Interplay between Cation–π and Coinage‐Metal–Oxygen Interactions: An Ab Initio Study and Cambridge Structural Database Survey

The interplay between cation–π and coinage‐metal–oxygen interactions are investigated in the ternary systems N???PhCCM???O (N=Li⁺, Na⁺, Mg²⁺; M=Ag, Au; O=water, methanol, ethanol). A synergetic effect is observed when cation–π and coinage‐metal–oxygen interactions coexist in the same complex. The cation–π interaction in most triads has a greater enhancing effect on the coinage‐metal–oxygen interaction. This effect is analyzed in terms of the binding distance, interaction energy, and electrostatic potential in the complexes. Furthermore, the formation, strength, and nature of both the cation–π and coinage‐metal–oxygen interactions can be understood in terms of electrostatic potential and energy decomposition. In addition, experimental evidence for the coexistence of both interactions is obtained from the Cambridge Structural Database (CSD).     

Nature and Strength of Weak O⋅⋅⋅O Interactions in Nitryl Halide Dimers

The use of real space functions and molecular graphs has pushed some chemists to wonder: Are interactions between negatively charged oxygen atoms possible? In this contribution we analyze whether there is a real interaction between oxygen atoms in nitryl halide dimers (XNO₂)₂ (X=F, Cl, Br and I) and in tetranitromethane and derivatives. Based on ab-initio and density functional theories (DFT) methods, we show these complexes are weakly stabilized. Energy decomposition analyses based on local molecular orbitals (LMOEDA) and interacting quantum atoms (IQA) reveal both dispersion and exchange play a crucial role in the stabilization of these complexes. Electron charge density and IQA analyses indicate that the oxygen atoms are connected by privileged exchange channels. In addition, electrostatic interactions between O and N atoms are also vital for the stabilization of the complexes. Finally, a reasonable explanation is given for the dynamic behavior of nitryl groups in tetranitromethane and derivatives.     

Luminescent Benzoquinolate‐Isocyanide Platinum(II) Complexes: Effect of Pt⋅⋅⋅Pt and π⋅⋅⋅π Interactions on their Photophysical Properties

The neutral compounds [Pt(bzq)(CN)(CNR)] (R=tBu ( 1 ), Xyl ( 2 ), 2‐Np ( 3 ); bzq= benzoquinolate, Xyl=2,6‐dimethylphenyl, 2‐Np=2‐napthyl) were isolated as the pure isomers with a trans‐C_bzq,CNR configuration, as confirmed by ¹³C{¹H} NMR spectroscopy in the isotopically marked [Pt(bzq)(¹³CN)(CNR)] (R=tBu ( 1′ ), Xyl ( 2′ ), 2‐Np ( 3′ )) derivatives (δ¹³C_CN≈110 ppm; ¹J(Pt,¹³C)≈1425 Hz]. By contrast, complex [Pt(bzq)(C≡CPh)(CNXyl)] ( 4 ) with a trans‐N_bzq,CNR configuration, has been selectively isolated from [Pt(bzq)Cl(CNXyl)] (trans‐N_bzq,CNR) using Sonogashira conditions. X‐ray diffraction studies reveal that while 1 adopts a columnar‐stacked chain structure with Pt–Pt distances of 3.371(1) Å and significant π???π interactions (3.262 Å), complex 2 forms dimers supported only by short Pt???Pt (3.370(1) Å) interactions. In complex 4 the packing is directed by weak bzq???Xyl and bzq???C≡E (C, N) interactions. In solid state at room temperature, compounds 1 and 2 both show a bright red emission (?=42.1 % 1 , 57.6 % 2 ). Luminescence properties in the solid state at 77 K and concentration‐dependent emission studies in CH₂Cl₂ at 298 K and at 77 K are also reported for 1 , 1·CHCl3 , 2 , 2' , 2·CHCl3 , 3 , 4 .     

Argentophilic Interactions

The decade 1990–2000 saw a growing interest in aurophilic interactions in gold chemistry. These interactions were found to influence significantly a variety of structural and other physical characteristics of gold(I) compounds. The attention paid to this unusual and counterintuitive type of intra‐ and intermolecular bonding between seemingly closed‐shell metal centers has rapidly been extended to also include silver chemistry. Hundreds of experimental and computational studies have since been dedicated to the argentophilicity phenomenon. The results of this development are reviewed herein focusing on molecular systems where two or more silver(I) centers are in close contact leading to specific structural characteristics and a variety of novel physical properties. These include strongly modified ligand‐to‐metal charge‐transfer processes observed in absorption and emission spectroscopy, but also colossal positive and negative thermal expansion on the one hand and unprecedented negative linear compressibility of crystal parameters on the other.     

电喷雾质谱的非共价键蛋白质复合物研究

电喷雾质谱(ESI-MS)已经成为检测和研究生物分子弱相互作用,即非共价键作用的一个重要分析手段.ESI-MS除了具有快速、灵敏、专属的特点以外,还有能够直接得出复合物的分子量和化学计量比的优点.本文通过蛋白质与蛋白质、配体、金属离子的非共价复合物的例子阐述了ESI-MS技术的主要特性,综述了ESI-MS在非共价键蛋白质复合物方面的早期和近期应用研究成果.引用文献34篇.     

Stabilizing Fluorine–π Interactions

A series of N-arylimide molecular balances were designed to study and measure fluorine–aromatic (F–π) interactions. Fluorine substituents gave rise to increasingly more stabilizing interactions with more electron-deficient aromatic surfaces. The attractive F–π interaction is electrostatically driven and is stronger than other halogen–π interactions.     

Electrostatics and Polarization in σ- and π-Hole Noncovalent Interactions: An Overview

The energetics of σ- and π-hole interactions can be described very well in terms of electrostatics and polarization, consistent with their Coulombic natures. When both of these components are taken into account, very good correlations with quantum-chemically computed interaction energies are obtained. If polarization is only minor, as when the interactions are quite weak, then electrostatics can suffice, as represented by the most positive electrostatic potential associated with the σ- or π-hole. For stronger interactions, the combination of electrostatics plus polarization is very effective even for interaction energies considerably greater in magnitude than what is normally considered noncovalent bonding. Several procedures for treating polarization are summarized, including the use of point charges and the direct inclusion of electric fields.     

Competition Between π–π and CH/π Interactions: A Comparison of the Structural and Electronic Properties of Alkoxy‐Substituted 1,8‐Bis((propyloxyphenyl)ethynyl)naphthalenes

The structural and electronic consequences of π–π and C?H/π interactions in two alkoxy‐substituted 1,8‐bis‐ ((propyloxyphenyl)ethynyl)naphthalenes are explored by using X‐ray crystallography and electronic structure computations. The crystal structure of analogue 4 , bearing an alkoxy side chain in the 4‐position of each of the phenyl rings, adopts a π‐stacked geometry, whereas analogue 8 , bearing alkoxy groups at both the 2‐ and the 5‐positions of each ring, has a geometry in which the rings are splayed away from a π‐stacked arrangement. Symmetry‐adapted perturbation theory analysis was performed on the two analogues to evaluate the interactions between the phenylethynyl arms in each molecule in terms of electrostatic, steric, polarization, and London dispersion components. The computations support the expectation that the π‐stacked geometry of the alkoxyphenyl units in 4 is simply a consequence of maximizing π–π interactions. However, the splayed geometry of 8 results from a more subtle competition between different noncovalent interactions: this geometry provides a favorable anti‐alignment of C?O bond dipoles, and two C?H/π interactions in which hydrogen atoms of the alkyl side chains interact favorably with the π electrons of the other phenyl ring. These favorable interactions overcome competing π–π interactions to give rise to a geometry in which the phenylethynyl substituents are in an offset, unstacked arrangement.     

Colorimetric calcium-response of β-lactosylated μ-oxo-bis-[5,15-meso-diphenylporphyrinatoiron(III)]

β-Lactosylated 5,15-meso-diphenylporphyrinatoiron(III) chloride was prepared by ironization of the corresponding free base porphyrin having acetylated lactoside-units followed by deacetylation with ammonia in a water-methanol mixture. The resultant 5,15-meso-bis(β-lactosylphenyl)porphyrinatoiron(III) chloride showed unique colorimetric response to calcium cation. This colorimetric response is calcium-specific and no other cations, such as sodium, potassium, or magnesium ions induced such colorimetric response. Lines of evidence including UV-vis spectra under different conditions and TEM images strongly indicate that interdigitations of the corresponding μ-oxo-dimers are responsible for this colorimetric change.     

Three-dimensional triazenido layers attained through classical and non-classical hydrogen interactions and its coordination to palladium under prolific occurrence of bifurcated hydrogen bonding

The new ligand 1,3-bis(3-methoxy-4-methylbenzoate) triazene (1, bmmbt), and the already known ligand 1,3-bis(4-acetylphenyl)triazene (bapht), yield the two new palladium(II) complexes [(bmmbt)Pd(PPh₃)₂Cl]·DMSO (2) and [(bapht)Pd(PPh₃)₂Cl] (3) (Ph = phenyl; DMSO = dimethylsulfoxide). Compound 1 shows the existence of more than one interaction promoting the coupling between the triazene chains. Other remarkable types of interactions in 1 are bifurcated hydrogen contacts and non-classical CH···π bonding. Complexes 2 and 3 present a planar geometry, supported also through bifurcated intramolecular Cl···H-C interactions, as well as the occurrence of trifurcated Cl···H-C intermolecular interactions.     

Large Stabilization Effects by Intramolecular Beryllium Bonds in Ortho-Benzene Derivatives

Intramolecular interactions are shown to be key for favoring a given structure in systems with a variety of conformers. In ortho-substituted benzene derivatives including a beryllium moiety, beryllium bonds provide very large stabilizations with respect to non-bound conformers and enthalpy differences above one hundred kJ·mol⁻¹ are found in the most favorable cases, especially if the newly formed rings are five or six-membered heterocycles. These values are in general significantly larger than hydrogen bonds in 1,2-dihidroxybenzene. Conformers stabilized by a beryllium bond exhibit the typical features of this non-covalent interaction, such as the presence of a bond critical point according to the topology of the electron density, positive Laplacian values, significant geometrical distortions and strong interaction energies between the donor and acceptor quantified by using the Natural Bond Orbital approach. An isodesmic reaction scheme is used as a tool to measure the strength of the beryllium bond in these systems in terms of isodesmic energies (analogous to binding energies), interaction energies and deformation energies. This approach shows that a huge amount of energy is spent on deforming the donor–acceptor pairs to form the new rings.     

Discrete π Stack of a Tweezer-Shaped Naphthalenediimide–Anthracene Conjugate

The design and synthesis of a tweezer-shaped naphthalenediimide (NDI)–anthracene conjugate ( 2NDI ) are reported. In the structure of the closed form (π_NDI ⋅⋅⋅ π_NDI stack) of 2NDI , which was elucidated by single-crystal XRD, the existence of C−H ⋅⋅⋅ O hydrogen bonding involving the nearest carbonyl oxygen atom of an NDI unit was suggested. The tunability of π_NDI ⋅⋅⋅ π_NDI interactions was studied by means of UV/Vis absorption, fluorescence and NMR spectroscopy and molecular modelling. This revealed that the π_NDI ⋅⋅⋅ π_NDI interactions in 2NDI affect the absorption and emission properties depending on the temperature. Furthermore, in polar solvents, 2NDI prefers the stronger π_NDI ⋅⋅⋅ π_NDI stack, whereas the π_NDI ⋅⋅⋅ π_NDI interaction is diminished in nonpolar solvents. Importantly, the conformational variations of 2NDI can be reversibly switched by variation in temperature, and this suggests potential application for fluorogenic molecular switches upon temperature changes.     

A cationic dye triplet as a unique "glue" that can connect fully matched termini of DNA duplexes

In this study, we propose that three consecutive cationic p‐methylstilbazoles tethered on D ‐threoninols ( Z residues) at 5′ termini act as a unique “glue” connecting DNA duplexes by their interstrand cluster formation. Interstrand clustering of p‐methylstilbazoles ( ZZZ triplets) induces narrowing and hypsochromic shift of bands at 350 nm, which can be assigned to the absorption of p‐methylstilbazole. However, single‐stranded DNA conjugates involving a ZZZ triplet at the 5′ terminus of 8‐mer native nucleotides is found not to induce such large spectral changes, which implies that the intrinsic self‐assembling property of ZZZ triplets is weak. Interestingly, when this conjugate is hybridized with a complementary 8‐mer native oligonucleotide, a remarkable spectral change is observed, indicating the dimerization of a duplex through the interstrand clustering of ZZZ triplets. Dimerization of the duplex is also evidenced by cold‐spray ionization mass spectrometry. This interstrand clustering is observed only when a ZZZ triplet is tethered to a 5′ rather than 3′ terminus. Furthermore, the stability of the interstrand cluster increases by increasing the number of nucleobases of the DNA portion, and when mismatched base pairs are incorporated or when a base next to the Z residue is deleted, the stability substantially drops. When we apply the ZZZ triplet to the formation of a nanowire using two complementary DNA conjugates, each of which has a ZZZ triplet at the 5′ termini as overhang, we demonstrate the successful formation of a nanowire by native PAGE analysis. Since native sticky ends that have three nucleotides do not serve as “glue”, ZZZ triplets with their unique glue‐like properties are prime candidates for constructing DNA‐based nanoarchitectures.     

Dual Association Modes of the 2,5,8‐Tris(pentafluorophenyl)phenalenyl Radical

The 2,5,8‐tris(pentafluorophenyl)phenalenyl radical was obtained by a straightforward synthesis in 11 steps from 2,7‐dibromonaphthalene. This radical crystallized as a σ dimer from a solution in MeCN and as a π‐stack from a melted liquid. The π stack was not confined to dimerization, but extended into a uniform 1D stack with an interplanar distance of 3.503 Å. This unique duality in association mode arose from the thermodynamic stability of the phenalenyl moiety.     

Structure–affinity relationships for the binding of actinomycin D to DNA

Molecular models of the complexes between actinomycin D and 14 different DNA hexamers were built based on the X-ray crystal structure of the actinomycin–d(GAAGCTTC)2 complex. The DNA sequences included the canonical GpC binding step flanked by different base pairs, nonclassical binding sites such as GpG and GpT, and sites containing 2,6-diamino- purine. A good correlation was found between the intermolecular interaction energies calculated for the refined complexes and the relative preferences of actinomycin binding to standard and modified DNA. A detailed energy decomposition into van der Waals and electrostatic components for the interactions between the DNA base pairs and either the chromophore or the peptidic part of the antibiotic was performed for each complex. The resulting energy matrix was then subjected to principal component analysis, which showed that actinomycin D discriminates among different DNA sequences by an interplay of hydrogen bonding and stacking interactions. The structure–affinity relationships for this important antitumor drug are thus rationalized and may be used to advantage in the design of novel sequence-specific DNA-binding agents.     

Proximity Effects in Organic Chemistry—The Photoelectron Spectroscopic Investigation of Non-Bonding and Transannular Interactions

Classical structural formulas often convey the impression only those relationships between the atoms are of importance which hold a molecule together as symbolized by the chemical bonds. However, many interactions between atoms or groups of atoms are not adequately denoted in this manner. Nevertheless, their existence can have important consequences for ground state energies (cis-difluoroethylene is more stable than trans-difluoroethylene), conformations (the syn form of methyl vinyl ether is more stable than the anti form), reactivities (an endo cyclopropane ring in 7-anti-norbornyl derivatives accelerates solvolysis by a factor of 10¹⁴), UV spectra (“superposition” of the π-systems of acridine and purine-bonded through a four-membered chain-results in hypochromism), CD spectra (the inherently symmetrical but dissymmetrically perturbed chromophore of 2-deuterionorbornadiene allows the observation of three transitions in the near UV), and ESR spectra (the long-range coupling with H-4 in the bridgehead bicyclo[2.1.1]hex-1-yl radical equals 22.5 G). Since orbital interactions are involved in most intramolecular effects of this kind, photoelectron spectroscopy has proven an informative and valuable extension to other methods.