Interior surface modification of bacteriophage MS2

An efficient strategy for the interior surface functionalization of MS2 viral capsids is reported, featuring a new hetero-Diels-Alder bioconjugation reaction. After virus isolation, the RNA genome was removed from the spherical particles by exposure to pH 11.8 conditions for a period of 4 h. Following this, 180 tyrosine residues on the interior surface of each "empty" capsid shell were modified by using a site-selective diazonium-coupling reaction. To attach additional functionality, the azo conjugate was reduced with Na2S2O4 to afford an ortho-amino tyrosine derivative. Oxidation of this moiety with NaIO4 produced an o-iminoquinone on the protein surface, which was found to undergo an efficient hetero-Diels-Alder reaction with N-(4-aminophenyl)acrylamide. This four-step procedure can be carried out in under 4 h, reaches high levels of conversion, and yields the desired conjugates in >60% overall yield.     

The Finite Subsets of Z2 Having the Extension Property

The paper considers finite subsets Z^d which possess the extensionproperty, namely that every collection {c_k}_k– of complexnumbers which is positive definite with respect to is the restrictionof the Fourier coefficients of some positive measure on T^d.All finite subsets of Z² which possess the extension propertyare described.     

Generic solvent sites in a crystal

A numerical procedure is described and tested for the determination of solvent sites in a crystal hydrate from computer simulation results. The method does not require the computation of density distributions.     

Requirements for prediction of peptide retention time in reversed-phase high-performance liquid chromatography: hydrophilicity/hydrophobicity of side-chains at the N- and C-termini of peptides are dramatically affected by the end-groups and location

The value of reversed-phase high-performance liquid chromatography (RP-HPLC) and the field of proteomics would be greatly enhanced by accurate prediction of retention times of peptides of known composition. The present study investigates the hydrophilicity/hydrophobicity of amino acid side-chains at the N- and C-termini of peptides while varying the functional end-groups at the termini. We substituted all 20 naturally occurring amino acids at the N- and C-termini of a model peptide sequence, where the functional end-groups were N(alpha)-acetyl-X- and N(alpha)-amino-X- at the N-terminus and -X-C(alpha)-carboxyl and -X-C(alpha)-amide at the C-terminus. Amino acid coefficients were subsequently derived from the RP-HPLC retention behaviour of these peptides and compared to each other as well as to coefficients determined in the centre of the peptide chain (internal coefficients). Coefficients generated from residues substituted at the C-terminus differed most (between the -X-C(alpha)-carboxyl and -X-C(alpha)-amide peptide series) for hydrophobic side-chains. A similar result was seen for the N(alpha)-acetyl-X- and N(alpha)-amino-X- peptide series, where the largest differences in coefficient values were observed for hydrophobic side-chains. Coefficients derived from substitutions at the C-terminus for hydrophobic amino acids were dramatically different compared to internal coefficients for hydrophobic side-chains, ranging from 17.1 min for Trp to 4.8 min for Cys. In contrast, coefficients derived from substitutions at the N-terminus showed relatively small differences from the internal coefficients. Subsequent prediction of peptide retention time, within an error of just 0.4 min, was achieved by a predictive algorithm using a combination of internal coefficients and coefficients for the C-terminal residues. For prediction of peptide retention time, the sum of the coefficients must include internal and terminal coefficients.     

Periodic trends within a series of five-coordinate thiolate-ligated [MII(SMe2N4(tren))]+ (M = Mn, Fe, Co, Ni, Cu, Zn) complexes, including a rare example of a stable CuII-thiolate

A series of five-coordinate thiolate-ligated complexes [M(II)(tren)N4S(Me2)]+ (M = Mn, Fe, Co, Ni, Cu, Zn; tren = tris(2-aminoethyl)amine) are reported, and their structural, electronic, and magnetic properties are compared. Isolation of dimeric [Ni(II)(SN4(tren)-RS(dang))]2 ("dang"= dangling, uncoordinated thiolate supported by H bonds), using the less bulky [(tren)N4S](1-) ligand, pointed to the need for gem-dimethyls adjacent to the sulfur to sterically prevent dimerization. All of the gem-dimethyl derivatized complexes are monomeric and, with the exception of [Ni(II)(S(Me2)N4(tren)]+, are isostructural and adopt a tetragonally distorted trigonal bipyramidal geometry favored by ligand constraints. The nickel complex uniquely adopts an approximately ideal square pyramidal geometry and resembles the active site of Ni-superoxide dismutase (Ni-SOD). Even in coordinating solvents such as MeCN, only five-coordinate structures are observed. The MII-S thiolate bonds systematically decrease in length across the series (Mn-S > Fe-S > Co-S > Ni-S approximately Cu-S < Zn-S) with exceptions occurring upon the occupation of sigma* orbitals. The copper complex, [Cu(II)(S(Me2)N4(tren)]+, represents a rare example of a stable CuII-thiolate, and models the perturbed "green" copper site of nitrite reductase. In contrast to the intensely colored, low-spin Fe(III)-thiolates, the M(II)-thiolates described herein are colorless to moderately colored and high-spin (in cases where more than one spin-state is possible), reflecting the poorer energy match between the metal d- and sulfur orbitals upon reduction of the metal ion. As the d-orbitals drop in energy proceeding across the across the series M(2+) (M= Mn, Fe, Co, Ni, Cu), the sulfur-to-metal charge-transfer transition moves into the visible region, and the redox potentials cathodically shift. The reduced M(+1) oxidation state is only accessible with copper, and the more oxidized M(+4) oxidation state is only accessible for manganese.     

Isobaric volume and enthalpy recovery of glasses. II. A transparent multiparameter theory

A multiordering parameter model for glass-transition phenomena has been developed on the basis of nonequilibrium thermodynamics. In this treatment the state of the glass is determined by the values of N ordering parameters in addition to T and P; the departure from equilibrium is partitioned among the various ordering parameters, each of which is associated with a unique retardation time. These times are assumed to depend on T, P, and on the instantaneous state of the system characterized by its overall departure from equilibrium, giving rise to the well-known nonlinear effects observed in volume and enthalpy recovery. The contribution of each ordering parameter to the departure and the associated retardation times define the fundamental distribution function (the structural retardation spectrum) of the system or, equivalently, its fundamental material response function. These, together with a few experimentally measurable material constants, completely define the recovery behavior of the system when subjected to any thermal treatment. The behavior of the model is explored for various classes of thermal histories of increasing complexity, in order to simulate real experimental situations. The relevant calculations are based on a discrete retardation spectrum, extending over four time decades, and on reasonable values of the relevant material constants in order to imitate the behavior of polymer glasses. The model clearly separates the contribution of the retardation spectrum from the temperature-structure dependence of the retardation times which controls its shifts along the experimental time scale. This is achieved by using the natural time scale of the system which eliminates all the nonlinear effects, thus reducing the response function to the Boltzmann superposition equation, similar to that encountered in the linear viscoelasticity. As a consequence, the system obeys a rate (time) -temperature reduction rule which provides for generalization within each class of thermal treatment. Thus the model establishes a rational basis for comparing theory with experiment, and also various kinds of experiments between themselves. The analysis further predicts interesting features, some of which have often been overlooked. Among these are the impossibility of extraction of the spectrum (or response function) from experiments involving cooling from high temperatures at finite rate; and the appearance of two peaks in the expansion coefficient, or heat capacity, during the heating state of three-step thermal cycles starting at high temperatures. Finally, the theory also provides a rationale for interpreting the time dependence of mechanical or other structure-sensitive properties of glasses as well as for predicting their long-range behavior.     

A chloride ion contained in a cobalt `claw': [Co3(DADIT)3]Cl(PF6)2

A trimeric compound containing Co^II is described, namely tris{μ‐2‐[3‐(di­methyl­amino)­propyl­imino]­propane‐1‐thiol­ato}­tricobalt(II) chloride bis­(hexa­fluoro­phosphate), [Co₃(C₁₀H₂₁N₂S)₃]Cl(PF₆)₂. Each Co atom is ligated by one 2‐[3‐(di­methyl­amino)­propyl­imino]­propane‐1‐thiol­ate ligand, an am­ine group and an imine group. The thiol­ate groups bridge the Co atoms, forming a six‐membered ring that encloses the chloride ion in a well defined binding pocket.     

How the Chemical Properties of GBCAs Influence Their Safety Profiles In Vivo

The extracellular class of gadolinium-based contrast agents (GBCAs) is an essential tool for clinical diagnosis and disease management. In order to better understand the issues associated with GBCA administration and gadolinium retention and deposition in the human brain, the chemical properties of GBCAs such as relative thermodynamic and kinetic stabilities and their likelihood of forming gadolinium deposits in vivo will be reviewed. The chemical form of gadolinium causing the hyperintensity is an open question. On the basis of estimates of total gadolinium concentration present, it is highly unlikely that the intact chelate is causing the T₁ hyperintensities observed in the human brain. Although it is possible that there is a water-soluble form of gadolinium that has high relaxitvity present, our experience indicates that the insoluble gadolinium-based agents/salts could have high relaxivities on the surface of the solid due to higher water access. This review assesses the safety of GBCAs from a chemical point of view based on their thermodynamic and kinetic properties, discusses how these properties influence in vivo behavior, and highlights some clinical implications regarding the development of future imaging agents.     

NIRS and Aquaphotomics Trace Robusta-to-Arabica Ratio in Liquid Coffee Blends

Coffee is both a vastly consumed beverage and a chemically complex matrix. For a long time, an arduous chemical analysis was necessary to resolve coffee authentication issues. Despite their demonstrated efficacy, such techniques tend to rely on reference methods or resort to elaborate extraction steps. Near infrared spectroscopy (NIRS) and the aquaphotomics approach, on the other hand, reportedly offer a rapid, reliable, and holistic compositional overview of varying analytes but with little focus on low concentration mixtures of Robusta-to-Arabica coffee. Our study aimed for a comparative assessment of ground coffee adulteration using NIRS and liquid coffee adulteration using the aquaphotomics approach. The aim was to demonstrate the potential of monitoring ground and liquid coffee quality as they are commercially the most available coffee forms. Chemometrics spectra analysis proved capable of distinguishing between the studied samples and efficiently estimating the added Robusta concentrations. An accuracy of 100% was obtained for the varietal discrimination of pure Arabica and Robusta, both in ground and liquid form. Robusta-to-Arabica ratio was predicted with R²CV values of 0.99 and 0.9 in ground and liquid form respectively. Aquagrams results accentuated the peculiarities of the two coffee varieties and their respective blends by designating different water conformations depending on the coffee variety and assigning a particular water absorption spectral pattern (WASP) depending on the blending ratio. Marked spectral features attributed to high hydrogen bonded water characterized Arabica-rich coffee, while those with the higher Robusta content showed an abundance of free water structures. Collectively, the obtained results ascertain the adequacy of NIRS and aquaphotomics as promising alternative tools for the authentication of liquid coffee that can correlate the water-related fingerprint to the Robusta-to-Arabica ratio.     

A novel approach to the calculation of the free energy due to molecular flexibility

The contribution of the molecular flexibility to the solvation excess free energy is expressed in terms of probabilities of reaching hard limits on intramolecular coordinates in a series of calculations successively relaxing those limits. Numerical tests on the harmonic oscillator are also presented and used to make suggestion about computational issues.