Luigi Cavallo

POPS: a fast algorithm for solvent accessible surface areas at atomic and residue level

POPS (Parameter OPtimsed Surfaces) is a new method to calculate solvent accessible surface areas, which is based on an empirically parameterisable analytical formula and fast to compute. Atomic and residue areas (the latter represented by a single sphere centered on the C(alpha) atom of amino acids and at the P atom of nucleotides) have been optimised versus accurate all-atom methods. The parameterisation has been derived from a selected dataset of proteins and nucleic acids of different sizes and topologies. The residue based approach POPS-R, has been devised as a useful tool for the analysis of large macromolecular assemblies like the ribosome and it is specially suited for the refinement of low resolution structures. POPS-R also allows for estimates of the loss of free energy of solvation upon complex formation, which should be particularly useful for the design of new protein-protein and protein-nucleic acid complexes. The program POPS is available at http://mathbio.nimr.mrc.ac.uk/~ffranca/POPS and at the mirror site http://www.cs.vu.nl/~ibivu/programs/popswww.

Flexibility of N-heterocyclic carbene ligands in ruthenium complexes relevant to olefin metathesis and their impact in the first coordination sphere of the metal.

We present a detailed static and dynamics characterization of 11 N-heterocyclic carbene (NHC) ligands in Ru complexes of the general formula (NHC)Cl(2)Ru horizontal lineCH(2). Analysis of the dynamic trajectories indicates that the nature of the N substituent can result in extremely different flexibilities of the Ru complexes. In almost all the cases the N substituent trans to the Ru-ylidene bond is severely folded so that it protects the vacant coordination position at the Ru center. Limited flexibility is instead associated with the N substituent on the side of the Ru-ylidene bond. NHCs with a single ortho substituent, either a simple Me or a bulkier i-Pr group, have a preferential folding that bends the unsubstituted side of the ring toward the halide-Ru-halide plane. Analysis of the dynamics trajectories in terms of buried volume indicates that the real bulkiness of these systems can be somewhat modulated, and this flexibility is a key feature that allows NHCs to modulate their encumbrance around the metal in order to make room for bulky substrates. Analysis of the buried volume in terms of steric maps showed that NHCs with mesityl or 2,6-diisopropylphenyl N substituents have quite different reactive pockets: rather flat with constant pressure on the halide-Ru-halide plane in the former and vault-shaped with higher pressure on the sides in the latter. Regarding the NHCs with an ortho tolyl or i-Pr group on the N substituent, the steric maps quantify the higher impact of the unsubstituted side of the ligand in the first coordination sphere of the metal and evidence the overall C(s)- and C(2)-symmetric reactive pockets of the corresponding complexes. We believe that a detailed characterization of the differently shaped reactive pockets is a further conceptual tool that can be used to rationalize the experimentally different performances of catalysts bearing these ligands or to devise new applications.

[Pd(IPr*)(cinnamyl)Cl]: An Efficient Pre‐catalyst for the Preparation of Tetra‐ortho‐substituted Biaryls by Suzuki–Miyaura Cross‐Coupling

The bigger the better: The new well-defined [Pd(IPr*)(cin)Cl] pre-catalyst is described. This complex proves to be highly active in the Suzuki-Miyaura cross-coupling for the synthesis of tetra-ortho-substituted biaryls under mild conditions. IPr* is reported as the largest N-heterocyclic carbene (NHC) to date for [Pd(NHC)(cin)Cl] complexes, explaining the high reactivity observed for this complex in this challenging transformation.

Gold‐ and Platinum‐Catalyzed Cycloisomerization of Enynyl Esters versus Allenenyl Esters: An Experimental and Theoretical Study

Ester-way to heaven: Unexpected formation of bicyclo[3.1.0]hexene 4 was the main focus of combined experimental and theoretical studies on the Au-catalyzed cycloisomerization of branched dienyne 1 (see scheme), which provided better understanding of the mechanistic details governing the cyclization of enynes bearing a propargylic ester group.Experimental and theoretical studies on Au- and Pt-catalyzed cycloisomerization of a branched dienyne with an acetate group at the propargylic position are presented. The peculiar architecture of the dienyne precursor, which has both a 1,6- and a 1,5-enyne skeleton, leads, in the presence of alkynophilic gold catalysts, to mixtures of bicyclic compounds 3, 4, and 5. Formation of unprecedented bicyclo[3.1.0]hexene 5 is the main focus of this study. The effect of the ancillary ligand on the gold center was examined and found to be crucial for formation of 5. Further mechanistic studies, involving cyclization of an enantioenriched dienyne precursor, (18)O-labeling experiments, and DFT calculations, allowed an unprecedented reaction pathway to be proposed. We show that bicyclo[3.1.0]hexene 5 is likely formed by a 1,3-OAc shift/allene-ene cyclization/1,2-OAc shift sequence, as calculated by DFT and supported by Au-catalyzed cyclization of isolated allenenyl acetate 7, which leads to improved selectivity in the formation of 5. Additionally, the possibility of OAc migration from allenyl acetates was supported by a trapping experiment with styrene that afforded the corresponding cyclopropane derivative. This unprecedented generation of a vinyl metal carbene from an allenyl ester supports a facile enynyl ester/allenenyl ester equilibrium. Further examination of the difference in reactivity between enynyl acetates and their corresponding [3,3]-rearranged allenenyl acetates toward Au- and Pt-catalyzed cycloisomerization is also presented.

SambVca 2. A Web Tool for Analyzing Catalytic Pockets with Topographic Steric Maps

Developing more efficient catalysts remains one of the primary targets of organometallic chemists. To accelerate reaching this goal, effective molecular descriptors and visualization tools can represent a remarkable aid. Here, we present a Web application for analyzing the catalytic pocket of metal complexes using topographic steric maps as a general and unbiased descriptor that is suitable for every class of catalysts. To show the broad applicability of our approach, we first compared the steric map of a series of transition metal complexes presenting popular mono-, di-, and tetracoordinated ligands and three classic zirconocenes. This comparative analysis highlighted similarities and differences between totally unrelated ligands. Then, we focused on a recently developed Fe(II) catalyst that is active in the asymmetric transfer hydrogenation of ketones and imines. Finally, we expand the scope of these tools to rationalize the inversion of enantioselectivity in enzymatic catalysis, achieved by point mutat...

Parameter optimized surfaces (POPS): analysis of key interactions and conformational changes in the ribosome

We present a new method for the calculation of solvent accessible surface areas at the atomic and residue levels, which we call parameter optimized surfaces (POPS-A and POPS-R ). Atomic and residue areas (the latter simulated with a single sphere centered at the C(alpha)s atom for amino acids and at the P atom for nucleotides) have been optimized versus accurate all-atoms methods. We concentrated on an analytical formula for the approximation of solvent accessibilities. The formula is simple, easily derivable and fast to compute, therefore it is practical for use in molecular dynamics simulations as an approximation to the first solvation shell. The residue based approach POPS-R has been derived as a useful tool for the analysis of large macromolecular assemblies like the ribosome, and is especially suited for use in refinement of low resolution structures. The structures of the 70S, 50S and 30S ribosomes have been analyzed in detail and most of the interactions within the subunits and at their interfaces were clearly identified. Some interesting differences between 30S alone and within the 70S have been highlighted. Owing to the presence of the P-tRNA in the 70S ribosome, localized conformational rearrangements occur within the subunits, exposing Arg and Lys residues to negatively charged binding sites of P-tRNA. POPS-R also allows for estimates of the loss of free energy of solvation upon complex formation, particularly useful in designing new protein-RNA complexes and in suggesting more focused experimental work.

[{Au(IPr)}2(μ‐OH)]X Complexes: Synthetic, Structural and Catalytic Studies

The synthesis of a series of dinuclear gold hydroxide complexes has been achieved. These complexes of type [{Au(IPr)}(2)(μ-OH)]X (X=BF(4), NTf(2), OTf, FABA, SbF(6); IPr=2,6-bis(disopropylphenyl)imidazol-2-ylidene; NTf(2)=bis(trifluoromethanesulfonyl)imidate; OTf=trifluoromethanesulfonate; FABA=tetrakis(pentafluorophenyl)borate) are easily formed in the presence of water and prove highly efficient in the catalytic hydration of nitriles. Their facile formation in aqueous media suggests they are of relevance in gold-catalyzed reactions involving water. Additionally, a series of [Au(IPr)(NCR)][BF(4)] (R=alkyl, aryl) complexes was synthesized as they possibly occur as intermediates in the catalytic reaction mechanism. (1)H and (13)C NMR data as well as key bond lengths obtained by X-ray diffraction studies are compared and reveal an interesting structure-activity relationship. The collected data indicate a negligible effect of the nature of the nitrile on the reactivity of [Au(L)(NCR)][X] complexes in catalysis.

Comparing the Enantioselective Power of Steric and Electrostatic Effects in Transition-Metal-Catalyzed Asymmetric Synthesis

The current approach to improve and tune the enantioselective performances of transition-metal catalysts for asymmetric synthesis is mostly focused to modifications of the steric properties of the ancillary ligands of the active metal. Nevertheless, it is also known that electrostatic effects can have a remarkable role to promote selectivity in asymmetric synthesis. Using the Rh-catalyzed asymmetric 1,4-addition of phenylboronic acid to 2-cyclohexenone leading to chiral 3-phenylcyclohexanone as an example, we could show that high enantioselectivity can be indeed achieved using catalysts essentially based either on steric or electrostatic effects as the main source of enantioselective induction. In this contribution we suggest that the analysis of the surface of interaction between the catalyst and the substrate could be a useful tool to quantify the power of steric and electrostatic effects of catalysts.

COCOMAPS: a web application to analyze and visualize contacts at the interface of biomolecular complexes.

SUMMARY Herein we present COCOMAPS, a novel tool for analyzing, visualizing and comparing the interface in protein-protein and protein-nucleic acids complexes. COCOMAPS combines traditional analyses and 3D visualization of the interface with the effectiveness of intermolecular contact maps. AVAILABILITY COCOMAPS is accessible as a public web tool at http://www.molnac.unisa.it/BioTools/cocomaps CONTACT romina.oliva@uniparthenope.it; lcavallo@unisa.it.

Mechanistic Features of Isomerizing Alkoxycarbonylation of Methyl Oleate

The weakly coordinated triflate complex [(P^P)Pd(OTf)](+)(OTf)(-) (1) (P^P = 1,3-bis(di-tert-butylphosphino)propane) is a suitable reactive precursor for mechanistic studies of the isomerizing alkoxcarbonylation of methyl oleate. Addition of CH(3)OH or CD(3)OD to 1 forms the hydride species [(P^P)PdH(CH(3)OH)](+)(OTf)(-) (2-CH(3)OH) or the deuteride [(P^P)PdD(CD(3)OD)](+)(OTf)(-) (2(D)-CD(3)OD), respectively. Further reaction with pyridine cleanly affords the stable and isolable hydride [(P^P)PdH(pyridine)](+)(OTf)(-) (2-pyr). This complex yields the hydride fragment free of methanol by abstraction of pyridine with BF(3)·OEt(2), and thus provides an entry to mechanistic observations including intermediates reactive toward methanol. Exposure of methyl oleate (100 equiv) to 2(D)-CD(3)OD resulted in rapid isomerization to the thermodynamic isomer distribution, 94.3% of internal olefins, 5.5% of α,β-unsaturated ester and <0.2% of terminal olefin. Reaction of 2-pyr/BF(3)·OEt(2) with a stoichiometric amount of 1-(13)C-labeled 1-octene at -80 °C yields a 50:50 mixture of the linear alkyls [(P^P)Pd(13)CH(2)(CH(2))(6)CH(3)](+) and [(P^P)PdCH(2)(CH(2))(6)(13)CH(3)](+) (4a and 4b). Further reaction with (13)CO yields the linear acyls [(P^P)Pd(13)C(═O)(12/13)CH(2)(CH(2))(6)(12/13)CH(3)(L)](+) (5-L; L = solvent or (13)CO). Reaction of 2-pyr/BF(3)·OEt(2) with a stoichiometric amount of methyl oleate at -80 °C also resulted in fast isomerization to form a linear alkyl species [(P^P)PdCH(2)(CH(2))(16)C(═O)OCH(3)](+) (6) and a branched alkyl stabilized by coordination of the ester carbonyl group as a four membered chelate [(P^P)PdCH{(CH(2))(15)CH(3)}C(═O)OCH(3)](+) (7). Addition of carbon monoxide (2.5 equiv) at -80 °C resulted in insertion to form the linear acyl carbonyl [(P^P)PdC(═O)(CH(2))(17)C(═O)OCH(3)(CO)](+) (8-CO) and the five-membered chelate [(P^P)PdC(═O)CH{(CH(2))(15)CH(3)}C(═O)OCH(3)](+) (9). Exposure of 8-CO and 9 to (13)CO at -50 °C results in gradual incorporation of the (13)C label. Reversibility of 7 + CO ⇄ 9 is also evidenced by ΔG = -2.9 kcal mol(-1) and ΔG(‡) = 12.5 kcal mol(-1) from DFT studies. Addition of methanol at -80 °C results in methanolysis of 8-L (L = solvent) to form the linear diester, 1,19-dimethylnonadecandioate, whereas 9 does not react and no branched diester is observed. DFT yields a barrier for methanolysis of ΔG(‡) = 29.7 kcal mol(-1) for the linear (8) vs ΔG(‡) = 37.7 kcal mol(-1) for the branched species (9).