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Molecular and crystal structure of 2-cyano-(2 E )-pentadien-2,4-oic acid and ethyl-2-cyano-(2 E )-pentadien-2,4-oate
Abstract
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 derivatives of 2-cyanoacrylic acid are of particular interest owing to their potential biological activity and great synthetic opportunities, especially in the field of heterocyclic and polymer chemistry [1][2][3]. ...
(E)-2-Сyano-5-phenylpent-2-en-4-ynoic acid esters and N-substituted amides were synthesized by the Knoevenagel condensation of 3-phenylpropiolaldehyde with the corresponding cyanoacetates or cyanoacetamides in the presence of basic alumina used as a catalyst. The IR and Raman spectra of the resulting compounds show strong absorption bands in the range of 1565–1580 cm–1 which are attributed to the vibrations of the C=C bond in the enyl moiety.
The central 2-cyanocarboxyaminoprop-2-enylic fragment of the title compound, 2-cyano-5,N-diphenylpent-2-en-4-ynamide, C18H12N2O, is planar. The phenyl rings are rotated with respect to this plane. Molecules are linked by N-H ... O hydrogen bonds and form stacks by translation along the crystallographic c axis.
Abstract The structure of 5-dimethylpyrazolo[1,5-a]pyrimidin-7(4H)-one 1 has been determined by X-ray crystallography. The compound 1 crystallizes in the space group P−1 with two molecules in the asymmetric unit solvated with one molecule of the acetic acid The unit cell parameters are a = 8.796(1) Å, b = 10.531(1) Å, c = 10.680(1) Å, α = 96.901(2)º, β = 98.135(2)º, γ = 107.248(2)º. In the crystal molecules A and B are linked into R
22(9) hydrogen bonded rings and these rings form chains parallel to [101] Overall, the supramolecular structure 1 consists of two hydrogen bonded and two π–π stacking dimers. An energetic interplay between these dimers has been studied
using B3LYP DFT calculations. In addition π–π interactions are analyzed using the Bader’s atoms in molecules’ (AIM) theory.
Graphical Abstract The structure of 5-dimethylpyrazolo[1,5-a]pyrimidin-7(4H)-one 1 has been determined by X-ray crystallography. The compound 1 crystallizes in the space group P−1 with two molecules in the asymmetric unit solvated with one molecule of the acetic acid The unit cell parameters are a = 8.796(1) Å, b = 10.531(1) Å, c = 10.680(1) Å, α = 96.901(2)º, β = 98.135(2)º, γ = 107.248(2)º. In the crystal molecules A and B are linked into R
22(9) hydrogen bonded rings and these rings form chains parallel to [101] Overall, the supramolecular structure 1 consists of two hydrogen bonded and two π–π stacking dimers. An energetic interplay between these dimers has been studied
using B3LYP DFT calculations. In addition π–π interactions are analyzed using the Bader’s atoms in molecules’ (AIM) theory.
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).
The molecular geometry of complex of cytosine with 14 water molecules was calculated within the density functional theory using the B3LYP functional. The standard 6-31G(d) basis set has been employed. It was found that the interaction with water molecules forming a locked chain around cytosine results in a significant change of its gas-phase geometry. The structure of the hydrated nucleobase cannot be described by canonical chemical formula, and it is best approximated as a superposition of the oxoamino and zwitterionic hydroxoimino resonance structures. The unique features of the interaction of water with cytosine are also revealed: the formation of three hydrogen bonds with the participation of the oxygen atom of the carbonyl group and the presence of weak CH···O hydrogen bonds between the water molecules and the hydrophobic part of cytosine.
Although the two polymorphic modifications, (I) and (II), of the title compound, C(13)H(10)N(2)O, crystallize in the same space group (P2(1)/c), their asymmetric units have Z' values of 1 and 2, respectively. These are conformational polymorphs, since the molecules in phases (I) and (II) adopt different rotations of the phenyl ring with respect the central 2-cyanocarboxyaminoprop-2-enyl fragment. Calculations of crystal packing using Cerius(2) [Molecular Simulations (1999). 9685 Scranton Road, San Diego, CA 92121, USA] have shown that (I) is more stable than (II), by 1.3 kcal mol(-1) for the crystallographically determined structures and by 1.56 kcal mol(-1) for the optimized structures (1 kcal mol(-1) = 4.184 kJ mol(-1)). This difference is mainly attributed to the different strengths of the hydrogen bonding in the two forms.
The title compound, C(36)H(35)N(5)O(7)S, is found to exist in a non-spirocyclic (ring-opened) form in the crystal, although equilibrium of ring-opened and ring-closed forms (or so-called ring-chain isomerization) is possible in solution. The 4-oxocyclohexa-2,5-diene ring has a flattened sofa conformation. The N.C intramolecular separation of the atoms which would be directly bonded in a ring-closed form is quite short [2.813 (5) A]. Topological analysis of charge density based on density-functional-theory calculations was used for consideration of shortened intramolecular contacts and indicates a strong attractive bonding interaction between these N and C atoms in the crystal structure.
A description of the ab initio quantum chemistry package GAMESS is presented. Chemical systems containing atoms through radon can be treated with wave functions ranging from the simplest closed-shell case up to a general MCSCF case, permitting calculations at the necessary level of sophistication. Emphasis is given to novel features of the program. The parallelization strategy used in the RHF, ROHF, UHF, and GVB sections of the program is described, and detailed speecup results are given. Parallel calculations can be run on ordinary workstations as well as dedicated parallel machines. © John Wiley & Sons, Inc.
π-Type hydrogen-bonded systems consisting of acetylene, ethylene, cyclopropane or benzene as proton acceptors and hydrogen fluoride as proton donor have been studied. The calculated π-type hydrogen-bond stabilization energies for C2H2·HF, C2H4·HF, C3H6·HF and C6H6·HF are 4.54, 4.71, 4.64 and 4.81 kcal mol−1, respectively, from MP2/6-31G∗∗/6-31G∗ calculations. The detailed bond connecting descriptions, which are taken from the molecular graphs, have been made on the basis of topological analysis of the electronic density distribution. The stabilization of C2H4·HF and C3H6·HF π-type hydrogen-bonded systems at the 3-21G level are discussed.
I-Adamantylmethyl 2-cyanoacrylate (1) was prepared by the reaction of 2-cyanoacryloyl chloride with 1-adamantylmethanol . 1,10-Decanediol bis-2-cyanoacrylate (2) was synthesized by transesterification of methyl 2-cyanoacrylate with 1,10-decanediol. Esters1 and2 were studied by X-ray structural analysis.
Distinctive patterns of C…C, Cl…Cl and C…Cl non-bonded short contacts are obtained for 4 Å short axis β-structures and for non-β-structures in a series of polychloro-aromatics, phenols and anilines. The directions of the shortest Cl…Cl and C…C contacts provide an insight into the role of the chloro-substituent as a steering group in the crystal engineering of β-structures.
The crystal structures of substituted cinnamic acids can be divided into three groups (α,β,γ) according to their cell dimensions. These structure groups coincide with the three types of photochemical behaviour reported in Part II: dimerisation to (1) α-truxillic or (2) β-truxinic acid, and (3) lightstability. -X-Ray analyses of members of the α- and β-classes indicate that in these photo-active structures the conformation of the diniers can be correlated with the packing arrangement of nearest-neighbours in the monomer lattice : dimerisation takes place at C=C separations of 3-6-4-1 Å and preserves in the (molecular) symmetry of the cyclobutane derivative the (crystallographic) symmetry element relating nearest-neighbour monomers. The separation between C=C of 4.7-5.1 Å in the light-stable γ-structures is interpreted as too long for dimerisation to be possible.
In C–H O hydrogen bonds, the average C O and H O separations depend on the nature of the acceptor O atoms: they obey the trends observed as for the conventional O–H and N–H donors, with a ranking of acceptor strengths CO > NO2 > SO > C–OH > C–O–C.
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.
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.
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.
Knoevenagel condensation of acrolein with NCCH2COOK or NCCH2CONH2 in 1M aqueous solutions of K and Na phosphates gave 2-cyanopenta-(2E,4)-dienoic acid and its amide, respectively.
trans,trans-Muconic acid, its monomethyl ester, and cis,cis-isomer, all of which crystallise in cells with shortest axes of 4 Å, react in the solid state on irradiation with λ > 290 mµ. At room temperature all give vinyl-substituted cyclobutanes of symmetry m, the configuration of which reproduces the geometry of the monomer molecules both in the attachment of the ring substituents and in the configuration of the vinyl side-chain. The all-trans-acid and its monomethyl ester give, in addition to dimers, various amounts of oligomers which, according to the spectroscopic evidence, are formed by both 1,4- and 1,2-addition of the butadiene chains. Dimethyl trans,trans-muconate, which does not crystallise in a 4 Å cell, is stable to λ > 290 mµ at 25°.
It is shown that the total charge density is a valid source to confirm hydrogen bonding without invoking a reference charge density. A set of criteria are proposed based on the theory of ''atoms in molecules'' to establish hydrogen bonding, even for multiple interactions involving C-H ... O hydrogen bonds. These criteria are applied to several van der Waals complexes. Finally a bifurcated intramolecular C-H ... O hydrogen bond is predicted in the anti-AIDS drug AZT, which may highlight a crucial feature of the biological activity of a whole class of anti-AIDS drugs.
Following a brief historical review of solid-state photochemistry current research is discussed under four parallel headings: first, analysis of the topochemical postulate according to which the course of the solid-state reaction and the stereochemistry of the photodimer (if any) can be predicted from the configuration and nearest-neighbour geometry of closest monomer molecules in the crystal lattice; secondly, the study of the locus of the reaction, that is the dependence of the course of the reaction or (dimerization, cis → trans isomerization) on crystal texture (dislocation, grain and phase boundaries); thirdly, a better understanding of the packing principles of organic molecules in their crystal structure to enable us to construct photoreactive (or lightstable) crystal structures of any given monomer as well as mixed crystals of potentially codimerizable monomers for synthetic purposes or energy-transfer studies. Several approaches to this problem of ‘crystal engineering’ based on generalizations of packing modes of primary amides and of dichlorophenyl derivatives are outlined, and their application to a systematic photochemistry of the solid state discussed.
Solid penta-1,3-diene-1-carboxylic acid (4), penta-1,3-diene-1-carboxamide (5), buta-1,3-diene-1,4-dicarbonitrile (6), styrylacrylic acid (10), its methyl ester (46), and amide (49)(all trans,trans-configurated), all photodimerise on irradiation (λ > 290 nm), to divinylcyclobutane (C4) derivatives. The structures of the fully characterised photoproducts from (4), (5), (6), and (49) and the light-stability of (N-phenyl)styrylacrylamide (53), are predictable from the known or postulated packing arrangements of their monomers.
A charge density study of the crystalline salt of methylammonium hydrogen succinate monohydrate has been carried out based on combined use of neutron and X-ray diffraction data at 110 K. The neutron data of a deuterated crystal showed that the O-D(H)-O hydrogen bond in the crystal is symmetrical with D(H) at a crystallographic inversion center. A charge density from the X-ray data with hydrogen positional and thermal parameters based on the neutron data proved to be informative on the topological properties of chemical bonding in the crystal. The Laplacian of the density was calculated and analyzed, and some of-the (3,-1) critical points in the crystal unit cell have been isolated and characterized. These results show that the short hydrogen bond has covalent character. The X-ray data also indicate that the electrostatic potential in the crystal adds to the stability of the short O-H-O hydrogen bond.
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Cured adhesive layers produced from ethyl-(ECA), allyl-(ACA), and allyloxyethyl-(AOECA) 2-cyanoacrylates were studied by means of thermogravimetry and differential scanning calorimetry. Polymer films of ECA-based adhesive compositions comprising various amounts and types of 2-cyano-2,4-pentadienoic acid (CPDA) esters were also examined. The influence of the modifier type, as well as the chemical structure of the cyanoacrylates used, was followed upon the glass transition temperatures (Tg) and the rates of thermal degradation of the corresponding polymers. In the case of cured adhesive mixtures containing unsaturated CPDA esters and when poly(ACA) and poly(AOECA) were studied, a significant increase of their heat resistance was established, as compared with poly(ECA). This fact was explained with the formation of three-dimensional structure of the polymer film due to crosslinking reactions. A different course and character of these reactions were found comparing the thermal behavior of poly(ACA) and cured compositions containing unsaturated CPDA esters. A good agreement was found between data from the thermal analyses and the tensile shear and impact strength tests. It was shown that the modification of ECA with unsaturated CPDA esters is a possible way of increasing the heat resistance of the basic adhesive. © 1993 John Wiley & Sons, Inc.
PC Version., A System of Computer Programs for the Determination of Crystal Structure from X-ray Diffraction Data
- G M Sheldrick
- Shelxtl Plus
- G. M. Sheldrick