Domain-specific incorporation of noninvasive optical probes into recombinant proteins

An integrated approach is described that allows the domain-specific incorporation of optical probes into large recombinant proteins. The strategy is the combination of two existing techniques, expressed protein ligation (EPL) and in vivo amino acid replacement of tryptophans with tryptophan (Trp) analogues. The Src homology 3 (SH3) domain from the c-Crk-I adaptor protein has been labeled with a Trp analogue, 7-azatryptophan (7AW), using Escherichia coli Trp auxotrophs. Structural, biochemical, and thermodynamic studies show that incorporation of 7AW does not significantly perturb the structure or function of the isolated domain. Ligation of the 7AW-labeled SH3 domain to the c-Crk-I Src homology 2 (SH2) domain, via EPL, generated the multidomain protein, c-Crk-I, with a domain-specific label. Studies of this labeled protein show that the biochemical and thermodynamic properties of the SH3 domain do not change within the context of a larger multidomain protein. The technology described here is likely to be a useful tool in enhancing our understanding of the behavior of modular domains in their natural context, within multidomain proteins.     

Stacking and separation of enantiomers by acetonitrile-salt mixtures in micellar electrokinetic chromatography

The feasibility of employing the "acetonitrile stacking" method in micellar electrokinetic chromatography (MEKC) for the on-line preconcentration and separation of enantiomers is demonstrated for the first time. The effects of various experimental parameters on the stacking and separation of three different pairs of optical isomers, i.e., two substituted naphthyl enantiomers and one dansylated-DL-amino acid, were examined. In particular, the effectiveness of the addition of acetonitrile and salt in the sample matrix to induce narrowing of the analyte bands was investigated in the presence of sodium cholate as the chiral surfactant micelle in the separation buffer. For example, it was found that the presence of both acetonitrile and 1% NaCl in the sample matrix (volume ratio = 2:1) led to a significant improvement of the peak height and resolution for the MEKC separation of a pair of R(-)/S(+)-1,1'-binaphthyl diyl hydrogen phosphate enantiomers when the injection sample size was relatively large (e.g., 12% capillary volume). Furthermore, the feasibility of combining salting-out solvent extraction (off-line) and acetonitrile stacking (on-line) as a novel approach for sample preconcentration in capillary electrophoresis was also demonstrated.     

Periodic trends in indirect nuclear spin-spin coupling tensors: relativistic density functional calculations for interhalogen diatomics

There have been significant advances in the calculation and interpretation of indirect nuclear spin-spin coupling (J) tensors during the past few years; however, much work remains to be done, especially for molecules containing heavy atoms where relativistic effects may play an important role. Many J tensors cannot be explained based solely on a nonrelativistic Fermi-contact mechanism. In the present work, the relativistic zeroth-order regular approximation density-functional (ZORA-DFT) implementation for the calculation of J has been applied to the complete series of homonuclear and heteronuclear diatomic halogen molecules: F(2), Cl(2), Br(2), I(2), At(2), ClF, BrF, IF, ClBr, ClI, and BrI. For all of these compounds, the reduced isotropic coupling constant (K(iso)) is positive and the reduced anisotropic coupling constant (DeltaK) is negative. With the exception of molecular fluorine, the magnitudes of K(iso) and DeltaK are shown to increase linearly with the product of the atomic numbers of the coupled nuclei. ZORA-DFT calculations of J for F(2) and ClF are in excellent agreement with the results obtained from multiconfigurational self-consistent-field calculations. The relative importance of the various coupling mechanisms is approximately constant for all of the compounds, with the paramagnetic spin-orbit term being the dominant contributor to K(iso), at approximately 70-80%. Available experimental stimulated resonant Raman spectroscopy data are exploited to extract the complete J((127)I,(127)I) tensor for iodine in two rotational states. The dependence of K(iso) and DeltaK on bond length and rovibrational state is investigated by using calculated results in combination with available experimental data. In addition to providing new insights into periodic trends for J coupling tensors, this work further demonstrates the utility of the ZORA-DFT method and emphasizes the necessity of spin-orbit relativistic corrections for J calculations involving heavy nuclei.     

The Amber biomolecular simulation programs

We describe the development, current features, and some directions for future development of the Amber package of computer programs. This package evolved from a program that was constructed in the late 1970s to do Assisted Model Building with Energy Refinement, and now contains a group of programs embodying a number of powerful tools of modern computational chemistry, focused on molecular dynamics and free energy calculations of proteins, nucleic acids, and carbohydrates.     

An extremely bent cyanide bridge in crystals of [(CN)3Pt(mu-CN)Cu(NH3)4]. Influence of electrostatic forces on the nature and geometry of bridging cyanides in the solid state

The dinuclear heterometallic complex [(CN)3Pt(mu-CN)Cu(NH3)4] has been obtained in the solid state, and its structure has been determined by X-ray diffraction techniques at two temperatures (102 and 233 K). C4H12CuN8Pt crystallizes in the orthorhombic system, with a = 14.554(3) A, b = 7.1901(12) A, c = 10.369(2) A, and V = 1085.1(3) A3 at 102 K (a = 14.5091(10) A, b = 7.2739(4) A, c = 10.4570(7) A, and V = 1103.61(12) A3 at 233 K), in space group Pnma, with Z = 4. The Pt and Cu atoms are linked by a CN bridge that presents a very bent C identical to N-Cu angle (120.1(6) degrees at 102 K). The C identical to N and N-Cu distances at 102 K are 1.147(10) and 2.394(7) A, respectively. [(CN)3Pt(mu-CN)Cu(NH3)4] is embedded in an extensive electrostatic net formed by (N)H...N(C) interactions which, it is concluded, play an important role in the extreme deviation from linearity observed for the C identical to N-Cu angle.     

Synthesis and characterization of new five-coordinate platinum nitrosyl derivatives: density functional theory study of their electronic structure

The neutral, five-coordinate platinum nitrosyl compounds [Pt(C(6)F(5))(3)(L)(NO)] (2) [L=CNtBu (2 a), NC(5)H(4)Me-4 (2 b), PPhMe(2) (2 c), PPh(3) (2 d) and tht (2 e)] have been prepared by the reaction of [NBu(4)][Pt(C(6)F(5))(3)(L)] (1) with NOClO(4) in CH(2)Cl(2). The ionic compound [N(PPh(3))(2)][Pt(C(6)F(5))(4)(NO)] (4) has been prepared in a similar way starting from the homoleptic species [N(PPh(3))(2)](2)[Pt(C(6)F(5))(4)] (3). Compounds 2 and 4 are all diamagnetic with [PtNO](8) electronic configuration and show nu(NO) stretching frequencies at around 1800 cm(-1). The crystal and molecular structures of 2 c and 4 have been established by X-ray diffraction methods. The coordination environment for the Pt center in both compounds can be described as square pyramidal (SPY-5). Bent nitrosyl coordination is observed in both cases with Pt-N-O angles of 120.1(6) and 130.2(7) degrees for 2 c and 4, respectively. The bonding mechanism of the nitrosyl ligand coordinated to various model [Pt(II)R(4)](2-) (R=H, Me, Cl, CN, C(6)F(5) or C(6)Cl(5)) and [Pt(C(6)F(5))(3)(L)](-) (L=CNMe, PH(3)) systems has been studied by density functional calculations at the B3LYP level of theory, using the SDD basis set. The R(4)Pt-NO and (C(6)F(5))(3)(L)Pt-NO interactions generally involve two components: i) a direct Pt-NO bonding interaction and ii) multicenter-bonding interactions between the N atom of the NO ligand and the donor atoms of the R and L ligands. Moreover, with the more complex R groups, C(6)F(5) or C(6)Cl(5), a third component has been found to arise, which involves multicenter electrostatic interactions between the positively charged NO ligand and the negatively charged halo-substituents in the ortho-position of the C(6)X(5) groups (X=F, Cl). The contribution of each component to the Pt-NO bonding in R(4)Pt-NO and (C(6)F(5))(3)(L)Pt-NO compounds seems to be modulated by the electronic and steric effects of the R and L ligands.     

Promotion effects in the oxidation of CO over zeolite-supported Pt nanoparticles

Well-defined Pt-nanoparticles with an average diameter of 1 nm supported on a series of zeolite Y samples containing different monovalent (H+, Na+, K+, Rb+, and Cs+) and divalent (Mg2+, Ca2+, Sr2+, and Ba2+) cations have been used as model systems to investigate the effect of promotor elements in the oxidation of CO in excess oxygen. Time-resolved infrared spectroscopy measurements allowed us to study the temperature-programmed desorption of CO from supported Pt nanoparticles to monitor the electronic changes in the local environment of adsorbed CO. It was found that the red shift of the linear Pt-coordinated CO vibration compared to that of gas-phase CO increases with an increasing cation radius-to-charge ratio. In addition, a systematic shift from linear (L) to bridge (B) bonded CO was observed for decreasing Lewis acidity, as expressed by the Kamlet-Taft parameter alpha. A decreasing alpha results in an increasing electron charge on the framework oxygen atoms and therefore an increasing electron charge on the supported Pt nanoparticles. This observation was confirmed with X-ray absorption spectroscopy, and the intensity of the experimental Pt atomic XAFS correlates with the Lewis acidity of the cation introduced. Furthermore, it was found that the CO coverage increases with increasing electron density on the Pt nanoparticles. This increasing electron density was found to result in an increased CO oxidation activity; i.e., the T(50%) for CO oxidation decreases with decreasing alpha. In other words, basic promotors facilitate the chemisorption of CO on the Pt particles. The most promoted CO oxidation catalyst is a Pt/K-Y sample, which has a T(50%) of 390 K and a L:B intensity ratio of 2.7. The obtained results provide guidelines to design improved CO oxidation catalysts.     

The crystallographic and magnetic characteristics of Sr2CrO4 (K2NiF4-type) and Sr10(CrO4)6F2 (apatite-type)

Solid-state reaction between SrCO₃, Cr₂O₃ and SrF₂ has produced the apatite phase Sr₁₀(CrO₄)₆F₂ and Sr₂CrO₄ which adopts the K₂NiF₄-type structure. The reaction outcome was very sensitive to the heating rate with rapid rise times favouring the formation of Sr₂CrO₄, which has been synthesised at ambient pressure for the first time. Powder X-ray diffraction and electron diffraction confirmed that Sr₂CrO₄ adopts a body centred tetragonal cell (space group I4/mmm) with lattice parameters a=3.8357(1) Å and c=12.7169(1) Å, while a combination of neutron and X-ray diffraction verified Sr₁₀(CrO₄)₆F₂ is hexagonal (space group P6₃/m) with lattice parameters a=9.9570(1) Å and c=7.4292(1) Å. X-ray photoelectron spectroscopy and magnetic measurements were used to characterise the oxidation states of chromium contained within these phases.     

Hyperpolarizability of the C60 fullerene cluster

Motivated by a discrepancy of five orders of magnitude between three different hyperpolarizability measurements on the C₆₀ fullerene, we calculated the optical response of this cluster using a tight-binding Hamiltonian and compared the results to those for a benzene molecule. Our Hamiltonian reproduces the linear polarizability and hyperpolarizability of benzene reasonably well. For C₆₀, our calculations of the bare polarizability agree only with two of the optical response measurements and indicate that the corresponding linear and nonlinear response of C₆₀ is much larger than that of C₆H₆. We find that screening effects decrease this difference strongly, and also reduce the calculated hyperpolarizability of C₆₀ to a value which is two orders of magnitude below the favored measurements.