Conformational analysis of five-membered rings by molecular mechanics: application to nitroxides

Siri, Didier; Gaudel‐Siri, Anouk; Tordo, Paul

doi:10.1016/s0166-1280(01)00773-4

Cited by 27 publications

(31 citation statements)

References 44 publications

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“…The latter values are in good agreement with the most common ones reported for other dithioamide compounds whose metrical parameters have been deposited with the Cambridge Structural Database [6] and are indicative of amide-type resonance. A puckering analysis of the vemembered rings according to Cremer & Pople [7] shows the adoption of 4 T 3 conformations in both cases ( C13 T C12 and C23 T C22 , respectively) [8]. The least-squares planes as de ned by the non-hydrogen atoms of both rings enclose an angle of 62.87(4)°.…”

Section: Atom Sitementioning

confidence: 99%

Crystal structure of di(pyrrolidin-1-yl)methane-thione, C9H16N2S

Lulama

Betz

2015

Zeitschrift Für Kristallographie - New Crystal Structures

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C 9 H 16 N 2 S, orthorhombic, Pbca (no. 61), a = 9.1580(4) Å, b = 11.8157(4) Å, c = 18.0202(8) Å, V = 1949.9 Å 3 , Z = 8, CCDC no.: 1267/4327 Source of materialThe compound was obtained commercially as "ammonium pyrrolidine dithiocarbamate" (APDC) from Hopkin & Williams Ltd. Crystals suitable for the di raction study were obtained directly from the crystalline reaction product. An explanation for the presence of the title compound in the provided product is not at hand. Experimental detailsCarbon-bound H atoms were placed in calculated positions (C-H 0.99 Å) and were included in the re nement in the riding model approximation, with U iso (H) set to 1.2Ueq(C).

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Section: Atom Sitementioning

confidence: 99%

Crystal structure of di(pyrrolidin-1-yl)methane-thione, C9H16N2S

Lulama

Betz

2015

Zeitschrift Für Kristallographie - New Crystal Structures

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“…The title compound is the endo-configured carboxylic acid of norbornane. A puckering analysis according to Cremer &Pople [4]showed the five-membered rings in the norbornane scaffold to adopt an E 3 and an E 5 conformation, respectively [5]. The flap atom in both cases is carbon atom C7.…”

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confidence: 99%

Redetermination of the crystal structure of endo-2-carboxy-bicyclo[2.2.1]- heptane, C8H12O2

Schalekamp

Hosten

Betz

2015

Zeitschrift Für Kristallographie - New Crystal Structures

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Source of materialThec ompoundw as obtained commercially (Frinton Laboratories). Crystals suitable for the diffraction study were obtained upon sublimation of the product at room temperature. Experimental detailsCarbon-bound Hatomswere placed in calculated positions (C-H 0.99 Åfor methylene groups and C-H 1.00 Åfor methine groups) and were included in the refinement in the riding model approximation, with U iso (H) setto1.2U eq (C). The Hatom of the carboxyl group was allowed to rotate with afixed angle around the C-O bond to best fit the experimental electron density (HFIX 147 in the SHELX program suite [11]), with U iso (H) sett o1 .5U eq (O). Due to very low residual electron densities after refinement of givenstructuralmodel,nodisorder model could be set up. DiscussionThe bicycloheptane scaffold has been afocusofresearch in organic chemistry for many decades. Especially questions centered around classicala nd non-classicalc arbocationsf ocusedo nt his keystructure andonlyveryrecentlythe existenceofpenta-coordinate carboncould be proven experimentally on grounds of diffraction experiments based on single crystals [1,2].T he latter finding motivated us to include bicycloheptane-derived ligands into our research efforts in synthesizing novel coordination compounds of transition metals. As aconvenient starting point for our studies, the title compound was chosen as it is commercially available. The molecular and crystal structure of endonorbornane-2-carboxylic acid have been mentioned in the literature once, however, no 3D coordinates have been provided [3]. As the structures of envisioned target molecules shall be elucidated by means of diffraction experiments on single crystals, the structure of the title compound was redetermined. The title compound is the endo-configured carboxylic acid of norbornane. A puckering analysis according to Cremer &Pople [4]showed the five-membered rings in the norbornane scaffold to adopt an E 3 and an E 5 conformation, respectively [5]. The flap atom in both cases is carbon atom C7. For the six-membered ring, a B 2,5 (B C2,C5 )conformation was found [6]. The C-O bond lengths were measured at 1.2130(14) Åa nd 1.3206(14) Åf or the doublebonded and the single-bonded oxygen atom.The latter two values are in good agreement with other values reported for carboxylic acidsw hose metrical parameters have been deposited with the Cambridge Structural Database [7].Inthe crystal, classical hydrogen bondso ft he O-H×××Ot ype arep redominant. There are C-H×××Oc ontacts whose range falls below the sum of van-derWaals radii of the atomsparticipating in them.While the hydrogen bonds give rise to the formation of centrosymmetric dimers as often observed for carboxylic acids [8], the C-H×××Ocontacts extend thesed imeric unitst os trands along the crystallographic a axis. The latter contacts are supported by one of the hydrogen atomsatabridge-head position of the norbornane scaffold and employ the carbonylic oxygen atom as acceptor thus giving rise to two anti-dromic C-H×××Oc ontact chains. In terms...

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“…The positive charge of the coordination unit is balanced by ab romide anionpresent in the crystal structure. Ac onformational analysis of the fivemembered chelate rings according to Cremer &Pople [5]shows the latter to invariably adopt E 1 conformations on the rhenium atom [6].R e-N bond lengthsc over an arrowr ange of 1.991(2)-2.0106(19) Åonly.The least-squares planes as defined by therespective carbon atomsofeach aromatic moiety enclose anglesof45.82(7)°,65.94(8)°and 68.82(9)°. In the crystal, classical hydrogen bonds of the N-H×××Br type are observed next to C-H×××Nc ontacts whose range falls below the sum of van-derWaals radii of the atomsparticipating in them [7].…”

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Crystal structure of tris(ortho-phenylenediamide-N,N’)-rhenium(VII) bromide, C18H18BrN6Re

Habarurema

Gerber

Hosten

et al. 2015

Zeitschrift Für Kristallographie - New Crystal Structures

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C 18 H 18 BrN 6 Re, monoclinic, P2 1 /n (no. 14), a =11.0894 ( Source of materialThe title compound was prepared upon reacting ReBr 3 (dab)(PPh 3 ) 2 (dab =1 ,2-diaminobenzene) with the symmetric two-fold Schiff-base derived from 1,3-diamino-propan-2-ol and 2-hydroxy-benzaldehyde in ethanol. Crystals suitable for the diffraction study were obtained upon free evaporation of the solvent at ambient conditions. Experimental detailsCarbon-bound Hatomswere placed in calculated positions (C-H 0.95 Å) and were included in the refinementinthe riding model approximation, with U iso (H) setto1.2U eq (C). All nitrogen-bound Ha toms were locatedo nad ifferenceF ourier mapa nd refined freely using DFIX instructions, the N-H distances set to 0.88 Å. DiscussionNext to cardiovascular diseases, cancer has become one of the main fatal diseases in industrialized countries. Apart fromclassical surgery,chemo-and radiotherapeutic treatments have entered the arsenal of possible cures for certain types of cancer. All methods, however, suffer from theirown setofproblematic side-effects and, as ac onsequence, the development of radiopharmaceuticals -combining the advantages of chemotherapy as well as radiation methods while at the sametimeavoiding their unique respectivendesiredside-effects -has been atopic of research [1,2]. Tailoring and fine-tuning of the envisioned radiopharmaceuticals' properties such as lipophilicity and, in particular, inertness is of paramount importance with respect to possible future in vivo applications in contemporary medicine and requires sound knowledge about structural parameters of the ligands applied if a more heuristic approach in the synthesis is to triumph over pure trial-and-error as it is encountered in this specific field of coordination chemistry up to the present day. In addition, the spatial requirements of pharmaceuticalsa re of importance as this factor influences on their interaction with enzymatic systems and, as a consequence, thep athway and rateo fc onjugation, functionalization and secretion from the body. In continuation of our ongoing research on the field of rhenium coordination compounds, the coordination of amultidentate ligand towards arhenium(V) startingm aterial was attempted [3].As tructural analysis of the crystalline reaction product showed the formation of an unexpected product. The crystal structures of two other comparable rhenium coordination compounds as found in the current reaction product are apparent in the literature [4].T he compound is ahomoleptic rhenium(VII) coordination compound featuringt hree chelating ortho-phenylenediamine ligands that are invariably two-folddeprotonated. The positive charge of the coordination unit is balanced by ab romide anionpresent in the crystal structure. Ac onformational analysis of the fivemembered chelate rings according to Cremer &Pople [5]shows the latter to invariably adopt E 1 conformations on the rhenium atom [6].R e-N bond lengthsc over an arrowr ange of 1.991(2)-2.0106(19) Åonly.The least-squares planes as defined by...

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Conformational analysis of five-membered rings by molecular mechanics: application to nitroxides

Cited by 27 publications

References 44 publications

Crystal structure of di(pyrrolidin-1-yl)methane-thione, C9H16N2S

Crystal structure of di(pyrrolidin-1-yl)methane-thione, C9H16N2S

Redetermination of the crystal structure of endo-2-carboxy-bicyclo[2.2.1]- heptane, C8H12O2

Crystal structure of tris(ortho-phenylenediamide-N,N’)-rhenium(VII) bromide, C18H18BrN6Re

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