Threefold Axis Research Articles

Crystal structures, spectroscopic characterization, and Hirshfeld surface analyses of three constrained cyclam compounds with perchlorate counteranions

Three constrained cyclam compounds with perchlorate anions, 3,14-diethyl-2,6,13,17-diazadiazoniatricyclo[16.4.0.07,12]docosa-2,13-diene diperchlorate [H2L1](ClO4)2 (1), 3,14-diethyl-2,13-diaza-6,17-diazoniatricyclo(16.4.0.07,12)docosane [H2L2](ClO4)2 (2), and bis(3,14-diethyl-2,6,13,17-tetraazatricyclo(16.4.0.07,12)docosane) di(sodium perchlorate) (L2)2·2NaClO4 (3), have been characterized by elemental analysis and single-crystal X-ray diffraction studies, as well as IR, Raman, and NMR spectroscopy. The asymmetric units of compounds 1 and 2 contain one half dication of [H2L1]2+ or [H2L2]2+ and one perchlorate anion, whereas the asymmetric unit of compound 3 comprises two free L2 molecules, two sodium cations, and two perchlorate anions. The ClO4− ions in 1 and 2 are doubly disordered about a noncrystallographic local threefold axis, and the two ClO4− ions in 3 are fully occupied, although distorted by interactions with adjacent Na+ ions and ligand NH groups. In 1 and 2, the crystals are stabilized by 3D networks of NH⋯O and NH⋯N hydrogen bonds, whereas the crystal structure of 3 is maintained by NH⋯N hydrogen bonds and Na+⋯O/N ion-dipole interactions. Hirshfeld surface analyses with 2D fingerprint plots reveal that the H⋯H and O⋯H interactions are the main intermolecular interactions.

Bis(nitrilotriacetamide-κ4 N,O,O′,O′′)silver(I) nitrate

In the centrosymmetric cation of the title compound, [Ag(C6H12N4O3)2]NO3, the AgI ion, lying on a threefold rotoinversion axis, is coordinated by two N atoms and six O atoms from two nitrilotriacetamide ligands, forming a distorted dodecahedral environment. In the crystal, cations and anions are linked through N—H...O hydrogen-bonding interactions, leading to a three-dimensional network structure.

Pinning, rotation, and metastability of BiFeO3 cycloidal domains in a magnetic field

Earlier models for the room-temperature multiferroic BiFeO3 implicitly assumed that a very strong anisotropy restricts the domain wavevectors q to the three-fold symmetric axis normal to the static polarization P. However, recent measurements demonstrate that the domain wavevectors rotate so that q rotates within the hexagonal plane normal to P away from the field orientation m. We show that the previously neglected three-fold anisotropy K3 restricts the wavevectors to lie along the three-fold axis in zero field. For m along a three-fold axis, the domain with q parallel to m remains metastable below Bc1 = 7 T. Due to the pinning of domains by non-magnetic impurities, the wavevectors of the other two domains start to rotate away from m above 5.6 T, when the component of the torque t = M x B along P exceeds a threshold value tpin. Since t =0 when m is perpendicular to q, the wavevectors of those domains never become completely perpendicular to the magnetic field. Our results explain recent measurements of the critical field as a function of field orientation, small-angle neutron scattering measurements of the wavevectors, as well as spectroscopic measurements with m along a three-fold axis.

Nonpolar-to-Polar Phase Transition of a Chiral Ionic Plastic Crystal and Switch of the Rotation Symmetry.

The synthesis of a new ionic plastic crystal, tetraethylammonium-d20 d-10-camphorsulfonate, is reported. The crystal has three solid phases, the structures of which were determined by single-crystal X-ray diffraction (XRD). XRD analysis revealed a phase transition from nonpolar space group P21212 to polar space group P21 with increasing temperature. The dynamics of the d-10-camphorsulfonate anion and the tetraethylammonium-d20 cation was investigated by variable-temperature 1H and 2H solid-state NMR spectroscopy. The anion showed swing motion in high-temperature phases, which is in good agreement with the disorder observed in XRD analysis. The cation showed uniaxial rotation even in the low-temperature phase. The rotation axis of the tetrahedral structure showed a transition from the two-fold axis to the three-fold axis with the phase transition.

Poly[bis(trimethylammonium) [hexa-μ-cyanido-cadmium(II)dicopper(I)

The title compound, {(C3H10N)2[CdCu2(CN)6]}n, has been synthesized as an alternative to the high-emitting complexes containing more expensive metals. The CN−ligands make linkages between the CuIand CdIIions to form the coordination polymer, [CdCu2(CN)6]n2−, which is a three-dimensional framework classified as pyrite net (pyr). The net has a void space for accommodating a trimethylammonium ion located on a threefold rotation axis. The CdIIion lies on a special position with site symmetry -3 and is octahedrally coordinated by six N atoms. The CuIion is located on a threefold rotation axis and has a trigonal-planar coordination geometry formed by three C atoms. In the three-dimensional net, two CuIions are arranged closely [Cu...Cu = 3.9095 (5) Å], but the distance is not short enough to suggest a CuI–CuIinteraction. The crystal studied was a merohedral twin (twin operation 2[101]), the refined component ratio being 0.9202 (7):0.0798 (7). A powder of the title compound shows strong luminescence with an emission maximum at 509 nm and a quantum yield of 98% at room temperature.

A Polyselenide with a Novel Se78– Unit: the Structure of Sr19–xPbxGe11Se44 with x = 5.0 and 6.4

An unprecedented, planar Se78– unit with a threefold rotation axis was discovered in the new polyselenide Sr19–xPbxGe11Se44. Sr12.6Pb6.4Ge11Se44 crystallizes in the non‐centrosymmetric hexagonal space group P63 with unit cell dimensions of a = b = 19.9867(2) Å, c = 12.0546(1) Å, V = 4170.28(7) Å3, with two formula units per cell. Its structure contains isolated [GeSe4] tetrahedra, [Ge2Se7] dimers, and a novel, planar propeller‐shaped Se78– unit. The latter is unprecedented, but reminiscent of the isoelectronic pyramidal Se78– and I7– units. It consists of a central Se atom, to which three Se2 pairs with a short Se–Se bond are attached through a longer Se–Se distance, resulting in a central Se atom featuring 120° bond angles, and bridging Se atoms featuring an approximately linear coordination with a 179° bond angle. It can thus be written as [Se(Se2)3]8–. We characterized this unit using Gaussian calculations in comparison to the pyramidal Se78– unit, which may be described also as [Se(Se2)3]8–. The solid‐state material is a black semiconductor with an optical band‐gap of 1.8 eV, which supports the assignment of this charge.

A new structural arrangement in proteins involving lysine NH3+ group and carbonyl

Screening of the Protein Data Bank led to identification of a recurring structural motif where lysine NH3+ group interacts with backbone carbonyl. This interaction is characterized by linear atom arrangement, with carbonyl O atom positioned on the three-fold symmetry axis of the NH3+ group (angle Cε-Nζ-O close to 180°, distance Nζ-O ca. 2.7-3.0 Å). Typically, this linear arrangement coexists with three regular hydrogen bonds formed by lysine NH3+ group (angle Cε-Nζ-acceptor atom close to 109°, distance Nζ-acceptor atom ca. 2.7-3.0 Å). Our DFT calculations using polarizable continuum environment suggest that this newly identified linear interaction makes an appreciable contribution to protein’s energy balance, up to 2 kcal/mol. In the context of protein structure, linear interactions play a role in capping the C-termini of α-helices and 310-helices. Of note, linear interaction involving conserved lysine is consistently found in the P-loop of numerous NTPase domains, where it stabilizes the substrate-binding conformation of the P-loop. Linear interaction NH3+ – carbonyl represents an interesting example of ion-dipole interactions that has so far received little attention compared to ion-ion interactions (salt bridges) and dipole-dipole interactions (hydrogen bonds), but nevertheless represents a distinctive element of protein architecture.

DFT, QTAIM, and NBO studies on the trimeric interactions in the protrusion domain of a piscine betanodavirus

Crystal structure of the protrusion domain (P-domain) of the grouper nervous necrosis virus (GNNV) shows the presence of three-fold trimeric protrusions with two asymmetrical calcium cations along the non-crystallographic three-fold axis. The trimeric interaction natures of the interacting residues and the calcium cations with the neighboring residues within the trimeric interface have been studied by the quantum theory of atoms in molecules (QTAIM) and natural bond orbital (NBO) analyses in the framework of the density-functional theory (DFT) approach. The results revealed that residues Leu259, Val274, Trp280, and Gln322 of subunit A, Arg261, Asp275, Ala277, and Gln322 of subunit B, Leu259, Asp260, Arg261, Ala277, Val278, and Leu324 of subunit C are the main residues involved in the trimeric interactions. Charge-dipole, dipole-dipole, and hydrogen bonding interactions make the significant contributions to these trimeric interactions. Among different interacting residues within trimeric interface, residue pair Arg261 B-Leu259C forms the strongest hydrogen bond inside the interface between subunits B and C. It was also found that calcium cations interact with residues Asp273, Val274, and Asp275 of subunits A, B, and C through charge-charge and charge transfer interactions.

The microscopic model of BiFeO3

Many years and great effort have been spent constructing the microscopic model for the room temperature multiferroic BiFeO3. However, earlier models implicitly assumed that the cycloidal wavevector q was confined to one of the three-fold symmetric axes in the hexagonal plane normal to the electric polarization. Because recent measurements indicate that q can be rotated by a magnetic field, it is essential to properly treat the anisotropy that confines q at low fields. We propose that the anisotropy energy −K3S6sin6θcos6ϕ confines the wavevectors q to the three-fold axis ϕ=0 and ±2π/3 within the hexagonal plane with θ=π/2.

An Ideal C3-Symmetric Sulfate Complex: Molecular Recognition of Oxoanions by m-Nitrophenyl- and Pentafluorophenyl-Functionalized Hexaurea Receptors.

The anion-binding properties of two tripodal-based hexaureas appended with the m-nitrophenyl (1) and pentafluorophenyl (2) groups have been studied both experimentally and theoretically, showing strong affinities for sulfate over other inorganic oxoanions such as hydrogen sulfate, dihydrogen phosphate, bicarbonate, nitrate, and perchlorate. The structural analysis of the sulfate complex with 1 reveals that the receptor organizes all urea-binding sites toward the cavity at precise orientations around a tetrahedral sulfate anion to form an ideal C3-symmetric sulfate complex that is stabilized by 12 hydrogen-bonding interactions. The receptor and the encapsulated sulfate are located on the threefold axis passing through the bridgehead nitrogen of 1 and the sulfur atom of the anionic guest. The high-level density functional theory calculations support the crystallographic results, demonstrating that the C3-symmetric conformation of the sulfate complex is achieved due to the complementary NH···O between the receptor and sulfate.

Study of the specific features of single-crystal boron microstructure

A complex study of the structure of β-boron single crystal grown by the floating-zone method, with sizes significantly exceeding the analogs known in the literature, has been performed. The study includes X-ray diffraction analysis and X-ray diffractometry (measurement of pole figures and rocking curves), performed on both laboratory and synchrotron sources; atomic-resolution scanning transmission electron microscopy with spherical aberration correction; and energy-dispersive microanalysis. X-ray diffraction analysis using synchrotron radiation has been used to refine the β-boron structure and find impurity Si atoms. The relative variations in the unit-cell parameters a and c for the crystal bulk are found to be δa/a ≈ 0.4 and δc/c ≈ 0.1%. X-ray diffractometry has revealed that the single-crystal growth axis coincides with the [\(2\bar 2013\)] crystallographic axis and makes an angle of 21.12° with the [0001] threefold axis. Electron microscopy data have confirmed that the sample under study is a β-boron crystal, which may contain 0.3–0.4 at % Si as an impurity. Planar defects (stacking faults and dislocations) are found. The results of additional measurements of the temperature dependence of the thermal conductivity of the crystal in the range of 50–300 K are indicative of its high structural quality.

The structure of the Pfp1 protease from the hyperthermophilic archaeon Thermococcus thioreducens in two crystal forms.

The Pfp1 protease, a cysteine protease of unknown specificity from the hyperthermophilic archaeon Thermococcus thioreducens, was crystallized in two distinctive crystal forms: from concentrated citrate in one case and PEG in the other. X-ray data were collected from both crystal forms at room temperature to about 1.9 Å resolution using a laboratory source and detector, and the structures were solved by molecular replacement using the Pfp1 protease from Pyrococcus horikoshii as the search model. In the T. thioreducens protease structures, Cys18 residues on adjacent molecules in the asymmetric units form intermolecular disulfide bonds, thereby yielding hexamers composed of three cross-linked, quasi-dyad-related dimers with crystallographically exact threefold axes and exhibiting almost exact 32 symmetry. The corresponding residue in P. horikoshii Pfp1 is Tyr18. An individual active site containing Cys100 and His101 also includes a Glu74 residue contributed by a quasi-twofold-related, non-cross-linked subunit. Two catalytic triads are therefore closely juxtaposed about the quasi-twofold axis at the interface of these subunits, and are relatively sequestered within the hexamer cavity. The cysteine in the active site is observed to be oxidized in both of the crystal forms that were studied.

Dead-end complex, lipid interactions and catalytic mechanism of microsomal glutathione transferase 1, an electron crystallography and mutagenesis investigation

Microsomal glutathione transferase 1 (MGST1) is a detoxification enzyme belonging to the Membrane Associated Proteins in Eicosanoid and Glutathione Metabolism (MAPEG) superfamily. Here we have used electron crystallography of two-dimensional crystals in order to determine an atomic model of rat MGST1 in a lipid environment. The model comprises 123 of the 155 amino acid residues, two structured phospholipid molecules, two aliphatic chains and one glutathione (GSH) molecule. The functional unit is a homotrimer centered on the crystallographic three-fold axes of the unit cell. The GSH substrate binds in an extended conformation at the interface between two subunits of the trimer supported by new in vitro mutagenesis data. Mutation of Arginine 130 to alanine resulted in complete loss of activity consistent with a role for Arginine 130 in stabilizing the strongly nucleophilic GSH thiolate required for catalysis. Based on the new model and an electron diffraction data set from crystals soaked with trinitrobenzene, that forms a dead-end Meisenheimer complex with GSH, a difference map was calculated. The map reveals side chain movements opening a cavity that defines the second substrate site.

Piezomagnetism and magnetoelastic memory in uranium dioxide

The thermal and magnetic properties of uranium dioxide, a prime nuclear fuel and thoroughly studied actinide material, remain a long standing puzzle, a result of strong coupling between magnetism and lattice vibrations. The magnetic state of this cubic material is characterized by a 3-k non-collinear antiferromagnetic structure and multidomain Jahn-Teller distortions, likely related to its anisotropic thermal properties. Here we show that single crystals of uranium dioxide subjected to strong magnetic fields along threefold axes in the magnetic state exhibit the abrupt appearance of positive linear magnetostriction, leading to a trigonal distortion. Upon reversal of the field the linear term also reverses sign, a hallmark of piezomagnetism. A switching phenomenon occurs at ±18 T, which persists during subsequent field reversals, demonstrating a robust magneto-elastic memory that makes uranium dioxide the hardest piezomagnet known. A model including a strong magnetic anisotropy, elastic, Zeeman, Heisenberg exchange, and magnetoelastic contributions to the total energy is proposed.

Heterometallic CoII-CoIII-MII alkoxido-bridged heptanuclear motifs (M = Cu, Zn). Syntheses, crystal structures and magnetic properties

Abstract Two new alkoxido-bridged heterometallic complexes of formula [CoIICoIII3CuII3(dea)6(CH3COO)3](ClO4)0.75(CH3COO)1.25 (1) and [CoII2CoIII2ZnII3(tea)2(piv)6(CH3O)2(OH)2(CH3OH)2]·H2O 2 (H2dea = diethanolamine, H3tea = triethanolamine and Hpiv = pivalic acid) have been assembled using aminoalcohol ligands. The cationic core in 1 possesses a threefold crystallographic axis, and it exhibits a set of three copper(II), one cobalt(II) and three cobalt(III) ions arranged as a hexagon of alternating copper(II) and cobalt(III) ions around the central cobalt(II) ion. Each edge of the hexagon is defined by a double alkoxido bridge, the outer one being bis-monodentate with copper(II)-cobalt(III) pair whereas the inner one adopts a tris-monodentate coordination mode linking the Cu(II)-Co(III) pair with the central cobalt(II) ion. The acetate groups act as bidentate ligands towards the copper(II) ions. The intramolecular cobalt(II)-copper(II) separation is 3.157 A. A hexagon of two cobalt(II), two cobalt(II) and two zinc(II) ions distributed along three types of edges with a central zinc(II) ion occurs in 2. A tris-modentate alkoxido bridge is involved in all edges together with another bis-monodentate alkoxido bridge (CoIII-CoII and CoII-ZnII pairs) and a carboxylate-pivalate bridge in the syn-syn conformation. The five coordination at each peripheral zinc(II) ion is completed by a monodentate carboxylate-pivalate ligand whereas a methoxo group allows to achieve the six-coordination at each cobalt(III) ion. The intramolecular cobalt(II)-cobalt(II) separation through the inner zinc(II) ion is 6.309 A. The magnetic properties of 1 and 2 have been investigated in the temperature range 1.9–300 K. The exchange interaction between the six-coordinate cobalt(II) and copper(II) ions through the double alkoxido bridges in 1 and that between the six-coordinate cobalt(II) ions across the diamagnetic zinc(II) ion in 2 are found to be ferromagnetic [J = +5.39(5) (1) and +1.05(2) cm−1 (2)], the accidental orthogonality between the interacting magnetic orbitals accounting for this behaviour in the two cases.

Structural basis for conductance through TRIC cation channels

Mammalian TRICs function as K+-permeable cation channels that provide counter ions for Ca2+ handling in intracellular stores. Here we describe the structures of two prokaryotic homologues, archaeal SaTRIC and bacterial CpTRIC, showing that TRIC channels are symmetrical trimers with transmembrane pores through each protomer. Each pore holds a string of water molecules centred at kinked helices in two inverted-repeat triple-helix bundles (THBs). The pores are locked in a closed state by a hydrogen bond network at the C terminus of the THBs, which is lost when the pores assume an open conformation. The transition between the open and close states seems to be mediated by cation binding to conserved residues along the three-fold axis. Electrophysiology and mutagenesis studies show that prokaryotic TRICs have similar functional properties to those of mammalian TRICs and implicate the three-fold axis in the allosteric regulation of the channel.

Measurement of 15N longitudinal relaxation rates in 15NH4+ spin systems to characterise rotational correlation times and chemical exchange

Many chemical and biological processes rely on the movement of monovalent cations and an understanding of such processes can therefore only be achieved by characterising the dynamics of the involved ions. It has recently been shown that 15N-ammonium can be used as a proxy for potassium to probe potassium binding in bio-molecules such as DNA quadruplexes and enzymes. Moreover, equations have been derived to describe the time-evolution of 15N-based spin density operator elements of 15NH4+ spin systems. Herein NMR pulse sequences are derived to select specific spin density matrix elements of the 15NH4+ spin system and to measure their longitudinal relaxation in order to characterise the rotational correlation time of the 15NH4+ ion as well as report on chemical exchange events of the 15NH4+ ion. Applications to 15NH4+ in acidic aqueous solutions are used to cross-validate the developed pulse sequence while measurements of spin-relaxation rates of 15NH4+ bound to a 41kDa domain of the bacterial Hsp70 homologue DnaK are presented to show the general applicability of the derived pulse sequence. The rotational correlation time obtained for 15N-ammonium bound to DnaK is similar to the correlation time that describes the rotation about the threefold axis of a methyl group. The methodology presented here provides, together with the previous theoretical framework, an important step towards characterising the motional properties of cations in macromolecular systems.

The crystal structure of N5O3 cryptand

The title compound, 1,4,13,22,27-pentaaza-6,9:17,20:29,32-tribenzo-10,16,33-trioxabicyclo [11,11,11] pentatriacontane (C33H45N5O3), is synthesized by [1+1] tripodal condensation of trialdehyde (4,4′,4″-triformyl-triphenoxytriethylamine) with tris(2-aminoethyl)amine (tren) in the presence of La(NO3)3·6H2O as a template, followed by reduction with KBH4. There are six unique molecules in the unit. The molecule has a threefold symmetry axis passing through the bridgehead nitrogen atoms in the structure. As a result, only one strand of the cryptand molecule is present in the asymmetric unit. The structure presents an endoendo conformation, with the distance between the two bridgehead nitrogen atoms of 10.030(8) A.

Multicell model of La3Ga5GeO14 crystal: A new approach to the description of the short-range order of atoms

The multicell model alternative to the model of mixed atomic sites used now is proposed for a single crystal of La3Ga5GeO14 belonging to the langasite family. The multicell consists of four unit cells. In three identical cells of the structure, atoms adapt to the Ge atom occupying one of the two 2d positions on the threefold symmetry axis. In the fourth cell, atoms surround the Ge atom located at the 1a position. The multicell model allows one to study the short-range order of atoms by the methods of classical structure analysis based on Bragg scattering. Four high-resolution data sets measured at 295 and 111.5 K are used in the study. The results are obtained with high relative precision (space group P321, Z = 1; at 295 K a = 8.2020(6) A and c = 5.1065(6) A, R/wR = 0.81/0.73% for 3829 unique ref lections; at 111.5 K a = 8.1939(1) A and c = 5.1022(4) A, R/wR = 0.85/0.76% for 3880 reflections).

(Invited) Dielectric Response and Quantum Motion of Lithium Cations Trapped inside Carbon Cages

Endohedral fullerenes trapping atoms and molecules with magnetic and electric moments have a potential to be used for quantum computing. A C60 fullerene trapping a Li+ cation has an electric monopole moment, and forms a rock-salt-type cubic crystal, [Li@C60](PF6). The dielectric response and quantum motion of the Li+ cations in the crystal at low temperature were revealed by the dielectric and X-ray diffraction measurements [1]. The Li+ cations are moving inside the C60 cages by the hopping and tunneling motion between the potential wells under 20 hexagons above 100 K. The Li+ motion is suppressed to be localized at two equivalent positions on the threefold inversion axis with decreasing temperature below 100 K. The simultaneous occupation of the Li+ cation at the two positions is mainly achieved by the tunneling motion. The hopping motion is slowing down and hindered by the energy barriers between the wells. The tunneling motion is also hindered below T C = 24 K by the antiferroelectric interactions among local electric dipole moments formed between the Li+ cations inside and the PF6 − anions outside the C60 cages. The tunneling motion and intermolecular interaction of the Li+ cation found in [Li@C60](PF6) show that Li+@C60 has a potential to be used as a qubit in a quantum computer using electric dipole moments. [1] S. Aoyagi, A. Tokumitu, K. Sugimoto, H. Okada, N. Hoshino, and T. Akutagawa, J. Phys. Soc. Jpn. 85, 094605 (2016)