New redox system: Trichloromethylarene —pyridine base

A redox reaction of trichloromethylarenes with pyridines results in respective N-(-chloroarylmethyl)substituted pyridiniurn chlorides which give, on hydrolysis, aromatic aidehydes and 4-chloropyridines or 1, 4-bipyridiniurn salts.N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 117913 Moscow, Russia. Published in Khimiya Geterotsiklicheskikh Soedinenii, No. 10, pp. 1373–1375, October, 1995. Original article submitted September 5, 1995.     

Amperometric urea biosensor based on urease and electropolymerized toluidine blue dye as a pH-sensitive redox probe

The electropolymerized toluidine blue film deposited on the glassy carbon electrode show amperometrically detectable pH sensitivity. This feature of polytoluidine blue (PTOB) film was used for a construction of an amperometric urea biosensor. We have observed a linear shift of the formal redox potential with increasing pH value between 4 and 8 giving the slope of 81 mV(Delta) pH(-1). Polytoluidine blue film has had a significantly increased stability and higher electrochemical activity compared to the adsorbed monomeric dye. The polytoluidine blue urea biosensor has been operating at a working potential of -200 mV vs. SCE. The sensitivity of the biosensor was 980 nA mM(-1) cm(-2). The biosensor showed linearity in concentration range up to 0.8 mM with the detection limit of 0.02 mM (S/N=3).     

Transfection mediated by gemini surfactants: engineered escape from the endosomal compartment

The structure of the lipoplex formed from DNA and the sugar-based cationic gemini surfactant 1, which exhibits excellent transfection efficiency, has been investigated in the pH range 8.8-3.0 utilizing small-angle X-ray scattering (SAXS) and cryo-electron microscopy (cryo-TEM). Uniquely, three well-defined morphologies of the lipoplex were observed upon gradual acidification: a lamellar phase, a condensed lamellar phase, and an inverted hexagonal (H(II)) columnar phase. Using molecular modeling, we link the observed lipoplex morphologies and physical behavior to specific structural features in the individual surfactant, illuminating key factors in future surfactant design, viz., a spacer of six methylene groups, the presence of two nitrogens that can be protonated in the physiological pH range, two unsaturated alkyl tails, and hydrophilic sugar headgroups. Assuming that the mechanism of transfection by synthetic cationic surfactants involves endocytosis, we contend that the efficacy of gemini surfactant 1 as a gene delivery vehicle can be explained by the unprecedented observation of a pH-induced formation of the inverted hexagonal phase of the lipoplex in the endosomal pH range. This change in morphology leads to destabilization of the endosome through fusion of the lipoplex with the endosomal wall, resulting in release of DNA into the cytoplasm.     

Photoinduced axial ligation and deligation dynamics of nonplanar nickel dodecaarylporphyrins

The ground- and excited-state metal-ligand dynamics of nonplanar nickel(II) 2,3,5,7,8,10,12,13,15,17,18,20-dodecaphenylporphyrin (NiDPP) and two fluorinated analogues (NiF(20)DPP and NiF(28)DPP) have been investigated using static and time-resolved absorption spectroscopy in toluene and in ligating media that differ in basicity, aromaticity, and steric encumbrance. Because of the electronic and steric consequences of nonplanarity, NiDPP does not bind axial ligands in the ground state, but metal coordination does occur after photoexcitation with multistep dynamics that depend on the properties of the ligand. Following the structural relaxations that occur in all nickel porphyrins within approximately 10 ps, ligand binding to photoexcited NiDPP is progressively longer in pyridine, piperidine, and 3,5-lutidine (25-100 ps) but does not occur at all in 2,6-lutidine in which the ligating nitrogen is sterically encumbered. The transient intermediate that is formed, which nominally could be either a five- or six-coordinate species, also has a ligand-dependent lifetime (200-550 ps). Decay of this intermediate occurs partially via ligand release to re-form the uncoordinated species, in competition with binding of the second axial ligand and/or conformational/electronic relaxations (of a six-coordinate intermediate) to give the ground state of the bis-ligated photoproduct. The finding that the photoproduct channel principally depends on ligand characteristics along with the time-evolving spectra suggests that the transient intermediate may involve a five-coordinate species. In contrast to NiDPP, the fluorinated analogues NiF(20)DPP and NiF(28)DPP do coordinate axial ligands in the ground state but eject them after photoexcitation. Collectively, these results demonstrate the sensitivity with which the electronic and structural characteristics of the macrocycle, substituents, and solvent (ligands) can govern the photophysical and photochemical properties of nonplanar porphyrins and open new avenues for exploring photoinduced ligand association and dissociation behavior.     

Miscibility of zinc sulfide and zinc phosphide

Solid solutions in the system zinc sulfide/zinc phosphide (Zn(2+)(x)S(2-2xP(2x)) were investigated using the cyclic cluster model within the semiempirical MSINDO method. Results of cyclic cluster calculations for binding energies of the perfect ZnS and Zn(3)P(2) are presented and compared with the experimental data. The miscibility of ZnS and Zn(3)P(2) over the whole composition range of 0 < x < 1 was investigated by calculating the Gibbs free energy of mixing Delta(M)G for different values of x. A miscibility gap was found at both ends of the composition range and compared with experimental data.     

Automated linkage of proteins and payloads producing monodisperse conjugates

Controlled protein functionalization holds great promise for a wide variety of applications. However, despite intensive research, the stoichiometry of the functionalization reaction remains difficult to control due to the inherent stochasticity of the conjugation process. Classical approaches that exploit peculiar structural features of specific protein substrates, or introduce reactive handles via mutagenesis, are by essence limited in scope or require substantial protein reengineering. We herein present equimolar native chemical tagging (ENACT), which precisely controls the stoichiometry of inherently random conjugation reactions by combining iterative low-conversion chemical modification, process automation, and bioorthogonal trans-tagging. We discuss the broad applicability of this conjugation process to a variety of protein substrates and payloads.

Controlled protein functionalization holds great promise for a wide variety of applications.

Applications of protein conjugates are limitless, including imaging, diagnostics, drug delivery, and sensing.^1–4 In many of these applications, it is crucial that the conjugates are homogeneous.⁵ The site-selectivity of the conjugation process and the number of functional labels per biomolecule, known as the degree of conjugation (DoC), are crucial parameters that define the composition of the obtained products and are often the limiting factors to achieving adequate performance of the conjugates. For instance, immuno-PCR, an extremely sensitive detection technique, requires rigorous control of the average number of oligonucleotide labels per biomolecule (its DoC) in order to achieve high sensitivity.⁶ In optical imaging, the performance of many super-resolution microscopy techniques is directly defined by the DoC of fluorescent tags.⁷ For therapeutics, an even more striking example is provided by antibody–drug conjugates, which are prescribed for the treatment of an increasing range of cancer indications.⁸ A growing body of evidence from clinical trials indicates that bioconjugation parameters, DoC and DoC distribution, directly influence the therapeutic index of these targeted agents and hence must be tightly controlled.⁹Standard bioconjugation techniques, which rely on nucleophile–electrophile reactions, result in a broad distribution of different DoC species (Fig. 1a), which have different biophysical parameters, and consequently different functional properties.¹⁰Open in a separate windowFig. 1Schematic representation of the types of protein conjugates.To address this key issue and achieve better DoC selectivity, a number of site-specific conjugation approaches have been developed (Fig. 1b). These techniques rely on protein engineering for the introduction of specific motifs (e.g., free cysteines,¹¹ selenocysteines,¹² non-natural amino acids,^13,14 peptide tags recognized by specific enzymes^15,16) with distinct reactivity compared to the reactivity of the amino acids present in the native protein. These motifs are used to simultaneously control the DoC (via chemo-selective reactions) and the site of payload attachment. Both parameters are known to influence the biological and biophysical parameters of the conjugates,¹¹ but so far there has been no way of evaluating their impact separately.The influence of DoC is more straightforward, with a lower DoC allowing the minimization of the influence of payload conjugation on the properties of the protein substrate. The lowest DoC that can be achieved for an individual conjugate is 1 (corresponding to one payload attached per biomolecule). It is noteworthy that DoC 1 is often difficult to achieve through site-specific conjugation techniques due to the symmetry of many protein substrates (e.g., antibodies). Site selection is a more intricate process, which usually relies on a systematic screening of conjugation sites for some specific criteria, such as stability or reactivity.¹⁷Herein, we introduce a method of accessing an entirely new class of protein conjugates with multiple conjugation sites but strictly homogenous DoCs (Fig. 1c). To achieve this, we combined (a) iterative low conversion chemical modification, (b) process automation, and (c) bioorthogonal trans-tagging in one workflow.The method has been exemplified for protein substrates, but it is applicable to virtually any native bio-macromolecule and payload. Importantly, this method allows for the first time the disentangling of the effects of homogeneous DoC and site-specificity on conjugate properties, which is especially intriguing in the light of recent publications revealing the complexity of the interplay between payload conjugation sites and DoC for in vivo efficacy of therapeutic bioconjugates.¹⁸ Finally, it is noteworthy that this method can be readily combined with an emerging class of site-selective bioconjugation reagents to produce site-specific DoC 1 conjugates, thus further expanding their potential for biotechnology applications.¹⁹     

NMR detection of intermolecular NH.OP hydrogen bonds between guanidinium protons and bisposphonate moieties in an artificial arginine receptor

Hydrogen bonding plays a major role in the selective recognition of guanidinium groups by receptor molecules. The present NMR investigation provides direct experimental evidence of hydrogen bonds in an artificial arginine receptor complex consisting of alpha-N-benzoylarginine ethyl ester and a bisphosphonate tweezers molecule. trans-Hydrogen bond 2hJHP couplings between the phosphonate moieties and individual guanidinium protons as well as the amide proton have been detected by [1H,31P]-HMBC and [31P,1H]-INEPT experiments. The detected hydrogen bonding network in the investigated artificial arginine receptor shows a symmetrical end-on interaction of the guanidinium moiety, which enables concerted rotations and deviates from the structure proposed for the biological arginine fork.     

The molecular geometries of some cyclic nitramines in the gas phase

The structural parameters of 1,3,5-trinitro-1,3,5-triazacyclohexane (RDX), (CH₂NNO₂)₃, 1,3-dinitro-1,3-diazacyclopentane (DDCP), CH₂(CH₂NNO₂)₂, andN-nitropyrrolidine (NP), (CH₂)₄NNO₂, have been determined by electron diffraction.The six-membered ring of RDX has a chair form with axial positions of the nitro groups and close to planar bond geometry of the amine nitrogen atoms. The overallC ₃ symmetry of the molecule is in agreement with the experimental data.The conformation of the five-membered ring in DDCP is a half-chair ofC ₂ symmetry, while that in NP is an envelope ofC _S symmetry. The nitro groups are in equatorial positions in both molecules. The conformations of pyrrolidine and imidazolidine cycles show interesting features.The pyramidal geometry of the amine nitrogen atom bonds flattens in going from pyrrolidine andN-chloropyrrolidine to NP and DDCP and then to RDX and to dimethylnitramine (DMNA), (CH₃)₂NNO₂.     

Rational Krylov methods for fractional diffusion problems on graphs

BIT Numerical Mathematics - In this paper we propose a method to compute the solution to the fractional diffusion equation on directed networks, which can be expressed in terms of the graph...     

Triazene proton affinities: A comparison between density functional,Hartree–Fock,and post-Hartree–Fock methods

The consistency of three density functional computational implementations (DMol, DGauss, and deMon) are compared with high-level Hartree–Fock and Møller–Plesset (MP) calculations for triazene (HN?NNH₂) and formyl triazene (HN?NNHCOH). Proton affinities on all electronegative sites are investigated as well as the geometries of the neutral and protonated species. Density functional calculations employing the nonlocal gradient corrections show agreement with MP calculations for both proton affinities and geometries of neutral and protonated triazenes. Local spin density approximation DMol calculations using numerical basis sets must employ an extended basis to agree with other density functional codes using analytic Gaussian basis sets. The lowest energy conformation of triazene was found to be nonplanar; however, the degree of nonplanarity, as well as some bond lengths, is dependent on the basis set, electron correlation treatment, and methods used for the calculation. © 1994 by John Wiley & Sons, Inc.

1 This article is a U.S. Government work and, as such, is in the public domain in the United States of America.