrogen ligands. The comparison of the results obtained from density functional theory computations on the one hand and SIBFA or SIBFA-LF on the other shows that SIBFA-LF gives geometric arrangements similar to those obtained from quantum mechanical computations. Moreover, the geometric improvement takes place without downgrading the energetic agreement obtained from SIBFA. The systems considered are Cu(II) interacting with six water molecules, four ammonia or four imidazoles, and four water plus two formate anions.     

Ligand effects in the non-alternating CO-ethylene copolymerization by palladium(II) catalysis

In this paper we report on a comparative study of the non-alternating CO-C(2)H(4) copolymerization catalyzed by neutral Pd(II) complexes with the phosphine-sulfonate ligands bis(o-methoxyphenyl)phosphinophenylenesulfonate and bis(o-methoxyphenyl)phosphino-ethylenesulfonate. The former ligand, featuring a lower skeletal flexibility, has been found to form more active catalysts as well as produce polyketones with higher molecular weight and higher extra-ethylene incorporation. Operando high-pressure NMR studies have allowed us to intercept, for the first time, Pd(II)(phosphine-sulfonate) beta-chelates in the non-alternating copolymerization cycle, while model organometallic reactions have contributed to demonstrate that Pd(II) (phosphine-sulfonate) fragments do not form stable carbonyl complexes. The opening of the beta-chelates has been found to be a viable process by either comonomer, which contrasts with the behaviour of Pd(II) (chelating diphosphine) catalysts for the perfectly alternating copolymerization.     

Quantitative structure-affinity relationship of 5-HT1A receptor ligands by the classification tree method

The influence of molecular structure of 346 ligands on their affinity for 5-HT1A receptors was investigated. It was shown that the effectiveness of the proposed novel approach for interpretation of decision tree models compared favourably with the PLS method. In the context of the proposed approach, molecular fragments and their values of the relative influence on the affinity for 5-HT1A receptors were defined.     

Mass spectra and fragmentation patterns of malonaldehydedianil and some of its metal complexes

Under electron impact malonaldehydedianil and its bis Co(II), Ni(II) and Zn(II) complexes produce a stable molecular ion. The Cu(II) complex appears to decompose prior to ionization. The free dianil molecular ion fragments by expulsion of the azomethine proton or by fission of C-N bonds. The molecular ions of the metal complexes usually expel a complete ligand before undergoing demetallation.     

Directed assembly of transition-metal-coordinated molecular loops and squares from salen-type components. Examples of metalation-controlled structural conversion

A series of transition-metal-containing molecular "loops" and "squares" has been prepared via a directed-assembly approach and characterized. The molecular loops were prepared from the reaction of cis-(PEt(3))(2)Pt(OTf)(2) with bis(4-pyridyl)-functionalized free-base salen-type ligands. Zn(II)-metalation of the salen-type ligands in the molecular loops converts the loops to molecular squares. Alternatively, the squares can be obtained by the directed assembly of cis-(PEt(3))(2)Pt(OTf)(2) and bis(4-pyridyl)-functionalized Zn(II)-salen-type ligands. A concentration-dependent dynamic equilibrium between cyclic species was observed when bis(3-pyridyl)-functionalized free-base salen-type ligand was employed in the reaction. Zn(II) or Cr(III) metalation of the free-base ligand shifted the equilibrium to the single dimeric species. The incorporation of multiple reactive metal sites into a single, cavity-containing supramolecular structure points toward catalytic applications for these new assemblies.     

Chemistry of Ruthenium Polypyridine Complexes: IV. Quantum-Chemical Simulation of the Effect of Solvation Shell on the Electronic Structure of Ru(II) Complexes with Nitrogen-containing Ligands

Ab initio quantum-chemical calculations of Ru(II) complexes have been fulfilled with consideration for solvation within the framework of the polarized continuum model. Energy levels of fragments of Ru(II) complexes with organic ligands are shifted relative to each other by electrostatic interactions with the solvation shells.     

Quantitative structure-affinity relationship of 5-HT1A receptor ligands by the classification tree method

The influence of molecular structure of 346 ligands on their affinity for 5-HT_1A receptors was investigated. It was shown that the effectiveness of the proposed novel approach for interpretation of decision tree models compared favourably with the PLS method. In the context of the proposed approach, molecular fragments and their values of the relative influence on the affinity for 5-HT_1A receptors were defined.     

The elusive phosphorescence of pyrromethene-BF2 dyes revealed in new multicomponent species containing Ru(II)-terpyridine subunits

The triplet emitting state of an indacene at 774 nm (of 50 ms life-time) was observed for the first time in new ruthenium(II) complexes based on bipartite ligands carrying one or two indacene subunits linked via phenylethynyl connectors to terpyridine fragments.     

New model potentials for sulfur-copper(I) and sulfur-mercury(II) interactions in proteins: from ab initio to molecular dynamics

We have developed new force field and parameters for copper(I) and mercury(II) to be used in molecular dynamics simulations of metalloproteins. Parameters have been derived from fitting of ab initio interaction potentials calculated at the MP2 level of theory, and results compared to experimental data when available. Nonbonded parameters for the metals have been calculated from ab initio interaction potentials with TIP3P water. Due to high charge transfer between Cu(I) or Hg(II) and their ligands, the model is restricted to a linear coordination of the metal bonded to two sulfur atoms. The experimentally observed asymmetric distribution of metal ligand bond lengths (r) is accounted for by the addition of an anharmonic (r3) term in the potential. Finally, the new parameters and potential, introduced into the CHARMM force field, are tested in short molecular dynamics simulations of two metal thiolates fragments in water. (Brooks BR et al. J Comput Chem 1983, 4, 1987.1).     

Synthesis,characterization and corrosion inhibition in acid medium of l‐histidine Schiff base complexes

Complexes of cobalt(II), nickel(II) and copper(II) of l ‐histidine Schiff base derived from 2,4‐dihydroxybenzaldehyde and 2‐hydroxy‐1‐naphthaldehyde have been synthesized. The structures of ligands and complexes have been characterized using elemental analysis, molar conductance, magnetic moment measurements, and spectral and thermal studies. The ligands behave as tridentate, coordinating through the azomethine nitrogen and α‐hydroxyl and carboxylic oxygen atoms. The obtained results show that the Cu(II) complexes have square planar geometry, the Co(II) complexes have octahedral and tetrahedral geometries and the Ni(II) complexes have square planar and octahedral geometries. The molecular geometries of the metal complexes are supported by three‐dimensional molecular modelling using molecular mechanics (MM+) and semiempirical molecular orbital calculations (PM3). The inhibition effect of ligands and complexes on the corrosion of aluminium in 2 M H₂SO₄ was investigated using weight loss. The inhibition efficiency is found to increase with increasing inhibitor concentration and temperature. The increase in inhibition efficiency with increasing temperature is suggestive of a chemical adsorption process. Copyright © 2014 John Wiley & Sons, Ltd.     

Formation of a 1-azaallenylidene ligand by reaction of an amido complex with tetracyanoethylene

Amido complexes of Mo(II) allyl carbonyl fragments containing monodentate amido ligands, prepared by reaction of suitable chloro precursors with potassium amides, react (for the N(H)(p-tolyl) derivative) with tetracyanoethylene to give a 1-azaallenylidene complex.     

Resorcarene-Based Nanoarchitectures: Metal-Directed Assembly of a Molecular Loop and Tetrahedron

Large cavities and portals are present in the nanoscale molecular architectures formed from dithiocarbamate-functionalized resorcarene ligands and zinc(II) or copper(III) ions. With Zn(II) a molecular loop based on a triangle of resorcarene cups is prepared-the cavity is circular (shown on the left). A molecular cage based on a distorted tetrahedron of four resorcarene ligands assembled by eight Cu(III) ions contains triangular-shaped portals suitable for guest passage (shown on the right).     

SVM and SVR-based MHC-binding prediction using a mathematical presentation of peptide sequences

At present, there are a number of methods for the prediction of T-cell epitopes and major histocompatibility complex (MHC)-binding peptides. Despite numerous methods for predicting T-cell epitopes, there still exist limitations that affect the reliability of prevailing methods. For this reason, the development of models with high accuracy are crucial. An accurate prediction of the peptides that bind to specific major histocompatibility complex class I and II (MHC-I and MHC-II) molecules is important for an understanding of the functioning of the immune system and the development of peptide-based vaccines. Peptide binding is the most selective step in identifying T-cell epitopes. In this paper, we present a new approach to predicting MHC-binding ligands that takes into account new weighting schemes for position-based amino acid frequencies, BLOSUM and VOGG substitution of amino acids, and the physicochemical and molecular properties of amino acids. We have made models for quantitatively and qualitatively predicting MHC-binding ligands. Our models are based on two machine learning methods support vector machine (SVM) and support vector regression (SVR), where our models have used for feature selection, several different encoding and weighting schemes for peptides. The resulting models showed comparable, and in some cases better, performance than the best existing predictors. The obtained results indicate that the physicochemical and molecular properties of amino acids (AA) contribute significantly to the peptide-binding affinity.     

LAMMA mass spectra of β-diketone,bis(benzoylacetone)ethylenediimine and bis(salicylidene)ethylenediimine complexes of some transition metals

Complexes of 2,4-pentanedione (acetylacetone, acac), [Cu(acac)₂], [VO(acac)₂] and [CO(acac)₃], and the chromium(III) derivative of 3-methyl-2,4-pentanedione (methylacetylacetone, meac), [Cr(meac)₃], the ligands bis(benzoylacetone)ethylenediimine and bis(salicylidene)ethylenediimine, and their cobalt(II), nickel(II) and copper(II) chelates were analysed by laser desorption mass spectrometry (LAMMA) and compared to electron impact (EI) results. The positive ion LAMMA spectra generally reveal mostly small fragments, although metal cationization peaks are seen for most complexes. Negative ion LAMMA produce carbon clusters and some structurally important fragments.     

Molecular modeling of the inhibitory mechanism of copper(II) on aggregation of amyloid β-peptide

Aggregation of amyloid β-peptide (Aβ) into insoluble fibrils is a key pathological event in Alzheimer’s disease (AD). Under certain conditions, Cu(II) exhibits strong inhibitory effect on the Zn(II)-induced aggregation, which occurs significantly even at nearly physiological concentrations of zinc ion in vitro. Cu(II) is considered as a potential factor in the normal brain preventing Aβ from aggregating. The possible mechanism of the inhibitory effect of Cu(II) is investigated for the first time by molecular modeling method. In the mono-ring mode, the Y10 residue promotes typical quasi-helix conformations of Aβ. Specially, [Cu-H13(NTT)-Y10(OH)] complex forms a local 3.0₁₀ helix conformation. In the multi-ring mode, the side chains of Q15 and E11 residues collaborate harmoniously with other chelating ligands producing markedly low energies and quasi-helix conformations. [Cu-3N-Q15(O)-E11(O1)] and [Cu-H13(NTT)-Y10(OH)] complex with quasi-helix conformations may prefer soluble forms in solution. In addition, hydrogen-bond interactions may be the main driving force for Aβ aggregation. All the results will provide helpful clues for an improved understanding of the role of Cu(II) in the pathogenesis of AD and contribute to the development of an “anti-amyloid” therapeutic strategy.     

Zn(II) ions bind very efficiently to tandem repeat region of "prion related protein" (PrP-rel-2) of zebra-fish. MS and potentiometric evidence

Multi-histidine peptide fragments of zebra-fish prion protein are effective ligands for Zn(II) ions. Moreover the formation of a dinuclear complex species with a longer peptide can suggest the existence of the cooperative effect in the metal ion binding.     

Exchange coupling through diamagnetic [Fe(CO)4]2- bridging ligands in a xenophilic cluster

The electronic structure of so-called 'xenophilic' clusters, which contain both organometallic fragments and Werner-type paramagnetic transition metal centres, presents a challenge to simple theories of bonding. Density functional theory shows clearly that the cluster Mn(2)(thf)(4)(Fe(CO)(4))(2) is best described as an exchange-coupled Mn(II)(2) dimer, the closed-shell organometallic [Fe(CO)(4)](2-) fragments acting simply as bridging ligands. The high-spin configuration of the Mn(II) ions leads to single occupation of the Mn-Fe σ* orbitals and therefore substantially weaker metal-metal bonding than in conventional low-valent organometallic clusters. The transition metal fragments are effective mediators of superexchange (J(calc) = -44 cm(-1)), leading to the measured effective magnetic moment of ~5 μ(B) at 300 K, considerably lower than the limiting value of 8.37 μ(B) for two uncoupled S = 5/2 Mn(II) centres.