Structures of XH4 + and XH6 + (X = B, Al and Ga) Cations

Structures and energies of XH₄ ⁺ and XH₆ ⁺ (X = B, Al and Ga) have been calculated at the density functional theory (DFT) B3LYP/6-311++G(3df,2pd) level. Calculations indicate that although the structure with a three center two electron (3c-2e) bond is the global minimum for BH₄ ⁺, the global minima of AlH₄ ⁺ and GaH₄ ⁺ are not those with one 3c-2e bond, but those with two 3c-2e bonds. For calibration, both structures of AlH₄ ⁺ were also calculated at the ab initio CCSD(T)/cc-pVTZ level and results in agreement with the DFT results were found. Similar calculations also indicate that although the C_2v symmetrical structure with two 3c-2e bonds is the global minimum for BH₆ ⁺, the global minima of AlH₆ ⁺ and GaH₆ ⁺ are not the C_2v symmetrical structures with two 3c-2e bonds but the C₂ symmetrical structures with three 3c-2e bonds.Electronic Supplementary Material available.     

New structures of low valent Al hypersilanides: A negatively charged isomer with a closo-Al4Si-structure potentially indicates a new entry in polyhedral AlmSin-frameworks

The reaction of lithium tris(trimethylsilyl)silanide with donor stabilized monovalent aluminium bromide leads to two isomeric closed polyhedral aluminium anions as reduction products (1a and 1b) and two new fourth-coordinate anionic aluminium(III) oxidation products (3 and 4). Evidence for a rearrangement reaction between the anionic polyhedral aluminium isomers is given. All of the structurally characterized compounds contain [Li(thf)₄]⁺ as counter cations in their neutral crystal lattices.     

Structural and electronic properties of diazonium functionalized (4, 4) single walled carbon nanotube: an ab initio study

In this work, ab initio density functional theory (DFT) calculations are performed to study the structural and electronic properties of diazonium reagent functionalized (4, 4) single-walled carbon nanotube (SWCNT). We find the aryl group covalently bonds with SWCNT and prefers to be perpendicular to the side wall of nanotube. It has a rotational barrier of 0.35 eV around the formed aryl-tube bond axis and should be thermodynamically stable at room temperature. Additionally, new peaks appeared around the Fermi energy in the density of state (DOS) due to the weak band dispersion. Increasing of the coverage of the functional group will result in significant upshift of the Fermi level.     

Crystal structure and physical properties of the new 2D polymeric compound bis(1,5-diaminotetrazole)dichlorocopper(II)

Two new coordination complexes, Cu(datz)Cl₂ and Cu(datz)₂Cl₂, where datz is 1,5-diaminotetrazole, have been obtained by the reaction of copper(II) chloride with datz. For one of them, Cu(datz)₂Cl₂, the crystal structure, magnetic susceptibility and thermal properties are reported. For the other compound only spectroscopic and thermal properties are presented. In Cu(datz)₂Cl₂ the Cu atoms were found to be octahedrally coordinated. Equatorial positions are occupied by two chloride anions and two tetrazole ligands via their N⁴ donor atoms. Surprisingly, the amino groups at the N¹ atom of the tetrazole ring of nearby molecules are in axial positions. Each copper atom is linked with four others through the datz molecules to form 2D polymeric networks parallel to the yz plane. Magnetic properties of Cu(datz)₂Cl₂ and the data of quantum-chemical calculations of molecular electrostatic potential and energies of hydronation of nitrogen atoms for datz using MP2/6-31G* and B3LYP/6-31G* levels of theory are in agreement with the structural data obtained.     

Oxidations of sulfur rich heterocycles - new S-oxides of the parent 1,2,4-trithiolane and its tetramethyl derivative: synthesis and structural investigations

Whereas oxidation of 1,2,4-trithiolane (1) with 1 molar equiv. of m-chloroperbenzoic acid (mCPBA) yielded 1,2,4-trithiolane 4-oxide (3) and a small amount of 1,2,4-trithiolane 1-oxide (2), the reaction with 2.5 molar equiv. of mCPBA afforded exclusively 1,2,4-trithiolane 1,4-dioxide (trans-7). The oxidation of 3,3,5,5-tetramethyl-1,2,4-trithiolane (4) with peroxyacetic acid (1 molar equiv. H₂O₂/AcOH) gave a mixture of regioisomeric 3,3,5,5-tetramethyl-1,2,4-trithiolane 4-oxide (6) as a major product and only traces of 1-oxide 5. Using 2.5 molar equiv. of peroxyacetic acid in reaction with 4 a mixture of both stereoisomers of 3,3,5,5-tetramethyl-1,2,4-trithiolane 1,4-dioxides cis-8 and trans-8 was isolated. Furthermore, 4 was oxidized to 3,3,5,5-tetramethyl-1,2,4-trithiolane 1,1,4,4-tetraoxide (9) using 6 molar equiv. of peroxyacetic acid. The molecular structures of 3, trans-7, trans-8 and 9 were unambiguously established by X-ray structure analysis. Compounds 1-4, trans-7, trans-8 and 9 were investigated by Raman spectroscopy. Ab initio calculations were used to obtain the optimized geometries and the vibrational wavenumbers of the title compounds. The vibrational assignment was accomplished by using the calculated harmonic wavenumbers and their Raman intensities. The calculated values of both structural parameters and the vibrational modes fitted in with experimental data. The spectroscopic changes observed in the spectra were correlated with the structural parameters in order to gain information about the influence of the oxidation on the molecule structure. The experimental data indicated, that in comparison with starting 1,2,4-trithiolanes 1 and 4 their oxidized derivatives showed remarkable shortening of the S-S bonds.     

On the “coloring problem” in YMgZn and related phases

During exploration in the Y-Mg-Zn system for quasicrystal approximants, three new phases, YMg_1−xZn_1+x (0 ? x ? 0.17) adopting the hexagonal ZrNiAl structure type, have been discovered. In these structures, the elements are completely ordered to minimize both the site energies and the bond energies as calculated by tight-binding calculations. Evaluation of the electron density in YMgZn suggests that Mg-Zn and Y-Zn bonding coupled with maximizing the Zn?Zn separations is the main factor influencing the atomic arrangements. Analysis of the electronic density of states of YMgZn indicates an optimized bonding situation for eight valence electrons per formula unit, e.g., as in YMgGa. Subsequently, YMgAl, YMgGa, and YMgIn were successfully prepared and structurally characterized. Their structures show relationships to both densely-packed structures common for intermetallics as well as three-dimensional networks common for valence compounds.     

An Investigation of the Structural Diversities of Lithiated HMPA Complexes of o-Mercaptopyridine and Trithiocyanuric Acid: Syntheses, Crystal structures and Model Molecular Orbital Calculations

Reaction of o-mercaptopyridine (o-MPH) and trithiocyanuric acid (TTCyH₃) with one equivalent of BuⁿLi in the presence of HMPA yields the mono-lithiated salts MPLi.HMPA (1) and TTCyH₂Li.2HMPA (2) respectively, which have been characterised by NMR spectroscopy and X-ray crystallography. Reaction of three equivalents of BuⁿLi with anhydrous TTCyH₃ in THF yields the tri-lithiated species TTCyLi₃.4THF (3). In all three compounds the lithium centres have N,S-bridged coordination modes. Whereas 1 is dimeric in the solid state, 2 has an unusual monomeric structure and 3, which is a very rare example of a structurally characterised tri-lithiated compound, has an unprecedented polymeric structure incorporating (NCSLi) _n (n = 1, 2) rings. The structural diversities displayed by 1 and 2 have been probed, and thereby in part rationalised, by ab initio (6-31G*/RHF, 6-31G**/RHF and 6-31G*/MP2 levels) MO calculations on both their thio-keto and thiol isomers and on their uncomplexed and complexed lithiated derivatives. In particular, the optimised structures predict and reproduce the N,S-bridging coordination modes found for lithium and explain why structure 1 is dimeric whereas 2 is monomeric.Electronic Supplementary Material available.     

Bis(2-methyltetrazole)dichlorocopper(II) is a layered coordination polymer built from dinuclear chloro-bridged Cu units linked by bridging tetrazoles. The first structurally and magnetically characterized complex of 2-monosubstituted tetrazoles

The data on synthesis, crystal structure, magnetic susceptibility and thermal properties of coordination compound of copper(II) chloride with 2-methyltetrazole (2mtet) of Cu(2mtet)₂Cl₂ composition are reported. The Cu atom environment forms an elongated octahedron, with two 2-methyltetrazole ligands (N4 bound) and two Cl atoms in the equatorial positions. Symmetry related 2-methyltetrazole ligand and Cl atom are in the axial positions. One of the two 2-methyltetrazole molecules of the asymmetric unit exhibits bridging properties being linked to two Cu atoms through two N atoms (i.e., N4 and N1) of the tetrazole ring, while the other ligand molecule is coordinated in monodentate fashion via one tetrazole N4 atom. The Cu-octahedra form dinuclear building bricks by sharing edges with equatorial and axial Cl atoms. These dinuclear units are linked together via bridging 2-methyltetrazole ligands to form infinite layers parallel to the plane. Magnetic properties of Cu(2mtet)₂Cl₂ and the data of quantum-chemical calculations of molecular electrostatic potential and energies of hydronation of nitrogen atoms for 2mtet using B3LYP/6-31G^* level of theory are in agreement with the structural data obtained.     

Crystal structures of cyclomaltohexaose (α-cyclodextrin) complexes with p-chlorophenol and p-cresol

Crystal structures of cyclomaltohexaose (α-cyclodextrin) complexes with p-chlorophenol and p-cresol have been determined by single-crystal X-ray diffraction studies. The space group of the α-cyclodextrin–p-chlorophenol complex is P2₁2₁2₁ with unit cell dimensions of a=15.299(3), b=24.795(5), c=13.447(5) Å, and that of the α-cyclodextrin–p-cresol complex is P2₁ with unit cell dimensions of a=7.927(7), b=13.568(7), c=24.54(1) Å, β=90.41(8)°. In spite of the similar structures of guest molecules, both complexes have different inclusion modes and packing structures.     

Structure and properties of a ferrocenylpyrimidine-bromanilic acid hydrogen-bonded supramolecular complex

A hydrogen-bonded assembly composed of ferrocenylpyrimidine (FcPM) and bromanilic acid (BA), represented as [FcPM](BA)(acetone)_0.5, was prepared and crystallographically characterized. The asymmetric unit of the crystal contained two crystallographically independent molecules of FcPM and BA, which were alternately connected to form one-dimensional zigzag chains via OH?N hydrogen bonds. The BA molecules were stacked to form one-dimensional columns. No charge transfer was observed between FcPM and BA. Acetone molecules, which were located in channels, were desorbed at 433 K.     

Template synthesis, structure and magnetic property of a new open-framework manganese borophosphate: (C4N2H12)Mn[B2P3O12(OH)]

A new manganese borophosphate compound, (C₄N₂H₁₂)Mn[B₂P₃O₁₂(OH)], has been hydrothermally synthesized, and structurally determined by single crystal X-ray diffractions. The crystal structure of the compound is characterized by corner-sharing BO₄ and PO₄ groups, leading to 1-D infinite chains built from alterative tetrahedra with a sequence of two corner-sharing borate tetrahedra, whose remaining corners are shared with two loop branching phosphate groups followed by a phosphate unit, which is interconnected by MnO₆ octahedral groups to construct a three-dimensional open-framework topology with unidimensional channels, which are occupied by diprotonated piperazinium ions. Magnetic measurement reveals an antiferromagnetic interaction system. Other characterizations by elemental analysis, IR and thermal analyses are also discussed.     

The novel 1D chain and 3D network of mercury carborane-diphenylphosphine complexes constructed by covalent bond or hydrogen bond interactions

The closo- and nido-carborane-diphenylphosphine complexes [Hg₂{1,2-(PPh₂)₂-1,2-C₂B₁₀H₁₀}₂(μ-Cl₂)₂(μ-HgCl₂)₃]·2CH₂Cl₂ (1) and [HgCl(PPh₃){7,8-(PPh₂)₂-7,8-C₂B₉H₁₀}] (2) have been synthesized and characterized by elemental analysis, FT-IR and X-ray structure determination. The X-ray structure analysis for these two complexes showed that the carborane cage ligand was coordinated bidentately to the Hg(II) center through its two phosphorus atoms. The coordination geometry of the mercury atom complexed by P₂Cl₂ unit in complex 1 or P₃Cl unit in complex 2 was a distorted tetrahedron, while the mercury atom in complex 2 coordinated to six Cl atoms was a slightly distorted octahedron. X-ray analysis reveals that the complex 1 forms a 1D chain coordination polymer via bridged Hg-Cl bonds. For complex 2, it displays a 3D network constructed by the C-H···Cl hydrogen bonds and C-H···H-B dihydrogen bonds.     

Extending the New Generation of Structure Predictors to Account for Dynamics and Allostery

Recent progress in structure-prediction methods that rely on deep learning suggests that the atomic structure of almost any protein may soon be predictable directly from its amino acid sequence. This much-awaited revolution was driven by substantial improvements in the reliability of methods for inferring the spatial distances between amino acid pairs from an analysis of homologous sequences. Improved reliability has been accompanied, however, by a reduced ability to detect amino acid relationships that are not due to direct spatial contacts, such as those that arise from protein dynamics or allostery. Given the central importance of dynamics and allostery to protein activity, we argue that an important future advance would extend modeling beyond predicting a single static structure. Here, we briefly review some of the developments that have led to the remarkable recent achievement in structure prediction and speculate what methods and sources of information may be leveraged in the future to develop a modeling framework that addresses protein dynamics and allostery.     

Novel porphyrin-thallium-platinum complex with “naked” metal-metal bond: multinuclear NMR characterization of [(tpp)Tl-Pt(CN)5] and [(thpp)Tl-Pt(CN)5] in solution

The novel porphyrin-thallium-platinum complexes with “naked” metal-metal bond, with the composition [(tpp)Tl-Pt(CN)₅]²⁻ (1) and [(thpp)Tl-Pt(CN)₅]²⁻ (2) (tpp = tetraphenylporphrin and thpp = tetrakis(4-hydroxyphenyl)-porphine), were synthesized and characterised by multinuclear NMR (²⁰⁵Tl, ¹⁹⁵Pt, ¹³C and ¹H) and Raman spectroscopies in solution. The presence of a direct Pt-Tl metal-metal bond in the complexes is convincingly confirmed by a very strong one-bond ¹⁹⁵Pt-²⁰⁵Tl spin-spin coupling (47.8 and 48.3 kHz for 1 and 2, respectively) detected in both Pt and Tl NMR spectra. The corresponding force constant in molecule 1, 1.92 N cm⁻¹, was calculated using Raman stretching frequency of the Pt-Tl vibration and is characteristic for a single metal-metal bond.     

Physico-chemical study of first row transition metal ions coordination compounds with N,N′-bis(2-tosylaminobenzylidene)-1,3-diaminopropanol. The crystal structure of bis-azomethine and its cobalt(II) complex

The novel Cu(II), Ni(II), Zn(II), Co(II) coordination compounds with Schiff base ligand - N,N′-bis(2-tosylaminobenzylidene)-1,3-diaminopropanol have been synthesized and studied. The structures of bis-azomethine as well as Co(II) and Zn(II) mononuclear metallochelates have been determined by X-ray analysis. The magnetic properties of all complexes were studied and interpreted in terms of HDVV theory. It was shown that exchange interaction in binuclear copper(II) complexes was affected by tosyl groups.     

Aldol additions with mutant lipase: analysis by experiments and theoretical calculations

A Ser105Ala mutant of Candida antarctica lipase B has previously been shown to catalyze aldol additions. Quantum chemical calculations predicted a reaction rate similar to that of natural enzymes, whereas experiments showed a much lower reaction rate. Molecular dynamics simulations, presented here, show that the low reaction rate is a consequence of the low frequencies of near attack complexes in the enzyme. Equilibrium was also considered as a reason for the slow product formation, but could be excluded by performing a sequential reaction to push the reaction towards product formation. In this paper, further experimental results are also presented, highlighting the importance of the entire active site for catalysis.     

Novel supramolecular compounds based on Cucurbit[6]uril, 1,8-diaminooctane and octahedral thiohydroxo anions with cluster core [Re6S8]

Supramolecular compounds {C₈N₂H₂₂@Cuc[6]}{Re₆S₈(H₂O)₂(OH)₄}·18H₂O (1), and K₂{C₈N₂H₂₂@Cuc[6]}{Re₆S₈(OH)₆}·14H₂O (2) were obtained by crystallization from aqueous solutions that contained the macrocyclic cavitand cucurbit[6]uril (C₃₆H₃₆N₂₄O₁₂), 1,8-diaminooctane and the cluster thiohydroxo complex [Re₆S₈(OH)₆]⁴⁻. The resultant composition of the formed compounds depends on the experiment technique. According to the X-ray diffraction analysis, 1,8-diaminooctane molecules are encapsulated within the cavity of the cucurbit[6]uril molecules in such a way that the aminogroups are above and below the plane of the cavitand. The 1,8-diaminooctane molecules formed hydrogen bonds with the cavitand and the cluster thiohydroxo complexes to give chains.     

Calculations of one-, two- and three-bond nuclear spin-spin couplings in a model peptide and correlations with experimental data

Summary We present ab initio calculations of the Fermi contact term and experimental correlations of six coupling constants, ³J_H ^N _H , ¹J_{C H} , ²J_CH , ¹J_{C N}, ²J_{C N} and ¹J_CN, in a peptide as functions of the backbone dihedral angles, and . Given estimates of experimental uncertainties, we find semiquantitative experimental correlations for ³J_H ^N _H , ¹J_{C N} and ²J_{C N}, qualitative correlations for ¹J_{C H} and ²J_CH , but no experimental correlations of practical utility for ¹J_CN, owing to its complex dependence on at least four dihedral angles. Errors in the estimation of dihedral angles from X-ray crystallographic data for proteins, which result from uncertainties in atom-to-atom distances, place substantial limitations on the quantitative reliability of coupling constant calculations fitted to such data. In the accompanying paper [Edison, A.S. et al., J. Biomol. NMR, 4, 543–551] we apply the results of the coupling constant calculations presented here to the estimation of and angles in staphylococcal nuclease from experimental coupling constants.Abbreviations AO atomic orbital - BPTI basic pancreatic trypsin inhibitor (bovine) - CI-2 chymotrypsin inhibitor 2 - E.COSY exclusive correlation spectroscopy (Griesinger et al., 1986) - ⁿJ_AB single bond (n=1), geminal (n=2), or vicinal (n=3) coupling constant between nuclei A and B - LCAO linear combination of atomic orbitals - NBO natural bond orbital - n lone pair orbitals - bonding orbitals - ^* antibonding orbitals - dihedral angle or molecular orbital wave function; r², correlation coefficient - RHF restricted Hartree-Fock; rmsd, root-mean-square deviation - 3-21G and 6-31G^* molecular orbital basis set designations (Hehre et al., 1986)     

Ab initio conformational maps for disaccharides in gas phase and aqueous solution

Ab initio conformational maps for beta-lactose in both the gas phase and in aqueous solution have been constructed at the HF/6-31G(d,p) level of calculation. The results of the gas-phase ab initio calculations allow us to conclude that a rigid conformational map is able to predict the regions of the minima in the potential energy surface of beta-lactose, in full agreement with those found in the relaxed conformational map. The solvation effects do not give rise to any new local minimum in the potential energy surface of beta-lactose, but just change the relative Boltzmann populations of the conformers found in the gas-phase calculations. The values obtained for heteronuclear spin coupling constant (3J(H,C)), using the seven most stable conformers in solution are in good agreement with the available experimental values. This is a good indication that ab initio rigid conformational maps can be reliably used to sort the most stable conformers of beta-lactose.