Molecular Threefold Axis Research Articles

Field- and Temperature-Dependent Paramagnetic Relaxation Enhancements in Co(II) Trispyrazolylmethanes.

A comprehensive field- and temperature-dependent examination of nuclear magnetic resonance paramagnetic relaxation enhancements (PREs) for the constitutive protons of [Co(Tpm)2][BF4]2 is presented. Data for an apically substituted derivative clearly establish that bis-Tpm complexes of Co(II) undergo Jahn-Teller dynamics about the molecular threefold axis. PREs from the parent Tpm complex were used to numerically extract the electron relaxation times (T1e). The Tpm complex showed field-dependent behavior, with an approximately 40% higher activation barrier than the related trispyrazolylborate (Tp) complex, based on fits to the T1e vs T, B0 data. Analysis of the field-dependent line widths revealed a surprisingly large contribution from susceptibility (Curie) relaxation (20-35% at the highest field), and a molecular radius (9.5 Å) that is consistent with a tightly associated counterion slowing rotation in solution. Density functional theory showed a shared vibration that is consistent with the Jahn-Teller and appears proportionately higher in energy in [Co(Tpm)2]2+. Complete active-space self-consistent field calculations support ascribing electron relaxation to enhanced mixing of the two Eg orbital sets that accompanies the tetragonal distortion and the differences in electron correlation times to the higher Jahn-Teller activation barrier in [Co(Tpm)2]2+.

Disordered Aragonite: The New High-Pressure, High-Temperature Phase of CaCO3

Phases of CaCO3 stabilized at high pressures and temperatures are the potential agents of the global carbon cycle, transferring oxidized carbon in deep Earth’s interiors and thus are of special interest for the Earth sciences. Here, we report finding of the new phase, named disarag, which is dynamically disordered aragonite with freely rotating CO3 groups, similar to that in the CaCO3-V phase with a calcite-like structure. Disarag has a stability field expanding from 3 to 10 GPa and from 1600 to 2000 K. Consideration of twinned structure enlarges this field, decreasing the transition temperature from aragonite to disarag at 100–300 K. At P–T parameters corresponding to the transition from aragonite to disarag, the marked disappearance of the diffraction peaks is observed in in situ experiments. We show that, among known phases of CaCO3, disarag is the best candidate for the explanation of this reconstruction of diffraction pattern. Also, for the first time, using ab initio molecular dynamics technique, we determine equilibrium curves between calcite and its disordered phases CaCO3-IV and CaCO3-V. We show that the transitions of alkaline-earth carbonates CaCO3, SrCO3, and BaCO3 to the disordered states start when the critical angle of librations of the CO3 group about the axis perpendicular to the molecular three-fold axis exceeds 45°. The calcite-like structure of CaCO3 is characterized by more intense librations than the aragonite-like structure of this compound and reaches the critical angle at lower temperatures. As a result, calcite transforms into the disordered state at lower temperatures than aragonite.

4-[(1E)-({[(Benzyl-sulfan-yl)methane-thio-yl]amino}-imino)-meth-yl]benzene-1,3-diol chloro-form hemisolvate: crystal structure, Hirshfeld surface analysis and computational study.

The title hydrazine carbodi-thio-ate chloro-form hemisolvate, 2C15H14N2O2S2·CHCl3, comprises two independent hydrazine carbodi-thio-ate mol-ecules, A and B, and a chloro-form mol-ecule; the latter is statistically disordered about its mol-ecular threefold axis. The common features of the organic mol-ecules include an almost planar, central CN2S2 chromophore [r.m.s. deviation = 0.0203 Å (A) and 0.0080 Å (B)], an E configuration about the imine bond and an intra-molecular hydroxyl-O-H⋯N(imine) hydrogen bond. The major conformational difference between the mol-ecules is seen in the relative dispositions of the phenyl rings as indicated by the values of the dihedral angles between the central plane and phenyl ring of 71.21 (6)° (A) and 54.73 (7)° (B). Finally, a difference is seen in the disposition of the outer hydroxyl-H atoms, having opposite relative orientations. In the calculated gas-phase structure, the entire mol-ecule is planar with the exception of the perpendicular phenyl ring. In the mol-ecular packing, the A and B mol-ecules assemble into a two-mol-ecule aggregate via N-H⋯S hydrogen bonds and eight-membered {⋯HNCS}2 synthons. The dimeric assemblies are connected into supra-molecular chains via hydroxyl-O-H⋯O(hydrox-yl) hydrogen bonds and these are linked into a double-chain through hy-droxy-O-H⋯π(phen-yl) inter-actions. The double-chains are connected into a three-dimensional architecture through phenyl-C-H⋯O(hydrox-yl) and phenyl-C-H⋯π(phen-yl) inter-actions. The overall assembly defines columns along the a-axis direction in which reside the chloro-form mol-ecules, which are stabilized by chloro-form-methine-C-H⋯S(thione) and phenyl-C-H⋯Cl contacts. The analysis of the calculated Hirshfeld surfaces, non-covalent inter-action plots and inter-action energies confirm the importance of the above-mentioned inter-actions, but also of cooperative, non-standard inter-actions such as π(benzene)⋯π(hydrogen-bond-mediated-ring) contacts.

A study of the pyramidality index in tris(2,4,6-triisopropylphenyl)phosphonium perchlorate

The title compound, C45H70P(+)·ClO4(-) or [Tripp3PH(+)][ClO4(-)], was produced from the perchlorate salt of the corresponding radical cation Tripp3P(·+) through very slow H-atom abstraction reactions in a solution of 1,2-dimethoxyethane (Tripp is 2,4,6-triisopropylphenyl). The H atom on the P atom was located in a difference map and was freely refined with an isotropic displacement consistent with full occupancy [P-H = 1.37 (3) Å]. It is the most sterically congested triarylphosphonium salt yet to be reported and has a `propeller' arrangement of the three Tripp groups around the P atom, with the protonation site located along the molecular threefold axis. There are short contacts between the flanking isopropyl methine H atoms and the P atom [P···H = 1.99 (2)-2.17 (2) Å]. The sum of the angles around the P atom [Σ(C-P-C) = 349.9 (6)°] is a convenient index of pyramidality for tricoordinate centres. This value is significantly larger than in analogous Mes3PH(+) salts (Mes is mesityl or 2,4,6-trimethylphenyl), for which the average of the three reported structures in the literature is Σ(C-P-C) = 345.3 (6)°. For comparison, in the ubiquitous Ph3PH(+) salts, this parameter has a typical average value of only 333.3 (9)°. The value of Σ(C-P-C) in the title compound is midway between that of the neutral phosphane Tripp3P [334.4 (6)°] and the phosphoniumyl radical cation Tripp3P(·+) [359.8 (2)°]. This geometrical feature provides additional support for the assignment as a phosphonium salt.

Ion Access Pathway to the Transmembrane Pore in P2X Receptors

P2X receptors are ATP-gated channels that mediate cation influx to evoke action potentials or trigger intracellular signaling, important in sensory signal transmission and inflammatory responses. However, the molecular mechanism of how cations penetrate the extracellular region of the receptor and access the transmembrane pore is unknown. Examination of the closed state crystal structure predicts two potential pathways: i) three fenestrations located above the membrane (lateral pathways) and ii) the central void along the molecular three-fold axis of symmetry (central pathway).

Identifying the Ion Access Pathway to the Transmembrane Pore in P2X Receptors

P2X receptors are trimeric ion channels activated by extracellular ATP. Upon activation, P2X receptors promote inward current of cations to evoke action potentials or trigger calcium mediated signaling that are important for pain sensing, inflammation, and the synaptic transmission. However, the molecular mechanism of how extracellular ions access the transmembrane pore of P2X receptors is unknown. According to the zebrafish P2X4 crystal structure in the closed state, extracellular ions appear to be readily accessible to the pore through three identical fenestrations located right above the membrane leaflet (lateral pathway). In addition, ions may access the pore through a second possible pathway that runs through the central voids along the molecular three-fold axis of symmetry (central pathway). While this pathway is hypothetical, as the constrictions flanking the central voids are too narrow for hydrated ions to pass (∼2.3 Å), agonist binding may expand these constrictions to enable ions to access the transmembrane pore. We have begun to explore the pathway ions use to move through the extracellular domain to enter the pore by inserting cysteine residues into rat P2X2 receptor channels and measuring reaction rates with a range of thiol-reactive reagents and ions. We found that MTSEA-Texas Red (MW=∼750) can access T336 in the transmembrane pore with an apparently fast modification rate when the channel is open. These results suggest a large access pathway exists between the extracellular solution and the transmembrane pore, consistent with the fenestrations observed in the crystal structure. We are currently testing whether reagents of various size may also move through the central pathway.

Crystal structure of the top domain of African horse sickness virus VP7: comparisons with bluetongue virus VP7

The baculovirus-expressed core protein VP7 of African horse sickness virus serotype 4 (AHSV-4) has been purified to homogeneity and crystallized in the presence of 2.8 M urea. The X-ray structure has been solved to a 2.3-Angstroms (1 Angstrom = 0.1 nm) resolution with an Rfactor of 19.8%. The structure of AHSV VP7 reveals that during crystallization, the two-domain protein is cleaved and only the top domain remains. A similar problem was encountered previously with bluetongue virus (BTV) VP7 (whose structure has been reported), showing that the connections between the top and the bottom domains are rather weak for these two distinct orbiviruses. The top domains of both BTV and AHSV VP7 are trimeric and structurally very similar. The electron density maps show that they both possess an extra electron density feature along their molecular threefold axes, which is most likely due to an unidentified ion. The characteristics of the molecular surface of BTV and AHSV VP7 suggest why AHSV VP7 is much less soluble than BTV VP7 and indicate the possibility of attachment to the cell via attachment of an Arg-Gly-Asp (RGD) motif in the top domain of VP7 to a cellular integrin for both of these orbiviruses.

Determination by electron diffraction of the molecular structures of chloro- and bromo-tri(trimethylsilyl)methane in the gas phase

The molecular structures of chloro- and bromo-tris (trimethylsilyl)methane in the gas phase have been determined by electron diffraction. Both molecules have inner Si–C bonds which are longer than normal and wide Si–C–Si angles. Principal parameters (ra) for CCl (SiMe3)3, with estimated standard deviations in parentheses, are r(C–Cl) 182.3 (15) pm, r(Si–Cinner) 193.9(6) pm, r(Si–Couter) 188.2(2) pm, and angles Cl–C–Si 102.7(5)° and Couter–Si–Couter 109.6(4)°. The three trimethylsilyl groups are twisted 14.6(7)° from the staggered positions, and tilted 1.3(6)° away from the molecular three-fold axis. For CBr(SiMe3)3 the major parameters are r(C–Br) 191.1(35) pm, r(Si–Cinner) 195.4(15) pm, r(Si–Couter) 187.7(3) pm, Br–C–Si 106.5(6)° and Couter–Si–Couter 109.3(5)°. The trimethylsilyl groupos are twisted 13.5(7)° from the stagtgered positions, but the tilt angle of these groups could not be determinded.

Molecular dynamics of a plastic crystal with two types of orientational disorder: Static and dynamic properties of plastic bicyclooctane

A molecular dynamics simulation of a realistic model of bicyclo-octane [HC(CH2–CH2)3CH] in its plastic phase has been performed at three different temperatures. The interactions between the molecules of the simulated system are calculated with phenomenological exp-6 additive atom–atom potentials. The molecules are considered rigid and their equations of motion are integrated using a method of constraints. A special attention is given to the problem of the C–H bond value. The static analysis of the molecular dynamics (MD) results yields a clear description of two types of orientational order: It confirms the experimental results about the equipartition of the molecular threefold axes around the eight 〈111〉 crystallographic axes and it furthermore unambiguously shows the existence of six preferred orientations for the orientational order of the molecules around their threefold axes where a previous experimental work concluded in favor of a quasifree rotation. The mean-square displacement amplitudes of the molecular centers of mass reveal that our simulation model is not impeded by the abnormal behavior of the exp-6 potentials at small interactive distances. From a dynamical point of view, the molecular dynamics scheme clearly shows that the jumps are not instantaneous and are slightly more diverse than previously assumed. In order to achieve a precise description of these jumps, we propose to make a conceptual distinction between the mean residence times and the correlation times. By contrast with a former MD simulation, our model gives two sets of distinct characteristic times which perfectly agree with the experimentally deduced values. Given the simplifying assumptions entering the experimental models, the quality of this latter agreement also shows a certain lack of sensitivity vis ā vis the exact nature of the underlying microscopic mechanisms. We also examined the ability of our model to simulate the behavior of a monovacancy. We found the influence of such a defect on its immediate neighborhood to be very small even when considering the nature of the complex orientational (dis)order.

Thermally stimulated depolarisation study of structural disorder in iodoform single crystals

Thermally stimulated depolarisation (TSD) and thermally stimulated polarisation (TSP) spectra have been measured for single-crystalline samples of iodoform. The spectra show a pronounced peak at c. 270K whose behaviour is consistent with an assumption that iodoform molecules can exhibit jumps between two orientations: that with the molecular threefold axis parallel to the crystal sixfold axis and that with the molecular axis antiparallel to the crystal axis. This dipolar motion seems to be well described by a simple Debye-like expression and the Arrhenium temperature dependence of the relaxation time seems to hold. The activation energy is c 0.69 eV and the frequency factor is c. 3*1010 s-1. It is concluded that the dipolar motions become frozen on lowering temperature but no order-disorder phase transition is present due to kinetic reasons.

Dynamical properties of 1-cyanoadamantane in the disordered phase

Coherent inelastic neutron scattering has been used to obtain the dispersion curves of 1-cyanoadamantane (C10D15C identical to N) at room temperature (disordered phase). Nearly complete dispersion curves of the librational motion (librons) have been measured. A phenomenological model is used to fit these dispersion curves. For a more general Q value the structure of the rotational scattering function contains three components: an elastic peak, a quasi-elastic peak and a damped oscillator corresponding to the librational mode. The authors show that the behaviour of the elastic intensity can be connected with the static scattering S(Q) due to the correlated reorientation of the molecular threefold axis (the tumbling motion) between the different (100) cubic directions.

A gas-phase electron diffraction study of the molecular structure of the sterically strained molecule tris(trimethylsilyl)methane, HC(SiMe3)3

The molecular structure of the sterically overcrowded molecule tris(trimethylsilyl)-methane has been studied using gas-phase electron diffraction data collected on the Balzers KDG2 instrument at UMEST. The diffraction data are compatible with a single conformer of point group C3 and local three-fold symmetry at the -CH3 and -SiMe3 groups. The three-fold axes of the —SLMe3 groups are inclined at 99.3(3)° to the molecular three-fold axis. The molecular overcrowding also leads to a slight lengthening of the central Si-C bonds (1.888(6)Å) compared with the Si-Me bonds (1.873(2)Å), and a deviation of the torsional angles from the values typifying staggered conformations. The torsional angle for H*CSiMe is 80.5(3)° (where H* denotes the unique H atom) and that for the methyl groups is −23(4)° (mean from preferred refinements). The three-fold axes of the -SiMe3 groups may deviate slightly (1.9(6)° ) from the line of the H*C-SiMe3 bonds. Other structural parameters are C-H = 1.114(2)Å, ∠CSiMe = 112.8° (average), and within SiMe3 groups: ∠MeSiMe = 105.8(3)°, ∠SiCH = 112.1(3)° and ∠HCH = 106.7(3)°.

An N.M.R. study of molecular motions in the plastic phases of 1-cyanoadamantane

Molecular motions have been studied in a powder sample of 1-cyanoadamantane, by using pulsed and continuous wave techniques, from 90 K to 480 K. Two very different types of motions are discussed: a fast uniaxial rotation around the three-fold axis of the molecule, and a slow isotropic reorientation of this molecular three-fold axis between the six [100] directions of the cubic lattice.

A nuclear magnetic resonance study of some solid alkylamines and their clathrate deuterates

A proton second-moment and spin-lattice relaxation data are reported on solid N,N-d 2 -isopropylamine, N,N-d 2 -isopropylamine clathrate deuterate, solid trimethylamine, and trimethylamine clathrate deuterate. The second-moment data on isopropylamine indicate that a nearly rigid structure exists at 77 K, and that a hindered rotation of both the methyl groups takes place around 165 K. The barrier hindering the methyl group rotation, as estimated from nonexponential spin-lattice relaxation data, is found to be 3.50 kcal mole −1 with τ c = (1.78 ± 0.22) × 10 −13, exp (3.50 ± 0.07)/ RT. In N-N-d 2 -isopropylamine deuterate there is, in addition to the methyl group rotation, a rotation of the molecule arond its pseudo threefold axis near 212 K. Measurements of T 1 on this deuterate exhibited a single broad minimum of 45 ± 1 msec in the temperature range of 170 to 178 K which we assign as a rotation of the isopropylamine molecule around its pseudo threefold axis. The activation energy associated with the pseudo-threefold-axis rotation was found to be > 1.63 ± 0.03 kcal mole −1. In solid trimethylamine there was found, in addition to methyl group reorientation, a reorientation of the molecule around its molecular threefold axis from ∼145 to 157 K. The barrier associated with methyl group reorientation in its upper limit was found from T 1 measurements to be 5.75 ± 0.14 kcal mole −1. The second-moment data on the trimethylamine clathrate deuterate gave a second moment of 8.46 ± 0.76 G 2 at 77 K (all three methyl groups rotating), 1.42 ± 0.02 G 2 (methyl plus rotation around the molecular threefold axis), and a plateau value of 0.6 G 2. Only a single broad minimum was noticed in the T 1 measurements, and this was assigned to rotation of methyl groups around the threefold axis of the whole trimethylamine molecule. The activation energy for this rotation was found to be ⩾2.90 ± 0.13 kcal mole −1.