N-H···π hydrogen-bonding and large-amplitude tipping vibrations in jet-cooled pyrrole-benzene

The N-H···π hydrogen bond is an important intermolecular interaction in many biological systems. We have investigated the infrared (IR) and ultraviolet (UV) spectra of the supersonic-jet cooled complex of pyrrole with benzene and benzene-d(6) (Pyr·Bz, Pyr·Bz-d(6)). DFT-D density functional, SCS-MP2 and SCS-CC2 calculations predict a T-shaped and (almost) C(s) symmetric structure with an N-H···π hydrogen bond to the benzene ring. The pyrrole is tipped by ω(S(0)) = ±13° relative to the surface normal of Bz. The N···ring distance is 3.13 ?. In the S(1) excited state, SCS-CC2 calculations predict an increased tipping angle ω(S(1)) = ±21°. The IR depletion spectra support the T-shaped geometry: The NH stretch is redshifted by -59 cm(-1), relative to the "free" NH stretch of pyrrole at 3531 cm(-1), indicating a moderately strong N-H···π interaction. The interaction is weaker than in the (Pyr)(2) dimer, where the NH donor shift is -87 cm(-1) [Dauster et al., Phys. Chem. Chem. Phys., 2008, 10, 2827]. The IR C-H stretch frequencies and intensities of the Bz subunit are very similar to those of the acceptor in the (Bz)(2) dimer, confirming that Bz acts as the acceptor. While the S(1)←S(0) electronic origin of Bz is forbidden and is not observable in the gas-phase, the UV spectrum of Pyr·Bz in the same region exhibits a weak 0 band that is red-shifted by 58 cm(-1) relative to that of Bz (38?086 cm(-1)). The origin appears due to symmetry-breaking of the π-electron system of Bz by the asymmetric pyrrole NH···π hydrogen bond. This contrasts with (Bz)(2), which does not exhibit a 0 band. The Bz moiety in Pyr·Bz exhibits a 6a band at 0 + 518 cm(-1) that is about 20× more intense than the origin band. The symmetry breaking by the NH···π hydrogen bond splits the degeneracy of the ν(6)(e(2g)) vibration, giving rise to 6a' and 6b' sub-bands that are spaced by ～6 cm(-1). Both the 0 and 6 bands of Pyr·Bz carry a progression in the low-frequency (10 cm(-1)) excited-state tipping vibration ω', in agreement with the change of the ω tipping angle predicted by SCS-MP2 and SCS-CC2 calculations.     

Rapid and accurate evaluation of the binding energies and the individual N-H···O=C, N-H···N, C-H···O=C, and C-H···N interaction energies for hydrogen-bonded peptide-base complexes

The binding energies of thirty-six hydrogen-bonded peptide-base complexes, including the peptide backbone-ase complexes and amino acid side chain-base complexes, are evaluated using the analytic potential energy function established in our lab recently and compared with those obtained from MP2, AMBER99, OPLSAA/L, and CHARMM27 calculations. The comparison indicates that the analytic potential energy function yields the binding energies for these complexes as reasonable as MP2 does, much better than the force fields do. The individual N H…O=C, N H…N, C H…O=C, and C H…N attractive interaction energies and C=O…O=C, N H…H N, C H…H N, and C H…H C repulsive interaction energies, which cannot be easily obtained from ab initio calculations, are calculated using the dipole-dipole interaction term of the analytic potential energy function. The individual N H…O=C, C H…O=C, C H…N attractive interactions are about 5.3±1.8, 1.2±0.4, and 0.8 kcal/mol, respectively, the individual N H … N could be as strong as about 8.1 kcal/mol or as weak as 1.0 kcal/mol, while the individual C=O…O=C, N H…H N, C H…H N, and C H…H C repulsive interactions are about 1.8±1.1, 1.7±0.6, 0.6±0.3, and 0.35±0.15 kcal/mol. These data are helpful for the rational design of new strategies for molecular recognition or supramolecular assemblies.     

Internucleotide J-couplings and chemical shifts of the N-H···N hydrogen-bonds in the radiation-damaged guanine-cytosine base pairs

Internucleotide ^2hJ_NN spin‐spin couplings and chemical shifts (δ(¹H) and Δδ(¹⁵N)) of N? H···N H‐bond units in the natural and radiation‐damaged G‐C base pairs were predicted using the appropriate density functional theory calculations with a large basis set. Four possible series of the damaged G‐C pairs (viz., dehydrogenated and deprotonated G‐C pairs, GC^?? and GC^?+ radicals) were discussed carefully in this work. Computational NMR results show that radicalization and anionization of the base pairs can yield strong effect on their ^2hJ_NN spin scalar coupling constants and the corresponding chemical shifts. Thus, variations of the NMR parameters associated with the N? H···N H‐bonds may be taken as an important criterion for prejudging whether the natural G‐C pair is radiation‐damaged or not. Analysis shows that ^2hJ_NN couplings are strongly interrelated with the energy gaps (ΔE_LP→σ*) and the second‐order interaction energies (E(2)) between the donor N lone‐pair (LP_N) and the acceptor σ^*_{N? H} localized NBO orbitals, and also are sensitive to the electron density distributions over the σ*(N? H) orbital, indicating that ^2hJ_NN couplings across the N? H···N H‐bonds are charge‐transfer‐controlled. This is well supported by variation of the electrostatic potential surfaces and corresponding charge transfer amount between G and C moieties. It should be noted that although the NMR spectra for the damaged G‐C pair radicals are unavailable now and the states of the radicals are usually detected by the electron spin resonance, this study provides a correlation of the properties of the damaged DNA species with some of the electronic parameters associated with the NMR spectra for the understanding of the different state character of the damaged DNA bases. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2011.     

Excited-state N-H···S hydrogen bond between indole and dimethyl sulfide: time-dependent density functional theory study

The intermolecular hydrogen bond N-H···S between indole and dimethyl sulfide is theoretically investigated. The formation of N-H···S hydrogen bonds between indole and dimethyl sulfide in ground and excited states is confirmed by the analysis of geometric structure, Mulliken charge, and infrared spectra. The result shows that the S(1) state of hydrogen bonded indole-Me(2)S is mainly a charger transfer state, while the S(2) state is a local excited state and also the state corresponding to the experiment. More importantly, it is demonstrated that the intermolecular hydrogen bond N-H···S of indole-Me(2)S is strengthened in the S(1) and S(2) states compared to that in ground state. Moreover, the strengthening of intermolecular N-H···S hydrogen bond in excited state induces the fluorescence emission peak of indole shifts to the red. These findings may provide insights for further study of N-H···S hydrogen bonds existing in many biomolecular systems.     

复合物HNO···H2O2内N-H···O蓝移氢键的理论研究

A theoretical study on the blue-shifted H-bond N-H…O and red-shifted H-bond O-H…O in the complexHNO…H_2O_2 was conducted by employment of both standard and counterpoise-corrected methods to calculate thegeometric structures and vibrational frequencies at the MP2/6-31G(d),MP2/6-31 G(d,p),MP2/6-311 q G(d,p),B3LYP/6-31G(d),B3LYP/6-31 G(d,p) and B3LYP/6-311 G(d,p) levels.In the H-bond N-H…O,the calcu-lated blue shift of N-H stretching frequency is in the vicinity of 120 cm~(-1) and this is indeed the largest theoreticalestimate of a blue shift in the X-H…Y H-bond ever reported in the literature.From the natural bond orbital analy-sis,the red-shifted H-bond O-H…O can be explained on the basis of the dominant role of the hyperconjugation.For the blue-shifted H-bond N-H…O,the hyperconjugation was inhibited due to the existence of significant elec-tron density redistribution effect,and the large blue shift of the N-H stretching frequency was prominently due tothe rehybridization of sp~n N-H hybrid orbital.     

Amino acid derivatives of perylenediimide and their N-H···O peptide bond dipoles-templated solid state assembly into stacks

A methodology is proposed to provide direct access in good yields to peptide residues-appended perylenediimides PDI-(Cl(4))-[Gly-Ala(OEt)](2), 2a, PDI-(Cl(4))-[Gly-Val(OEt)](2), 2b and PDI-(Cl(4))-[Gly-Gly(OEt)](2), 2c from a generic perylenediimide (PDI) platform symmetrically functionalized with carboxylic acids at the imide sites, PDI-(Cl(4))-[Gly(OH)](2), 1. The latter is obtained in good purity by a non classical two-steps route avoiding the many, notoriously cumbersome successive chromatography steps typical of PDI chemistry, and including a single final purification allowing to crystallize the water soluble pure diacid 1, of great interest in its own right for further developments in a variety of fields. Then, the synthesis, crystallization and analysis of the crystal structures of 2a and 2b reveal a common pattern of self-assembly of the outer peptide residues based on collections of parallel N-H···O peptidic hydrogen bonds running alongside stacks where the constraints imposed upon on the inner PDI skeletons by long range interaction of these parallel electric dipoles reduce the dihedral angles around the bay regions by as much as 11% down to 32°.     

Location of protons in N-H···N hydrogen-bonded systems: a theoretical study on intramolecular pyridine-dihydropyridine and pyridine-pyridinium pairs

Two-dimensional potential energy surfaces (PESs) were calculated for the degenerate intramolecular proton transfer (PT) in two N-H···N hydrogen-bonded systems, (Z)-2-(2-pyridylmethylidene)-1,2-dihydropyridine (1) and monoprotonated di(2-pyridyl) ether (2), at the MP2/cc-pVDZ level of theory. The calculated PES had two minima in both cases. The energy barrier in 1 was higher than the zero-point energy (ZPE) level, while that in 2 was close to the ZPE. Vibrational wavefunctions were obtained by solving time-independent Schr?dinger equations with the calculated PESs. The maximum points of the probability density were shifted from the energy minima towards the region where the covalent N-H bond was elongated and the N···N distance shortened. The effects of a polar solvent on the PES were investigated with the continuum or cluster models in such a way that the solute-solvent electrostatic interactions could be taken into account under non-equilibrated conditions. A solvated contact ion-pair was modelled by a cluster consisting of one cation 2, one chloride ion and 26 molecules of acetonitrile. The calculation with this model suggested that the bridging proton is localised in the deeper well due to the significant asymmetry of the PES and the high potential barrier.     

Pressure-induced collapse of guanidinium nitrate N-H···O bonded honeycomb layers into a 3-D pattern with varied H-acceptor capacity

Highly favoured N-H···O bonded honeycomb layers in guanidinium nitrate, C(NH(2))(3)(+)NO(3)(-), have been destabilized by a pressure of 0.6 GPa, and the novel motif of 3-dimensional N-H···O bonded aggregation in high-pressure phase IV determined for in situ grown single-crystal by X-ray diffraction. The mechanism of the transition involves the collapse of voids present in phases I, II and III. In the P/T phase diagram a large hysteresis of the phase IV boundaries is caused by the strongly reconstructive character of the transition and pressure dependent H-accepting capacity of oxygen atoms.     

氮自由基化学新进展:光催化N-H键活化途径

氮自由基作为一种高活性的中间体,为新型化学反应的设计及含氮化合物的合成提供了新的机遇.光催化条件活化N-H键直接产生氮自由基具有绿色、高效、经济等优点,相关方法学的研究在近年来取得了重要进展.本综述就2016年至今报道的几例最新的研究成果进行亮点评述.     

含氮杂环的N-H和O-H二氟甲基化反应

有机氟化合物具有独特的化学、物理和生物性能,被广泛应用于医药、农药、新型功能材料、生命科学等领域.因此,发展便捷高效的合成方法,将单个的氟原子（-F）、二氟甲基（-CF₂H）或者三氟甲基（-CF₃）引入有机小分子,是有机合成领域的热点.相对于发展相对成熟的三氟甲基化反应,二氟甲基化反应发展相对滞后.利用廉价、易保存的溴二氟乙酸乙酯在Na₂CO₃的条件下产生二氟卡宾,并顺利发生N-H,O-H的二氟甲基化反应,成功的将二氟甲基引入到有机小分子中.该反应的底物适用性很广,官能团的兼容性也很好,卤素、醛基、硝基、腈基等取代的底物均能顺利的发生反应.     

Exchange coupling mediated by N-H···Cl hydrogen bonds: experimental and theoretical study of the frustrated magnetic system in bis(o-phenylenediamine)nickel(II) chloride

The title compound crystallizes in the monoclinic P2(1)/c space group with a = 11.2470(3) ?, b = 5.9034(2) ?, c = 12.0886(3) ?, β = 115.143(1)°, and V = 726.58(4) ?(3) and consists of discrete monomeric NiCl(2)(o-phenylendiamine)(2) molecules. Each o-phen ligand coordinates in a bidentate mode with the chloride ions occupying trans positions in the resulting tetragonally distorted octahedral coordination sphere. Two discrete sets of N-H···Cl hydrogen bonds link the octahedral molecules into a two-dimensional network, with type 1 interactions linking adjacent monomers along the c axis and type 2 interactions linking monomers along the diagonals in the bc plane. Analysis of the magnetic data reveals the existence of weak antiferromagnetic coupling within the layers via these hydrogen bonds, in addition to the presence of zero field splitting, with the best fit obtained for a 1d antiferromagnetic model with g = 2.0917(7), J/k = -2.11(4) K [J = -1.47(3) cm(-1)], and D = 1.05(3) cm(-1) [β = D/|J| = 0.72(6)] for the model with D > 0 and g = 2.0911(6), J/k = -2.26(1) K [J = -1.57(1) cm(-1)], and D = -0.86(1) cm(-1) [β = D/|J| = 0.55(6)] for the model with D < 0. Theoretical calculations of the exchange coupling confirm the experimental results, yielding values of J(1) = -1.39 cm(-1) for the type 1 hydrogen bonds and J(2)/k = -0.56 cm(-1) for the type 2 hydrogen bonds.     

Five- and six-membered N-H?S hydrogen bonding in aromatic amides

The capacity of sulfur to form intramolecular five- or six-membered S?H-N hydrogen bonding in aromatic amides is assessed. The five-membered S?H-N hydrogen bonding is observed in crystal structures of five compounds, whereas the six-membered S?H-N hydrogen bonding is revealed in crystal structures of three compounds. The trityl group has been used to promote formation of the weak hydrogen bonding because it efficiently inhibits the competition of the intermolecular CO?H-N hydrogen bonding. (2D) ¹H NMR experiments indicate that both patterns also exist in chloroform.     

Crystallographic and theoretical studies of 1-(1-naphthyl)-2-thiourea with intermolecular N-H...S heteroatom interaction and N-H...π interaction

A single crystal X-ray diffraction study of 1-(1-naphthyl)-2-thiourea (1) C₁₁H₁₀N₂S indicates crystallization in the monoclinic space group C2/c, Z = 8, with unit cell parameters a = 15.3864(14) Å, b = 7.6090(7) Å, c = 17.0836(16) Å, β = 91.7420(30)°. In the crystal structure, two components of 1 are connected via intermolecular NH...S hydrogen bonds (the N...S distance of 3.371 Å). In 1 there is an NH...π interaction (with the N...π distance of 3.804 Å and a possible N-H...π distance of 3.196 Å). The calculations of 1 at the B3LYP/cc-pVTZ, RHF/cc-pVTZ, RIMP2/cc-pVDZ, and RIMP2/cc-pVTZ levels of theory can almost reproduce the X-ray geometry. In addition, the binding energies of a dimer of 1 calculated by RIMP2 using the cc-pVDZ and cc-pVTZ corrected BSSE basis sets are ?36.1 kJ/mol and ?41.7 kJ/mol. The results suggest that complex 1 is significantly important for the attractive intermolecular interaction in 1.     

Theoretical study of the N-H…O red-shifted and blue-shifted hydrogen bonds

Theoretical calculations are performed to study the nature of the hydrogen bonds in complexes HCHO…HNO, HCOOH…HNO, HCHO…NH3, HCOOH…NH3, HCHO…NH2F and HCOOH…NH2F. The geometric structures and vibrational frequencies of these six complexes at the MP2/6-31 G(d,p), MP2/6-311 G(d,p), B3LYP/6-31 G(d,p) and B3LYP/6-311 G(d,p) levels are calculated by standard and counterpoise-corrected methods, respectively. The results indicate that in complexes HCHO…HNO and HCOOH…HNO the N-H bond is strongly contracted and N-H…O blue-shifted hydrogen bonds are observed. While in complexes HCHO…NH3, HCOOH…NH3, HCHO…NH2F and HCOOH…NH2F, the N-H bond is elongated and N-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, and the other three factors belong to the bond shortening effects. In complexes HCHO…HNO and HCOOH…HNO, the shortening effects dominate which lead to the blue shift of the N-H stretching frequencies. In complexes HCHO…NH3, HCOOH…NH3, HCHO…NH2F and HCOOH…NH2F where elongating effects are dominant, the N-H…O hydrogen bonds are red-shifted.     

Urea activation of α-nitrodiazoesters: an organocatalytic approach to N-H insertion reactions

The combination of a urea catalyst and an α-nitro-α-diazo ester gives rise to a reactive species able to undergo insertion into the N-H bonds of anilines. This new strategy to achieve N-H insertion reactivity is in contrast to typical metal-catalyzed conditions for the generation of carbenoids from α-diazocarbonyl compounds. This report includes the extension of the insertion reaction to a three-component coupling for the construction of α-amino-α-aryl esters in high yield.     

Bidentate Surface Structures of Glycylglycine on Si(111)7×7 by High-Resolution Scanning Tunneling Microscopy: Site-Specific Adsorption via N-H and O-H or Double N-H Dissociation

The early adsorption stage of glycylglycine on Si(111)7×7 surface has been studied by scanning tunneling microscopy (STM). Filled-state imaging shows that glycylglycine adsorbs dissociatively in a bidentate fashion on two adjacent Si adatoms across a dimer wall or an adatom-restatom pair, with the dissociated H atoms on neighboring restatoms. The present STM result validates our hypothesis that both bidentate configurations involving N-H and O-H dissociation and double N-H dissociation are equally probable. Our STM results further show that the relative surface concentrations of the five bidentate configurations follow a specific ordering. This suggests that N-H dissociation at a center adatom site would likely be followed by N-H dissociation at an adjacent restatom, while N-H dissociation at a corner adatom site would be succeeded by O-H dissociation at an adatom across the dimer wall. Evidently, the strong bidentate interactions also inhibit surface diffusion of the adsorbed glycylglycine fragment, and the adsorption apparently follows random sequential adsorption statistics. The random nature of adsorption is also supported by the similar relative occupancies of the center adatom and corner adatom sites, indicating that the relative reactivities of these adatom sites do not play a significant role. Our DFT computational study shows that all three bidentate (Si-)NHCH(2)CONHCH(2)COO(-Si) adatom-adatom configurations (center-center, corner-corner, center-corner) have similar adsorption energies for a double adatom-adatom pair across the dimer wall, while the (Si-)NHCH(2)CON(-Si)CH(2)COOH bidentate adatom-restatom configuration is energetically favorable. The free -CONH- and -COOH groups remaining on the respective bidentate adstructures could facilitate adsorption of the second adlayer through the formation of hydrogen bonding.     

Unexpected Side Reaction in the Intermolecular N-H Insertion of Phenyl Diazoacetates with Arylamines

Unexpected side reaction is discovered from the N-H insertion of phenyl diazoacetates with arylamines in the presence of Rh2(OAc)4 catalyst. This side reaction is not evident with copper catalysts such as Cu(acac)2 or Cu(OTf)2. Good yield of the N-H insertion was obtained by using 0.2% of copper catalyst.     

Selective recognition of aromatic hydrocarbons by endo-functionalized molecular tubes via C/N-H…π interactions

Aromatic hydrocarbons can be selectively recognized by four endo-functionalized molecular tubes through C/N-H...π interactions in nonpolar media with binding constants up to 1580 L/mol.     

Tetramidocavitand: strong anion receptor by well-organized four -(CO)N-H?X interactions

Resorcin[4]arene-based tetramidocavitands containing four secondary amide groups on their upper rim showed strong (R = methyl or ethyl) binding properties. The caviplex formation through hydrogen bonds of -(CO)N-H?X⁻ was supported by ¹H NMR and crystal structure analyses. In a mixture of C₂D₂Cl₄/DMSO/D₂O = 5:15:2 at 25 °C, the thermodynamic parameters for caviplex @1, ΔG (kcal mol⁻¹), ΔH (kcal mol⁻¹), and ΔS (cal K⁻¹ mol⁻¹), are −3.7, −8.6, and −16.7, respectively.     

N-H…O,C-H… O hydrogen-bonded supramolecular frameworks in 4-fluoroanilinium and dicyclohexylaminium picrate salts

The asymmetric unit of compound (I), 4-fluoroanilinium picrate, C₆H₇NF⁺.C₆H₂N₃O₇^? contain one 4-fluoroanilinium cation and one picrate anion whereas in compound (II), dicyclohexylaminium picrate, C₁₂H₂₂N⁺.C₆H₂N₃O₇^? the asymmetric unit contains two sets of dicyclohexylaminium cation and picrate anion due to conformational difference between the molecules. In (I), all three nitro groups of the picrate anion are positionally disordered over two sites refined to major and minor components. The molecular ions of (I), interlinked through N–H???O and C–H???O hydrogen bonds forming two-dimensional supramolecular sheet along (-1 0 1) plane. Whereas in (II), the symmetry-independent molecules labeled as A and B molecule form independent one-dimensional supramolecular tape extending along (1 1 0) and (1 0 0) direction. The supramolecular tapes are interlinked through C–H???O interaction to form three-dimensional network in the crystalline solid in (II).