2-Methyl-<i>N</i>-phenylbenzamide

Gowda, B.T.; Foro, Sabine; Sowmya, B.P.; Fueß, H.

doi:10.1107/s1600536807068821

Cited by 14 publications

(23 citation statements)

References 5 publications

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“…In structural chemistry, a multitude of crystal structure studies have been reported to date on a variety of organic molecular classes and with a particular emphasis on polymorphism, pseudopolymorphism and isomers (Gelbrich et al, 2007;Wardell et al, 2007Wardell et al, , 2008Chopra & Row, 2008). The variety and sizes of structural series reported are expanding rapidly and notable examples include benzoate esters (Gowda, Foro, Sowmya & Fuess, 2008) and both mono/dimethyl-and chlorobenzamides (Gowda, Foro, Babitha & Fuess, 2008). Series such as these provide a 'goldmine' of structural data for ongoing data analyses.…”

Section: Commentmentioning

confidence: 99%

A structural systematic study of four isomers of difluoro-N-(3-pyridyl)benzamide

McMahon¹,

Gallagher²,

Anderson³

et al. 2009

Acta Crystallogr C

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The four isomers 2,4‐, (I), 2,5‐, (II), 3,4‐, (III), and 3,5‐difluoro‐N‐(3‐pyridyl)benzamide, (IV), all with formula C12H8F2N2O, display molecular similarity, with interplanar angles between the C6/C5N rings ranging from 2.94 (11)° in (IV) to 4.48 (18)° in (I), although the amide group is twisted from either plane by 18.0 (2)–27.3 (3)°. Compounds (I) and (II) are isostructural but are not isomorphous. Intermolecular N—H...O=C interactions form one‐dimensional C(4) chains along [010]. The only other significant interaction is C—H...F. The pyridyl (py) N atom does not participate in hydrogen bonding; the closest H...Npy contact is 2.71 Å in (I) and 2.69 Å in (II). Packing of pairs of one‐dimensional chains in a herring‐bone fashion occurs viaπ‐stacking interactions. Compounds (III) and (IV) are essentially isomorphous (their a and b unit‐cell lengths differ by 9%, due mainly to 3,4‐F2 and 3,5‐F2 substitution patterns in the arene ring) and are quasi‐isostructural. In (III), benzene rotational disorder is present, with the meta F atom occupying both 3‐ and 5‐F positions with site occupancies of 0.809 (4) and 0.191 (4), respectively. The N—H...Npy intermolecular interactions dominate as C(5) chains in tandem with C—H...Npy interactions. C—H...O=C interactions form R22(8) rings about inversion centres, and there are π–π stacks about inversion centres, all combining to form a three‐dimensional network. By contrast, (IV) has no strong hydrogen bonds; the N—H...Npy interaction is 0.3 Å longer than in (III). The carbonyl O atom participates only in weak interactions and is surrounded in a square‐pyramidal contact geometry with two intramolecular and three intermolecular C—H...O=C interactions. Compounds (III) and (IV) are interesting examples of two isomers with similar unit‐cell parameters and gross packing but which display quite different intermolecular interactions at the primary level due to subtle packing differences at the atom/group/ring level arising from differences in the peripheral ring‐substitution patterns.

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Section: Commentmentioning

confidence: 99%

A structural systematic study of four isomers of difluoro-N-(3-pyridyl)benzamide

McMahon¹,

Gallagher²,

Anderson³

et al. 2009

Acta Crystallogr C

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“…We assume that realistic conformations explaining the crystallographic data will be within a limited RMSD distance of the published PDB structure; this follows similar assumptions in previous work [7,10]. However, hinge motion, if present in a single crystal specimen, can also be detected by sampling in a larger conformational space around the PDB structure.…”

Section: Methodsmentioning

confidence: 87%

“…Multi-conformer approaches have long been the norm when modeling NMR data. It has been suggested that, for an accurate representation of the physical heterogeneity in a protein, such multiple-conformer models also be used to explain X-ray crystallography data [8-10]. …”

Section: Introductionmentioning

confidence: 99%

“…The key problem is that limited sampling (i.e. number of conformations) and multiplicity of the problem make for weak statistical estimates [8,10,13]. While a growing number of tools address the problem of using ensembles to implicitly model conformational variability [7,10,12,14,15], they generally do not distinguish between variability due to noise vs. physical motion.…”

Section: Introductionmentioning

confidence: 99%

“…A number of methods have been proposed to model multiple conformations that might give rise to X-ray crystallographic data from a single crystal [7,9,10,12]. Although independently optimized multi-conformer representations prove to be a very attractive solution, interpretation of what the ensemble represents is a gray area [9,12].…”

Section: Introductionmentioning

confidence: 99%

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Sparse estimation for structural variability

Hosur¹,

Singh²,

Berger

2011

Algorithms Mol Biol

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BackgroundProteins are dynamic molecules that exhibit a wide range of motions; often these conformational changes are important for protein function. Determining biologically relevant conformational changes, or true variability, efficiently is challenging due to the noise present in structure data.ResultsIn this paper we present a novel approach to elucidate conformational variability in structures solved using X-ray crystallography. We first infer an ensemble to represent the experimental data and then formulate the identification of truly variable members of the ensemble (as opposed to those that vary only due to noise) as a sparse estimation problem. Our results indicate that the algorithm is able to accurately distinguish genuine conformational changes from variability due to noise. We validate our predictions for structures in the Protein Data Bank by comparing with NMR experiments, as well as on synthetic data. In addition to improved performance over existing methods, the algorithm is robust to the levels of noise present in real data. In the case of Human Ubiquitin-conjugating enzyme Ubc9, variability identified by the algorithm corresponds to functionally important residues implicated by mutagenesis experiments. Our algorithm is also general enough to be integrated into state-of-the-art software tools for structure-inference.

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2-Methyl-N-(3-methylphenyl)benzamide

et al. 2008

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In the structure of the title compound (N3MP2MBA), C15H15NO, the conformation of the N—H bond is anti to the meta-methyl substituent in the aniline ring and that of the C=O bond is syn to the ortho-methyl substituent in the benzoyl ring, while the conformations of the N—H and C=O bonds are anti to each other. The bond parameters in N3MP2MBA are similar to those in 2-methyl-N-phenylbenzamide, N-(3,4-dimethylphenyl)benzamide and other benzanilides. The amide group, –NHCO–, makes a dihedral angle of 55.2 (7)° with the benzoyl ring, while the dihedral angle between the two benzene rings (benzoyl and aniline) is 36.2 (1)°. N—H⋯O hydrogen bonds give rise to infinite chains running along the b axis of the crystal structure.

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2-Methyl-N-phenylbenzamide

Cited by 14 publications

References 5 publications

A structural systematic study of four isomers of difluoro-N-(3-pyridyl)benzamide

A structural systematic study of four isomers of difluoro-N-(3-pyridyl)benzamide

Sparse estimation for structural variability

2-Methyl-N-(3-methylphenyl)benzamide

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