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.     

The molecular geometries of some cyclic nitramines in the gas phase

The structural parameters of 1,3,5-trinitro-1,3,5-triazacyclohexane (RDX), (CH₂NNO₂)₃, 1,3-dinitro-1,3-diazacyclopentane (DDCP), CH₂(CH₂NNO₂)₂, andN-nitropyrrolidine (NP), (CH₂)₄NNO₂, have been determined by electron diffraction.The six-membered ring of RDX has a chair form with axial positions of the nitro groups and close to planar bond geometry of the amine nitrogen atoms. The overallC ₃ symmetry of the molecule is in agreement with the experimental data.The conformation of the five-membered ring in DDCP is a half-chair ofC ₂ symmetry, while that in NP is an envelope ofC _S symmetry. The nitro groups are in equatorial positions in both molecules. The conformations of pyrrolidine and imidazolidine cycles show interesting features.The pyramidal geometry of the amine nitrogen atom bonds flattens in going from pyrrolidine andN-chloropyrrolidine to NP and DDCP and then to RDX and to dimethylnitramine (DMNA), (CH₃)₂NNO₂.     

The dimer,trimer and 1,2,4‐tri­thiol­ane of adamantane­thione

The mol­ecules of di­spiro­[1,3‐dithietane‐2,2′:4,2′′‐diadamantane], C₂₀H₂₈S₂, have crystallographic C_i symmetry, as well as local D_2h symmetry, and a planar 1,3‐dithietane ring. The mol­ecules of tri­spiro­[1,3,5‐tri­thia­ne‐2,2′:4,2′′:6,2′′′‐triadamantane], C₃₀H₄₂S₃, have approximate C₂ symmetry and the 1,3,5‐tri­thia­ne ring has a twist–boat conformation. The C—S—C bond angles within the ring are about 8° larger than observed in most related 1,3,5‐tri­thia­ne structures. In di­spiro­[1,2,4‐tri­thiol­ane‐3,2′:5,2′′‐diadamantane], C₂₀H₂₈S₃, the mol­ecules have local C₂ symmetry and the 1,2,4‐tri­thiol­ane ring has a half‐chair conformation.     

A dynamic nuclear magnetic resonance spectroscopic study of conformational properties of 1,3-dioxepane and 4,4,7,7-tetramethyl-1,3-dioxepane

The 251 MHz ¹H and the natural abundance 63.1 MHz ¹³C NMR spectra of 1,3-dioxepane (1) and 4,4,7,7-tetramethyl-1,3-dioxepane (2) have been investigated over the temperature range of 5 to ?180 °C. While the spectra of 1 show no dynamic NMR effect, compound 2 exists in solution as a 1:1 mixture of a symmetrical (C₂) twist-chair and its mirror image conformation. The free energy barrier for the conformational racemization of 2 is 43 kJ mol^?1 (10.3 kcal mol^?1). Interconversion paths between various conformations of 2 are discussed. Compound 1 is suggested to have a symmetrical (C₂) twist-chair conformation which is rapidly pseudorotating via a chair conformation to achieve a time averaged symmetry of C_2v, even at ?180 °C.     

2,5‐O‐Methyl­ene‐d‐mannitol: two polymorphs and the NaI complex

Two polymorphs of the title compound, (4R,5R,6R,7R)‐4,7‐bis­(hydroxy­methyl)‐1,3‐dioxepane‐5,6‐diol, C₇H₁₄O₆, both have Z′ = 2 at 100 K, and differ in their hydrogen‐bonding patterns. The sodium iodide complex, NaI·C₇H₁₄O₆, is isomorphous with the NaCl complex, and has the mannitol, cation and anion all lying on twofold axes. The dioxepane rings of all three mol­ecules are in the twist‐chair conformation.     

1,3(R):4,6(R)‐Di‐O‐benzyl­idene‐d‐mannitol

The title compound, C₂₀H₂₂O₆, has crystallographic twofold symmetry. The central six‐C‐atom chain has an extended conformation similar to that of d ‐mannitol, with two independent C—C—C—C torsion angles of 165.69 (14) and 177.60 (12)°. The 1,3‐dioxane ring has a chair conformation. All chiral centers have the R configuration.     

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.     

Cyclodimerization of 1-(Dimethoxyniethyl)-5,6-dimethylidene-7-oxa-bicyclo[2.2.1]hept-2-ene Induced by Nonacarbonyldiiron. Crystal Structure of (1RS, 2SR, 3RS, 4RS, 4aRS, 9aSR)- Tricarbonyl[C, 2,3, C-η-(1,4-epoxy-1,5-bis(dimethoxymethyl)-2,3-dimethylidene-1,2,3,4,4a,9,9a,10-octahydroanthracene)]iron

The transition-metal-carbonyl-induced cyclodimerization of 5,6-dimethylidene-7-oxabicyclo[2.2.1]hept-2-ene is strongly affected by substitution at C(1) While 5,6-dimethylidene-7-oxabicyclo[2.2.1]hept–2-ene-l-methanol ( 7 ) refused to undergo [4 + 2]-cyclodimerization in the presence of [Fe₂(CO)⁹] in MeOH, 1-(dimethoxymethyl)-5,6-di-methylidene-7-oxabicyclo[2.2.1]hept-2-ene ( 8 ) led to the formation of a 1.7:1 mixture of ‘trans’ ( 19, 21, 22 ) vs. ‘cis’ ( 20, 23, 24 ) products of cyclodimerization together with tricarbonyl[C, 5,6, C-η-(l-(dimethoxymethyl)-5,6-di-methylidenecyclohexa-1,3-diene)]iron ( 25 ) and tricarbonyl[C,3,4, C-η-(methyl 5-(dimethoxymethyl)-3,4-di-methylidenecyclohexa-1,5-diene-l-carboxylate)]iron ( 26 ). The structures of products 19 and of its exo ( 21 ) and endo ( 22 ) [Fe(CO)₃(1,3-diene)]complexes) and 20 (and of its exo ( 23 ) and endo (24) (Fe(CO)₃(1,3-diene)complexes) were confirmed by X-ray diffraction studies of crystalline (1RS, 2SR, 3RS, 4RS, 4aRS, 9aSR)-tricarbonyl[C, 2,3, C-η-(1,4-epoxy-1,5-bis(dimethoxymethyl])-2,3-dimethylidene-1,2,3,4,4a,9,9a,10-octahydroanthracene)iron ( 21 ). In the latter, the Fe(CO)₃(1,3-diene) moiety deviates significantly from the usual local C_s symmetry. Complex 21 corresponds to a ‘frozen equilibrium’ of rotamers with η-alkyl, η³-allyl bonding mode due to the acetal unit at the bridgehead centre C(1).     

Spatial structure of some 6-alkyl-6-phenyl-tetrahydro-1,3-oxazines

It is shown from ¹³C NMR spectra and molecular mechanical calculations that 5,6-dialkyl-(or 6-alkyl-)-3-methyl-6-phenyltetrahydro-1,3-oxazines exist in a conformation with the phenyl group orientated axially. The relative configuration of the substituents on the C₍₅₎ and C₍₆₎ atoms of 5,6-dialkyl-3-methyl-6-phenyltetrahydro-1,3-oxazines is established.Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 2, pp. 246–249, February, 1993.     

Simulated Raman spectra of four tetraphenylbutadiene polymorphs

We report a combined experimental and theoretical investigation on the Raman spectra of the polymorphs α, β, γ, and δ of 1,1,4,4‐tetraphenyl‐1,3‐butadiene (TPB), in the region of the intramolecular modes. The interpretation of the polarized spectra is supported by ab‐initio calculations for the isolated molecules and by lattice dynamics calculations for the crystals. The calculations reproduce the peculiar, and surprisingly large, differences among the spectra of the various polymorphs. The phenyl groups of 1,1,4,4‐tetraphenyl‐1,3‐butadiene may arrange themselves around the butadiene skeleton in 2 stable conformers, which have either inversion (C_i) or 2‐fold (C₂) symmetry and therefore exhibit intramolecular vibrations with quite different Raman selection rules and spectra. The compound forms 4 crystalline polymorphs (α, β, γ, and δ) with different combinations of C_i and C₂ conformers, and correspondingly different intramolecular spectra. The theoretical calculations provide a quantitative analysis of the various spectra.     

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     

2,2‐Dimethyl‐5‐nitroso‐1,3‐dioxan‐5‐yl benzoate, 2,2‐dimethyl‐5‐nitroso‐1,3‐dioxan‐5‐yl 4‐chlorobenzoate and 5‐nitroso‐1,3‐dioxan‐5‐yl 4‐chlorobenzoate

The crystal structures of 2,2‐dimethyl‐5‐nitroso‐1,3‐dioxan‐5‐yl benzoate, C₁₃H₁₅NO₅, (I), 2,2‐dimethyl‐5‐nitroso‐1,3‐dioxan‐5‐yl 4‐chlorobenzoate, C₁₃H₁₄ClNO₅, (II), and 5‐nitroso‐1,3‐dioxan‐5‐yl 4‐chlorobenzoate, C₁₁H₁₁NO₅, (III), have been determined in order to gain insight into the conformational preference of α‐benzoyloxynitroso. Unfavourable 1,3‐diaxial interactions force (I) and (II) to crystallize in the 2,5 twist‐boat conformation, whereas compound (III), lacking this destabilizing interaction, crystallizes in the chair conformation.     

Synthesis and three-dimensional structure of 5,5-disubstituted 2-alkoxy-1,3-dioxanes

It was established by PMR spectroscopy that a chair conformation with an axial orientation of the alkoxy substituent is the primary conformation for 5,5-disubstituted (and unsubstituted) 2-alkoxy-1,3-dioxanes. As compared with alkyl-1,3-dioxanes, 2-alkoxy-1,3-dioxanes are characterized by reversal of the chemical shifts of the axial and equatorial protons attached to C₄, and C₆.Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 9, pp. 1182–1185, September, 1981.     

Molecular conformation of cyclenes: Part VI. MINDO/2' study of 1,3-cycloheptadiene,cis- and trans-cyclooctene

Quantum mechanical calculations indicate that the most stable conformation for 1,3-cycloheptadiene is a C_s semi-planar form, for trans-cyclooctene a C₂ twist form and for cis-cyclooctene a form without symmetry. An equilibrium between two C₁ forms and the C_s form can be suggested as a consequence of the negligible rotational barrier in 1,3-cycloheptadiene; no obviously preferred conformations exist in cis-cyclooctene, where the molecule is quite flexible. Theoretical results are consistent with the experimental data available.     

Vibrational spectroscopic studies on some 2-substituted 1,3-dithi a-2-boracyclopentanes

Infrared and Raman spectra are reported for 2-X-1,3-dithia-2-boracyclopentanes, where X = Br, Cl, Ph or NMe₂. In all cases the vibrations of the heterocyclic ring unit can be assigned in terms of C₂ symmetry, corresponding to a “twisted-ring” conformation similar to that found for the related molecule 1,3-dithiolan-2-thione. The internal modes of the B-Ph unit are in agreement with C_2v “local” symmetry, while those for B-NMe₂ suggest a considerably lower symmetry.     

2‐(1,3‐Dithian‐2‐yl)benzaldehyde and N‐{2‐[2‐(1,3‐dioxan‐2‐yl)phenoxy]­ethyl}phthalimide

The crystal structures of two elaborated‐porphyrin precursors have been determined. In the crystalline state, 2‐(1,3‐di­thian‐2‐yl)­benz­aldehyde, C₁₁H₁₂OS₂, has its di­thiane ring in a slightly distorted chair conformation. The mol­ecules pack in anti‐parallel chains. N‐{2‐[2‐(1,3‐Dioxan‐2‐yl)­phenoxy]­ethyl}­phthal­imide, C₂₀H₁₉NO₅, is in a folded conformation. The dihedral angle between the phthal­imide and phenyl planes is 80.07 (3)°. In the crystalline states, mol­ecules stack on top of one another.     

Approximate symmetry characteristics using fuzzy-subset theory study for chiral transitions of allene-1,3,-dihalides

Based on our study of the application of fuzzy-subset theory to the characterization of imperfect symmetry in some stable molecular systems and simple dynamic molecular systems, we analyze the internal rotation process of allene-1,3- dihalides. Allene-1,3-dihalides (CHX=C=CHY, where X and Y may be the same or different halogen atoms) are optically chiral nonplanar molecules. The two end-groups may internally rotate about the near straight linear C=C=C axis, and the molecule may change its chirality. The internal rotation process may pass through two different planar transition state (TS): cis-TS and trans-TS, which belong to C_2v and C_2h point groups (as X and Y to be same), respectively. The intrinsic reaction coordinate (IRC) corresponding to the two TS processes is denoted as cis-IRC and trans-IRC. However, for the whole IRC reaction process, only their subgroup C₂ well-defined symmetry remains. Other symmetry transformations in C_2v and C_2h point groups can only be examined in terms of imperfect symmetry, although there appear certain reaction reversal joint point group G(R_cC_2v) and G(R_tC_2h) well-defined symmetry in the dynamics through the IRC processes. If X and Y are different, the stable molecule has no conventional nontrivial point group symmetry. The internal rotation processes may pass through two different planar TS’s (cis-and trans-TS). The TS will still be a planar molecule belonging to C_S point group with the molecule plane as its symmetry plane. Other states in the IRC may belong to certain reaction reversal joint point groups, G(RM)_C and G(RM)_T. We have thus examined the approximate symmetry of MO’s related to C₂ point group. Moreover, we have also analyzed the membership functions, representation components, and their relationships shown in the MO fuzzy main representation correlation diagrams.     

2‐Phenyl­malonpiperadide and 2‐phenyl­malonmorpholide

The structures of 2‐phenyl­malonpiperadide [systematic name: 2‐phenyl‐1,3‐bis­(piperidin‐1‐yl)­propane‐1,3‐dione, C₁₉H₂₆N₂O₂, (I)] and 2‐phenyl­malonmorpholide [systematic name: 1,3‐dimorpholino‐2‐phenyl­propane‐1,3‐dione, C₁₇H₂₂N₂O₄, (II)], have been determined and both their molecular conformations and packing arrangements compared. Although chemically similar, compounds (I) and (II) exhibit different molecular conformations. The only general conformational similarities are that their respective carbonyl groups are orientated in the same direction and the heterocyclic rings exist in the chair arrangement. General similarities in the packing arrangements arise due to both compounds having the same space group (P2₁2₁2₁) and a similar alignment of their phenyl‐substituted backbone with respect to the c axis. Similar C—H⋯O hydrogen‐bonding associations are listed for the carbonyl O atoms, while only one of the morpholine O atoms is involved in any such association.     

Conformational analysis of mesocyclic polythioethers : Crystal and molecular structures of 1,4-dithiacycloheptane, 1,5-dithiacyclononane and 1,6-dithiacyclodecane

The crystal and molecular structures of 1,4-dithiacycloheptane (1,4-DTCH), 1,5-dithiacyclononane (1,5-DTCN), and 1,6-dithiacyclodecane (1,6-DTCD) have been determined by single crystal X-ray studies. These compounds crystallize in the space groups P2₁2₁2₁ (No. 19), P2₁/c (No. 14), and P2₁/n, respectively with a = 5.409(1), b = 10.883(2), c = 11.390(2) Å, Z = 4; a = 9.600(4), b = 12.378(8), c = 7.904(3) Å, /gb = 113.31(3)°, Z = 4; and a = 5.290(1), b = 12.853(3), c = 6.850(2) Å, β = 93.39(2)°, Z = 2, respectively. The nonhydrogen atoms were located using direct methods and the hydrogen atoms were found by Fourier difference maps. Full-matrix least-squares refinement led to conventional R factors of 0.0459, 0.0558 and 0.0314, respectively. The conformations adopted by 1,4-DTCH, 1,5-DTCN and 1,6-DTCD, in the crystalline slate, are twist chair (C₂ symmetry), twist boat chair (C₂ symmetry), and boat chair boat (C_2k symmetry), respectively. The transannular S-S distances are 3.583, 4.108 and 4.864 Å, respectively.     

3,3,6,6‐Tetra­methyl‐1,2,4,5‐tetroxane: a twinned crystal structure

The title compound, C₆H₁₂O₄, also known as dimeric acetone peroxide, Me₂(C₂O₄)Me₂, has crystallographically imposed inversion symmetry and adopts a chair conformation in the solid state. This structure contrasts with that of the sulfur homologue Me₂(C₂S₄)Me₂, which has crystallographically imposed symmetry and crystallizes in a twist‐boat conformation. Crystals of the title compound are twinned along the reciprocal c* axis.