Charge Density Studies of Weak Interactions in Dipicrylamine

Strategic Synthesis of 'Picket Fence' Porphyrins Based on Nonplanar Macrocycles

Traditional 'picket fence' porphyrin systems have been a topic of interest for their capacity to direct steric shielding effects selectively to one side of the macrocycle. Sterically overcrowded porphyrin systems that adopt macrocycle deformations have recently drawn attention for their applications in organocatalysis and sensing. Here we explore the combined benefits of nonplanar porphyrins and the old molecular design to bring new concepts to the playing field. The challenging ortho-positions of meso-phenyl residues in dodecasubstituted porphyrin systems led us to transition to less hindered para- and meta-sites and develop selective demethylation based on the steric interplay. Isolation of the symmetrical target compound [2,3,7,8,12,13,17,18-octaethyl-5,10,15,20-tetrakis(3,5-dipivaloyloxyphenyl)porphyrin] was investigated under two synthetic pathways. The obtained insight was used to isolate unsymmetrical [2,3,7,8,12,13,17,18-octaethyl-5,10,15,20-tetrakis(2-nitro-5-pivaloyloxyphenyl)porphyrin]. Upon separation of the atropisomers, a detailed single-crystal X-ray crystallographic analysis highlighted intrinsic intermolecular interactions. The nonplanarity of these systems in combination with 'picket fence' motifs provides an important feature in the design of supramolecular ensembles.

Serendipitous isolation of a triazinone-based air stable organic radical: synthesis, crystal structure, and computation

Here we report the synthesis, isolation, and characterization of a dication salt, namely 4,6-bis(4,4′-bipyridinium)-1,3,5-triazin-2-one {1²⁺(PF₆)₂²⁻·2H₂O1(PF6)2·2H2O}, and its radical cation salt, namely 4,6-bis(4,4′-bipyridinium)-1,3,5-triazin-2-one (1+˙PF₆⁻1˙PF6).

Dipicrylamine as a colorimetric sensor for anions: experimental and computational study

Dipicrylamine exhibited colorimetric sensing of F⁻, OAc⁻ and H₂PO₄⁻, detectable by bared-eye, out of a large number of anions. Interestingly, F⁻ binds with one of the phenyl carbon of dipicrylamine.

Systematic experimental charge density analysis of anion receptor complexes

The first systematic electronic resolution study of a series of urea-based anion receptor complexes is presented and shows the binding strength to be greater for more basic anion–receptor pairs in the solid state.

X-ray crystallographic, FT-IR, and density functional theory studies of the salt formed between dipicrylamine and 1,5,7-triazabicyclo[4.4.0]dec-1-ene

The DPA-TBD (dipicrylamine-1,5,7-triazabicyclo[4.4.0]dec-1-ene) salt has been synthesized and characterized by FT-IR spectroscopy, X-ray single-crystal diffraction, and theoretical study. In the FT-IR spectrum of the crystalline DPA-TBD salt, an unexpected intense band at 1742 cm(-1) is present. The optimized geometry and the FT-IR spectra of the DPA salt were calculated at the B3LYP/6-31G+(d) level and give an explanation of the nature of this band as the ν(C═N═C) vibration. For comparison, the calculated IR spectra of the DPA anion, hydrogen-bonded DPA anion, and neutral DPA and TBD molecules as well as for the TBD cation are also shown. The presence of the free DPA anion in the gas phase was directly detected in the negative ion mode electrospray ionization MS spectra. The fragmentation of the DPA anion is also discussed.

Neutron single crystal diffraction: techniques and applications in molecular systems

Single crystal neutron diffraction is a powerful method for the investigation of molecular structure, and in many cases is found to be an excellent complement to X-ray diffraction. The ability of neutron diffraction to determine the position of the atomic nucleus, rather than the electron density, is key to its use in structural studies. Among other advantages, this lends the neutron the ability to determine accurately the positions (and displacement parameters) of light atoms. In the context of molecular systems, neutron diffraction is thus very well suited to the determination of hydrogen atom parameters, which are key to many applications in molecular structure determination, including hydrogen bonded systems, organometallic materials and in macromolecular structures.

This article briefly summarises some of the applications to which single crystal neutron diffraction has been put in the study of molecular structure, together with an account of the techniques and instrumentation used for these experiments. Particular account is taken of recent developments in instrumentation, and the new scientific applications that have resulted from these, along with a forward look to some of the exciting developments currently taking place in this field. These include instruments with dramatically enhanced detector arrays, other optimisations to improve count-rate and performance, the construction of new neutron sources and exciting new instruments being planned for these sources.

Fluorescence Spectroscopic Properties and Crystal Structure of a Series of Donor−Acceptor Diphenylpolyenes

A series of p-nitro-p'-alkoxy(OR)-substituted (E,E,E)-1,6-diphenyl-1,3,5-hexatrienes (1a, R = Me; 1b, R = Et; 1c, R = n-Pr; 1d, R = n-Bu) were prepared. The absorption and fluorescence spectra in solution were almost independent of the alkoxy chain length. The absorption maximum showed only a small dependence on the solvent polarity, whereas the fluorescence maximum red-shifted largely as the polarity increased. The solid-state absorption and fluorescence spectra were red-shifted relative to those in low polar solvents and were clearly dependent on the alkoxy chain length. The fluorescence maxima for the crystals of 1b and 1d were observed at 635-650 nm, which were red-shifted by 40-50 nm relative to those for 1a and 1c. The Stokes shifts were all relatively small (3000-3500 cm-1). For all four compounds, the fluorescence decay curves in the solid state were able to be analyzed by single-exponential fitting to give the lifetimes of 1.1-1.3 ns. This indicates that the emission of 1a-d is not originated from an excimer or molecular aggregates, but from only one emitting monomeric species. The fluorescence quantum yields of 1a-d were considerably high compared with the values for organic solids, which is consistent with their monomeric origin of emission. Single-crystal X-ray structure analyses of 1a, 1c, and 1d showed that the crystal packing was dependent on the alkoxy chain length. The crystals of 1a and 1c had herringbone structure, whereas that of 1d had pi-stacked structure. Strong pi-pi interaction in the crystal of 1d would be the cause of the spectral red shifts relative to those for 1a and 1c. No observation of excimer fluorescence from crystal 1d can be attributed to the limited overlap between the pi-planes of the molecules due to its "slipped-parallel" structure.

Role of Triple Bond in 1,2-Diphenylacetylene Crystal: A Combined Experimental and Theoretical Study

We have performed a combined experimental and theoretical study of the molecular system of 1,2-diphenylacetylene. The occurrence of two different geometries of the molecule in the crystal structure, one being planar and the other tilted by approximately 6 degrees , has been investigated in relation to the nature of the acetylenic linker. The experimental charge density analysis shows that the acetylenic linker exhibits a noncylindrical density reminiscent of the strong conjugation present in the molecule. The pi-orbitals of the acetylenic linker derived from density functional theory (DFT) calculations are found to sustain a variety of conjugation lengths between the phenyl rings, thereby giving flexibility to the molecule to arrange itself in various packing conformations in the crystal. It is interesting that the energy involved for such distortions is only kBT, allowing several polymorphic forms of the crystal structure as reported in the literature. The distortions entertained by the molecule and the corresponding changes in the charge density distribution and energy are all relevant to molecular electronics.

Intermolecular interactions of nitrobenzene-benzene complex and nitrobenzene dimer: Significant stabilization of slipped-parallel orientation by dispersion interaction

The CCSD(T) level interaction energies of eight orientations of nitrobenzene-benzene complexes and nine orientations of nitrobenzene dimers at the basis set limit have been estimated. The calculated interaction energy of the most stable slipped-parallel (C(s)) nitrobenzene-benzene complex was -4.51 kcal/mol. That of the most stable slipped-parallel (antiparallel) (C(2h)) nitrobenzene dimer was -6.81 kcal/mol. The interaction energies of these complexes are significantly larger than that of the benzene dimer. The T-shaped complexes are substantially less stable. Although nitrobenzene has a polar nitro group, electrostatic interaction is always considerably weaker than the dispersion interaction. The dispersion interaction in these complexes is larger than that in the benzene dimer, which is the cause of the preference of the slipped-parallel orientation in these complexes.

Elusive contribution of the experimental surface molecular electrostatic potential and promolecule approximation in the empirical estimate of the crystal density

The aim of this study is to probe the crystal density (D(c)) description in terms of pertinent molecular characteristics and properties. In this purpose, the electrostatic potential was derived from available experimental electron density multipole parameters of molecular compounds with different D(c) magnitudes. The surface electrostatic potential has been analyzed through the positive and negative statistical variances. The surface of the molecule is here corresponding to particular isodensity values according to Bader's topological theory. Following the successful Politzer's method based on quantum mechanics calculations to empirically describe macroscopic properties, the crystal density was regressed on the molecular density and the surface electrostatic potential variance. This latter appears to be a poor statistical descriptor of the crystal density when the experimentally derived electrostatic potential is used and it does not significantly improve the fit of D(c) to molecular density alone. Compared to Politzer's approach based on gas phase isolated molecules, the experimental electrostatic potential is biased by the interactions in the crystal lattice. As an alternative to other sophisticated methods, the promolecule isodensity surface offers a quite useful and straightforward way to define the molecular volumes. The reported description of the crystal density for a set of 50 molecules using the promolecule approach yields satisfactory results.

Orthogonal Multipolar Interactions in Structural Chemistry and Biology

The past few decades of molecular recognition studies have greatly enhanced our knowledge on apolar, ion-dipole, and hydrogen-bonding interactions. However, much less attention has been given to the role that multipolar interactions, in particular those with orthogonal dipolar alignment, play in organizing a crystal lattice or stabilizing complexes involving biological receptors. By using results from database mining, this review attempts to give an overview of types and structural features of these previously rather overlooked interactions. A number of illustrative examples of these interactions found in X-ray crystal structures of small molecules and protein-ligand complexes demonstrate their propensity and thus potential importance for both, chemical and biological molecular recognition processes.

The first observation of nitrogen–carbonyl bonding: self-assembly of N-oxalyl 2,4-dinitroanilide assisted by a weak N⋯OC interaction

A new type of weak bond, i.e., the N...O=C interaction, that determines the crystal packing of N-oxalyl 2,4-dinitroanilide (1) in cooperation with C-H...O hydrogen bonds, has been found and is rationalized by ab initio calculations as being the result of electrostatic interactions.