Intermolecular interactions in group 14 hydrides: Beyond C?H···H?C contacts

In line with previous work in which we established the factors that enhance attractive C? H···H? C dihydrogen interactions in alkanes, an extended theoretical analysis of noncovalent intermolecular interactions in group 14 hydrides is presented here. Remarkably, these weak interactions may play a major role in determining the crystal structures adopted by several families of molecules. A combined structural and computational analysis at the MP2 level allowed us to identify and characterize different interactions of the type E? H···H? E and E···H? E (E = Si, Ge, Sn, and Pb), and to find also the most suitable scenario for the establishment of each particular type. The nature of the interactions has been analyzed in terms of natural charges of the atoms involved and a topological analysis of the electron density of several dimers confirms the existence of H···H and H···E attractive contacts. We have observed that the interaction strength increases when descending down the periodic group and that silicon has a marked tendency to establish Si···H? Si interactions. A size‐dependent backbone effect that reinforces H···H dihydrogen interactions in polyhedral systems has also been found.     

Characterization of the N?H···ON and N?H···NO H‐bonds in nitrosamine dimers

Ab initio molecular orbital and DFT calculations have been carried out for three most stable dimers of parent nitrosamine (NA) in order to elucidate the structures and energetics of the dimers. The structures were optimized using HF, B3LYP, and MP2 methods with 6‐311+G(d,p) and 6‐311++G(2d,2p) basis sets. At the optimized geometries obtained at MP2/6‐311++G(2d,2p) level of theory, the energies were evaluated at QCISD/aug‐cc‐pVDZ and CCSD/aug‐cc‐pVDZ levels. The most stable dimer has two N? H···O?N hydrogen bonds and the least stable dimer has two N? H···N?O hydrogen bonds. The natural bond orbital analysis showed that the lpO(N) → BD*(N? N) and lpO(N) → BD*(N? H_b) interactions play a decisive role in the stabilization of the NH···O(N) hydrogen bonds in dimers. The atoms in molecules results reveal that the intermolecular N? H···O(N) H‐bonds in dimers have electrostatic character. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2008     

N?H···S and S?H···N intramolecular hydrogen bond in β‐thioaminoacrolein: A quantum chemical study

The conformational study of β‐thioaminoacrolein was performed at various theoretical levels, HF, B3LYP, and MP2 with 6‐311++G(d,p) basis set, and the equilibrium conformations were determined. To have more reliable energies, the total energies of all conformers were recomputed at high‐level ab initio methods, G2MP2, G3, and CBS‐QB3. According to these calculations, the intramolecular hydrogen bond is accepted as the origin of conformational preference in thialamine (TAA) and thiolimine groups. The hydrogen bond strength in various resonance‐assisted hydrogen bond systems was evaluated by HB energy, geometrical parameters, topological parameters, and charge transfers corresponding to orbital interactions. Furthermore, our results reveal that the TAA tautomer has extra stability with respect to the other tautomers. The population analyses of the possible conformations by NBO predict that the origin of this preference is mainly due to the π‐electron delocalization in framework of TAA forms, especially usual π_C?C → π*_C?S and Lp (N) → π*_C?C charge transfers. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Theoretical study of the S?H···O blue‐shifted hydrogen bond

Theoretical calculations were performed to study the nature of the hydrogen bonds in the complexes HCHO···HSO, HCOOH···HSO, HCHO···HOO, and HCOOH···HOO. The geometric structures and vibrational frequencies of these four complexes at the MP2/6‐31G(d,p) and MP2/6‐311+G(d,p) levels are calculated by standard and counterpoise‐corrected methods, respectively. The results indicate that in the complexes HCHO···HSO and HCOOH···HSO the S? H bond is strongly contracted. In the S? H···O hydrogen bonds, the calculated blue shifts for the S? H stretching frequencies are in the vicinity of 50 cm^?1. While in the complexes HCHO···HOO and HCOOH···HOO, the O? H bond is elongated and O? H···O red‐shifted hydrogen bonds are found. From the natural bond orbital analysis it can be seen that the X? H bond length in the X? H···Y hydrogen bond is controlled by a balance of four main factors in the opposite directions: hyperconjugation, electron density redistribution, rehybridization, and structural reorganization. Among them hyperconjugation has the effect of elongating the X? H bond. Electron density redistribution and rehybridization belong to the bond shortening effects, while structural reorganization has an uncertain influence on the X? H bond length. In the complexes HCHO···HSO and HCOOH···HSO, the shortening effects dominate which lead to the blue shift of the S? H stretching frequencies. In the complexes HCHO···HOO and HCOOH···HOO where elongating effects are dominant, the O? H···O hydrogen bonds are red‐shifted. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2009     

Investigation on the individual contributions of N?H···OC and C?H···OC interactions to the binding energies of β‐sheet models

In this article, the binding energies of 16 antiparallel and parallel β‐sheet models are estimated using the analytic potential energy function we proposed recently and the results are compared with those obtained from MP2, AMBER99, OPLSAA/L, and CHARMM27 calculations. The comparisons indicate that the analytic potential energy function can produce reasonable binding energies for β‐sheet models. Further comparisons suggest that the binding energy of the β‐sheet models might come mainly from dipole–dipole attractive and repulsive interactions and VDW interactions between the two strands. The dipole–dipole attractive and repulsive interactions are further obtained in this article. The total of N? H···H? N and C?O···O?C dipole–dipole repulsive interaction (the secondary electrostatic repulsive interaction) in the small ring of the antiparallel β‐sheet models is estimated to be about 6.0 kcal/mol. The individual N? H···O?C dipole–dipole attractive interaction is predicted to be ?6.2 ± 0.2 kcal/mol in the antiparallel β‐sheet models and ?5.2 ± 0.6 kcal/mol in the parallel β‐sheet models. The individual C^α? H···O?C attractive interaction is ?1.2 ± 0.2 kcal/mol in the antiparallel β‐sheet models and ?1.5 ± 0.2 kcal/mol in the parallel β‐sheet models. These values are important in understanding the interactions at protein–protein interfaces and developing a more accurate force field for peptides and proteins. © 2009 Wiley Periodicals, Inc. J Comput Chem 2010     

Synthesis,Crystal Structure,and IR Investigations of [(NH3)5V?O?V(NH3)5]I4 · NH3 and [(NH3)5Ti?O?Ti(NH3)5]I4 · NH3

The reaction of VI₂ or TiI₃, respectively, with ammonia in the presence of traces of water or oxygen, respectively, leads to [(NH₃)₅M? O? M(NH₃)₅]I₄ · NH₃ with M = V, Ti. Their structures were solved by X-ray single crystal data: Pbca (No. 61), Z = 4, M = V: a = 12.482(4) Å, b = 14.819(6) Å, c = 13.286(5) Å, N(F ? 3σF) = 983, N(variables) = 88, R/R_w = 0.053/0.063, M = Ti: a = 12.628(4) Å, b = 14.970(4) Å, c = 13.359(3) Å, N(F ? 3σF) = 1188, N(variables) = 88, R/R_w = 0.043/0.047. The structures consist of corner sharing octahedra double units [(NH₃)₅M? O? M(NH₃)₅]⁴⁺ with eclipsed conformation which are stacked together according to the motif of a distorted cubic face centered arrangement for the bridging oxygen atoms. IR spectroscopic investigations of the undeuterated vanadium compound and of 5% deuterated samples hint to N? H … I hydrogen bridge bonds and to remarkable π-bonding between the transition metal and the bridging oxygen atoms.     

Effect of Al?H···H?O dihydrogen bond on the reaction between diphenylmethanol and pyrazolate‐bridged dialuminum complex. An ONIOM DFT/AM1 study

To elucidate the nature of the Al? H···H? O dihydrogen bond and its effect on the reaction between diphenylmethanol and pyrazolate‐bridged dialuminum complex, a theoretical study was carried out using the ONIOM(B3LYP/6‐31+G(d,p):AM1) method. Calculations indicate that this reaction is a two‐step process. The first step is nucleophilic addition and the resulting intermediate is stabilized by an Al? H···H? O dihydrogen bond. Topology analyses based on the “atoms‐in‐molecules” theory show that the Al? H···H? O dihydrogen bond in dialuminum intermediate is stronger than normal hydrogen bond. This step is not barrierless, which is contrary to the result predicted by using simplified model. The second step, eliminating a molecule of dihydrogen, requires an activation free energy of 9.9 kcal/mol in gas phase, which implies the simplified model underestimates the energy barrier of this elimination step. ONIOM calculations also show that, using the simplified model without zero‐point energy correction, the dihydrogen bonding strength has been underestimated and unreliable results have been obtained. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2008     

Cooperative influence of water binding to peptides by N?H···OH2 and CO···HOH hydrogen bonds: Study by Ab Initio calculations

In this article, the geometry structures of hydrogen bond chains of formamide and N‐methylacetamide and their hydrogen‐bonded complexes with water were optimized at the MP2/6‐31G* level. Then, we performed Møller–Plesset perturbation method with 6‐311++g**, aug‐cc‐pvtz basis sets to study the cooperative influence to the total hydrogen bond energy by the N? H ··· OH₂ and C?O ··· HOH hydrogen bonds. On the basis of our results, we found that the cooperativity of the hydrogen‐bonded complexes become weaker as N? H ··· OH₂ and C?O ··· HOH hydrogen bonds replacing N? H ··· O?C hydrogen bonds in protein and peptide. It means that the N? H and C?O bonds in peptide prefer to form N? H ··· O?C hydrogen bond rather than to form C?O ··· HOH and N? H ··· OH₂. It is significant for understanding the structures and properties of the helical or sheet structures of protein and peptide in biological systems. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

An insight into C?H···N hydrogen bond and stability of the complexes formed by trihalomethanes with ammonia and its monohalogenated derivatives

A theoretical study of the C? H···N hydrogen bond in the interactions of trihalomethanes CHX₃ (X = F, Cl, Br) with ammonia and its halogen derivatives NH₂Y (Y = F, Cl, Br) has been carried out thoroughly. The complexes are quite stable, and their stability increases in going from CHF₃ to CHCl₃ then to CHBr₃ when Y keeps unchanged. With the same CHX₃ proton donor, enhancement of the gas phase basicity of NH₂Y strengthens stability of the CHX₃···NH₂Y complex. The C? H···N hydrogen bond strength is directly proportional to the increase of proton affinity (PA) at N site of NH₂Y and the decrease of deprotonation enthalpy (DPE) of C? H bond in CHX₃. The CHF₃ primarily appears to favor blue shift while the red‐shift is referred to the CHBr₃. The blue‐ or red‐shift of CHCl₃ strongly depends on PA at N site of NH₂Y. We suggest the ratio of DPE/PA as a factor to predict which type of hydrogen bond is observed upon complexation. The SAPT2+ results show that all C? H···N interactions in the complexes are electrostatically driven regardless of the type of hydrogen bond, between 48% and 61% of the total attractive energy, and partly contributed by both induction and dispersion energies.     

Luminescent Cyanoruthenate(II)?Diimine and Cyanoruthenium(II)?Diimine Complexes

To improve the emission and excited‐state properties of luminescent cyanometalates, new classes of highly solvatochromic luminescent cyanoruthenium(II) and cyanoruthenate(II) complexes of the general formulae [Ru(PR₃)₂(CN)₂($\widehat{NN}$ )] and K[Ru(PR₃)(CN)₃($\widehat{NN}$ )], respectively, were developed. These complexes could be readily synthesized through the ligand‐substitution reaction of K₂[Ru(CN)₄(PR₃)₂] with a diimine ligand. The geometrical isomerism of these complexes was characterized by using various spectroscopic techniques. Their photophysical properties, solvatochromism, and electrochemistry have also been investigated. Our detailed study showed that many of these complexes exhibited extremely environmentally sensitive emissions and significantly improved emission quantum efficiencies and lifetimes compared with the well‐studied tetracyanoruthenate systems.     

Alkyne Insertion into the M?P and M?H Bonds (M=Pd,Ni, Pt,and Rh): A Theoretical Mechanistic Study of the C?P and C?H Bond‐Formation Steps

In hydrogen‐metal‐phosphorus (H M P) transition metal complexes (proposed as intermediates of H P bond addition to alkynes in the catalytic hydrophosphorylation, hydrophosphinylation, and hydrophospination reactions), alkyne insertion into the metal‐hydrogen bond was found much more facile compared to alkyne insertion into the metal‐phosphorus bond. The conclusion was verified for different metals (Pd, Ni, Pt, and Rh), ligands, and phosphorus groups at various theory levels (B3LYP, B3PW91, BLYP, MP2, and ONIOM). The relative reactivity of the metal complexes in the reaction with alkynes was estimated and decreased in the order of Ni>Pd>Rh>Pt. A trend in relative reactivity was established for various types of phosphorus groups: PR₂>P(O)R₂>P(O)(OR)₂, which showed a decrease in rate upon increasing the number of the oxygen atoms attached to the phosphorus center.     

MHSe: The First Hydride Selenides of the Lanthanides (M = La?Nd; Gd?Er,Lu)

The oxidation of most of the lanthanide dihydrides MH₂ (M = La? Nd; Gd? Er, Lu) with equimolar amounts of selenium results in the formation of the first lanthanide hydride selenides MHSe. The presence of alkali chlorides (e.g., NaCl or CsCl) as fluxes secures complete and fast reactions (7 d) at 700–850°C in sealed, arc-welded tantalum capsules (protected by evacuated silica vessels) as well as single-crystalline products (pale bluish-gray hexagonal columns or platelets). Two different structures were determined from X-ray single crystal data for the examples of 2H? CeHSe (hexagonal, P6₃/mmc (no. 194), Z = 2, a = 406.36(4), c = 794.81(9) pm, R1 = 0.0365, wR2 = 0.0766) and 1H? HoHSe (hexagonal, P6 m2 (no. 187), Z = 1, a = 381.56(3), c = 387.28(5) pm, R1 = 0.0140, wR2 = 0.0337). According to X-ray powder data, the hydride selenides MHSe with M = La? Nd proved to be isostructural with 2H-CeHSe, those with M = Gd? Er and Lu crystallize isotypically with 1H? HoHSe just like YHSe. Both structures contain hydrogen in half of the trigonal planar interstices within closest-packed mono-layers of the metals. These layers [(M³⁺)(H^?)_3/3]²⁺ (a,β or b,α) are alternatively sheethed with closest-packed mono-layers of Se^2? (C) along [001], and only the stacking sequence decides whether a “stuffed” WC- (C(a,β)C ? 1 H-MHSe) or a “stuffed” anti-NiAs-type arrangement (C(a,β)C(b,α)C ? 2H? MHSe) emerges.     

A novel single‐electron sodium bond system of H3C···Na?Y (YH,OH, F,CCH, CN,and NC)

A novel single‐electron sodium bond system of H₃C···Na? H (I), H₃C···Na? OH(II), H₃C···Na? F(III), H₃C···Na‐CCH(IV), H₃C···Na? CN (V) and H₃C···Na? NC (VI) complexes has been studied by using MP2/6‐311++G** and MP2/aug‐cc‐pVTZ methods for the first time. We demonstrated that the single‐electron sodium bond H₃C···Na? Y formed between H₃C and Na? Y (Y?H, OH, F, CCH, CN, and NC) could induce the Na? Y increased and stretching frequencies of I–IV and VI are red‐shifted, including the Na? N bond in complex V is blue‐shifted abnormally. The interaction energies are calculated at two levels of theory [MP2, CCSD(T)] with different basis. The results shows that the strength of binding bond in group 2 (IV–VI) with π electrons are stronger than that of group 1 (I–III) without π electrons. For all complexes, the main orbital interactions between moieties H₃C and Na? Y are LP₁(C)→LP*₁(Na). By comparisons with some related systems, it is concluded that the strength of single‐electron bond is increased in the order: hydrogen bond < bromine bond < sodium bond < lithium bond. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Homolytic S?S Bond Dissociation of 11 Bis(thiocarbonyl)disulfides R‐C(S)?S?S?C(S)R and Prediction of A Novel Rubber Vulcanization Accelerator

The structures and energetics of eight substituted bis(thiocarbonyl)disulfides (RCS₂)₂, their associated radicals RCS₂^., and their coordination compounds with a lithium cation have been studied at the G3X(MP2) level of theory for R=H, Me, F, Cl, OMe, SMe, NMe₂, and PMe₂. The effects of substituents on the dissociation of (RCS₂)₂ to RCS₂^. were analyzed using isodesmic stabilization reactions. Electron‐donating groups with an unshared pair of electrons have a pronounced stabilization effect on both (RCS₂)₂ and RCS₂^.. The S? S bond dissociation enthalpy of tetramethylthiuram disulfide (TMTD, R=NMe₂) is the lowest in the above series (155 kJ mol^?1), attributed to the particular stability of the formed Me₂NCS₂^. radical. Both (RCS₂)₂ and the fragmented radicals RCS₂^. form stable chelate complexes with a Li⁺ cation. The S? S homolytic bond cleavage in (RCS₂)₂ is facilitated by the reaction [Li(RCS₂)₂]⁺+Li⁺→2 [Li(RCS₂)]^.+. Three other substituted bis(thiocarbonyl) disulfides with the unconventional substituents R=OSF₅, Gu¹, and Gu² have been explored to find suitable alternative rubber vulcanization accelerators. Bis(thiocarbonyl)disulfide with a guanidine‐type substituent, (Gu¹CS₂)₂, is predicted to be an effective accelerator in sulfur vulcanization of rubber. Compared to TMTD, (Gu¹CS₂)₂ is calculated to have a lower bond dissociation enthalpy and smaller associated barrier for the S? S homolysis.     

Catalytic C?C,C?N,and C?O Ullmann‐Type Coupling Reactions

Copper‐catalyzed Ullmann condensations are key reactions for the formation of carbon–heteroatom and carbon–carbon bonds in organic synthesis. These reactions can lead to structural moieties that are prevalent in building blocks of active molecules in the life sciences and in many material precursors. An increasing number of publications have appeared concerning Ullmann‐type intermolecular reactions for the coupling of aryl and vinyl halides with N, O, and C nucleophiles, and this Minireview highlights recent and major developments in this topic since 2004.     

M4(CH2)4 Cubane‐Type Rare‐Earth Methylidene Complexes: Unique Reactivity toward Unsaturated C?O,C?N,and C?S Bonds

The reactivity of the cubane‐type rare‐earth methylidene complex [Cp′Lu(μ₃‐CH₂)]₄ ( 1 , Cp′=C₅Me₄SiMe₃) with various unsaturated electrophiles was investigated. The reaction of 1 with CO (1 atm) at room temperature gave the bis(ketene dianion)/dimethylidene complex [Cp′₄Lu₄(μ₃‐CH₂)₂(μ₃,η²‐O‐C?CH₂)₂] ( 2 ) in 86 % yield through the insertion of two molecules of CO into two of the four lutetium–methylidene units. In the reaction with the sterically demanding N,N‐diisopropylcarbodiimide at 60 °C, only one of the four methylidene units in 1 reacted with one molecule of the carbodiimide substrate to give the mono(ethylene diamido)/trimethylidene complex [Cp′₄Lu₄(μ₃‐CH₂)₃{iPrNC(=CH₂)NiPr}] ( 3 ) in 83 % yield. Similarly, the reaction of 1 with phenyl isothiocyanate gave the ethylene amido thiolate/trimethylidene complex [Cp′₄Lu₄(μ₃‐CH₂)₃{PhNC(S)=CH₂}] ( 4 ). In the case of phenyl isocyanate, two of the four methylidene units in 1 reacted with four molecules of the substrate at ambient temperature to give the malonodiimidate/dimethylidene complex [Cp′₄Lu₄(μ₃‐CH₂)₂{PhN=C(O)CH₂(O)C?NPh}₂] ( 5 ) in 87 % yield. In this reaction, each of the two lutetium–methylidene bonds per methylidene unit inserted one molecule of phenyl isocyanate. All the products have been fully characterized by NMR spectroscopy, X‐ray diffraction, and microelemental analyses.     

Synthesis and Structure of Amido‐ and Imido(pentafluorophenyl)borane Zirconocene and Hafnocene Complexes: N?H and B?H Activation

Treatment of Me₂S ? B(C₆F₅)_nH_3?n (n=1 or 2) with ammonia yields the corresponding adducts. H₃N ? B(C₆F₅)H₂ dimerises in the solid state through N? H???H? B dihydrogen interactions. The adducts can be deprotonated to give lithium amidoboranes Li[NH₂B(C₆F₅)_nH_3?n]. Reaction of the n=2 reagent with [Cp₂ZrCl₂] leads to disubstitution, but [Cp₂Zr{NH₂B(C₆F₅)₂H}₂] is in equilibrium with the product of β‐hydride elimination [Cp₂Zr(H){NH₂B(C₆F₅)₂H}], which proves to be the major isolated solid. The analogous reaction with [Cp₂HfCl₂] gives a mixture of [Cp₂Hf{NH₂B(C₆F₅)₂H}₂] and the N? H activation product [Cp₂Hf{NHB(C₆F₅)₂H}]. [Cp₂Zr{NH₂B(C₆F₅)₂H}₂] ? PhMe and [Cp₂Hf{NH₂B(C₆F₅)₂H}₂] ? 4(thf) exhibit β‐B‐agostic chelate bonding of one of the two amidoborane ligands in the solid state. The agostic hydride is invariably coordinated to the outside of the metallocene wedge. Exceptionally, [Cp₂Hf{NH₂B(C₆F₅)₂H}₂] ? PhMe has a structure in which the two amidoborane ligands adopt an intermediate coordination mode, in which neither is definitively agostic. [Cp₂Hf{NHB(C₆F₅)₂H}] has a formally dianionic imidoborane ligand chelating through an agostic interaction, but the bond‐length distribution suggests a contribution from a zwitterionic amidoborane resonance structure. Treatment of the zwitterions [Cp₂MMe(μ‐Me)B(C₆F₅)₃] (M=Zr, Hf) with Li[NH₂B(C₆F₅)_nH_3?n] (n=2) results in [Cp₂MMe{NH₂B(C₆F₅)₂H}] complexes, for which the spectroscopic data, particularly ¹J(B,H), again suggest β‐B‐agostic interactions. The reactions proceed similarly for the structurally encumbered [Cp′′₂ZrMe(μ‐Me)B(C₆F₅)₃] precursor (Cp′′=1,3‐C₅H₃(SiMe₃)₂, n=1 or 2) to give [Cp′′₂ZrMe{NH₂B(C₆F₅)_nH_3?n}], both of which have been structurally characterised and show chelating, agostic amidoborane coordination. In contrast, the analogous hafnium chemistry leads to the recovery of [Cp′′₂HfMe₂] and the formation of Li[HB(C₆F₅)₃] through hydride abstraction.     

A simple model for the band structure and D.C. conductivity of an infinite CO···H?N chain perpendicular to the protein backbone

The¹ Hartree–Fock crystal orbital (CO) method in its linear combination of atomic orbitals form was applied to determine the band structure of histone proteins taking 0.041e charge transfer per nucleotide base from the PO groups of poly(guanilic acid) to the arginine, and lysine side chains in histones (see text). Assuming that there are infinite COs, perpendicular to the main chain, formed by the amide groups of one segment of the protein chain bound together by H‐bonds with the C?O groups of another segment of the chain, we have calculated the band structure. From this, we have determined the mobility using the deformation potential approximation. Multiplying this with the mobile electron concentration due to the charge transfer between the PO groups of DNA and the positive side chains in histones, we have obtained for the direct current (D.C.) electron conductivity σ_fib = 1.07 × 10^?9 Ω^?1 cm for a single fiber and after division by the cross‐section of 9.10 × 10^?16 cm², σ_spec = 1.18 × 10⁶ Ω^?1 cm^?1 for the specific conductivity. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2009