Qualitative and quantitative analysis of intermolecular interactions in xanthenedione derivatives

The existence of intermolecular interactions and the conformational geometry adopted by molecules are related to biological activity. Xanthenedione molecules are promising and emerging antioxidants and acetylcholinesterase inhibitors. To examine the role of different functional groups involved in the intermolecular interactions and conformational geometries adopted in xanthenediones, a series of three substituted xanthenediones have been crystallized [9‐(3‐hydroxyphenyl)‐3,3,6,6‐tetramethyl‐3,4,5,6,7,9‐hexahydro‐1H‐xanthene‐1,8(2H)‐dione, C₂₃H₂₆O₄, 9‐(5‐bromo‐2‐methoxyphenyl)‐3,3,6,6‐tetramethyl‐3,4,6,7‐tetrahydro‐2H‐xanthene‐1,8(5H,9H)‐dione, C₂₄H₂₇BrO₄, and 3,3,6,6‐tetramethyl‐9‐(pyridin‐2‐yl)‐3,4,6,7‐tetrahydro‐2H‐xanthene‐1,8(5H,9H)‐dione, C₂₂H₂₅NO₃] and their intermolecular interactions analyzed via Hirshfeld analysis. The results show that all the derivatives adopt the same structural conformation, where the central ring has a shallow boat conformation and the outer rings have a twisted boat conformation. The intermolecular interactions in the molecules are predominantly O—H…O, C—H…O and π–π interactions. The optimized structures of the derivatives from theoretical B3LYP/6‐311G** calculations show a good correlation with the experimental structures. The lattice energy involved in the intermolecular interactions has been explored using PIXELC.     

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.     

Remarks on the analysis of torsional energy surfaces of cycloheptane and cyclooctane by molecular mechanics

A modified version (MM 2′) of the Allinger's 1977 force field is checked against cycloheptane and cyclooctane. Cycloheptane is characterized by two pseudorotating itineraries, chair/twist-chair and boat/twist-boat, separated by a barrier of 8.5 kcal mol^?1. The activation energy in the C/TC pseudorotation is estimated to be 0.96 kcal mol^?1, while B and TB transform into each other freely at an energy level 3.8 kcal mol^?1 above the global energy minimum (TC). With cyclooctane the lowest energy is calculated for the boat-chair form which participates in a pseudorotational process with TBC through a saddle point lying 3.5 kcal mol^?1 above BC. The chair/chair and boat/boat families contain only one local minimum, crown and BB, respectively, on the MM 2′ surface. The results are presented as an illustration for quick coverage of torsional energy surface by two-bond driver calculation with the block-diagonal Newton–Raphson minimization, followed by the force search of stationary points by full-matrix Newton–Raphson optimization.     

SYNTHESIS AND CONFORMATIONAL ANALYSIS OF 16H-DINAPHTHO AND 12 H-DIBENZO [D,G][1,3,2]DIOXASILOCINE

Abstract

The conformation of the heterocyclic eight-membered ring in 16H-dinaphtho and 12H-dibenzo [d,g][1,3,2]dioxasilocine was investigated in solution by ¹H NMR spectroscopy. The barrier to ring inversion in the 16H-dinaphtho compound 3a was found to be 8.6±0.2 Kcal/mol and for the 12 H-dibenzo compound 4a, 8±0.2 Kcal/mol. Molecular mechanics calculations show three energy minima conformations for both compounds, boat chair(BC), twist boat(TB) and twist boat boat(TBB). Twist boat form is estimated to be the global minimum for the dibenzo compounds while TBB is the global conformation of the dinaphtho compounds. The result of molecular mechanics calculations are supported by analysis of the ¹H-NMR spectra.     

Interactions Intramoleculaires—X: Etude par RMN des Équilibres Conformationnels de Cyclohexènes Monosubstitutés en 4 et du Dicyano-1,2 Cyclohexane trans

The conformational free energies of CN, Cl and COOC₂H₅ substituents have been evaluated from the PMR spectra of 4-substituted 3,3,6,6-d₄-cyclohexene. The PMR spectra of trans-1,2-dicyano-3,3,6,6-d₄-cyclohexane permit the conformational equilibrium (in different solvents) and the gauche diequatorial interaction energy between the two CN substituents to be estimated.     

Ab initio molecular orbital study of dications of 1,5‐dichalcogenacyclooctanes

The molecular and electronic structures of the dications of three homonuclear and three heteronuclear dichalcogenacyclooctanes (chalcogen = S, Se, or Te) were investigated by ab initio molecular orbital calculations. Four energy‐minimum structures were located for each dication. Three of those (chair‐chair, boat‐boat, and boat‐chair) have the cis configuration with respect to the chalcogen lone pairs, and the remaining one has the trans configuration. The cis isomers were found to be much more stable than the trans isomer. Among the three cis structures, the stability is in the order of boat‐chair > boat‐boat > chair‐chair for all dications. This order can be explained by considering the nonbonding H···H interactions. The chair‐chair structure (C_2v symmetry) of the 1,5‐dithiacyclooctane dication has a very low vibrational frequency of a₂ symmetry, and its LUMO energy is lower than those of boat‐boat and boat‐chair. These can rationalize the fact that in the crystalline state the dication adopts a distorted C₂ chair‐chair conformation. The transition states between the three conformers of the homonuclear dications were also located. The corresponding energy barriers are relatively low, which is consistent with their NMR spectra. The relative stabilities of the homonuclear and heteronuclear dications were elucidated on the basis of their energies and those of the corresponding neutral compounds. © 2000 John Wiley & Sons, Inc. Heteroatom Chem 11:31–41, 2000     

Hydroacridines and related compounds

3,3-Dimethyl-2-oxa-1,2,3,4-tetrahydroacridine and its N-oxide and 3,3,6,6-tetramethyl-2,7-dioxa-sym-octahydroacridine N-oxide were synthesized. On heating with acetic anhydride, the N-oxides form, respectively, acetates of 3,3-dimethyl-2-oxa-1,2,3,4-tetrahydro-4-acridinol and 3,3,6,6-tetramethyl-2,7-dioxa-sym-octahydro-4-acridinol. Hydrolysis of the acetates gives the alcohols themselves. Oxidation of 3,3,6,6-tetramethyl-2,7-dioxa-sym-octahydro-4-acridinol acetate gives the corresponding N-oxide. Oxidation of 3,3,6,6-tetramethyl-2,7-dioxa-sym-octahydro-4-acridinol with manganese dioxide gives 3,3,6,6-tetramethyl-2,7-dioxa-sym-octahydro-4-acridinone.See [9] for communication VII.Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 9, pp. 1218–1221, September, 1971.     

Conformational properties of permethylcyclohexane as compared to cyclohexane: A force field study

The conformational properties of the recently synthesized highly strained permethylcyclohexane molecule 2 have been studied by empirical force field calculations using three different potentials (CFF, MM2, MM2′) and second-derivative optimization methods. A comparison of the results with the conformational behavior of parent cyclohexane 1 leads to the following conclusions: The best conformation of 2 is a chair minimum whose six-membered ring is flatter than that of 1 , due to the strong H…H repulsions introduced by the methyl groups. The twist minimum of 2 is energetically less favorable than the chair by an amount similar to 1 . A potential energy barrier Δ V^# for the chair inversion of 2 of 15.32 kcal/mol results with the CFF, only about three kcal/mol higher than for 1 . The free energy of activation ΔG^# for this process obtained with the CFF is 16.96 kcal/mol (at 333 K) and agrees well with the experimental value of 16.7(2) kcal/mol.¹ MM2 and MM2′ give substantially lower and higher potential energy inversion barriers Δ V^# of 9.03 and 20.29 kcal/mol, respectively, which is attributed to inappropriate torsional energy terms in these force fields. The characteristic difference in the conformational behavior of 2 and 1 concerns the boat forms which are substantially less favorable in the per-methyl compound than in 1 . Expectedly, strong H…H repulsions between the 1,4 diaxial flagpole–bowsprit methyl groups in 2 are responsible for this difference. The particularly high strain of the boat forms of 2 leads to flexibility differences as compared to 1 which in turn affect the relative entropies of the various statiomers (stationary point conformations); e.g., the chair ring inversion activation entropies of 2 and 1 are predicted by the CFF calculations to have opposite signs (?4.82 and 3.41 cal/mol K, respectively, at 298 K). The twist and half-twist statiomers of 2 are much more rigid than those of 1 , which is a consequence of the substantially larger boat barriers along their pseudorotational interconversion paths. The boat transition state separating two enantiomeric twist minima represents a barrier calculated to be more than tenfold higher for 2 than for 1 (CFF Δ V^# values 11.14 and 0.92 kcal/mol, respectively); likewise the half-boat chair inversion barrier of 2 is calculated 5.07 kcal/mol less favorable than the respective half-twist barrier. These statiomers are practically equienergetic in the case of 1 . Except for the axial flagpole–bowsprit CH₃ substituents of the boat forms, the methyl groups of all the relevant calculated statiomers of 2 are more or less staggered. The rotational barrier of the equatorial methyl groups of the chair minimum of 2 is computationally predicted to be 5.78 kcal/mol (ΔG^#), i.e., unusually high. Interesting vibrational effects are brought about by the strong H…H repulsions in 2 ; thus the chair minimum has a largest C? H stretching frequency estimated to be 3050 cm^?1 and involves several particularly low frequencies which have a substantial influence on its entropy. CFF calculations for the lower homologue permethylcyclopentane 5 indicate that its pseudorotational properties are similar to those of cyclopentane 4 , in contradistinction to the pair 2/1 .     

Mechanisms of conformational chirality inversion in bicyclo[4.2.1]nonan-9-one and bicyclo[4.2.2]decane as studied in two-parametric torsional energy surfaces

With the purpose of deciphering conformational inversion processes of typical mobile bicyclic molecules, torsional energy surfaces near the enantiomers of bicyclo[4.2.1]nonan-9-one ( 1 ) and bicyclo-[4.2.2]decane ( 2 ) were prepared using molecular mechanics with an improved two-bond drive technique. Inversion of 1 takes place most favorably via a C_s transition state with the tetramethylene chain over the ethano bridge [ 1B , ΔH^± 6.1 (calculated) vs. 6.8 (observed) kcal/mol]. An alternative pathway involving a C_s local energy minimum ( 1C ), in which the tetramethylene chain is bent over the carbonyl, has a barrier 2.4 kcal higher than 1B . The global energy minimum conformation of 2 has boat–chair cyclooctane and twist–boat cyclohexane rings (BCTB ), and enantiomerizes into its mirror image (BCTB ') via three intermediates: TCTB , CB , and TCTB '. The highest point in the proposed pathway, a saddlepoint CB , is calculated to lie 8.0 kcal/mol above BCTB (observed ΔH^± 7.8 kcal/mol). The advantage of the two-parametric over the one-parametric torsional energy surface is discussed.     

Metallacycloalkanes : II. Reactions of α,α′-bipyridyl-5-nickela-3,3,7,7-tetramethyl-trans-tricyclo[4.1.0.02,4]heptane

The title compound (II) underwent reductive elimination on treatment with maleic anhydride, tetracyanoethylene or triphenylphosphite to give 3,3,6,6,-tetramethyl-trans-tricyclo[3.1.0.0^2,4]hexane (III). With triphenylphosphite bi(2,2-dimethylcyclopropyl) (V) and 1-(2,2-dimethylcyclopropyl)-3-methyl-1,3-butadiene (VI) were also formed. Acidolysis of II with either HCl, malonic acid or methanol gave V. An intermediate complex α,α′-bipyridyl(phenoxy)-3-nickel-1,1′-bi-(2,2′-dimethylcyclopropyl) (VIII) was isolated by reaction of II with phenol. Methylene dibromide reacts with II to give III and 3,3,7,7-tetramethyl-trans-tricyclo[4.1.0.0^2,4]heptane (IV). With triethylaluminum and II complete exchange of the alkyl groups occurred and V was released on hydrolysis. Trifluoroborane diethyl ether and II gave 3,3,6,6-tetramethylcyclohexa-1,4-diene in a rearrangement-displacement reaction. The cyclodimerisation of 3,3-dimethylcyclopropene (I) to III catalysed by II and the fact that II can be recovered from the reaction mixture provides strong evidence for the intermediacy of metallacyclopentanes in these transition-metal-catalysed [2π + 2π] cyclo-additions.     

Photochemical transformations of 3-alkyl-3-ferrocenylcyclopropenes

Photolysis of 3-ferrocenyl-3-methyl- and 3-ferrocenyl-3-isopropylcyclopropenes was studied. Sensitized irradiation (triplet excitation) afforded [2+2]-cycloaddition products, viz., tricyclohexane derivatives. Direct irradiation (singlet excitation) of methyl-substituted ferrocenylcyclopropene gave rise to 2-ferrocenylbut-1-en-3-yne and trans-2-ferrocenylbut-2-ene. The isopropyl analog was converted into 1-ferrocenyl-4,4-dimethylcyclobutene. The reaction of this cyclopropene with 2-ferrocenyl-3-methylbut-1-ene afforded 1,3-diferrocenyl-3-isopropyl-6,6-dimethylcyclohexene. The latter compound and 3,6-diferrocenyl-3,6-diisopropyltricyclo[3.1.0.0^2,4]hexane were studied by X-ray diffraction analysis. Possible reaction pathways are discussed.     

Ab initio conformational analysis of 1,5‐dithiacyclooctane, 1,5‐diselenacyclooctane,and 1,5‐ditelluracyclooctane

Energy‐minimum structures of 1,5‐dithiacyclooctane (1,5‐DTCO), 1,5‐diselenacyclooctane (1,5‐DSeCO), and 1,5‐ditelluracyclooctane (1,5‐DTeCO) were calculated by the ab initio molecular orbital method. Nine energy‐minimum structures were obtained for each compound. A twist‐boat–chair (TBC) structure is the most stable for 1,5‐DTCO and 1,5‐DSeCO, whereas a boat–boat (BB) structure is the most stable in 1,5‐DTeCO. The TBC conformer of 1,5‐DTCO has received little attention so far. The energy gap between HOMO and NHOMO in the TBC conformer of 1,5‐DTCO is in good agreement with the experimental data (photoelectron spectrum). For 1,5‐DTCO and 1,5‐DSeCO, the boat–chair (BC) conformer in which two chalcogen atoms face each other has the highest HOMO energy among the nine conformers, and the energy barriers between the TBC and BC conformers were calculated to be relatively low for these compounds. Therefore, a conformational change from the TBC to the BC is predicted to occur before these compounds are oxidized in solution. © 1999 John Wiley & Sons, Inc. Heteroatom Chem 10: 159–166, 1999     

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.     

Kinetics of thermal gas-phase isomerizations and fragmentations of cis- and trans-1-(E)-propenyl-2-methylcyclobutanes at 275 degrees C

Kinetic studies of the thermal isomerization and fragmentation reactions exhibited by cis- and trans-1-(E)-propenyl-2-methylcyclobutanes at 275 degrees C in the gas phase have provided first-order rate constants for cis,trans interconversions of the cyclobutanes, 1,3-carbon migrations leading to 3,4- and 3,6-dimethylcyclohexenes, isomerizations providing directly and indirectly four acyclic dienes, and fragmentations to ethylene, propene, and mixtures of pentadienes and hexadienes. Both cis and trans isomers of 1-(E)-propenyl-2-methylcyclobutane form trans-3,4-dimethylcyclohexene faster than they are converted to cis-3,4-dimethylcyclohexene; the trans reactant gives rise to cis-3,6-dimethylcyclohexene in preference to its trans isomer, while the cis starting material gives neither at measurable rates; both form the relatively minor product 1,6-(Z)-octadiene. The rate constants derived from 35 kinetic runs starting with four distinct 1-(E)-propenyl-2-methylcyclobutane samples are consistent to within narrow error limits. The stereomutations, isomerizations, and fragmentations of the 1-(E)-propenyl-2-methylcyclobutanes are interpreted in terms of competitive processes involving conformationally flexible short-lived 2-(E)-octene-4,7-diyl and 3-methyl-5-(E)-heptene-1,4-diyl diradicals.     

The crystal and molecular structure and solid state conformation of 2,2,4,4,6,6,-hexamethylcyclohexanetrione

The crystal and molecular structure of the title compound have been determined by X-ray methods. Crystals are monoclinic, space group P2₁/n with a= 6.076(2), b=14.927(3), c = 13.200(3) Å, β=96.71(5)⁰. The structure was solved by direct methods and refined by least-squares to a final R value of 0.05 using 1358 significant (I 1.5σ(I)) reflections out of a total 2095 measured. The molecule adopts a slightly distorted unsymmetric boat conformation, in between two (of three) degenerate perfect C₂ boat structures which it is proposed are intercon-vertible by a confonnational ripple of low energy.     

Restricted rotation of the amino group and ring inversion in highly substituted anilines. A dynamic NMR and computational study

The reaction of cyclic ylidene malononitriles with acetylene (di)carboxylic acid esters led to the production of nine bicyclic systems incorporating highly substituted (5/6) anilines. The free energy of activation (ΔG^#) for the restricted rotation about the aniline-NH₂ bond was experimentally measured in each case and a correlation was evident between the increase in steric strain in the ground state, the electron withdrawing capabilities of the ring substituents, and a reduction in the rotational barrier. For four of the compounds, the slow ring interconversion (chair?chair) for the annelated saturated seven-membered ring that formed part of the bicyclic system was also evident. In these four compounds, both dynamic processes were also studied theoretically using ab initio methods whilst the ring interconversion was additionally studied using molecular dynamic simulations. The interconversion between the two stable chair forms was deemed to occur via a conformation series consisting of chair?boat?twist-boat?boat?chair.     

Catalytic effect of cuprous ions on the thermal decomposition of 3,3,6,6-tetramethyl-1,2,4,5-tetraoxane in methanol solution

Thermal decomposition of 3,3,6,6-tetramethyl-1,2,4,5-tetraoxane was examined in methanol solution (1.69×10⁻² M) containing cuprous ions (5.05×10⁻⁷ M) in the temperature range from 130 to 166°C using UV spectroscopy as analytical method. The ion-catalyzed reaction follows first-order kinetics with respect to the peroxide and added cuprous ions. The temperature effect on the rate of thermal decomposition of the title compound was described by the corresponding Arrhenius equations, and its stability in solution was estimated on a quantitative level. The activation parameters of the initial step of decomposition of 3,3,6,6-tetramethyl-1,2,4,5-tetraoxane were determined (ΔH ^≠ = 14.7±0.8 kcal mol⁻¹; ΔS ^≠ = −38.9±1.4 cal mol⁻¹ K⁻¹; ΔG ^≠ = 31.0±0.8 kcal mol⁻¹). Electron-transfer mechanism was proposed for the reaction under study. The text was submitted by the authors in English.     

Kinetics and mechanism of the thermal decomposition reaction of acetone cyclic diperoxide in the gas phase

The kinetics of the thermal decomposition reaction of gaseous 3,3,6,6-tetramethyl-1,2,4,5-tetroxane (ACDP) in the presence of n-octane was studied in the 403.2–523.2 K temperature range. This reaction yields acetone as the organic product. Under optimum conditions, first-order kinetics were observed, included when the S/V ratio of the Pyrex reaction vessel was increased by a nearly six-fold factor. In the range 443.2–488.2 K the temperature dependence of the rate constants for the unimolecular reaction in conditioned vessels is given by In k₁/(s^?1) = (31.8 ± 2.5) ? [(39.0 ± 2.5)/RT]. The value of the energy of activation in kcal/mol correspond to one O? O bond homolysis of the ACDP molecule in a stepwise biradical initiated decomposition mechanism. At the lower reaction temperatures as well in preliminary experiments participation of a surface catalyzed ACDP decomposition process could be detected. © 1994 John Wiley & Sons, Inc.     

Synthesis of new highly organosoluble metallophthalocyanines with 1,8-dioxo-octahydroxanthene substituents

New highly organosoluble metallophthalocyanines (M = Zn, Co, Ni and Cu) bearing four [4-(3,3,6,6-tetramethyl-1,8-dioxo-2,3,4,5,6,7,8,9-octahydro-1H-xanthen-9-yl)phenoxy] substituents at peripheral positions have been prepared by tetramerization of 4-[4-(3,3,6,6-tetramethyl-1,8-dioxo-dodecahydro-1H-xanthen-9-yl)phenoxy]phthalonitrile in 2-(dimethylamino)ethanol using microwave irradiation or conventional heating. Ni(II), Co(II), and Cu(I) chloride were employed in order to synthesize the corresponding metal phthalocyanines and Zn(OAc)₂ was used for the preparation of the zinc phthalocyanines. 4-[4-(3,3,6,6-Tetramethyl-1,8-dioxo-2,3,4,5,6,7,8,9-octahydro-1H-xanthen-9-yl)phenoxy]phthalonitrile was obtained by nucleophilic displacement of the nitro group in 4-nitrophthalonitrile with 9-(4-hydroxyphenyl)-3,3,6,6-tetramethyl-3,4,6,7-tetrahydro-2H-xanthene-1,8(5H,9H)-dione. 9-(4-Hydroxyphenyl)-3,3,6,6-tetramethyl-3,4,6,7-tetrahydro-2H-xanthene-1,8(5H,9H)-dione was synthesized efficiently from dimedone and 4-hydroxybenzaldehyde. All the phthalocyanines are soluble in DMSO, DMF, CHCl₃, THF, CH₂Cl₂, and CH₃CN. The new compounds were characterized by IR, NMR, and UV–vis spectroscopy, elemental analysis, and thermogravimetric analysis.