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     

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     

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     

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.     

Attempted 1,3-trimethylsilyl migration in Me3Si?PSN?R system

A dimer of thioxo-N-t-butylimino(trimethylsiloxy)-phosphorane 5 has been prepared by reaction of tris(trimethylsilyl) phosphine with N-sulfinyl-N-tert-butylamine. The structure of 5 has been confimed by X-ray analysis data. 1-Aza-2-thia-3-phosphaallene 1 , thiaphosphaziridine 3 , iminophosphine P-sulfide 4 are postulated as intermediates of the reaction studied.     

Does a Stabilising Interaction Favouring the Z,Z Configuration of ?S‐NSN‐S? Systems Exist?

The existence of the orbital interaction presented in the literature as being the cause for the stabilisation of the Z,Z configuration of Ph-S-N=S=N-S-Ph (1) and its derivatives in the crystal phase, has been investigated. The results of theoretical calculations at the DFT/B3LYP/6-311+G* level of theory suggest that such a stabilising interaction might not exist or be extremely weak and that packing forces must be the main cause of the observed Z,Z configuration in the solid. To reach this conclusion structural and energetic parameters were combined to study the bonding in these -S-N=S=N-S- systems. For the analogous Ph-Se-N=S=N-Se-Ph (2) in particular the isomeric equilibrium in solution found in the variable-temperature 77Se NMR spectrum indicates that, in the gas phase or in solution, the observed Z,Z configuration is not stabilised to a greater extent than the Z,E configuration.     

Methylidene Rare‐Earth‐Metal Complex Mediated Transformations of CN,NN and N?H Bonds: New Routes to Imido Rare‐Earth‐Metal Clusters

Three new patterns of reactivity of rare‐earth metal methylidene complexes have been established and thus have resulted in access to a wide variety of imido rare‐earth metal complexes [L₃Ln₃(μ₂‐Me)₃(μ₃‐Me)(μ ‐ NR)] (L=[PhC(NC₆H₃iPr₂‐2,6)₂]^?; R=Ph, Ln=Y ( 2 a ), Lu ( 2 b ); R=2,6‐Me₂C₆H₃, Ln=Y ( 3 a ), Lu ( 3 b ); R=p‐ClC₆H₄, Ln=Y ( 4 a ), Lu ( 4 b ); R=p‐MeOC₆H₄, Ln=Y ( 5 a ), Lu ( 5 b ); R=Me₂CHCH₂CH₂, Ln=Y ( 6 a ), Lu ( 6 b )) and [{L₃Lu₃(μ₂‐Me)₃(μ₃‐Me)}₂(μ ‐ NR′N)] (R′=(CH₂)₆ ( 7 b ), (C₆H₄)₂ ( 8 b )). Complex 2 b was treated with an excess of CO₂ to give the corresponding carboxylate complex [L₃Lu₃(μ‐η¹:η¹‐O₂CCH₃)₃(μ‐η¹:η²‐O₂C‐CH₃)(μ‐η¹:η¹:η²‐O₂CNPh)] ( 9 b ) easily. Complex 2 a could undergo the selective μ₃‐Me abstraction reaction with phenyl acetylene to give the mixed imido/alkynide complex [L₃Y₃(μ₂‐Me)₃(μ₃‐η¹:η¹:η³‐NPh)(μ₃‐C?CPh)] ( 10 a ) in high yield. Treatment of 2 with one equivalent of thiophenol gave the selective μ₃‐methyl‐abstracted products [L₃Ln₃(μ₂‐Me)₃(μ₃‐η¹:η¹:η³‐NPh)(μ₃‐SPh)] (Ln=Y ( 11 a ); Lu ( 11 b ). All new complexes have been characterized by elemental analysis, NMR spectroscopy, and most of the structures confirmed by X‐ray diffraction.     

N-alkyl-C-polyfluoroalkyl-C-chlorosulfinimides RFC(Cl)SN?R

The N-alkyl-C-polyfluoroalkyl-C-chlorosulfinimides R_FC(Cl)SN R have been investigated. Some aspects of their thermal stability and their [3 + 2] and [3 + 1] cycloaddition reactions have been examined.     

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     

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.     

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.     

Transition‐metal‐catalyzed aminations and aziridinations of C?H and CC bonds with iminoiodinanes

Catalytic insertion or addition of a metal‐imido/nitrene species, generated from reaction of a transition‐metal catalyst with iminoiodanes, to C? H and C?C bonds offers a convenient and atom economical method for the synthesis of nitrogen‐containing compounds. Following this groundbreaking discovery during the second half of the last century, the field has received an immense amount of attention with a myriad of impressive metal‐mediated methods for the synthesis of amines and aziridines having been developed. This review will cover the significant progress made in improving the efficiency, versatility and stereocontrol of this important reaction. This will include the various iminoiodanes, their in situ formation, and metal catalysts that could be employed and new ligands, both chiral and non‐chiral, which have been designed, as well as the application of this functional group transformation to natural product synthesis and the preparation of bioactive compounds of current therapeutic interest. DOI 10.1002/tcr.201100018     

Ab initio and density functional studies on bonding nature of the N?N bonds in 1,2,5‐trinitroimidazole and 1,2,4,5‐tetranitroimidazole

The bonding nature of the N N bonds in 1,2,5‐trinitroimidazole ( I ) and 1,2,4,5‐tetranitroimidazole ( II ) was examined with various levels of ab initio and density functional (DF) theories. The second‐order Møller–Plesset perturbation method (MP2) with the 6‐31G** basis set has predicted significantly long N N bond lengths in I and II , that is, 1.737 and 1.824 Å, respectively. Two DF theories, BLYP/6‐31G** and BP86/6‐31G**, provided similar results to those of MP2/6‐31G**. On the other hand, Hartree–Fock (HF) calculation with the 6‐311++G** basis set evaluated these bond lengths of I and II to be 1.443 and 1.414 Å, respectively. Bond properties including the bond critical density are strongly dependent on the equilibrium bond length. Thus, accurate prediction of geometric parameters is of particular importance to derive reliable bond properties. Especially, a substantial difference in bonding properties is observed when the electron correlation effect is included. According to our analyses with bonding natures and CHELPG charges at the MP2 level, (1) the N N bonds of I and II appear to have a significant ionic nature, and (2) the 1‐nitro group bears a considerable positive charge and has attractive electrostatic interactions with O atoms of adjacent nitro groups. Although all the theories utilized in this study predict that both I and II are stable in their potential‐energy surfaces, significantly long N N bond lengths calculated with MP2 and DF theories imply a strong hyperconjugation effect, which may explain a tendency to form a salt in these compounds easily. ©1999 John Wiley & Sons, Inc. Int J Quant Chem 72: 145–154, 1999     

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     

The nature of the N?O bond in amine oxides

Despite the ubiquitous presence of amine oxides in chemistry, there is no consensus about the nature of the N O bond in these compounds. In this work, we have used electron density analysis to investigate the nature of this bond in substituted amine oxides, R₃NO, and have compared it with the nature of the N O bond in hydroxylamines, R₂NOR, and model molecules that have well-established chemical bond character. The results showed that the N O bond length and relative stability are proportional to the inductive effect of the substituents. Quantum chemical topology, natural bond orbitals (NBO), and natural resonance theory (NRT) analyses indicated that the N O bond is polar covalent in all the studied amine oxides, but the ionic contribution is different. NBO and NRT analyses revealed that molecules with more electronegative substituents have strongly delocalized N O and N R bonds, whereas molecules with electropositive substituents have localized bonds.     

Protonation of 2H‐Azaphosphirene Complexes: P?N Bond Activation and Ring‐Expansion Reactions

P? N bond activation of 2H‐azaphosphirene complexes 1 and 2 by using triflic acid led to ring expansion in the presence of nitriles. In the absence of nitriles, the reaction surprisingly afforded two haptomeric N‐protonated 1‐aza‐3‐phospha‐butadiene complexes in the case of complex 1 , whereas the N‐protonated 2H‐azaphosphirene complex [H‐ 2 ]⁺ was characterized by NMR spectroscopy.

     

Mechanistic Insight into the NN Bond‐Cleavage of Azo‐Compounds that was Induced by an Al?Al‐bonded Compound [L2−AlII?AlIIL2−]

An α‐diimine‐stabilized Al? Al‐bonded compound [L^2?Al^II? Al^IIL^2?] (L=[{(2,6‐iPr₂C₆H₃)NC(Me)}₂]; 1 ) consists of dianionic α‐diimine ligands and sub‐valent Al²⁺ ions and thus could potentially behave as a multielectron reductant. The reactions of compound 1 with azo‐compounds afforded phenylimido‐bridged products [L^?Al^III(μ₂‐NPh)(μ₂‐NAr)Al^IIIL^?] ( 2 – 4 ). During the reaction, the dianionic ligands and Al²⁺ ions were oxidized into monoanions and Al³⁺, respectively, whilst the [NAr]^2? imides were produced by the four‐electron reductive cleavage of the N?N double bond. Upon further reduction by Na, the monoanionic ligands in compound 2 were reduced to the dianion to give [(L^2?)₂Al^III₂(μ₂‐NPh)₂Na₂(thf)₄] ( 5 ). Interestingly, when asymmetric azo‐compounds were used, the asymmetric adducts were isolated as the only products (compounds 3 and 4 ). DFT calculations indicated that the reaction was quite feasible in the singlet electronic state, but the final product with the triplet‐state monoanionic ligands could result from an exothermic singlet‐to‐triplet conversion during the reaction process.