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

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.

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

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.

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

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.

Unravelling strong temperature-dependence of JHD in transition metal hydrides: solvation and non-covalent interactions versus temperature-elastic H-H bonds.

A number of transition metal hydrides reveal intriguing temperature-dependent JHD in their deuterated derivatives and possibly the temperature dependent hydrogen-hydrogen distance (r(H-H)) as well. Previously, theoretical studies rationalized JHD and r(H-H) changes in such compounds through a "temperature-elastic" structure model with a significant population of vibrational states in an anharmonic potential. Based on the first variable temperature neutron diffraction study of a relevant complex, (p-H-POCOP)IrH2, observation of its elusive counterpart with longer r(H-H), crystallized as an adduct with C6F5I, and thorough spectroscopic and computational study, we argue that the model involving isomeric species in solution at least in some cases is more relevant. The existence of such isomers is enabled or enhanced by solvation and weak non-covalent interactions with solvent, such as halogen or dihydrogen bonds. "Non-classical" hydrides with r(H-H) ≈ 1.0-1.6 Å are especially sensitive to the above-mentioned factors.

Dynamics and thermodynamics of crystalline polymorphs: α-glycine, analysis of variable-temperature atomic displacement parameters.

Multitemperature synchrotron diffraction data to 0.5 Å resolution in the temperature range 10-298 K and neutron data at 18 K of the α-glycine polymorph have been collected at the KEK photon factory (PF), SPring-8 and the Institut Laue Langevin (ILL) for the study of molecular motion in the crystal and of the associated thermodynamic functions. Atomic displacement parameters (ADPs) of non-H atoms are obtained from refinements based on nonspherical atomic scattering factors (invariom model) to minimize correlation between parameters describing thermal motion and valence electron density. The ADPs in the temperature range 50-298 K from SPring-8 connect smoothly with those from neutron diffraction at 18 K and 288-323 K. The combined ADPs from both sources covering the temperature range 18-323 K are used for a normal-mode analysis in the molecular mean field approximation. The lattice vibration frequencies from the ADP analysis and the internal vibration frequencies from an ONIOM (B3LYP/6-311+G(2d,p):PM3) calculation together with the Einstein, Debye, and Nernst-Lindemann models of heat capacity are used to calculate Cp, Hvib, and Svib values that are in good agreement with those from calorimetry.

The spontaneous self-assembly of a molecular water pipe in 3D space.

The self-assembly and self-organization of water molecules are relevant in many fields of research. When water spontaneously reacts with 2,2,6,6-tetra-methyl-piperidine (TMP) to form colourless and crystalline discrete needles, only in the exact ratio of 2:1, it is important to understand the phenomenon. Single-crystal X-ray and neutron diffraction data have unveiled that TMP self-assembles around columns of water molecules, and as such, the resulting adduct may be described as a series of molecular water pipes.

Thermal neutron cross sections of amino acids from average contributions of functional groups.

The experimental thermal neutron cross sections of the 20 proteinogenic amino acids have been measured over the incident-neutron energy range spanning from 1 meV to 10 keV and data have been interpreted using the multi-phonon expansion based on first-principles calculations. The scattering cross section, dominated by the incoherent inelastic contribution from the hydrogen atoms, can be rationalised in terms of the average contributions of different functional groups, thus neglecting their correlation. These results can be used for modelling the total neutron cross sections of complex organic systems like proteins, muscles, or human tissues from a limited number of starting input functions. This simplification is of crucial importance for fine-tuning of transport simulations used in medical applications, including boron neutron capture therapy as well as secondary neutrons-emission induced during proton therapy. Moreover, the parametrized neutron cross sections allow a better treatment of neutron scattering experiments, providing detailed sample self-attenuation corrections for a variety of biological and soft-matter systems.

Crystal structure of the insect neuropeptide proctolin.

The crystal structure of the neuropeptide proctolin (Arg-Tyr-Leu-Pro-Thr) is reported revealing the solid-state conformation of its molecules and their association in the crystal.

X-ray diffraction data as a source of the vibrational free-energy contribution in polymorphic systems.

In this contribution we attempt to answer a general question: can X-ray diffraction data combined with theoretical computations be a source of information about the thermodynamic properties of a given system? Newly collected sets of high-quality multi-temperature single-crystal X-ray diffraction data and complementary periodic DFT calculations of vibrational frequencies and normal mode vectors at the Γ point on the yellow and white polymorphs of di-methyl 3,6-di-chloro-2,5-di-hydroxy-terephthalate are combined using two different approaches, aiming to obtain thermodynamic properties for the two compounds. The first approach uses low-frequency normal modes extracted from multi-temperature X-ray diffraction data (normal coordinate analysis), while the other uses DFT-calculated low-frequency normal mode in the refinement of the same data (normal mode refinement). Thermodynamic data from the literature [Yang et al. (1989), Acta Cryst. B45, 312-323] and new periodic ab initio DFT supercell calculations are used as a reference point. Both approaches tested in this work capture the most essential features of the systems: the polymorphs are enantiotropically related, with the yellow form being the thermodynamically stable system at low temperature, and the white form at higher temperatures. However, the inferred phase transition temperature varies between different approaches. Thanks to the application of unconventional methods of X-ray data refinement and analysis, it was additionally found that, in the case of the yellow polymorph, anharmonicity is an important issue. By discussing contributions from low- and high-frequency modes to the vibrational entropy and enthalpy, the importance of high-frequency modes is highlighted. The analysis shows that larger anisotropic displacement parameters are not always related to the polymorph with the higher vibrational entropy contribution.

Cooperativity in the Iron(II) Spin-Crossover Compound [Fe(ptz)(6)](PF(6))(2) under the Influence of External Pressure (ptz = 1-n-Propyltetrazole).

The iron(II) spin-crossover compound [Fe(ptz)(6)](PF(6))(2) (ptz = 1-propyltetrazole) crystallizes in the triclinic space group P&onemacr;, with a = 10.6439(4) Å, b = 10.8685(4) Å, c = 11.7014(4) Å, alpha = 75.644(1) degrees, beta = 71.671(1) degrees, gamma = 60.815(1) degrees, and Z = 1. In [Fe(ptz)(6)](PF(6))(2), the thermal spin transition is extremely steep because of cooperative effects of elastic origin. The transition temperature at ambient pressure is 74(1) K. An external pressure of 1 kbar shifts the transition temperature to 102(1) K, corresponding to a stabilization of the low-spin state, which is smaller in volume. The volume difference between the high-spin and the low-spin state, DeltaV degrees (HL), is 24(2) Å(3)/molecule. The interaction constant Gamma, as a measure of cooperativity, is within experimental error independent of external pressure and has a value of 101(5) cm(-)(1). In contrast to the case of the related compound [Fe(ptz)(6)](BF(4))(2) (Decurtins et al. Inorg. Chem.1985, 24, 2174), there is no hysteresis due to a first-order crystallographic phase transition, nor is there a hysteresis induced by external pressure as in the mixed crystal [Zn(1)(-)(x)()Fe(x)()(ptz)(6)](BF(4))(2), x = 0.1 (Jeftic et al. J. Phys.Chem. Solids 1996, 57, 1743). However, in [Fe(ptz)(6)](PF(6))(2), the interaction constant Gamma is found to be very close to the critical value above which a hysteresis solely due to the cooperative effects is expected. In addition, high-spin --> low-spin relaxation measurements were performed under external pressures of up to 1 kbar in the temperature interval between 50 and 60 K. An external pressure of 1 kbar accelerates the high-spin --> low-spin relaxation by 1 order of magnitude.

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

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.

Hirshfeld atom refinement.

Hirshfeld atom refinement (HAR) is a method which determines structural parameters from single-crystal X-ray diffraction data by using an aspherical atom partitioning of tailor-made ab initio quantum mechanical molecular electron densities without any further approximation. Here the original HAR method is extended by implementing an iterative procedure of successive cycles of electron density calculations, Hirshfeld atom scattering factor calculations and structural least-squares refinements, repeated until convergence. The importance of this iterative procedure is illustrated via the example of crystalline ammonia. The new HAR method is then applied to X-ray diffraction data of the dipeptide Gly-l-Ala measured at 12, 50, 100, 150, 220 and 295 K, using Hartree-Fock and BLYP density functional theory electron densities and three different basis sets. All positions and anisotropic displacement parameters (ADPs) are freely refined without constraints or restraints - even those for hydrogen atoms. The results are systematically compared with those from neutron diffraction experiments at the temperatures 12, 50, 150 and 295 K. Although non-hydrogen-atom ADPs differ by up to three combined standard uncertainties (csu's), all other structural parameters agree within less than 2 csu's. Using our best calculations (BLYP/cc-pVTZ, recommended for organic molecules), the accuracy of determining bond lengths involving hydrogen atoms from HAR is better than 0.009 Šfor temperatures of 150 K or below; for hydrogen-atom ADPs it is better than 0.006 Å(2) as judged from the mean absolute X-ray minus neutron differences. These results are among the best ever obtained. Remarkably, the precision of determining bond lengths and ADPs for the hydrogen atoms from the HAR procedure is comparable with that from the neutron measurements - an outcome which is obtained with a routinely achievable resolution of the X-ray data of 0.65 Å.

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

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.

Electron distribution and molecular motion in crystalline benzene: an accurate experimental study combining CCD X-ray data on C6H6 with multitemperature neutron-diffraction results on C6D6.

The electronic properties of the benzene molecule, for example its quadrupole moment and the electric field gradients (EFG's) at the H nuclei, are of fundamental importance in theoretical and experimental chemistry. With this in mind, single-crystal X-ray diffraction data on C(6)H(6) were collected with a charge-coupled device detector at T approximately 110 K. As accurate modelling of the thermal motion in the crystal was regarded as vital, especially for the hydrogen atoms, anisotropic-displacement parameters (ADP's) for the C and H atoms in C(6)H(6) were derived in a straightforward fashion from analysis of the temperature dependence of ADP's for the C and D atoms in C(6)D(6) at 15 K and 123 K obtained by neutron diffraction. Agreement between C-atom ADP's derived from thermal-motion analysis of neutron data and those obtained from multipole refinement by using the X-ray data is extraordinarily good; this gives confidence in the modelling of vibrational motion for the H atoms. The molecular quadrupole moment derived from the total charge density of the molecule in the crystal is (-29.7+/-2.4)x10(-40) C m(2), in excellent agreement with measurements made in the gas phase and in solution. The average deuterium nuclear quadrupole coupling constant (DQCC) derived from EFG tensors at H atoms is 182+/-17 kHz, also in excellent agreement with independent measurements. The strategy employed in this work may be of more general applicability for future accurate electron density studies.