Lone Pair Interactions Research Articles

Role of lone pair and π-orbital interaction in formation of water nanostructures confined in carbon nanotubes

A detailed analysis on the geometrical and electronic properties of confined water nanostructures in pristine and functionalized (7,0) and (10,0) carbon nanotubes (CNT) is presented. Confined water molecules within these CNTs form similar ‘water-chain’, ‘water-cluster’ and ‘water-tube’ like nanostructures. From the analysis of electronic properties it is clearly evident that the formation of these nanostructures is determined by the interplay between water lone-pair–CNT π orbital interaction and hydrogen bonding between water molecules.

Theoretical and experimental study of lone pair interactions in THF/chloranilic acid system

Crystallization of a multi-component molecular crystal that consists of chloranilic acid with THF as solvate afforded the general formula C6H2O4Cl2� THF. Its crystal structure is new and reveals new example of cooperative lone pair-p interactions (oxygen of THF to centroid of chloranilic distance of 3.258 A u ) beside others (e.g., hydrogen bonding OH��� O) with new experimental evi- dence of receptor/solvent as a lone pair donor. This has been supported by computational methods, mainly, DFT and RIMP2 levels of theory (-48.3 kJ/mol). In addition, several potential curve surfaces are obtained to test the strength and type of every notable interaction in the lattice.

The effect of the nitrogen non-bonding electron pair on the NMR and X-ray in 1,3-diazaheterocycles

The effect of the nitrogen nonbonding electron pair on the 1JC,H values of 1,3-diazaheterocycles was analyzed and compared to 1,5-diazabiciclo[3.2.1]octanes, which have a restricted conformation. The 1JC,H values were measured by observing the 13C satellites in the 1H NMR spectra and then determining the 1H-coupled 13C NMR spectra. The 1JC,H values are 10Hz larger when the α-hydrogen is synperiplanar rather than antiperiplanar to the nonbonding electron pair on the nitrogen, which serves as experimental evidence of the orbital nN→σ∗C,Hap interactions. In addition, the homoanomeric effect from the interactions of the nitrogen lone pair with the antibonding orbital of the equatorial hydrogen, which was in the β position, was discussed (nN→σ∗C(β),Heq).

Molecular structures of antitumor active Pd(II) and Pt(II) complexes of N,N-donor benzimidazole methyl ester

[MLCl2] · zH2O · C2H5OH (L = 2-[(1H-benzimidazol-2-ylmethyl)-amino]-benzoic acid methyl ester; M = Pd, z = 2; M = Pt, z = 0) complexes were synthesized as potential antitumor compounds and their structures were elucidated by elemental analysis and spectroscopic data. Theoretical molecular structures were investigated by the DFT/B3LYP method using the LANL2DZ basis set. The calculated molecular parameters, bond distances, and angles, revealed a square-planar geometry around the metal through pyridine-type nitrogen (Npy) of benzimidazole and the secondary amino group (NHsec). The lone pair interaction LP(2)O48 of ethanol with anti-bonding σ*(C(16)–H(29)) is an evidence for charge transfer from ethanol to platinum. The electronic movement and assignment of electronic spectra were carried out by TD-DFT calculations. The ligand in comparison to its metal complexes was screened for antibacterial activity and cytotoxicity.

Complexes of germanium chlorides (RnGeCl4-n, n=0-3; R=Me, Ph) with redox active N-hetero­aromatic ligands: an electrochemical study

Methyl and phenyl germanium chlorides (RnGeCl4-n, n=1, 2, 3), just like GeCl4, form complexes with electroactive bidentate (2,2'-bipyridine) and monodentate (imidazole, pyrimidine and 2,6-dichloro-pyridine) ligands, RnGeCl4-n‧Lx (x=1 or 2 for bi- and monodentate Ls, respectively), which were studied by cyclic voltammetry and electron paramagnetic resonance (EPR) spectroscopy supported by density functional theory (DFT) calculations. Dative interactions of lone pair of N of these heteroaromatic ligands towards Ge lower the reduction potential Ep of such complexes by about 1 V compared to own reduction potential Eo of L. Electron transfer to these complexes is reversible, resulting in corresponding anion radicals. Elimination of Cl- anion from these species leads to L-coordinated radicals whose one-electron reduction is also reversible. Real-time, time-dependent EPR spectro­electrochemistry of electrogenerated anion radicals of complexes with 2,2'-bipyridine (bipy) has shown that spin in these species is delocalized on the bipy moiety; nitrogen hfc constants suggest that two N atoms are non-equivalent and occupy different positions in the Ge environment. These findings are supported by DFT calculations.

Coordination chemistry of Ag(i) with bridging ligands based on pyrazolyl–pyridine termini: polymers, helicates and a bow-tie

A series of Ag(I) complexes has been prepared containing bridging ligands based on two pyrazolyl–pyridine ligands connected by a flexible spacer. Crystallographic investigations reveal a remarkable range of structural types from simple mononuclear complexes to dinuclear double helicates, a distorted ‘bow-tie’ metallamacrocycle, and one-dimensional chains including a triple helical chain based on double helical molecular units linked by Ag⋯Ag contacts. The different structures arise as a result of the different interactions dominating in each complex, including aromatic π-stacking, Ag⋯Ag interactions, exocyclic lone pair interactions and inter-ligand π-stacking.

(B15c5)BiI3(I2): Molecular Benzo-15-Crown-5―BiI3 Complexes Bridged by Iodine Molecules to Chains

The reaction of bismuth triiodide with iodine and benzo-15-crown-5 in ethanol/dichloromethane yielded red single crystals of (b15c5)BiI3(I2) (monoclinic, P21/c (no. 14), a = 1376.9(1), b = 1172.7(1), c = 1700.2(2) pm, b = 115.197(6), V = 2484.1(4)·106 pm3, Z = 4). Neutral pseudo-octahedral complexes (b15c5)BiI3 are connected by secondary bonding interactions via iodine molecules to chains. Electronic structure calculations of the neutral complex (b15c5)BiI3 reveal that the compound can indeed be described as b15c5 interacting with a molecular BiI3 unit. However, bonding has to be mainly electrostatic as the interactions of the bismuth 6s lone pair with the 2p orbitals of the oxygen atoms of the crown ether are clearly antibonding.

Theoretical study of hydrazine adsorption on Pt(111): Anti or cis?

Hydrazine (N 2H 4) adsorption on metal surface is important due to its application in the direct hydrazine fuel cell technology. First principles DFT calculations have been carried out to understand the structure and mechanism of hydrazine adsorption on Pt(111). Calculations revealed that configuration with hydrazine adsorbed on its anti-conformation yields the largest adsorption energy suggesting it to be the most stable structure on Pt(111). This result was found to be in disagreement with available XPS results which favor the adsorption on cis-conformation as the most stable configuration. However, by taking into account the energy cost for orbital re-hybridization and internal rotation involves in the adsorption, it was found that the interaction strength between adsorbate and substrate is comparably equal for adsorption on both anti and cis-conformations that indicates the feasibility of the adsorption in cis-conformation to occur. Charge transfers from lone-pair orbitals belong to the highest occupied molecular orbital (HOMO) and second highest occupied molecular orbital (S-HOMO) were found to be important in the formation of the bonding. The π-anti-bonding HOMO lone-pair transfers its charge to the surface which stabilizes the internal structure of the molecule and responsible for the stable anti-conformation adsorption structure. The interaction of the π-bonding S-HOMO lone pair with the surface was found to be dative type and plays an important role in the stabilization of cis-conformation adsorption structure.

Theoretical study on the interaction of sulfur‐ and aminopyridine‐containing chelating resins with Hg(II) and Pb(II)

AbstractThe geometries and energetics of complexes of Hg(II) and Pb(II) with sulfur‐ and aminopyridine‐containing chelating resin including crosslinked polystyrene immobilizing 2‐aminopyridine via sulfur‐containing (PVBS‐AP), sulfoxide‐containing (PVBSO‐AP), and sulfone‐containing (PVBSO2‐AP) spacer arms have been investigated theoretically, and thus interactions of the metal ions with chelating resins were evaluated. The results indicate that PVBS‐AP behaves as a tridentate ligand to coordinate with the metal ions by S and two N atoms to form chelating compounds with S atom playing a dominant role in the coordination, whereas PVBSO‐AP and PVBSO2‐AP interact with metal cations, respectively, in a tricoordinate manner by O and two N atoms forming chelating complexes. Furthermore, it is revealed that O and N2 atoms of PVBSO‐AP are the main contributor of coordination to Hg(II), whereas N2 atom of PVBSO2‐AP is mainly responsible for the coordination to Hg(II). For PVBSO‐AP‐Pb2+ and PVBSO2‐AP‐Pb2+ complex, the coordination is dominated by the synergetic effect of N1, N2, and O atoms. Natural bond orbital and second‐order perturbation analyses suggest that the charge transfer from the chelating resins to metal ions is mainly dominated by the interactions of lone pair of electrons of the donor atoms with the unoccupied orbitals of metal ions. Hg(II) complexes exhibit larger binding energies than the corresponding Pb(II) complexes, implying the chelating resins exhibit higher affinity toward Hg(II), which is consistent with the experimental results. Combined the theoretical and experimental results, further understanding of the structural information of the complexes and the coordination mechanism was achieved. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011

Supramolecular assemblies involving anion–π and lone pair–π interactions: experimental observation and theoretical analysis

Two nickel(II) malonate coordination compounds, namely (C5H7N2)4[Ni(C3H2O4)2(H2O)2](ClO4)2 (1) and (C5H7N2)4[Ni(C3H2O4)2(H2O)2](PF6)2 (2) [where C5H7N2 = protonated 2-aminopyridine, C3H4O4 = malonic acid, ClO4− = perchlorate, PF6− = hexafluoridophosphate], have been synthesized from purely aqueous media, and their single-crystal structures have been determined by X-ray diffraction. As anticipated, various weak forces, i.e. lone pair–π, π–π and anion–π interactions, play a key role in stabilizing the self-assembly process observed for both compounds. Intricate combinations of lone pair–π, π–π and anion–π interactions of the type lone pair–π/π–π/π–anion–π/π–lone pair and lone pair–π/π–π/π–anion are observed that are fully described, including by computational methods. The theoretical calculations allow estimating the strength of these π contacts.

ChemInform Abstract: The Role of Lone-Pair Interactions in the Chemistry of the Monosaccharides. Stereoelectronic Effects in Unsaturated Monosaccharides.

ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.

Synthesis and characterization of nitrogen‐linked carbazole‐containing fluorescent polymers

AbstractWe have prepared four light‐emitting polymers bearing a chromophore composed of carbazole and fluorene by the Suzuki coupling polycondensation. Two nonconjugated polymers (P3CzBFXy and P2CzFXy) had a chromophore tethered by the p‐xylylene spacer, whose connection point between carbazole and fluorene in addition to the number of fluorene unit was systematically changed to investigate the emission wavelength and intensity. The red‐shifted absorption and emission maximum wavelengths together with the improved fluorescence quantum yield of polymers P3CzBFXy and P2CzFXy indicate that the increment of the number of para‐connected benzene rings included in the chromophore effectively extends the conjugation length. The fact that polymer P3CzBFXy has longer wavelength absorption and emission spectra also indicates the interaction of the carbazole nitrogen lone pair with the oligophenylene moiety. Other two polymers P3CzFPy and P3CzFPym having the heterocycle directly bound to the carbazole nitrogen were prepared to know the character of the carbazole nitrogen lone pair and their influence on the fluorescence behavior. The fluorescence spectra of polymer P3CzFPym bearing the pyrimidine ring gradually red‐shifted in conjunction with the decrease of fluorescence quantum yield on going from toluene solution to CHCl3 solution because of the intramolecular charge transfer at the excited state. © 2010 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 48: 3729–3735, 2010

Synthesis of a d-Ala-d-Ala peptide isostere via olefin cross-metathesis and evaluation of vancomycin binding

The alkene peptide isostere for the d-Ala-d-Ala dipeptide was synthesized via a convergent approach utilizing olefin cross-metathesis. The new isostere was then evaluated for binding to the last resort antibiotic, vancomycin. The alkene isostere exhibited a KD=90μM in comparison to the native peptide (KD=2.3μM) and Lac mutant (KD=2300μM). This study demonstrates that loss of binding in vancomycin resistant strains as a result of a d-Ala to d-Lac mutation is from both the loss of a crucial hydrogen bond and introduction of a repulsive lone pair interaction.

Supramolecular Assembly of Mg(II) Complexes Directed by Associative Lone Pair−π/π−π/π−Anion−π/π−Lone Pair Interactions

Two Mg(II) malonate complexes with protonated 2-aminopyridine and protonated 2-amino-4-picoline as counterions, namely, (C(5)H(7)N(2))(4)[Mg(C(3)H(2)O(4))(2)(H(2)O)(2)](ClO(4))(2) (1) and (C(6)H(8)N(2)H)(2)[Mg(C(3)H(2)O(4))(2)(H(2)O)(2)] x 4 H(2)O (2) [C(5)H(7)N(2) = protonated 2-aminopyridine, C(3)H(4)O(4) = malonic acid, C(6)H(8)N(2)H = protonated 2-amino-4-picoline], have been synthesized from purely aqueous media, and their crystal structures have been determined by single-crystal X-ray diffraction. The role of lone pair...pi interactions in stabilizing the self-assembly process appears to be of great importance in both complexes. Additional weak forces like anion...pi and noncovalent O...O interactions are also found to be operating in 1. A rare combination of lone pair...pi and anion...pi interactions in 1, of the type lone pair...pi/pi...pi/pi...anion...pi/pi...lone pair, is observed, and this unusual supramolecular network is fully described here. An attempt to prepare an analogous complex with 2-amino-4-picoline resulted in 2, which is isomorphous with our recently reported transition-metal complexes of the type (C(6)H(8)N(2)H)(2)[M(C(3)H(2)O(4))(2)(H(2)O)(2)] x 4 H(2)O (M = Ni/Co/Mn). A high-level DFT-D study (RI-B97-D/TZVP) has been used to characterize the different noncovalent interactions present in the solid state. We have also analyzed some crystal fragments to examine energetically some important assemblies that drive the crystal packing. Finally, we have studied the influence of magnesium on some hydrogen-bonding interactions.

Reaction of 2,5-bis-trifluoromethyl-1,3,4-oxadiazole with 7-oxanorbornenes revisited: Experimental and quantum-chemical study of reaction stereoselectivity

The stereochemical outcome of reaction of 2,5-bis-trifluoromethyl-1,3,4-oxadiazole with 7-oxanorbornenes under various conditions was investigated. For the first time, microwave irradiation in carrying this type of reactions was used, resulting in comparable yields in significantly shorter reaction times. Regardless on substrate, in all reactions mixtures of the two isomeric O3-[3]polynorbornanes, bent and linear were obtained, with slight preference for bent structure. In some cases, retro Diels–Alder fragmentation was observed resulting in formation of isobenzofuran species. Reaction mechanism was also studied computationally (RHF/6-31G* method), and the origin of stereoselectivity explained by repulsive lone pair interactions between oxygen bridges in the transition state of the 1,3-dipolar addition.

Synthesis and Characterization of Lead(II) Complexes with the 4-Methoxybenzoyltrifluoroacetonate Ligand

To investigate the intermolecular interactions of ligands in lead(II) complexes featuring stereochemical activity of the lone electron pair and noncovalent donor-acceptor interactions giving rise also to multidimensional networks, the compounds [Pb2(phen)2(mbtfa)4] (1) and [Pb2(dmp)2 (mbtfa)4] (2) (phen, dmp and mbtfa− for 1,10-phenanthroline, 2,9-dimethyl-1,10-phenanthroline and 4-methoxybenzoyltrifluoroacetonate ligands, respectively) have been prepared and characterized by elemental analysis and their crystal structures investigated. The structures show the coordination number of Pb(II) to be seven and eight, respectively. Supramolecular structures of 1 and 2 are realized by weak directional intermolecular interactions.

Halogen Bonded Supramolecular Assemblies of [Ru(bipy)(CN)4]2− Anions and N-Methyl-Halopyridinium Cations in the Solid State and in Solution

The interactions between the [Ru(bipy)(CN)(4)](2-) anion and N-methyl-halopyridinium cations have been examined in both the solid state and in solution. In the solid state, crystal structures of [Ru(bipy)(CN)(4)](2-) salts containing iodinated cations (N-methyl-3-iodopyridinium and N-methyl-3,5-diiodopyridinium) show clear C-I...NC(Ru) halogen bonds between the externally directed cyanide lone pairs of the anion and the iodine atoms of the cation which dominates the structures. In contrast the analogous brominated cations (N-methyl-3-bromopyridinium and N-methyl-3,5-dibromopyridinium) do not exhibit C-Br...NC(Ru) interactions in the solid state, with the cyanide groups instead involved in hydrogen bonding, principally to lattice water molecules. The charge-assisted C-I...NC(Ru) interactions are therefore clearly of value as synthons in crystal engineering applications. In CH(2)Cl(2) solution, spectroscopic titrations between [Ru(4,4'-(t)Bu(2)-bipy)(CN)(4)](2-) and both N-methyl-3-iodopyridinium and N-methyl-3-bromopyridinium cations show clear evidence for formation of distinct 1:1, 3:2, and then 2:1 cation/anion adducts with high association constants (>10(7) M(-1) for the first 1:1 association constant). However the presence of identical results using the non-halogenated cation N-methyl-pyridinium indicates that this strong cation/anion association in CH(2)Cl(2) is dominated by electrostatic effects: either C-H...NC(Ru) hydrogen bonds or C-X...NC(Ru) halogen bonds could be involved in the ion pairs but it is the charge-assistance that makes the association strong. This is confirmed by a titration between [Ru(4,4'-(t)Bu(2)-bipy)(CN)(4)](2-) and the neutral halogen-bond acceptor C(6)F(5)I for which the first association constant is very low (ca. 6 M(-1)). The formation of adducts between [Ru(4,4'-(t)Bu(2)-bipy)(CN)(4)](2-) and the various N-methyl-pyridinium cations in solution results in a clear blue-shift of the (1)MLCT absorption maxima associated with the Ru(II) unit, a characteristic consequence of interaction of the cyanide lone pairs with a Lewis-acidic site on the cation. The (3)MLCT luminescence from the [Ru(4,4'-(t)Bu(2)-bipy)(CN)(4)](2-) center, however, does not show the usual associated increase in intensity associated with this blue shift in the (1)MLCT absorptions, most likely because of electron-transfer quenching by the N-methyl-pyridinium cations in the assemblies.

Structures and Energetics of the Cation−π Interactions of Li+, Na+, and K+ with Cup-Shaped Molecules: Effect of Ring Addition to Benzene and Cavity Selectivity

The interactions of alkali metal cations (Li (+), Na (+), and K (+)) with the cup-shaped molecules, tris(bicyclo[2.2.1]hepteno)benzene and tris(7-azabicyclo[2.2.1]hepteno)benzene have been investigated using MP2(FULL)/6-311+G(d,p)//MP2/6-31G(d) level of theory. The geometries and interaction energies obtained for the metal ion complexation with the cup-shaped systems trindene and benzotripyrrole are compared with the results for benzene-metal ion complexes to examine the effect of ring addition to the benzene on structural and binding affinities. The cup-shaped molecules exhibit two faces or cavities (top and bottom). Except for one of the conformers of tris(7-azabicyclo[2.2.1]hepteno)benzene), the metal ions prefer to bind with the top face over bottom face of the cup-shaped molecules. The selectivity of the top face is due to strong interaction of the cation with the pi cloud not only from the central six-membered ring but also from the pi electrons of rim C=C bonds. In contrast, the metal ions under study exhibit preference to bind with the bottom face rather than top face of tris(7-azabicyclo[2.2.1]hepteno)benzene) when the lone pair of electrons of three nitrogen atoms participates in binding with metal ions. This bottom face selectivity could be ascribed to the combined effect of the cation-pi and strong cation-lone pair interactions. As evidenced from the values of pyramidalization angles, the host molecule becomes deeper bowl when the lone pair of electrons of nitrogen atoms participates in binding with cation. Molecular electrostatic potential surfaces nicely explain the cavity selectivity in the cup-shaped systems and the variation of interaction energies for different ligands. Vibrational frequency analysis is useful in characterizing different metal ion complexes and to distinguish top and bottom face complexes of metal ions with the cup-shaped molecules.

Two derivatives of 1,5-disubstituted tetrazoles: 1-(4-nitrophenyl)-1H-tetrazol-5-amine and {(E)-[1-(4-ethoxyphenyl)-1H-tetrazol-5-yl]iminomethyl}dimethylamine

The geometric features of 1-(4-nitrophenyl)-1H-tetrazol-5-amine, C(7)H(6)N(6)O(2), correspond to the presence of the essential interaction of the 5-amino group lone pair with the pi system of the tetrazole ring. Intermolecular N-H...N and N-H...O hydrogen bonds result in the formation of infinite chains running along the [110] direction and involve centrosymmetric ring structures with motifs R(2)(2)(8) and R(2)(2)(20). Molecules of {(E)-[1-(4-ethoxyphenyl)-1H-tetrazol-5-yl]iminomethyl}dimethylamine, C(12)H(16)N(6)O, are essentially flattened, which facilitates the formation of a conjugated system spanning the whole molecule. Conjugation in the azomethine N=C-N fragment results in practically the same length for the formal double and single bonds.

Potential Energy Surfaces for All-trans P5H6+ and P5Me6+ May Be Less Complicated than Anticipated

Burford and co-workers recently (2007) investigated the synthesis, structure, and pseudorotation of a family of cyclotetraphosphinophosphonium ions comprehensively. We now report theoretical computations through the CCSD(T) level to study the conformations of the parent model rings, P5H6(+) and P5Me6(+). The all-trans conformations on the full pseudorotational cycle for the cyclotetraphosphinophosphonium cation (P5H6(+)) and for its methyl-substituted derivative (P5Me6(+)) were located systematically on their potential energy surfaces. The potential energy for the pseudorotational circuit of P5H6(+) is smooth and monotonic with only one minimum ((3)T4) and one maximum ((4)T3), but the analogous P5Me6(+) circuit has two minima. The P5H6(+) and P5Me6(+) potential surfaces appear to be qualitatively very different from that for the well investigated tetrahydrofuran. Since the (3)T4 form of P5H6(+)avoids unfavorable eclipsing PH-PH and lone pair-lone pair interactions, it is the global minimum among all possible P5H6(+) configurations and conformations.