Intramolecular Resonance-assisted Hydrogen Bonds Research Articles

Experimental and theoretical comparison of the vibrational and NMR spectra of novel 6-6’-(1E-1’E)-(Propane-1,3Diylbis (Azanylyidene)) Bis (Phenylmethylylidene)) Bis (3-Octyloxy) Phenol), NBO and molecular docking studies

The characterization study of the synthesized novel compound 6-6’-(1E-1’E)-(Propane-1,3Diylbis(Azanylyidene))Bis(Phenylmethylylidene))Bis(3-Octyloxy)Phenol) (C45H58N2O4) was done by FT-IR, Raman and NMR spectra. Vibrational analysis was realized with normal coordinate treatment, and vibrational modes were assigned in the mid-IR region. The 13C and 1H -NMR spectra of the title compound were measured in DMSO and chloroform, and the corresponding chemical shifts were calculated in the different basis sets (6-31++G(d,p), 6-311G(2d,p), 6-311++G(2d,p), TZVPP) of DFT-B3LYP with continuum models. The vibrational and NMR spectroscopies show that the existence of the intramolecular resonance-assisted hydrogen bonds(O-H...N) results in the redshift of OH vibrational modes and its high proton chemical shifts (ca. 16 ppm), as confirmed by X-ray crystal structure and NRT studies.13C NMR chemical shifts of the Schiff base bond are determined as ca. 174 ppm. The calculations indicate that both the intramolecular hydrogen bond strength and the OH-proton chemical shift increase with increasing solvent polarity. The molecular docking studies reveal that the title ligand has the potency of inhibition against the VIM-2 and NDM-1 active sites of metallo-β-lactamase receptor.

Halogen Bonding in the Decoration of Secondary Coordination Sphere of Zinc(II) and Cadmium(II) Complexes: Catalytic Application in Cycloaddition Reaction of CO2 with Epoxides.

Three new zinc(II) complexes [Zn(H2L3)2(H2O)3] (Zn2), [Zn(H3L2a)(H2O)3]n (Zn3) (H3L2a = 2,4-diiodo-5-(2-(2,4,6-trioxotetrahydropyrimidin-5(2H)-ylidene)hydrazineyl)isophthalate) and [Zn(HL4)(DMF)(H2O)]n (Zn4) were synthesized by the reaction of Zn(II) salts with 5-(2-(2,4-dioxopentan-3-ylidene)hydrazineyl) isophthalic acid (H3L3), 2,4,6-triiodo-5-(2-(2,4,6-trioxotetrahydropyrimidin-5(2H)-ylidene)hydrazineyl) isophthalic acid (H5L2) (in the presence of NH2OH·HCl) and 5-(2-(2,4-dioxopentan-3-ylidene)hydrazineyl)-2,4,6-triiodoisophthalic acid (H3L4), respectively. According to the X-ray structural analysis, the intramolecular resonance-assisted hydrogen bond ring remains intact, with N···O distances of 2.562(5) and 2.573(5) Å in Zn2, 2.603(6) Å in Zn3, and 2.563(8) Å in Zn4. In the crystal packing of Zn3, the cooperation of I···O and I···I types of halogen bonds between tectons leads to a one-dimensional supramolecular polymer, while I···O interactions aggregate 1D chains of coordination polymer Zn4. These new complexes (Zn2, Zn3, and Zn4) and known [Zn(H3L1)(H2O)2]n (Zn1) (H3L1 = 5-(2-(2,4,6-trioxotetrahydropyrimidin-5(2H)-ylidene) hydrazineyl)isophthalate), {[Zn(H3L1)(H2O)3]·3H2O}n (Zn5), [Cd(H3L1)(H2O)2]n (Cd1), {[Cd(HL3)(H2O)2(DMF)]·H2O}n (Cd2), [Cd(H3L3)]n (Cd-3), {[Cd2(μ-H2O)2(μ-H2L4)2(H2L4)2]·2H2O}n (Cd4), and {[Cd(H3L1)(H2O)3]·4H2O}n (Cd5) were tested as catalysts in the cycloaddition reaction of CO2 with epoxides in the presence of tetrabutylammonium halides as the cocatalyst. The halogen-bonded catalyst Zn4 is the most efficient one in the presence of tetrabutylammonium bromide by affording a high yield (85-99%) of cyclic carbonates under solvent-free conditions after 48 h at 40 bar and 80 °C.

Intramolecular resonance-assisted hydrogen bonds: Insights from symmetry adapted perturbation theory

The accurate description of hydrogen bonds (H-bonds) is one of the primary challenges when describing intermolecular forces. Intramolecular hydrogen bonds (IMHB) are even more challenging because of their ill-defined energy and their interplay with π-systems. In this contribution, we investigate the role of π-resonance in the enhancement of IMHBs. This is accomplished by comparing a number of π-conjugated systems to their saturated planar counterparts using intramolecular symmetry adapted perturbation theory (I-SAPT). The change in the composition of the IMHB energies (electrostatics, exchange, induction, and dispersion) due to π-conjugation is examined in detail. The biggest changes are observed in the induction and electrostatics contributions. However, electrostatics is nearly canceled by its exchange counterpart. The importance of induction term is also observed when plotting rotational potential curves for the different energy components. Once the distance between the H-bond donor and acceptor is frozen, the stabilization of IMHBs mostly occurs through the decrease in the exchange term leading to less repulsion. In any case, all results are consistent with expected trends in the resonance-assisted hydrogen bonds (RAHBs), and corroborate the fragmentation procedures used in this study. The closeness of induction contribution to the whole interaction energy and the existence of a linear correlation between the IMHB energy and the induction component show that the induction term is a good predictor of the intramolecular RAHBs stability trends.

Intramolecular resonance assisted N–H⋅⋅⋅O=C hydrogen bond and weak noncovalent interactions in two asymmetrically substituted geminal amido-esters: Crystal structures and quantum chemical exploration

Two asymmetrically substituted geminal amido-esters, namely ethyl (2E)-2-[(2,5-dimethoxy phenyl)carbamoyl]-3-[(4-nitrophenyl)amino] prop-2-enoate (I) and ethyl (2E)-2-[(9,10-dioxo-9,10-dihydroanthracen-1-yl)carbamoyl]-3-(phenylamino) prop-2-enoate (II) were synthesized and the nature and strength of intramolecular resonance assisted hydrogen bond (RAHB) and non-RAHB was studied. X-ray analysis revealed that intramolecular N–H⋅⋅⋅O, and C–H⋅⋅⋅O interactions lead to the formation of angularly fused pseudo tricyclic (A-C) motif in compound I and fused pseudo pentacyclic (A-E) motif in compound II. Intramolecular RAHB; non-RAHB interactions are characterized and quantified by Bader's quantum theory of atoms-in-molecules approach (QTAIM). In both compounds, ring A was found to exhibit intramolecular RAHB characteristics. Crystal structures of I and II are stabilized by weak intermolecular C–H⋅⋅⋅O, C–H⋅⋅⋅π, and π⋅⋅⋅π interactions. Intermolecular interaction energies for different molecular dimers in I and II have been quantified by using the PIXEL, QTAIM, and DFT methods. The pseudoring stacking interaction is observed only in compound II whereas no such stacking interactions are seen in compound I. Hirshfeld surface (HS) analysis suggested that the H⋅⋅⋅H and O⋅⋅⋅H contacts are the first and second dominant contacts in both crystal structures. The theoretical charge density analysis revealed that the C–H⋅⋅⋅O and C–H⋅⋅⋅C(π) interactions produce closed-shell characteristics. Further, the crystal packing of compounds I and II analyzed based on the energy frameworks.

Tuning the Strength of the Resonance-Assisted Hydrogen Bond in Acenes and Phenacenes with Two o-Hydroxyaldehyde Groups-The Importance of Topology.

The fact that intramolecular resonance-assisted hydrogen bonds (RAHBs) are stronger than conventional ones is attributed to the partial delocalization of the π-electrons within the hydrogen bond (HB) motif, the so-called quasi-ring. If an aromatic ring is involved in the formation of the RAHB, previous studies have shown that there is an interplay between aromaticity and HB strength. Moreover, in 1,3-dihydroxyaryl-2-aldehydes, some of us found that the position of the quasi-ring formed by the substituents interacting through RAHB influences the strength of the H bonding, the HBs being stronger when a kinked-like structure is generated by formation of the quasi-ring. In this work, we explore this concept further by considering a set of acenes and phenacenes of different sizes with two o-hydroxyaldehyde substituents. Calculations with the CAM-B3LYP/6-311++G(d,p) + GD3B method show that for long acenes or phenacenes, once the substituent effect loses importance because quasi-rings are pulled apart far from each other, the different topologies rule the HB distances. This fact can be explained in most cases using an extended Clar's aromatic π-sextet model. In some kinked systems, however, the justification from the Clar model has to be complemented by taking into account the repulsion between hydrogen atoms. Triphenylene-like compounds with different numbers of benzene rings have been studied, finding out a very good relationship between aromaticity of the ipso- and quasi-rings with the RAHB distances. This result confirms the importance of the communication of the π-systems of the ipso- and quasi-rings.

Tuning the Strength of the Resonance-Assisted Hydrogen Bond in o-Hydroxybenzaldehyde by Substitution in the Aromatic Ring1.

Intramolecular resonance-assisted hydrogen bonds (RAHBs) are stronger than conventional hydrogen bonds (HBs) thanks to the extra stabilization connected with the partial delocalization of the π-electrons within the HB motif containing conjugated formally single and double bonds. When these conjugated bonds are part of an aromatic ring, there is an interplay between resonance-assisted hydrogen bonding and the aromaticity of the ring. The main aim of the present work is to analyze the changes in RAHB strength by substitution in the aromatic ring. For this purpose, we use density functional theory methods to study all possible mono- and disubstitutions in the four free positions of the aromatic ring of o-hydroxybenzaldehyde. As substituents, we consider three π-electron donating groups (EDG: NH2, OH, and F) and three π-electron withdrawing groups (EWG: NO2, NO, and CN). We show that it is possible to tune the HB bond distance in the RAHB by locating different substituents in given positions of the aromatic ring. Indeed, certain combinations of EDG and EWD result in a reduction or increase of the HB distance by up to 0.05 Å. Results found can be explained by considering the existence of a resonance effect of the π-electrons within the HB motif.

CoII, NiII and UO2II complexes with β-diketones and their arylhydrazone derivatives: Synthesis, structure and catalytic activity in Henry reaction

The new uranyl, nickel and cobalt complexes, [UO2(L1)2(R)] (1), [Ni(L1)2((CH3)2SO)2] (2), [Co(H2O)4(HL2)2]·2H2O (3) and [UO2(H2O)2(HL2)2]·2H2O (4), were prepared by reaction of UO2(CH3COO)2·2H2O, Ni(CH3COO)2·4H2O or Co(CH3COO)2·4H2O with 1,3-diphenyl-propane-1,3-dione (H2L1) or 4-(2-(2,4-dioxopentan-3-ylidene)hydrazinyl)benzoic acid (H2L2) in the presence of N,N-diethylnicotinamide (R) (for 1). Complexes 1–4 were characterized by elemental analysis, IR spectroscopy, ESI-MS and single crystal X-ray diffraction technique. In both 1 and 2 the (L1)− coordinates in a bidentate chelating mode where the UO22+ in 1 exhibits a distorted pentagonal bipyramidal and Ni2+ in 2 a distorted octahedral geometries. In 3 and 4 a hydrazone moiety containing an intramolecular resonance assisted hydrogen bond, with N–H⋯O distances of 2.5469(18) and 2.549(7)Å, respectively, was found in the coordinated ligand (HL2)−. The supramolecular networks (packing diagrams) of 1–4 are constructed via hydrogen bonding, CH–π or π–π interactions. All the four complexes (1–4) act as a good catalyst towards the diastereoselective nitroaldol (Henry) reaction of aliphatic and aromatic aldehydes with nitroethane in different solvents such as acetonitrile, methanol or water. Complex 3 was found to be efficient catalyst for the Henry reaction in aqueous medium, providing β-nitroalcohols with good yields (68–91%) and diastereoselectivities (syn/anti 77:23–73:27).

A computational study of the structure, aromaticity and enthalpy of formation of UVA filter 4-tert-butyl-4′-methoxydibenzoylmethane

In this study we have performed a density functional theory (DFT) study of the molecular structure and energetics of the enol and keto tautomers of UVA filter 4-tert-butyl-4′-methoxydibenzoylmethane (BMDBM) and for comparison and validation purposes a similar study has been carried out for the parent molecule: dibenzoylmethane (DBM). The molecular structure of the enol and keto tautomers were obtained at the B3LYP/6-311++G(d,p) level. The enol forms were found to have a strong intramolecular resonance assisted hydrogen bond that accounts for the greater energetic stability of the enol relative to the keto form. The aromatic character of the six-membered enol rings has been analyzed by calculation of Nucleus Independent Chemical Shifts (NICS). The standard molar enthalpy of formation in the gas phase of BMDBM was derived from appropriately chosen reactions.

Intramolecular resonance-assisted hydrogen bonds: A theoretical description by means of atomic charges and charge fluxes

The characterization of intramolecular H-bonds in terms of atomic charges and charge fluxes (at the B3LYP/cc-pVTZ level of theory) has been extended to the case of the so called resonance-assisted (RA) H-bonds. A quadratic correlation between the charge fluxes ϕH and the molecular IR absorption coefficients E that includes the entire family of the studied systems (31 of them) containing both intra- and intermolecular hydrogen bonds (O–H⋯O/N) confirmed the critical importance of the charge fluxes on the IR intensity enhancements. Since they reflect changing of the atomic charge distribution during the normal modes of vibrations, the dynamic nature of hydrogen bonding properties has been re-emphasized. The changes of the charge flux of the hydroxyl hydrogen in an RA intramolecular H-bond are between those for “free” OH bonds and the values calculated for intermolecular H-bonds. The transition “free”→intramolecular→intermolecular is gradual and therefore the hydrogen charge flux can be considered as practically sufficient to give quantitative measure to the intuitively obvious statement that “intramolecular H-bonding is somehow in between no H-bonding situation and intermolecular H-bonding” and thus provide a quantitative and yet simple parameterization of H-bond strength. In strictly planar molecules, the difference of the sums of charges of atoms participating in the 6-membered H-bond ring ΔΣ can serve as a measure of the charge delocalization after the H-bond is formed. The electronic charge is withdrawn from the group of six atoms when the H-bond is formed in nitrophenol (ΔΣ=−0.07), while the opposite is true (ΔΣ=+0.03) for 2-hydroxy benzylidene amine. The corresponding values of the geometrical resonance parameter Δ are 0.39 and 0.37, respectively, similar to those found for 2-hydroxy acetophenone and 2-hydroxy benzaldehyde. The extent of the π-electron delocalization as measured by the resonance parameter Δ does not follow the strength of H-bond as measured by the charge flux ϕH.

Synthesis and Structural Characterisation of New Bifunctional o-Hydroxyacetophenones – Potential Linker Molecules for Coordinative Framework Construction

Two new linker-type molecules 1a and 1b composed of o-hydroxyacetophenone coordinative groups attached to linear ethynylene or 1,4-phenylenediethynylene spacer units have been synthesised and structurally characterised. An X-ray crystallographic study for both compounds has shown structures with strong intramolecular hydrogen bonds fitting in the model of ‘Intramolecular Resonance Assisted Hydrogen Bond (IRHAB)’. Initial coordination experiments with Cu(II) were performed and the resulting materials characterised by PXRD. The similarity of the copper coordination between these compounds and copper(II) acetylacetonate complexes was demonstrated by XPS measurements. Based on the evidence of these studies, and on elemental analysis, the formation of the corresponding coordination polymers comprising Cu(II) and the linkers has been proposed

Total synthesis of marinomycin A using salicylate as a molecular switch to mediate dimerization

Antibiotics play a significant role in human health because of their ability to treat life-threatening bacterial infections. The growing problems with antibiotic resistance have made the development of new antibiotics a World Health Organization priority. Marinomycin A is a member of a new class of bis-salicylate-containing polyene macrodiolides, which have potent antibiotic activity against methicillin-resistant Staphylococcus aureus and vancomycin-resistant Enterococcus faecium. Herein, we describe a triply convergent synthesis of this agent using the salicylate as a novel molecular switch for the chemoselective construction of the macrodiolide. This strategy raises new questions regarding the biosynthetic role of the salicylate and its potential impact on the mechanism of action of these types of agents. For instance, in contrast to penicillin, which enhances the electrophilicity of the cyclic amide through ring strain, salicylates reduce the electrophilicity of the aryl ester through an intramolecular resonance-assisted hydrogen bond to provide an amide surrogate.

Properties, aromaticity, and substituents effects in poly nitro- and amino-substituted benzenes

Geometrical parameters, aromaticity, and conformational flexibility of the set of polysubstituted benzenes with different number and position of nitro and amino groups were calculated at the MP2/cc-pvdz level of theory. The key factor for structural and energetic changes has been identified. This is related to the presence of nitro and amino groups in vicinal positions that forms strong intramolecular resonance-assisted hydrogen bonds with a binding energy of 7–14 kcal/mol. Increasing number of such bonds facilitates a cooperative effect, inducing notable changes in molecular geometry (particularly increasing bond alternation within H2N–C–C–NO2 fragment and planarization of amino group), drastic increasing of conformational flexibility and decreasing of aromaticity. In spite of well-known π-electron effects of nitro and amino substituents, influence of their push–pull interaction through aromatic moiety is negligible compared to the effect of the hydrogen bonding. That results in great difference of the ortho-isomers as compared to meta- and para-isomers.

分子内共鳴支援水素結合における共役効果と芳香族性(5) 三重項状態における配置依存性

分子内共鳴支援水素結合における共役効果と芳香族性(5) 三重項状態における配置依存性

分子内共鳴支援水素結合における共役効果と芳香族性(4) 水素移動と反芳香族性

分子内共鳴支援水素結合における共役効果と芳香族性(4) 水素移動と反芳香族性

H-Bonding-Assisted Substituent Effect

In this paper we investigate the influence of intramolecular noncovalent interaction, i.e., H-bonding and Li-bonding, on the properties of substituents communicating through the resonance (mesomeric) effect in such molecular systems as salicylaldehyde, o-hydroxy Schiff base, o-nitrosophenol, and their lithium analogues. The investigated systems are usually considered as molecular patterns of intramolecular resonance-assisted hydrogen bonds (or its analogues in the case of Li-bonded systems). We show that the relation between intramolecular noncovalent interactions, A-H...B and A-Li...B, and the pi-electron delocalization in the sequence of pi-conjugated covalent bonds linking A and B can be considered in terms of the Hammett-like substituent effect in which electron-donating and electron-withdrawing properties of substituents are affected by the noncovalent interaction.

The effect of formation of second hydrogen bond in adjacent two-ring resonance-assisted hydrogen bonds – Ab initio and QTAIM studies

Two-ring intramolecular resonance-assisted hydrogen bonds (RAHBs) existing in 1,5-dihydroxy-1,4-diene-3-pentanone and some its symmetrically substituted derivatives have been studied at the MP2/6-311++G∗∗ level of theory. The influence of the coexistence of two intramolecular hydrogen bonded rings in these molecular systems on the structure, intramolecular hydrogen bonding and π-electron delocalization was investigated. The results of calculations show that such coexistence increases the π-electron delocalization but it leads also to the weakening of hydrogen bonding. The Quantum Theory of ‘‘Atoms in Molecules’’ (QTAIM) of Bader was also applied here to get more details about the nature of hydrogen bonds. Correlations between the hydrogen bond strength and different parameters were also analyzed. It was found that topological characteristics of critical points (bond critical points and ring critical points) are also useful to estimate the strength of intramolecular hydrogen bonds in two-ring RAHB systems.

分子内共鳴支援水素結合における共役効果と芳香族性(2) 鎖長依存性

分子内共鳴支援水素結合における共役効果と芳香族性(2) 鎖長依存性

Close shell interactions in 3-ethoxycarbonyl-4-hydroxy-6-methoxymethyleneoxy-1-methyl-2-quinolone: 100 K single crystal neutron diffraction study and ab initio calculations

The molecular and crystal structures of the title compound have been determined from a single crystal neutron diffraction experiment at 100 K. A comparison between the main geometrical features and related properties of the in-crystal and the ab initio optimized free molecule structures has shown that crystal packing induces a significant distortion in the molecular geometry. Packing instead would only have a moderate effect on the observed intramolecular resonance assisted hydrogen bond. Supermolecular ab initio molecular orbital calculations have been performed on the six different dimers one molecule forms with its nine nearest neighbours. The obtained results clearly show that dispersion contributions dominate in the most strongly interacting dimers, in good qualitative accord with the predictions made by using different empirical potentials. A qualitative description of the most prominent inductive effects determined from the electron density deformation upon dimer formation is presented. Topological analyses of the dimers charge densities have been performed in the framework of the Bader's AIM theory and all the intermolecular bond critical points have been identified. An attempt to determine some of the interaction energies only from topological quantities made evident the practical limitations of such an approach.

π‐Electron delocalisation for intramolecular resonance assisted hydrogen bonds

Abstractπ‐Electron delocalisation for the intramolecular resonance assisted hydrogen bonds (IRAHBs) is analysed here. The investigation is based on MP2/6‐311++G** calculations as well as on the results derived from the Bader theory. The Mulliken analysis of the change in natural population atomic charges for the IRAHB systems shows that there is a transfer of the electron charge from the R1CCR2CR3region into the OH…O hydrogen bond. The results of calculations also show that the strength of IRAHBs depends mainly on the process of the π‐electron delocalisation. Copyright © 2003 John Wiley & Sons, Ltd.

Intramolecular resonance assisted hydrogen bond and aggregation of 2-quinolones: a neutron diffraction study

Fil: Punte, Graciela Maria. Consejo Nacional de Investigaciones Cientificas y Tecnicas. Centro Cientifico Tecnologico Conicet - La Plata. Instituto de Fisica La Plata. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Instituto de Fisica La Plata; Argentina