Crystal Structures Of Methyl Research Articles

Crystal structures of methyl 3,5-di-methyl-benzoate, 3,5-bis-(bromo-meth-yl)phenyl acetate and 5-hy-droxy-benzene-1,3-dicarbaldehyde.

The crystal structures of the title compounds, methyl 3,5-di-methyl-benzoate (C10H12O2; 1), 3,5-bis-(bromo-meth-yl)phenyl acetate (C10H10Br2O2; 2) and 5-hy-droxy-benzene-1,3-dicarbaldehyde (C8H6O3; 3) were determined by single-crystal X-ray analysis. The crystals of 1 are composed of strands of C-H⋯O=C bonded mol-ecules, which are further arranged into layers. As a result of the presence of two bromo-methyl substituents in compound 2, mol-ecular dimers formed by crystallographically non-equivalent mol-ecules are connected to structurally different two-dimensional aggregates in which the bromine atoms participate in Br⋯Br bonds of type I and type II. In the case of compound 3, which possesses three donor/acceptor substituents, the mol-ecular association in the crystal creates a close three-dimensional network comprising Car-yl-H⋯Ohy-droxy, Cform-yl-H⋯Oform-yl and O-H⋯Oform-yl bonds.

N–H⋯O hydrogen bonding to the alkoxy oxygen of a carboxylic ester group: crystal structures of methyl 2,6-diaminobenzoate and its derivatives

Molecules with hydrogen bonds from amino groups to both oxygens of a carboxylic ester are described, and other examples of hydrogen bonding to an ester's alkoxy oxygen atom are highlighted.

Synthesis and Crystal Structures of Methyl 3,4,5-Trimethoxybenzoate and 1,2-Dihydro-2,2,4-Trimethylquinoline Derivatives

Two 1,2-dihydro-2,2,4-trimethylquinoline derivatives and two methyl 3,4,5-trimethoxybenzoate derivatives have been synthesized and their crystal structure determined by X-ray single crystal diffraction. Both methyl 3,4,5-trimethoxybenzoate derivatives: methyl 2,6-dibromo-3,4,5-trimethoxybenzoate (1) and methyl 3,4,5-trimethoxy-2-nitrobenzoate (2) crystallize in the monoclinic crystal system with a = 17.2605(5) A, b = 8.9082 (3) A, c = 8.9920 (3) A, β = 105.922 (2)°, space group Cc for 1, and a = 20.4898 (4) A, b = 9.7348 (2) A, c = 24.3911 (5) A, β = 99.457 (1)°, space group C2/c for 2. 1,2-Dihydro-8-methoxy-2,2,4-trimethylquinoline (3) crystallizes in the orthorhombic, space group Pna21, with a = 11.3745 (2) A, b = 8.0638 (1) A and c = 12.0019 (2) A, while 6-chloro-1,2-dihydro-2,2,4-trimethylquinoline (4) crystallizes in the monoclinic, space group P21/c, with a = 7.8063 (10) A, b = 17.757 (3) A, c = 7.8675 (10) A and β = 91.559 (8)°. The three-dimensional crystal packing structures of all four compounds are consolidated by a combination of van der Waals forces and weak directional hydrogen bonds, mostly though the overlap of peripheral groups with the centroids of the aromatic rings as the planar aromatic systems appeared to be displaced from each other resulting in the absence of π–π stacking intereactions usually found in the structural stacking of aromatic systems. This report deals with a comparative analysis of the crystal structures and crystal packing of two pairs of closely related molecules (1, 2) and (3, 4).

Crystal structures of methyl and benzyl 5-ferrocenyl-3,5-dimethyl-2-pyrazoline-1-dithiocarboxylate

Reactions of E-4-ferrocenylpent-3-en-2-one with S-methyldithiocarbazate or S-benzyldithiocarbazate result in the formation of methyl 5-ferrocenyl-3,5-dimethyl-2-pyrazoline-1-dithiocarboxylate (1) or benzyl 5-ferrocenyl-3,5-dimethyl-2-pyrazoline-1-dithiocarboxylate (2). The single crystals of both products are obtained and their structures are identified by X-ray diffraction method with triclinic P-1 space groups. The cell parameters for compound 1 are as follows: a = 7.7029(8) A, b = 10.1631(11) A, c = 10.7305(12) A, α = 101.3270(10)°, β = 90.6740(10)°, γ = 94.8390(10)°, and V = 820.40(15) A3. For compound 2, the crystallographic data are: a = 7.953(3) A, b = 10.970(5) A, c = 12.534(3) A, α = 84.718(5)°, β = 81.651(3)°, γ = 76.274(4)A, and V = 1049.1(7) A3.

ChemInform Abstract: Synthesis and the Molecular and Crystal Structures of Methyl 2‐Substituted 7,7‐Dimethyl‐5‐oxo‐5,6,7,8‐tetrahydroquinoline‐4‐carboxylates (III).

ChemInform Abstract: Synthesis and the Molecular and Crystal Structures of Methyl 2‐Substituted 7,7‐Dimethyl‐5‐oxo‐5,6,7,8‐tetrahydroquinoline‐4‐carboxylates (III).

Synthesis and Crystal Structures of Methyl 3-(Benzoylamino)-6-methyl-2-oxo-2H-pyran-5-carboxylate and N-[5-(3,4-Dimethoxyphenyl)-6-methyl-2-oxo-2H-pyran-3-yl]benzamide

The compounds methyl 3-(benzoylamino)-6-methyl-2-oxo-2H-pyran-5-carboxylate (1), C15H13NO5, and N-[5-(3,4-dimethoxyphenyl)-6-methyl-2-oxo-2H-pyran-3-yl]benzamide (2), C21H19NO5, crystallize as a centrosymmetric hydrogen-bonded dimer facilitated by N–H···O interactions involving the amide and carbonyl moiety of the lactone group of adjacent molecules. Supramolecular aggregation in 1 is controlled by a combination of π–π interactions [centroid–centroid distance = 4.0745(11) A] and weak C–H···O hydrogen bonding between the phenyl ring of the benzoylamino group and the carbonyl atom of the methoxycarbonyl group and in 2 by a combination of π–π interactions [centroid–centroid distance = 4.0699(8) and 4.1556(10) A], weak C–H···O interactions between the methoxy substituents of the adjacent dimethoxyphenyl group and weak C–H··· π interactions. 2H-Pyran-2-ones represent an important class of compounds useful for various ring transformations, the titled compounds crystallize as a centrosymmetric hydrogen-bonded dimers.

Crystal Structures of Methyl (Methyl 3-azido-2,3-dideoxy-β-L-lyxo- and -β-D-arabino-hexopyranosid)uronates

Single-crystal x-ray diffraction data for methyl (methyl 3-azido-2,3-dideoxy-β-L-lyxo- and β-D-arabino-hexopyranosid)uronates are presented. Three independent molecules in the asymmetric part of the unit cell of the β-D-arabino stereoisomer were found. These differ slightly in the geometry of the groups bound to the pyranose rings. Conformations and the geometry parameters of all the molecules as well as the planarity of the carbomethoxy group, the linearity of the azido group, and the orientation of the aglycone in the crystal lattice are discussed. Influence of the hybridization, resonance, and crystal packing on the geometry parameters is shown.

Straight-chain alkyl isocyanides open the distal histidine gate in crystal structures of myoglobin .

Crystal structures of methyl, ethyl, propyl, and butyl isocyanide bound to sperm whale myoglobin (Mb) reveal two major conformations. In the in conformer, His(E7) is in a "closed" position, forcing the ligand alkyl chain to point inward. In the out conformer, His(E7) is in an "open" position, allowing the ligand side chain to point outward. A progressive increase in the population of the out conformer is observed with increasing ligand length in P2(1) crystals of native Mb at pH 7.0. This switch from in to out with increasing ligand size also occurs in solution as measured by the decrease in the relative intensity of the low-frequency ( approximately 2075 cm(-1)) versus high-frequency ( approximately 2125 cm(-1)) isocyano bands. In contrast, all four isocyanides in P6 crystals of wild-type recombinant Mb occupy the in conformation. However, mutating either His64 to Ala, creating a "hole" to solvent, or Phe46 to Val, freeing rotation of His64, causes bound butyl isocyanide to point completely outward in P6 crystals. Thus, the unfavorable hindrance caused with crowding a large alkyl side chain into the distal pocket appears to be roughly equal to that for pushing open the His(E7) gate and is easily affected by crystal packing. This structural conclusion supports the "side path" kinetic mechanism for O(2) release, in which the dissociated ligand first moves toward the protein interior and then encounters steric resistance, which is roughly equal to that for escaping to solvent through the His(E7) channel.

Synthetic applications of aryl radical building blocks for cyclisation onto azoles

2-(2-Bromophenyl)ethyl groups have been used as building blocks in radical cyclisation reactions onto azoles to synthesise tri- and tetra-cyclic heterocycles. 2-(2-Bromophenyl)ethyl methanesulfonate was used to alkylate azoles (imidazoles, pyrroles, indoles and pyrazoles) for the synthesis of the radical precursors. Cyclisations of the intermediate aryl radicals yield new 6-membered rings attached to the azoles. The aryl radicals undergo intramolecular homolytic aromatic substitution onto the azole rings. Tributylgermanium hydride has been used with success to replace the toxic and troublesome tributyltin hydride. Initial studies show that the protocol can be used on solid phase resins. The molecular and crystal structures of methyl 5,6-dihydroimidazo[5,1- a]iso-quinoline-1-carboxylate and methyl 5,6-dihydroimidazo[2,1- a]isoquinoline-3-carboxylate were determined by X-ray crystallography.

Studies on the conformation of α-arylcinnamic acids and their esters: Crystal structures of methyl (E)-2,3-bis(3,4-dimethoxyphenyl)propenoate and methyl (Z)-2,3-bis(3,4-dimethoxyphenyl)propenoate

The conformations of stereoisomers of α-arylcinnamic acids and their esters are discussed based on crystal structures of the E and Z forms of 2,3-bis(3,4-dimethoxyphenyl)propenoic acid and its methyl ester. In the E forms of the cinnamic acid and the cinnamic acid ester, the plane of the α-aryl substituent is approximately perpendicular to that of the rest of the molecule. In the Z forms the plane of the carboxyl or methoxycarbonyl group is approximately perpendicular to that of the ethylenic group, and both the aromatic group planes are significantly twisted out of the ethylenic group plane. Crystal structures of methyl (E)-2,3-bis(3,4-dimethoxyphenyl)propenoate (space group P21/n with a = 8.1697(5), b = 11.3882(9), c = 19.7766(9) A, β = 90.058(4)°, V = 1840.0(2) A3, and Z = 4), monoclinic methyl (Z)-2,3-bis(3,4-dimethoxyphenyl)propenoate (space group P21/n with a = 11.183(2), b = 5.640(2), c = 29.737(7) A, β = 99.19(2)°, V = 1851.4(9) A3, and Z = 4), and orthorhombic methyl (Z)-2,3-bis(3,4-dimethoxyphenyl)propenoate (space group P212121 with a = 8.849(4), b = 24.288(9), c = 8.734(3) A, V = 1877(1) A3, and Z = 4) are reported.

C–H group acidity and the nature of C–H···N interactions: crystal structural analysis of pyrazine and methyl substituted pyrazines

Crystal structures of methyl-, 2,3-, 2,5- and 2,6-dimethyl-, and trimethylpyrazine (2–6) have been determined by X-ray diffraction analysis. Four of these compounds (2–4 and 6) are liquids and their single crystals have been grown in situ on the diffractometer using a miniature zone melting procedure. These structures are analysed together with those of pyrazine (1) and tetramethylpyrazine (7) in the context of C–H···N interactions. Compounds 1–7 were chosen because they contain only C, H and N atoms, and also C–H groups of variable acidity. This facilitates the comparison of C–H···N geometries with respect to the C–H group acidity. Compounds 1 and 2 are dominated by sp2 C–H groups in their molecules and their supramolecular structures are generated by sp2 C–H···N. On the other hand the domination of sp3 C–H groups at the molecular level in 6 and 7 results in crystal structures that are governed by sp3 C–H···N. A balance of sp2 and sp3 C–H groups in the dimethyl derivatives 3–5 leads to a situation where both kinds of C–H groups play a structure directing role. While the sp2 C–H groups form C–H···N, the sp3 C–H groups are involved in C–H···π interactions. Thus the C–H group interactions follow a property unique to hydrogen bonds—stronger donors interact with stronger acceptors while weaker donors approaching weaker acceptors. Inter-structural comparison revealed that H···N distances decrease with increasing C–H acidity and therefore C–H···N interactions could be considered as weak hydrogen bonds.

The Cubane Cage – A Sensitive Probe for Assessing Substituent Effects on a Four-Membered Ring, Part II

The crystal structures of methyl 4-methoxycubane-1-carboxylate (1), 1-acetamido-4-fluorocubane (2), methyl 4-acetoxycubane-1-carboxylate (3), 1,4-difluorocubane (4), 1,4-dichlorocubane (5), and N,N-diisopropylcubane-1,4-dicarboxamide (6) have been investigated by means of X-ray diffraction analysis. Fluorine and chlorine substituents cause a shortening of the vicinal bonds, as is seen in the 4-halocubane-1-carboxylates. The cage bonds vicinal to the ester substituent, with a favorable orientation with regard to the π-acceptor influence of this group become longer than the CH–CH bonds. Furthermore, the influence on bond length with respect to the orientation of this group relative to bonds within the cubane skeleton has been investigated experimentally. The effect of the methoxy group has also been found to depend on the orientation. The cage bond antiperiplanar to the methyl group is shortened, while the cage bonds in gauche orientation to this group are lengthened. As seen in the case of the halogen-substituted derivatives, the bonds bearing the acetoxy substituent are shortened due to the σ-acceptor property of this group. Ab initio calculations on compounds 1, 2, 4, and 5 performed at the 6-31G* level confirm the experimental results.

Crystal Structures of Methyl and EthylN-(2,3-Dimethoxybenzyl)-N-(p-toluenesulfonyl)-2-phenylglycinates

The crystal structures of methyl and ethyl N-(2,3-dimethoxybenzyl)-N-(p-toluenesulfonyl)-2-phenylglycinates 4a and 4b respectively, have been determined by X-ray diffraction analysis. The presence of different alkyl ester groups in both molecules does not affect the geometry retaining a synclinal conformation for the N atom and the O atom of the C=O group [N—C17—C18—O5 38.1(5)° for 4a and 33.3(4)° for 4b].

Crystal structures of methyl [formula omitted

The crystal structures of methyl 6-O- n-octanoyl-α- d-galactopyranoside ( 1) and methyl 6-O- n-decanoyl-α- d-galactopyranoside ( 2) were investigated by X-ray analysis. Anhydrous crystals obtained from methanol solution by slow evaporation are monoclinic, and the space group is P2 1 with Z = 2. The cell dimensions are as follows, 1: a = 5.774(1), b = 8.013(1), c = 19.183(1) A ̊ , β = 98.50(1)°; 2: a = 5.762(1), b = 8.003(1), c = 21.227(2) A ̊ , β = 93.93(1)° . The galactopyranoside ring is nearly in a 4C 1 chair conformation but slightly distorted to twist boat and the alkyl chain is in all- trans conformation. In these crystals, molecules are arranged in a bilayer structure with interdigitated alkyl chains. The hydrogen bonding linkages between sugar moieties, which are found only between the layers, form an infinite chain through the crystal. 1 and 2 show higher melting points than those of corresponding β- d-glucopyranosides. The results indicate the important role of the sugar in the crystal.

Two [7.3.1]azabicyclo-z-3-ene-1,5-diyne analogues of dynemicin A.

The crystal structures of methyl 6-methoxy-17-oxo-2-azatricyclo[7.7.1.0(3,8)]heptadeca-3(8),4 ,6,13-tetraene- 11,15-diyne-2-carboxylate ethyl acetate solvate, (1), 2C19H15NO4.0.5C4H8O2, and tricyclo[3.3.1.1(3,7)]decyl 6-methoxy-17-oxo-2-azatricyclo[7.7.1.0(3,8)]heptadeca-3(8),4 ,6,13-tetraene- 11,15-diyne-2-carboxylate ethyl acetate solvate, (2), C28H27NO4.0.5C4H8O2, are reported. For compound (1), two crystallographically independent molecules are observed. Interestingly, for both compounds (1) and (2), a molecule of ethyl acetate is found in the crystal lattice disordered about an inversion center. The azabicyclo[7.3.1]enediyne core appears to be fairly rigid. Only minor differences are observed in the ring conformation between the two independent molecules in (1) and between compounds (1) and (2) themselves. The conformation is also similar to that found in deoxydynemicin A [Shiomi, Iinuma, Naganawa, Hamada, Hattori, Nakamura, Takeuchi & Iitaka (1990). J. Antibiot. 43, 1000-1005] and triacetyldynemicin A [Konishi, Ohkuma, Tsuno, Oki, Van Duyne & Clardy (1990). J. Am. Chem. Soc. 112, 3715-3716]. The transannular diyne distance (C3...C8) averages 3.428 (2) A for compound (1) and is 3.403 (3) A for compound (2).

Crystal structures of methyl [formula omitted

The crystal structures of methyl 6-O-n- octanoyl-β- d- glucopyranoside 1 and methyl 6-O-n- decanoyl-β- d- glucopyranoside 2, which are types of glycosurfactants, were determined by X-ray analysis. Anhydrous crystals were obtained from a diethyl ether-acetone solution. The crystals are monoclinic, and the space group is P2 1 with Z = 2. The cell dimensions are as follows: 1, a = 7.760(1), b = 7.373(1), c = 15.514(1) A ̊ , β = 102.91(1)° ; 2, a = 7.724(1), b = 7.351(1), c = 16.957(2) A ̊ , β = 94.81(1)° . The glucopyranoside moieties are in a 4 C 1 chair conformation and the conformation of the alkyl chain is the all- trans type. The molecules are arranged parallel to the a– c plane in a bilayer structure where alkyl chains are interdigitated. The sugar moieties are stacked to form a hydrophilic zone elongated parallel to the ab plane and arranged with a packing structure similar to that of methyl β- d-glucopyranoside in spite of a substituted long alkyl chain. Hydrogen bondings of sugar moieties are found only between the bilayers.

ChemInform Abstract: Stereoselectivity in Fragmentation and Rearrangement of α‐ Hydroxyiminophosphinates and ‐phosphonates. A Synthetic Approach to Acylphosphon‐ and ‐phosphor‐amidates. Crystal Structures of Methyl (E)‐ α‐Hydroxyiminobenzylphenylphosphinate and Methyl Benzoylphenylphosphonamidate.

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Stereoselectivity in fragmentation and rearrangement of α-hydroxyimino-phosphinates and -phosphonates. A synthetic approach to acylphosphon- and phosphor-amidates. Crystal structures of methyl (E)-α-hydroxyimino-benzylphenylphosphinate and methyl benzoylphenylphosphonamidate

Reaction of methyl benzoylphenylphosphinate 1 with hydroxylamine gave methyl α-hydroxy-iminobenzylphenylphosphinate 2 as a mixture of E and Z isomers with the E isomer predominating. Pure (E)-2 when heated gave methyl N-benzoylphenylphosphonamidate 3 as the sole product. In contrast, (Z)-2 when heated gave, as a result of fragmentation, mainly methyl hydrogen phenylphosphonate 4 and benzonitrile, together with methyl N-phenylcarbamoylphenylphosphinate 5 as the minor product; the latter results from Beckmann rearrangement of (Z)-2. Analogous behaviour is exhibited by the two geometrical isomers of dimethyl α-hydroxyiminobenzylphosphonate 8. The crystal structures of methyl (E)-α-hydroxyiminobenzylphenylphosphinate (E)-2 and methyl benzoylphenylphosphonamidate 3 are reported.

Crystal structures of methyl 4,6-O-(S)-benzylidene-2-chloro-2-deoxy-α-D-idopyranoside

Crystal structures of methyl 4,6-<i>O</i>-(<i>S</i>)-benzylidene-2-chloro-2-deoxy-α-<scp>D</scp>-idopyranoside

Structural studies of some serrulatane diterpenes

The crystal structures of methyl (15S)-7,8,16-trihydroxyserrulatan-19-oate (1) and 2,7,8,20-tetrahydroxyserrulat-14-ene (2) have been established by single crystal X-ray diffraction techniques at 295 K, being refined by least squares to residuals of 0.046 and 0.053 for 1 153 and 1 513 ‘observed’ reflections respectively. Crystals of (1) are orthorhombic, P212121, a= 21.78(2), b= 18.42(2), c= 5.101(3)A, Z= 4 while those of (2) are monoclinic, C2, a= 14.96(1), b= 12.315(6), c= 21.75(1)A, β= 107.21(5)°, Z= 8. As well as establishing total relative stereochemistry in (1), an interesting intramolecular hydrogen-bonding system is observed, together with an alicyclic ring conformation differing from that found in the previously studied dihydroxyserrulatic acid (3). In (2), the two independent molecules of the asymmetric unit have different conformations, corresponding broadly to those of (1) and (3).