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     

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     

A new unconventional halogen bond C?X···H?M between HCCX (X = Cl and Br) and HMH (M = Be and Mg): An ab initio study

In this article, a new type of halogen‐bonded complex YCCX···HMY (X = Cl, Br; M = Be, Mg; Y = H, F, CH₃) has been predicted and characterized at the MP2/aug‐cc‐pVTZ level. We named it as halogen‐hydride halogen bonding. In each YCCX···HMY complex, a halogen bond is formed between the positively charged X atom and the negatively charged H atom. This new kind of halogen bond has similar characteristics to the conventional halogen bond, such as the elongation of the C? X bond and the red shift of the C? X stretch frequency upon complexation. The interaction strength of this type of halogen bond is in a range of 3.34–10.52 kJ/mol, which is smaller than that of dihydrogen bond and conventional halogen bond. The nature of the electrostatic interaction in this type of halogen bond has also been unveiled by means of the natural bond orbital, atoms in molecules, and energy decomposition analyses. © 2009 Wiley Periodicals, Inc. J Comput Chem 2010     

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.     

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.     

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.     

Why is N···Be distance of NH3H+···DBeH shorter than that of NH3D+···HBeH? paradoxical geometrical isotope effects for partially isotope‐substituted dihydrogen‐bonded isotopomers

The partial isotope substitution for the change of geometrical parameters, interaction energies, and nuclear magnetic shielding tensors (σ) of dihydrogen‐bonded NH₃X⁺···YBeH (X, Y = H, D, and T) systems is analyzed. Based on the theoretical calculation, the distance between heavy atoms R_N···Be of NH₃H⁺···DBeH is clearly found to be shorter than that in NH₃D⁺···HBeH. Such apparently paradoxical geometrical isotope effect (GIE) on R_N···Be is revealed by the cooperative effect of two kinds of (1) primary covalent‐bonded GIE and (2) secondary dihydrogen‐bonded one. We have demonstrated that (1) the covalent bond lengths become shorter by heavier isotope‐substitution and (2) the dihydrogen‐bonded distance R_X···Y becomes shorter by heavier Y and lighter X isotope‐substitution due to the difference of electronic structure reflected by the nuclear distribution. We have also found that interaction energy of NH₃H⁺···DBeH is stronger than that of NH₃D⁺···HBeH and isotopic deshielding effect of magnetic shielding becomes large in lighter isotope. © 2013 Wiley Periodicals, Inc.     

Amide‐Directed Tandem C?C/C?N Bond Formation through C?H Activation

The transformation of C? H bonds into other chemical bonds is of great significance in synthetic chemistry. C? H bond‐activation processes provide a straightforward and atom‐economic strategy for the construction of complex structures; as such, they have attracted widespread interest over the past decade. As a prevalent directing group in the field of C? H activation, the amide group not only offers excellent regiodirecting ability, but is also a potential C? N bond precursor. As a consequence, a variety of nitrogen‐containing heterocycles have been obtained by using these reactions. This Focus Review addresses the recent research into the amide‐directed tandem C? C/C? N bond‐formation process through C? H activation. The large body of research in this field over the past three years has established it as one of the most‐important topics in organic chemistry.     

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     

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     

An efficient synthesis of phosphenimidous esters,RO?PN?Ar

Trimethylsilyltrifluoromethane sulfonate is shown to be an efficient catalyst for the elimination of Me₃SiCl from N-trimethylsilyl-N-(2,4,6-tri-tert-butylphenyl)amidochlorophosphites la-f , leading to the phosphenimidous esters 3a–f. The crystal structures of phosphites 1a and 1d provide a stereochemical explanation for the better thermal stability of 1d On the basis of these observations a convenient and general synthesis of phosphenimidous esters 3a–f is presented.     

Rhodium‐Catalyzed ortho‐Selective C?F Bond Borylation of Polyfluoroarenes with Bpin?Bpin

An ortho‐selective C F bond borylation between N‐heterocycle‐substituted polyfluoroarenes and Bpin‐Bpin with simple and commercially available [Rh(cod)₂]BF₄ as a catalyst is now reported. The reaction proceeds under mild reaction conditions with high efficiency and broad substrate scope, even toward monofluoroarene, thus providing a facile access to a wide range of borylated fluoroarenes that are useful for photoelectronic materials. Preliminary mechanistic studies reveal that a Rh^III/V catalytic cycle via a key intermediate rhodium(III) hydride complex [(H)Rh^IIIL_n(Bpin)] may be involved in the reaction.     

The Morita?Baylis?Hillman Reaction of Chiral Highly Oxygenated Cyclopent‐2‐enones

The Morita? Baylis? Hillman (MBH) reactions of (4S,5R,7R,8R)‐ and (4R,5R,7R,8R)‐4‐hydroxy‐7,8‐dimethoxy‐7,8‐dimethyl‐6,9‐dioxaspiro[4.5]dec‐2‐en‐1‐ones ( 2 and 3 , resp.) with aldehydes using various catalysts were studied. A combination of Bu₃P/phenol in THF was found being optimum conditions giving the corresponding MBH adducts with high diastereoisomeric ratios. After separation, each stereomerically pure isomer of the MBH adducts was subjected to hydrolysis employing 1% aq. CF₃COOH (TFA) in a water bath of an ultrasonic cleaner to afford the corresponding polyhydroxylated cyclopentenones in good yields.