Molecules in crystals

Abstract

Hirshfeld surface analysis has developed from the serendipitous discovery of a novel partitioning of the crystal electron density into discrete molecular fragments, to a suite of computational tools used widely for the identification, analysis and discussion of intermolecular interactions in molecular crystals. The relationship between the Hirshfeld surface and very early ideas on the internal structure of crystals is outlined, and applications of Hirshfeld surface analysis are presented for three molecules of historical importance in the development of modern x-ray crystallography: hexamethylbenzene, hexamethylenetetramine and diketopiperazine.

Functionalization of Bambusurils by a Thiol–Ene Click Reaction and a Facile Method for the Preparation of Anion‐Free Bambus[6]urils

“…This arrangement is similart ot hat previously found in Cl@Me 12 BU [6], [2] and I@Pr 12 BU [6]. [3] The interactions between the included anion and the macrocycle can be analyzed through calculation of Hirshfeld surfaces (HSs) [14] with Crysta-lExplorer. [15] As shown in Figure 2, the HSs of the anions mapped with d norm show only four conspicuous red spots (only two of which are seen in the figure,t he others being related to these by inversion) corresponding to contacts shorter than the van der Waals separation with four methine hydrogen [4] and BU [6]studied in this work: allyl 8 BU[4] 1,R= CH 2 CH=CH 2 , m = 0, no TBAX; I@allyl 12 BU[6]·TBA 2, R = CH 2 ÀCH=CH 2 , m = 1, X À = I À ;Cl@allyl 12 BU[6]·TBA 3,R= CH 2 ÀCH=CH 2 , m = 1, X À = Cl À ;Br@allyl 12 BU[6]·TBA 4,R= CH 2 ÀCH=CH 2 , m = 1, X À = Br À ; Cl@Pr 12 BU[6]·TBA 5,R= (CH 2 ) 2 CH 3 , m = 1, X À = Cl À ;Br@Pr 12 BU[6]·TBA 6, R = (CH 2 ) 2 CH 3 , m = 1, X À = Br À ;( OAc) 8 BU[4] 8,R= (CH 2 ) 3 S(CH 2 ) 2 OAc, m = 0, no TBAX,I @(OAc) 12 BU[6]·TBA 9,R= (CH 2 ) 3 S(CH 2 ) 2 OAc, m = 1, X À = I À ;Cl@(OAc) 12 BU [6]·TBA 10,R= (CH 2 ) 3 S(CH 2 ) 2 OAc, m = 1, X À = Cl À ;B r@(OAc) 12 BU[6]·TBA 11,R= (CH 2 ) 3 S(CH 2 ) 2 OAc, m = 1, X À = Br À ;I@(CO 2 Me) 12 BU[6]·TBA 12; R = (CH 2 ) 3 S(CH 2 ) 2 CO 2 Me, m = 1, X À = I À ;Cl@(CO 2 Me) 12 BU[6]·TBA 13, R = (CH 2 ) 3 S(CH 2 ) 2 CO 2 Me, m = 1, X À = Cl À ;B r@(CO 2 Me) 12 atoms (the other methine hydrogen atoms are at distances larger than 3 anda re not involved in interactions stronger than dispersion).…”

“…However, when bambusuril 21,c ontaining 1.15 equivalents of TBACl, is titrated by TBAI, as low exchange is observed on the N-CH signal ( Figure S8, Supporting Information). This denotes ac ompetition between guests.B oth signals are assigned to i) bambusuril 21 binding chloride or athioether arm and ii)iodide, respectively.U sing the N-CH 2 signal, also in slow exchange but much closer to the coalescence, it has been deducedt hat iodide is ab etter guest than chloride to bambusuril 21,b ut only by af actor 4( the fit is in accordance with values in the range of [3][4][5][6][7][8][9][10][11][12][13][14][15]. We note that this is al esser ratio than that observedi nt he case of allyl 12 BU [6] 17,b earing much smaller arms.…”

Unusual hydrogen bond patterns contributing to supramolecular assembly: conformational study, Hirshfeld surface analysis and density functional calculations of a new steroid derivative

“…The main intermolecular interactions presented in I were analyzed using the Hirshfeld surface 48,49 and the corresponding two-dimensional fingerprint plots. 50,51 In previous work we used this methodology to understand the role of hydrogen bonds in the molecular conformation of a steroid derivative and acylthioureas.…”

Luminogens for Aggregation‐Induced Emission via Titanium‐Mediated Double Nucleophilic Addition to 2,5‐Dialkynylpyridines: Formation and Transformation of the Emitting Aggregates

“…The overall fluorescence intensity (vide infra) can therefore be seen as the net outcome of competing RIM and ACQ processes upon aggregation . In order to visualize the intermolecular interactions in the crystal, normalized contact distances (d norm ) were mapped onto the molecular Hirschfeld surface (Figure ) . As expected, the local minima of d norm are often associated with fluorine substituents involved in weak intermolecular H⋅⋅⋅F bonds (Figure ).…”