Controlling the outcome of an N-alkylation reaction by using N-oxide functional groups

Covalent modifiers of proteins are of importance in chemical proteomics, an emerging chemical technology used to assign protein function. In this study, high-field (1)H NMR techniques were used to analyze the reaction of the bioactive compound, 2,3-bis(bromomethyl)quinoxaline 1,4-dioxide, with amines (a model system for proteins containing nitrogen-based nucleophiles). Unexpectedly, the results show that a double nucleophilic substitution reaction involving 2 equiv of the amine is preferred to an intramolecular cyclization pathway. A direct comparison with the reaction carried out on a substrate lacking the N-oxide functional groups is also provided. X-ray crystal structures and computational studies are used to rationalize the observed differences in reactivity between the two systems.     

The proton affinity of proline analogs using the kinetic method with full entropy analysis

The proton affinity of proline analogs, L-azetidine-2-carboxylic acid (Aze), L-proline (Pro), and L-pipecolic acid (Pip), have been measured using the Armentrout modification of the extended kinetic method in a quadrupole ion trap instrument. Experimental values of 223.0 +/- 1.5, 224.9 +/- 1.6, and 225.6 +/- 1.6 kcal/mol have been determined for the 298K proton affinities of Aze, Pro, and Pip respectively. High level theoretical calculations using both MP2 and B3LYP methods at a variety of basis sets were carried out in order to give theoretical predictions for the 298 K proton affinity and gas phase basicity of all three analogs. Recommended values for the gas phase basicity and proton affinity for proline based on our work and other recent determinations are 216 +/- 2 and 224 +/- 2 kcal/mol.     

Theoretical study of “protonated pyruvate”: A methylhydroxycarbene—carbon dioxide complex—implications for the decarboxylation of pyruvic acid

Two conformers of protonated pyruvate, CH₃C⁺(OH)COO, with the OH group either trans or cis to the methyl group and the carboxylate group in the C? C? C plane have been studied using the ab initio SCF/3-21G method, as well as by some semiempirical AM1 calculations. Both ab initio SCF and AM1 curves for the potential energy as a function of the C? COO distance exhibit a minimum corresponding to a complex of methylhydroxycarbene, CH₃COH, associated with carbon dioxide, but only the AM1 curves predict an inner minimum corresponding to a covalently bonded protonated pyruvate molecule with a C? COO distance of 1.6–1.7 Å. The two models also disagree on the dissociation pathway for pyruvic acid, with the AM1 calculations predicting formation of acetyl and HOCO radicals while the ab initio method predicts dissociation into methylhydroxycarbene and carbon dioxide following an initial intramolecular proton transfer. The weakly bound complexes of methylhydroxycarbene and carbon dioxide have been studied in some detail using ab initio SCF and MP2 methods in conjunction with 6-311G** basis sets, obtaining equilibrium geometries and vibrational frequencies. In addition, the lactone-type isomer of protonated pyruvate, which contains a C? C? O ring, was also studied. The conclusions of these calculations are consistent with those from earlier work using the smaller 3-21G basis set. The most stable complex is predicted to occur between trans-methylhydroxycarbene and carbon dioxide where substantial stabilization is provided by an OH ? OC hydrogen bond. © 1993 John Wiley & Sons, Inc.     

GROMACS: fast, flexible, and free

This article describes the software suite GROMACS (Groningen MAchine for Chemical Simulation) that was developed at the University of Groningen, The Netherlands, in the early 1990s. The software, written in ANSI C, originates from a parallel hardware project, and is well suited for parallelization on processor clusters. By careful optimization of neighbor searching and of inner loop performance, GROMACS is a very fast program for molecular dynamics simulation. It does not have a force field of its own, but is compatible with GROMOS, OPLS, AMBER, and ENCAD force fields. In addition, it can handle polarizable shell models and flexible constraints. The program is versatile, as force routines can be added by the user, tabulated functions can be specified, and analyses can be easily customized. Nonequilibrium dynamics and free energy determinations are incorporated. Interfaces with popular quantum-chemical packages (MOPAC, GAMES-UK, GAUSSIAN) are provided to perform mixed MM/QM simulations. The package includes about 100 utility and analysis programs. GROMACS is in the public domain and distributed (with source code and documentation) under the GNU General Public License. It is maintained by a group of developers from the Universities of Groningen, Uppsala, and Stockholm, and the Max Planck Institute for Polymer Research in Mainz. Its Web site is http://www.gromacs.org.     

Influence of antibody immobilization strategy on molecular recognition force microscopy measurements

A systematic evaluation of the effects of antibody immobilization strategy on the binding efficiency and selectivity (e.g., ability to distinguish between specific and nonspecific interactions) of immunosurfaces prepared with F(ab') antibody fragments of rabbit Immunoglobulin G (IgG) is described. F(ab') was attached to gold surfaces either (1) directly via the formation of a gold-thiolate bond or (2) indirectly through a series of a bifunctional linkers containing an alkane chain or ethylene glycol spacer. Immobilization of F(ab') via the sulfhydryl reactive group located opposite the antigen binding site ensured optimum orientation of the antigen binding site. X-ray photoelectron spectroscopy (XPS) and surface plasmon resonance (SPR) were used to confirm surface modification with the bifunctional linkers and antibody immobilization, respectively. Binding efficiency assays performed with SPR indicated that increasing the length of the linker increased the antigen binding efficiency. Atomic force microscopy (AFM) adhesion force measurements indicated that AFM probes functionalized with directly immobilized F(ab') more effectively discriminated between specific and nonspecific surface-bound proteins than probes modified indirectly via linker-immobilized F(ab'). In addition, a greater number of antibody-antigen binding events were observed with directly immobilized F(ab')-functionalized probes.     

Tetrakis(imidazolyl)borate-based coordination polymers: group II network solids,M[B(Im)4]2(H2O)2 (M = Mg,Ca, Sr)

We are using the coordinating anion tetrakis(imidazolyl)borate to construct new metal-organic framework structures. In this report, we present three alkaline earth metal network solids incorporating this anion. All three compounds have the same formula, M[B(Im)(4)](2)(H(2)O)(2) (M = Mg, Ca, Sr), and the same coordination environment about the metal. However, the three compounds have different network structures with different degrees of hydrogen bonding; the Mg material forms a two-dimensional network and the Ca and Sr compounds form one-dimensional chains. In addition, we present the structure of the protonated anion B(HIm)(Im)(3) as a model for the default structure of this anion and discuss how the conformation of tetrakis(imidazolyl)borate can affect the structure of network solids.     

Relativistic all-electron configuration interaction calculations on the gold atom

We present the results of relativistic and non-relativistic self-consistent field and configuration interaction calculations for the gold atom, using the spin-free no-pair Hamiltonian in a basis set expansion. A new basis set for the gold atom is discussed and its results in relativistic and non-relativistic self-consistent field calculations are compared to those of numerical Dirac-Hartree-Focic and Hartree-Fock calculations, respectively. Excitation energies, electron affinities and ionization potentials were calculated using a multi-reference configuration interaction technique and are in reasonable agreement with experiment in the relativistic case.     

Platinum(IV)-mediated nitrile-sulfimide coupling: a route to heterodiazadienes

Pt(IV)-mediated addition of the sulfimide Ph2S = NH and the mixed sulfide/sulfimides o- and p-[PhS(=NH)](PhS)-C6H4 by the S=NH group to the metal-bound nitriles in the platinum(IV) complexes [PtCl4(RCN)2] proceeds smoothly at room temperature in CH2Cl2 and results in the formation of the heterodiazadiene compounds [PtCl4[NH=C(R)N=SR'Ph]2] (R' = Ph, R = Me, Et, CH2Ph, Ph; R' = o- and p-(PhS)C6H4; R = Et). While trans-[PtCl4(RCN)2] (R = Et, CH2Ph, Ph) reacting with Ph2S=NH leads exclusively to trans-[PtCl4[NH=C(R)N=SPh2]2], cis/trans-[PtCl4(MeCN)2] leads to cis/trans mixtures of [PtCl4[NH=C(Me)N=SPh2]2] and the latter have been separated by column chromatography. Theoretical calculations at both HF/HF and MP2//HF levels for the cis and trans isomers of [PtCl4[NH=C(Me)N=SMe2]2] indicate a higher stability for the latter. Compounds trans-[PtCl4[E-NH=C(R)N=SPh2]2] (R = Me, Et) and cis-[PtCl4[E-NH=C(Me)N=SPh2][Z-NH=C(Me)N=SPh2]] have been characterized by X-ray crystallography. The complexes [PtCl4[NH=C(R)N=SPh2]2] undergo hydrolysis when treated with HCl in nondried CH2Cl2 to achieve the amidines [PtCl4[NH=C(NH2)R]2] the compound with R = Et has been structurally characterized) and Ph2SO. The heterodiazadiene ligands, formed upon Pt(IV)-mediated RCN/sulfimide coupling, can be liberated from their platinum(IV) complexes [PtCl4[NH=C(R)N=SR'Ph]2] by reaction with Ph2PCH2CH2PPh2 (dppe) giving free NH=C(R)=SR'Ph and the dppe oxides, which constitutes a novel route for such rare types of heterodiazadienes whose number has also been extended. The hybrid sulfide/sulfimide species o- and p-[PhS(=NH)](PhS)C6H4 also react with the Pt(II) nitrile complex [PtCl2(MeCN)2] but the coupling--in contrast to the Pt(IV) species--gives the chelates [PtCl2[M-I=C(Me)N=S(Ph)C6H4SPh]]. The X-ray crystal structure of [PtCl2[M-I=C(Me)N=S(Ph)C6H4SPh-o]] reveals the bond parameters within the metallacycle and shows an unusual close interaction of the sulfide sulfur atom with the platinum.