Publications by authors named "Sax A Mason"

36 Publications

Macromolecular structure phasing by neutron anomalous diffraction.

Sci Rep 2016 08 11;6:31487. Epub 2016 Aug 11.

Faculty of Natural Sciences, Keele University, Staffordshire, ST5 5BG, United Kingdom.

In this report we show for the first time that neutron anomalous dispersion can be used in a practical manner to determine experimental phases of a protein crystal structure, providing a new tool for structural biologists. The approach is demonstrated through the use of a state-of-the-art monochromatic neutron diffractometer at the Institut Laue-Langevin (ILL) in combination with crystals of perdeuterated protein that minimise the level of hydrogen incoherent scattering and enhance the visibility of the anomalous signal. The protein used was rubredoxin in which cadmium replaced the iron at the iron-sulphur site. While this study was carried out using a steady-state neutron beam source, the results will be of major interest for capabilities at existing and emerging spallation neutron sources where time-of-flight instruments provide inherent energy discrimination. In particular this capability may be expected to offer unique opportunities to a rapidly developing structural biology community where there is increasing interest in the identification of protonation states, protein/water interactions and protein-ligand interactions - all of which are of central importance to a wide range of fundamental and applied areas in the biosciences.
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http://dx.doi.org/10.1038/srep31487DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4980602PMC
August 2016

Binding site asymmetry in human transthyretin: insights from a joint neutron and X-ray crystallographic analysis using perdeuterated protein.

IUCrJ 2014 Nov 21;1(Pt 6):429-38. Epub 2014 Oct 21.

Facility of Natural Sciences, Institute of Science and Technology in Medicine, Keele University , Staffordshire ST5 5BG, United Kingdom ; Institut Laue-Langevin , 71, avenue des Martyrs, Grenoble, CS 20156, France ; Partnership for Structural Biology , 71, avenue des Martyrs, Grenoble, CS 20156, France.

Human transthyretin has an intrinsic tendency to form amyloid fibrils and is heavily implicated in senile systemic amyloidosis. Here, detailed neutron structural studies of perdeuterated transthyretin are described. The analyses, which fully exploit the enhanced visibility of isotopically replaced hydrogen atoms, yield new information on the stability of the protein and the possible mechanisms of amyloid formation. Residue Ser117 may play a pivotal role in that a single water molecule is closely associated with the γ-hydrogen atoms in one of the binding pockets, and could be important in determining which of the two sites is available to the substrate. The hydrogen-bond network at the monomer-monomer interface is more extensive than that at the dimer-dimer interface. Additionally, the edge strands of the primary dimer are seen to be favourable for continuation of the β-sheet and the formation of an extended cross-β structure through sequential dimer couplings. It is argued that the precursor to fibril formation is the dimeric form of the protein.
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http://dx.doi.org/10.1107/S2052252514021113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4224461PMC
November 2014

Glycyl-L-alanine: a multi-temperature neutron study.

Acta Crystallogr C Struct Chem 2014 Oct 28;70(Pt 10):949-52. Epub 2014 Sep 28.

School of Chemistry and Biochemistry, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia.

Neutron diffraction data have been collected at 12, 50, 150 and 295 K for the dipeptide glycyl-L-alanine, C5H10N2O3, in order to obtain accurate positional and anisotropic displacement parameters for the H atoms. The values of these parameters serve as a benchmark for assessing the equivalent parameters obtained from a so-called Hirshfeld-atom refinement of X-ray diffraction data described elsewhere [Capelli et al. (2014). IUCrJ, 1, 361-379]. The flexibility of the glycyl-L-alanine molecule in the solid and the hydrogen-bonding interactions as a function of temperature are also considered.
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http://dx.doi.org/10.1107/S2053229614019809DOI Listing
October 2014

CNN pincer ruthenium catalysts for hydrogenation and transfer hydrogenation of ketones: experimental and computational studies.

Chemistry 2014 Oct 4;20(42):13603-17. Epub 2014 Sep 4.

Dipartimento di Chimica, Fisica e Ambiente, Università di Udine, Via Cotonificio 108, 33100 Udine (Italy), Fax: (+39) 0432-558803.

Reaction of [RuCl(CNN)(dppb)] (1-Cl) (HCNN=2-aminomethyl-6-(4-methylphenyl)pyridine; dppb=Ph2 P(CH2 )4 PPh2 ) with NaOCH2 CF3 leads to the amine-alkoxide [Ru(CNN)(OCH2 CF3 )(dppb)] (1-OCH2 CF3 ), whose neutron diffraction study reveals a short RuO⋅⋅⋅HN bond length. Treatment of 1-Cl with NaOEt and EtOH affords the alkoxide [Ru(CNN)(OEt)(dppb)]⋅(EtOH)n (1-OEt⋅n EtOH), which equilibrates with the hydride [RuH(CNN)(dppb)] (1-H) and acetaldehyde. Compound 1-OEt⋅n EtOH reacts reversibly with H2 leading to 1-H and EtOH through dihydrogen splitting. NMR spectroscopic studies on 1-OEt⋅n EtOH and 1-H reveal hydrogen bond interactions and exchange processes. The chloride 1-Cl catalyzes the hydrogenation (5 atm of H2 ) of ketones to alcohols (turnover frequency (TOF) up to 6.5×10(4) h(-1) , 40 °C). DFT calculations were performed on the reaction of [RuH(CNN')(dmpb)] (2-H) (HCNN'=2-aminomethyl-6-(phenyl)pyridine; dmpb=Me2 P(CH2 )4 PMe2 ) with acetone and with one molecule of 2-propanol, in alcohol, with the alkoxide complex being the most stable species. In the first step, the Ru-hydride transfers one hydrogen atom to the carbon of the ketone, whereas the second hydrogen transfer from NH2 is mediated by the alcohol and leads to the key "amide" intermediate. Regeneration of the hydride complex may occur by reaction with 2-propanol or with H2 ; both pathways have low barriers and are alcohol assisted.
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http://dx.doi.org/10.1002/chem.201402229DOI Listing
October 2014

L-Arabinose binding, isomerization, and epimerization by D-xylose isomerase: X-ray/neutron crystallographic and molecular simulation study.

Structure 2014 Sep 14;22(9):1287-1300. Epub 2014 Aug 14.

Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA. Electronic address:

D-xylose isomerase (XI) is capable of sugar isomerization and slow conversion of some monosaccharides into their C2-epimers. We present X-ray and neutron crystallographic studies to locate H and D atoms during the respective isomerization and epimerization of L-arabinose to L-ribulose and L-ribose, respectively. Neutron structures in complex with cyclic and linear L-arabinose have demonstrated that the mechanism of ring-opening is the same as for the reaction with D-xylose. Structural evidence and QM/MM calculations show that in the reactive Michaelis complex L-arabinose is distorted to the high-energy (5)S1 conformation; this may explain the apparent high KM for this sugar. MD-FEP simulations indicate that amino acid substitutions in a hydrophobic pocket near C5 of L-arabinose can enhance sugar binding. L-ribulose and L-ribose were found in furanose forms when bound to XI. We propose that these complexes containing Ni(2+) cofactors are Michaelis-like and the isomerization between these two sugars proceeds via a cis-ene-diol mechanism.
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http://dx.doi.org/10.1016/j.str.2014.07.002DOI Listing
September 2014

SPINE-compatible `carboloops': a new microshaped vitreous carbon sample mount for X-ray and neutron crystallography.

Acta Crystallogr F Struct Biol Commun 2014 May 15;70(Pt 5):681-4. Epub 2014 Apr 15.

European Synchrotron Radiation Facility, 6 Rue Jules Horowitz, 38000 Grenoble, France.

A novel vitreous carbon mount for macromolecular crystallography, suitable for neutron and X-ray crystallographic studies, has been developed. The technology described here is compatible both with X-ray and neutron cryo-crystallography. The mounts have low density and low background scattering for both neutrons and X-rays. They are prepared by laser cutting, allowing high standards of production quality, the ability to custom-design the mount to specific crystal sizes and large-scale production.
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http://dx.doi.org/10.1107/S2053230X14005901DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4014346PMC
May 2014

The self-assembling zwitterionic form of L-phenylalanine at neutral pH.

Acta Crystallogr C Struct Chem 2014 Mar 22;70(Pt 3):326-31. Epub 2014 Feb 22.

Partnership for Structural Biology, Institut Laue-Langevin, 38042 Grenoble, France.

The title zwitterion (2S)-2-azaniumyl-1-hydroxy-3-phenylpropan-1-olate, C9H11NO2, also known as L-phenylalanine, was characterized using synchrotron X-rays. It crystallized in the monoclinic space group P21 with four molecules in the asymmetric unit. The 0.62 Å resolution structure is assumed to be closely related to the fibrillar form of phenylalanine, as observed by electron microscopy and electron diffraction. The structure exists in a zwitterionic form in which π-π stacking and hydrogen-bonding interactions are believed to form the basis of the self-assembling properties.
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http://dx.doi.org/10.1107/S2053229614002563DOI Listing
March 2014

Nature of Si-H interactions in a series of ruthenium silazane complexes using multinuclear solid-state NMR and neutron diffraction.

Inorg Chem 2014 Jan 6;53(2):1156-65. Epub 2014 Jan 6.

LCC (Laboratoire de Chimie de Coordination), CNRS , 205 Route de Narbonne, F-31077 Toulouse, France.

Three new N-heterocyclic-silazane compounds, 1a-c, were prepared and employed as bidentate ligands to ruthenium, resulting in a series of [Ru(H){(κ-Si,N-(SiMe2-N-heterocycle)}3] complexes (3a-c) featuring the same RuSi3H motif. Detailed structural characterization of the RuSi3H complexes with X-ray diffraction, and in the case of triazabicyclo complex [Ru(H){κ-Si,N-(SiMe2)(C7H12N3)}3] (3a), neutron diffraction, enabled a reliable description of the molecular geometry. The hydride ligand of (3a) is located closer to two of the silicon atoms than it is to the third. Such a geometry differs from that of the previously reported complex [Ru(H){(κ-Si,N-(SiMe2)N(SiMe2H)(C5H4N)}3] (3d), also characterized by neutron diffraction, where the hydride was found to be equidistant from all three silicon atoms. A DFT study revealed that the symmetric and less regular isomers are essentially degenerate. Information on the dynamics and on the Ru···H···Si interactions was gained from multinuclear solid-state ((1)H wPMLG, (29)Si CP MAS, and 2D (1)H-(29)Si dipolar HETCOR experiments) and solution NMR studies. The corresponding intermediate complexes, [Ru{κ-Si,N-(SiMe2-N-heterocycle)}(η(4)-C8H12)(η(3)-C8H11)] (2a-c), involving a single silazane ligand were isolated and characterized by multinuclear NMR and X-ray diffraction. Protonation of the RuSi3H complexes was also studied. Reaction of 3a with NH4PF6 gave rise to [Ru(H)(η(2)-H -SiMe2)κ-N-(C7H12N3){κ-Si,N-(SiMe2)(C7H12N3)}2](+)[PF6](-)(4aPF6) which was isolated and characterized by NMR spectroscopy, X-ray crystallography, and DFT studies. The nature of the Si-H interactions in this silazane series was analyzed in detail.
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http://dx.doi.org/10.1021/ic4027199DOI Listing
January 2014

A highly hydrated α-cyclodextrin/1-undecanol inclusion complex: crystal structure and hydrogen-bond network from high-resolution neutron diffraction at 20 K.

Acta Crystallogr B Struct Sci Cryst Eng Mater 2013 Apr 26;69(Pt 2):214-27. Epub 2013 Feb 26.

UMR CNRS 8612, LabEx LERMIT Universite Paris-Sud, 5 rue Jean-Baptiste Clément, F-92296 Chatenay-Malabry CEDEX, France.

The monoclinic C2 crystal structure of an α-cyclodextrin/1-undecanol host-guest inclusion complex was solved using single-crystal neutron diffraction. Large high-quality crystals were specially produced by optimizing temperature-controlled growth conditions. The hydrate crystallizes in a channel-type structure formed by head-to-head dimer units of α-cyclodextrin molecules stacked like coins in a roll. The alkyl chain of the guest lipid is entirely embedded inside the tubular cavity delimited by the α-cyclodextrin dimer and adopts an all-trans planar zigzag conformation, while the alcohol polar head group is outside close to the α-cyclodextrin primary hydroxyl groups. The cyclodextrin dimer forms columns, which adopt a quasi-square arrangement much less compact than the quasi-hexagonal close packing already observed in the less hydrated α-cyclodextrin channel-type structures usually found with similar linear guests. The lack of compactness of this crystal form is related to the high number of interstitial water molecules. The replacement of 1-undecanol by 1-decanol does not modify the overall crystal structure of the hydrate as shown by additional X-ray diffraction investigations comparing the two host-guest assemblies. This is the first study that analyses the entire hydrogen-bonding network involved in the formation of a cyclodextrin dimer surrounded by its shell of water molecules.
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http://dx.doi.org/10.1107/S2052519213001772DOI Listing
April 2013

Step-by-step introduction of silazane moieties at ruthenium: different extents of Ru-H-Si bond activation.

Inorg Chem 2013 Mar 19;52(5):2654-61. Epub 2013 Feb 19.

LCC (Laboratoire de Chimie de Coordination), CNRS, 205 Route de Narbonne, F-31077 Toulouse, France.

The coordination of pyridine-2-amino(methyl)dimethylsilane ligands to ruthenium has afforded access to a family of novel complexes that display multicenter Ru-H-Si interactions according to the number of incorporated ligands. The new complexes Ru[κ-Si,N-(SiMe2)N(Me)(C5H4N)](η(4)-C8H12)(η(3)-C8H11) (1), Ru2(μ-H)2(H)2[κ-Si,N-(SiMe2)N(Me)(C5H4N)]4 (2), and Ru(H)[κ-Si,N-(SiMe2)N(Me)(C5H4N)]3 (3) were isolated and fully characterized. The complexes exhibit different degrees of Si-H activation: complete Si-H cleavage, secondary interactions between the atoms (SISHA), and η(2)-Si-H coordination. Reversible protonation of 3 leading to the cationic complex [RuH{(η(2)-H-SiMe2)N(Me)κ-N-(C5H4N)}{κ-Si,N-(SiMe2)N(Me)(C5H4N)}2](+)[BAr(F)4](-) (5) was also demonstrated. The coordination modes in these systems were carefully studied with a combination of X-ray and neutron diffraction analysis, DFT geometry optimization, and multinuclear NMR spectroscopy.
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http://dx.doi.org/10.1021/ic302682fDOI Listing
March 2013

Probing highly selective H/D exchange processes with a ruthenium complex through neutron diffraction and multinuclear NMR studies.

Inorg Chem 2013 Jul 20;52(13):7329-37. Epub 2012 Dec 20.

CNRS , LCC (Laboratoire de Chimie de Coordination), 205 route de Narbonne, BP 44099, F-31077 Toulouse Cedex 4, France.

Deuterium labeling is a powerful way to gain mechanistic information in biology and chemistry. However, selectivity is hard to control experimentally, and labeled sites can be difficult to assign both in solution and in the solid state. Here we show that very selective high-deuterium contents can be achieved for the polyhydride ruthenium phosphine complex [RuH2(H2)2(PCyp3)2] (1) (PCyp3 = P(C5H9)3). The selectivity of the H/D exchange process is demonstrated by multinuclear NMR and neutron diffraction analyses. It has also been investigated through density functional theory (DFT) calculations. The reactions are performed under mild conditions at room temperature, and the extent of deuterium incorporation, involving selective C-H bond activation within the cyclopentyl rings of the phosphine ligands, can easily be tuned (solvent effects, D2 pressure). It is shown that D2 gas can inhibit the C-H/C-D exchange process.
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http://dx.doi.org/10.1021/ic302307mDOI Listing
July 2013

The role of order-disorder transitions in the quest for molecular multiferroics: structural and magnetic neutron studies of a mixed valence iron(II)-iron(III) formate framework.

J Am Chem Soc 2012 Dec 19;134(48):19772-81. Epub 2012 Nov 19.

Instituto de Ciencia de Materiales de Aragón, CSIC-Universidad de Zaragoza, C/Pedro Cerbuna 12, E-50009, Zaragoza, Spain.

Neutron diffraction studies have been carried out to shed light on the unprecedented order-disorder phase transition (ca. 155 K) observed in the mixed-valence iron(II)-iron(III) formate framework compound [NH(2)(CH(3))(2)](n)[Fe(III)Fe(II)(HCOO)(6)](n). The crystal structure at 220 K was first determined from Laue diffraction data, then a second refinement at 175 K and the crystal structure determination in the low temperature phase at 45 K were done with data from the monochromatic high resolution single crystal diffractometer D19. The 45 K nuclear structure reveals that the phase transition is associated with the order-disorder of the dimethylammonium counterion that is weakly anchored in the cavities of the [Fe(III)Fe(II)(HCOO)(6)](n) framework. In the low-temperature phase, a change in space group from P31c to R3c occurs, involving a tripling of the c-axis due to the ordering of the dimethylammonium counterion. The occurrence of this nuclear phase transition is associated with an electric transition, from paraelectric to antiferroelectric. A combination of powder and single crystal neutron diffraction measurements below the magnetic order transition (ca. 37 K) has been used to determine unequivocally the magnetic structure of this Néel N-Type ferrimagnet, proving that the ferrimagnetic behavior is due to a noncompensation of the different Fe(II) and Fe(III) magnetic moments.
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http://dx.doi.org/10.1021/ja3082457DOI Listing
December 2012

Inhibition of D-xylose isomerase by polyols: atomic details by joint X-ray/neutron crystallography.

Acta Crystallogr D Biol Crystallogr 2012 Sep 18;68(Pt 9):1201-6. Epub 2012 Aug 18.

Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.

D-Xylose isomerase (XI) converts the aldo-sugars xylose and glucose to their keto analogs xylulose and fructose, but is strongly inhibited by the polyols xylitol and sorbitol, especially at acidic pH. In order to understand the atomic details of polyol binding to the XI active site, a 2.0 Å resolution room-temperature joint X-ray/neutron structure of XI in complex with Ni(2+) cofactors and sorbitol inhibitor at pH 5.9 and a room-temperature X-ray structure of XI containing Mg(2+) ions and xylitol at the physiological pH of 7.7 were obtained. The protonation of oxygen O5 of the inhibitor, which was found to be deprotonated and negatively charged in previous structures of XI complexed with linear glucose and xylulose, was directly observed. The Ni(2+) ions occupying the catalytic metal site (M2) were found at two locations, while Mg(2+) in M2 is very mobile and has a high B factor. Under acidic conditions sorbitol gains a water-mediated interaction that connects its O1 hydroxyl to Asp257. This contact is not found in structures at basic pH. The new interaction that is formed may improve the binding of the inhibitor, providing an explanation for the increased affinity of the polyols for XI at low pH.
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http://dx.doi.org/10.1107/S0907444912024808DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3489103PMC
September 2012

Uranium and thorium hydride complexes as multielectron reductants: a combined neutron diffraction and quantum chemical study.

Inorg Chem 2012 Mar 24;51(6):3613-24. Epub 2012 Feb 24.

Department of Chemistry, University of Minnesota and Supercomputing Institute, Minneapolis, Minnesota 55455, USA.

The unusual uranium reaction system in which uranium(4+) and uranium(3+) hydrides interconvert by formal bimetallic reductive elimination and oxidative addition reactions, [(C(5)Me(5))(2)UH(2)](2) (1) ⇌ [(C(5)Me(5))(2)UH](2) (2) + H(2), was studied by employing multiconfigurational quantum chemical and density functional theory methods. 1 can act as a formal four-electron reductant, releasing H(2) gas as the byproduct of four H(2)/H(-) redox couples. The calculated structures for both reactants and products are in good agreement with the X-ray diffraction data on 2 and 1 and the neutron diffraction data on 1 obtained under H(2) pressure as part of this study. The interconversion of the uranium(4+) and uranium(3+) hydride species was calculated to be near thermoneutral (~-2 kcal/mol). Comparison with the unknown thorium analogue, [(C(5)Me(5))(2)ThH](2), shows that the thorium(4+) to thorium(3+) hydride interconversion reaction is endothermic by 26 kcal/mol.
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http://dx.doi.org/10.1021/ic202503hDOI Listing
March 2012

(+)-syn-Benzotriborneol an enantiopure C3-symmetric receptor for water.

Org Biomol Chem 2012 Mar 20;10(12):2464-9. Epub 2012 Feb 20.

Dipartimento di Scienze Molecolari e Nanosistemi, Università Ca' Foscari di Venezia Dorsoduro 2137, I-30123, Venezia, Italy.

(+)-syn-Benzotriborneol forms stable complexes with one molecule of water. This is due to the ability of the host to form three hydrogen bonds with water, to act simultaneously as a hydrogen-bond acceptor and donor, and to a perfect geometrical match between the pair. We report experimental (X-ray and neutron diffraction, VT NMR, DSC, TGA) and stereochemical studies carried out to elucidate and quantify the molecular and thermodynamic aspects of this supramolecular complex.
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http://dx.doi.org/10.1039/c2ob06774aDOI Listing
March 2012

Preliminary neutron crystallographic study of human transthyretin.

Acta Crystallogr Sect F Struct Biol Cryst Commun 2011 Nov 27;67(Pt 11):1428-31. Epub 2011 Oct 27.

EPSAM, Keele University, Keele, Staffordshire ST5 5BG, England.

Preliminary studies of perdeuterated crystals of human transthyretin (TTR) have been carried out using the LADI-III and D19 diffractometers at the Institut Laue-Langevin in Grenoble. The results demonstrate the feasibility of a full crystallographic analysis to a resolution of 2.0 Å using Laue diffraction and also illustrate the potential of using monochromatic instruments such as D19 for higher resolution studies where larger crystals having smaller unit cells are available. This study will yield important information on hydrogen bonding, amino-acid protonation states and hydration in the protein. Such information will be of general interest for an understanding of the factors that stabilize/destabilize TTR and for the design of ligands that may be used to counter TTR amyloid fibrillogenesis.
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http://dx.doi.org/10.1107/S1744309111036244DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3212468PMC
November 2011

Molecular heterometallic hydride clusters composed of rare-earth and d-transition metals.

Nat Chem 2011 Sep 18;3(10):814-20. Epub 2011 Sep 18.

Organometallic Chemistry Laboratory and Advanced Catalyst Research Team, RIKEN Advanced Science Institute, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.

Heteromultimetallic hydride clusters containing both rare-earth and d-transition metals are of interest in terms of both their structure and reactivity. However, such heterometallic complexes have not yet been investigated to a great extent because of difficulties in their synthesis and structural characterization. Here, we report the synthesis, X-ray and neutron diffraction studies, and hydrogen addition and release properties of a family of rare-earth/d-transition-metal heteromultimetallic polyhydride complexes of the core structure type 'Ln(4)MH(n)' (Ln = Y, Dy, Ho; M = Mo, W; n = 9, 11, 13). Monitoring of hydrogen addition to a hydride cluster such as [{(C(5)Me(4)SiMe(3))Y}(4)(μ-H)(9)Mo(C(5)Me(5))] in a single-crystal to single-crystal process by X-ray diffraction has been achieved for the first time. Density functional theory studies reveal that the hydrogen addition process is cooperatively assisted by the Y/Mo heteromultimetallic sites, thus offering unprecedented insight into the hydrogen addition and release process of a metal hydride cluster.
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http://dx.doi.org/10.1038/nchem.1147DOI Listing
September 2011

The structure of water in p-sulfonatocalix[4]arene.

Chemistry 2011 Sep 11;17(37):10259-71. Epub 2011 Aug 11.

Department of Chemistry, Durham University, South Road, Durham, DH1 3LE, UK.

Tetrasodium p-sulfonatocalix[4]arene exists as a hydrate with approximately 14 water molecules and has three polymorphic modifications, all of which contain a water molecule in the molecular cavity that is engaged in OH···π interactions. Single-crystal neutron structures are reported for two of these three forms and reveal a "compressed" water molecule with short OH bonds. Partial atomic charges and hardness analysis (PACHA) calculations based on the neutron coordinates give an OH···π interaction energy of 6.9-7.5 kJ mol(-1). The PACHA analysis also reveals the dominance of the charge-assisted hydrogen bonds from the Na(+)-coordinated water molecules. The instability of the crystal towards dehydration can be traced to an uncoordinated lattice water site. The remarkable calixarene-Na(+)-hydrate motif is conserved almost unchanged across all three polymorphs. A single-crystal neutron structure is also reported for pentasodium p-sulfonatocalix[4]arene·12H(2)O, which exhibits an intracavity water molecule that is engaged in both OH···π and OH···O hydrogen bonding. The shorter covalent bond to the hydrogen atom that forms the interaction with the aromatic ring is again apparent.
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http://dx.doi.org/10.1002/chem.201101748DOI Listing
September 2011

Square-planar iridium(II) and iridium(III) amido complexes stabilized by a PNP pincer ligand.

Angew Chem Int Ed Engl 2011 Aug 8;50(35):8184-7. Epub 2011 Jul 8.

Department Chemie und Pharmazie, Friedrich-Alexander-Universität, Erlangen, Germany.

Squaring the circle: the novel dienamido pincer ligand N(CHCHPtBu(2))(2)(-) affords the isolation of the unusual square-planar iridium(II) and iridium(III) amido complexes [IrCl{N(CHCHPtBu(2))(2)}](n) (n=0 (1), +1 (2)). In contrast, the corresponding iridium(I) complex of the redox series (n=-1) is surprisingly unstable. The diamagnetism of 2 is attributed to strong N→Ir π donation.
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http://dx.doi.org/10.1002/anie.201102795DOI Listing
August 2011

Low-temperature neutron diffraction structures of N-glycoprotein linkage models and analogues: structure refinement and trifurcated hydrogen bonds.

J Am Chem Soc 2011 Jul 15;133(26):10042-5. Epub 2011 Jun 15.

European Synchrotron Radiation Facility, BP220 Grenoble, France.

The biological addition of oligosaccharide moieties to asparagine residues of N-glycoproteins influences the properties and bioactivities of these macromolecules. The low-temperature neutron crystal structures of three N-glycoprotein linkage models and analogues provide accurate characterization of the three-dimensional structure of the conserved GlcNAc-Asn linkage. These first crystal structures of N-acetylated carbohydrates obtained by neutron diffraction provide high-resolution geometrical parameters that can be used for force-field parametrization and subsequent molecular dynamics simulation of N-glycoproteins. The correct localization of hydrogen atoms demonstrates the occurrence of trifurcated hydrogen bonds and hydrophobic contacts.
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http://dx.doi.org/10.1021/ja203239jDOI Listing
July 2011

High-resolution neutron crystallographic studies of the hydration of the coenzyme cob(II)alamin.

Acta Crystallogr D Biol Crystallogr 2011 Jun 19;67(Pt 6):584-91. Epub 2011 May 19.

Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI 02912, USA.

The hydration of the coenzyme cob(II)alamin has been studied using high-resolution monochromatic neutron crystallographic data collected at room temperature to a resolution of 0.92 Å on the original D19 diffractometer with a prototype 4° × 64° detector at the high-flux reactor neutron source run by the Institute Laue-Langevin. The resulting structure provides hydrogen-bonding parameters for the hydration of biomacromolecules to unprecedented accuracy. These experimental parameters will be used to define more accurate force fields for biomacromolecular structure refinement. The presence of a hydrophobic bowl motif surrounded by flexible side chains with terminal functional groups may be significant for the efficient scavenging of ligands. The feasibility of extending the resolution of this structure to ultrahigh resolution was investigated by collecting time-of-flight neutron crystallographic data during commissioning of the TOPAZ diffractometer with a prototype array of 14 modular 2° × 21° detectors at the Spallation Neutron Source run by Oak Ridge National Laboratory.
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http://dx.doi.org/10.1107/S090744491101496XDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3107055PMC
June 2011

Dispersion-driven hydrogen bonding: predicted hydrogen bond between water and platinum(II) identified by neutron diffraction.

Angew Chem Int Ed Engl 2010 Oct;49(41):7440-3

Dip. di Chimica Strutturale e Stereochimica Inorganica, Università di Milano, 20133 Milano, Italy.

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http://dx.doi.org/10.1002/anie.201001892DOI Listing
October 2010

Metal ion roles and the movement of hydrogen during reaction catalyzed by D-xylose isomerase: a joint x-ray and neutron diffraction study.

Structure 2010 Jun;18(6):688-99

Bioscience Division, Los Alamos National Laboratory, MS M888, Los Alamos, NM 87545, USA.

Conversion of aldo to keto sugars by the metalloenzyme D-xylose isomerase (XI) is a multistep reaction that involves hydrogen transfer. We have determined the structure of this enzyme by neutron diffraction in order to locate H atoms (or their isotope D). Two studies are presented, one of XI containing cadmium and cyclic D-glucose (before sugar ring opening has occurred), and the other containing nickel and linear D-glucose (after ring opening has occurred but before isomerization). Previously we reported the neutron structures of ligand-free enzyme and enzyme with bound product. The data show that His54 is doubly protonated on the ring N in all four structures. Lys289 is neutral before ring opening and gains a proton after this; the catalytic metal-bound water is deprotonated to hydroxyl during isomerization and O5 is deprotonated. These results lead to new suggestions as to how changes might take place over the course of the reaction.
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http://dx.doi.org/10.1016/j.str.2010.03.011DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2887347PMC
June 2010

Neutron diffraction studies on a 4-coordinate hydrogen atom in an yttrium cluster.

J Am Chem Soc 2008 Mar 29;130(12):3888-91. Epub 2008 Feb 29.

Department of Chemistry, University of Southern California, Los Angeles, California, USA.

A four-coordinate hydrogen atom has been unambiguously located, by single-crystal neutron diffraction for the first time, in the center of the tetrahedral metal complex Y4H8(Cp')4(THF) [Cp'=C5Me4(SiMe3)]. The core of the molecule consists of a tetranuclear cluster with one interstitial, one face-bridging, and six edge-bridging hydride ligands. The compound was prepared via the reaction of YCp'(CH2SiMe3)2(THF) with gaseous H2. Neutron data were collected on a 4 mm3 crystal at the Quasi-Laue diffractometer VIVALDI at ILL (Grenoble)1a and on an 8 mm3 crystal at the SXD diffractometer at ISIS (Didcot). The final agreement factor is R = 8.9% for 4171 reflections. The existence of 4-coordinate hydrogen now completes the series of high-connectivity hydride ligands located in the interstitial cavities of molecular cluster complexes. We had previously reported the existence of 6-coordinate hydrogen in the octahedral cavity of [HCo6(CO)15]- in 1979, and 5-coordinate hydrogen in the square pyramidal cavities of [H2Rh13(CO)24]3- in 1997, also via single-crystal neutron analyses.
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http://dx.doi.org/10.1021/ja076520cDOI Listing
March 2008

Syntheses and structures of asymmetric Bis(silyl) niobocene hydrides.

Inorg Chem 2007 Jan;46(1):147-60

Chemistry Department, Moscow State University, Vorob'evy Gory, 119992 Moscow, Russia.

This paper deals with the preparation and structural investigation of asymmetric bis(silyl) niobocene hydrides, Cp2Nb(SiHMe2)(H)(SiXMe2) (2; X = F (a), Cl (b), Br (c), I (d)) and Cp2Nb(SiXMe2)(H)(SiYMe2) (X,Y= F-I; X not equal Y). Complexes 2a-d were prepared by selective electrophilic activation of the Si-H bond in Cp2Nb(SiHMe2)2(H). The Cp2Nb(SiXMe2)(H)(SiYMe2) complexes were prepared by electrophilic activation of the Si-H bond in 2a-d and, in some cases, by electrophilic exchange of the X halides in Cp2Nb(SiXMe2)2(H) (1) for other halides, Y. The structures of complexes 2b and 2c have been studied by X-ray and neutron diffraction (ND). The ND results unequivocally established that the hydride ligand in 2c is shifted toward the SiBrMe2 ligand and that in 2b is positioned symmetrically between two nonequivalent silyl groups, with the H...SiClMe2 distance being shorter because of the shorter Nb-SiClMe2 bond length. Analysis of the X-ray structures of complexes 2a-d and complexes Cp2Nb(SiXMe2)(H)(SiYMe2) shows that the largest structural distortions are observed for the silyl groups substituted by heavy halogen atoms. These trends are rationalized in terms of stronger interligand hypervalent interactions (IHI) Nb-H...Si-X for heavy atoms X from Group 7.
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http://dx.doi.org/10.1021/ic061314bDOI Listing
January 2007

Molecular motion in crystalline naphthalene: analysis of multi-temperature X-ray and neutron diffraction data.

J Phys Chem A 2006 Oct;110(41):11695-703

European Synchrotron Radiation Facility, BP220, F-38043 Grenoble, France.

Single crystals of h8-naphthalene have been examined by both X-ray and neutron diffraction over a range of temperatures from 5 to 295 K. The aim of this case study was to measure the anisotropic displacement parameters (ADPs) of carbons and hydrogens and to interpret them using the model of thermal motion proposed by Bürgi and Capelli (Acta Cryst. 2000, A56, 403). The traditional rigid-body analysis expresses the low-frequency motions in terms of molecular translations and librations only, whereas the Bürgi-Capelli treatment also includes the high-frequency internal modes. We show that a considerable improvement occurs by representing the internal modes by a single second-rank tensor and that a further improvement follows by including a Grüneisen parameter to account for volume thermal expansion. By applying the treatment to multi-temperature diffraction data, there is a considerable reduction in the ratio of number of adjustable parameters/number of independent observations.
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http://dx.doi.org/10.1021/jp062953aDOI Listing
October 2006

A neutron diffraction study of [OsClH3(PPh3)3]: a complex containing a highly "stretched" dihydrogen ligand.

Angew Chem Int Ed Engl 2005 Nov;44(44):7227-30

Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA.

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http://dx.doi.org/10.1002/anie.200502297DOI Listing
November 2005

Cooperative hydrogen-bonding effects in a water square: a single-crystal neutron and partial atomic charges and hardness analysis study.

J Am Chem Soc 2005 Aug;127(31):11063-74

Department of Chemistry, University of Durham, South Road, Durham DH1 3LE, U.K.

Four isomorphous complexes of formula [M(L)(4)(H(2)O)(2)]SO(4).2H(2)O (M = Co, 1a; Ni, 1b; Cu, 1c; Zn, 1d) have been isolated and characterized by single-crystal X-ray diffraction and neutron diffraction using the quasi-Laue diffractometer VIVALDI at the Institut Laue-Langevin as well as by thermogravimetric analysis. The structures contain a discrete, strongly hydrogen-bonded water tetramer which causes a significant distortion of the metal coordination sphere in each case. Partial atomic charges and hardness analysis (PACHA) calculations reveal that the shortest hydrogen bonds are not the strongest in this constrained, cyclic solid-state structure and show that the distortion at the metal center is caused by the drive to maintain the integrity of the water tetramer. The system undergoes a disorder-order transition on slow cooling that provides insight into the nature of communication between water squares.
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http://dx.doi.org/10.1021/ja052081aDOI Listing
August 2005

Nonclassical vs classical metal...H3C-C interactions: accurate characterization of a 14-electron ruthenium(II) system by neutron diffraction, database analysis, solution dynamics, and DFT studies.

J Am Chem Soc 2004 May;126(17):5549-62

Dipartimento di Scienze e Tecnologie Chimiche, Università di Udine, Via Cotonificio 108, I-33100 Udine, Italy.

A neutron diffraction study of the complex RuCl(2)[PPh(2)(2,6-Me(2)C(6)H(3))](2) (1) defines the precise nature of the delta agostic interactions between the unsaturated metal center and two o-methyl groups of the xylyl substituents. The CH(3) carbon atoms lie in the RuP(2) equatorial plane with Ru...C distances of 2.637(7) and 2.668(6) A, whereas four short Ru.H distances (from 2.113(11) to 2.507(11) A) indicate that each methyl group interacts with two C-H bonds. A survey of the X-ray structures with beta, gamma, delta, and epsilon M...H(3)C-C moieties (no neutron data have been previously reported) shows a linear correlation between the angle M.C-C and the torsion of the methyl group about the C-C bond. Thus, the agostic interactions span the range between the classical (M...eta(2)-HC) and the nonclassical (M...eta(3)-H(2)C) types. A solution study of 1 shows intramolecular rearrangement of each xylyl substituent that equilibrates the environments of its two ortho CH(3) groups. Activation parameters, evaluated from the analysis of (1)H NMR line shape as a function of temperature, are Delta H(++) = 9.6 +/- 0.2 kcal mol(-1) with Delta S(++) = -15.4 +/- 0.7 eu (CDCl(3)). The related 14-electron complexes RuX(2)[PPh(2)(2,6-Me(2)C(6)H(3))](2) (X = I, 2; NCO, 3), prepared from 1 and NaX, show a similar dynamic process in solution, with the iodo derivative displaying the most hindered rotation of the xylyl group. A DFT optimization of the complex RuCl(2)[PH(2)(2,6-Me(2)C(6)H(3))](2) (1a) reproduces well the nonclassical Ru...eta(3)-H(2)C agostic mode, whereas the classical Ru...eta(2)-HC one corresponds to a transition state 1b, destabilized by 3.4 kcal mol(-1). A similar barrier (ca. 3.8 kcal mol(-1)) is calculated for the xylyl rotation in the further simplified model RuCl(2)[PH(2)(2,6-Me(2)C(6)H(3))][PH(2)CH[double bond]CHCH(3)] (1c), the absence of bulky phenyl substituents being largely responsible for the difference with respect to the experimental value. Finally, the MO analysis addresses the intrinsic stability of the 14-electron complex RuCl(2)(PH(3))(2) and, in agostic complexes, accounts for the different interactions between the methyl group and the metal atom in relation to the length of their interconnecting chain.
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http://dx.doi.org/10.1021/ja038986aDOI Listing
May 2004