Intermolecular N–H...O hydrogen bonds assisted by resonance. Heteroconjugated systems as hydrogen-bond-strengthening functional groups

Copper(I)-Mediated Divergent Synthesis of Pyrroquinone Derivatives and 2-Halo-3-amino-1,4-quinones

A divergent transformation of 2-amino-1,4-quinones for the synthesis of pyrroquinone derivatives and 2-halo-3-amino-1,4-quinones was disclosed. The mechanistic study showed that both the tandem cyclization and halogenation involved a Cu(I)-catalyzed oxidative radical process. This protocol not only constructed a series of novel pyrroquinone derivatives with high atom economy but also provided a new method of halogenation via directed C(sp²)-H functionalization with CuX (X = I, Br, Cl) serving as the X (X = I, Br, Cl) source.

Resonance-Assisted Hydrogen Bond-Revisiting the Original Concept in the Context of Its Criticism in the Literature

In the presented research, we address the original concept of resonance-assisted hydrogen bonding (RAHB) by means of the many-body interaction approach and electron density delocalization analysis. The investigated molecular patterns of RAHBs are open chains consisting of two to six molecules in which the intermolecular hydrogen bond stabilizes the complex. Non-RAHB counterparts are considered to be reference systems. The results show the influence of the neighbour monomers on the unsaturated chains in terms of the many-body interaction energy contribution. Exploring the relation between the energy parameters and the growing number of molecules in the chain, we give an explicit extrapolation of the interaction energy and its components in the infinite chain. Electron delocalization within chain motifs has been analysed from three different points of view: three-body delocalization between C=C-C, two-body hydrogen bond delocalization indices and also between fragments (monomers). A many-body contribution to the interaction energy as well as electron density helps to establish the assistance of resonance in the strength of hydrogen bonds upon the formation of the present molecular chains. The direct relation between interaction energy and delocalization supports the original concept, and refutes some of the criticisms of the RAHB idea.

The synthesis and crystal structures of two μ-oxo iron(III) porphyrin complexes

Two [Formula: see text]-oxo iron(III) porphyrin complexes, [Formula: see text]-oxo-bis[meso-tetra-[Formula: see text],[Formula: see text],[Formula: see text],[Formula: see text]-([Formula: see text]-nicotina-midophenyl)porphinatoiron(III)] ([Fe(TPyPP)]2O) and its copper adduct ([Fe(TPyPP)(CuCl)]2O[CF3SO3][Formula: see text], which are derived from Gunter’s porphyrin model for cytochrome [Formula: see text]oxidase are reported. The two complexes were isolated and characterized by single crystal X-ray diffraction, UV-vis and IR spectroscopies. Crystal structural analysis including comparisons to [Formula: see text]-oxo analogues and Hirshfeld surface calculations revealed several noteworthy structural features [Formula: see text] the various picket orientations which are partially attributed to intra- and/or inter-molecular nonbonded interactions.

Bis(1-methylimidazole)[meso-α,α,α,α-tetrakis(o-nicotinamidophenyl)porphinato]iron(II)–1-methylimidazole–tetrahydrofuran (1/1/1.5)

The crystal structure of the bis­(1-methyl­imidazole)-ligated iron(II) picket-fence porphyrin derivative [Fe^II(C₆₈H₄₄N₁₂O₄)(C₄H₆N₂)₂]·C₄H₆N₂·1.5C₄H₈O is investigated.

In the title compound, [Fe^II(C₆₈H₄₄N₁₂O₄)(C₄H₆N₂)₂]·C₄H₆N₂·1.5C₄H₈O, the central Fe^II ion is coordinated by four pyrrole N atoms of the porphyrin core and two N atoms of the 1-methyl­imidazole ligands in the axial sites. One 1-methyl­imidazole and one and a half tetra­hydro­furan solvent mol­ecules are also present in the asymmetric unit. The complex exhibits a near planar porphyrin core conformation, in which the iron centre is slightly displaced towards the hindered porphyrin side (0.01 Å). The average Fe—N_p (N_p refers to the pyrrole nitro­gen atoms in the porphyrin) bond length is 1.990 (9) Å, and the axial Fe—N_Im (N_Im refers to the imidazole nitro­gen atoms) bond lengths are 1.993 (3) and 2.004 (3) Å. The dihedral angle between the two coordinated 1-methyl­imidazole planes is 56.6 (2)°. The dihedral angles between the 1-methyl­imidazole planes and the planes of the closest Fe—N_p vector are 16.8 (2) and 39.8 (2)°. N—H⋯N and N—H⋯O inter­actions are observed in the crystal structure.

Co-crystallization of a neutral mol-ecule and its zwitterionic tautomer: structure and Hirshfeld surface analysis of 5-methyl-4-(5-methyl-1H-pyrazol-3-yl)-2-phenyl-2,3-di-hydro-1H-pyrazol-3-one 5-methyl-4-(5-methyl-1H-pyrazol-2-ium-3-yl)-3-oxo-2-phenyl-2,3-di-hydro-1H-pyrazol-1-ide monohydrate

The title compound, 2C14H14N4O·H2O, comprises a neutral mol-ecule containing a central pyrazol-3-one ring flanked by an N-bound phenyl group and a C-bound 5-methyl-1H-pyrazol-3-yl group (at positions adjacent to the carbonyl substituent), its zwitterionic tautomer, whereby the N-bound proton of the central ring is now resident on the pendant ring, and a water mol-ecule of crystallization. Besides systematic variations in geometric parameters, the two independent organic mol-ecules have broadly similar conformations, as seen in the dihedral angle between the five-membered rings [9.72 (9)° for the neutral mol-ecule and 3.32 (9)° for the zwitterionic tautomer] and in the dihedral angles between the central and pendant five-membered rings [28.19 (8) and 20.96 (8)° (neutral mol-ecule); 11.33 (9) and 11.81 (9)°]. In the crystal, pyrazolyl-N-H⋯O(carbon-yl) and pyrazolium-N-H⋯N(pyrazol-yl) hydrogen bonds between the independent organic mol-ecules give rise to non-symmetric nine-membered {⋯HNNH⋯NC3O} and {⋯HNN⋯HNC3O} synthons, which differ in the positions of the N-bound H atoms. These aggregates are connected into a supra-molecular layer in the bc plane by water-O-H⋯N(pyrazolide), water-O-H⋯O(carbon-yl) and pyrazolyl-N-H⋯O(water) hydrogen bonding. The layers are linked into a three-dimensional architecture by methyl-C-H⋯π(phen-yl) inter-actions. The different inter-actions, in particular the weaker contacts, formed by the organic mol-ecules are clearly evident in the calculated Hirshfeld surfaces, and the calculated electrostatic potentials differentiate the tautomers.

Accurate prediction of bulk properties in hydrogen bonded liquids: amides as case studies

In this contribution we show that it is possible to build accurate force fields for small organic molecules allowing the reliable reproduction of a large panel of bulk properties, which are seldom addressed in the same context. Starting from the results obtained in recent studies, we developed a protocol for charge estimation and virtual site generation for the amide class of molecules. The parametrization of electrostatic properties is based on population analysis and orbital localization of quantum mechanical computations rooted in density functional theory and the polarizable continuum model, without any additional external information. The new protocol, coupled to other recent studies in our group targeted at an accurate fitting of internal degrees of freedom, makes available a method for building force fields from scratch (excluding for the moment intermolecular van der Waals interactions) with focus on reproducing the structure and dynamics of hydrogen bonded liquids, yielding results that are in line or better than those delivered by current general force fields. The approach is tested on the demanding series formed by formamide and its two N-methyl derivatives, N-methylformamide and N,N-dimethylformamide. We show that the atomistic structure of the liquids arising from classical molecular dynamics (MD) simulations employing the new force field is in full agreement with X-ray and neutron diffraction experiments and the corresponding spatial distribution functions are in remarkable agreement with the results of ab initio MD simulations. It is noteworthy that the latter result has never been obtained before without using ad hoc (and system dependent) scale factors and that, in addition, our parameter-free procedure is able to reproduce static dielectric constants over a wide range of values without sacrificing the force field accuracy with respect to other observables. Finally, we are able to explain the trend of static dielectric constants followed by the three amides in terms of properties obtained from the simulations, namely hydrogen bond patterns and reorientational lifetimes.

Crystal structure of (5-{3-[(1,4,7,10,13-penta-oxa-16-aza-cyclo-octa-decan-16-yl)carbonyl-amino]-phen-yl}-10,15,20-tri-phenyl-porphyrinato)cobalt(II)

In the title compound, [Co(C57H52N6O6)], the central CoII atom is coordinated by four pyrrole N atoms of the porphyrin core and one O atom of the crown ether. The complex has a distorted porphyrin core, with mean absolute core-atom displacements of 0.14 (10) (Ca), 0.20 (10) (Cb), 0.24 (4) (Cm) and 0.18 (10) Å (Cav), respectively. The axial Co-O bond length is 2.3380 (15) and the average Co-Np bond length is 1.968 (5) Å. Intra-molecular N-H⋯O and inter-molecular C-H⋯π inter-actions are observed.

Resonance-Assisted Hydrogen Bonding as a Driving Force in Synthesis and a Synthon in the Design of Materials

Resonance-assisted hydrogen bonding (RAHB), a concept introduced by Gilli and co-workers in 1989, concerns a kind of intramolecular H-bonding strengthened by a conjugated π-system, usually in 6-, 8-, or 10-membered rings. This Review highlights the involvement of RAHB as a driving force in the synthesis of organic, coordination, and organometallic compounds, as a handy tool in the activation of covalent bonds, and in starting moieties for synthetic transformations. The unique roles of RAHB in molecular recognition and switches, E/Z isomeric resolution, racemization and epimerization of amino acids and chiral amino alcohols, solvatochromism, liquid-crystalline compounds, and in synthons for crystal engineering and polymer materials are also discussed. The Review can provide practical guidance for synthetic chemists that are interested in exploring and further developing RAHB-assisted synthesis and design of materials.

Crystal structure of bis-(2-methyl-1H-imidazole-κN (3))(meso-tetra-p-tol-ylporphyrinato-κ(4) N)iron(III) perchlorate tetra-hydro-furan sesquisolvate

In the title compound, [Fe(C48H36N4)(C4H6N2)2]ClO4·1.5C4H8O, the iron(III) metal is coordinated in a distorted octa-hedral geometry by four pyrrole N atoms of the porphyrin ligand in the equatorial plane and two N atoms of 2-methyl-imidazole ligands in the axial sites. The complex has a highly ruffled porphyrin core with mean absolute core-atom displacements C a, C b, C m and C av of 0.25 (5), 0.17 (12), 0.432 (16) and 0.25 (13) Å, respectively. One of the four phenyl groups of the porphyrin is disordered over two sets of sites with refined occupancy ratio of 0.718 (7):0.282 (7). The mean Fe-Np (Np is a porphyrin N atom) bond length [1.975 (9) Å] indicates the low-spin state of the iron atom. The two 2-methyl-imidazole ligands are nearly perpendicular and form a dihedral angle of 86.93 (10)°. The dihedral angles between the 2-methyl-imidazole ligands and the closest Fe-Np vector are 38.04 (9) and 35.00 (7)°. In the crystal, the complex cations inter-act with the perchlorate anions through N-H⋯O hydrogen bonds, forming chains running parallel to [110].

3-Phenylpyridinium hydrogen squarate: experimental and computational study of a nonlinear optical material

The detailed investigation of an organic nonlinear optical (NLO) squarate salt of 3-phenylpyridinium hydrogen squarate (1), C11H10N+·C4HO4(-), was reported in this study. The XRD data indicates that the crystal structure of the title compound is in the triclinic P-1 space group. In the asymmetric unit, the 3-phenylpyridine molecule is protonated by one hydrogen atom donation of squaric acid molecule, forming the salt (1). The X-ray analysis shows that the crystal packing has hydrogen bonding ring pattern of D2(2)(10) (α-dimer) through NH···O interactions. The structural and vibrational properties of the compound were also studied by computational methods of ab initio at DFT/B3LYP/6-31++G(d,p) (2) and HF/6-31++G(d,p) (3) levels of theory. The calculation results on the basis of two models for both the optimized molecular structure and vibrational properties for the 1 are presented and compared with the experimental results. Non-linear optical properties (NLO) of the title compound together with the molecular electrostatic potential (MEP), electronic absorption spectrum, frontier molecular orbitals (FMOs) and conformational flexibility were also studied at the 2 level and the results were reported. In order to evaluate the suitability for NLO applications thermal analysis (TG, DTA and DTG) data of 1 were also obtained.

2-Pyridinium propanol hydrogen squarate: experimental and computational study of a nonlinear optical material

The experimental and theoretical investigation of a novel organic nonlinear optical (NLO) squarate salt of 2-pyridinium propanol hydrogen squarate (1), C8H12ON(+)·C4HO4(-), were reported in this study. The crystal structure of the title compound was found to crystallize in the triclinic P-1 space group. In the asymmetric unit each squaric acid molecules have donated one H atom to the pyridines N1 and N2 atoms of a 2-pyridine propanol molecule, forming the salt (1). The X-ray analysis clearly indicated that the crystal packing has shown the hydrogen bonding ring pattern of D2(2)(10) (α-dimer) through N-H⋯O interactions. The structural and vibrational properties of the compound were also studied by computational methods of ab initio performed on the compound at DFT/B3LYP/6-31++G(d,p) (2) and HF/6-31++G(d,p) (3) level of theory. The calculation results on the basis of two models for both the optimized molecular structure and vibrational properties for the 1 are presented and compared with the X-ray analysis result. The molecular electrostatic potential (MEP), electronic absorption spectra, frontier molecular orbitals (FMOs), conformational flexibility and non-linear optical properties (NLO) of the title compound were also studied at the 2 level and the results are reported. In order to evaluate the suitability for NLO applications thermal analysis (TG, DTA and DTG) data of 1 were also obtained.

Synthesis, an experimental and quantum chemical computational study: proton sharing in 4-Morpholinium bis(hydrogen squarate)

The experimental and theoretical investigation results of a novel organic squarate salt of 4-Morpholinium bis(hydrogen squarate) (1), C₆H₁₄ON(+)·C₈H₃O₈(-), were reported in this study. The crystal structure of the title compound was found to crystallize in the triclinic P-1 space group. In the crystals of 1 the morpholine ring adopts the chair conformation with the ethyl group in the equatorial and hydrogen atoms in axial positions. The hydrogen squarate anions are linked into a homoconjugated anion, [(HSQ)₂H], by a short symmetric, nonlinear O₈⋯H₂⋯O₂ hydrogen bond of 2.444 (2)Å. The structural and vibrational properties of the compound were also studied by computational methods of ab-initio performed on the compound at DFT/B3LYP/6-31++G(d,p) (2) and HF/6-31++G(d,p) (3) level of theory. The obtained calculation results on the basis of two models for both the optimized molecular structure and vibrational properties for the 1 obtained are presented and compared with the X-ray analysis result. On the other hand the molecular electrostatic potential (MEP), electronic absorption spectra, frontier molecular orbitals (FMOs), conformational flexibility and non-linear optical properties (NLO) of the title compound were also studied at the 2 level and the results are reported. In order to evaluate the suitability for NLO applications thermal analysis (TG, DTA and DTG) data of 1 were also obtained.

Chemical and computational methods for the characterization of covalent reactive groups for the prospective design of irreversible inhibitors

Interest in drugs that covalently modify their target is driven by the desire for enhanced efficacy that can result from the silencing of enzymatic activity until protein resynthesis can occur, along with the potential for increased selectivity by targeting uniquely positioned nucleophilic residues in the protein. However, covalent approaches carry additional risk for toxicities or hypersensitivity reactions that can result from covalent modification of unintended targets. Here we describe methods for measuring the reactivity of covalent reactive groups (CRGs) with a biologically relevant nucleophile, glutathione (GSH), along with kinetic data for a broad array of electrophiles. We also describe a computational method for predicting electrophilic reactivity, which taken together can be applied to the prospective design of thiol-reactive covalent inhibitors.

Synthesis, an experimental and quantum chemical computational study of a new nonlinear optical material: 2-picolinium hydrogensquarate

The experimental and theoretical investigation results of a novel organic non-linear optical (NLO) organic squarate salt of 2-Picolinium hydrogensquarate (1), C6H8N+·C4HO4-, were reported in this study. The space group of the title compound was found in the monoclinic C2/c space group. It was found that the asymmetric unit consists of one monohydrogen squarate anion together with mono protonated 2-Picolinium, forming the (1) salt. The X-ray analysis clearly indicated that the crystal packing has shown the hydrogen bonding ring pattern of D2(2)(10) (α-dimer) through NH⋯O interactions. The hydrogensquarate anions form α-dimer, while 2-Picolinium molecule interacts through NH⋯O and CH⋯O with the hydrogensquarate anion. The structural and vibrational properties of the compound were also studied by computational methods of ab initio performed on the compound at DFT/B3LYP/6-31++G(d,p) (2) and HF/6-31++G(d,p) (3) level of theory. The calculation results on the basis of two models for both the optimized molecular structure and vibrational properties for the 1 obtained are presented and compared with the X-ray analysis result. On the other the molecular electrostatic potential (MEP), electronic absorption spectra, frontier molecular orbitals (FMOs), conformational flexibility and non-linear optical properties (NLO) of the title compound were also studied at the 2 level and the results are reported. In order to evaluate the suitability for NLO applications thermal analysis (TG, DTA and DTG) data of 1 were also obtained.

Structure and vibrational analysis of methyl 3-amino-2-butenoate

The molecular structure and vibrational spectra of methyl 3-(amino)-2-butenoate (MAB) and its deuterated analogous, D(3)MAB, were investigated using density functional theory (DFT) calculations. The geometrical parameters and harmonic vibrational wavenumbers of MAB and D(3)MAB were obtained at the B3LYP/6-311++G(d,p) level. The calculated vibrational wavenumbers were compared with the corresponding experimental results. The assignment of the IR and Raman spectra of MAB and D(3)MAB was facilitated by calculating the anharmonic wavenumbers at the B3LYP/6-311G(d,p) level as well as recording and calculating the MAB spectra in CCl(4) solution. The assigned normal modes were compared with a similar molecule, 4-amino-3-penten-2-one (APO). The theoretical results were in good agreement with the experimental data. All theoretical and experimental results indicate that substitution of a methyl group with a methoxy group considerably weakens the intramolecular hydrogen bond and reduces the π-electron delocalization in the chelated ring system. The IR spectra also indicate that in the solid state, MAB is not only engaged in an intramolecular hydrogen bond, but also forms an intermolecular hydrogen bond. However, the intermolecular hydrogen bond will be removed in dilute CCl(4) solution.

Directionality of inter- and intramolecular OHO hydrogen bonds: DFT study followed by AIM and NBO analysis

The directionality of inter- and intramolecular OHO hydrogen bonds has been compared. For intramolecular bridges it is determined by an orbital formed in the proton transfer process. For intermolecular bonds, the hydrogen-bonded proton is attached to two lone pairs of the acceptor and the OHO angle is not fixed but can change in a broad range. Depending on the OHO angle, the interaction changes continuously from electrostatic interaction to strong OHO hydrogen bond.

2-(4-Chloro-phen-yl)-4-[1-(4-chloro-phen-yl)-3-methyl-1H-pyrazol-5-yl]-5-methyl-1H-pyrazol-3(2H)-one

The title compound, C₂₀H₁₆Cl₂N₄O, has two mol­ecules in the asymmetric unit. The two five-membered rings form a dihedral angle of 54.2 (3)° in one mol­ecule and 56.8 (3)° in the other independent mol­ecule. The amino group of the dihydro­pyrazolone unit of one mol­ecule acts as a hydrogen-bond donor to the carbonyl group of the dihydro­pyrazolone system of the other mol­ecule. The resulting N—H⋯O hydrogen bonds generate a chain running along the c axis. The crystal selected was a pseudo-merohedral twin with a 44.9 (3)% twin component.

Interplay between intramolecular resonance-assisted hydrogen bonding and aromaticity in o-hydroxyaryl aldehydes

In this work, we analyze a series of o-hydroxyaryl aldehydes to discuss the interrelation between the resonance-assisted hydrogen bond (RAHB) formation and the aromaticity of the adjacent aromatic rings. As compared to the nonaromatic reference species (malonaldehyde), the studied compounds can be separated into two groups: first, the set of systems that have a stronger RAHB than that of the reference species, for which there is a Kekulé structure with a localized double CC bond linking substituted carbon atoms; and second, the systems having a weaker RAHB than that of the reference species, for which only pi-electrons coming from a localized Clar pi-sextet can be involved in the RAHB. As to aromaticity, there is a clear reduction of aromaticity in the substituted ipso ring for the former group of systems due to the formation of the RAHB, while for the latter group of species only a slight change of local aromaticity is observed in the substituted ipso ring.

Cocrystal Design Gone Awry? A New Dimorphic Hydrate of Oxalic Acid

The crystal chemistry of oxalic acid has been studied since 1880, including 37 published structure determinations of the two anhydrous forms (alpha, beta) and the dihydrate, the latest in 2000. In attempts to cocrystallize asparagine or glutamine with oxalic acid, utilizing the particular hydrogen bond synthon R(4)(2)(8), we unexpectedly obtained two previously unreported sesquihydrates of oxalic acid. Form 1 is orthorhombic, Pnma, and the unit cell is a = 11.231(2) A, b = 12.330(2) A, c = 6.908(1) A. Form 2 crystallizes in the triclinic crystal system in space group P, and the unit cell is a = 6.337(2) A; b = 7.247(3) A, c = 10.571(4)A, alpha = 94.34(1) degrees, beta = 100.244(9) degrees, gamma = 97.67(1) degrees. Both of the new hydrate forms of oxalic acid utilized the R(4)(2)(8) hydrogen bonded synthon.

Prediction of aqueous solubility based on large datasets using several QSPR models utilizing topological structure representation

Several QSPR models were developed for predicting intrinsic aqueous solubility, S(o). A data set of 5,964 neutral compounds was sub-divided into two classes, aromatic and non-aromatic compounds. Three models were created with different methods on both data sets: two regression models (multiple linear regression and partial least squares) and an artificial neural network model. These models were based on 3343 aromatic and 1674 non-aromatic compounds for training sets; 938 compounds were used in external validation testing. The range in -log S(o) is -1.6 to 10. Topological structure descriptors were used with all models. A genetic algorithm was used for descriptor selection for regression models. For the artificial neural network (ANN) model, descriptor selection was done with a backward elimination process. All models performed well with r2 values ranging 0.72 to 0.84 in external validation testing. The mean absolute errors in validation ranged from 0.44 to 0.80 for the classes of compounds for all the models. These statistical results indicate a sound ANN model. Furthermore, in a comparison with eight other available models, based on predictions using a validation test set (442 compounds), the artificial neural network model presented in this work (CSLogWS) was clearly superior based on both the mean absolute error and the percentage of residuals less than one log unit. In the ANN model both E-State and hydrogen E-State descriptors were found to be important.

Photoinduced Intramolecular Charge Transfer in 9-Aminoacridinium Derivatives Assisted by Intramolecular H-Bond

Fluorochromic dyes derived from 9-aminoacridinium containing a vinylene function with electron withdrawing groups such as diethyl [(acridinium-9-ylamino)methylene]malonate (I), ethyl [(acridinium-9-ylamino)methylene]cyanoacetate (II), [(acridinium-9-ylamino)methylene]malononitrile (III), are prepared and studied in their monoprotonated form. Absorption spectra of the new dyes are red shifted compared to that of the precursor dye. The observed dual fluorescence and multiexponential decay are ascribed to normal emission from the acridinium chromophore in addition to excited-state intramolecular charge transfer (ESICT) process. However, biexponential decay character is observed only for the dicyano derivative (compound III), whereas for the two other systems, more complex kinetics and a three-component decay is recovered. The analysis of the fluorescence decays in different solvents for the first two compounds reveals two short-lived components in the range of 160-350 ps and 1.1-3.0 ns, related to formation and decay of the ESICT state, plus a third one with decay time of about 9 ns, which is ascribed to the normal emission from the acridinium chromophore as an enol tautomer or as an intramolecular H-bond conformer (closed form tautomer). For the dicyano derivative, in which the absence of carbonyl group precludes the H-bond interaction, the biexponential fitting reveals a slightly fast formation rate of the ESICT state with values on the order of 10(10) s(-1), whereas its decay time is between 0.6 and 3.2 ns, depending on the solvent used.