Color Polymorphism: Understanding the Diverse Solid‐State Packing and Color in Dimethyl‐3,6‐dichloro‐2,5‐dihydroxyterephthalate

Dimethyl‐3,6‐dichloro‐2,5‐dihydroxyterephthalate (MCHT) is known to exist in three differently packed crystals having three different colors, namely yellow (Y), light yellow (LY), and white (W). Apart from the difference in their color, the molecules in the crystals also differ in their intramolecular O?H???O and O?H???Cl hydrogen bonds. Time‐dependent DFT calculations reveal the role of the various types of hydrogen bonds in controlling the color of the polymorphs. Mechanistic pathways that lead to such transformations in the crystal are elucidated by solid‐state dispersion‐corrected DFT studies. Relative stabilities of the various polymorphs rationalize the experimentally observed transformations between them. Calculations reveal that the minimum‐energy pathway for the conversion of the Y form to a W form is through stepwise disrotatory motion of the two ?OH groups through a hybrid intermediate having one intramolecular O?H???O and one O?H???Cl bond. The LY form is shown to exist on the higher‐energy pathway involving a concerted Y→W transformation.     

“Hummingbird” Behaviour of N‐Heterocyclic Carbenes Stabilises Out‐of‐Plane Bonding of AuCl and CuCl Units

An N‐heterocyclic carbene substituted by two expanded 9‐ethyl‐9‐fluorenyl groups was shown to bind an AuCl unit in an unusual manner, namely with the Au?X rod sitting out of the plane defined by the heterocyclic carbene unit. As shown by X‐ray studies and DFT calculations, the observed large pitch angle (21°) arises from an easy displacement of the gold(I) atom away from the carbene lone‐pair axis, combined with the stabilisation provided by weak CH???Au interactions involving aliphatic and aromatic H atoms of the NHC wingtips. Weak, intermolecular Cl???H bonds are likely to cooperate with the H???Au interactions to stabilise the out‐of‐plane conformation. A general belief until now was that tilt angles in NHC complexes arise mainly from steric effects within the first coordination sphere.     

Cooperative Effect of a Classical and a Weak Hydrogen Bond for the Metal‐Induced Construction of a Self‐Assembled β‐Turn Mimic

A novel metal‐induced template for the self‐assembly of two independent phosphane ligands by means of unprecedented multiple noncovalent interactions (classical hydrogen bond, weak hydrogen bond, metal coordination, π‐stacking interaction) was developed and investigated. Our results address the importance and capability of weak hydrogen bonds (WHBs) as important attractive interactions in self‐assembling processes based on molecular recognition. Together with a classical hydrogen bond, WHBs may serve as promoters for the specific self‐assembly of complementary monomeric phosphane ligands into supramolecular hybrid structures. The formation of an intermolecular C? H???N hydrogen bond and its persistence in the solid state and in solution was studied by X‐ray crystal analysis, mass spectrometry and NMR spectroscopy analysis. Further evidence was demonstrated by DFT calculations, which gave specific geometric parameters for the proposed conformations and allowed us to estimate the energy involved in the hydrogen bonds that are responsible for the molecular recognition process. The presented template can be regarded as a new type of self‐assembled β‐turn mimic or supramolecular pseudo amino acid for the nucleation of β‐sheet structures when attached to oligopeptides.     

Cooperative Catalysis of Metal and O?H⋅⋅⋅O/sp3‐C?H⋅⋅⋅O Two‐Point Hydrogen Bonds in Alcoholic Solvents: Cu‐Catalyzed Enantioselective Direct Alkynylation of Aldehydes with Terminal Alkynes

Catalyst–substrate hydrogen bonds in artificial catalysts usually occur in aprotic solvents, but not in protic solvents, in contrast to enzymatic catalysis. We report a case in which ligand–substrate hydrogen‐bonding interactions cooperate with a transition‐metal center in alcoholic solvents for enantioselective catalysis. Copper(I) complexes with prolinol‐based hydroxy amino phosphane chiral ligands catalytically promoted the direct alkynylation of aldehydes with terminal alkynes in alcoholic solvents to afford nonracemic secondary propargylic alcohols with high enantioselectivities. Quantum‐mechanical calculations of enantiodiscriminating transition states show the occurrence of a nonclassical sp³‐C? H???O hydrogen bond as a secondary interaction between the ligand and substrate, which results in highly directional catalyst–substrate two‐point hydrogen bonding.     

Intramolecular Hydrogen Bonds in Low‐Molecular‐Weight Polyethylene Glycol

We used static DFT calculations to analyze, in detail, the intramolecular hydrogen bonds formed in low‐molecular‐weight polyethylene glycol (PEG) with two to five repeat subunits. Both red‐shifted O?H???O and blue‐shifting C?H???O hydrogen bonds, which control the structural flexibility of PEG, were detected. To estimate the strength of these hydrogen bonds, the quantum theory of atoms in molecules was used. Car–Parrinello molecular dynamics simulations were used to mimic the structural rearrangements and hydrogen‐bond breaking/formation in the PEG molecule at 300 K. The time evolution of the H???O bond length and valence angles of the formed hydrogen bonds were fully analyzed. The characteristic hydrogen‐bonding patterns of low‐molecular‐weight PEG were described with an estimation of their lifetime. The theoretical results obtained, in particular the presence of weak C?H???O hydrogen bonds, could serve as an explanation of the PEG structural stability in the experimental investigation.     

Importance of CH/π hydrogen bonds in recognition of the core motif in proline-recognition domains: an ab initio fragment molecular orbital study

We examined CH/π hydrogen bonds in protein/ligand complexes involving at least one proline residue using the ab initio fragment molecular orbital (FMO) method and the program CHPI. FMO calculations were carried out at the Hartree–Fock (HF)/6‐31G*, HF/6‐31G**, second‐order Møller–Plesset perturbation (MP2)/6‐31G*, and MP2/6‐31G** levels for three Src homology 3 (SH3) domains and five proline‐recognition domains (PRDs) complexed with their corresponding ligand peptides. PRDs use a conserved set of aromatic residues to recognize proline‐rich sequences of specific ligands. Many CH/π hydrogen bonds were identified in these complexes. CH/π hydrogen bonds occurred, in particular, in the central part of the proline‐rich motifs. Our results suggest that CH/π hydrogen bonds are important in the recognition of SH3 and PRDs by their ligand peptides and play a vital role in the signal transduction system. Combined use of the FMO method and CHPI analysis is a valuable tool for the study of protein/protein and protein/ligand interactions and may be useful in rational drug design. © 2011 Wiley Periodicals, Inc. J Comput Chem 2011     

π‐Hole Bonds: Boron and Aluminum Lewis Acid Centers

MP2/aug‐cc‐pVTZ calculations were performed on complexes of boron and aluminum trihydrides and trihalides with hydrogen cyanide (ZH₃‐NCH and ZX₃‐NCH; Z=B, Al; X=F, Cl). The complexes are linked through the B???N and Al???N interactions, which are named as triel bonds and which are classified as π‐hole bonds. It was found that they possess numerous characteristics of typical covalent bonds, since they are ruled mainly by processes of the electron charge shift from the Lewis base to the Lewis acid unit. Other configurations of the ZH₃‐NCH and ZX₃‐NCH complexes linked by the dihydrogen, hydrogen, and halogen bonds were found. However, these interactions are much weaker than the corresponding π‐hole bonds. The quantum theory of atoms in molecules and the natural bond orbital approaches were applied to characterize the complexes and interactions analyzed. The crystal structures of triel trihydrides and triel trihalides were also analyzed for comparison with the results of calculations.     

A Carbohydrate–Anion Recognition System in Aprotic Solvents

A carbohydrate–anion recognition system in nonpolar solvents is reported, in which complexes form at the B‐faces of β‐D ‐pyranosides with H1‐, H3‐, and H5‐cis patterns similar to carbohydrate–π interactions. The complexation effect was evaluated for a range of carbohydrate structures; it resulted in either 1:1 carbohydrate–anion complexes, or 1:2 complex formation depending on the protection pattern of the carbohydrate. The interaction was also evaluated with different anions and solvents. In both cases it resulted in significant binding differences. The results indicate that complexation originates from van der Waals interactions or weak CH ??? A^? hydrogen bonds between the binding partners and is related to electron‐withdrawing groups of the carbohydrates as well as increased hydrogen‐bond‐accepting capability of the anions.     

Comprehensive Analysis of Fragment Orbital Interactions to Build Highly π‐Conjugated Thienylene‐Substituted Phenylene Oligomers

π‐Conjugated thienylene? phenylene oligomers with fluorinated and dialkoxylated phenylene fragments have been designed and prepared to understand the interactions in fragment orbitals, the influence of the substituents (F, OMe) on the HOMO–LUMO gap, and the role of intramolecular non‐covalent cumulative interactions in the construction of π‐conjugated nanostructures. Their strong conjugation was also evidenced in the gas phase by UV photoelectron spectroscopy and theoretical calculations. These results can be explained by the crucial role of the relative energetic positions of the π orbitals of the dimethoxyphenylene, which was used to model the dialkoxyphenylene entity, in determining the π/π^* orbital levels of the fluorinated phenylene entity. Dialkoxyphenylenes raise the HOMO orbitals, whereas fluorinated phenylenes lower the LUMO orbitals in the oligomers. In addition, the presence of S???F and H???F interactions in the fluorinated phenylene? thienylene compounds add to the S???O interactions in the mixed targets and contribute to the full conjugation in the oligomer, inducing weak inter‐ring angles between the involved aromatic cycles. These results, which showed extended conjugation of the π system, were corroborated by a narrow HOMO–LUMO gap (according to DFT calculations) and by a relatively strong maximum wavelength (as obtained by TD‐DFT calculations and experimental UV/Vis measurements). The crystallographic data of two mixed thienylene? (fluorinated and dialkoxylated phenylene) five‐ring oligomers agree with the above results and show the formation of quasi‐planar conformations with non‐covalent S???O, H???F, and S???F interactions. These studies in the solid and gas phases show the relevance of associating dialkoxyphenylene and fluorinated phenylene fragments with thiophene to lead to oligomers with improved electronic delocalization for electronic or optoelectronic devices.     

Recognition of N‐Alkyl and N‐Aryl Acetamides by N‐Alkyl Ammonium Resorcinarene Chlorides

N‐Alkyl ammonium resorcinarene chlorides are stabilized by an intricate array of intra‐ and intermolecular hydrogen bonds that leads to cavitand‐like structures. Depending on the upper‐rim substituents, self‐inclusion was observed in solution and in the solid state. The self‐inclusion can be disrupted at higher temperatures, whereas in the presence of small guests the self‐included dimers spontaneously reorganize to 1:1 host–guest complexes. These host compounds show an interesting ability to bind a series of N‐alkyl acetamide guests through intermolecular hydrogen bonds involving the carbonyl oxygen (C?O) atoms and the amide (NH) groups of the guests, the chloride anions (Cl^?) and ammonium (NH₂⁺) cations of the hosts, and also through CH ??? π interactions between the hosts and guests. The self‐included and host–guest complexes were studied by single‐crystal X‐ray diffraction, NMR titration, and mass spectrometry.     

Hydrogen‐Bonding Interactions and Properties of Energetic Nitroamino[1,3,5]triazine‐Based Guanidinium Salts: DFT‐D and QTAIM Studies

The intramolecular hydrogen‐bonding interactions and properties of a series of nitroamino[1,3,5]triazine‐based guanidinium salts were studied by using the dispersion‐corrected density functional theory method (DFT‐D). Results show that there are evident LP(N or O; LP=lone pair)→σ*(N? H) orbital interactions related to O???H? N or N???H? N hydrogen bonds. Quantum theory of atoms in molecules (QTAIM) was applied to characterize the intramolecular hydrogen bonds. For the guanidinium salts studied, the intramolecular hydrogen bonds are associated with a seven‐ or eight‐membered pseudo‐ring. The guanylurea cation is more helpful for improving the thermal stabilities of the ionic salts than other guanidinium cations. The contributions of different substituents on the triazine ring to the thermal stability increase in the order of ? NO₂23 (? ONO₂)2. Energy decomposition analysis shows that the salts are stable owing to electrostatic and orbital interactions between the ions, whereas the dispersion energy has very small contributions. Moreover, the salts exhibit relatively high densities in the range of 1.62–1.89 g cm^?3. The detonation velocities and pressures lie in the range of 6.49–8.85 km s^?1 and 17.79–35.59 GPa, respectively, which makes most of them promising explosives.     

Preparing Gold(I) for Interactions with Proton Donors: The Elusive [Au]⋅⋅⋅HO Hydrogen Bond

MP2 and DFT calculations with correlation consistent basis sets indicate that isolated linear anionic dialkylgold(I) complexes form moderately strong (ca. 10 kcal mol^?1) Au???H hydrogen bonds with single H₂O molecules as donors in the absence of sterically demanding substituents. Relativistic effects are critically important in the attraction. Such bonds are significantly weaker in neutral, strong σ‐donor N‐heterocyclic carbene (NHC) complexes (ca. 5 kcal mol^?1). The overall association (>11 kcal mol^?1), however, is strengthened by co‐operative, synergistic classical hydrogen bonding when the NHC ligands bear NH units. Further manipulation of the interaction by ligands positioned trans to the carbene, is possible.     

On the Nature of Blueshifting Hydrogen Bonds

The block‐localized wave function (BLW) method can derive the energetic, geometrical, and spectral changes with the deactivation of electron delocalization, and thus provide a unique way to elucidate the origin of improper, blueshifting hydrogen bonds versus proper, redshifting hydrogen bonds. A detailed analysis of the interactions of F₃CH with NH₃ and OH₂ shows that blueshifting is a long‐range phenomenon. Since among the various energy components contributing to hydrogen bonds, only the electrostatic interaction has long‐range characteristics, we conclude that the contraction and blueshifting of a hydrogen bond is largely caused by electrostatic interactions. On the other hand, lengthening and redshifting is primarily due to the short‐range n(Y)→σ*(X?H) hyperconjugation. The competition between these two opposing factors determines the final frequency change direction, for example, redshifting in F₃CH ??? NH₃ and blueshifting in F₃CH ??? OH₂. This mechanism works well in the series F_nCl_3?nCH ??? Y (n=0–3, Y=NH₃, OH₂, SH₂) and other systems. One exception is the complex of water and benzene. We observe the lengthening and redshifting of the O?H bond of water even with the electron transfer between benzene and water completely quenched. A distance‐dependent analysis for this system reveals that the long‐range electrostatic interaction is again responsible for the initial lengthening and redshifting.     

Homonuclear chalcogen–chalcogen bond interactions in complexes pairing YO3 and YHX molecules (Y = S,Se; X = H,Cl, Br,CCH, NC,OH, OCH3): Influence of substitution and cooperativity

MP2/aug‐cc‐pVTZ calculations are performed on complexes of YO₃ (Y = S, Se) with a series of electron‐donating chalcogen bases YHX (X = H, Cl, Br, CCH, NC, OH, OCH₃). These complexes are formed through the interaction of a positive electrostatic potential region (π‐hole) on the YO₃ molecule with the negative region in YHX. Interaction energies of the binary O₃Y???YHX complexes are in the range of ?4.37 to ?12.09 kcal/mol. The quantum theory of atoms in molecules and the natural bond orbital analysis were applied to characterize the nature of interactions. It was found that the formation and stability of these binary complexes are ruled mainly by electrostatic effects, although the electron charge transfer from YHX to YO₃ unit also seems to play an important role. In addition, mutual influence between the Y???N and Y???Y interactions is studied in the ternary HCN???O₃Y???YHX complexes. The results indicate that the formation of a Y???N interaction tends to weaken Y???Y bond in the ternary systems. Although the Y???Y interaction is weaker than the Y???N one, however, both types of interactions seem to compete with each other in the HCN???O₃Y???YHX complexes. © 2016 Wiley Periodicals, Inc.     

Cooperativity between the Halogen Bond and the Hydrogen Bond in H3N⋅⋅⋅XY⋅⋅⋅HF Complexes (X,Y=F,Cl, Br)

Ab initio calculations are used to provide information on H₃N???XY???HF triads (X, Y=F, Cl, Br) each having a halogen bond and a hydrogen bond. The investigated triads include H₃N???Br₂‐HF, H₃N???Cl₂???HF, H₃N???BrCI???HF, H₃N???BrF???HF, and H₃N???ClF???HF. To understand the properties of the systems better, the corresponding dyads are also investigated. Molecular geometries, binding energies, and infrared spectra of monomers, dyads, and triads are studied at the MP2 level of theory with the 6‐311++G(d,p) basis set. Because the primary aim of this study is to examine cooperative effects, particular attention is given to parameters such as cooperative energies, many‐body interaction energies, and cooperativity factors. The cooperative energy ranges from ?1.45 to ?4.64 kcal mol^?1, the three‐body interaction energy from ?2.17 to ?6.71 kcal mol^?1, and the cooperativity factor from 1.27 to 4.35. These results indicate significant cooperativity between the halogen and hydrogen bonds in these complexes. This cooperativity is much greater than that between hydrogen bonds. The effect of a halogen bond on a hydrogen bond is more pronounced than that of a hydrogen bond on a halogen bond.     

Influence of the Li⋅⋅⋅π Interaction on the H/X⋅⋅⋅π Interactions in HOLi⋅⋅⋅C6H6⋅⋅⋅HOX/XOH (X=F,Cl, Br,I) Complexes

The influences of the Li???π interaction of C₆H₆???LiOH on the H???π interaction of C₆H₆???HOX (X=F, Cl, Br, I) and the X???π interaction of C₆H₆???XOH (X=Cl, Br, I) are investigated by means of full electronic second‐order Møller–Plesset perturbation theory calculations and “quantum theory of atoms in molecules” (QTAIM) studies. The binding energies, binding distances, infrared vibrational frequencies, and electron densities at the bond critical points (BCPs) of the hydrogen bonds and halogen bonds prove that the addition of the Li???π interaction to benzene weakens the H???π and X???π interactions. The influences of the Li???π interaction on H???π interactions are greater than those on X???π interactions; the influences of the H???π interactions on the Li???π interaction are greater than X???π interactions on Li???π interaction. The greater the influence of Li???π interaction on H/X???π interactions, the greater the influences of H/X???π interactions on Li???π interaction. QTAIM studies show that the intermolecular interactions of C₆H₆???HOX and C₆H₆???XOH are mainly of the π type. The electron densities at the BCPs of hydrogen bonds and halogen bonds decrease on going from bimolecular complexes to termolecular complexes, and the π‐electron densities at the BCPs show the same pattern. Natural bond orbital analyses show that the Li???π interaction reduces electron transfer from C₆H₆ to HOX and XOH.     

Using (FH)2 and (FH)3 to Bridge the σ‐Hole and the Lone Pair at P in Complexes with H2XP,for X=CH3, OH,H, CCH,F, Cl,NC, and CN

Ab initio MP2/aug′‐cc‐pVTZ calculations are used to investigate the binary complexes H₂XP:HF, the ternary complexes H₂XP:(FH)₂, and the quaternary complexes H₂XP:(FH)₃, for X=CH₃, OH, H, CCH, F, Cl, NC, and CN. Hydrogen‐bonded (HB) binary complexes are formed between all H₂XP molecules and FH, but only H₂FP, H₂ClP, and H₂(NC)P form pnicogen‐bonded (ZB) complexes with FH. Ternary complexes with (FH)₂ are stabilized by F?H???P and F?H???F hydrogen bonds and F???P pnicogen bonds, except for H₂(CH₃)P:(FH)₂ and H₃P:(FH)₂, which do not have pnicogen bonds. All quaternary complexes H₂XP:(FH)₃ are stabilized by both F?H???P and F?H???F hydrogen bonds and P???F pnicogen bonds. Thus, (FH)₂ with two exceptions, and (FH)₃ can bridge the σ‐hole and the lone pair at P in these complexes. The binding energies of H₂XP:(FH)₃ complexes are significantly greater than the binding energies of H₂XP:(FH)₂ complexes, and nonadditivities are synergistic in both series. Charge transfer occurs across all intermolecular bonds from the lone‐pair donor atom to an antibonding σ* orbital of the acceptor molecule, and stabilizes these complexes. Charge‐transfer energies across the pnicogen bond correlate with the intermolecular P?F distance, while charge‐transfer energies across F?H???P and F?H???F hydrogen bonds correlate with the distance between the lone‐pair donor atom and the hydrogen‐bonded H atom. In binary and quaternary complexes, charge transfer energies also correlate with the distance between the electron‐donor atom and the hydrogen‐bonded F atom. EOM‐CCSD spin‐spin coupling constants ^2hJ(F–P) across F?H???P hydrogen bonds, and ^1pJ(P–F) across pnicogen bonds in binary, ternary, and quaternary complexes exhibit strong correlations with the corresponding intermolecular distances. Hydrogen bonds are better transmitters of F–P coupling data than pnicogen bonds, despite the longer F???P distances in F?H???P hydrogen bonds compared to P???F pnicogen bonds. There is a correlation between the two bond coupling constants ^2hJ(F–F) in the quaternary complexes and the corresponding intermolecular distances, but not in the ternary complexes, a reflection of the distorted geometries of the bridging dimers in ternary complexes.     

The nido‐Cage⋅⋅⋅π Bond: A Non‐covalent Interaction between Boron Clusters and Aromatic Rings and Its Applications

Non‐covalent interactions involving multicenter multielectron skeletons such as boron clusters are rare. Now, a non‐covalent interaction, the nido‐cage???π bond, is discovered based on the boron cluster C₂B₉H₁₂^? and an aromatic π system. The X‐ray diffraction studies indicate that the nido‐cage???π bonding presents parallel‐displaced or T‐shaped geometries. The contacting distance between cage and π ring varies with the type and the substituent of the aromatic ring. Theoretical calculations reveal that this nido‐cage???π bond shares a similar nature to the conventional anion???π or π???π bonds found in classical aromatic ring systems. This nido‐cage???π interaction induces variable photophysical properties such as aggregation‐induced emission and aggregation‐caused quenching in one molecule. This work offers an overall understanding towards the boron cluster‐based non‐covalent bond and opens a door to investigate its properties.     

Synthesis,Coordination Chemistry and Bonding of Strong N‐Donor Ligands Incorporating the 1H‐Pyridin‐(2E)‐Ylidene (PYE) Motif

A range of N‐donor ligands based on the 1H‐pyridin‐(2E)‐ylidene (PYE) motif have been prepared, including achiral and chiral examples. The ligands incorporate one to three PYE groups that coordinate to a metal through the exocyclic nitrogen atom of each PYE moiety, and the resulting metal complexes have been characterised by methods including single‐crystal X‐ray diffraction and NMR spectroscopy to examine metal–ligand bonding and ligand dynamics. Upon coordination of a PYE ligand to a proton or metal‐complex fragment, the solid‐state structures, NMR spectroscopy and DFT studies indicate that charge redistribution occurs within the PYE heterocyclic ring to give a contribution from a pyridinium–amido‐type resonance structure. Additional IR spectroscopy and computational studies suggest that PYE ligands are strong donor ligands. NMR spectroscopy shows that for metal complexes there is restricted motion about the exocyclic C? N bond, which projects the heterocyclic N‐substituent in the vicinity of the metal atom causing restricted motion in chelating‐ligand derivatives. Solid‐state structures and DFT calculations also show significant steric congestion and secondary metal–ligand interactions between the metal and ligand C? H bonds.