Three-center Bonds Research Articles

Electronic Structure and Effectively Unpaired Electron Density Topology in closo-Boranes: Nonclassical Three-Center Two-Electron Bonding.

This article provides a detailed study of the structure and bonding in closo-borane cluster compounds X2B3H3 (X = BH(-), P, SiH, CH, N), with particular emphasis on the description of the electron distribution using the topology of the quantum many-body effectively unpaired density. The close relationship observed between the critical points of this quantity and the localization of the electron cloud allows us to characterize the nonclassical bonding patterns of these systems. The obtained results confirm the suitability of the local rule to detect three-center two-electron bonds, which was conjectured in our previous study on boron hydrides.

A Hypervalent Pentacoordinate Boron Compound with an N−B−N Three-Center Four-Electron Bond

For the purpose of synthesizing and characterizing hypervalent boron compounds with strong hypervalent interaction, we have prepared a boron compound with a tridentate ligand bearing two pyrimidine rings as nitrogen donors. X-ray analysis and molecular orbital calculations suggested that the boron compound was of hypervalent pentacoordinate structure with an N-B-N hypervalent bond. Thus, we have prepared the first hypervalent second row element compound with apical N coordination. A breakdown of energy contributions by DFT calculations revealed that the N-B-N bond energy of the pentacoordinate state ground state (13) was 2.8 kcal mol(-1). Implications were that the conjugation energy difference of 6.6 kcal mol(-1) (14.2-7.6 kcal mol(-1)) with the tetracoordinate state was a crucial factor for shifting stability toward the pentacoordinate structure.

Mild route to generate gaseous metal anions

Gaseous metal anions such as Na(-), K(-), Cs(-), and Ag(-) can be generated at ambient temperatures by the collision-induced dissociation of the anions of several dicarboxylic acid salts, including oxalate, maleate, fumarate, succinate, and glutamate salts. The formation of gaseous metal anions in this way is unprecedented because the metal is initially present in its cationic form. The mild process described here could facilitate novel applications of metal anions as selective reagents for gas-phase ion-molecule and ion-ion reactions. Ab initio calculations were used to describe the dissociation process for anions of the oxalate salts. The formation of alkalides occurs via production of a metal-carbon dioxide anion intermediate with a bidentate three-center two-electron bond to the metal. The metal atom acquires a partial negative charge in the intermediate structure.

Lomefloxacinium picrate.

In the cation of the title compound [systematic name: (RS)-4-(3-carb­oxy-1-ethyl-6,8-difluoro-4-oxo-1,4-dihydro­quinolin-7-yl)-2-methyl­piperazin-1-ium 2,4,6-trinitro­phenolate], C17H20F2N3O3 +·C6H2N3O7 −, the piper­azine ring adopts a slightly distorted chair conformation and contains a protonated N atom. An intra­molecular O—H⋯O hydrogen bond occurs in the cation. The dihedral angles between the mean planes of the six-atom piperazine ring and the 10-atom fused ring system is 43.3 (5)°. The picrate anion inter­acts with the protonated N atom of an adjacent cation through a bifurcated N—H⋯(O,O) three-center hydrogen bond. Strong N—H⋯O hydrogen bonds in concert with weak π–π stacking inter­actions [centroid–centroid distance = 3.6460 (14) Å] dominate the crystal packing, creating a two-dimensional network structure along [011].

Enrofloxacinium picrate.

There is one cation–anion pair in the asymmetric unit of the title compound [systematic name: 4-(3-carb­oxy-6-fluoro-4-oxo-1,4-dihydroquinolin-7-yl)-1-ethyl­piperazin-1-ium 2,4,6-tri­nitro­phenolate], C19H23FN3O3 +·C6H2N3O7 −. The six-membered piperazine group in the cation adopts a slightly distorted chair conformation and contains a protonated N atom. The dihedral angles between the mean planes of the cyclo­propyl and piperazine rings in the cation with the 10-atom ring system of the quinolone group are 48.1 (1) and 69.9 (5)°, respectively. The picrate anion inter­acts with the protonated N atom of an adjacent cation through a bifurcated N—H⋯O three-center hydrogen bond, forming an R 1 2(6) ring motif. Furthermore, there is an intra­molecular O—H⋯O hydrogen bond. The dihedral angle between the mean planes of the anion benzene and cation piperizine, quinoline and cyclo­propyl rings are 61.3 (6), 31.1 (4) and 70.4 (9)°, respectively. The mean planes of the two o-NO2 and single p-NO2 groups in the picrate anion are twisted by 6.7 (6), 38.3 (9) and 12.8 (7)° with respect to the mean plane of the benzene ring. Strong N—H⋯O and weak inter­molecular C—H⋯O hydrogen bonds in concert with weak π–π stacking inter­actions [centroid–centroid distances = 3.5785 (13), 3.7451 (12) and 3.6587 (13) Å] dominate the crystal packing.

Experimental and database studies of three-centered halogen bonds with bifurcated acceptors present in molecular crystals, cocrystals and salts

We present a database and experimental study of three-centered halogen bonds involving bifurcated halogen bond acceptors. Our study encompasses three cocrystals with nitrogen, oxygen and sulfur atoms as acceptors and iodine atoms as donors, as well as an overview of three-centered halogen-bonded systems contained within the Cambridge Structural Database based on organic iodine as the donor atom and nitrogen, oxygen, fluorine, sulfur, chlorine, bromine or iodine atoms as acceptors. The results demonstrate that three-centered halogen bonding arrangements are a possible outcome of cocrystallisation experiments and that they exhibit well-defined geometries. The occurrence of such three-centered interactions is considerably rarer for halogen bonds than for hydrogen bonds and, at the current level of understanding, their formation cannot be readily predicted. The strong preference for binary two-center interactions makes a clear difference between halogen and hydrogen bonds. However, as potential guidelines towards developing halogen-bonded architectures based on bifurcated acceptors, the database search indicates particular preference for bifurcation of neutral sulfur or anionic chloride and bromide acceptors.

Stereochemical control in the structures of linear δ ,α -hybrid tripeptides containing tetrahydrofuran amino acids

Structural and electronic properties of diastereomers of tetrahydrofuran amino acids (TAA) derived tripeptide, Boc-TAA-Leu-Val-OMe, are studied using density functional theory. Predicted secondary folding patterns with hydrogen bonded pseudocycles of different sizes in peptides containing (2R,5S)-cis-TAA and (2S,5R)-cis-TAA are confirmed by detailed NMR studies of both, and single crystal X-ray analysis of the former. A novel unusual folding pattern emanating from three-centered hydrogen bond is found in peptide with (2R,5S)-cis relationship. Stereochemical control on the orientation of interacting sites is substantiated by structural analysis of the peptides. Using natural bonding orbital and atoms in molecules analyses, charge transfer interactions are analyzed. Copyright © 2010 John Wiley & Sons, Ltd.

Real-Space Indicators for Chemical Bonding. Experimental and Theoretical Electron Density Studies of Four Deltahedral Boranes

In an approach combining high-resolution X-ray diffraction at low temperatures with density functional theory calculations, two closo-borates, B(12)H(12)(2-) (1) and B(10)H(10)(2-) (2), and two arachno-boranes, B(10)H(12)L(2) [L = amine (3) or acetonitrile (4)], were analyzed by means of the atoms-in-molecules (AIM) theory and electron localizability indicator (ELI-D). The two-electron three-center (2e3c) bonds of the borane cages are investigated with the focus on real-space indicators for chemical bonding and electron delocalization. In compound 2, only two of the three expected bond critical points (bcp's) are found. However, a weakly populated ELI-D basin is found for this pair of adjacent B atoms and the delocalization index and the Source contributions are on the same order of magnitude as those for the other pairs. The opposite situation is found in the arachno-boranes, where no ELI-D basins are found for two types of B-B pairs, which, in turn, exhibit a bcp. However, again the delocalization index is on the same order of magnitude for this bonding interaction. The results show that an unambiguous real-space criterion for chemical bonding is not given yet for this class of compounds. The arachno-boranes carry a special B-B bond, which is the edge of the crown-shaped molecule. This bond is very long and extremely curved inward the B-B-B ring. Nevertheless, the corresponding bond ellipticity is quite small and the ELI-D value at the attractor position of the disynaptic valence basin is remarkably larger than those for all other B-B valence basins. Furthermore, the value of the ED is large in relation to the B-B bond length, so that only this bond type does not follow a linear relationship of the ED value at the bcp versus B-B bond distances, which is found for all other B-B bcp's. The results indicate that both 2e2c and 2e3c bonding play a distinct role in borane chemistry.

SOME EARLY-DAYS MEMORIES AND THEN A SMALL DIVERSION INTO BORON CHEMISTRY, AND FINALLY SOME NEW CHEMISTRY OF CARBON NANOTUBES

A brief personal account of the relation of the author with Professor Gordon Stone is described. Then the two parts of the scientific presentation of the symposium talk is given. The first part shows that there are two classes of two-electron three-centre bonds. And the manner in which the se two types of bonds differ in their interaction with each other is shown. For example in the Class II 2e-3c bond the central bridging atom formally contributes two electrons to each of the other two atoms, in terms of electron counting considerations. The second part describes how carbon nanotubes, decorated with sugar molecules on the outside and filled with radioactive iodine, sealed in the interior of the SWNTs can be delivered selectively to the lungs of a mouse. The radio nuclei are selectively located in exceptionally high concentrations and this has implications for applications in radio surgery.

Boron fullerenes with 32-56 atoms: irregular cage configurations and electronic properties

Unbiased search by first-principles simulated annealing revealed irregular cage configurations for medium-sized B n clusters (namely, boron fullerene) with n=32-56, which are more stable than the previously proposed symmetric cages. The stability of these irregular cages can be understood by the three-center bonds as well as the polygonal holes on the cage surface. The delocalized distribution of molecular orbitals as well as the negative nucleus-independent chemical shifts (NICS) values for each boron cage indicates strong aromaticity.

Tri- and Tetraprotonated Ethane (C2H93+ and C2H104+) Containing Five- and Six-Coordinate Carbons

Triprotonated ethane (C(2)H(9)(3+)) 4 and tetraprotonated ethane (C(2)H(10)(4+)) 6 were found by ab initio MP2/cc-pVTZ calculations as viable energy minima. Their structure has three and four two-electron three-center (2e-3c) bonds, respectively. In contrast, calculations showed no minimum-energy structure on the potential energy surface of pentaprotonated ethane (C(2)H(11)(5+)). Charge-charge repulsion may approach its limit in this case. Sufficient stabilization of polycations by Schmidbaur-type auration with (C(6)H(5))(3)PAu, an isolobal analogue of H(+), should be possible for the preparation of the polyaurate derivatives of poly protonated ethane allowing their structural study.

Amine-rich Silver Complexes of rac-trans-1,2-Diaminocyclohexane

The use of the diamine rac-trans-1,2-diaminocyclohexane (LL) as a major component of the solvent system allows the isolation of crystalline silver complexes with higher ratios of LL to silver (up to 4 : 1, compared to the previously obtained 1 : 1 in ethanolic solution). The complexes obtained and crystallographically characterized were (LL)2AgNO3 (1), (LL)3Ag(OAc)(H2O)2 (2) and (LL)4AgBr(H2O)3 (3). Additionally, the silver-free compounds (LL)・(H2O) (4) and (LL)3・HCl (5) were obtained as by-products. Complex 1 is a chain polymer with one bridging and one terminal LL ligand; the chains are homochiral. Complex 2 contains isolated [(LL)3Ag]+ cations with one chelating and two monodentate ligands. Complex 3 contains dimeric [(LL)2AgBr]2 units; the additional LL molecules are not coordinated to the metal. Compound 5 consists of one diamine with imposed twofold symmetry, one half-protonated diamine in which the acidic hydrogen site is half-occupied (it is involved in a disordered hydrogen bond N-H・ ・ ・N across a twofold axis) and a chloride anion on a twofold axis. In all five structures, the components pack so as to form clearly defined hydrophilic and hydrophobic areas. In the former, classical hydrogen bonds are formed. Except for a few borderline cases of three-center bonds, these are all two-center systems. The appreciable number of these (e. g. 20 for compound 3) renders the layer structures quite complex, but in most cases they can be analyzed in terms of smaller units.

ChemInform Abstract: A Phosphoranide (10-P-4) Anion Coordinating to Transition Metals, as a Lewis Base and a π-Acceptor.

The reaction of 10-P-5 hydridophosphorane 6 with KH provides the 10-P-4 potassium phosphoranide anion 7a. Anion 7a reacts with CpFe(CO)2I and BrAu(PEt3) to replace the halide with the phosphoranide as a monodentate ligand forming 8 and 9. The X-ray structure of 8 shows that the equatorial—Fe(CO)2Cp ligand of 8 makes the apical PO bonds (1.824 A) longer than the PO bonds (1.80 A) of the phosphoranide oxide anion 10. The PO bonds (1.75 A) of 6, with an equatorial proton ligand, are still shorter. This provides evidence that the—Fe(CO)2Cp ligand is not only a sigma-acceptor Lewis acid ligand, but also a pi-donor that transfers electrons into the OPO three-center bond's anti-bonding orbital to increase its P—O bond lengths. It is a better pi-donor than the O− pi-donor of phosphoranide oxide 10.

ChemInform Abstract: Coordination Compounds Formed Using Three-Center Hydrogen Bridge Bonds: An Extension of the Lewis Donor-Acceptor Coordinate Bond

Abstract In 1959 it was suggested by Parry and Edwards that the concept of a coordinate covalent bond could be extended to include three-center bridge bonds. Although the bond was soon seen in metal borohydrides and salts of metals with other boron hydride anions, questions about ionic contributions to bonding in these structures rendered questionable the concept of valid coordination to a metal through a [boron-hydrogen-metal] three-center bond. Now complexes have been characterized with formulas of ZnCl2·L, (CuClL)2, CuPφ3LCl, Ni(CO)2L, Cr(CO)4L, Mo(CO)4L, and W(CO)4L where L is the bidentate, neutral, σ-bonding ligand which can be compared in some sense to ethylenediamine: In these compounds, as in some of the boron hydrides such as B2H6, the linkage is clearly and unequivocally the basis for compound stability. Relatively unstable complexes of the formula M(CO)5[B2H4 · 2P(CH3)3] have also been characterized where M is Cr and W, and where the [B2H4 · 2P(CH3)3] is a monodentate ligand. Even less stable monodentate complexes of formula Cr(CO)5(H3B · Base) and W(CO)5(H3B · Base) have been characterized where the bases fastened to BH3 are P(CH3)3, N(CH3), and P(C6H5)3. These borane ligands are excellent leaving groups.

Chemical Bonding in Compounds of the CuAl2 Family: MnSn2, FeSn2 and CoSn2

A model for the chemical bonding in the isostructural intermetallic compounds MnSn(2), FeSn(2) and CoSn(2), crystallising in the CuAl(2)-type structure, is developed. The description is based on quantum-chemical calculations applying the electron localisability approach as well as on experimental results obtained from Raman spectroscopy, Hall effect and electrical resistivity measurements on oriented single crystals. The analysis of the chemical bonding reveals four different covalent interactions leading to the formation of interpenetrating 6(3) nets of tin and chains of transition-metal atoms T (T=Mn, Fe or Co) along [001], which are interconnected by three-centre bonds. Polarised Raman measurements on oriented single crystals allowed the determination of the bond strengths, resulting in a bond order of 0.5 within the 6(3) nets, while the three-centre interactions show bond orders of up to 1. Measurements show a metal-like temperature dependence of the resistivity. A comparison of the results with the bonding models obtained for the isostructural compounds CuAl(2), TiSb(2) and VSb(2) reveals the influence of the main-group element on the connectivity pattern.

Monoborane NHC Adducts in the Coordination Sphere of Transition Metals

Irradiation of various carbonyl complexes in the presence of 1,3-dimethylimidazol-2-ylideneborane (IMe·BH3) afforded the new borane complexes [CpMn(CO)2(η1-H3B−IMe)] and [M(CO)5(η1-H3B−IMe] (M = Cr, Mo, W). With the exception of [Mo(CO)5(η1-H3B−IMe], which was detected only in solution, the solid-state structures of all species were validated by single-crystal X-ray diffraction. The NHC−BH3 moiety was found to be coordinated to the metal center through a B−H−M three-center two-electron bond presumably without any B−M interaction. π-Back-donation from the metal center to the boron-containing ligand is most likely negligible.

Dichloridobis(N,N′-diethylthiourea-κS)mercury(II)

There are two mol­ecules in the asymmetric unit of the title compound, [HgCl2(C5H12N2S)2]. In both mol­ecules, the N,N′-diethyl­thio­urea ligands exhibit a cis,trans geometry around their C—N amide bonds. The shapes of the mol­ecules are, to a large extent, determined by intra­molecular N—H⋯Cl hydrogen bonds formed by the N—H groups from the cis amide groups. In one mol­ecule, these groups are involved in three-center hydrogen bonds involving both chloride ligands, whereas in the other mol­ecule only one Cl ligand takes part in intra­molecular hydrogen bonding. The coordination around the Hg atom is distorted tetra­hedral with an S2Cl2 donor set. Inter­molecular hydrogen bonds between N—H groups from the trans amide units of the thio­amide ligands and the chloride ligands connect the mol­ecules into a polymeric chain extending along the c axis. One of the ethyl groups of the N,N′-diethyl­thio­urea ligands is disordered over two positions in one of the mol­ecules, with an occupancy of 0.654 (17) for the major component.

Theoretical Study of Hypervalent Bonds in 1,6-Diaza-1,6-dihydro- and 1,6-Dihydro-1,6-dioxapentalene Systems with a Heteroatom X at 6a Position (X = 14–16 Group Atoms)

Abstract The present study theoretically investigated hypervalent bonding systems with the skeleton of pentalene. Geometries and energetics were examined by density functional theory calculations with triple-zeta class basis sets. The bond energies of the O–X and N–X hypervalent three-center four-electron bonds were estimated. Furthermore, the relationships between the bond-switching equilibration reactions and the stabilities of the hypervalent bonding intermediates were examined.

N′-[Bis(benzylsulfanyl)methylidene]-4-methoxybenzohydrazide

In the title compound, C23H22N2O2S2, the dihedral angles between the 4-meth­oxy-substituted phenyl ring and the other two phenyl rings are 84.4 (4) and 77.7 (1)°, respectively, while the dihedral angle between the two phenyl rings is 57.5 (2)°. The amino group is not involved in an N—H hydrogen bond. The crystal packing is established by inter­molecular C—H⋯O packing inter­actions involving a relatively rare weak three-center hydrogen bond between the keto O atom and H atoms of the two nearby phenyl rings, which link the mol­ecules into chains running along the a axis. Additional weak inter­molecular hydrogen-bond inter­actions between the 4-meth­oxy O atom and one of the phenyl rings and provide added stability to the crystal packing.

Bifurcated Hydrogen Bonds Stabilize Fibrils of Poly(l-glutamic) Acid

Model fibrillating homopolypeptides have been providing many insightful analogies to the clinically important phenomena of protein misfolding and amyloidogenesis. Here we show that the beta(2) structural variant of poly(l-glutamic) acid forms fibrils with an amyloid-like morphology, ability to enhance fluorescence of thioflavin T, and seeding properties. The beta(2) fibrils are formed upon heating of aqueous solutions of alpha-helical poly(l-glutamic) acid, which leads to a significant increase of pD (pH) of unbuffered samples and a concomitant precipitation of fibrils with unusual infrared traits: amide I' band being dramatically red-shifted to 1596 cm(-1), and the -COOD stretching band split into two peaks around 1730 and 1719 cm(-1). We are proposing that formation of three-center hydrogen bonds involving bifurcated peptide carbonyl acceptors (>C=O) and main chains' NH, as well as side chains' -COOH proton donors is likely to underlie the observed infrared characteristics of beta(2) fibrils. Such bonds provide additional conformational constraints in a tightly packed environment around glutamate side chains resulting in the decreased overall acidity of the polypeptide. The presence of bifurcated hydrogen bonds in amyloid fibrils may be an overlooked factor in fibrils' robustness, thermodynamic stability and the ability to propagate their own growth.