A polarizable dipole–dipole interaction model for evaluation of the interaction energies for NH···OC and CH···OC hydrogen‐bonded complexes

In this article, a polarizable dipole–dipole interaction model is established to estimate the equilibrium hydrogen bond distances and the interaction energies for hydrogen‐bonded complexes containing peptide amides and nucleic acid bases. We regard the chemical bonds N? H, C?O, and C? H as bond dipoles. The magnitude of the bond dipole moment varies according to its environment. We apply this polarizable dipole–dipole interaction model to a series of hydrogen‐bonded complexes containing the N? H···O?C and C? H···O?C hydrogen bonds, such as simple amide‐amide dimers, base‐base dimers, peptide‐base dimers, and β‐sheet models. We find that a simple two‐term function, only containing the permanent dipole–dipole interactions and the van der Waals interactions, can produce the equilibrium hydrogen bond distances compared favorably with those produced by the MP2/6‐31G(d) method, whereas the high‐quality counterpoise‐corrected (CP‐corrected) MP2/aug‐cc‐pVTZ interaction energies for the hydrogen‐bonded complexes can be well‐reproduced by a four‐term function which involves the permanent dipole–dipole interactions, the van der Waals interactions, the polarization contributions, and a corrected term. Based on the calculation results obtained from this polarizable dipole–dipole interaction model, the natures of the hydrogen bonding interactions in these hydrogen‐bonded complexes are further discussed. © 2013 Wiley Periodicals, Inc.     

Two‐component molecular crystals composed of chloronitrobenzoic acids and 4‐aminopyridine

The crystal structures of the four isomeric organic salts 4‐amino­pyridinium 2‐chloro‐4‐nitro­benzoate, (I), 4‐amino­pyridinium 2‐chloro‐5‐nitro­benzoate, (II), 4‐amino­pyridinium 5‐chloro‐2‐nitro­benzoate, (III), and 4‐amino­pyridinium 4‐chloro‐2‐nitro­benzoate, (IV), all C₅H₇N₂⁺·C₇H₃ClNO₄^?, are presented. Compound (I) has one intramolecular hydrogen bond, one intermolecular C—H?O hydrogen bond and π–π‐stacking interactions. Compound (II) has N—H?O, C—H?O and C—H?Cl hydrogen bonds, and Cl?O—C electrostatic interactions. Compound (III) has N—H?O and C—H?O hydrogen bonds. Compound (IV) has a π–π‐stacking interaction, but no C—H?O hydrogen bonds.     

2‐Iodo‐N‐(3‐nitrobenzyl)aniline and 3‐iodo‐N‐(3‐nitrobenzyl)aniline exhibit entirely different patterns of supramolecular aggregation

In 2‐iodo‐N‐(3‐nitro­benzyl)­aniline, C₁₃H₁₁IN₂O₂, the mol­ecules are linked into a three‐dimensional structure by a combination of C—H?O hydrogen bonds, iodo–nitro interactions and aromatic π–π‐stacking interactions, but N—H?O and C—H?π(arene) hydrogen bonds are absent. In the isomeric 3‐iodo‐N‐(3‐nitro­benzyl)­aniline, a two‐dimensional array is generated by a combination of N—H?O, C—H?O and C—H?π(arene) hydrogen bonds, but iodo–nitro interactions and aromatic π–π‐stacking interactions are both absent.     

Atomistic understanding of the C·T mismatched DNA base pair tautomerization via the DPT: QM and QTAIM computational approaches

It was established that the cytosine·thymine (C·T) mismatched DNA base pair with cis‐oriented N1H glycosidic bonds has propeller‐like structure (|N3C4C4N3| = 38.4°), which is stabilized by three specific intermolecular interactions–two antiparallel N4H…O4 (5.19 kcal mol^?1) and N3H…N3 (6.33 kcal mol^?1) H‐bonds and a van der Waals (vdW) contact O2…O2 (0.32 kcal mol^?1). The C·T base mispair is thermodynamically stable structure (ΔG_int = ?1.54 kcal mol^?1) and even slightly more stable than the A·T Watson–Crick DNA base pair (ΔG_int = ?1.43 kcal mol^?1) at the room temperature. It was shown that the C·T ? C*·T* tautomerization via the double proton transfer (DPT) is assisted by the O2…O2 vdW contact along the entire range of the intrinsic reaction coordinate (IRC). The positive value of the Grunenberg's compliance constants (31.186, 30.265, and 22.166 Å/mdyn for the C·T, C*·T*, and TS_{C·T ? C*·T*}, respectively) proves that the O2…O2 vdW contact is a stabilizing interaction. Based on the sweeps of the H‐bond energies, it was found that the N4H…O4/O4H…N4, and N3H…N3 H‐bonds in the C·T and C*·T* base pairs are anticooperative and weaken each other, whereas the middle N3H…N3 H‐bond and the O2…O2 vdW contact are cooperative and mutually reinforce each other. It was found that the tautomerization of the C·T base mispair through the DPT is concerted and asynchronous reaction that proceeds via the TS_{C·T ? C*·T*} stabilized by the loosened N4? H? O4 covalent bridge, N3H…N3 H‐bond (9.67 kcal mol^?1) and O2…O2 vdW contact (0.41 kcal mol^?1). The nine key points, describing the evolution of the C·T ? C*·T* tautomerization via the DPT, were detected and completely investigated along the IRC. The C*·T* mispair was revealed to be the dynamically unstable structure with a lifetime 2.13·× 10^?13 s. In this case, as for the A·T Watson–Crick DNA base pair, activates the mechanism of the quantum protection of the C·T DNA base mispair from its spontaneous mutagenic tautomerization through the DPT. © 2013 Wiley Periodicals, Inc.     

Experimental and Theoretical Charge Density Study on Di‐2‐pyrazylamine (Hdpza) Molecule in Crystal

Electron density distribution of Di‐2‐pyrazylamine ( Hdpza ) is studied both by single‐crystal X‐ray diffraction method at 100K and theoretical calculation. Structural determination reveals that Hdpza molecules crystalize in a syn‐anti conformation with an intramolecular C? H?N hydrogen bond between two pyrazine rings and then gather together via two intermolecular N? H?N and C? H?N hydrogen interaction and π? π stacking interaction between pyrazine rings. Charge density analysis is made in terms of deformation density (Δπ), Laplacian distribution and topological analysis of total electron density based on multipole model and theoretical calculation. The agreement between experiment and theory is good. The topological properties at bond critical points of C? C and C? N bonds reveal a covalent bond character, and those of intermolecular interactions, such as hydrogen bonds and π? π stacking interactions, reveal a closed‐shell interaction. The potential energy curve of Hdpza molecule shows that the syn‐anti conformation is the most stable one (global minima) than the other two of syn‐syn and anti‐anti conformations.     

Theoretical Studies on the Intermolecular Interactions of Potentially Primordial Base‐Pair Analogues

Recent experimental studies on the Watson–Crick type base pairing of triazine and aminopyrimidine derivatives suggest that acid/base properties of the constituent bases might be related to the duplex stabilities measured in solution. Herein we use high‐level quantum chemical calculations and molecular dynamics simulations to evaluate the base pairing and stacking interactions of seven selected base pairs, which are common in that they are stabilized by two N? H???O hydrogen bonds separated by one N? H???N hydrogen bond. We show that neither the base pairing nor the base stacking interaction energies correlate with the reported pK_a data of the bases and the melting points of the duplexes. This suggests that the experimentally observed correlation between the melting point data of the duplexes and the pK_a values of the constituent bases is not rooted in the intrinsic base pairing and stacking properties. The physical chemistry origin of the observed experimental correlation thus remains unexplained and requires further investigations. In addition, since our calculations are carried out with extrapolation to the complete basis set of atomic orbitals and with inclusion of higher electron correlation effects, they provide reference data for stacking and base pairing energies of non‐natural bases.     

The 1:1 adduct of 4‐aminobenzoic acid with 4‐aminobenzonitrile

The 1:1 adduct of 4‐amino­benzoic acid (PABA) with 4‐am‐inobenzonitrile (PABN), C₇H₇NO₂·C₇H₆N₂, consists of a primary centrosymmetric cyclic hydrogen‐bonded PABA dimer interaction [O?O 2.640 (3) Å] peripherally linked into chains by weaker hydrogen bonds via a head‐to‐tail PABN interaction [N?N 3.179 (4) and N?O 3.062 (4) Å], and is linked between the chains by amine‐N (PABN) to amine‐N (PABA) interactions [N?N 3.233 (5) Å]. No proton transfer occurs.     

Supramolecular Assemblies of (±-2,2''''-Dihydroxy-1,1''''-binaphthyl with 2,2''''-Bipyridine and Naphthodiazine

Introduction Optically active 1,1'-bi-2-naphthol (BINOL) and its derivatives have been widely used as chiral ligands of catalysts for asymmetric reactions and effective host compounds for the isolation or optical resolution of a wide range of organic guest molecules through the for-mation of crystalline inclusion complexes.1,2 The wide-ranging and important applications of these com-pounds in organic synthesis have stimulated great inter-est in developing efficient methods for their prepara-…     

Photophysical Processes in ‘Supramolecular Balls’ Formed by Lanthanide Chloride with 2,2′‐Bipyridine

The europium complex [EuCl₂(bpy)₂(H₂O)₂]Cl?1.25 C₂H₆O?0.37 H₂O, where bpy is 2,2′‐bipyridine, was synthesized and investigated with the aim to relate its molecular geometry and crystal packing to the efficiency of energy‐transfer processes. The presence of H‐bonds between noncoordinated Cl^? ions and coordinated H₂O molecules leads to the formation of discrete trimers assembled by a number of C? H???Cl and stacking interactions into ‘supramolecular balls’ which contain Cl^? ions and solvate molecules (H₂O and EtOH). The additional stabilization of the complex is due to intramolecular N???C interactions between two bpy ligands that causes some shortening of the Eu? N bonds. Deciphering the luminescence properties of the Eu complex was performed under consideration of both the composition of the inner coordination sphere and the peculiarities of the crystal packing. The influence of the latter and the bpy orientation on the energy of the ligand→Eu charge‐transfer state (LMCT) was established, and an additional excited state induced by the π‐stacking interaction (SICT) was identified.     

Supramolecular hydrogen‐bonding patterns in the organic–inorganic hybrid compound bis(4‐amino‐5‐chloro‐2,6‐dimethylpyrimidinium) tetrathiocyanatozinc(II)–4‐amino‐5‐chloro‐2,6‐dimethylpyrimidine–water (1/2/2)

Zinc thiocyanate complexes have been found to be biologically active compounds. Zinc is also an essential element for the normal function of most organisms and is the main constituent in a number of metalloenzyme proteins. Pyrimidine and aminopyrimidine derivatives are biologically very important as they are components of nucleic acids. Thiocyanate ions can bridge metal ions by employing both their N and S atoms for coordination. They can play an important role in assembling different coordination structures and yield an interesting variety of one‐, two‐ and three‐dimensional polymeric metal–thiocyanate supramolecular frameworks. The structure of a new zinc thiocyanate–aminopyrimidine organic–inorganic compound, (C₆H₉ClN₃)₂[Zn(NCS)₄]·2C₆H₈ClN₃·2H₂O, is reported. The asymmetric unit consist of half a tetrathiocyanatozinc(II) dianion, an uncoordinated 4‐amino‐5‐chloro‐2,6‐dimethylpyrimidinium cation, a 4‐amino‐5‐chloro‐2,6‐dimethylpyrimidine molecule and a water molecule. The Zn^II atom adopts a distorted tetrahedral coordination geometry and is coordinated by four N atoms from the thiocyanate anions. The Zn^II atom is located on a special position (twofold axis of symmetry). The pyrimidinium cation and the pyrimidine molecule are not coordinated to the Zn^II atom, but are hydrogen bonded to the uncoordinated water molecules and the metal‐coordinated thiocyanate ligands. The pyrimidine molecules and pyrimidinium cations also form base‐pair‐like structures with an R₂²(8) ring motif via N—H…N hydrogen bonds. The crystal structure is further stabilized by intermolecular N—H…O, O—H…S, N—H…S and O—H…N hydrogen bonds, by intramolecular N—H…Cl and C—H…Cl hydrogen bonds, and also by π–π stacking interactions.     

Investigating Alanine–Silica Interaction by Means of First‐Principles Molecular‐Dynamics Simulations

In our attempts to achieve a detailed understanding of protein–silica interactions at an atomic level we have, as a first step, simulated a small system consisting of one alanine in different protonation states, and a hydroxylated silica surface, using a first‐principles molecular‐dynamics technique. The simulations are carried out in vacuo as well as in the presence of water molecules. In the case of a negatively charged surface and an alanine cation, an indirect proton transfer from the alanine carboxylic group to the surface takes place. The transfer involves several water molecules revealing an alanine in its zwitterionic state interacting with the neutral surface through indirect hydrogen bonds mediated by water molecules. During the simulation of the zwitterionic state the ammonium group eventually establishes a direct ? N? H???O? Si interaction, suggesting that the surface–amino group interaction is stronger than the interaction between the surface and the carboxylic group. In vacuum simulations, the amino group exhibits clearly stronger interactions with the surface than the carboxylic group.     

Hydrogen‐Bond Cooperativity in Formamide2–Water: A Model for Water‐Mediated Interactions

The rotational spectrum of formamide₂–H₂O formed in a supersonic jet has been characterized by Fourier‐transform microwave spectroscopy. This adduct provides a simple model of water‐mediated interaction involving the amide linkages, as occur in protein folding or amide‐association processes, showing the interplay between self‐association and solvation. Mono‐substituted ¹³C, ¹⁵N, ¹⁸O, and ²H isotopologues have been observed and their data used to investigate the structure. The adduct forms an almost planar three‐body sequential cycle. The two formamide molecules link on one side through an N?H???O hydrogen bond and on the other side through a water‐mediated interaction with the formation of C=O???H?O and O???H?N hydrogen bonds. The analysis of the quadrupole coupling effects of two ¹⁴N‐nuclei reveals the subtle inductive forces associated to cooperative hydrogen bonding. These forces are involved in the changes in the C=O and C?N bond lengths with respect to pure formamide.     

The Mechanism of NO Bond Cleavage in Rhodium‐Catalyzed CH Bond Functionalization of Quinoline N‐oxides with Alkynes: A Computational Study

Metal‐catalyzed C?H activation not only offers important strategies to construct new bonds, it also allows the merge of important research areas. When quinoline N‐oxide is used as an arene source in C?H activation studies, the N?O bond can act as a directing group as well as an O‐atom donor. The newly reported density functional theory method, M11L, has been used to elucidate the mechanistic details of the coupling between quinoline N?O bond and alkynes, which results in C?H activation and O‐atom transfer. The computational results indicated that the most favorable pathway involves an electrophilic deprotonation, an insertion of an acetylene group into a Rh?C bond, a reductive elimination to form an oxazinoquinolinium‐coordinated Rh^I intermediate, an oxidative addition to break the N?O bond, and a protonation reaction to regenerate the active catalyst. The regioselectivity of the reaction has also been studied by using prop‐1‐yn‐1‐ylbenzene as a model unsymmetrical substrate. Theoretical calculations suggested that 1‐phenyl‐2‐quinolinylpropanone would be the major product because of better conjugation between the phenyl group and enolate moiety in the corresponding transition state of the regioselectivity‐determining step. These calculated data are consistent with the experimental observations.     

Correlated one‐electron wave functions

Using four basis sets, 6‐311G(d,p), 6‐31+G(d,p), 6‐311++G(2d,2p), and 6‐311++G(3df,3pd), the optimized structures with all real frequencies were obtained at the MP2 level for dimers CH₂O? HF, CH₂O? H₂O, CH₂O? NH₃, and CH₂O? CH₄. The structures of CH₂O? HF, CH₂O? H₂O, and CH₂O? NH₃ are cycle‐shaped, which result from the larger bend of σ‐type hydrogen bonds. The bend of σ‐type H‐bond O…H? Y (Y?F, O, N) is illustrated and interpreted by an attractive interaction of a chemically intuitive π‐type hydrogen bond. The π‐type hydrogen bond is the interaction between one of the acidic H atoms of CH₂O and lone pair(s) on the F atom in HF, the O atom in H₂O, or the N atom in NH₃. By contrast with above the three dimers, for CH₂O? CH₄, because there is not a π‐type hydrogen‐bond to bend its linear hydrogen bond, the structure of CH₂O? CH₄ is a noncyclic shaped. The interaction energy of hydrogen bonds and the π‐type H‐bond are calculated and discussed at the CCSD(T)/6‐311++G(3df,3pd) level. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

Rhodium(III)‐Catalyzed CC and CO Coupling of Quinoline N‐Oxides with Alkynes: Combination of CH Activation with O‐Atom Transfer

[Cp*Rh^III]‐catalyzed C? H activation of arenes assisted by an oxidizing N? O or N? N directing group has allowed the construction of a number of hetercycles. In contrast, a polar N? O bond is well‐known to undergo O‐atom transfer (OAT) to alkynes. Despite the liability of N? O bonds in both C? H activation and OAT, these two important areas evolved separately. In this report, [Cp*Rh^III] catalysts integrate both areas in an efficient redox‐neutral coupling of quinoline N‐oxides with alkynes to afford α‐(8‐quinolyl)acetophenones. In this process the N? O bond acts as both a directing group for C? H activation and as an O‐atom donor.     

Triclinic and orthorhombic polymorphs of 2‐iodo‐4‐nitro­aniline: interplay of hydrogen bonds,nitro⃛I interactions and aromatic π–π‐stacking interactions

In the triclinic polymorph of 2‐iodo‐4‐nitro­aniline, C₆H₅IN₂O₂, space group P, the mol­ecules are linked by paired N—­H?O hydrogen bonds into C(8)[R(6)] chains of rings. These chains are linked into sheets by nitro?I interactions, and the sheets are pairwise linked by aromatic π–π‐stacking interactions. In the orthorhombic polymorph, space group Pbca, the mol­ecules are linked by single N—H?O hydrogen bonds into spiral C(8) chains; the chains are linked by nitro?O interactions into sheets, each of which is linked to its two immediate neighbours by aromatic π–π‐stacking inter­actions, so producing a continuous three‐dimensional ­structure.     

Contrasting the supramolecular structures in the isomeric pair 5‐bromo‐3‐nitrosalicylaldehyde phenylhydrazone and 3‐bromo‐5‐nitrosalicylaldehyde phenylhydrazone

Isomeric 5‐bromo‐3‐nitrosalicylaldehyde phenylhydrazone and 3‐bromo‐5‐nitrosalicylaldehyde phenylhydrazone, C₁₃H₁₀BrN₃O₃, both crystallize with two molecules in the asymmetric unit. In both isomers, an intramolecular O—H...N hydrogen bond links the hydroxy group and the imine N atom. In the 5‐bromo‐3‐nitro isomer, there are two independent N—H...O hydrogen‐bonded chains, each molecule in the asymmetric unit forming its own chain. These chains are then linked to form a three‐dimensional framework by a combination of weak C—H...O, C—H...Br, C—H...π and π–π stacking interactions. In the 3‐bromo‐5‐nitro isomer, N—H...O hydrogen bonds link the independent molecules alternately into a zigzag chain, which is reinforced by a weak C—H...O interaction. Individual chains are linked by a C—H...Br interaction and a three‐dimensional framework is generated by π–π stacking interactions.     

Hydrogen‐bonded sheet structures in methyl 4‐(4‐chloroanilino)‐3‐nitrobenzoate and methyl 1‐benzyl‐2‐(4‐chlorophenyl)‐1H‐benzimidazole‐5‐carboxylate

In methyl 4‐(4‐chloroanilino)‐3‐nitrobenzoate, C₁₄H₁₁ClN₂O₄, (I), there is an intramolecular N—H...O hydrogen bond and the intramolecular distances provide evidence for electronic polarization of the o‐quinonoid type. The molecules are linked into sheets built from N—H...O, C—H...O and C—H...π(arene) hydrogen bonds, together with an aromatic π–π stacking interaction. The molecules of methyl 1‐benzyl‐2‐(4‐chlorophenyl)‐1H‐benzimidazole‐5‐carboxylate, C₂₂H₁₇ClN₂O₂, (II), are also linked into sheets, this time by a combination of C—H...π(arene) hydrogen bonds and aromatic π–π stacking interactions.     

Remote C−H Activation of Quinolines through Copper‐Catalyzed Radical Cross‐Coupling

Achieving site selectivity in carbon–hydrogen (C?H) functionalization reactions is a formidable challenge in organic chemistry. Herein, we report a novel approach to activating remote C?H bonds at the C5 position of 8‐aminoquinoline through copper‐catalyzed sulfonylation under mild conditions. Our strategy shows high conversion efficiency, a broad substrate scope, and good toleration with different functional groups. Furthermore, our mechanistic investigations suggest that a single‐electron‐transfer process plays a vital role in generating sulfonyl radicals and subsequently initiating C?S cross‐coupling. Importantly, our copper‐catalyzed remote functionalization protocol can be expanded for the construction of a variety of chemical bonds, including C?O, C?Br, C?N, C?C, and C?I. These findings provide a fundamental insight into the activation of remote C?H bonds, while offering new possibilities for rational design of drug molecules and optoelectronic materials requiring specific modification of functional groups.     

Concomitant polymorphic forms of 3‐cyclopropyl‐5‐(2‐hydrazinylpyridin‐3‐yl)‐1,2,4‐oxadiazole

The dipharmacophore compound 3‐cyclopropyl‐5‐(2‐hydrazinylpyridin‐3‐yl)‐1,2,4‐oxadiazole, C₁₀H₁₁N₅O, was studied on the assumption of its potential biological activity. Two concomitant polymorphs were obtained on crystallization from isopropanol solution and these were thoroughly studied. Identical conformations of the molecules are found in both structures despite the low difference in energy between the four possible conformers. The two polymorphs differ crucially with respect to their crystal structures. A centrosymmetric dimer formed due to both stacking interactions of the `head‐to‐tail' type and N—H…N(π) hydrogen bonds is the building unit in the triclinic structure. The dimeric building units form an isotropic packing. In the orthorhombic polymorphic structure, the molecules form stacking interactions of the `head‐to‐head' type, which results in their organization in a column as the primary basic structural motif. The formation of N—H…N(lone pair) hydrogen bonds between two neighbouring columns allows the formation of a double column as the main structural motif. The correct packing motifs in the two polymorphs could not be identified without calculations of the pairwise interaction energies. The triclinic structure has a higher density and a lower (by 0.60 kcal mol^?1) lattice energy according to periodic calculations compared to the orthorhombic structure. This allows us to presume that the triclinic form of 3‐cyclopropyl‐5‐(2‐hydrazinylpyridin‐3‐yl)‐1,2,4‐oxadiazole is the more stable.