Bond Angles Range Research Articles

Development of charge-transfer interatomic potential for O-Fe-P-Zn systems and its application to tribochemical reactions between ZnDTP-derived tribofilm and iron oxide

ZnDTP (zinc dialkyl-dithiophosphate) is added to lubricants to reduce wear in automobile engines. However, the atomistic understanding of its formation and effect on wear resistance remains incomplete. We have developed a charge-transfer interatomic potential for O-Fe-P-Zn systems to reproduce the tribochemical reactions between zinc phosphate and iron oxide. Since our potential function can handle a mixed system of covalent and ionic bonds, it can successfully reproduce structural changes in phosphate chains at the interface. To increase the potential’s accuracy and robustness, we employ three types of training data: target structures of stable crystalline and molecular structures, standard structures of various crystal structures covering a wide range of coordination numbers and bond angles, and annealed random structures with various compositions. The developed potential well reproduces energies, forces, and atomic charges for O-Fe and O-P-Zn systems as well as polyphosphate chain structures. We then apply this developed potential to ZnDTP-derived tribofilm on iron oxide, revealing that the long-chain phosphate turns into a dense network of short chains under high shear and normal stress conditions. Fe atoms are incorporated into the zinc metaphosphate network, creating a hard Fe/Zn mixed layer. Our results indicate that the short-chain layer acts as an easily sheared lubricant while the Fe/Zn mixed layer prevents wear on the iron oxide substrate.

Local and Bulk Probe of Vanadium-Substituted α-Manganese Oxide (α-KxVyMn8-yO16) Lithium Electrochemistry.

A series of V-substituted α-MnO2 (KxMn8-yVyO16·nH2O, y = 0, 0.2, 0.34, 0.75) samples were successfully synthesized without crystalline or amorphous impurities, as evidenced by X-ray diffraction (XRD) and Raman spectroscopy. Transmission electron microscopy (TEM) revealed a morphological evolution from nanorods to nanoplatelets as V-substitution increased, while electron-energy loss spectroscopy (EELS) confirmed uniform distribution of vanadium within the materials. Rietveld refinement of synchrotron XRD showed an increase in bond lengths and a larger range of bond angles with increasing V-substitution. X-ray absorption spectroscopy (XAS) of the as-prepared materials revealed the V valence to be >4+ and the Mn valence to decrease with increasing V content. Upon electrochemical lithiation, increasing amounts of V were found to preserve the Mn-Mnedge relationship at higher depths of discharge, indicating enhanced structural stability. Electrochemical testing showed the y = 0.75 V-substituted sample to deliver the highest capacity and capacity retention after 50 cycles. The experimental findings were consistent with the predictions of density functional theory (DFT), where the V centers impart structural stability to the manganese oxide framework upon lithiation. The enhanced electrochemistry of the y = 0.75 V-substituted sample is also attributed to its smaller crystallite size in the form of a nanoplatelet morphology, which promotes facile ion access via reduced Li-ion diffusion path lengths.

Crystal structure of bis-[2-(1H-benzimidazol-2-yl-κN 3)aniline-κN]bis-(nitrato-κO)cadmium(II).

In the title compound, [Cd(NO3)2(C13H11N3)2], the CdII atom lies on a twofold rotation axis and is coordinated by four N atoms and two O atoms, provided by two bidentate 2-(1H-benzimidazol-2-yl)aniline ligands, and two nitrato O atoms, forming a distorted octa-hedral geometry [range of bond angles around the Cd atom = 73.82 (2)-106.95 (8)°]. In the ligand, the dihedral angle between the aniline ring and the benzimidazole ring system is 30.43 (7)°. The discrete complex mol-ecule is stabilized by an intra-molecular N-H⋯O hydrogen bond. In the crystal, inter-molecular N-H⋯O hydrogen bonds link the mol-ecules, forming a three-dimensional network.

N-Heterocyclic Germylenes: Structural Characterisation of Some Heavy Analogues of the Ubiquitous N-Heterocyclic Carbenes

The X-ray crystal structures of three N-heterocyclic germylenes (NHGes) have been elucidated including the previously unknown 1,3-bis(2,6-dimethylphenyl)diazagermol-2-ylidene (1). In addition, the X-ray crystal structures of the previously synthesised 1,3-bis(2,4,6-trimethylphenyl)diazagermol-2-ylidene (2) and 1,3-bis(2,6-diisopropylphenyl)diazagermol-2-ylidene (3) are also reported. The discrete molecular structures of compounds 1 to 3 are comparable, with Ge-N bond lengths in the range 1.835-1.875 Å, while the N-Ge-N bond angles range between 83.6 and 85.2°. Compound 2 was compared to the analogous N-heterocyclic carbene species, 1,3-bis(2,4,6-trimethylphenyl)imidazol-2-ylidene (IMes). The major geometrical difference observed, as expected, was the bond angle around the divalent group 14 atom. The N-Ge-N bond angle was 83.6° for compound 2 versus the N-C-N bond angle of 101.4° for IMes. The Sn equivalent of (1), 1,3-bis(2,6-dimethylphenyl)diazastannol-2-ylidene (4), has also been synthesised and its crystal structure is reported here. In order to test their suitability as ligands, compounds 1 to 3 were reacted with a wide range of transition metal complexes. No NHGes containing metal complexes were observed. In all cases the NHGe either degraded or gave no reaction.

Synthesis, characterization, and structural properties of mercury(II), cadmium(II) and zinc(II) tripiperidinophosphine chalcogenide complexes

Reaction of metal chlorides (MCl2) with tripiperidinophosphine chalcogenides (Pip3PE) produces new dimer species (1–6) of the formula [MCl2(Pip3PE)]2 (Pip = piperidinyl; E = S or Se; M = Hg, Cd or Zn). These coordination complexes were characterized by elemental analysis, IR, multinuclear (31P, 113Cd and 199Hg) NMR spectroscopy and single crystal X-ray analysis. Compounds 1–6 exist as centrosymmetric homobimetallic dimers, [M(µ-Cl)Cl(Pip3PE)]2. Each dimer incorporates two µ2-chloro atoms and two terminal MCl bonds. The E atom of Pip3PE forms terminal ME bonds {S; 2.305(11); Se: 2.412(6)−2.589(15) Å} and thus the geometry about each metal centre is distorted tetrahedral and the range of tetrahedral bond angles is 102.83(3)° to 113.32(3)°. The PSe bond lengths of 2.183(9)–2.205(2) Å in the selenide complexes are slightly elongated compared to those in the free ligands [2.1090(4) Å]. The results are discussed and compared with those obtained for related analogues.

Crystal structures of 2-bromo-1,1,1,3,3,3-hexa-methyl-2-(tri-methyl-sil-yl)tris-ilane and 2-bromo-1,1,1,3,3,3-hexa-isopropyl-2-(triiso-propyl-sil-yl)tri-silane.

The synthesis and crystal structures of two tris-(tri-alkyl-sil-yl)silyl bromide compounds, C9H27BrSi4 (I, HypSiBr) and C27H63BrSi4 (II, TipSiBr), are described. Compound I was prepared in 85% yield by free-radical bromination of 1,1,1,3,3,3-hexa-methyl-2-(tri-methyl-sil-yl)tris-ilane using bromo-butane and 2,2'-azobis(2-methyl-propio-nitrile) as a radical initiator at 333 K. The mol-ecule possesses threefold rotational symmetry, with the central Si atom and the Br atom being located on the threefold rotation axis. The Si-Br bond distance is 2.2990 (12) Å and the Si-Si bond lengths are 2.3477 (8) Å. The Br-Si-Si bond angles are 104.83 (3)° and the Si-Si-Si bond angles are 113.69 (2)°, reflecting the steric hindrance inherent in the three tri-methyl-silyl groups attached to the central Si atom. Compound II was prepared in 55% yield by free-radical bromination of 1,1,1,3,3,3-hexa-isopropyl-2-(triiso-propyl-sil-yl)tris-ilane using N-bromo-succinimide and 2,2'-azobis(2-methyl-propio-nitrile) as a radical initiator at 353 K. Here the Si-Br bond length is 2.3185 (7) Å and the Si-Si bond lengths range from 2.443 (1) to 2.4628 (9) Å. The Br-Si-Si bond angles range from 98.44 (3) to 103.77 (3)°, indicating steric hindrance between the three triiso-propyl-silyl groups.

2,2′,2″-Thiotris(acetic acid) betaine, S(CH2COOH)2(CH2COO), and 2,2′,2″-selenotris(acetic acid) betaine, Se(CH2COOH)2(CH2COO)

The title compounds, X(CH2COOH)2(CH2COO), X = S, 1, and X = Se, 2, have been characterised by FTIR, NMR and MS and by their crystal structures at 123(2) K. The FTIR spectra show two major peaks, at 1396 and 1731 cm−1 in 1 and at 1390 and 1721 cm−1 in 2. The 77Se NMR signal of 2 at 325.5 ppm is 83.4 ppm downfield from the signal of Se(CH2COOH)2 indicating a substantial selenonium character of 2. The two compounds are isostructural and have a pyramidal configuration. The C—X—C bond angles range from 99.29 to 103.14° in 1 and from 97.56 to 99.87° in 2. The XCCO torsion angles for the three substituents are most different; one of the carboxylic acid groups attains the anti-conformation with rather short S⋯O(H) and Se⋯O(H) distances, 2.744 and 2.750 Å, the other acid group is synclinal and with longer S⋯OC and Se⋯OC distances, 3.063 and 3.090 Å, whereas the carboxylate group is in the XCC plane with X⋯OC distances of 2.869 and 2.908 Å in 1 and 2. The presence of these strong X⋯O interactions is suggested to be the cause for the very low Bronsted basicity of this class of betaines preventing salts of the corresponding acids, the presently unknown [X(CH2COOH)3]+ - cations, to be isolated. The molecules are linked together with two fairly strong but different hydrogen bonds to the carboxylate oxygen atoms with O⋯O distances of 2.493 and 2.580 Å in 1 and 2.489 and 2.581 Å in 2 and with one X⋯OC contact, 3.244 Å in 1 and 3.209 Å in 2. The carbonyl oxygen atoms do not participate significantly in intermolecular hydrogen bonding and there are no contacts between the heteroatoms.

Application of polarizable ellipsoidal force field model to pnicogen bonds.

Noncovalent interactions, such as hydrogen bonds and halogen bonds, are frequently used in drug designing and crystal engineering. Recently, a novel noncovalent pnicogen bonds have been identified as an important driving force in crystal structures with similar bonding mechanisms as hydrogen bond and halogen bond. Although the pnicogen bond is highly anisotropic, the pnicogen bond angles range from 160° to 180° due to the complicated substituent effects. To understand the anisotropic characters of pnicogen bond, a modification of the polarizable ellipsoidal force field (PEff) model previously used to define halogen bonds was proposed in this work. The potential energy surfaces (PESs) of mono- and polysubstituted PH3 -NH3 complexes were calculated at CCSD(T), MP2, and density functional theory levels and were used to examine the modified PEff model. The results indicate that the modified PEff model can precisely characterize pnicogen bond. The root mean squared error of PES obtained with PEff model is less than 0.5 kcal/mol, compared with MP2 results. In addition, the modified PEff model may be applied to other noncovalent bond interactions, which is important to understand the role of intermolecular interactions in the self-assembly structures.

Thermodynamic perturbation theory for associating fluids with small bond angles: Effects of steric hindrance, ring formation, and double bonding

We develop a comprehensive approach to model associating fluids with small bond angles using Wertheim's perturbation theory. We show theoretically and through Monte Carlo simulations that as bond angle is varied various modes of association become dominant. The theory is shown to be in excellent agreement with Monte Carlo simulation for the prediction of the internal energy, pressure, and fractions in rings and chains, double bonded over the full range of bond angles.

Bis[O-isopropyl (4-ethoxyphenyl)dithiophosphonato-κ2S,S′]lead(II)

The title compound, [Pb(C11H16O2PS2)2], is a neutral four-coordinate mononuclear complex with a distorted square-pyramidal geometry of the PbS4 core. The apical PbII atom of each pyramid is 1.33059 (3) Å above the basal S4 plane. The metal atom is surrounded by two chelating dithio­phospho­nate ligands binding through the S-donor atoms. The ligands are anisobidentate as the pyramid is comprised of Pb—S bond lengths that vary substanti­ally [2.6999 (7), 2.7128 (6), 2.8877 (7) and 2.9472 (7) Å], clearly indicating two short and two longer bond lengths. The P—S bond lengths are also paired as shorter [1.9959 (9) and 1.9877 (8) Å] and slightly longer [2.0115 (9) and 2.0245 (9) Å], indicating an anisobidentate nature of the ligand whereby the shorter P—S bond has more double-bond character than the other. The S—Pb—S (chelating) bond angles range from 71.841 (18) to 72.692 (19)°, whilst the Pb—S—P bond angles range from 84.70 (3) to 90.51 (3)°.

(E)-N-Benzylideneadamantan-1-amine

In the title compound, C17H21N, the dihedral angle between the benzene ring and the imine group (—N=) is 5.1 (4)°. In the adamantane group, the C—C—C bond angles range from 107.88 (19) to 111.33 (17)°. Only weak van der Waals inter­actions contribute to the contribute to the packing of the molecules in the crystal..

Synchrotron radiation infrared microscopic study of non-bridging oxygen modes associated with laser-induced breakdown of fused silica

Nanosecond pulse laser-driven optical breakdown at SiO2 surfaces as probed by synchrotron-based Fourier transform infrared (SRFTIR) and photoluminescence (PL) microscopies is presented. SRFTIR mapping of laser damage identified localized non-bridging Si-O vibrational modes at ∼950 cm−1 which became stiffer as 355 nm laser pulse lengths were increased from 5 to 20 ns. The bridging Si-O-Si transverse optic mode frequency varied significantly across damaged regions indicating a wide range of average bond angles, softening slightly with increasing pulse length. 355 nm-excited PL images of laser modified regions could be directly correlated with the structural modifications identified through SRFTIR.

Bis{2-[(2-hydroxy-2-methylpropyl)iminomethyl]-4-nitrophenolato}nickel(II) dimethylformamide monosolvate

In the title compound, [Ni(C11H13N2O4)2]·C3H7NO, the NiII ion is octa­hedrally coordinated in an N2O4 environment by two identical Schiff base ligands. The Ni—O bond lengths range from 2.004 (2) to 2.106 (2) Å, while the Ni—N bond lengths are 2.038 (2) and 2.0465 (19) Å. The cis bond angles range from 78.64 (8) to 97.30 (8)°, with the former being due to the small bite of the amino­alcohol ligand, while the trans bond angles range from 167.86 (8) to 171.23 (8)°. One of the alcohol H atoms forms a hydrogen bond with the dimethyl­formamide (DMF) solvent mol­ecule, while the other links mol­ecules into chains along the b axis through inter­molecular O—H⋯O hydrogen bonds. There are bifurcated C—H⋯O inter­actions involving one of the nitro groups between parallel stacks of mol­ecules in the b-axis direction.

Crystal Structure of HugZ, a Novel Heme Oxygenase from Helicobacter pylori

The crystal structure of a heme oxygenase (HO) HugZ from Helicobacter pylori complexed with heme has been solved and refined at 1.8 Å resolution. HugZ is part of the iron acquisition mechanism of H. pylori, a major pathogen of human gastroenteric diseases. It is required for the adaptive colonization of H. pylori in hosts. Here, we report that HugZ is distinct from all other characterized HOs. It exists as a dimer in solution and in crystals, and the dimer adopts a split-barrel fold that is often found in FMN-binding proteins but has not been observed in hemoproteins. The heme is located at the intermonomer interface and is bound by both monomers. The heme iron is coordinated by the side chain of His(245) and an azide molecule when it is present in crystallization conditions. Experiments show that Arg(166), which is involved in azide binding, is essential for HugZ enzymatic activity, whereas His(245), surprisingly, is not, implying that HugZ has an enzymatic mechanism distinct from other HOs. The placement of the azide corroborates the observed γ-meso specificity for the heme degradation reaction, in contrast to most known HOs that have α-meso specificity. We demonstrate through sequence and structural comparisons that HugZ belongs to a new heme-binding protein family with a split-barrel fold. Members of this family are widespread in pathogenic bacteria and may play important roles in the iron acquisition of these bacteria.

Tetra-μ(3)-methano-lato-tetra-kis-[(2-formyl-6-meth-oxy-phenolato)methano-lnickel(II)

The molecule of the title compound, [Ni4(CH3O)4(C8H7O3)4(CH3OH)4], has S 4 symmetry. Each of the four NiII atoms occupies every other corner of a cube, with the alternate corners occupied by μ3-methano­late bridging groups linking to three NiII atoms. Each NiII atom is in an O6 octa­hedral coordination environment formed by three O atoms from three μ3-methano­late groups, one from methanol, and two others from a bidentate 2-formyl-6-meth­oxy­phenolate ligand. The Ni—O bond distances range from 2.0020 (14) to 2.0938 (14) Å, the cis bond angles range from 81.74 (6) to 97.63°, and the trans bond angles range from 168.76 (5) to 175.22 (6)°. There are bifurcated hydrogen-bonding inter­actions between the coordinated methanol OH groups and both the phenolic and meth­oxy O atoms of an adjoining 2-formyl-6-meth­oxy­phenolate moiety. In addition, there are weak inter­molecular C—H⋯O inter­actions involving the meth­oxy O atoms.

1,1,2,2-Tetrakis(di-o-tolylphosphino)ethane

The complete molecule of title compound, C58H58P4, is generated by a crystallographic twofold rotation axis that passes through the center of the C(methine)—C(methine) bond of length 1.582 (4) Å. The C—P bond lengths are 1.8824 (19) and 1.8991 (19) Å. The P—C—P angle of 109.69 (9)° is essentially equal to the expected value of 109.5° for a tetra­hedral C atom. Although the C(methine)—P—C(aromatic) bond angles range from 102.67 (9) to 107.04 (9)°, the C(aromatic)—P—C(aromatic) bond angles of 96.72 (9) and 97.29 (9)° are significantly smaller. The steric demands of the o-tolyl groups cause deviations from the bond lengths and angles reported for its phenyl analog.

Statistical analysis of structural characteristics of protein Ca2+-binding sites.

To better understand the biological significance of Ca(2+), we report a comprehensive statistical analysis of calcium-binding proteins from the Protein Data Bank to identify structural parameters associated with EF-hand and non-EF-hand Ca(2+)-binding sites. Comparatively, non-EF-hand sites utilize lower coordination numbers (6 +/- 2 vs. 7 +/- 1), fewer protein ligands (4 +/- 2 vs. 6 +/- 1), and more water ligands (2 +/- 2 vs. 1 +/- 0) than EF-hand sites. The orders of ligand preference for non-EF-hand and EF-hand sites, respectively, were H(2)O (33.1%) > side-chain Asp (24.5%) > main-chain carbonyl (23.9%) > side-chain Glu (10.4%), and side-chain Asp (29.7%) > side-chain Glu (26.6%) > main-chain carbonyl (21.4%) > H(2)O (13.3%). Less formal negative charge was observed in the non-EF-hand than in the EF-hand binding sites (1 +/- 1 vs. 3 +/- 1). Additionally, over 20% of non-EF-hand sites had formal charge values of zero due to increased utilization of water and carbonyl oxygen ligands. Moreover, the EF-hand sites presented a narrower range of ligand distances and bond angles than non-EF-hand sites, possibly owing to the highly conserved helix-loop-helix motif. Significant differences between ligand types (carbonyl, side chain, bidentate) demonstrated that angles associated with each type must be classified separately, and the EF-hand side-chain Ca-O-C angles exhibited an unusual bimodal quality consistent with an Asp distribution that differed from the Gaussian model observed for non-EF-hand proteins. The results of this survey more accurately describe differences between EF-hand and non-EF-hand proteins and provide new parameters for the prediction and design of different classes of Ca(2+)-binding proteins.

Tetraphenylantimony(V) hexachloroplatinate, tetrachloroaurate, and hexachlorostannate [Ph4Sb] 2 + [PtCl6]2−, [Ph4Sb]+[AuCl4]−, and [Ph4Sb] 2 + [SnCl6]2−: Synthesis and crystal structures

The reactions of tetraphenylantimony with hexachloroplatinic and chloroauric acids in benzene afford bis(tetraphenylantimony) hexachloroplatinate (I) and tetraphenylantimony tetrachloroaurate (II), respectively. Compound II is also synthesized from tetraphenylantimony chloride and chloroauric acid in acetone. Bis(tetraphenylantimony) hexachlorostannate (III) is synthesized from tin dichloride and tetraphenylantimony chloride in acetone or from tin tetrachloride and tetraphenylantimony chloride in benzene. The crystal structures of compounds I–III are determined by X-ray diffraction analysis. The antimony atoms in the [Ph4Sb]+ cations have a distorted tetrahedral coordination (CSbC bond angles range from 105.7(1)° to 118.5(1)° (I), from 106.2(3)° to 114.4(3)° (II), and from 106.0(1)° to 117.1(1)° (III)). The Sb-C bond lengths vary in intervals of 2.094(2)–2.098(2), 2.087(7)–2.111(7), and 2.093–2.100(3) A, respectively. The coordination of the Pt and Sn atoms in complexes I and III is close to an ideal octahedral coordination with ClPtCl and ClSnCl bond angles of 88.68(2)°–91.32(3)° and 88.84(3)°–91.16(3)°, respectively. The square coordination of the Au atom in complex II is slightly distorted: the Au-Cl bond lengths are 2.266(2)–2.277(2) A, the ClAuCl bond angles are equal to 89.7(1)°–90.5(1)°, the root-mean-square deviation of the atoms from the coordination plane being 0.004 A.

1-Benzhydryl-4-(4-chlorophenylsulfonyl)piperazine

The title compound, C23H23ClN2O2S, was synthesized by the nucleophilic substitution of 1-benzhydrylpiperazine with 4-chloro­phenyl­sulfonyl chloride. The piperazine ring is in a chair conformation. The geometry around the S atom is that of a distorted tetra­hedron. There is a large range of bond angles around the piperazine N atoms. The dihedral angle between the least-squares plane (p1) defined by the four coplanar C atoms of the piperazine ring and the benzene ring is 81.6 (1)°. The dihedral angles between p1 and the phenyl rings are 76.2 (1) and 72.9 (2)°. The two phenyl rings make a dihedral angle of 65.9 (1)°. Intramolecular C—H⋯O hydrogen bonds are present.

Characterisation of the supramolecular structure of chemically and physically modified regenerated cellulosic fibres by means of high-resolution Carbon-13 solid-state NMR

Carbon-13 high-resolution solid-state NMR techniques have been invaluable in elucidating the structure of regenerated cellulosic materials. Studies of a range of fibres have shown systematic changes in chemical shifts, which can be related to the influences of physical processing or chemical modification. A constrained curve fitting method has been applied, where the C4 spectral envelope is represented as the sum of contributions from polymer in ordered, partially-ordered and disordered environments, associated with differing conformational arrangements of the cellulose hydroxymethyl and glycocidic bonds. The empirical gamma- gauche effect seems likely to provide the best rationalization for the relationship between C4 shifts and conformational order, taking into account the increased range of bond angles in disordered environments. The quantification of proportions of polymer units within different conformational groupings will provide new insights into the development of supramolecular texture. This will allow better appreciation of the relationships between fibre processing and ultimate fibre performance.