Unprecedented Synthesis of 1,3-Dimethylcyclobutadiene in the Solid State and Aqueous Solution

Pathological crystal structures

Recent decades have seen enormous changes in the technology of crystal structure analysis, but the interpretation of these data still depends on human judgment, and errors are far from uncommon. Although analysing the crystallographic results with available software tools can catch many types of errors, others can be detected only by combining knowledge of both crystallography and chemistry. We discuss several such examples from the published literature, and for each of them we identify what lessons they teach us. The examples are categorized by the type of error: correct crystallography but incorrect chemistry, mis-assignment of atoms, high-symmetry superstructures with included guest molecules, incorrect choice of space group, incorrect choice of unit-cell size, and unresolved problems. These examples are intended to counteract the aura of infallibility that crystal structures sometimes assume and to alert the reader to features to look for in detecting pathological structures.

Progressive Folding and Adaptive Multivalent Recognition of Alkyl Amines and Amino Acids in p-Sulfonatocalix[4]arene Hosts: Solid-State and Solution Studies

Calix[4]arenes have the ability to encapsulate biomimetic guests, offering interesting opportunities to explore their molecular recognition, very close to biological scenarios. In this study, p-sulfonatocalix[4]arene (C4 A) anions and hydrated alkali cations have been used for the in situ recognition of cationic 1,ω-diammonium-alkanes and 1,ω-amino-acids of variable lengths. NMR spectroscopy illustrates that these systems are stable in aqueous solution and the interaction process involves several binding states or stabilized conformations within the C4 A anion, depending of the nature of the guest. DOSY experiments showed that monomeric 1 : 1 host-guest species are present, while the cation does not influence their self-assembly in solution. The folded conformations observed in the solid-state X-ray single-crystal structures shed light on the constitutional adaptivity of flexible chains to environmental factors. Futhermore, a comprehensive screening of 30 single crystal structures helped to understand the in situ conformational fixation and accurate determination of the folded structures of the confined guest molecules, with a compression up to 40 % compared with their linear conformations.

“Calix[4]-box” cages promote the formation of amide bonds in water in the absence of coupling reagents

Calix[4]box cages promote template synthesis via accelerated amide bond formation upon encapsulation in water.

Pyrene-box capsules for adaptive encapsulation and structure determination of unstable or non-crystalline guest molecules

“Pyrene-box” cages easily crystallize from aqueous solutions and readily encapsulate compounds of biological interest.

New "pyrene box" cages for adaptive guest conformations

The possibility of controlling the compression extent and the coiling shape of the 1,12-diammoniumdodecane guest is shown by changing the dimensions of the internal space of the host guanidinium 1,3,5,8 pyrene-tetrasulfonate PTS(4-) crystalline capsules by using guanidinium (G(+)), amino-guanidinium (AG(+)), and diaminoguanidinium (A2G(+)) cations.

Adaptive binding and selection of compressed 1,ω-diammonium-alkanes via molecular encapsulation in water

Guest molecules confined inside hollow molecular assemblies and thus protected from their environment can show unexpected structural behavior or special reactivity compared to their behavior in a bulk, unprotected environment. A special case is the coiling behavior of variable-length alkane chains in rigid hydrogen-bonded molecular cages. It has been found before that coiling may occur in such circumstances, but no experimental evidence concerning the exact conformation of the chains has yet been presented. We reveal in this study the self-assembly of a molecular cage in water and the crystalline state from three distinct components in which linear 1,ω-diammonium-alkanes chains are confined with different degrees of compression. The exact coiling behavior is determined from atomic resolution X-ray diffraction showing crenel-like conformations in the compressed state. Chemical selection can be obtained from mixtures of alkane chains via the encapsulation of kinetically stable conformations observed during the encapsulation of pure components. Moreover, it was found that uncompressed and compressed chains can be competitively trapped inside the capsule. These findings may provide insight in areas to a better understanding of biological processes, such as the fatty acid metabolism.

Reply to A computational evaluation of the evidence for the synthesis of 1,3-dimethylcyclobutadiene in solid state and aqueous solution--beyond the experimental reality

Following earlier reports on the photochemical synthesis of 1,3-dimethylcyclobutadiene in a protective host matrix, theoretical calculations for the formation of that adduct have been recently performed by Rzepa. The author formulated criticisms based mainly on density functional theory calculations of (1)H NMR spectra. According to Rzepa the calculated spectra do not correspond with our measured spectra, which leads him to the conclusion that our interpretation is wrong, and that mainly cyclobutadiene has not been stabilized or even synthesized; we believe, however, that the initial model that Rzepa used for his calculations does not correspond to chemical reality or is at the very least a crude simplification of it, which implies that his calculations cannot match, in every point, our experimental spectra. Rzepa's simplified models might be 'reasonable' from the theoretical point of view; however, in the case of assessment in the solid state, the theoretical setup does not force the system to preserve the confined stabilizing space defined by the crystalline matrix for encapsulated hosts in the solid state. Inversely, in the case of solution modeling, the theoretical setup is too rigid to properly assess the complex equilibria occurring in solution and to accurately determine the NMR spectra of exchanging species in solution. The inconsistency between our experimental results and the results of the theoretical models proposed by Rzepa is such that his conclusions are considered to be too far from experimental reality. Accurate modeling taking in account "reasonable" experimental details would be a worthwhile endeavor.

A constrained disorder refinement: "Reinvestigation of "Single-crystal X-ray structure of 1,3-dimethylcyclobutadiene" by M. Shatruk and I. V. Alabugin"

Shatruk and Alabugin propose an alternative structural model for the observed electron density that we have attributed to the photochemical formation of 1,3-dimethylcyclobutadiene in a protective solid crystalline matrix. The main criticism from Shatruk and Alabugin concerns the modeling of the disorder in the calixarene cavity and in particular the neglect of a residual electron density close to the O1 atom. We published (Chem. Eur. J. 2011, 17, 10021) our opinion concerning this "ignored peak" in the Supporting Information of the paper. The current response to the Correspondence demonstrates that Shatruk and Alabugin have over-modeled our data by assigning a small electron density peak, which is hardly more than the density corresponding to a hydrogen atom, to an under-occupied oxygen site, using inappropriate refinement contraints.

Organic aspects. Oxygen-containing functions

In this chapter, most of the reported work deals with the photochemistry of carbonyl compounds; however, the photoreactions of other functions, such as the photo-Claisen rearrangement or the photocleavage of cyclic ethers, are also included. In the present volume, time coverage is 2010–2011, and only original research articles are quoted. In general, reviews or purely theoretical calculations are not systematically included. As usually, the material is organized according to established types of reactions (e.g., Norrish I/II, hydrogen abstraction, Paternò-Büchi, photoelimination, photo-Fries/photo-Claisen, etc.). After presenting the basic photochemical aspects, more specific findings are reported. They include synthetic applications, stereoselectivity, and biological or technological implications. Next, the attention is focused on photochemical reactions in anisotropic media, including (micro)heterogeneous or supramolecular systems, solid matrixes or fully organized crystals. Finally, mechanistic studies based on direct experimental evidence are highlighted, especially when transient absorption spectroscopy or related ultrafast detection are employed.