Aromaticity-controlled tautomerism and resonance-assisted hydrogen bonding in heterocyclic enaminone-iminoenol systems

The contribution of aromaticity and intramolecular hydrogen bonding to relative stability, for a set of (1H-azahetero-2-ylidene)-acetaldehyde and 2-azahetero-2-yl-ethanol tautomeric pairs, has been investigated by means of quantum chemical DFT and ab initio methods up to the MP4(SDTQ)/AUG-cc-pVDZ and MP2/AUG-cc-pVTZ levels of theory. It is found that the relative energy of the tautomers is governed by the change in the degree of heterocycle aromaticity upon intramolecular hydrogen transfer. An analysis of geometrical parameters of a hydrogen-bonded system reveals a clear relationship between the aromaticity of the heterocycle, the conjugation in a resonant spacer, and the strengths of the intramolecular hydrogen bonds. This allows the conclusion to be drawn that intramolecular N-H...O and O-H...N hydrogen bonds formed are found to be resonance-assisted and their strength is dependent on the pi-donating/accepting properties of the heterocycle. On the basis of the results of the calculations, a simple model describing the mechanism of resonance assistance of hydrogen bonding has been suggested.     

配位化学中新型金属配合物的电子结构与成键特点

研究配合物的几何电子构型、阐明配位键的本质是配位化学中重要的理论组成部分。本文在回顾配位化学基本的成键理论基础上,介绍几例近年来具有教科书级别的国内高水平原创工作,重点阐述具有独特芳香性、低氧化态、高配位数以及锕系金属的新型金属配合物的电子结构和成键特点,对丰富和拓展配位化学的基本理论具有重要意义。     

Analysis of the structures,energetics, and vibrational frequencies for the hydrogen-bonded interaction of nucleic acid bases with Carmustine pharmaceutical agent: a detailed computational approach

In the present study, it is attempted to scrutinize the hydrogen bonding interaction between Carmustine drug and DNA pyrimidine bases by means of density functional theory calculations regarding their geometries, binding energies, vibrational frequencies, and topological features of the electron density in the gas phase and the water solution. Based on the density functional theory results, it is found that the process of intermolecular interaction between Carmustine drug and nucleobases is exothermic and all of the optimized configurations are stable. Furthermore, the negative stability energy represented by a polarizable continuum model shows the significant increase in the solubility of the nucleobase after hydrogen bonding intermolecular interaction in the presence of water solvent. It is also found that the intermolecular hydrogen bonds between drug and the nucleobases play the significant role in the stability of the physisorption configurations. Hydrogen bond energies for hydrogen-bonded complexes are obtained from Espinosa method and the atoms-in-molecules theory are also applied to get a more precise insight into the nature of the intermolecular hydrogen bond interactions.     

The intramolecular hydrogen bond in 2-hydroxy-benzamides

The two crystal structures of 5-chloro-2-hydroxy-benzamide and 2-hydroxy-N,N-diethyl-benzamide were determined by X-ray diffraction at 100 K. The intramolecular and intermolecular hydrogen bonds were found in these structurally similar 2-hydroxy-benzamides. Analysis of the hydrogen bonding was carried out on the basis of X-ray data, infrared spectra, and DFT calculations. Disruption of the intramolecular hydrogen bonding in the solid state by a steric effect is shown. Conformational analysis and potential energy calculations as functions of the turning angle around the C_aryl–C_alkyl bond were conducted. The values obtained for the HOMA index indicate mutual compensation of the amide and hydroxyl groups (due to the high degree aromaticity of the phenyl ring).     

氢键准则在DMSO水溶液中应用的评价

利用分子动力学模拟方法, 分别采用几何准则和能量准则分析了不同浓度下的二甲基亚砜(DMSO)水溶液的氢键统计和动力学等特性. 结果显示, 两种氢键准则可以很好地反映出溶液的氢键性质随浓度的变化趋势. 通过分析比较发现, 由于几何准则不能有效地排除具有弱对势能的分子对, 因此其统计的氢键数量要大于能量准则的结果.此外, 能量准则对于分子间相对取向的区分存在不足, 进而引起氢键寿命的计算结果偏大.因此,为使氢键分析更加准确, 本文建议使用几何-能量混合型氢键准则.     

Highly Stable Double‐Stranded DNA Containing Sequential Silver(I)‐Mediated 7‐Deazaadenine/Thymine Watson–Crick Base Pairs

The oligonucleotide d(TX)₉, which consists of an octadecamer sequence with alternating non‐canonical 7‐deazaadenine (X) and canonical thymine (T) as the nucleobases, was synthesized and shown to hybridize into double‐stranded DNA through the formation of hydrogen‐bonded Watson–Crick base pairs. dsDNA with metal‐mediated base pairs was then obtained by selectively replacing W‐C hydrogen bonds by coordination bonds to central silver(I) ions. The oligonucleotide I adopts a duplex structure in the absence of Ag⁺ ions, and its stability is significantly enhanced in the presence of Ag⁺ ions while its double‐helix structure is retained. Temperature‐dependent UV spectroscopy, circular dichroism spectroscopy, and ESI mass spectrometry were used to confirm the selective formation of the silver(I)‐mediated base pairs. This strategy could become useful for preparing stable metallo‐DNA‐based nanostructures.     

Bond formation in diatomic transition metal hydrides: Insights from the analysis of domain‐averaged fermi holes

The analysis of domain‐averaged Fermi holes (DAFHs) is used to provide detailed insights into the electron reorganization that accompanies the splitting of the bonding electron pairs in simple diatomic transition metal hydrides MH (M = Sc–Cr). The dissociation process is followed by monitoring the geometry dependence of the dominant DAFH functions, as well as their populations and overlaps. In addition to providing a highly appealing visual picture of the geometry‐induced changes in the bonding interactions, the DAFH approach clearly confirms the close link between the progress of the dissociation and the extent of electron sharing. The results of the various DAFH analyses straightforwardly reveal the anticipated close parallel in the nature of the M? H bonds in the different systems studied, as well as the smooth character of the splitting of the associated shared electron pairs. In addition to a very basic resemblance between the different cases, subtle differences are revealed for individual systems. © 2012 Wiley Periodicals, Inc.     

High‐Field NMR Spectroscopy Reveals Aromaticity‐Modulated Hydrogen Bonding in Heterocycles

From DNA base pairs to drug–receptor binding, hydrogen (H‐)bonding and aromaticity are common features of heterocycles. Herein, the interplay of these bonding aspects is explored. H‐bond strength modulation due to enhancement or disruption of aromaticity of heterocycles is experimentally revealed by comparing homodimer H‐bond energies of aromatic heterocycles with analogs that have the same H‐bonding moieties but lack cyclic π‐conjugation. NMR studies of dimerization in C₆D₆ find aromaticity‐modulated H‐bonding (AMHB) energy effects of approximately ±30 %, depending on whether they enhance or weaken aromatic delocalization. The attendant ring current perturbations expected from such modulation are confirmed by chemical shift changes in both observed ring C−H and calculated nucleus‐independent sites. In silico modeling confirms that AMHB effects outweigh those of hybridization or dipole–dipole interaction.     

Nitrogen-15 NMR spectroscopy of N-metallated nucleic acids: insights into 15N NMR parameters and N-metal bonds

It was recently demonstrated spectroscopically that RNA/DNA nucleobases can bind to metal cations in aqueous solution through coordination bonds and covalent bonds. Nitrogen-15 ((15)N) NMR spectroscopy was employed and shown to be a powerful tool for determining the mode of metal ion binding to nitrogen atoms in RNA/DNA molecules. This review describes (15)N NMR spectroscopic characteristics in accordance with the mode of metal ion binding to nitrogen atoms. The general rules for (15)N chemical shift changes, which are applicable to the determination of the metal ion binding mode of N-metallated compounds, are also described.     

Structures of nucleobases trapped within Au triangles and its effects on hydrogen bonding in base pairs of DNA

Nucleobases (adenine (A), thymine (T), cytosine (C), and guanine (G)) trapped within two metal clusters such as Au(3) undergo expansion. Our investigation reveals that this primarily arises due to the concomitant increase in all the bond lengths in molecules. Such expansion of the molecules can be qualitatively understood on the basis of classical harmonic potentials in the bonds and loss of aromaticity in the rings. Specifically, the highly electronegative O and N elements in the base pairs anchor to Au atoms and form X-Au bonds, which leads to charge redistribution within the molecules. As a very important consequence of this, the nature of the hydrogen bonds (in Au(3)-A...T-Au(3) and in Au(3)-G...C-Au(3)) change substantially within these electrodes in comparison to gas-phase structures. These hydrogen bonds have a single-well potential energy profile (of the type N...H...O and N...H...N) instead of double-well potentials (like N-H...O or N-H...N/ N...H-N types). A detailed energy calculation along the proton movement pathway supports our conclusions.     

Evaluation of the individual hydrogen bonding energies in N-methylacetamide chains

The individual hydrogen bonding energies in N-methylacetamide chains were evaluated at the MP2/6-31+G** level including BSSE correction and at the B3LYP/6-311++G(3df,2pd) level including BSSE and van der Waals correction. The calculation results indicate that compared with MP2 results, B3LYP calculations without van der Waals correction underestimate the individual hydrogen bonding energies about 5.4 kJ mol^?1 for both the terminal and central hydrogen bonds, whereas B3LYP calculations with van der Waals correction produce almost the same individual hydrogen bonding energies as MP2 does for those terminal hydrogen bonds, but still underestimate the individual hydrogen bonding energies about 2.5 kJ mol^?1 for the hydrogen bonds near the center. Our calculation results show that the individual hydrogen bonding energy becomes more negative (more attractive) as the chain becomes longer and that the hydrogen bonds close to the interior of the chain are stronger than those near the ends. The weakest individual hydrogen bonding energy is about ?29.0 kJ mol^?1 found in the dimer, whereas with the growth of the N-methylacetamide chain the individual hydrogen bonding energy was estimated to be as large as ?62.5 kJ mol^?1 found in the N-methylacetamide decamer, showing that there is a significant hydrogen bond cooperative effect in N-methylacetamide chains. The natural bond orbital analysis indicates that a stronger hydrogen bond corresponds to a larger positive charge for the H atom and a larger negative charge for the O atom in the N-H?O=C bond, corresponds to a stronger second-order stabilization energy between the oxygen lone pair and the N-H antibonding orbital, and corresponds to more charge transfer between the hydrogen bonded donor and acceptor molecules.     

π-Orbital electron–energy contributions to chemical reaction heats,I. Reactions involving only linear molecules containing up to three first–row atoms

Ab initio calculations of various expectation energies have been made for the reactant and product species in six reactions that involve only small linear molecules. The reactions include fission by hydrogen, addition of hydrogen, exchange of triply bonded atoms, fluorination, and oxygen atom transfer. The change in total electronic energy is not invariably the result of changes in inner shell energy and outer shell σ- and π-electron energies simply augmenting each other, but in several cases there is a complex interplay of opposing effects. This approach gives a different insight into the energetic aspects of changes in bonding from that derived from the concept of shared electron pairs in σ and π bonds together with lone pairs in valence shells. Changes in π-electron energy are shown to be important in a reaction in which neither reactant nor product molecules contain π bonds in the usual chemical sense. While in a reaction in which there is a complete change in the nature of the triple bonds, and hence the π bonding, the change in π-electron energy makes a smaller contribution than either the change in inner shell or the outer shell σ-electron energies.     

Analytic models of domain-averaged Fermi holes: a new tool for the study of the nature of chemical bonds

Simple analytical models are introduced that significantly enhance the ability to understand and rationalise the nature of bonding interactions depicted by domain-averaged Fermi hole (DAFH) analysis. The examples presented show that besides shedding new light on the role of electron-sharing in ordinary two-centre two-electron (2c-2e) chemical bonds that are well represented by the classical Lewis model, the proposed approach also provides interesting new insights into the nature of bonding interactions that go beyond the traditional Lewis paradigm. This is, for example, the case of 3c-2e multicentre bonding, but a straightforward extension of the approach also reveals for direct metal-metal bonding the existence of a completely new type of bonding interaction that involves the mutual exchange of electrons between the lone pairs on adjacent metal atoms.     

Aromatic gold and silver "rings": hydrosilver(I) and hydrogold(I) analogues of aromatic hydrocarbons

Quantum chemical calculations suggest that a series of molecules with the general formula cyclo-Mn(mu-H)n (M = Ag, Au; n = 3-6) are stable. All cyclo-MnHn species, except cyclo-Au(3)H(3), have the same symmetry with the respective aromatic hydrocarbons but differ in that the hydrogen atoms are in bridging positions between the metal atoms and not in terminal positions. The aromaticity of the hydrosilver(I) and hydrogold(I) analogues of aromatic hydrocarbons was verified by a number of established criteria of aromaticity, such as structural, energetic, magnetic, and chemical criteria. In particular, the nucleus-independent chemical shift, the relative hardness, Deltaeta, the electrophilicity index, omega, and the chemical reactivity toward electrophiles are indicative for the aromaticity of the hydrosilvers(I) and hydrogolds(I). A comprehensive study of the structural, energetic, spectroscopic (IR, NMR, electronic, and photoelectron spectra), and bonding properties of the novel classes of inorganic compounds containing bonds that are characterized by a common ring-shaped electron density, more commonly seen in organic molecules, is presented.     

Glucose interaction with Au,Ag, and Cu clusters: Theoretical investigation

Interactions of α‐D ‐glucose with gold, silver, and copper metal clusters are studied theoretically at the density functional theory (CAM‐B3LYP) and MP2 levels of theory, using trimer clusters as simple catalytic models for metal particles as well as investigating the effect of cluster charge by studying the interactions of cationic and anionic gold clusters with glucose. The bonding between α‐D ‐glucose and metal clusters occurs by two major bonding factors; the anchoring of M atoms (M = Cu, Ag, and Au) to the O atoms, and the unconventional M…H? O hydrogen bond. Depending on the charge of metal clusters, each of these bonds contributes significantly to the complexation. Binding energy calculations indicate that the silver cluster has the lowest and gold cluster has the highest affinity to interact with glucose. Natural bond orbital analysis is performed to calculate natural population analysis and charge transfers in the complexes. Quantum theory of atoms in molecules was also applied to interpret the nature of bonds. © 2012 Wiley Periodicals, Inc.     

How resonance assists hydrogen bonding interactions: an energy decomposition analysis

Block-localized wave function (BLW) method, which is a variant of the ab initio valence bond (VB) theory, was employed to explore the nature of resonance-assisted hydrogen bonds (RAHBs) and to investigate the mechanism of synergistic interplay between pi delocalization and hydrogen-bonding interactions. We examined the dimers of formic acid, formamide, 4-pyrimidinone, 2-pyridinone, 2-hydroxpyridine, and 2-hydroxycyclopenta-2,4-dien-1-one. In addition, we studied the interactions in beta-diketone enols with a simplified model, namely the hydrogen bonds of 3-hydroxypropenal with both ethenol and formaldehyde. The intermolecular interaction energies, either with or without the involvement of pi resonance, were decomposed into the Hitler-London energy (DeltaEHL), polarization energy (DeltaEpol), charge transfer energy (DeltaECT), and electron correlation energy (DeltaEcor) terms. This allows for the examination of the character of hydrogen bonds and the impact of pi conjugation on hydrogen bonding interactions. Although it has been proposed that resonance-assisted hydrogen bonds are accompanied with an increasing of covalency character, our analyses showed that the enhanced interactions mostly originate from the classical dipole-dipole (i.e., electrostatic) attraction, as resonance redistributes the electron density and increases the dipole moments in monomers. The covalency of hydrogen bonds, however, changes very little. This disputes the belief that RAHB is primarily covalent in nature. Accordingly, we recommend the term "resonance-assisted binding (RAB)" instead of "resonance-assisted hydrogen bonding (RHAB)" to highlight the electrostatic, which is a long-range effect, rather than the electron transfer nature of the enhanced stabilization in RAHBs.     

Hydrogen bonding mediated ion pairs of some aprotic ionic liquids and their structural transition in aqueous solution

Ion pair speciation of ionic liquids(ILs) has an important effect on the physical and chemical properties of ILs and recognition of the structure of ion pairs in solution is essential. It has been reported that ion pairs of some ILs can be formed by hydrogen bonding interactions between cations and anions of them. Considering the fact that far-IR(FIR) spectroscopy is a powerful tool in indicating the intermolecular and intramolecular hydrogen bonding, in this work, this spectroscopic technique has been combined with molecular dynamic(MD) simulation and nuclear magnetic resonance hydrogen spectroscopy(~1H NMR) to investigate ion pairs of aprotic ILs [Bmim][NO_3], [BuPy][NO_3], [Pyr_(14)][NO_3], [PP_(14)][NO_3] and [Bu-choline][NO_3] in aqueous IL mixtures. The FIR spectra have been assigned with the aid of density functional theory(DFT) calculations, and the results are used to understand the effect of cationic nature on the structure of ion pairs. It is found that contact ion pairs formed in the neat aprotic ILs by hydrogen bonding interactions between cation and anion, were still maintained in aqueous solutions up to high water mole fraction(say 0.80 for [BuPy][NO3]). When water content was increased to a critical mole fraction of water(say 0.83 for [BuPy][NO3]), the contact ion pairs could be transformed into solvent-separated ion pairs due to the formation of the hydrogen bonding between ions and water. With the further dilution of the aqueous ILs solution, the solvent-separated ion pairs was finally turned into free cations and free anions(fully hydrated cations or anions). The concentrations of the ILs at which the contact ion pairs were transformed into solvent-separated ion pairs and solvent-separated ion pairs were transformed into free ions(fully hydrated ion) were dependent on the cationic structures. These information provides direct spectral evidence for ion pair structures of the aprotic ILs in aqueous solution. MD simulation and ~1H NMR results support the conclusion drawn from FIR spectra investigations.     

catena‐Poly[[[(di‐2‐pyridylamine‐κ2N2,N2′)copper(II)]‐μ‐benzene‐1,3‐dicarboxylato‐κ3O1,O1′:O3] monohydrate], a zigzag coordination polymer with strong π–π interactions

The novel title coordination polymer, {[Cu(C₈H₄O₄)(C₁₀H₉N₃)]·H₂O}_n, synthesized by the slow‐diffusion method, takes the form of one‐dimensional zigzag chains built up of Cu^II cations linked by benzene‐1,3‐dicarboxylate (ipht) anions. An exceptional characteristic of this structure is that it belongs to a small group of metal–organic polymers where ipht is coordinated as a bridging tridentate ligand with monodentate and chelate coordination of individual carboxylate groups. The Cu^II cation has a highly distorted square‐pyramidal geometry formed by three O atoms from two ipht anions and two N atoms from a di‐2‐pyridylamine (dipya) ligand. The zigzag chains, which run along the b axis, further construct a three‐dimensional metal–organic framework via strong face‐to‐face π–π interactions and hydrogen bonds. A solvent water molecule is linked to the different carboxylate groups via hydrogen bonds. Thermogravimetric and differential scanning calorimetric analyses confirm the strong hydrogen bonding.     

Cyano‐Functionalized Triarylamines on Coinage Metal Surfaces: Interplay of Intermolecular and Molecule–Substrate Interactions

The self‐assembly of cyano‐functionalized triarylamine derivatives on Cu(111), Ag(111) and Au(111) was studied by means of scanning tunnelling microscopy, low‐energy electron diffraction, X‐ray photoelectron spectroscopy and density functional theory calculations. Different bonding motifs, such as antiparallel dipolar coupling, hydrogen bonding and metal coordination, were observed. Whereas on Ag(111) only one hexagonally close‐packed pattern stabilized by hydrogen bonding is observed, on Au(111) two different partially porous phases are present at submonolayer coverage, stabilized by dipolar coupling, hydrogen bonding and metal coordination. In contrast to the self‐assembly on Ag(111) and Au(111), for which large islands are formed, on Cu(111), only small patches of hexagonally close‐packed networks stabilized by metal coordination and areas of disordered molecules are found. The significant variety in the molecular self‐assembly of the cyano‐functionalized triarylamine derivatives on these coinage metal surfaces is explained by differences in molecular mobility and the subtle interplay between intermolecular and molecule–substrate interactions.