A Conformational Study on Silacyclohexane. Comparison of ab initio (HF,MP2), DFT,and Molecular Mechanics Calculations. Conformational Energy Surface of Silacyclohexane

The structures and relative energies for the basic conformations of silacyclohexane 1 have been calculated using HF, RI‐MP2, RI‐DFT and MM3 methods. All methods predict the chair form to be the dominant conformation and all of them predict structures which are in good agreement with experimental data. The conformational energy surface of 1 has been calculated using MM3. It is found that there are two symmetric lowest energy pathways for the chair‐to‐chair inversion. Each of them consists of two sofa‐like transition states, two twist forms with C₁ symmetry (twist‐C₁), two boat forms with Si in a gunnel position (C₁ symmetry), and one twist form with C₂ symmetry (twist‐C₂). All methods calculate the relative energy to increase in the order chair < twist‐C₂ < twist‐C₁ < boat. At the MP2 level of theory and using TZVP and TZVPP (Si atoms) basis sets the relative energies are calculated to be 3.76, 4.80, and 5.47 kcal mol^–1 for the twist‐C₂, twist‐C₁, and boat conformations, respectively. The energy barrier from the chair to the twisted conformations of 1 is found to be 6.6 and 5.7 kcal mol^–1 from MM3 and RI‐DFT calculations, respectively. The boat form with Si at the prow (C_s symmetry) does not correspond to a local minimum nor a saddle point on the MM3 energy surface, whereas a RI‐DFT optimization under C_s symmetry constraint resulted in a local minimum. In both cases its energy is above that of the chair‐to‐twist‐C₁ transition state, however, and it is clearly not a part of the chair‐to‐chair inversion.     

Conformational analysis of cyclic sulphites. 2-Oxo 1,3,2-dioxathiane-4-spiro-4-tert-butyl-cyclohexanes

Three series of 4-spirosulphites, a new class of cyclic sulphites, were synthesized and five couples of diastereoisomers isolated. Their structural analysis, using ¹H NMR coupling constants and SO stretching vibration as conformational probes, shows a large variety of ananchomeric chair forms and multicomponent equilibria for the cyclic sulphite moiety, the cyclohexane part of the molecule remaining in the chair form. Related to the occurrence of severe interactions involving the 5-methyl or 6-tert. butyl substituent, several twist forms were encountered, with 2,5-axis and isoclinal SO or 1,4-axis and axial or equatorial SO as a consequence of the weak free energy difference between chair and twist conformations in the cyclic sulphite series.     

Die Konformeren des 5,5-Dimethyl-3,7-dithia-1,2-benzocycloheptens-(1) und ihre Umwandlungen Konformative Beweglichkeit flexibler Ringsysteme—XV. Untersuchungen mit Hilfe der Protonenresonanzspektroskopie

The temperature dependence of the NMR spectrum of 5,5-dimethyl-3,7-dithia-1,2-benzocyclo-heptene-( 1 ) is described and discussed. This compound occurs in two conformers with different topographies of the seven membered ring. From the chemical shift of the 2 geminal methyl groups (obtained by low-temperature spectra) it can be shown that the ring occurs in one case in the chair form and in the other case in the twist form. The free conformational energy of the twist form is only about 20 cal/mole. Two conformational changes can be distinguished: the conversion between chair and twist forms and the pseudorotation of the twist forms. The free activation enthalpies of the conversion (ΔG_V^≠) and the pseudorotation (ΔG_P^≠) are 12·6 ± 0·1 Kcal/mole (at ?12°C) and 8·3 ± 0·3 Kcal/mole (at ?95°C) respectively.     

Conformational analysis: XIV—A 1H n.m.r. conformational study of methyl substituted 2-oxo-1,3,2-dioxathians to confirm the predominance of chair forms in the trimethylene sulphite series

Seven isomeric 4,5,6-trimethyl-2-oxo-1,3,2-dioxathians, cis-4-trans-6-dimethyl-r-2-oxo-1,3,2-dioxathian and two isomeric 4,5,5,6-tetramethyl-2-oxo-1,3,2-dioxathians were prepared and their ¹H n.m.r. spectra analysed. The values of the vicinal coupling constants reported earlier for the cis-4-trans-6 compound were shown to be erroneous. In all cases the values of the vicinal coupling constants (and those of the chemical shifts) are indicative of a single chair conformation or a chair-chair equilibrium, in contrast to earlier reports on the significant contribution of twist forms but in agreement with an electron diffraction study. The chair form is ? 31 kJ mol^?1 thermochemically more stable than the twist form.     

Steric structure of phosphorus-containing heterocycles Communication 36. 2-dialkylamino-1,3,2-dioxaphosphepines with tetracoordinated phosphorus

Conclusions In conformity with the data of¹H NMR, DM, and the Kerr effect for 2-dialkylamino-2-oxo(thiono, seleno)-1,3,2-dioxaphosphepines, a conformational equilibrium of two forms of twist and chair with an equatorial dialkylamino group is observed in solutions. The equilibrium is displaced in favor of the latter.Then the products were crystallized after removing a part of the solvent in vacuo.Translated from Izvestiya Akademii Nauk SSSR, Seriya Khimicheskaya, No. 4, pp. 799–803, April, 1985.     

AB INITIO MOLECULAR ORBITAL STUDY OF 1,2-DITHIANE AND 1,2,4,5-TETRATHIANE

Ab initio calculations at HF/6-31+G? level of theory for geometry optimization, and MP2/6-31+G?//HF/6-31+G? and B3LYP/6-31+G?//HF/6-31+G? levels for a single-point total energy calculation, are reported for the chair and twist conformations of 1,2-dithiane (1), 3,3,6,6-tetramethyl-1,2-dithiane (2), 1,2,4,5-tetrathiane (3), and 3,3,6,6-tetramethyl-1,2,4,5-tetrathiane (4). The C₂ symmetric chair conformations of 1 and 2 are calculated to be 21.9 and 8.6 kJ mol^?1 more stable than the corresponding twist forms. The calculated energy barriers for chair-to-twist processes in 1 and 2 are 56.3 and 72.8 kJ mol^?1, respectively. The C_2h symmetric chair conformation of 3 is 10.7 kJ mol^?1 more stable than the twist form. Interconversion of these forms takes place via a C₂ symmetric transition state, which is 67.5 kJ mol^?1 less stable than 3-Chair. The D₂ symmetric twist-boat conformation of 4 is calculated to be 4.0 kJ mol^?1 more stable than the C_2h symmetric chair form. The calculated strain energy for twist to chair process is 61.1 kJ mol^?1.     

Vibrational spectra and conformational analysis of 1,3-dithia-5,6-benzocycloheptenes

The equilibrium between the chair and boat forms of 1,3-dithia-5,6-benzocycloheptene and its 2-Me, t-Bu, and Ph derivatives has been established by Raman and IR spectroscopy, and their spectroscopic characteristics have been revealed. In liquids the chair forms of 1,3-dithia(or dioxa)-5,6-benzocycloheptenes have C_s symmetry for the ring, and the twist forms of the seven-membered acetals have C₂ symmetry.Translated from Izvestiya Akademii Nauk SSSR, Seriya Khimicheskaya, No. 9, pp. 2014–2019, September, 1989.     

Analyse Conformationnelle par RMN du Proton des Oxo-2 Oxathiazannes-1,2,3 (Sulfinamates Cycliques) Diversement Substitués en 3, 4 et 6

In this study, carried out with 16 compounds, the chair form with an axial S?O group (CA) is found, in the absence of C-4, C-5 and C-6 substituents, to be the most stable (ΔG>8,4 kJ mole^?1), as previously reported for analogous cyclic sulfites. When methyl or tert-butyl substituents are present on the 4 and 6 carbon atoms, the conformation of the ring depends on their respective orientation towards the S?O group, and on the nature of the substituent of the nitrogen atom. For the trans isomers, the conformation remains anancomeric chair (CA) except when important gauche interactions exist: thus the strong Me/tBu gauche interaction in the 3-tert-butyl-4-t-methyl-2-r-oxo-1,2,3-oxathiazan induces a twist form with a 3,6-axis and an axial S?O group (CNA). When the 4- or 6-substituent is cis, the conformation of the sulfinamate may be either a chair form with an axial S?O group (CA), if the 4-substituent is a methyl, (even with a tert-butyl group in the 3-position which would be in the axial orientation) or a twist form with a 1,4-axis and an axial S?O group (COA) if the 4-substituent is a tert-butyl. Unlike cyclic sulfites, the equatorial SO chair form (CE) and the twist forms with a 2,3-axis and an isoclinal S?O group (CS, CS′) are rarely involved.     

The structure of the antibiotic hedamycin—III : C NMR spectra of hedamycin and kidamycin

The ¹³C NMR spectra of hedamycin, kidamycin and some of their derivatives have been fully assigned. Proton coupling constants and ¹³C NMR acetylation shifts indicate that the conformations of the highly substituted tetrahydropyran rings in solution are chair forms for ring E, as well as for ring F in isokidamycins, but a twist form for ring F in hedamycins and kidamycins.     

Effects of methyl groups on the geometry and conformational equilibrium of 1,3-dioxanes

The geometries and energies of polymethyl-1,3-dioxanes were studied by molecular mechanics calculations. Buttressing effects of the Me groups are discussed. The chair/twist conformational equilibrium of 1,3-dioxanes having two syn-axial Me groups in the chair were calculated, and a twist form (the 1,4-twist) is found to be more stable than the chair only for 9 and 14, chair and 2,5-twist form are of comparable energies for 10 and 13, and the chair is considerably favored in 11 and 12. The chair/1,4-twist energy difference of 1 was calculated to be only 16.4 kJ mol^?1. Ring inversion of 1 goes through a transition state with C-C-C-O coplanar with a calculated activation enthalpy of 28.3 kJ mol^?1.     

1H NMR spectra,dipole moments,and conformations of 3-oxo-6,7-benzo-1,5,3-dioxaphosphepines

¹H NMR spectroscopy, measurements of dipole moments, and the Kerr effect have been used to study the conformational structure in solutions of 3-X-3-oxo-6,7-benzo-1,5,3-dioxaphosphepines (X=Me, Et, Ph, Cl, NEt₂, OEt, OPh). On the basis of x-ray diffraction data, by means of the Dillen-Geise method, possible conformers of the seven-membered ring have been described quantitatively: chair, twist, and twist-boat. It has been shown that the compounds are characterized by a three-component equilibrium of chair and flexible forms. The relative populations of the conformers depend on the nature of the substituent X. The relationships in internal rotation around the P-Ph and P-O(R) bonds are discussed.Translated from Izvestiya Akademii Nauk SSSR, Seriya Khimicheskaya, No. 7, pp. 1517–1523, July, 1991.     

cis‐[(4R,5R)‐4,5‐Bis­(amino­methyl)‐2,2‐di­methyl‐1,3‐dioxolane‐N,N′](malonato‐O,O′)­platinum(II), an anticancer agent

In the title compound, [Pt(C₃H₂O₄)(C₇H₁₆N₂O₂)], the Pt atom is coordinated to two O and two N atoms in a square‐planar arrangement. The two independent mol­ecules, which have very similar structures, are approximately related by pseudo‐twofold screw‐axis symmetry. The six‐membered chelate ring in the leaving ligand assumes a conformation intermediate between the half‐chair and boat forms. The seven‐membered ring in the carrier ligand assumes a twist‐chair conformation and the oxolane ring assumes an envelope conformation. The crystal packing consists of extensive hydrogen‐bonding networks which form two‐dimensional molecular layers, and there are weak van der Waals interactions between these layers.     

(24R)‐24,25‐Dihydroxycyclo­artan‐3‐one

In the title compound, C₃₀H₅₀O₃, the three six‐membered rings adopt chair, twist and twist‐boat conformations. The five‐membered ring is in a slightly distorted envelope conformation. The substituent on the five‐membered ring is in an extended conformation, with its two hydroxyl O atoms forming an intramolecular hydrogen bond. One of these O atoms also forms an intermolecular hydrogen bond with the oxy­gen of the carbonyl group in a neighbouring mol­ecule.     

π–π Stacking Interaction in an Oxidized CuII–Salen Complex with a Side-Chain Indole Ring: An Approach to the Function of the Tryptophan in the Active Site of Galactose Oxidase

In order to gain new insights into the effect of the π–π stacking interaction of the indole ring with the Cu^II–phenoxyl radical as seen in the active form of galactose oxidase, we have prepared a Cu^II complex of a methoxy-substituted salen-type ligand, containing a pendent indole ring on the dinitrogen chelate backbone, and characterized its one-electron-oxidized forms. The X-ray crystal structures of the oxidized Cu^II complex exhibited the π–π stacking interaction of the indole ring mainly with one of the two phenolate moieties. The phenolate moiety in close contact with the indole moiety showed the characteristic phenoxyl radical structural features, indicating that the indole ring favors the π–π stacking interaction with the phenoxyl radical. The UV/Vis/NIR spectra of the oxidized Cu^II complex with the pendent indole ring was significantly different from those of the complex without the side-chain indole ring, and the absorption and CD spectra exhibited a solvent dependence, which is in line with the phenoxyl radical–indole stacking interaction in solution. The other physicochemical results and theoretical calculations strongly support that the indole ring, as an electron donor, stabilizes the phenoxyl radical by the π–π stacking interaction.     

Computational study of sulfoxides of thiacyclohexane, 4‐silathiacyclohexane, 4‐fluoro‐4‐silathiacyclohexane,and 4,4‐difluoro‐4‐silathiacyclohexane: Relative energies of conformations and sulfinyl oxygen stabilized pentacoordinate silicon in boat and twist structures

Second‐order Møller‐Plesset theory (MP2) has been used to calculate the equilibrium geometries and relative energies of the chair, 1,4‐twist, 2,5‐twist, 1,4‐boat, and 2,5‐boat conformations of thiacyclohexane 1‐oxide (tetrahydro‐2H‐thiopyran 1‐oxide), 4‐silathiacyclohexane 1‐oxide, cis‐ and trans‐4‐fluoro‐4‐silathiacyclohexane 1‐oxide, and 4,4‐difluoro‐4‐silathiacyclohexane 1‐oxide. At the MP2/6‐311+G(d,p) level of theory, the chair conformer of axial thiacyclohexane 1‐oxide is 0.99, 5.61, 5.91, 8.57, and 7.43 kcal/mol more stable (ΔE) than its respective equatorial chair, 1,4‐twist, and 2,5‐twist conformers and 1,4‐boat and 2,5‐boat transition states. The chair conformer of equatorial thiacyclohexane 1‐oxide is 4.62, 6.31, 7.56, and 7.26 kcal/mol more stable (ΔE) than its respective 1,4‐twist and 2,5‐twist conformers and 1,4‐boat and 2,5‐boat transition states. The chair conformer of axial 4‐silathiacyclohexane 1‐oxide is 1.79, 4.26, 3.85, and 5.71 kcal/mol more stable (ΔE) than its respective equatorial chair, 1,4‐twist, and 2,5‐twist conformers and 2,5‐boat transition state. The 2,5‐twist conformer of axial 4‐silathiacyclohexane 1‐oxide is stabilized by a transannular interaction between the sulfinyl oxygen and silicon, to give trigonal bipyramidal geometry at silicon. The chair conformer of equatorial 4‐silathiacyclohexane 1‐oxide is 2.47, 7.90, and 8.09 kcal/mol more stable (ΔE) than its respective 1,4‐twist, and 2,5‐twist conformers and 2,5‐boat transition state. The chair conformer of axial cis‐4‐fluoro‐4‐silathiacyclohexane 1‐oxide is 4.18 and 5.70 kcal/mol more stable than its 1,4‐twist conformer and 2,5‐boat transition state and 1.51 kcal/mol more stable than the chair conformer of equatorial cis‐4‐fluoro‐4‐silathiacyclohexane 1‐oxide. The chair conformer of axial trans‐4‐fluoro‐4‐silathiacyclohexane 1‐oxide is 5.02 and 6.11 kcal/mol more stable than its respective 1,4‐twist conformer and 2,5‐boat transition state, but is less stable than its 2,5‐twist conformer (ΔE = ?1.77 kcal/mol) and 1,4‐boat transition state (ΔE = ?1.65 kcal/mol). The 2,5‐twist conformer and 1,4‐boat conformer of axial trans‐4‐fluoro‐4‐silathiacyclohexane 1‐oxide are stabilized by intramolecular coordination of the sulfinyl oxygen with silicon that results in trigonal bipyramidal geometry at silicon. The chair conformer of axial 4,4‐difluoro‐4‐silathiacyclohexane 1‐oxide is 3.02, 5.16, 0.90, and 6.21 kcal/mol more stable (ΔE) than its respective equatorial chair, 1,4‐twist, and 1,4‐boat conformers and 2,5‐boat transition state. The 1,4‐boat conformer of axial 4,4‐difluoro‐4‐silathiacyclohexane 1‐oxide is stabilized by a transannular coordination of the sulfinyl oxygen with silicon that results in a trigonal bipyramidal geometry at silicon. The relative energies of the conformers and transition states are discussed in terms of hyperconjugation, orbital interactions, nonbonded interactions, and intramolecular sulfinyl oxygen–silicon coordination. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

Konformative Beweglichkeit Flexibler Ringsysteme—XIII: Untersuchungen mit Hilfe der Protonenresonanzspektroskopie die Konformation des Ungesättigten Siebenringes im Benzocyclohepten und in symmetrisch substituierten derivaten

The confromations of the unsaturated seven membered ring in 4,4,6,6-tetradeuterium-1,2-benzocycloheptene-(1) ( 1 ) and five benzocycloheptene derivatives were determined by NMR spectroscopy. For all investigated compounds at ?80°C only one conformer was present in detectable quantity. By analysis of the NMR data – molecular symmetry, coupling constants and chemical shift – it can be shown that the conformation is always the chair form. The free conformational enthalpy of both the other conformations with boat or twist form of the ring is for all six compounds more than 1.8 kcal/mole. The experimental results agree with those from model calculations: thus for benzocycloheptene, the 5,5-dimethyl derivative ( 2 ) and the 4,4,6,6-tetramethyl derivative ( 4 ) the lowest energy was found for the chair conformation; the second most stable conformations were found to be the boat for 1 and 4 , and the twist form for 2 .     

Molecular mechanics conformational analysis of cyclononane using the RIPS method and comparison with quantum-mechanical calculations

The recently reported Random Incremental Pulse Search (RIPS) technique has been used to probe the conformational energy surface of cyclononane. The stochastic method permits searching of the potential energy surface for all minimum-energy conformations. The search located all previously reported structures together with three additional conformations that were not found by earlier, primitive searching techniques. Two of these structures are high-nergy skew forms, and the third is a low-energy conformer that should contribute significantly to the overall equilibrium set of cyclononane conformations. The global minimum has been found to be the D₃ symmetrical twist chair-boat (TBC) form in accordance with previous studies. The newly discovered low-energy structure, which lies only 2.2 kcal/mol above the global minimum, has been designated twist chair-twist chair (TCTC). The two higher energy conformers are skewed chair-chair (SCC) and skewed boat-boat (SBB) forms that are 5.7 kcal/mol and 10.4 kcal/mol above the global minimum, respectively. The seven reported conformations were reanalyzed quantum mechanically (AM 1), and a comparison between MM 2 and AM 1 results is presented.     

Fragmentation and isomerization reactions of phenyl substituted 2-oxo-1,3,2-dioxathianes (trimethylene sulfites)

The preparation and Grob-like fragmentation of several phenyl substituted 2-oxo-1,3,2-dioxathianes (trimethylene sulfites) have been examined. Preparation of the 4,4,6-triphenyl derivatives gives a chair S = O equatorial isomer which fragments readily in polar solvents to produce benzaldehyde and 1,1-diphenylethylene. Isomerization to an unreactive twist boat isomer occurs as a minor reaction in solution and in the solid state on prolonged storage. Activation parameters and substituent effects on the fragmentation reaction are consistent with an ionic mechanism. The diphenyl derivatives react only in the presence of boron trifluoride etherate giving mainly isomerization to the stable chair, S = O axial form; fragmentation is a minor pathway.     

Gas phase structures, energetics, and potential energy surfaces of disilacyclohexanes

The molecular structures of 1,4-, 1,3-, and 1,2-disilacyclohexanes (denoted as 14, 13, and 12, respectively) were investigated by means of gas electron diffraction (GED). Each molecule was found to possess a chair as the most stable conformation in the gas phase, the point group being C(2h), C(s), and C(2), respectively. Experimental GED structures are in good agreement with theoretical calculations (MP2/cc-pVTZ and B3LYP/cc-pVTZ). A qualitative ring strain analysis suggests 14 to be the most stable and 12 the least stable of the parent disilacyclohexanes. Relative energy calculations with the G4 model chemistry protocol, on the other hand, predict 13 to be the most stable isomer, 5.9 and 14.2 kcal/mol more stable than 14 and 12, respectively. The enhanced stability of 13 compared to 14 is in agreement with an analysis on endocyclic bond lengths and bond polarities. The heats of formation (G4 calculations) are predicted to be -12.3, -18.1, and -3.9 kcal/mol for 14, 13, and 12, respectively. The potential energy surface (PES) and the lowest energy path for the chair-to-chair inversion have been calculated for each isomer. In addition to the two chair forms in each case and some half-chair or sofa-like transition states (four in the case of 14, and two in the case of 13), there are two twist forms found as stationary points on the PES of 14, six twist and six boat forms on the PES of 13, and four twist and six boat forms on the PES of 12.