Minimization of organocuprate complexity through self-organization: remarkable orientation effect in mixed cuprate π complexes

They "know" where to go: a powerful orientation effect has been observed in complexes of mixed organocuprates [R(T)R(NT)CuLi] and substrates with C-C, C-N, and C-S double bonds (see scheme; Th=thienyl). The preferred geometry of the intermediate complex sets up the facile addition of R(T) to the double bond, rather than addition of the "dummy ligand", R(NT) .     

Theoretical and experimental investigation of the energetics of cis-trans proline isomerization in peptide models

The energetics of cis-trans proline isomerization in small peptide models have been investigated using the hybrid density functional theory method B3LYP with a 6-31+G* basis set. The molecules studied are models for the phospho-Ser/Thr-Pro substrate for Pin-1, a peptidyl-prolyl isomerase (PPIase) involved in cell division. Pin-1 requires phosphorylation of a Ser or Thr residue adjacent to a Pro residue in the substrate and catalyzes cis-trans isomerization about the proline amide bond. The dihedral angle that would correspond to the reaction coordinate for isomerization of the omega peptide bond was investigated for several small models. Relaxed potential energy scans for this dihedral angle in N-methylacetamide, 1, N,N-dimethylacetamide, 2, acetylpyrrolidine, 3 and acetylproline, 4, were carried out in 20 degrees steps using the B3LYP/6-31+G* level of theory. In addition, similar scans were carried out for 1-4 protonated on the acetylamide carbonyl oxygen. Optimized structures for 1-4 protonated on the amide nitrogen were also obtained at B3LYP/6-31+G*. Relative proton affinities were determined for each site at various angles along the reaction coordinate for isomerization. The relative proton affinities were anchored to experimental gas phase proton affinities, which were taken from the literature for 1 and 2, or determined in an electrospray ionization-quadrupole ion trap instrument using the extended kinetic method for 3 and 4. Proton affinities of 925 +/- 10 and 911 +/- 12 kJ/mol were determined for 3 and 4, respectively. These studies suggest that the nitrogen atom in these amides becomes the most basic site in the molecule at a dihedral angle of ca. 130 degrees . In addition, the nitrogen atoms in 2-4 are predicted to attain basicities in the range 920-950 kJ/mol, making them basic enough to be the preferred site for hydrogen bonding in the Pin-1 active site, in support of the proposed mechanism for PPIases.     

Ab initio molecular dynamics of excited-state intramolecular proton transfer around a three-state conical intersection in malonaldehyde

Excited-state potential energy surface (PES) characterization is carried out at the CASSCF and MRSDCI levels, followed by ab initio dynamics simulation of excited-state intramolecular proton transfer (ESIPT) on the S2(pipi*) state in malonaldehyde. The proton-transfer transition state lies close to an S2/S1 conical intersection, leading to substantial coupling of proton transfer with electronic relaxation. Proton exchange proceeds freely on S2, but its duration is limited by competition with twisting out of the molecular plane. This rotamerization pathway leads to an intersection of the three lowest singlet states, providing the first detailed report of ab initio dynamics around a three-state intersection (3SI). There is a significant energy barrier to ESIPT on S1, and further pyramidalization of the twisted structure leads to the minimal energy S1/S0 intersection and energetic terminal point of excited-state dynamics. Kinetics and additional mechanistic details of these pathways are discussed. Significant depletion of the spectroscopic state and recovery of the ground state is seen within the first 250 fs after photoexcitation.     

On the size-dependent behavior of nanocrystal-ligand bonds

Recent experiments have indicated that 3-mercapto-1-propanol ligands display a size-dependent binding energy of attachment to the surface of II-VI semiconductor nanocrystals. Using semiempirical calculations, we exhaustively calculate the energy of this bond at each surface site, for CdSe and CdSe/CdS core/shell nanocrystals ranging from 1.8 to 4.1 nm in diameter. Our results suggest that the experimentally observed changes in binding energy are due to the distribution of surface facets on the nanocrystals, and not related to the band gap, as proposed in the experimental paper.     

Electron bubbles in helium clusters. II. Probing superfluidity

In this paper we present calculations of electron tunneling times from the ground electronic state of excess electron bubbles in ((4)He)(N) clusters (N=6500-10(7), cluster radius R=41.5-478 A), where the equilibrium bubble radius varies in the range R(b)=13.5-17.0 A. For the bubble center located at a radial distance d from the cluster surface, the tunneling transition probability was expressed as A(0)phi(d,R)exp(-betad), where beta approximately 1 A(-1) is the exponential parameter, A(0) is the preexponential factor for the bubble located at the cluster center, and phi(d,R) is a correction factor which accounts for cluster curvature effects. Electron tunneling dynamics is grossly affected by the distinct mode of motion of the electron bubble in the image potential within the cluster, which is dissipative (i.e., tau(D)tau(0)) in superfluid ((4)He)(N) clusters, where tau(D) is the bubble motional damping time (tau(D) approximately 4 x 10(-12) s for normal fluid clusters and tau(D) approximately 10 s for superfluid clusters), while tau(0) approximately 10(-9)-10(-10) s is the bubble oscillatory time. Exceedingly long tunneling lifetimes, which cannot be experimentally observed, are manifested from bubbles damped to the center of the normal fluid cluster, while for superfluid clusters electron tunneling occurs from bubbles located in the vicinity of the initial distance d near the cluster boundary. Model calculations of the cluster size dependence of the electron tunneling time (for a fixed value of d=38-39 A), with lifetimes increasing in the range of 10(-3)-0.3 s for N=10(4)-10(7), account well for the experimental data [M. Farnik and J. P. Toennies, J. Chem. Phys. 118, 4176 (2003)], manifesting cluster curvature effects on electron tunneling dynamics. The minimal cluster size for the dynamic stability of the bubble was estimated to be N=3800, which represents the threshold cluster size for which the excess electron bubble in ((4)He)(N) (-) clusters is amenable to experimental observation.     

Conductance of single alkanedithiols: conduction mechanism and effect of molecule-electrode contacts

The conductance of single alkanedithiols covalently bound to gold electrodes has been studied by statistical analysis of repeatedly created molecular junctions. For each molecule, the conductance histogram reveals two sets of well-defined peaks, corresponding to two different conductance values. We have found that (1) both conductance values decrease exponentially with the molecular length with an identical decay constant, beta approximately equal to 0.84 A(-1), but with a factor of 5 difference in the prefactor of the exponential function. (2) The current-voltage curves of the two sets can be fit with the Simmons tunneling model. (3) Both conductance values are independent of temperature (between -5 and 60 degrees C) and the solvent. (4) Despite the difference in the conductance, the forces required to break the molecular junctions are the same, 1.5 nN. These observations lead us to believe that the conduction mechanism in alkanedithiols is due to electron tunneling or superexchange via the bonds along the molecules, and the two sets of conductance peaks are due to two different microscopic configurations of the molecule-electrode contacts.     

A nitridoniobium(V) reagent that effects acid chloride to organic nitrile conversion: synthesis via heterodinuclear (Nb/Mo) dinitrogen cleavage, mechanistic insights, and recycling

The transformation of acid chlorides (RC(O)Cl) to organic nitriles (RC[triple bond]N) by the terminal niobium nitride anion [N[triple bond]Nb(N[Np]Ar)3]- ([1a-N]-, where Np = neopentyl and Ar = 3,5-Me2C6H3) via isovalent N for O(Cl) metathetical exchange is presented. Nitrido anion [1a-N]- is obtained in a heterodinuclear N2 scission reaction employing the molybdenum trisamide system, Mo(N[R]Ar)3 (R = t-Bu, 2a; R = Np, 2b), as a reaction partner. Reductive scission of the heterodinuclear bridging N2 complexes, (Ar[R]N)3Mo-(mu-N2)Nb(N[Np]Ar)3 (R = t-Bu, 3b; R = Np, 3c) with sodium amalgam provides 1 equiv each of the salt Na[1a-N] and neutral N[triple bond]Mo(N[R]Ar)3 (R = t-Bu, 2a-N; R = Np, 2b-N). Separation of 2-N from Na[1a-N] is readily achieved. Treatment of salt Na[1a-N] with acid chloride substrates in tetrahydrofuran (THF) furnishes the corresponding organic nitriles concomitant with the formation of NaCl and the oxo niobium complex O[triple bond]Nb(N[Np]Ar)3 (1a-O). Utilization of 15N-labeled 15N2 gas in this chemistry affords a series of 15N-labeled organic nitriles establishing the utility of anion [1a-N]- as a reagent for the 15N-labeling of organic molecules. Synthetic and computational studies on model niobium systems provide evidence for the intermediacy of both a linear acylimido and niobacyclobutene species along the pathway to organic nitrile formation. High-yield recycling of oxo 1a-O to a niobium triflate complex appropriate for heterodinuclear N2 scission has been developed. Specifically, addition of triflic anhydride (Tf2O, where Tf = SO2CF3) to an Et2O solution of 1a-O provides the bistriflate complex, Nb(OTf)2(N[Np]Ar)3 (1a-(OTf)2), in near quantitative yield. One-electron reduction of 1a-(OTf)2 with either cobaltocene (Cp2Co) or Mg(THF)3(anthracene) provided the monotriflato complex, Nb(OTf)(N[Np]Ar)3 (1a-(OTf)), which efficiently regenerates complexes 3b and 3c when treated with the molybdenum dinitrogen anions [N2Mo(N[t-Bu]Ar)3]- ([2a-N2]-) or [N2Mo(N[Np]Ar)3]- ([2b-N2]-), respectively.     

Heterologous production of fosfomycin and identification of the minimal biosynthetic gene cluster

Fosfomycin is a clinically utilized, highly effective antibiotic, which is active against methicillin- and vancomycin-resistant pathogens. Here we report the cloning and characterization of a complete fosfomycin biosynthetic cluster from Streptomyces fradiae and heterologous production of fosfomycin in S. lividans. Sequence analysis coupled with gene deletion and disruption revealed that the minimal cluster consists of fom1-4, fomA-D. A LuxR-type activator that was apparently required for heterologous fosfomycin production was also discovered approximately 13 kb away from the cluster and was named fomR. The genes fomE and fomF, previously thought to be involved in fosfomycin biosynthesis, were shown not to be essential by gene disruption. This work provides new insights into fosfomycin biosynthesis and opens the door for fosfomycin overproduction and creation of new analogs via biomolecular pathway engineering.