Accurate redox potentials of mononuclear iron, manganese, and nickel model complexes*

Density functional theory (DFT) was combined with solution of the Poisson equation for continuum dielectric media to compute accurate redox potentials for several mononuclear transition metal complexes (TMCs) involving iron, manganese, and nickel. Progress was achieved by altering the B3LYP DFT functional (B4(XQ3)LYP-approach) and supplementing it with an empirical correction term G(X) having three additional adjustable parameters, which is applied after the quantum-chemical DFT computations. This method was used to compute 58 redox potentials of 48 different TMCs involving different pairs of redox states solvated in both protic and aprotic solvents. For the 58 redox potentials the root mean square deviation (RMSD) from experimental values is 65 mV. The reliability of the present approach is also supported by the observation that the energetic order of the spin multiplicities of the electronic ground states is fulfilled for all studied TMCs, if the influence from the solvent is considered as well.     

A tris(pyrazolyl) eta6-arene ligand that selects Cu(I) over Cu(II)

1,3,5-Tris{2'-[(pyrazol-1-yl)methyl]phenyl}benzene, 4, and its complexes with Cu(I) and Ag(I) have been prepared and characterized. Both CuI4 and AgI4 triflate crystallize in the rhombohedral space group R3, with the cations and anions each exhibiting crystallographically imposed 3-fold (C3) symmetry. In both complexes, 4 behaves as a tris(pyrazolyl) eta6-arene ligand whose arms act as three-pronged tweezers to form chiral, propeller-like cations with pyramidal MN(pyrazole)3 coordination geometries. Centers of symmetry in the space group ensure that the crystals are racemates, with equal numbers of P,P,P and M,M,M enantiomers. In broad outline, each cation is shaped like a three-legged stool, with the metal ion centered at the top and pointed downward from a triangular N(pyrazole) plane toward the center of gravity (Cg) of the central benzene ring (a metal-endo conformation), which constitutes the bottom shelf of the stool. The Cu(I)...Cg and Ag(I)...Cg distances, 3.195(2) and 3.165(2) A, respectively, support the existence of an eta6 bonding interaction with Ag(I) and, to a lesser extent, with Cu(I). NMR data for AgI4 suggest rapid interconversion of this cation in solution between P,P,P and M,M,M enantiomers. Our inability to prepare any Cu(II) complexes with 4 is consistent with cyclovoltammetric results, which suggest that the ligand is more easily oxidized than Cu(I).     

Protein secondary structure prediction with SPARROW

A first step toward predicting the structure of a protein is to determine its secondary structure. The secondary structure information is generally used as starting point to solve protein crystal structures. In the present study, a machine learning approach based on a complete set of two-class scoring functions was used. Such functions discriminate between two specific structural classes or between a single specific class and the rest. The approach uses a hierarchical scheme of scoring functions and a neural network. The parameters are determined by optimizing the recall of learning data. Quality control is performed by predicting separate independent test data. A first set of scoring functions is trained to correlate the secondary structures of residues with profiles of sequence windows of width 15, centered at these residues. The sequence profiles are obtained by multiple sequence alignment with PSI-BLAST. A second set of scoring functions is trained to correlate the secondary structures of the center residues with the secondary structures of all other residues in the sequence windows used in the first step. Finally, a neural network is trained using the results from the second set of scoring functions as input to make a decision on the secondary structure class of the residue in the center of the sequence window. Here, we consider the three-class problem of helix, strand, and other secondary structures. The corresponding prediction scheme "SPARROW" was trained with the ASTRAL40 database, which contains protein domain structures with less than 40% sequence identity. The secondary structures were determined with DSSP. In a loose assignment, the helix class contains all DSSP helix types (α, 3-10, π), the strand class contains β-strand and β-bridge, and the third class contains the other structures. In a tight assignment, the helix and strand classes contain only α-helix and β-strand classes, respectively. A 10-fold cross validation showed less than 0.8% deviation in the fraction of correct structure assignments between true prediction and recall of data used for training. Using sequences of 140,000 residues as a test data set, 80.46% ± 0.35% of secondary structures are predicted correctly in the loose assignment, a prediction performance, which is very close to the best results in the field. Most applications are done with the loose assignment. However, the tight assignment yields 2.25% better prediction performance. With each individual prediction, we also provide a confidence measure providing the probability that the prediction is correct. The SPARROW software can be used and downloaded on the Web page http://agknapp.chemie.fu-berlin.de/sparrow/ .     

The role of group 14 element hydrides in the activation of C-h bonds in cyclic olefins

Formally, triple-bonded dimetallynes ArEEAr [E = Ge (1), Sn (2); Ar = C(6)H(3)-2,6-(C(6)H(3)-2,6-(i)Pr(2))(2)] have been previously shown to activate aliphatic, allylic C-H bonds in cyclic olefins, cyclopentadiene (CpH), cyclopentene (c-C(5)H(8)) and 1,4-cyclohexadiene, with intriguing selectivity. In the case of the five-membered carbocycles, cyclopentadienyl species ArECp [E = Ge (3), Sn (4)] are formed. In this study, we examine the mechanisms for activation of CpH and c-C(5)H(8) using experimental methods and describe a new product found from the reaction between 1 and c-C(5)H(8), an asymmetrically substituted digermene ArGe(H)Ge(c-C(5)H(9))Ar (5), crystallized in 46% yield. This compound contains a hydrogenated cyclopentyl moiety and is found to be produced in a 3:2 ratio with 3, explaining the fate of the liberated H atoms following triple C-H activation. We show that when these C-H activation reactions are carried out in the presence of tert-butyl ethylene (excess), compounds {ArE(CH(2)CH(2)tBu)}(2) [E = Ge(8), Sn(9)] are obtained in addition to ArECp; in the case of CpH, the neohexyl complexes replace the production of H(2) gas, and for c-C(5)H(8) they displace cyclopentyl product 5 and account for all the hydrogen removed in the dehydroaromatization reactions. To confirm the source of 8 and 9, it was demonstrated that these molecules are formed cleanly between the reaction of (ArEH)(2) [E = Ge(6), Sn(7)] and tert-butyl ethylene, new examples of noncatalyzed hydro-germylation and -stannylation. Therefore, the presence of transient hydrides of the type 6 and 7 can be surmised to be reactive intermediates in the production of 3 and 4, along with H(2), from 1 and 2 and CpH (respectively), or the formation of 3 and 5 from 1. The reaction of 6 or 7 with CpH gave 3 or 4, respectively, with concomitant H(2) evolution, demonstrating the basic nature of these low-valent group 14 element hydrides and their key role in the 'cascade' of C-H activation steps. Additionally, during the course of these studies a new polycyclic compound (ArGe)(2)(C(7)H(12)) (10) was obtained in 60% yield from the reaction of 1,6-heptadiene and 1 via double [2 + 2] cycloaddition and gives evidence for a nonradical mechanism for these types of reactions.     

High-frequency and -field electron paramagnetic resonance of high-spin manganese(III) in axially symmetric coordination complexes

High-frequency and -field electron paramagnetic resonance (HFEPR) has been used to study several complexes of high-spin manganese(III) (3d⁴,S = 2): [Mn(Me₂dbm)X] and [Mn(OEP)X] (X = Cl^?, Br^?), where Me₂dbm^? is the anion of 4,4′-dimethyldibenzoylmethane and OEP^2? is the dianion of 2,3,7,8,12,13,17,18-octaethylporphine. These non-Kramers (integer spin) systems are not EPR-active with conventional magnetic fields and microwave frequencies. However, use of fields up to 15 T in combination with multiple frequencies in the range of 95–550 GHz allows observation of richly detailed EPR spectra. Analysis of the field- and frequency-dependent HFEPR data allows accurate determination of the following spin Hamiltonian parameters for these complexes: [Mn(Me₂dbm)Cl],D = ?2.45(3) cm^?1; [Mn(Me₂dbm)Br],D = ?1.40(2) cm^?1; [Mn(OEP)Cl],D = ?2.40(1) cm^?1; [Mn(OEP)Br],D = ?1.07(1) cm^?1 (E ≈ 0, andg ≈ 2.0 in all cases). Comparison of structural data with the electronic parameters for these and related complexes shows quantitatively the effects of axial and equatorial ligation on the electronic structure of Mn(III). These high-spin complexes can be employed as building blocks in the construction of single-molecule magnets. Thus the accurate determination and understanding of the electronic properties, best obtainable by HFEPR, of these monomeric units is important in understanding and improving the properties of the polynuclear single-molecule magnets which can be formed from them.     

Stereoelectronic Features of a Complex Ketene Dimerization Reaction

The amidation reaction of a tetrahydroisoquinolin-1-one-4-carboxylic acid is a key step in the multi-kilogram-scale preparation of the antimalarial drug SJ733, now in phase 2 clinical trials. In the course of investigating THIQ carboxamidations, we found that propanephosphonic acid anhydride (T3P) is an effective reagent, although the yield and byproducts vary with the nature and quantity of the base. As a control, the T3P reaction of a 3-(2-thienyl) THIQ was performed in the absence of the amine, and the products were characterized: among them are three dimeric allenes and two dimeric lactones. A nucleophile-promoted ketene dimerization process subject to subtle steric and stereoelectronic effects accounts for their formation. Two novel monomeric products, a decarboxylated isoquinolone and a purple, fused aryl ketone, were also isolated, and mechanisms for their formation from the ketene intermediate are proposed.     

A procedure for “iodolactamization”

Treatment of an unsaturated amide with TMS-OTf, then iodine in THF gives the iodolactam.     

Confidence Regions on Variance Components in an Extended ANOVA Model for Combining Information

In this paper we consider a general variance components model for combining experiments that allows for a possible interaction of responses with groups. The variance estimate from each experiment cannot take into account this interaction which can additionally be different from experiment to experiment. The interaction term can be interpreted as an additional variance component so that we consider an extended ANOVA model. We derive confidence regions and test of hypotheses on the variance components which – at least approximately – hold the nominal significance level.