Protonated primary amines induced thymine quintets studied by electrospray ionization mass spectrometry and density functional theory calculations

As the novel magic number clusters of nucleobases, the thymine quintets induced by ammonium ion (NH₄⁺), and particularly by its derivatives such as protonated alkyl amines and protonated aryl amines, have been studied by electrospray ionization mass spectrometry (ESI‐MS) and density functional theory (DFT) calculations. The DFT‐optimized geometry of NH₄⁺ induced thymine quintet ([T₅ + NH₄]⁺) reveals some new features including three additional hydrogen bonds between NH₄⁺ and its surrounding thymine molecules when compared with that of the alkali metal ions induced thymine quintets. In addition, the fourth hydrogen atom of NH₄⁺ is sticking out the assembly, and, thus, it might be replaced by an organic group R to form the protonated primary amine induced thymine quintet ([T₅ + R ? NH₃]⁺), a hypothesis that has been confirmed by both DFT calculations and ESI‐MS experiments. Furthermore, the relative abilities of the different protonated primary amines for inducing the thymine quintets are investigated by ESI‐MS competition experiments, and the results have shown a clear trend of stronger ability as the alkyl chain gets longer or as the aryl ring gets larger for the alkyl amines or the aryl amines. Two basic influence factors are consequently identified: one is the ability of the alkyl amine to accept proton, another is the π–π stacking interaction between the aryl ring and the π‐surface of the thymine molecule(s), whose explanations are strongly supported by multiple types of thermochemical data, various control experiments and DFT calculations. Copyright © 2014 John Wiley & Sons, Ltd.     

The choice of appropriate density functional for the calculation of static first hyperpolarizability of azochromophores and stacking dimers

The effect of the stacked azo‐chromophore dimer formation on the values of static first hyperpolarizability is studied in the framework of the DFT‐based approach; calculations were also performed at the MP2 level. A number of dispersion‐corrected density functionals—В97D, ωВ97X‐D, and M06‐2X—is tested to calculate the structure of the dimer, the value of binding energy, and molecular nonlinear optical characteristics. According to the QTAIM analysis, the presence of bond critical points is revealed in the intermolecular region, the signs and values of topological characteristics giving evidence for the noncovalent van der Waals interaction between the chromophores. The formation of stacks results in moderate increase of dimer static first hyperpolarizability as compared to that of a single chromophore, the effect depending on the relative shift of the chromophores in dimer. In a special case of greatly shifted chromophores, this enhancement of the first hyperpolarizability becomes appreciable and achieves 72%. © 2015 Wiley Periodicals, Inc.     

Interpreting geometric preferences in π‐stacking interactions through molecular orbital analysis

The preference of π‐stacking interactions for parallel‐displaced (PD) and twisted (TW) conformations over the fully eclipsed sandwich (S) in small π‐stacked dimers of benzene, pyridine, pyrimidine, 1,3,5‐trifluorobenzene, and hexafluorobenzene are examined in terms of enhancement of the inter‐ring density through mixing of the monomer orbitals (MOs). PD and/or TW conformations are consistent with a non‐zero “stack bond order” (SBO), defined in analogy to the bond order of conventional MO theory, as the difference in the occupation of bonding and antibonding π‐type dimer MOs. In the S conformation, the equal number of bonding and antibonding MOs cancel overall stack bonding character between the monomers for an SBO of zero and an overall repulsive interaction. PD from the S shifts the character of at least one antibonding combination of monomer π‐type MOs with nodes perpendicular to the coordinate for PD to bonding, leading to an attractive nonzero SBO. The inter‐ring density measured through the Wiberg bond index analysis shows an enhancement at the PD conformations consistent with greater interpenetration of the monomer densities. This intuitive bonding model for π‐stacking interactions is complementary to highly accurate calculations of π‐stacking energies and allows a predictive understanding of relative stability using cheaper quantum chemical methods.     

Hybrid density functional theory for pi-stacking interactions: application to benzenes, pyridines, and DNA bases

The suitability of a hybrid density functional to qualitatively reproduce geometric and energetic details of parallel pi-stacked aromatic complexes is presented. The hybrid functional includes an ad hoc mixture of half the exact (HF) exchange with half of the uniform electron gas exchange, plus Lee, Yang, and Parr's expression for correlation energy. This functional, in combination with polarized, diffuse basis sets, gives a binding energy for the parallel-displaced benzene dimer in good agreement with the best available high-level calculations reported in the literature, and qualitatively reproduces the local MP2 potential energy surface of the parallel-displaced benzene dimer. This method was further critically compared to high-level calculations recently reported in the literature for a range of pi-stacked complexes, including monosubstituted benzene-benzene dimers, along with DNA and RNA bases, and generally agrees with MP2 and/or CCSD(T) results to within +/-2 kJ mol(-1). We also show that the resulting BH&H binding energy is closely related to the electron density in the intermolecular region. The net result is that the BH&H functional, presumably due to fortuitous cancellation of errors, provides a pragmatic, computationally efficient quantum mechanical tool for the study of large pi-stacked systems such as DNA.     

2H‐Azirines as Ligands: Structural Characterization of the First Neutral and Cationic (η5‐C5Me5)Rh(III) 2H‐Azirine Complexes

The synthesis and structural characterization of two azirine rhodium(III ) complexes are described. The stabilization, N‐coordination and phenylgroup π‐stacking of the highly reactive and strained 3‐phenyl‐2H‐azirine by transition metal coordination is observed. The reaction of the dimeric complex [(η⁵‐C₅Me₅)RhCl₂]₂ with 3‐phenyl‐2H‐azirine (az) in CH₂Cl₂ at room temperature in a 1:2 molar ratio afforded the neutral mono‐azirine complex [(η⁵‐C₅Me₅)RhCl₂(az)]. The subsequent reaction of [(η⁵‐C₅Me₅)RhCl₂]₂ with six equivalents of az and 4 equivalents of AgOTf yielded the cationic tris‐azirine complex [(η⁵‐C₅Me₅)Rh(az)₃](OTf)₂. After purification, all complexes have been fully characterized. The molecular structures of the novel rhodium(III ) complexes exhibit slightly distorted octahedral coordination geometries around the metal atoms.     

Competition between hydrogen and halogen bonding in halogenated 1‐methyluracil: Water systems

The competition between hydrogen‐ and halogen‐bonding interactions in complexes of 5‐halogenated 1‐methyluracil (XmU; X = F, Cl, Br, I, or At) with one or two water molecules in the binding region between C5‐X and C4?O4 is investigated with M06‐2X/6‐31+G(d). In the singly‐hydrated systems, the water molecule forms a hydrogen bond with C4?O4 for all halogens, whereas structures with a halogen bond between the water oxygen and C5‐X exist only for X = Br, I, and At. Structures with two waters forming a bridge between C4?O and C5‐X (through hydrogen‐ and halogen‐bonding interactions) exist for all halogens except F. The absence of a halogen‐bonded structure in singly‐hydrated ClmU is therefore attributed to the competing hydrogen‐bonding interaction with C4?O4. The halogen‐bond angle in the doubly‐hydrated structures (150–160°) is far from the expected linearity of halogen bonds, indicating that significantly non‐linear halogen bonds may exist in complex environments with competing interactions. © 2016 Wiley Periodicals, Inc.     

A New Succinato‐bridged Supramolecular Helix Chain: Crystal Structure of [Mn(H2O)2(bpy)(C4H4O4)] · H2O with bpy = 2,2′‐bipyridine

Yellow crystals of [Mn(H₂O)₂(bpy)(C₄H₄O₄)] · H₂O were obtained by the reaction of 2,2′‐bipyridine, succinic acid, MnSO₄ · H₂O and Na₂CO₃ in an aqueous methanol solution. The crystal structure (monoclinic, P2₁/c (no. 14), a = 8.294(1), b = 11.556(1), c = 17.064(1)Å, β = 95.181(6)°, Z = 4, R = 0.0349, wR² = 0.0887) consists of 1D supramolecular helix chains [Mn(H₂O)₂(bpy)(C₄H₄O₄)_2/2] and hydrogen bonded H₂O molecules. The Mn atoms are octahedrally coordinated by two N atoms of one bidentate chelating bpy ligand and four O atoms of two H₂O molecules and two bis‐monodentate bridging succinato ligands with d(Mn–O) = 2.139–2.237Å and d(Mn–N) = 2.268, 2.281 Å. The helix chains are held together by π‐π stacking interactions and hydrogen bonds.     

Tuning the π‐π stacking distance and J‐aggregation of DPP‐based conjugated polymer via introducing insulating polymer

The close π–π stacking and the high J‐aggregation during the formation of fibrillar morphology in films of the poly[[2,5‐bis(2‐octyldodecyl)?2,3,5,6‐tetrahydro‐3,6‐dioxopyrrolo[3,4‐c]pyrrole‐1,4‐diyl]‐alt–[[2,2′‐(2,5‐thiophene)bis‐thieno[3,2‐b]thiophen]‐5,5′‐diyl]] (PDPPTT‐T) are demonstrated via blending with polystyrene (PS). The hydrodynamic radius (R_h) of PDPPTT‐T is decreased from 16.7 nm in the neat solution to 12.7 nm in the blend solution at the ratio of 1/20(PDPPTT‐T/PS). This phenomenon suggests that blending PS is beneficial for the disentanglement of PDPPTT‐T. The disentanglement of PDPPTT‐T facilitates the formation of fibrillar morphology. The growth of the fibrils occurs along the molecular backbones and the width of the fibrils is parallel to the π–π stacking direction. The disentanglement of PDPPTT‐T helps the molecules adjust conformation to improve J‐aggregation and decrease the π–π stacking distance. The maximum absorption is red‐shifted from 825 nm to 849 nm and the relative intensity of J‐aggregation (the 0‐0/0‐1 ratio) is increased from 1.19 to 1.60. The π–π stacking distance decreases from 3.57 to 3.52 Å. The charge‐carrier mobility will be improved in the fibrillar morphology with close π–π stacking and high J‐aggregation. © 2016 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2016 , 54, 838–847     

Hydroxo Bridged Dinuclear Rare Earth Complexes: Syntheses and Crystal Structures of [Ln2(phen)4(H2O)4(OH)2](NO3)4(phen)2 with Ln = Er,Lu

Reactions of phenanthroline (phen) and Er(NO₃)₃ · 5 H₂O or Lu(NO₃)₃ · H₂O in CH₃OH/H₂O yield [Ln₂(phen)₄(H₂O)₄(OH)₂](NO₃)₄(phen)₂ with Ln = Er ( 1 ), Lu ( 2 ). Both isostructural complex compounds crystallize in the triclinic space group P 1 (no. 2) with the cell dimensions: a = 11.257(2) Å, b = 11.467(2) Å, c = 14.069(2) Å, α = 93.93(2)°, β = 98.18(1)°, γ = 108.14(1)°, V = 1696.0(6) ų, Z = 1 for ( 1 ) and a = 11.251(1) Å, b = 11.476(1) Å, c = 14.019(1) Å, α = 93.83(1)°, β = 98.27(1)°, γ = 108.27(1)°, V = 1689.0(3) ų, Z = 1 for ( 2 ). The crystal structures consist of the hydroxo bridged dinuclear [Ln₂(phen)₄(H₂O)₄(OH)₂]⁴⁺ complex cations, hydrogen bonded NO₃^– anions and π‐π stacking (phen)₂ dimers. The rare earth metal atoms are coordinated by four N atoms of two phen ligands and four O atoms of two H₂O molecules and two μ‐OH groups to complete tetragonal antiprisms. Via two common μ‐OH groups, two neighboring tetragonal antiprisms are condensed to a centrosymmetric dinuclear [Ln₂(phen)₄(H₂O)₄(OH)₂]⁴⁺ complex cation. Based on π‐π stacking interactions and hydrogen bonding, the complex cations and (phen)₂ dimers form 2 D layers parallel to (1 0 1), between which the hydrogen bonded NO₃^– anions are sandwiched. The structures can be simplified into a distorted CsCl structure when {[Ln₂(phen)₄(H₂O)₄(OH)₂](NO₃)₄} and (phen)₂ are viewed as building units.     

Interdigitated crystalline MMT‐MCA: Preparation and characterization

A novel nanomaterial, montmorillonite–melamine cyanurate (MMT‐MCA), was successfully synthesized, in which the number of MCA layers in between 2 MMT layers can be controlled at 1 or a very large value (over 100 nm thick). Its interdigitated crystalline structure was thoroughly characterized. The MMT‐MCA shows outstanding dispersion ability in different polymers to easily prepare MMT nanocomposites by melt blending due to the π‐π stacking exfoliation between MCA layers. The paper opens the way to the synthesis of novel interdigitated nanomaterials.     

Structure,stability, and nature of bonding in carbon monoxide bound complexes (E = group 14 element; X = H,F, Cl,Br, I)

A density functional theory study is performed to predict the structures and stability of carbon monoxide (CO) bound (E = C, Si, Ge, Sn, Pb; X = H, F, Cl, Br, I) complexes. The possibility of bonding through both C‐ and O‐sides of CO is considered. Thermochemical analysis reveals that all the dissociation processes producing CO and are endothermic in nature whereas most of the dissociation reactions are endergonic in nature at room temperature. The nature of bonding in E? C/O bonds is analyzed via Wiberg bond index, natural population analysis, electron density, and energy decomposition analyses in conjunction with natural orbitals for chemical valence scheme. In comparison to C? O stretching frequency ( ) in free CO, while a red shift is noted in O‐side binding, the C‐side binding results in a blue shift in . The relative change in values in CO bound complexes on changing either E or X is scrutinized and possible explanation is provided in terms of polarization in the σ‐ and π‐orbitals and the relative strength of C→E or O→E σ‐donation and E→C or E→O π‐back‐donation. © 2016 Wiley Periodicals, Inc.     

Coumarin‐tethered (benz)imidazolium salts and their silver(I) N‐heterocyclic carbene complexes: Synthesis,characterization, crystal structure and antibacterial studies

A series of new sterically modulated chlorocoumarin‐substituted (benz)imidazolium salts and their bis‐N‐heterocyclic carbene silver(I) complexes were prepared and characterized. The complexes were prepared in good yields following the in situ deprotonation method by treating azolium salts with silver(I) oxide in the dark. All the compounds were characterized using various spectroscopic and analytical methods. Additionally, one of the benzimidazolium salts was characterized using single‐crystal X‐ray diffraction technique. In this salt, intermolecular π–π stacking interactions operate between benzimidazole as well as coumarin heterocyclic systems with adjacent molecules. In the preliminary antibacterial studies, the silver complexes were found more active than the corresponding salts against a panel of bacterial strains. Interestingly, the complexes displayed improved antibacterial efficacy against Escherichia coli strain, comparable with that of the standard drug ampicillin.     

Crystal Structures of [Mn2(H2O)4(bpy)2(C8H12O4)2] · 2 H2O and [Mn(H2O)2(bpy)(C8H12O4)2/2] · H2O with bpy = 2,2′‐bipyridine

Reaction of MnSO₄ · H₂O, 2,2′‐bipyridine (bpy), suberic acid and Na₂CO₃ in CH₃OH/H₂O yielded a mixture of [Mn₂(H₂O)₄(bpy)₂(C₈H₁₂O₄)₂] · 2 H₂O ( 1 ) and [Mn(H₂O)₂‐ (bpy)(C₈H₁₂O₄)_2/2] · H₂O ( 2 ). In both complexes, the Mn atoms are octahedrally coordinated by two N atoms of one bpy ligand and four O atoms of two trans positioned H₂O molecules and two suberato ligands (d(Mn–O) = 2.107–2.328 Å; d(Mn–N) = 2.250–2.330 Å). The bis‐monodentate suberato ligands bridge Mn atoms to form dinuclear [Mn₂(H₂O)₄(bpy)₂(C₈H₁₂O₄)₂] complex molecules in 1 and 1D [Mn(H₂O)₂(bpy)(C₈H₁₂O₄)_2/2] chains in 2 . Via the intermolecular hydrogen bondings and π‐π stacking interactions, the dinuclear molecules in 1 are assembled into 2D networks parallel to (100), between which the crystal H₂O molecules are sandwiched. The polymeric chains in 2 are linked together by interchain hydrogen bonding and π‐π stacking interactions into 3D networks with the crystal H₂O molecules located in tunnels along [010]. Crystal data for 1 : P2₁/c (no. 14), a = 10.092(1) Å, b = 11.916(2) Å, c = 17.296(2) Å, β = 93.41(1)° and Z = 2. Crystal data for 2 : P2₁/c (no. 14), a = 11.176(2) Å, b = 9.688(1) Å, c = 37.842(6) Å, β = 90.06(1)° and Z = 8.     

The theoretical study on anionic polymerization mechanism of maleimide: Chain propagation by p‐π conjugation process

A complete research on the mechanism of the anionic polymerization of maleimide was performed, not only including the chain initiation, but the propagation as well. The density functional theory method is employed to investigate the reaction pathway using 6‐311+G* basis set, and the Onsager model is also applied to imitate the effect of solvent on the structures and thermodynamic functions of the key steps. It is found that the initiation starts with a nucleophilic reaction, in which the key transition state shows a π‐complex structure. In contrast, the calculated chain propagation (both dimer and trimer process) employs a p‐π conjugation chain propagation mechanism (p‐π CCPM), characterized by the formation of p‐π conjugation orbital between the chain terminal C atom and monomer C?C double bond. This mechanism is in good agreement with the frontier molecular theory and the principle of conservation of molecular orbital symmetry. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2008     

Hydroxo‐bridged Tetranuclear CuII Complexes: {[Cu(bpy)(OH)]4Cl2}Cl2 · 6 H2O and {[Cu(phen)(OH)]4(H2O)2}]Cl4 · 4 H2O

The blue tetranuclear Cu^II complexes {[Cu(bpy)(OH)]₄Cl₂}Cl₂ · 6 H₂O ( 1 ) and {[Cu(phen)(OH)]₄(H₂O)₂}Cl₄ · 4 H₂O ( 2 ) were synthesized and characterized by single crystal X‐ray diffraction. ( 1 ): P 1 (no. 2), a = 9.240(1) Å, b = 10.366(2) Å, c = 12.973(2) Å, α = 85.76(1)°, β = 75.94(1)°, γ = 72.94(1)°, V = 1152.2(4) ų, Z = 1; ( 2 ): P 1 (no. 2), a = 9.770(3) Å, b = 10.118(3) Å, c = 14.258(4) Å, α = 83.72(2)°, β = 70.31(1)°, γ = 70.63(1)°, V = 1252.0(9) ų, Z = 1. The building units are centrosymmetric tetranuclear {[Cu(bpy)(OH)]₄Cl₂}²⁺ and {[Cu(phen)(OH)]₄(H₂O)₂}⁴⁺ complex cations formed by condensation of four elongated square pyramids CuN₂(OH)₂L^ap with the apical ligands L^ap = Cl, H₂O, OH. The resulting [Cu₄(μ₂‐OH)₂(μ₃‐OH)₂] core has the shape of a zigzag band of three Cu₂(OH)₂ squares. The cations exhibit intramolecular and intermolecular π‐π stacking interactions and the latter form 2D layers with the non‐bonded Cl^– anions and H₂O molecules in between (bond lengths: Cu–N = 1.995–2.038 Å; Cu–O = 1.927–1.982 Å; Cu–Cl^ap = 2.563; Cu–O^ap(OH) = 2.334–2.369 Å; Cu–O^ap(H₂O) = 2.256 Å). The Cu…Cu distances of about 2.93 Å do not indicate direct interactions, but the strongly reduced magnetic moment of about 2.74 B.M. corresponds with only two unpaired electrons per formula unit of 1 (1.37 B.M./Cu) and obviously results from intramolecular spin couplings (χ_m(T‐θ) = 0.933 cm³ · mol^–1 · K with θ = –0.7 K).