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1.  Analysis of rapidly synthesized guest-filled porous complexes with synchrotron radiation: practical guidelines for the crystalline sponge method 
This report describes complete practical guidelines and insights for the crystalline sponge method, which have been derived through the first use of synchrotron radiation on these systems, and includes a procedure for faster synthesis of the sponges. These guidelines will be applicable to crystal sponge data collected at synchrotrons or in-house facilities, and will allow researchers to obtain reliable high-quality data and construct chemically and physically sensible models for guest structural determination.
A detailed set of synthetic and crystallographic guidelines for the crystalline sponge method based upon the analysis of expediently synthesized crystal sponges using third-generation synchrotron radiation are reported. The procedure for the synthesis of the zinc-based metal–organic framework used in initial crystal sponge reports has been modified to yield competent crystals in 3 days instead of 2 weeks. These crystal sponges were tested on some small molecules, with two being unexpectedly difficult cases for analysis with in-house diffractometers in regard to data quality and proper space-group determination. These issues were easily resolved by the use of synchrotron radiation using data-collection times of less than an hour. One of these guests induced a single-crystal-to-single-crystal transformation to create a larger unit cell with over 500 non-H atoms in the asymmetric unit. This led to a non-trivial refinement scenario that afforded the best Flack x absolute stereochemical determination parameter to date for these systems. The structures did not require the use of PLATON/SQUEEZE or other solvent-masking programs, and are the highest-quality crystalline sponge systems reported to date where the results are strongly supported by the data. A set of guidelines for the entire crystallographic process were developed through these studies. In particular, the refinement guidelines include strategies to refine the host framework, locate guests and determine occupancies, discussion of the proper use of geometric and anisotropic displacement parameter restraints and constraints, and whether to perform solvent squeezing/masking. The single-crystal-to-single-crystal transformation process for the crystal sponges is also discussed. The presented general guidelines will be invaluable for researchers interested in using the crystalline sponge method at in-house diffraction or synchrotron facilities, will facilitate the collection and analysis of reliable high-quality data, and will allow construction of chemically and physically sensible models for guest structural determination.
PMCID: PMC4283468  PMID: 25537388
X-ray crystallography; crystalline sponge method; metal–organic framework; single-crystal-to-single-crystal transformation; synchrotron radiation
2.  The synthesis of open-shell, bimetallic Mn/Fe trinuclear clusters 
Journal of the American Chemical Society  2013;135(38):10.1021/ja408003d.
Concomitant deprotonation and metallation of hexadentate ligand platform tbsLH6 (tbsLH6 = 1,3,5-C6H9(NHC6H4-o-NHSiMe2 tBu)3) with divalent transition metal starting materials Fe2(Mes)4 (Mes = mesityl) or Mn3(Mes)6 in the presence of tetrahydrofuran (THF) resulted in isolation of homotrinuclear complexes (tbsL)Fe3(THF) and (tbsL)Mn3(THF) respectively. In the absence of coordinating solvent (THF) the deprotonation and metallation exclusively afforded dinuclear complexes of the type (tbsLH2)M2 (M = Fe or Mn). The resulting dinuclear species were utilized as synthons to prepare bimetallic trinuclear clusters. Treatment of (tbsLH2)Fe2 complex with divalent Mn source (Mn2(N(SiMe3)2)4) afforded the bimetallic complex (tbsL)Fe2Mn(THF) which established the ability of hexamine ligand tbsLH6 to support mixed metal clusters. The substitutional homogeneity of (tbsL)Fe2Mn(THF) was determined by 1H NMR, 57Fe Mössbauer, and X-ray fluorescence. Anomalous scattering measurements were critical for the unambiguous assignment of the trinuclear core composition. Heating a solution of (tbsLH2)Mn2 with a stoichiometric amount of Fe2(Mes)4 (0.5 mol equiv) affords a mixture of both (tbsL)Mn2Fe(THF) and (tbsL)Fe2Mn(THF) as a result of the thermodynamic preference for heavier metal substitution within the hexa-anilido ligand framework. These results demonstrate for the first time the assembly of mixed metal cluster synthesis in an unbiased ligand platform.
PMCID: PMC3822335  PMID: 23984911
3.  Trigonal Mn3 and Co3 Clusters Supported by Weak-Field Ligands: A Structural, Spectroscopic, Magnetic, and Computational Investigation into the Correlation of Molecular and Electronic Structure 
Inorganic chemistry  2012;51(19):10290-10299.
Transamination of divalent transition metal starting materials (M2(N(SiMe3)2)4, M = Mn, Co) with hexadentate ligand platforms RLH6 (RLH6 = MeC(CH2NPh-o-NR)3 where R = H, Ph, Mes (Mes = Mesityl)) or H,CyLH6 = 1,3,5-C6H9(NHPh-o-NH2)3 with added pyridine or tertiary phosphine co-ligands afforded trinuclear complexes of the type (RL)Mn3(py)3 and (RL)Co3(PMe2R’)3 (R’ = Me, Ph). While the sterically less encumbered ligand varieties, HL or PhL, give rise to local square-pyramidal geometries at each of the bound metal atoms, with four anilides forming an equatorial plane and an exogenous pyridine or phosphine in the apical site, the mesityl-substituted ligand (MesL) engenders local tetrahedral coordination. Both the neutral Mn3 and Co3 clusters feature S = 1/2 ground states, as determined by dc magnetometry, 1H NMR spectroscopy, and low-temperature EPR spectroscopy. Within the Mn3 clusters, the long internuclear Mn–Mn separations suggest minimal direct metal-metal orbital overlap. Accordingly, fits to variable-temperature magnetic susceptibility data reveal the presence of weak antiferromagnetic superexchange interactions through the bridging anilide ligands with exchange couplings ranging from J = −16.8 to −42 cm−1. Conversely, the short Co–Co interatomic distances suggest a significant degree of direct metal-metal orbital overlap, akin to the related Fe3 clusters. With the Co3 series, the S = 1/2 ground state can be attributed to population of a single molecular orbital manifold that arises from mixing of the metal- and o-phenylenediamide (OPDA) ligand-based frontier orbitals. Chemical oxidation of the neutral Co3 clusters affords diamagnetic cationic clusters of the type [(RL)Co3(PMe2R)3]+. DFT calculations on the neutral (S = ½) and cationic (S = 0) Co3 clusters reveal that oxidation occurs at an oribital with contributions from both the Co3 core and OPDA subunits. The predicted bond elongations within the ligand OPDA units are corroborated by the ligand bond perturbations observed by X-ray crystallography.
PMCID: PMC3479444  PMID: 22991939
Trinuclear; Clusters; Cobalt; Manganese; Electronic structure; Coordinatively Unsaturated; Open-shell configurations
4.  Selenium as a Structural Surrogate of Sulfur: Template-Assisted Assembly of Five Types of Tungsten-Iron-Sulfur/Selenium Clusters and the Structural Fate of Chalcogenide Reactants 
Syntheses of five types of tungsten-iron-sulfur/selenium clusters–incomplete cubanes, single cubanes, edge-bridged double cubanes (EBDCs), PN-type clusters, and double-cuboidal clusters–have been devised based on the concept of template-assisted assembly. The template reactant is six-coordinate [(Tp*)WVIS3]1−, which in the assembly systems organizes FeII,III and sulfide/selenide into cuboidal [(Tp*)WFe2S3] or cubane [(Tp*)WFe3S3Q] units. With appropriate terminal iron ligation, these units are capable of independent existence or may be transformed into higher nuclearity species. Selenide is used as a surrogate for sulfide in cluster assembly in order to determine by X-ray structures the position occupied by an external chalcogenide nucleophile or an internal chalcogenide atom in product clusters. Specific incorporation of selenide is demonstrated by formation of [WFe3S3Se]2+,3+ cubane cores. Reductive dimerization of the cubane leads to the EBDC core [W2Fe6S6Se2]2+ containing μ4-Se sites. Reaction of these species with HSe− affords the PN-type cores [W2Fe6S6Se3]1+ in which selenide occupies μ6-Se and μ2-Se sites. Reaction of [(Tp*)WS3]1−, FeCl2, and Na2Se results in the double cuboidal [W2Fe4S6Se3]2+,0 core with μ2-Se and μ4-Se bridges. It is highly probable that in analogous sulfide-only assembly systems, external and internal sulfide reactants occupy corresponding positions in cluster products. The results further demonstrate the viability of template-assisted cluster synthesis inasmuch as the reduced (Tp*)WS3 unit is present in all clusters. Structures, zero-field Mössbauer data, and redox potentials are presented for all cluster types. (Tp* = tris(pyrazolyl)hydroborate(1−))
PMCID: PMC3353770  PMID: 22424175
5.  Cubane-type Fe4S4 Clusters with Chiral Thiolate Ligation: Formation by Ligand Substitution, Detection of Intermediates by 1H NMR, and Solid State Structures Including Spontaneous Resolution Upon Crystallization 
Inorganic chemistry  2011;50(21):11082-11090.
Cubane-type clusters [Fe4S4(SR*)4]2− containing chiral thiolate ligands with R* = CH(Me)Ph (1), CH2CH(Me)Et (2), and CH2CH(OH)CH2OH (3) have been prepared by ligand substitution in the reaction systems [Fe4S4(SEt)4]/R*SH (1–3, acetonitrile) and [Fe4S4Cl4]2−/NaSR*(3, Me2SO). Reactions with successive equivalents of thiol or thiolate generate the species [Fe4S4L4-n(SR*)n]2− (L = SEt, Cl) with n = 1–4. Clusters 1 and 2 were prepared with racemic thiols leading to the possible formation of one enantiomeric pair (n = 1) and seven diastereomers and their enantiomers (n = 2–4). Reactions were monitored by isotropically shifted 1H NMR spectra in acetonitrile or Me2SO. In systems affording 1 and 2 as final products, individual mixed-ligand species could not be detected. However, crystallization of (Et4N)2[1] afforded 1-[SS(RS)(RS)] in which two sites are disordered because of occupancy of R and S ligands. Similarly, (Et4N)2[2] led to 2-[SSSS], a consequence of spontaneous resolution upon crystallization. The clusters 3-[RRRR] and 3- [SSSS] were obtained from enantiomerically pure thiols. Successive reactions lead to detection of species with n = 1–4 by appearance of four pairs of diastereotopic SCH2 signals in both acetonitrile and Me2SO reaction systems. Identical spectra were obtained with racemic, R-(−), and S-(+) thiols, indicating that ligand-ligand interactions are too weak to allow detection of diastereomers (e.g., [SSSS] vs. [SSRR]). The stability of 3 in Me2SO/H2O media is described.
PMCID: PMC3215100  PMID: 21942299
6.  Oxidative group transfer to a triiron complex to form a nucleophilic μ3-nitride, [Fe3(μ3-N)]− 
Utilizing a hexadentate ligand platform, a high-spin trinuclear iron complex of the type (tbsL)Fe3(thf) was synthesized and characterized ([tbsL]6− = [1,3,5-C6H9(NPh-o-NSitBuMe2)3]6−). The silyl-amide groups only permit ligation of one solvent molecule to the tri-iron core, resulting in an asymmetric core wherein each iron ion exhibits a distinct local coordination environment. The triiron complex (tbsL)Fe3(thf) rapidly consumes inorganic azide ([N3]NBu4) to afford an anionic, trinuclear nitride complex [(tbsL)Fe3(μ3-N)]NBu4. The nearly C3-symmetric complex exhibits a highly pyramidalized nitride ligand that resides 1.205(3) Å above the mean triiron plane with short Fe–N (1.871(3) Å) distances and Fe–Fe separation (2.480(1) Å). The nucleophilic nitride can be readily alkylated via reaction with methyl iodide to afford the neutral, trinuclear methylimide complex (tbsL)Fe3(μ3-NCH3). Alkylation of the nitride maintains the approximate C3-symmetry in the imide complex, where the imide ligand resides 1.265(9) Å above the mean triiron plane featuring lengthened Fe–Nimide bond distances (1.892(3) Å) with nearly equal Fe–Fe separation (2.483(1) Å).
PMCID: PMC3056537  PMID: 21332160
7.  Time-resolved synchrotron diffraction and theoretical studies of very short-lived photo-induced molecular species 
Excited-state geometries determined by time-resolved synchrotron diffraction are summarized with emphasis on their comparison with a series of theoretical results. The relative merits of monochromatic and polychromatic (Laue) techniques are discussed.
Definitive experimental results on the geometry of fleeting species are at the time of writing still limited to monochromatic data collection, but methods for modifications of the polychromatic Laue data to increase their accuracy and their suitability for pump–probe experiments have been implemented and are reviewed. In the monochromatic experiments summarized, excited-state conversion percentages are small when neat crystals are used, but are higher when photoactive species are embedded in an inert framework in supramolecular crystals. With polychromatic techniques and increasing source brightness, smaller samples down to tenths of a micrometre or less can be used, increasing homogeneity of exposure and the fractional population of the excited species. Experiments described include a series of transition metal complexes and a fully organic example involving excimer formation. In the final section, experimental findings are compared with those from theoretical calculations on the isolated species. Qualitative agreement is generally obtained, but the theoretical results are strongly dependent on the details of the calculation, indicating the need for further systematic analysis.
PMCID: PMC2824528  PMID: 20164641
pump–probe experiments; time-resolved diffraction; excited-state molecular geometries; excimers
8.  Direct Observation of a Photo-Induced Non-Stabilized Nitrile Imine Structure in the Solid State 
Journal of the American Chemical Society  2009;131(50):18036-18037.
We report the direct observation of a bent geometry for a non-stabilized nitrile imine in a metal-coordination crystal. The photoinduced tetrazole ring rupture to release N2 appears to depend on the size of voids around the N3-N4 bond in the crystal lattice. We further observed the selective formation of 1,3-addition product when a reactive nitrile imine was photo-generated in water. Taken together, the bent nitrile imine geometry agrees with the 1,3-dipolar structure, a transient reactive species that mediates the photoinduced 1,3-dipolar cycloaddition in the aqueous medium.
PMCID: PMC2797338  PMID: 19928921
9.  Syntheses of α-Pyrones Using Gold-Catalyzed Coupling Reactions 
Organic Letters  2011;13(11):2834-2836.
Sequential alkyne activation of terminal alkynes and propiolic acids by gold(I) catalysts yields compounds having α-pyrone skeletons. Novel cascade reactions involving propiolic acids are reported that give rise to α-pyrones with different substitution patterns.
PMCID: PMC3103191  PMID: 21534543
10.  Structure and Biosynthesis of Amychelin, an Unusual Mixed-Ligand Siderophore from Amycolatopsis sp. AA4 
Journal of the American Chemical Society  2011;133(30):11434-11437.
Actinobacteria generate a large number of structurally diverse small molecules with potential therapeutic value. Genomic analyses of this productive group of bacteria show that their genetic potential to manufacture small molecules exceeds their observed ability by roughly an order of magnitude, and this revelation has prompted a number of studies to identify members of the unknown majority. As a potential window into this cryptic secondary metabolome, pairwise assays for developmental interactions within a set of 20 sequenced actinomycetes were carried out. These assays revealed that Amycolatopsis sp. AA4, a so-called “rare” actinomycete, produces a novel siderophore, amychelin, which alters the developmental processes of several neighboring streptomycetes. Using this phenotype as an assay, we isolated amychelin and solved its structure by NMR and MS methods coupled with an X-ray crystallographic analysis of its Fe-complex. The iron binding affinity of amychelin was determined using EDTA competition assays, and a biosynthetic cluster was identified and annotated to provide a tentative biosynthetic scheme for amychelin.
PMCID: PMC3144690  PMID: 21699219
11.  Multicomponent Assembly of Proposed DNA Precursors in Water 
Journal of the American Chemical Society  2012;134(33):13889-13895.
We propose a novel pathway for the prebiotic synthesis of 2′-deoxynucleotides. Consideration of the constitutional chemical relationships between glycolaldehyde and β-mercapto-acetaldehyde, and the corresponding proteinogenic amino acids, serine and cysteine, led us to explore the consequences of the corresponding sulfur substitution for our previously proposed pathways leading to the canonical ribonucleotides. We demonstrate that just as 2-aminooxazole–an important prebiotic ribonucleotide precursor–is readily formed from glycolaldehyde and cyanamide, so is 2-aminothiazole formed from β-mercapto-acetaldehyde and cyanamide in water at neutral pH. Indeed, both the oxazole and the thiazole can be formed together in a one-pot reaction, and can be co-purified by crystallization or sublimation. We then show that 2-aminothiazole can take part in a 3-component carbon–carbon bond-forming reaction in water that leads to the diastereoselective synthesis of masked 2′-thiosugars regiospecifically tethered to purine precursors, which would lead to 2′-deoxynucleotides upon desulfurization. The possibility of an abiotic route to the 2′-deoxynucleotides provides a new perspective on the evolutionary origins of DNA. We also show that 2-aminothiazole is able to sequester, through reversible aminal formation, the important nucleotide precursors glycolaldehyde and glyceraldehyde in a stable, crystalline form.
PMCID: PMC3424849  PMID: 22839703

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