Density functional study of indole–pyrrole heterodimer potential energy hypersurface

A density‐functional study of indole–pyrrole heterodimer potential energy hypersurface (PES) was performed. Eight stationary points were located on the B3LYP/6‐31++G(d,p) PES, three of which correspond to real minima, all of them being characterized with an N? H … π type hydrogen bonding. In two of these minima (the local ones), pyrrole subunit acts as a hydrogen bond proton donor, while the global minimum corresponds to indole–H … π(‐pyrrole) arrangement. Besides the interaction and dissociation energies corrected for BSSE and the monomer relaxation energies and the relevant structural parameters, anharmonic N? H and N? H … π vibrational frequencies were calculated for various N? H oscillators involved in this interaction from the 1‐D DFT vibrational potentials. On the basis of anharmonic vibrational frequency analysis, it was concluded that the two types of N? H … π hydrogen bonded dimers (indole vs. pyrrole being a proton donor) should be distinguishable with spectroscopic methods. Various contributions to the overall anharmonic frequency shifts upon hydrogen bonding were calculated and discussed as well. The charge field perturbation (CFP) technique was employed to study the electrostatic + polarization influence of the proton accepting unit on the N? H(… π) vibrational potential. The second‐order perturbation theory analysis (SOPT) of the Fock matrix (i.e., its Kohn–Sham analog) within the natural bond orbital (NBO) basis, as well as various NBO deletion analyses revealed an essentially one‐directional charge transfer (CT) of a π(C? C) → σ*(N? H) type in the case of all three minima. © 2003 Wiley Periodicals, Inc. Int J Quantum Chem, 2003     

A Combined Experimental and Theoretical Electron Density Study of Intra‐ and Intermolecular Interactions in Thiourea S,S‐Dioxide

The thiourea S,S‐dioxide molecule is recognized as a zwitterion with a high dipole moment and an unusually long C? S bond. The molecule has a most interesting set of intermolecular interactions in the crystalline state—a relatively strong O???H? N hydrogen bond and very weak intermolecular C???S and N???O interactions. The molecule has C_s symmetry, and each oxygen atom is hydrogen‐bonded to two hydrogen atoms with O???H? N distances of 2.837 and 2.826 Å and angles of 176.61 and 158.38°. The electron density distribution is obtained both from Xray diffraction data at 110 K and from a periodic density functional theory (DFT) calculation. Bond characterization is made in terms of the analysis of topological properties. The covalent characters of the C? N, N? H, C? S, and S? O bonds are apparent, and the agreement on the topological properties between experiment and theory is adequate. The features of the Laplacian distributions, bond paths, and atomic domains are comparable. In a systematic approach, DFT calculations are performed based on a monomer, a dimer, a heptamer, and a crystal to see the effect on the electron density distribution due to the intermolecular interactions. The dipole moment of the molecule is enhanced in the solid state. The typical values of ρ_b and H_b of the hydrogen bonds and weak intermolecular C???S and N???O interactions are given. All the interactions are verified by the location of the bond critical point and its associated topological properties. The isovalue surface of Laplacian charge density and the detailed atomic graph around each atomic site reveal the shape of the valence‐shell charge concentration and provide a reasonable interpretation of the bonding of each atom.     

Hydrogen‐bonded bilayers in 7‐benzyl‐3‐tert‐butyl‐1‐phenyl‐4,5,6,7‐tetrahydro‐1H‐spiro[pyrazolo[3,4‐b]pyridine‐5,2′‐indan]‐1′,3′‐dione

In the title compound, C₃₁H₂₉N₃O₂, the reduced pyridine ring adopts a conformation intermediate between the envelope and half‐chair forms. The aryl rings of the benzyl and phenyl substituents are nearly parallel and overlap, indicative of an intramolecular π–π stacking interaction. A combination of two C—H...O hydrogen bonds and one C—H...N hydrogen bond links the molecules into a bilayer having tert‐butyl groups on both faces.<!?tpb=19.5pt>     

Comparative analysis of blue‐shifted hydrogen bond versus conventional hydrogen bond in methyl radical complexes

Methyl radical complexes H₃C…HCN and H₃C…HNC have been investigated at the UMP2(full)/aug‐cc‐pVTZ level to elucidate the nature of hydrogen bonds. To better understand the intermolecular H‐bond interactions, topological analysis of electron density at bond critical points (BCP) is executed using Bader's atoms‐in‐molecules (AIM) theory. Natural bond orbital (NBO) analysis has also been performed to study the orbital interactions and change of hybridization. Theoretical calculations show that there is no essential difference between the blue‐shift H‐bond and the conventional one. In H₃C…HNC complex, rehybridization is responsible for shortening of the N? H bond. The hyperconjugative interaction between the single electron of the methyl radical and N? H antibonding orbital is up to 7.0 kcal/mol, exceeding 3.0 kcal/mol, the upper limit of hyperconjugative n(Y)→σ*(X–H) interaction to form the blue‐shifted H‐bond according to Alabugin's theory. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007     

Exo conformers of N‐(pyridin‐2‐yl)‐ and N‐(pyridin‐3‐yl)norbornene‐5,6‐dicarboximide crystals

Two isomeric pyridine‐substituted norbornenedicarboximide derivatives, namely N‐(pyridin‐2‐yl)‐exo‐norbornene‐5,6‐dicarboximide, (I), and N‐(pyridin‐3‐yl)‐exo‐norbornene‐5,6‐dicarboximide, (II), both C₁₄H₁₂N₂O₄, have been crystallized and their structures unequivocally determined by single‐crystal X‐ray diffraction. The molecules consist of norbornene moieties fused to a dicarboximide ring substituted at the N atom by either pyridin‐2‐yl or pyridin‐3‐yl in an anti configuration with respect to the double bond, thus affording exo isomers. In both compounds, the asymmetric unit consists of two independent molecules (Z′ = 2). In compound (I), the pyridine rings of the two independent molecules adopt different conformations, i.e. syn and anti, with respect to the methylene bridge. The intermolecular contacts of (I) are dominated by C—H...O interactions. In contrast, in compound (II), the pyridine rings of both molecules have an anti conformation and the two independent molecules are linked by carbonyl–carbonyl interactions, as well as by C—H...O and C—H...N contacts.     

Modulation of Stacking Interactions by Transition‐Metal Coordination: Ab Initio Benchmark Studies

A series of ab initio calculations are used to determine the C? H???π and π???π‐stacking interactions of aromatic rings coordinated to transition‐metal centres. Two model complexes have been employed, namely, ferrocene and chromium benzene tricarbonyl. Benchmark data obtained from extrapolation of MP2 energies to the basis set limit, coupled with CCSD(T) correction, indicate that coordinated aromatic rings are slightly weaker hydrogen‐bond acceptors but are significantly stronger hydrogen‐bond donors than uncomplexed rings. It is found that π???π stacking to a second benzene is stronger than in the free benzene dimer, especially in the chromium case. This is assigned, by use of energy partitioning in the local correlation method, to dispersion interactions between metal d and benzene π orbitals. The benchmark data is also used to test the performance of more efficient theoretical methods, indicating that spin‐component scaling of MP2 energies performs well in all cases, whereas various density functionals describe some complexes well, but others with errors of more than 1 kcal mol^?1.     

Theoretical Studies on the Hydrogen‐bonding and π‐Stacking Interactions in the m‐Nisoldipine Polymorphism Dimers

The intermolecular interactions in the dimers of m‐nisoldipine polymorphism were studied by B3LYP calculations and quantum theory of "atoms in molecules" (QTAIM) studies. Four geometries of dimers were obtained: dimer I (a‐dimer, O···H? N), dimer II (b‐dimer, O···H? N), dimer III (b‐dimer, π‐stacking‐c), and dimer IV (b‐dimer, π‐stacking‐p). The interaction energies of the four dimers are along the sequence of II>I>III>IV. The intermolecular distance of the interactions follows the order: I (O···H? N)II>III>IV, and the electrostatic character decreases along the sequence: I>II>III>IV.     

Self‐assembly of 2‐pivaloyl‐6‐chloro­pterin

In the title compound, N‐(6‐chloro‐4‐oxo‐3,4‐di­hydro­pteridin‐2‐yl)­‐2,2‐di­methyl­propan­amide, C₁₁H₁₂ClN₅O₂, the rings in the pterin moiety are planar. The amide carbonyl O atom is in syn‐periplanar conformation while the C—N—C—C propanamide linkage is antiperiplanar. The N—H?N and N—H?O intermolecular hydrogen bonds transform the mol­ecules into infinite chains.     

The Conformational Landscape of Nicotinoids: Solving the Conformational Disparity of Anabasine

The conformational landscape of the alkaloid anabasine (neonicotine) has been investigated by using rotational spectroscopy and ab initio calculations. The results allow a detailed comparison of the structural properties of the prototype piperidinic and pyrrolidinic nicotinoids (anabasine vs. nicotine). Anabasine adopts two most stable conformations in isolation conditions, for which we determined accurate rotational and nuclear quadrupole coupling parameters. The preferred conformations are characterized by an equatorial pyridine moiety and additional N–H equatorial stereochemistry at the piperidine ring (eq‐eq; eq=equatorial). The two rings of anabasine are close to a bisecting arrangement, with the observed conformations differing by an approximately 180° rotation of the pyridine subunit, denoted either syn or anti. The preference of anabasine for the eq‐eq‐syn conformation has been established by relative intensity measurements (syn/anti～5(2)). The conformational preferences of free anabasine are directed by a weak N???H? C hydrogen bond interaction between the nitrogen lone pair at piperidine and the closest C? H bond in pyridine, with N???H distances ranging from 2.686 (syn) to 2.667 Å (anti). Supporting ab initio calculations by using MP2 and the recent M05‐2X density functional are provided, evaluating the predictive performance of both methods.     

Study of conformations and hydrogen bonds in the configurational isomers of pyrrole‐2‐carbaldehyde oxime by 1H, 13C and 15N NMR spectroscopy combined with MP2 and DFT calculations and NBO analysis

The ¹H, ¹³C and ¹⁵N NMR studies have shown that the E and Z isomers of pyrrole‐2‐carbaldehyde oxime adopt preferable conformation with the syn orientation of the oxime group with respect to the pyrrole ring. The syn conformation of E and Z isomers of pyrrole‐2‐carbaldehyde oxime is stabilized by the N? H···N and N? H···O intramolecular hydrogen bonds, respectively. The N? H···N hydrogen bond in the E isomer causes the high‐frequency shift of the bridge proton signal by about 1 ppm and increase the ¹J(N, H) coupling by ～3 Hz. The bridge proton shows further deshielding and higher increase of the ¹J(N, H) coupling constant due to the strengthening of the N? H···O hydrogen bond in the Z isomer. The MP2 calculations indicate that the syn conformation of E and Z isomers is by ～3.5 kcal/mol energetically less favorable than the anti conformation. The calculations of ¹H shielding and ¹J(N, H) coupling in the syn and anti conformations allow the contribution to these constants from the N? H···N and N? H···O hydrogen bondings to be estimated. The NBO analysis suggests that the N? H···N hydrogen bond in the E isomer is a pure electrostatic interaction while the charge transfer from the oxygen lone pair to the antibonding orbital of the N? H bond through the N? H···O hydrogen bond occurs in the Z isomer. Copyright © 2010 John Wiley & Sons, Ltd.     

Crystallographic study of self‐organization in the solid state including quasi‐aromatic pseudo‐ring stacking interactions in 1‐benzoyl‐3‐(3,4‐dimethoxyphenyl)thiourea and 1‐benzoyl‐3‐(2‐hydroxypropyl)thiourea

1‐Benzoylthioureas contain both carbonyl and thiocarbonyl functional groups and are of interest for their biological activity, metal coordination ability and involvement in hydrogen‐bond formation. Two novel 1‐benzoylthiourea derivatives, namely 1‐benzoyl‐3‐(3,4‐dimethoxyphenyl)thiourea, C₁₆H₁₆N₂O₃S, (I), and 1‐benzoyl‐3‐(2‐hydroxypropyl)thiourea, C₁₁H₁₄N₂O₂S, (II), have been synthesized and characterized. Compound (I) crystallizes in the space group P , while (II) crystallizes in the space group P 2₁/c . In both structures, intramolecular N—H…O hydrogen bonding is present. The resulting six‐membered pseudo‐rings are quasi‐aromatic and, in each case, interact with phenyl rings via stacking‐type interactions. C—H…O, C—H…S and C—H…π interactions are also present. In (I), there is one molecule in the asymmetric unit. Pairs of molecules are connected via two intermolecular N—H…S hydrogen bonds, forming centrosymmetric dimers. In (II), there are two symmetry‐independent molecules that differ mainly in the relative orientations of the phenyl rings with respect to the thiourea cores. Additional strong hydrogen‐bond donor and acceptor –OH groups participate in the formation of intermolecular N—H…O and O—H…S hydrogen bonds that join molecules into chains extending in the [001] direction.     

Ab initio and AIM studies on typical π‐type and pseudo‐π‐type halogen bonds: Comparison with hydrogen bonds

Series of typical π‐type and pseudo‐π‐type halogen‐bonded complexes B ··· ClY and B ··· BrY and hydrogen‐bonded complex B ··· HY (B = C₂H₄, C₂H₂, and C₃H₆; Y = F, Cl, and Br) have been investigated using the MP2/aug‐cc‐pVDZ method. A striking parallelism was found in the geometries, vibrational frequencies, binding energies, and topological properties between B ··· XY and B ··· HY (X = Cl and Br). It has been found that the lengths of the weak bond d(X ··· π)/d(H ··· π), the frequencies of the weak bond ν(X ··· π)/ν(H ··· π), the frequency shifts Δν(X? Y)/Δν(H? Y), the electron densities at the bond critical point of the weak bonds ρ_c(X ··· π)/ρ_c(H ··· π), and the electron density changes Δρ_c(X? Y)/Δρ_c(H? Y) could be used as measures of the strengths of typical π‐type and pseudo‐π‐type halogen/hydrogen bonds. The typical π‐type and pseudo‐π‐type halogen bond and hydrogen bond are noncovalent interactions. For the same Y, the halogen bond strengths are in the order B ··· ClY < B ··· BrY. For the same X, the halogen bond strength decreases according to the sequence F > Cl > Br that is in agreement with the hydrogen bond strengths B ··· HF > B ··· HCl > B ··· HBr. All of these typical π‐type and pseudo‐π‐type hydrogen‐bonded and halogen‐bonded complexes have the “conflict‐type” structure. Contour maps of the Laplacian of π electron density indicate that the formation of B ··· XY halogen‐bonded complex and B ··· HY hydrogen‐bonded complex is very similar. Charge transfer is observed from B to XY/HY and both the dipolar polarization and the volume of the halogen atom or hydrogen atom decrease on B ··· XY/B ··· HY complex formation. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

N‐(4‐Bi­phenyl­yl)­urea

In the crystal structure of the title compound, C₁₃H₁₂N₂O, N—H(anti)?O hydrogen bonds produce the so‐called urea α‐network and the N—H(syn) donor forms an unconventional N—H?π hydrogen bond.     

Theoretical study of the red‐ and blue‐shifted hydrogen bonds of nitroxyl and acetylene dimers

Ab initio molecular orbital and density functional theory (DFT) in conjunction with different basis sets calculations were performed to study the C? H…O red‐shifted and N? H…π blue‐shifted hydrogen bonds in HNO? C₂H₂ dimers. The geometric structures, vibrational frequencies and interaction energies were calculated by both standard and counterpoise (CP)‐corrected methods. In addition, the G3B3 method was employed to calculate the interaction energies. The topological and natural bond orbital (NBO) analysis were investigated the origin of N? H…π blue‐shifted hydrogen bond. From the NBO analysis, the electron density decrease in the σ* (N? H) is due to the significant electron density redistribution effect. The blue shifts of the N? H stretching frequency are attributed to a cooperative effect between the rehybridization and electron density redistribution. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2006     

Three sterically hindered 6‐amino‐5‐cyano‐2‐methyl‐4‐(1‐naphthyl)‐4H‐pyran‐3‐carboxylate derivatives

In the title compounds, 2‐methoxyethyl 6‐amino‐5‐cyano‐2‐methyl‐4‐(1‐naphthyl)‐4H‐pyran‐3‐carboxylate, C₂₁H₂₀N₂O₄, (II), isopropyl 6‐amino‐5‐cyano‐2‐methyl‐4‐(1‐naphthyl)‐4H‐pyran‐3‐carboxylate, C₂₁H₂₀N₂O₃, (III), and ethyl 6‐amino‐5‐cyano‐2‐methyl‐4‐(1‐naphthyl)‐4H‐pyran‐3‐carboxylate, C₂₀H₁₈N₂O₃, (IV), the heterocyclic pyran ring adopts a flattened boat conformation. In (II) and (III), the carbonyl group and a double bond of the heterocyclic ring are mutually anti, but in (IV) they are mutually syn. The ester O atoms in (II) and (III) and the carbonyl O atom in (IV) participate in intramolecular C—H...O contacts to form six‐membered rings. The dihedral angles between the naphthalene substituent and the closest four atoms of the heterocyclic ring are 73.3 (1), 71.0 (1) and 74.3 (1)° for (II)–(IV), respectively. In all three structures, only one H atom of the NH₂ group takes part in N—H...O [in (II) and (III)] or N—H...N [in (IV)] intermolecular hydrogen bonds, and chains [in (II) and (III)] or dimers [in (IV)] are formed. In (II), weak intermolecular C—H...O and C—H...N hydrogen bonds, and in (III) intermolecular C—H...O hydrogen bonds link the chains into ladders along the a axis.     

How the oxazole fragment influences the conformation of the tetraoxazocane ring in a cyclohexanespiro‐3′‐(1,2,4,5,7‐tetraoxazocane): single‐crystal X‐ray and theoretical study

Single crystals of (2S,5R)‐2‐isopropyl‐5‐methyl‐7‐(5‐methylisoxazol‐3‐yl)cyclohexanespiro‐3′‐(1,2,4,5,7‐tetraoxazocane), C₁₆H₂₆N₂O₅, have been studied via X‐ray diffraction. The tetraoxazocane ring adopts a boat–chair conformation in the crystalline state, which is due to intramolecular interactions. Conformational analysis of the tetraoxazocane fragment performed at the B3LYP/6‐31G(d,2p) level of theory showed that there are three minima on the potential energy surface, one of which corresponds to the conformation realized in the solid state, but not to a global minimum. Analysis of the geometry and the topological parameters of the electron density at the (3,?1) bond critical points (BCPs), and the charge transfer in the tetraoxazocane ring indicated that there are stereoelectronic effects in the O—C—O and N—C—O fragments. There is a two‐cross hyperconjugation in the N—C—O fragment between the lone electron pair of the N atom (lpN) and the antibonding orbital of a C—O bond (σ*_C—O) and vice versa between lpO and σ*_C—N. The oxazole substituent has a considerable effect on the geometry and the topological parameters of the electron density at the (3,?1) BCPs of the tetraoxazocane ring. The crystal structure is stabilized via intermolecular C—H…N and C—H…O hydrogen bonds, which is unambiguously confirmed with PIXEL calculations, a quantum theory of atoms in molecules (QTAIM) topological analysis of the electron density at the (3,?1) BCPs and a Hirshfeld analysis of the electrostatic potential. The molecules form zigzag chains in the crystal due to intermolecular C—H…N interactions being electrostatic in origin. The molecules are further stacked due to C—H…O hydrogen bonds. The dispersion component in the total stabilization energy of the crystal lattice is 68.09%.     

1,4,4‐Tri­methyl‐9‐phenyl‐8‐oxa‐9‐aza­bi­cyclo­[3.2.2]­non‐6‐en‐2‐one

The structure of the adduct of eucarvone with nitro­so­benzene, C₁₆H₁₉NO₂, is reported. The [3.2.2] bicyclic system corresponds to two seven‐membered rings in boat and distorted chair conformations and a six‐membered ring that adopts a distorted boat conformation. No conjugation is observed between the phenyl group and the N—O system. The packing is directed mainly by a C?O hydrogen bond, C—H?O‐(1 ? x, ?y, z) and by intermolecular C—H?π interactions.     

A comparative study of some lithium and hydrogen‐bonded complexes: Ab initio and QTAIM studies

The nature of the interactions of cyanide with lithium and hydrogen halides was investigated using ab initio calculations and topological analysis of electron density. The computed properties of the lithium‐bonded complexes RCN···LiX (R = H, F, Cl, Br, C?CH, CH?CH₂, CH₃, C₂H₅; X = Cl, Br) were compared with those of corresponding hydrogen‐bonded complexes RCN···HX. The results show that both types of intermolecular interactions are “closed‐shell” noncovalent interactions. The effect of substitution on the interaction energy and electron density at the bond critical points of the lithium and hydrogen bonding interactions is similar. In comparison, the interaction energies of lithium‐bonded complexes are more negative than those of hydrogen‐bonded counterparts. The electrostatic interaction plays a more important role in the lithium bond than in the hydrogen bond. On complex formation, the net charge and energy of the Li atom decrease and the atomic volume increases, while the net charge and energy of the H atom increase and the atomic volume decreases. © 2013 Wiley Periodicals, Inc.     

Van Der Waals heterogeneous layer‐layer carbon nanostructures involving π···H‐C‐C‐H···π···H‐C‐C‐H stacking based on graphene and graphane sheets

Noncovalent interactions involving aromatic rings, such as π···π stacking, CH···π are very essential for supramolecular carbon nanostructures. Graphite is a typical homogenous carbon matter based on π···π stacking of graphene sheets. Even in systems not involving aromatic groups, the stability of diamondoid dimer and layer‐layer graphane dimer originates from C − H···H − C noncovalent interaction. In this article, the structures and properties of novel heterogeneous layer‐layer carbon‐nanostructures involving π···H‐C‐C‐H···π···H‐C‐C‐H stacking based on [n ]‐graphane and [n ]‐graphene and their derivatives are theoretically investigated for n = 16–54 using dispersion corrected density functional theory B3LYP‐D3 method. Energy decomposition analysis shows that dispersion interaction is the most important for the stabilization of both double‐ and multi‐layer‐layer [n ]‐graphane@graphene. Binding energy between graphane and graphene sheets shows that there is a distinct additive nature of CH···π interaction. For comparison and simplicity, the concept of H‐H bond energy equivalent number of carbon atoms (noted as NHEQ), is used to describe the strength of these noncovalent interactions. The NHEQ of the graphene dimers, graphane dimers, and double‐layered graphane@graphene are 103, 143, and 110, indicating that the strength of C‐H···π interaction is close to that of π···π and much stronger than that of C‐H···H‐C in large size systems. Additionally, frontier molecular orbital, electron density difference and visualized noncovalent interaction regions are discussed for deeply understanding the nature of the C‐H···π stacking interaction in construction of heterogeneous layer‐layer graphane@graphene structures. We hope that the present study would be helpful for creations of new functional supramolecular materials based on graphane and graphene carbon nano‐structures. © 2017 Wiley Periodicals, Inc.     

C?H···N and C?H···O intramolecular hydrogen bonding effects in the 1H, 13C and 15 N NMR spectra of the configurational isomers of 1‐vinylpyrrole‐2‐carbaldehyde oxime substantiated by DFT calculations

According to the ¹H, ¹³C and ¹⁵N NMR spectroscopic data and DFT calculations, the E‐isomer of 1‐vinylpyrrole‐2‐carbaldehyde adopts preferable conformation with the anti‐orientation of the vinyl group relative to the carbaldehyde oxime group and with the syn‐arrangement of the carbaldehyde oxime group with reference to the pyrrole ring. This conformation is stabilized by the C? H···N intramolecular hydrogen bond between the α‐hydrogen of the vinyl group and the oxime group nitrogen, which causes a pronounced high‐frequency shift of the α‐hydrogen signal in ¹H NMR (～0.5 ppm) and an increase in the corresponding one‐bond ¹³C–¹H coupling constant (ca 4 Hz). In the Z‐isomer, the carbaldehyde oxime group turns to the anti‐position with respect to the pyrrole ring. The C? H···O intramolecular hydrogen bond between the H‐3 hydrogen of the pyrrole ring and the oxime group oxygen is realized in this case. Due to such hydrogen bonding, the H‐3 hydrogen resonance is shifted to a higher frequency by about 1 ppm and the one‐bond ¹³C–¹H coupling constant for this proton increases by ～5 Hz. Copyright © 2008 John Wiley & Sons, Ltd.