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C-H ⋯ O interactions and the adoption of 4 Å short-axis crystal structures by oxygenated aromatic compounds
Abstract
Oxygen atoms, pendant as substituents or occurring within the ring systems of planar aromatic molecules, have a pronounced tendency to direct crystallisation patterns of such compounds to the β-structure, characterised by a 4 Å short axis. They seem to perform this function by stabilising a critical number of hydrogen atoms, covalently bonded to carbon, through short and directionally specific intermolecular C–H O hydrogen bonds. Consequently, the number of ‘free’ hydrogen atoms which contribute to crystal stabilisation through non-β steering C H interactions is reduced. Both these factors result in the formation of C–H O stabilised two-dimensional entities such as sheets and ribbons. Such entities may be stacked at 4 Å translational separation to generate the entire structure. These concepts are illustrated for some methylenedioxy and alkoxy aromatic systems, quinones, and heterocycles. However, both intra- and inter-sheet C–H O interactions may sometimes be present and the unusual crystal structure of 7-acetoxycoumarin (5) shows how a significantly non-planar molecule may still adopt the β-structure if it is particularly well suited for the formation of C–H O bonds. Yet 4-acetoxycinnamic acid (6), the crystal structure of which was determined in this work and which has almost the same C:H:O ratio as (5), adopts a non-β structure because the number of oxygen atoms available for C–H O bond formation is greatly reduced. The crucial role of the number of such ‘available’ oxygen atoms and ‘H-bonded’ and ‘free’(C–)H atoms vis-à-vis the carbon content is exemplified by the β-steering behaviour of oxygen in some large fused-ring quinones and heterocycles. These trends may also be extended to nitrogen and sulphur heterocycles.
... Following the study by Taylor and Kennard, another group to focus on the subject of C-H. . .O bonds was that of Gautam Desiraju, who was then at the University of Hyderabad [63,64]. He became particularly interested in the occurrence of such bonds in intermolecular contacts in crystals and the possibilities of crystal engineering [65,66]. ...
Hydrogen bonds constitute a unique type of non-covalent interaction, with a critical role in biology. Until fairly recently, the canonical view held that these bonds occur between electronegative atoms, typically O and N, and that they are mostly electrostatic in nature. However, it is now understood that polarized C-H groups may also act as hydrogen bond donors in many systems, including biological macromolecules. First recognized from physical chemistry studies, C-H…X bonds were visualized with X-ray crystallography sixty years ago, although their true significance has only been recognized in the last few decades. This review traces the origins of the field and describes the occurrence and significance of the most important C-H…O bonds in proteins and nucleic acids.
... Figure 9 displays the close contacts for HH, CH, and HO interactions are found at 41.1, 25.6 and 25.2 percent, respectively. In this study the fingerprint plots indicated that the interactions in the molecular packing of curcumin are longer contact distances which are in agreement with Desiraju (2005) that the aromatic hydroxyl does not form a good CHO contact (Sarma & Desiraju, 1987). The crystal molecular packing of curcumin is linked by the weak interactions. ...
... They have been confirmed by ab-initio calculations [163,164] and molecular beam studies of van der Waals complexes [165,166]. Desiraju and Sarma showed that oxygen atoms on the periphery of a planar aromatic hydrocarbon exert a significant effect in steering from a Herringbone to a stack structure through the formation of weak C-H⋅⋅⋅⋅O hydrogen bonds [122,167]. Later, Desiraju and Kishan [168,169], suggested that this effect could be analyzed in terms of a reduction in the number of peripheral hydrogen atoms which tend to form Herringbone-directing C⋅⋅⋅⋅H contacts. They observed that several alkoxy-substituted phenylpropiolic acids presented a stack structure while the unsubstituted acid crystallizes in the Herringbone pattern. ...
Background
Molecular organic photochemistry is concerned with the description of physical and chemical processes generated upon the absorption of photons by organic molecules. Recently, it has become an important part of many areas of science: chemistry, biology, biochemistry, medicine, biophysics, material science, analytical chemistry, among others. Many synthetic chemists are using photochemical reactions in crystals to generate different types of organic compounds since this methodology represents a green chemistry approach.
Objective & Method
Chemical reactions in crystals are quite different from reactions in solution. The range of organic solid state reactions and the degree of control which could be achieved under these conditions are quite wider and subtle. Therefore, for a large number of molecular crystals, the photochemical outcome is not the expected product based on topochemical principles. To explain these experimental results, several physicochemical factors in crystal structure have been proposed such as defects, reaction cavity, dynamic preformation or photoinduced lattice instability and steric compression control. In addition, several crystal engineering strategies have been developed to bring molecules into adequate orientations with reactive groups in good proximity to synthesize complex molecules that in many cases are not available by conventional methods. Some strategies involve structural modifications like intramolecular substitution with different functional groups to modify intermolecular interactions. Other strategies involve chemical techniques such as mixed crystal formation, charge transfer complexes, ionic and organometallic interactions. Furthermore, some examples of the single crystal to single crystal transformations have also been developed showing an elegant method to achieve regio and stereoselectivity in a photochemical reaction.
Conclusion
The several examples given in this review paper have shown the wide scope of photochemical reactions in organic molecular crystals. There are several advantages of carrying photochemical reaction in the solid state. Production of materials unobtainable by the traditional solution phase reactions, improved specificity, reduction of impurities, and enhancement in the yields by the reduction of side reactions. These advantages and the multidisciplinary nature of solid-state photochemistry make this discipline quite likely to develop a lot in the future.
Developing broad spectrum white-light emitting materials was always considered a challenge in terms of color stability and reproducibility. Here, we report the design and optical properties of two materials bearing an ethynylbiphenyl group. The two materials exhibited excellent thermal stability and showed liquid crystal (LC) behavior. Promisingly, temperature-dependent photoluminescence results demonstrated distinct thermochromic behavior which switches the emission color from deep blue in the crystal phase to white in the LC phase. It was revealed that the overall effect of the intermolecular interactions forming a new excited state in the LC phase of the ethynylbiphenyl moiety is the main cause for the white-light emission. The emission behavior of the studied materials was tuned by thermal stimuli, and the emission color was regulated by changing the aggregate structure. These present findings open a door to develop more appealing single-molecule white-light emitters.
Single crystal X-ray crystallographic analysis of 7,8-dihydro-6H-[1,4]diazepino[1,2-a:4,3-a 0 ]diindole-14,15-dione (propano-bridged indigo [PBI]) reveals the presence of two homopolar intermolecular dihydrogen C-H···H-C interactions of distances 2.38 and 2.89 Å. Hirshfeld surface analysis indicates a significant contribution of C-H···H-C interactions (49%) to the total molecular contact surface. Theoretical analysis of the topology of electron density reveals the existence of two closed shell dihydrogen interactions per dimer. The values of the AIM charges on the H···H interacting atoms are similar (0.172). The calculated dihydrogen interaction energy is found to be significant (3.76 kcal mol −1). London dispersion forces are the dominant contributor to the homopolar C-H···H-C interactions.
Almost hundred years old concepts on hydrogen bonding are brought into light to be compared to the contemporary views and theories. The first findings were based on qualitative grounds and relied upon observations of simple experiments and very much on human imagination. It is a challenge to contrast the old and new views and to see if they could be verified or revised. Over the last decades there has been tremendous development of methods for structure elucidation and many hydrogen bonded molecular structures were determined and deposited in structural data bases. The structural aspect of hydrogen bond in the solid state is well defined. However, the knowledge of hydrogen bonded structures in the liquid state is still limited. Studies on hydrogen bond dynamics, which are in progress, with new experimental methods will help to better understand processes in solutions. In many systems the functioning of hydrogen bonding at atomic level has been still an enigma. In biological reactions the proton transfer is a key issue of acid-base enzyme catalysis and ribozymic function, transport reactions such as "water wires" functioning through the membrane protein channels and photosynthetic reaction centres. The paramount example for the unique role of the proton in specificity and rates is the storage life's genetic information: hydrogen bonds define the complementarities of G with C and A with T whereas the hydrogen transfer controls the genetic mutations. Ultra-fast time-resolved spectroscopies of hydrogen bonds and proton-transfer processes accompanied by very sophisticated theoretical frameworks such as multidimensional quantum dynamics and combined quantum mechanics/molecular mechanics are offering new insights into functioning of hydrogen bond.
Guanidinium and organosulfonate ions self-assemble into crystalline lattices described by robust two-dimensional hydrogen-bonded networks with the general formula [C(NH2)(3)]+RSO3-. These networks, which typically have quasihexagonal symmetry due to favourable hydrogen bonding between six guanidinium proton donors and six sulfonate electron lone pair accepters, assemble in the third dimension by stacking in a manner which maximizes van der Waals interactions between R groups. The steric requirements of the R groups dictate whether this assembly results in interdigitated bilayer stacking in which all the R groups are orientated to one side of a given sheet or interdigitated single layer stacking in which R groups are orientated to both sides of a given hydrogen-bonded sheet. The two-dimensional network tolerates very different steric requirements of the R groups due to the ability to form either of these stacking motifs and to the inherent flexibility of the hydrogen-bonded network about one-dimensional hydrogen-bonding 'hinges'. This flexibility allows the sheets to pucker in order to accommodate steric strain between R groups within the layers. We describe here the influence of substituents on the R groups whose steric and hydrogen bonding capacity influence the puckering of the two-dimensional guanidinium sulfonate network. In particular, we examine the X-ray crystal structures of the guanidinium salts of ferrocenesulfonate and methyl- and nitro-substituted benzenesulfonates. The retention of the hydrogen-bonding motif in spite of steric and hydrogen bonding interference by the R group substituents illustrates the robustness of the guanidinium sulfonate network. However, additional competing hydrogen bonding and sterics influence the crystal packing, and in the case of multiple substituents on the R groups, these factors may disrupt the guanidinium sulfonate network. Overall, this work demonstrates that the use of robust two-dimensional supramolecular modules can reduce the crystal engineering problem to the last remaining dimension, which can simplify the design of functional molecular materials.
The structure of 1-indanone has been studied by X-ray crystallography,
vibrational analysis and theoretical calculations. The crystal structure
(determined at 120 K) is stabilised by an extensive network of weak
hydrogen bonds of the C-HctdotO and C-Hctdotπ type. The molecular
structure has been optimised in the frame of the isolated molecule
approximation using ab initio RHF and DFT/B3LYP and BLYP methods with an
assortment of basis sets, i.e. 6-31G(d), 6-31G(d,p), 6-31++G(2d,p),
6-311G(2d,p) and 6-311++G(2d,p). This allows to compare the theoretical
molecular structure and that obtained through X-ray diffraction in such
a way that conclusions about the magnitude of the intermolecular
interactions can follow. Furthermore, a proposal of assignment of the
vibrational spectrum is given since the only early studies available so
far are non-conclusive and incomplete. This proposal is assessed by a
molecular force field which has been performed according to the SQM
methodology starting from the theoretical B3LYP/6-31G(d) and
BLYP/6-31G(d) force fields and using a set of experimental IR and Raman
spectra.
1078 C O non-bonded distances, retrieved from the Cambridge Structural Database for the series (Cl3 –nCn)C–H O where 0 n 3, are found to decrease smoothly with increasing donor group acidity.
The crystal structure of trans-4-(trifluoromethyl) cinnamic acid (1) has been determined in the triclinic space groupP. Differential scanning calorimetry showed that 1 undergoes a single fully reversible temperature induced phase transition at around 132/131 K (cooling/heating). Single crystal structure determinations, carried out at 200, 145 and 120 K, revealed that the volume of the unit cell quadruples as the crystal is cooled through the phase transition with Z′ increasing from 2 to 8. The structures are stabilised by the presence of O–HO hydrogen bonding and C–HO interactions. The results of DSC, single crystal and powder X-ray diffraction studies on 1 are reported.
The stereochemistry in the conversion of (E)-alpha,beta-unsaturated esters into the corresponding beta,gamma-unsaturated esters, and that in the conversion of aldehydes into the silyl enol ethers, were investigated. The Z/E ratios of the resulting beta, gamma-unsaturated esters and the silyl enol ethers varied according to the gamma-substituents of the (E)-alpha, beta-unsaturated esters and the alpha-substituents of the aldehydes, respectively. This phenomenon was rationalized by a "syn-effect", which may be attributed primarily to a sigma --> pi* interaction and/or 6pi-electron homoaromaticity.
4a-[2-(3-Indolyl)ethyl]-1,3,6,8-tetramethyl-4a,4b,8a,8b-tetrahydrocyclobuta[1,2-d:4,3-d']dipyrimidine-2,4,5,7(1H,3H,6H,8H)-tetrone, C22H25N5O4, M(r) = 423.52, triclinic, P1BAR, a = 8.116 (4), b = 15.888 (6), c = 16.226 (7) angstrom, alpha = 87.05 (3), beta = 86.28 (3), gamma = 87.79 (3)-degrees, V = 2083.8 (15) angstrom 3, Z = 4, D(m) = 1.34, D(x) = 1.35 g cm-3, lambda-(Mo K-alpha) = 0.71073 angstrom, mu = 0.9 cm-1, F(000) = 896, T = 298 K, R = 0.0872 for 3779 observed data [F(o) > 3-sigma-(F(o))] of 7155 unique data collected. Hydrogen bonding is observed between the indolyl N-H and the uracil C(4)-O as well as attractive interaction between the uracil C(5)-H and C(4)-O atoms. It is assumed that van der Waals interactions hold layers of hydrogen-bonded molecules that lie parallel to the (011).
The crystal chemistry and engineering of a new family of host–guest complexes is described. 4,4′-Dicyanobiphenyl (DCBP) forms a 1:1 complex, 1 with urea wherein the DCBP host forms large hexagonal channels via C–H· · ·N hydrogen bonds and the urea guest molecules are arranged in N–H· · ·O ribbons which fit completely within the host channels. By analogy, 4,4′-bipyridine N,N′-dioxide (BPNO) was selected as a molecule that can form a corresponding C-H· · ·O based channel. BPNO forms complexes with urea (2), thiourea (3) and water (4). Structures 2 and 3 provide some points of comparison with the structure of 1 but are not fully equivalent to it. In structure 4, the smaller guest water is able to fit neatly within the smaller hexagonal channel of BPNO and in this sense, the degree of structural predictability is satisfactory. To obtain another structure similar to that of 1, 4,4′-dinitrobiphenyl (DNBP) was identified as an alternative host compound. This choice was justified by the structure of its 1:1 complex, 5 with urea. In all cases, the guest molecules interact with each other via strong hydrogen bonds and form an essential template for the weak hydrogen bonded assembly of the host network structure but the latter is still of some significance. One finds consequently, in complexes 1-5, a constructive interplay of strong and weak hydrogen bonds.
The presence of a chloro substituent in a planar aromatic molecule tends to favour its crystallisation in the 4 Å short axis β-structure. This structure is stabilised by inter-stack Cl Cl interactions which are weakly attractive yet directional in nature, and by intra-stack dispersive C C interactions. The balance between intra- and inter-sheet interactions is revealed in the crystal structures of 6-chloro-3,4-methylenedioxycinnamic acid (2a), its 2:1 complex (1a) with 2,4-dichlorocinnamic acid, and its 1:1 complex (1b) with 3,4-dichlorocinnamic acid. The acid (2a) is dimorphic with both forms triclinic and with short axes ca. 4 Å; the structure of one form has been determined by X-ray diffraction methods. Solid-state u.v. irradiation of the complexes (1a and b) affords mixtures of mirror and pseudomirror symmetrical cyclobutanes; the formation of these products is consistent only with an ordered sheet-disordered stack structure, derived from the completely ordered structure of (2a), for these complexes. The structures of (1a and b) have been deduced thus on the basis of topochemical, kinetic, and crystallographic evidence, and provide important corroboration of inter-stack stabilisation as a prerequisite for β-structure adoption. Mixed crystalline complexes such as (1a) permit a comparative kinetic study of topochemical reactions, a procedure normally difficult in solid-state chemistry.
X-ray study of 2-cyano-(2E)-pentadien-2,4-oic acid (1) and its ethyl ester (2) showed that the molecules of1 and2 in the crystalline phase form stacks by translating along the shortest crystallographic axis. The nature of the intermolecular
interactions favoring the formation of such β-structures was analyzed within the framework of the Bader topological theory.
Possible routes of topochemical reactions of compounds1 and2 are considered.
The structure of barbituric acid (1,4)-dioxane solvate has been determined by X-ray diffraction at 100 K. The compound crystallizes in the triclinic space group P
$$\overline 1$$
, with cell dimensions of a = 6.7770(16) Å, b = 9.583(2) Å, c = 9.697(2) Å, a = 85.868(5)°, ß = 82.566(5)°, ? = 70.675(5)°, V = 589.0(2) Å3, and Z = 1. In the solid state, one asymmetric unit consists of C4H4N2O3 · 3/2(C4H8O2), each barbituric acid molecule being involved in two hydrogen bonds. The two nitrogen atoms of the acid act as hydrogen donors to two oxygen atoms, each from a different molecule of (1,4)-dioxane, which serve as the acceptors. Not all of the hydrogen-bonding capacity of the chemical moieties is used, and the principal feature of the supramolecular structure is a sawtooth ribbon composed of alternating barbituric acid and (1,4)-dioxane molecules, connected through hydrogen bonds and C
$$---$$
H ··· O interactions.
A new simple model of porphyrin ring current effect was proposed based on a line current approximation. It can reproduce the porphyrin-induced shifts for several Sn(IV)(tpp) and Sn(IV)(oep) dicarboxylate complexes quite satisfactorily. Perpendicular arrangement of the aromatic rings in the diaromatic-carboxylate complexes of Sn(IV)(tpp) and Sn(IV)(oep) was clarified with this porphyrin ring current effect model. There are two structures, exo and endo, in solution in dinaphthalene-1- and 2- carboxylate complexes of Sn(IV)(tpp) and Sn(IV)(oep). The exo conformer is in dynamic equilibrium with the endo form in solution. Thermodynamic data of these conformational equilibria are given.
The crystal and molecular structures of mono- and di-quaternary salts ofa-isosparteine have been determined by X-ray analysis. Both N(1)-methyl-a-isosparteine iodide and 1,16-endomethylenea-isosparteine diiodide crystallize in the space groupC2221. The N-methylation does not change the configuration of parenttrans-cisoid-trans-a-isosparteine. The crystallographic twofold symmetry axis coincides with molecular symmetry of the diquaternary cation. Thetrans-cisoid-trans-1,16-endomethylene-a-isosparteine diiodide and its stereoisomer,trans-cisoid-cis-1,16-endo-methylenesparteine diiodide, form isomorphous crystals. Short cation-anion contacts in crystal structures suggest existence of C-H-?-I- hydrogen bonds in the solid state. In the N(1)-methyl-a-isosparteine iodide crystal, 7C?I- distances in the range 3.85-4.15 Å have been found, while 17 distances of this type have been observed in 1,16-endomethylene-a-isosparteine diiodide.
The crystal structures of two quaternary salts,trans,trans- andcis,trans-N,N'-dimethylthiobinupharidine diiodide, whose stereochemistries have been previously characterized by13C NMR spectroscopy, have now been determined by X-ray analysis. Differences in the nitrogen atom configuration of the AB quinolizidine fragment result in different conformations of the central part of the cations, the spiro tetrahydrothiophene ring, and specific selectivity toward solvent molecules. Thetrans,trans isomer crystals obtained from an acetone/methanol/water solution contained two water and one acetone molecule, while thecis,trans cocrystallized from the same solvent mixture with methanol and two water molecules. Very weak hydrogen bonds of the C-H?I- type determine interactions between the quaternary cations and the I- anions in the solid state. Water molecules form a dimer, and this dimer is hydrogen bonded to the I- anions. Organic solvent molecules included in crystals show different type of interactions with surrounding molecules: (i) the acetone molecule is trapped in the cavity of thetrans,trans cation by very weak C-H?O interactions; (ii) methanol is hydrogen bonded to a water molecule while with thecis,trans cation and I- anion interacts only by van der Waals forces.
An analysis of 105 and 622 C–H O bond geometries retrieved from 69 alkyne and 131 alkene structures in the Cambridge Structural Database shows that more acidic C–H groups tend to form stronger bonds but that even weak C–H O bonds have pronounced linearity.
The crystal structure of a supramolecular system consisting of indole-2,3-dione 1-(2-oxopropyl)-3-ethylene ketal (I) and indole-2,3-dione 1-(2-oxopropyl)-3-ethylene ketal thiosemicarbazone (II) molecules that are linked together by hydrogen bonds is determined using X-ray diffraction. The crystal is monoclinic, and
the unit cell parameters are as follows: a = 12.8360(3) Å, b = 10.7330(3) Å, c = 19.4610(3) Å, β = 99.566(1), space group P21/c, and Z = 4 (C27H29N5O7S). In molecules I and II, the indole-2,3-dione 3-ethylene ketal fragments have a virtually identical structure. The pyrrole and dioxolane fragments
are spiro-linked through the carbon atom with a dihedral angle close to 90. The adjacent pyrrole and benzene rings are coplanar
to within 4.4. In molecule II, the oxygen atom of the dioxolane fragment and the terminal nitrogen atom of the thiosemicarbazide fragment are involved
in the N-HO intramolecular hydrogen bond [3.294(2) Å]. The key role in the formation of the crystal structure is played by
intermolecular hydrogen bonds of the N-H⋯dO, C-H⋯O, C-H⋯N, and N-H⋯S types.
The coumarin and benzoxazole ring systems in the title compound, C16H9NO3, are planar. The angle between them is 5.24 (8)°. The crystal structure is stabilized by intermolecular C—H⋯O and C—H⋯N attractive interactions.
A 2-D croconato bridged complex of Cu(II), [{Cu(C5O5)(bpee)}·0.5H2O]n
(1)
[bpee, trans-1,2-bis(4-pyridyl)ethylene] has been synthesized by in situ hydrothermal reaction and characterized by X-ray diffraction analysis, variable temperature magnetic susceptibility measurement and EPR study. The structure determination reveals that the adjacent 2-D sheets are extended to 3-D supramolecular architecture through π–π and trifurcated C–HO interactions, which inhibit the oxygen atom of croconate from forming the usual bridging mode.
3,5-Dimethylidene-1,2,2,6,6-pentamethyl-4-oxopiperidine was shown by the kinetic method to be less reactive than 3,5-dimethylidene-2,2,6,6-tetramethyl-4-oxopiperidin-1-oxyl
in the nucleophilic addition of secondary amines and Diels—Alder dimerization. According to the quantum-chemical AM1 calculations,
this is due to the difference in the structures of the activated complexes (in the reactions with amines) and to the “press”
effect created by theN-methyl group that impedes the necessary cycle flattening (in the Diels—Alder reaction).
Nitrobenzene derivatives pack in two main motifs: stacks [see Andre, Foces-Foces, Cane & Martinez-Ripoll (1997). Acta Cryst. B53, 984-995] and 'pseudo-herringbone' together account for some 61.5% of the structures classified as BCLASS = 15 by the Cambridge Structural Database. Several geometrical parameters allow the classification of the 'pseudo-herringbone' category into four main motifs. Weak interactions appear to play an important role in this packing mode.
The structural information collected by X-ray (or neutron) diffraction studies of metallic, ionic, molecular and macromolecular crystals has increased beyond any previously imagined limit. Data are presently compiled in computer-based crystal structure databases. Making particular reference to molecular crystals, it is shown that the information collected may possess a great heuristic value, that is a great potential for guiding the discovery of new chemical facts or the formulation of new chemical theories, provided systematic methods of database analysis and crystal structure interpretation are made available. It is suggested that such methods consist of systematic correlations of structural data pertaining to single molecular fragments as found in many different crystal structures and can be collectively called (crystal) structure correlation methods (SCMs). SCMs are based on the search for and recognition of correlations among the geometrical descriptors of the fragment (structural correlations) and other physical properties of the fragment itself or of the molecule the fragment belongs to (structure-properties correlations).
SCMs are systematically reviewed from the point of view of their chemical applications. Chemical themes so far investigated include chemical bonding, molecular interactions, reaction pathways and transition states, conformational interconversions, and reversible or irreversible transformations occurring in the crystalline state. Methodological aspects of SCMs are treated by means of a formalization of the structural correlation concept based on simple analytical mechanics considerations. The meaning of structural correlations, is dicussed in terms of chemical bond theories and potential energy hypersurfaces (principle of structure correlation) and their degree of applicability to chemical kinetics is analyzed in the frame of the Marcus rate-equilibrium theory. In the final section a number of selected SCM applications are discussed in detail, paying particular attention to the chemical relevance of the results obtained.
The synthesis and characterization of a nickel-(0) complex of 5,6,11,12,17,18-hexadehydro-1,4,7,10,13, 16-hexamethoxytribenzo[a,e,i]cyclododecene (2) is described. The crystal structure revealed the presence of intermolecular agostic C-H---Ni and intermolecular C-H---O interactions.
Treatment of a dimethylnaphthalene (DMN) isomer mixture with 2,4,7-trinitrofluorenone (TNF) resulted in the predominant formation of 2,6-DMN-TNF (1:1) complex (3) accompanied by a small amount of 2,7-DMN-TNF (1:1) (4). X-ray structural analyses of these charge-transfer crystals showed that coplanar "ribbon"-like networks are formed by C-H...0 hydrogen bonding of TNF and that 3 is thermodynamically more stable than 4 due to the larger interactions through C-H...0 contacts.
Crystal structures of planar oxygenated aromatic compounds are determined by an interplay of C⋯H interactions which steer to herringbone structures, characterized by adjacent inclined molecules, and C-H⋯O interactions, which being lateral, steer to stacked-sheet structures with short axes of 3.8-4.2 Å. The number of hydrogen and oxygen atoms in the molecule seems to determine which of these two preferences is exercised, a smaller number of hydrogens and a greater number of oxygens leading to the stack structure. Accordingly, if an alkoxycinnamic acid has a stack structure, the corresponding phenylpropiolic acid will, in all likelihood, have the same structure. This is exemplified by the pair of nearly isomorphous compounds 3,4-(methylenedioxy)cinnamic acid and [3,4-(methylenedioxy)phenyl]propiolic acid. The structure of the latter is triclinic, P1, Z = 2, a = 3.807 (2) Å, b = 10.297 (2) Å, c = 10.995 (3) Å, α = 84.07 (2)°, β = 96.46 (3)°, γ = 98.13 (3)°. Even if a cinnamic acid does not have a 4-Å structure, the removal of two hydrogen atoms to give the propiolic acid could result in the stack structure for the latter. Accordingly, (3,4-dimethoxyphenyl)propiolic acid is triclinic, P1, Z = 2, a = 3.891 (1) Å, b = 11.361 (3) Å, c = 12.089 (4) Å, α = 112.50 (2)°, β = 92.53 (3)°, γ = 96.12 (3)°. A large number of oxygen atoms acting as C-H⋯O bond acceptors can lead to a stack structure for significantly nonplanar molecules. An example is (3,4,5-trimethoxyphenyl)propiolic acid which is monoclinic, P21/n, Z = 4, a = 20.806 (6) Å, b = 14.159 (3) Å, c = 3.942 (5) Å, β = 94.79 (7)°. In contrast, (4-methoxyphenyl)propiolic acid, which does not have the critical number of oxygen atoms, does not have a 4-Å stack structure being triclinic, P1, Z = 2, with a = 10.767 (3) Å, b = 8.494 (3) Å, c = 7.499 (2) Å, α = 99.01 (2)°, β = 125.62 (2)°, γ = 112.42 (2)°. The crystal structures of these and other phenylpropiolic acids are closely paralleled by their solid-state thermal reactivities. Acids with a 4-Å stack structure participate in an intermolecular Diels-Alder reaction to give derivatives of 1-phenylnaphthalene-2,3-dicarboxylic acid anhydride, while those with short axes greater than 4.2 Å are unreactive. The products of these reactions may be rationalized by assuming that adjacent double and triple bonds, within a threshold distance of ca. 4.5 Å in the crystal, are potentially reactive. In general, any crystalline phenylpropiolic acid may be expected to form Diels-Alder products upon heating if the triple bonds are sufficiently close for topochemical reaction. The formation of these lignan derivatives from acetylenic precursors under mild conditions could be of biosynthetic significance.
The intermolecular contacts between chalcogen atoms and cyano lone pairs were found to stabilize the crystalline state by electrostatic interaction. This interaction is one of the sources of the directionality in crystal packing of organic molecules and causes the formation of various types of inclusion lattices in the charge-transfer (CT) crystals of 1-3. By using highly selective formation of CT crystals with substituted aromatic hydrocarbons, particular isomers such as p-xylene or 2,6-dimethylnaphthalene (2,6-DMN) could be separated from the corresponding isomer mixtures. Lattice-related interaction plays a more significant role than molecular orbital interaction in the observed selectivity for para-disubstituted benzenes. However, the latter interaction is important for the recognition of 2,6-DMN from the 2,7 isomer.
Crystal structures of N,N-dipicrylamine and its ionic complexes with N,N-di(2-pyridyl)amine, 1,8-bis(N,N-dimethylamino)naphthalene, 2,3-di(2-pyridyl)-6,7-dimethylquinoxaline, and 4-(dimethylamino)pyridine have been determined by single-crystal X-ray diffraction and infrared and solid-state NMR spectroscopies. in addition to intra- and intermolecular hydrogen bonds, all structures are stabilized by intra- and intermolecular N...O contacts resulting from electrostatic interactions between partially positively charged nitrogens and partially negatively charged oxygens in the nitro groups of symmetry-related molecules. Resonance structures of the nitro groups are used to rationalize these interactions. We consider the configuration of the oxygen atoms around the central nitrogen. Mesomerism of ionic structures and different types of hydrogen bonds are the main factors governing the 3D arrangement of dipicrylamine and its complexes. Principal structural features of the cations are discussed.
There is a very strong tendency for carboxylic acids to form centrosymmetric, hydrogen-bonded dimers in the solid state, and recent studies have attempted to use this dimeric building block in the crystal engineering of molecular solids. However, hydrogen-bonded molecules of (4-chlorophenyl)propiolic acid, p-ClCâHâC{triple bond}CCOâH, do not pack in the crystal according to the predicted dimer motif but, in an unusual manner for this category of molecule, in the catemer arrangement. Crystals of this compound are triclinic, space group P{anti 1}, Z = 2, a = 6.120 (4) â«, b = 17.323 (13) â«, c = 3.944 (2) â«, α = 90.47 (6)°, β = 92.70 (5)°, γ = 102.26 (6)°, R = 0.065, R{sub w} = 0.071, with 831 nonzero reflections. The catemer arrangement observed in this case might have been anticipated for some other carboxylic acids, but it is unexpected here and could arise due to the inability of the molecules to form C-H{hor ellipsis}O hydrogen bonds.
This review considers the correlation between the reactivity of nitroxyl radicals (piperidine, pyrroline, pyrrolidine, imidazoline, dihydroquinoline, tetrahydroquinoline, diphenyl nitroxide, etc.) and their chemical structure in terms of the rate constants of reactions between these radicals and hydrazobenzene. 4,4′-Di(tert-butyl)diphenyl nitroxyl has the highest reactivity, and the nitroxyl radical of benzoindolopyrrolidine is the least reactive (the difference is a factor of ∼104). The effects of the metal atom in stable organometallic nitroxyl radicals and of the halogen atom in halogenated nitroxyl radicals on the reactivity of the nitroxyl center are considered. Data on the effect of the nitroxyl center on the reactivity of functional groups in the piperidine nitroxyl radical are generalized. Nitroxyl radicals with an activated double bond are shown by quantum chemical calculations to form cyclic transition complexes with amines, involving both the paramagnetic center and a double bond. This explains why the activated double bond in nitroxyl radicals is more reactive in nucleophilic additions of amines than the same bond in their diamagnetic analogues. The rate constants of nitroxyl reduction with hydrazobenzene and of nitroxyl oxidation with tetranitromethane are related to the σESR constant derived from isotropic hyperfine coupling constants HFC(aN), and their correlation with Hammett constants is demonstrated. The role of solvents in the reduction and oxidation of the nitroxyl radicals is considered. The influence of hydroxyl radical-polar solvent complexes and hydroxylamine-polar solvent H complexes on the course of reactions is considered for hydrogen atom transfer in systems of a sterically hindered nitroxyl radical and hydroxylamine.
Crystal packing calculations have been carried out on a number of commercially important organic pigments in an attempt to determine the important interactions and structural features holding pigment molecules together in selected arrangements in the solid state. The high performance pigments were found to be those with the most efficient packing and with the highest lattice energies. The most important intermolecular interactions identified were π–π stacking forces, traditional hydrogen bonds and weak hydrogen bonds.
The high potential of self-assembly processes of molecular building blocks is reflected in the vast variety of different functional nanostructures reported in the literature. The constituting units must fulfill several requirements like synthetic accessibility, presence of functional groups for appropriate intermolecular interactions and depending on the type of self-assembly processsignificant chemical and thermal stability. It is shown that oligopyridines are versatile building blocks for two- and three-dimensional (2D and 3D) self-assembly. They can be employed for building up different architectures like gridlike metal complexes in solution. By the appropriate tailoring of the heterocycles, further metal coordinating and/or hydrogen bonding capabilities to the heteroaromatic molecules can be added. Thus, the above-mentioned architectures can be extended in one-step processes to larger entities, or in a hierarchical fashion to infinite assemblies in the solid state, respectively. Besides the organizational properties of small molecules in solution, 2D assemblies on surfaces offer certain advantages over 3D arrays. By precise tailoring of the molecular structures, the intermolecular interactions can be fine-tuned expressed by a large variety of resulting 2D patterns. Oligopyridines prove to be ideal candidates for 2D assemblies on graphite and metal sufaces, respectively, expressing highly ordered structures. A slight structural variation in the periphery of the molecules leads to strongly changed 2D packing motifs based on weak hydrogen bonding interactions. Such 2D assemblies can be exploited for building up host-guest networks which are attractive candidates for manipulation experiments on the single-molecule level. Thus, "erasing" and "writing" processes by the scanning tunneling microscopy (STM) tip at the liquid/solid interface are shown. The 2D networks are also employed for performing coordination chemistry experiments at surfaces.
C5H6N2O3, Mr = 142.11, monoclinic, P2(1)/n, a = 3.862 (1), b = 16.329 (2), c = 10.088 (1) A, beta = 98.77 (2) degrees, V = 628.7 (2) A3, Z = 4, Dx = 1.50 g cm-3, lambda(Mo K alpha) = 0.71069 A, mu = 1.18 cm-1, F(000) = 296, T = 296 K, R = 0.035 for 1124 independent reflections with I greater than 3 sigma(I). The structure is a hydantoin derivative with a methoxymethylene group substituted at the 5-position. Excluding the H atoms, the molecule is planar to within 0.032 A. All of the N and O atoms are involved in an intermolecular hydrogen-bonding network via N--H...O and C--H...O interactions. The packing arrangement is a linear ribbon motif with the ribbons stacked to form the short a axis.
The crystal structures (determined from single-crystal X-ray diffraction studies) and hydrogen-bond patterns of three crystalline 1,2-dialkyl-3-hydroxy-4-pyridones and their 1:1 formic acid solvates are elucidated. The primary hydrogen-bond connectivities observed are explained by a model that predicts that the best donor bonds to the best acceptor. Relative hydrogen-bond donating and accepting abilities of the functional groups observed in these compounds are evaluated by a combination of pKas, energy calculations, resonance arguments, and crystallographic evidence. The primary (O--H ... O) hydrogen-bond patterns are described by graph set notation, and brief explanations of the graph set assignments are also included. A total of 17 secondary (C--H ... O) hydrogen bonds are also observed in these six structures. Correlations are drawn between the observed C--H ... O hydrogen bonds and the molecular packing. The possible role of these secondary hydrogen bonds in influencing molecular packing is discussed.
A novel pi-conjugated organic compound, 1-phenyl-2,5-bis[5-(tricyanoethenyl)-2-thienyl]pyrrole, which bears two powerful electron-withdrawing tricyanoethenyl substitutents, readily yielded gold-like metal-lustrous inclusion crystals with a series of aromatic guest molecules such as toluene, p-xylene, anisole, dimethoxybenzenes and indene. All the inclusion compounds have a common stoichiometric ratio (host/guest) of 2 : 1. X-Ray structural analyses demonstrate that the structural feature for toluene included crystal is similar to those containing p-xylene, anisole, dimethoxybenzenes and indene.
Hydrogen bonds, X–H⋯A, formed by weak donors (X = C) and acceptors (A =
π system) were generally dismissed as being of little consequence before and even during the 1970s. This situation changed in the early 1980s, and during the two following decades they were implicated as being significant in many small molecule crystal structures, and also in solution. Today, knowledge gained about these interactions is being used to understand the structure of biomolecules with implications for structure based drug design.
Since an activated C-H group may take part in hydrogen bonding, the angles involved in the "short" interaction have been calculated for various compounds of known crystal structure containing activated C-H groups and "short" C ⋯ O distances. In these compounds, the conditions for hydrogen bonding are satisfied by the methylidyne group and probably by the methylene and the methyl group. This type of hydrogen bond occurs rather widely and may be of importance in the structures of biological molecules.
The photo-dimerisation of the two crystal modifications of trans-cinnamic acid has been re-investigated and clarified. The stable (α) form gives α-truxillic acid only; the metastable (β) form yields pure β-truxinic acid at temperatures where the β → α phase transformation of the monomer is sufficiently slow; at higher temperatures a-truxillic acid is also formed from the α-modification which arises via the β → α phase change. The dimers of o-hydroxycinnamic acid and of its methyl, n- and isopropyl, and allyl ethers have been related to α-truxillic acid. The ethoxy-acid occurs in three modifications: one form (γ) is light-stable; the second (α) gives an α-truxillic acid derivative; the third (least stable) β-form gives mainly a β-truxinic acid if irradiation is conducted at temperatures at which the phase transformation β → α is slow. The 5-bromo-2-hydroxy-, 5-bromo-2-methoxy-, and 5-chloro-2-methoxy-derivatives of cinnamic acid dimerise to derivatives of β-truxinic acid. m- and p-Hydroxy-trans-cinnamic acids dimerise to dihydroxy-α-truxillic acids while their methyl ethers are light-stable. The photochemical behaviour of o-, m-, and p-nitro-trans-cinnamic acids has been re-investigated; o-, (β) m-, and (β) p-nitrocinnamic acids give dimers which have been identified as truxinic rather than the α-truxillic acids suggested by Tanasescu and Hodosan. Light-stable modifications of m- and p-nitrocinnamic acids are described. o -, (β) m-, p-Chloro-, 2,4-, 3,4-, 2,6-dichloro-, o-, (β) m-, and p-bromotrans-ciimamic acids give photo-dimers all of which are derivatives of β-truxinic acid. m-Chloro- and m-bromo-cinnamic acids also occur in lightstable (γ)modifications. o-Methylcinnamic acid is light-stable while the p-isomer dimerises to the corresponding α-truxillic acid.
The presence of a chloro substituent in a planar aromatic molecule tends to favour its crystallisation in the 4 Å short axis β-structure. This structure is stabilised by inter-stack Cl Cl interactions which are weakly attractive yet directional in nature, and by intra-stack dispersive C C interactions. The balance between intra- and inter-sheet interactions is revealed in the crystal structures of 6-chloro-3,4-methylenedioxycinnamic acid (2a), its 2:1 complex (1a) with 2,4-dichlorocinnamic acid, and its 1:1 complex (1b) with 3,4-dichlorocinnamic acid. The acid (2a) is dimorphic with both forms triclinic and with short axes ca. 4 Å; the structure of one form has been determined by X-ray diffraction methods. Solid-state u.v. irradiation of the complexes (1a and b) affords mixtures of mirror and pseudomirror symmetrical cyclobutanes; the formation of these products is consistent only with an ordered sheet-disordered stack structure, derived from the completely ordered structure of (2a), for these complexes. The structures of (1a and b) have been deduced thus on the basis of topochemical, kinetic, and crystallographic evidence, and provide important corroboration of inter-stack stabilisation as a prerequisite for β-structure adoption. Mixed crystalline complexes such as (1a) permit a comparative kinetic study of topochemical reactions, a procedure normally difficult in solid-state chemistry.
It has been shown that the presence of a methylenedioxy substituent in a planer aromatic molecule tends to favour its crystallisation in highly overlapped structures. Thus, in a series of methylenedioxycinnamic acid derivatives, there is a preference for the β-structure over the α-and γ-forms. It is suggested that this substituent is a good steering device towards the β-form since, in this form, the oxygen atoms of the substituent can participate in stabilising non-bonded interactions involving p electrons and further, the compactness of the substituent allows the molecules to crystallise with a 4 Å repeat. The crystal-structure determination of 3,4-methylenedioxycinnamic acid, (1), illustrates these concepts. The crystals of (1) are triclinic, the space group is P, Z= 2, a= 3.804(3),b= 10.502(5), c= 11.112(4)Å, α= 77.84(4), β= 84.26(9),γ= 80.17(5)°. The structure was solved, not without difficulty, and has been refined to an R-factor of 0.067 on 742 non-zero reflections. Molecules related by translation along [100] are within photoreactive distance and the β-structure leads to the formation of a mirror-symmetry cyclobutane on solid-state irradiation. If the oxygenated substituents are bulky, crystallisation in the β-form is not easy. The crystal structure of 3,4-dimethoxycinnamic acid, (2), demonstrates an alternative packing. Acid (2) is triclinic, the space group is P, Z= 4, a= 8.448(3), b= 15.072(8),c= 8.437(6)Å, α= 99.44(5),β= 94.71(5),γ= 101.59(4)°. The structure solution was non-trivial and only possible with the use of the program YZARC 80. The structure has been refined to an R-factor of 0.107 on 725 non-zero reflections. Pairs of pseudo-centrosymmetric molecules in the asymmetric unit are hydrogen bonded to form cyclic dimers. Nearest neighbours are related by a pseudo-translation (γ) and centres of inversion (α). Only half the molecules in the structure are potentially reactive; for each these there are two inversion-related near neighbours. However, only one of these is within photoreactive distance to give the topochemical inversion-symmetry cyclobutane on irradiation.