An idealized molecular geometry library for refinement of poorly behaved molecular fragments with constraints

An idealized molecular geometry library with 40 geometries of molecules and ions optimized by density functional theory methods has been created. All geometries are accessible through a web site. The library entries are tailored for constrained (also known as rigid body) refinements of problematic small-molecule structures with theOLEX2andSHELXLsoftware packages. The library application is demonstrated with the refinement of a Pd complex,trans-Pd(dimethyl sulfoxide)(OH2)(trifluoroacetate)2, that co-crystallizes in a 2:1 ratio with a solvent molecule of ethyl acetate disordered over an inversion center. Alternative approaches to constrained refinements are discussed.

Aminodiols via stereocontrolled oxidation of methyleneaziridines

A highly diastereoselective Ru-catalyzed oxidation/reduction sequence of bicyclic methyleneaziridines provides a facile route to complex 1-amino-2,3-diol motifs. The relative anti stereochemistry between the amine and the vicinal alcohol are proposed to result from 1,3-bischelation in the transition state by the C1 and C3 heteroatoms.

Phosphinogold(I) dithiocarbamate complexes: effect of the nature of phosphine ligand on anticancer properties

The reactions of potassium salts of the dithiocarbamates L {where L = pyrazolyldithiocarbamate (L1), 3,5-dimethylpyrazolyldithiocarbamate (L2), or indazolyldithiocarbamate (L3)} with the gold precursors [AuCl(PPh3)], [Au2Cl2(dppe)], [Au2Cl2(dppp)], or [Au2Cl2(dpph)] lead to the new gold(I) complexes [AuL(PPh3)] (1-3), [Au2L2(dppe)] (4-6), [(Au2L2)(dppp)] (7-9), and [Au2(L)2(dpph)] (10-12) {where dppe = 1,2-bis(diphenylphosphino)ethane, dppp = 1,3-bis(diphenylphosphino)propane, and dpph = 1,6-bis(diphenylphosphino)hexane}. These gold compounds were characterized by a combination of NMR and infrared spectroscopy, microanalysis, and mass spectrometry; and in selected cases by single-crystal X-ray crystallography. Compounds 4-6, which have dppe ligands, are unstable in solution for prolonged periods, with 4 readily transforming to the Au18 cluster [Au18S8(dppe)6]Cl2 (4a) in dichloromethane. Compounds 1-3 and 7-12 are all active against human cervical epithelioid carcinoma (HeLa) cells, but the most active compounds are 10 and 11, with IC50 values of 0.51 μM and 0.14 μM, respectively. Compounds 10 and 11 are more selective toward HeLa cells than they are toward normal cells, with selectivities of 25.0 and 70.5, respectively. Further tests, utilizing the 60-cell-line Developmental Therapeutics Program at the National Cancer Institute (U.S.A.), showed 10 and 11 to be active against nine other types of cancers.

(Phenoxyimidazolyl-salicylaldimine)iron complexes: synthesis, properties and iron catalysed ethylene reactions

(Salicyladimine)iron(iii) pre-catalysts, from iron(ii) precursors, form catalysts for ethylene oligomerisation, polymerisation and alkylation of aromatic solvents by the ethylene oligomers.

Ferrocenylpyrazolyl palladium complexes as catalysts for the polymerisation of 1-heptene and 1-octene to highly branched polyolefins

(Ferrocenylpyrazolyl)palladium complexes that catalyse the polymerization of 1-heptene and 1-octene to highly branched polyolefins are reported.

Evaluation of a cyclopentane-based γ-amino acid for the ability to promote α/γ-peptide secondary structure

We report the asymmetric synthesis of the γ-amino acid (1R,2R)-2-aminomethyl-1-cyclopentane carboxylic acid (AMCP) and an evaluation of this residue's potential to promote secondary structure in α/γ-peptides. Simulated annealing calculations using NMR-derived distance restraints obtained for α/γ-peptides in chloroform reveal that AMCP-containing oligomers are conformationally flexible. However, additional evidence suggests that an internally hydrogen-bonded helical conformation is partially populated in solution. From these data, we propose characteristic NOE patterns for the formation of the α/γ-peptide 12/10-helix and discuss the apparent conformational frustration of AMCP-containing oligomers.

Transfer of chirality in the rhodium-catalyzed intramolecular [5+2] cycloaddition of 3-acyloxy-1,4-enynes (ACEs) and alkynes: synthesis of enantioenriched bicyclo[5.3.0]decatrienes

Chiral bicycles: Enantioenriched bicyclo[5.3.0]decatrienes were prepared from readily available chiral 3-acyloxy-1,4-enynes (ACEs) for the first time. In most cases, the chirality of the ACEs could be transferred to the bicyclic products with high efficiency. Inversion of the configuration was observed, thus confirming the predictions of previous computational studies.

Structure-activity studies of divin: an inhibitor of bacterial cell division

We describe the synthesis and SAR studies of divin-a small molecule that blocks bacterial division by perturbing the assembly of proteins at the site of cell septation. The bacteriostatic mechanism of action of divin is distinct from other reported inhibitors of bacterial cell division and provides an opportunity for assessing the therapeutic value of a new class of antimicrobial agents. We demonstrate a convenient synthetic route to divin and its analogs, and describe compounds with a 10-fold increase in solubility and a 4-fold improvement in potency. Divin analogs produce a phenotype that is identical to divin, suggesting that their biological activity comes from a similar mechanism of action. Our studies indicate that the 2-hydroxynaphthalenyl hydrazide portion of divin is essential for its activity and that alterations and substitution to the benzimidazole ring can increase its potency. The SAR study provides a critical opportunity to isolate drug resistant mutants and synthesize photoaffinity probes to determine the cellular target and biomolecular mechanism of divin.

Stereoselective halocyclization of alkenes with N-acyl hemiaminal nucleophiles

Halocyclization of alkenes was realized using N-acylhemiaminal nucleophiles. High diastereoselectivity could be achieved for the formation of three stereogenic centers in this halogen-mediated cyclization reaction. We also demonstrated that enantioselective bromocyclization of alkenes using N-acylhemiaminal nucleophiles was possible.

Positional and compositional disorder in a ruthenium(II) piano-stool complex

In (η⁶-p-cymene)(difluorophosphinato-κO){2-[(1H-pyrazol-1-yl)methyl-κN²]pyridine-κN}ruthenium(II) 0.85-hexafluorophosphate 0.15-tetrafluoroborate, [Ru(PO₂F₂)(C₁₀H₁₄)(C₉H₉N₃)](PF₆)0.85(BF₄)0.15, (I), the [PO₂F₂]⁻ ligand exhibits positional disorder due to one F atom and one O atom sharing the same two positions related by a mirror reflection across the O-P-F plane. The correct composition of this coordinated anion was successfully determined to be [PO₂F₂]⁻ by refining the complex with various tetrahedral anions in which terminal atoms have similar atomic form factors. The noncoordinated counter-ion is compositionally disordered between [PF₆]⁻ and [BF₄]⁻. The difficulty in determining the correct composition of this anion illustrates the importance of a crystallographer remaining impartial and open to encountering unexpected moieties in the process of elucidating a structure.

Structural, spectroscopic, and computational characterization of the azide adduct of Fe(III)(2,6-diacetylpyridinebis(semioxamazide)), a functional analogue of iron superoxide dismutase

We have prepared and thoroughly characterized, using X-ray crystallographic, spectroscopic, and computational methods, the diazide adduct of [Fe(III)(dapsox)(H2O)2](+) [dapsox = 2,6-diacetylpyridinebis(semioxamazide)], (1), a low-molecular weight, functional analogue of iron superoxide dismutase (FeSOD). The X-ray crystal structure of the dimeric form of 1, (Na[Fe(III)(dapsox)(N3)2]·DMF)2 (2) shows two axially coordinated, symmetry inequivalent azides with differing Fe-N3 bond lengths and Fe-N-N2 bond angles. This inequivalence of the azide ligands likely reflects the presence of an interdimer hydrogen bonding interaction between a dapsox NH group and the coordinated nitrogen of one of the two azide ligands. Resonance Raman (rR) data obtained for frozen aqueous solution and solid-state samples of 2 indicate that the azides remain inequivalent in solution, suggesting that one of the azide ligands of 1 engages in an intermolecular hydrogen bonding interaction with a water molecule. Density functional theory (DFT) and time-dependent DFT calculations have been used to study two different computational models of 1, one using coordinates taken from the X-ray crystal structure of 2, and the other generated via DFT geometry optimization. An evaluation of these models on the basis of electronic absorption, magnetic circular dichroism, and rR data indicates that the crystal structure based model yields a more accurate electronic structure description of 1, providing further support for the proposed intermolecular hydrogen bonding of 1 in the solid state and in solution. An analysis of the experimentally validated DFT results for this model reveals that the azides have both σ- and π-bonding interactions with the Fe(III) center and that more negative charge is located on the Fe-bound, rather than on the terminal, nitrogen atom of each azide. These observations are reminiscent of the results previously reported for the azide adduct of FeSOD and provide clues regarding the origin of the high catalytic activity of Fe-dapsox for superoxide disproportionation.

n→π* interactions of amides and thioamides: implications for protein stability

Carbonyl-carbonyl interactions between adjacent backbone amides have been implicated in the conformational stability of proteins. By combining experimental and computational approaches, we show that relevant amidic carbonyl groups associate through an n→π* donor-acceptor interaction with an energy of at least 0.27 kcal/mol. The n→π* interaction between two thioamides is 3-fold stronger than between two oxoamides due to increased overlap and reduced energy difference between the donor and acceptor orbitals. This result suggests that backbone thioamide incorporation could stabilize protein structures. Finally, we demonstrate that intimate carbonyl interactions are described more completely as donor-acceptor orbital interactions rather than dipole-dipole interactions.

Generation of rhodium(I) carbenes from ynamides and their reactions with alkynes and alkenes

Rh(I) carbenes were conveniently generated from readily available ynamides. These metal carbene intermediates could undergo metathesis with electron-rich or neutral alkynes to afford 2-oxopyrrolidines or be trapped by tethered alkenes to yield 3-azabicyclo[3.1.0]hexanes, a common skeleton in numerous bioactive pharmaceuticals. Although the scope of the former is limited, the latter reaction tolerates various substituted alkenes.

Pyramidalization of a carbonyl C atom in (2S)-N-(seleno-acet-yl)proline methyl ester

The title compound, C8H13NO2Se, crystallizes as a non-merohedral twin with an approximate 9:1 component ratio with two symmetry-independent mol-ecules in the asymmetric unit. Our density-functional theory (DFT) computations indicate that the carb-oxy C atom is expected to be slightly pyramidal due to an n→ π* inter-action, wherein the lone pair (n) of the Se atom overlap with the anti-bonding orbital (π*) of the carbonyl group. Such pyramidalization is observed in one mol-ecule of the title compound but not the other.

Dichlorido{2-[(3,5-diphenyl-1H-pyrazol-1-yl-κN2)methyl]pyridine-κN}palladium(II)

The title compound, [PdCl(2)(C(21)H(17)N(3))], is a member of a sequence of Pd, Pt and Co dichloride complexes bearing polysubstituted (pyrazol-1-ylmethyl)pyridine ligands. It is shown that there is a correlation between the steric bulkiness of the bidentate (pyrazol-1-ylmethyl)pyridine ligands and the Pd-N(pyrazole) distances, i.e. the larger the ligand, the longer the bond. In contrast, no trend is observed between the steric properties of the ligand and the Pd-N(pyridine) bond lengths.

Solvent-Free Synthesis of 3,5-Di-Tert-Butylpyrazole and 3,5-Di-Substituted-Butylpyrazol-1-Ylethanol

A high-yield, solvent-free approach to the synthesis of 1,3,5-trisubstituted pyrazoles is reported. Four compounds, (3,5-di-tert-butyl-1H-pyrazole, (2-(3,5-dimethyl-1H-pyrazol-1-yl)ethanol, 2-(3,5-di-tert-butyl-1H-pyrazol-1-yl)ethanol, 2-(3,5-diphenyl-1H-pyrazol-1-yl)ethanol were readily prepared by solvent-free condensation of the appropriate dike-tone and the respective hydrazine. The crystal structures of the three pyrazolyl-ethanols are typical of N-substituted pyrazoles. All three pyrazolyl compounds show interesting inter-molecular hydrogen bonding. For the 3,5-dimethyl compound the molecules form discrete hydrogen bonded dimers within a unit cell, while for the others the hydrogen bonding is in a head-to-tail arrangement resulting in the formation of chains.

1,2-Bis[(3,5-diphenyl-1H-pyrazol-1-yl)methyl]benzene

The title compound, C₃₈H₃₀N₄, a potentially mono- and bidentate ligand, does not seem to form palladium complexes similar to other poly(pyrazol-1-ylmeth­yl)benzenes due to the large steric size of the phenyl substituents on the pyrazole rings. The pyrazole rings have a 21.09 (5)° angle between their mean planes and exhibit a trans-like geometry in which the in-plane lone pairs of electrons on the 2-N nitrogen atoms point in opposite directions.

(3,5-Di-tert-butyl-2-ethoxybenzylidene)[2-(3,5-di-tert-butyl-1H-pyrazol-1-yl)ethyl]amine

The angles within the benzene ring in the title compound, C₃₀H₄₉N₃O, ranging from 116.34 (16) to 124.18 (16)°, reflect the presence of electron-donating and electron-withdrawing substituents. The angles at the two electron-donating tert-butyl substituents are smaller than 120°, at the electron-withdrawing eth­oxy substituent larger than 120°, and at the imine substituent equal to 119.59 (16)°. The latter does not reflect the electron-donating nature of the imine group due to the presence of other substituents.

Rhodium-catalyzed carbonylation of cyclopropyl substituted propargyl esters: a tandem 1,3-acyloxy migration [5 + 1] cycloaddition

We have developed two different types of tandem reactions for the synthesis of highly functionalized cyclohexenones from cyclopropyl substituted propargyl esters. Both reactions were initiated by rhodium-catalyzed Saucy-Marbet 1,3-acyloxy migration. The resulting cyclopropyl substituted allenes derived from acyloxy migration then underwent [5 + 1] cycloaddition with CO. The acyloxy group not only eased the access to allene intermediates but also provided a handle for further selective functionalizations.

An example of the refinement of positional disorder modeled as compositional disorder in [5-(2-formylphenyl)-10,15,20-triphenylporphyrinato]nickel(II)

The title compound, [Ni(C(45)H(28)N(4)O)], crystallizes in the space group I ̅42d and resides on a crystallographic fourfold rotoinversion axis with only a quarter of the complex in the asymmetric unit. The complex displays positional disorder as the one aldehyde group on the ligand can be located at four different positions. It was necessary to model this as compositional disorder to obtain a correct model and refinement. The practical approach to the refinement is explained.

Modular functionalization of allenes to aminated stereotriads

Nitrogen-containing stereotriads, compounds with three adjacent stereodefined carbons, are commonly found in biologically important molecules. However, the preparation of molecules bearing these motifs can be challenging. Herein, we describe a modular oxidation protocol which converts a substituted allene to a triply functionalized amine of the form C-X/C-N/C-Y. The key step employs a Rh-catalyzed intramolecular conversion of the allene to a strained bicyclic methylene aziridine. This reactive intermediate is further elaborated to the target products, often in one reaction vessel and with effective transfer of the axial chirality of the allene to point chirality in the stereotriad.

New preorganized γ-amino acids as foldamer building blocks

An asymmetric synthesis of two new diastereomeric γ-amino acids is described. Both molecules contain a cyclohexyl ring to limit conformational flexibility about the Cα-Cβ bond; they differ in having cis vs trans stereochemistry on the ring. Residues derived from the cis γ isomer are shown to support helical secondary structures in α/γ-peptide oligomers.

2-[(3,5-Diphenyl-1H-pyrazol-1-yl)meth-yl]pyridine

The title compound, C(21)H(17)N(3), crystallizes with the phenyl ring in the 3-position coplanar with the pyrazole ring within 4.04 (5)°, whereas the phenyl ring in the 5-position forms a dihedral angle of 50.22 (3)° with the pyrazole ring. There is no ambiguity regarding the position of pyridine N atom, which could have exhibited disorder between the ortho positions of the ring.

An asymmetric synthesis of L-pyrrolysine

An efficient asymmetric synthesis of the 22nd amino acid L-pyrrolysine has been accomplished. The key stereogenic centers were installed by an asymmetric conjugate addition reaction. A Staudinger/aza-Wittig cyclization was used to form the acid-sensitive pyrroline ring. Pyrrolysine was synthesized in 13 steps in 20% overall yield.

1,4-Diazaspiro[2.2]pentanes as a flexible platform for the synthesis of diamine-bearing stereotriads

Nitrogen-containing stereotriads occur in a number of biologically active compounds, but general and flexible methods to access these compounds are limited mainly to the manipulation of chiral olefins. An alternative approach is to employ a highly chemo-, regio-, and stereocontrolled allene oxidation that can install a new carbon-heteroatom bond at each of the three original allene carbons. In this paper, an intramolecular/intermolecular allene bis-aziridination is described that offers the potential to serve as a key step for the construction of stereotriads containing vicinal diaminated motifs. The resultant 1,4-diazaspiro[2.2]pentane (DASP) scaffolds contain two electronically differentiated aziridines that undergo highly regioselective ring openings at C1 with a variety of heteroatom nucleophiles to give chiral N,N-aminals. Alternatively, the same DASP intermediate can be induced to undergo a double ring-opening reaction at both C1 and C3 to yield vicinal diaminated products corresponding to formal ring opening at C3. The chirality of a propargyl alcohol is easily transferred to the DASP with good fidelity, providing a new paradigm for the construction of enantioenriched nitrogen-containing stereotriads.