Determination of the molecular packing in the crystal of N,N'-dicyclohexylurea by means of potential-energy calculations

Coiro, V. M.; Giacomello, Pierluigi; Giglio, E.

doi:10.1107/s0567740871005430

Cited by 27 publications

(21 citation statements)

References 7 publications

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“…Table 3. Relevant intramoleeular torsion angles (°) Table 3 the corresponding values are -13.0 ° and 169.6°, which indicate a relatively large deviation from planarity, as has been found in other crystal structures (Ganis, Avitable, Benedetti, Pedone & Goodman, 1970; Coiro, Giacomello & Giglio, 1971;Winkler & Dunitz, 1971;Ramachandran & Kolaskar, 1973, and references cited therein; Pattabhi, Venkatesan & Hall, 1973;Stenkamp & Jensen, 1973). All the experimental results suggest that the crystal field as well as the intramolecular interactions can easily distort the OC-NH group from planarity.…”

Section: Molecular Geometrymentioning

confidence: 97%

“…The conformation of a molecule may be established by intramolecular potential energy calculations as for N,N'-dicyclohexylurea (Coiro, Giacomello & Giglio, 1971) by fixing bond lengths and angles at standard values. ZLNP has 11 degrees of freedom if the methyl group is considered as one atom.…”

Section: Conformational Analysismentioning

confidence: 99%

“…Finally this procedure was repeated by including the nitrophenyl group and allowing two more rotation angles (~ua,~'9) to vary against the other previously fixed ~u's. The van der Waals energy was computed by means of potentials previously verified in known and unknown crystal structures (Coiro, Giacomello & Giglio, 1971;Coiro, Giglio, Lucano & Puliti, 1973;Gavuzzo, Mazza & Giglio, 1974; and references cited therein). Their coefficients, which refer to the generalized form:…”

Section: Conformational Analysismentioning

confidence: 99%

“…The other reason is connected with the study of the OC-NH group planarity which is important in the conformational analysis of cyclic and acyclic oligopeptides as well as polypeptides (Ramachandran, 1968;Coiro, Giacomello & Giglio, 1971;Ramachandran & Kolaskar, 1973). ZLNP is suitable for such investigation because of the presence of the bulky Leu residue which may cause a torsion around the ~ angle of the peptide group.…”

Section: Introductionmentioning

confidence: 99%

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The crystal structure and the conformational analysis of carbobenzoxyl-L-leucyl-p-nitrophenyl ester

Coiro¹,

Mazza²,

Mignucci³

1974

Acta Crystallogr Sect B

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Carbobenzoxy-L-leucyl-p-nitrophenyl ester crystallizes in space group P212121 with a= 8"498, b= 9"40j and c=25"217 A. 1398 independent reflexions were collected on a Philips automatic diffractometer. The structure was solved by direct methods, and refined isotropically by full-matrix least-squares calculations. The final R is 0.105. The molecule assumes a 'folded-back' conformation in the crystal, the folding occurring at the Leu residue. The two parts of the molecule departing from the Leu residue are in the extended conformation. The OC-NH group deviates significantly from planarity. The molecules are held together by hydrogen bonds and dipole-dipole and van der Waals interactions. The prediction of the conformational analysis, particularly for the fragment containing the Leu residue, is in accordance with the actual structure.

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Section: Molecular Geometrymentioning

confidence: 97%

Section: Conformational Analysismentioning

confidence: 99%

Section: Conformational Analysismentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

The crystal structure and the conformational analysis of carbobenzoxyl-L-leucyl-p-nitrophenyl ester

Coiro¹,

Mazza²,

Mignucci³

1974

Acta Crystallogr Sect B

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“…Since the stereochemistry of the cholanic acids may be related to their remarkable chemical and biological behaviour we are interested in predicting the conformation of the side chain and ring D. Furthermore it may be useful to establish, even approximately, their conformation in order to decrease the degrees of freedom in solving the phase problem in crystals by means of potential-energy calculations (Coiro, Giglio & Quagliata, 1972;Coiro, Giacomello & Giglio, 1971;Coiro, Giglio, Lucano & Puliti, 1973;Gavuzzo, Mazza & Giglio, 1974).…”

Section: Introductionmentioning

confidence: 99%

Side-chain and ring D conformation in cholanic acids

Giglio¹,

Quagliata²

1975

Acta Crystallogr Sect B

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The conformations of some cholanic acids and related compounds are discussed. The intramolecular van der Waals energy surface of desoxycholic acid, computed as a function of four internal rotation .angles of the side chain, presents several minima indicating a remarkable conformational flexibility. The agreement with the experimental conformations is satisfactory. The arrangement of the carboxyl group in the crystals mainly depends on its ability to form hydrogen bonds rather than on the intramolecular van der Waals energy. Ring D shows different conformations which may chiefly arise from short-range intramolecular interactions. However, anisotropic packing forces could also influence the conformation of ring D in the crystals.

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Structure of guanosine‐3′,5′‐cytidine monophosphate. I. Semi‐empirical potential energy calculations and model‐building

et al. 1973

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synopsisThe conformation and packing scheme for guanosine-3',5'-cytidine monophosphate, GpC, were computed by minimizing the classical potential energy. The lowest energy conformation of the isolated molecule had dihedral angles in the range of helical RNA's, and the sugar pucker was C3' endo. This was used as the starting conformation in a packing search over orientation space, the dihedral angles being flexible in this step also.The packing search was restricted by constraints from our x-ray data, namely, (1) the dimensions of the monoclinic unit cell and its pseudo-C2 symmetry (the real space group is P21), (2) t,he location of the phosphorous atom, and (3) the orientation of the bases.In addition, a geometric function was devised to impose Watson-Crick base pairing. Thus, a trial structure could be sought without explicit inclusion of intermolecular potentials. An interactive computer graphics system was used for visualizing the calculated structures.The packing searches yielded two lowest energy schemes in which the molecules had the same conformation (similar to double-helical RNA) but different orientations within the unit cell. One of these was refined by standard x-ray methods to a discrepancy index of 14.4% in the C2 pseudocell. This served as the starting structure for the subsequent refinement in the real P21 cell.5

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Determination of the molecular packing in the crystal of N,N'-dicyclohexylurea by means of potential-energy calculations

Cited by 27 publications

References 7 publications

The crystal structure and the conformational analysis of carbobenzoxyl-L-leucyl-p-nitrophenyl ester

The crystal structure and the conformational analysis of carbobenzoxyl-L-leucyl-p-nitrophenyl ester

Side-chain and ring D conformation in cholanic acids

Structure of guanosine‐3′,5′‐cytidine monophosphate. I. Semi‐empirical potential energy calculations and model‐building

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