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     

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     

Conformational analysis of cycloheptane,oxacycloheptane, 1,2‐dioxacycloheptane, 1,3‐dioxacycloheptane,and 1,4‐dioxacycloheptane

The conformational analysis of cycloheptane (1), oxacycloheptane (2), 1,2‐dioxacycloheptane (3), 1,3‐dioxacycloheptane (4), and 1,4‐dioxacycloheptane (5) has been carried out using B3LYP, CCD, CCSD, and QCISD with the 6‐311+G(d,p) and cc‐pVDZ basis sets. The twist chair conformers are predicted to be lower in energy than their corresponding boat and chair conformations. All levels of theory predict (4) to be lower in energy than (3) and (5). CCSD predicts remarkably similar activation barriers for the conformational interconversion of the twist chair conformers to their corresponding boat conformers. Small barriers to pseudorotation are also predicted. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2008     

The endo and exo isomers of 1‐(4‐isopropyl‐3,5‐dioxa‐8‐aza­bicyclo­[5.1.0]octan‐8‐yl)pyrrolidine‐2,5‐dione

The crystal structures of the title compounds, C₁₂H₁₈N₂O₄, have been determined in order to establish the relative configurations. In both structures, the isopropyl substituent strongly prefers the quasi‐equatorial position. Therefore, the exo isomer adopts a dioxepanoaziridine pattern of a chair–chair (CC) conformation and the endo isomer a boat–chair (BC) conformation.     

Computational study of 4‐fluoro‐4‐chloro‐ and 4‐fluoro‐4‐bromo‐4‐silathiacyclohexane S‐oxides: Effect of halogen on the SO→Si intramolecular coordination in the boat and twist conformers

Chair, twist, and boat conformations of axial and equatorial 4‐fluoro‐4‐chloro‐ and 4‐fluoro‐4‐bromo‐4‐silathiacyclohexane S‐oxides have been calculated at the second‐order Møller–Plesset (MP2) and density functional theory (DFT) levels of theory. The 2,5‐twist and 1,4‐boat conformers of the axial sulfoxides are stabilized by transannular interaction between the sulfinyl oxygen and silicon to give trigonal bipyramidal geometry at silicon. The stability of conformers containing pentacoordinate silicon is governed by the balance of the transannular sulfinyl oxygen–silicon coordination, nonbonded H…H and O…Hlg_ax interactions, electronegativity of Hlg_ax and nucleofugality of Hlg_eq, and may approach the stability of the lowest‐energy chair conformers. The effect of pentacoordination on the energy and geometry of Si‐halogenated 4‐silathiane S‐oxides is analyzed as a function of the halogen nature and position. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007     

rac‐5‐Diphenylacetyl‐2,2,4‐trimethyl‐2,3,4,5‐tetrahydro‐1,5‐benzothiazepine and rac‐5‐formyl‐2,2,4‐trimethyl‐2,3,4,5‐tetrahydro‐1,5‐benzothiazepine

rac‐5‐Diphenylacetyl‐2,2,4‐trimethyl‐2,3,4,5‐tetrahydro‐1,5‐benzothiazepine, C₂₆H₂₇NOS, (I), and rac‐5‐formyl‐2,2,4‐trimethyl‐2,3,4,5‐tetrahydro‐1,5‐benzothiazepine, C₁₃H₁₇NOS, (II), are both characterized by a planar configuration around the heterocyclic N atom. In contrast with the chair conformation of the parent benzothiazepine, which has no substituents at the heterocyclic N atom, the seven‐membered ring adopts a boat conformation in (I) and a conformation intermediate between boat and twist‐boat in (II). The molecules lack a symmetry plane, indicating distortions from the perfect boat or twist‐boat conformations. The supramolecular architectures are significantly different, depending in (I) on C—H...O interactions and intermolecular S...S contacts, and in (II) on a single aromatic π–π stacking interaction.     

A theoretical study on the conformation of 3‐phosphinoxido‐ and 3‐phosphono‐1,2,3,4,5,6‐hexahydrophosphinine 1‐oxides

The title compounds ( 2 and 4 ) obtained by the diastereoselective hydrogenation of the corresponding 1,2,3,6‐tetrahydrophosphinine oxides ( 1 and 3 ) were subjected to a detailed quantum chemical study. The possible chair conformers were calculated at the HF/6‐31G* level of theory, according to which, the 1‐phenyl‐3‐P(O)Y₂‐substituted products ( 2 ) exist in the trans₁ form, in which all substituents are equatorial. At the same time, the 1‐ethoxy‐3‐dialkylphosphono compounds ( 4 ) adopt the cis conformations, in which the 1‐ethoxy group is axial and the 3‐P(O)(OR)₂ moiety is equatorial. The major diastereomer ( 4–1 ) is cis₃, in which the 5‐methyl group is axial, while the minor one is cis₁ with an equatorial methyl substituent. It is noteworthy that the rotational position of the exocyclic P(O)Z₂ function affected the energy content of the chair conformer to a high extent. The possibility of the involvement of the twist conformers was also considered. © 2005 Wiley Periodicals, Inc. Heteroatom Chem 16:520–524, 2005; Published online in Wiley InterScience ( www.interscience.wiley.com ). DOI 10.1002/hc.20148     

4‐Deoxy‐4‐fluoro‐β‐d‐glucopyranose

4‐Deoxy‐4‐fluoro‐β‐d ‐glucopyranose, C₆H₁₁FO₅, (I), crystallizes from water at room temperature in a slightly distorted ⁴C₁ chair conformation. The observed chair distortion differs from that observed in β‐d ‐glucopyranose [Kouwijzer, van Eijck, Kooijman & Kroon (1995). Acta Cryst. B 51 , 209–220], (II), with the former skewed toward a B^C3,O5 (boat) conformer and the latter toward an ^O5TB_C2 (twist–boat) conformer, based on Cremer–Pople analysis. The exocyclic hydroxymethyl group conformations in (I) and (II) are similar; in both cases, the O—C—C—O torsion angle is ∼−60° (gg conformer). Intermolecular hydrogen bonding in the crystal structures of (I) and (II) is conserved in that identical patterns of donors and acceptors are observed for the exocyclic substituents and the ring O atom of each monosaccharide. Inspection of the crystal packing structures of (I) and (II) reveals an essentially identical packing configuration.     

Conformational features and chemical behavior of 5H, 7H-dibenzo[B,g][1,5] dithiocin oxides: 1,5-Oxygen shift via a dithiodication intermediate

Some 5H,7H-dibenzo[b,g][1,5]dithiocin oxides ( 4–8 ) and their related compounds 9–13 were prepared and the assignment of the most favorable conformation was carried out on the basis of the characteristic ¹H NMR spectral data. Only a single conformer (BC: boatchair form) exists for 4 , 5 , and 8–13 , while two conformers (BC and TB: twist-boat form) are apparent for 6 and 7 . Oxidation and methylation of 4 gave exclusively a single geometrical isomer ( 8 and 13 , respectively). These results are interpreted as a sterically preferential attack of electrophiles on the BC conformer of the starting material. A 1,5-oxygen shift of 4 occurred smoothly to give 6 in the presence of trifluoroacetic acid in CDCl₃ solution. The mechanistic investigation is described briefly. Differences in chemical behavior between dibenzodithiocin 12-oxide 4 and dibenzothiazocine 12-oxide 2 are also discussed on the basis of the conformational features.     

[1,5‐Bis(1‐methyl‐1H‐imidazol‐2‐yl­methyl‐κN3)‐1,5‐di­aza­cyclo­octane‐N,N′]chlorocobalt(II) perchlorate

The crystal structure of the title compound, [CoCl‐(C₁₆H₂₆N₆)]ClO₄, consists of discrete [CoCl­(C₁₆­H₂₆N₆)]⁺ cations and perchlorate anions. The five‐coordinate Co^II atom has four nitro­gen donors from the new mesocyclic ligand 1,5‐bis(1‐methyl‐1H‐­imidazol‐2‐ylmethyl)‐1,5‐di­aza­cyclo­octane [Co—N 2.046 (3)–2.214 (4) Å], and a chloride anion at the apical site [Co—Cl 2.3184 (13) Å]. The coordination geometry of the complex is essentially square pyramidal. The mesocyclic ligand takes a boat–chair configuration and the two imidazole pendants are not coplanar. The dihedral angle between the two imidazole planes is 15.97°. An H atom from the 1,5‐diaza­cyclo­octane group effectively blocks the axial coordination site opposite the Cl ligand.     

Theoretical study of the structures,conformations, and spectroscopic properties of 2‐formylthiophene‐N‐acetylhydrazone and 2‐thiophenecarboxaldehyde‐2‐thienylhydrazone

2‐Formylthiophene‐N‐acetylhydrazone (Hait) and 2‐thiophenecarboxaldehyde‐2‐thienylhydrazone (Htit) in the cis and trans conformations were investigated in the gas‐phase by density functional method using B3LYP as the functional set and 6‐311++G(d,p) as the basis set. The cis and trans structures were fully optimized in the C₁ and C_s symmetries. Transition states were also modeled for the cis–trans isomerization of the title compounds and the barriers to internal rotation were calculated. This work reports the structural, energetics, and spectroscopic parameters of all the optimized geometries. Some of the structural parameters are in good agreement with experimental literature data. The computed parameters for these compounds are also in good agreement with a related molecule, namely, acetohydrazide. For both Hait and Htit, the trans conformers are more stable than the cis conformers and the energy barriers are larger compared with the energy differences between the cis and trans conformers. This accounts for Hait and Htit existing mostly in the trans conformation. © 2009 Wiley Periodicals, Inc. Heteroatom Chem 20:144–150, 2009; Published online in Wiley InterScience ( www.interscience.wiley.com ). DOI 10.1002/hc.20526     

Conformational effects of 1,5,9-substitution in symmetric bicyclo[3.3.1]nonane analogues

The high-level ab initio calculations on several derivatives of bicyclo[3.3.1]nonane, 1-aza- and 1,5-diazabicyclo[3.3.1]-nonanes show the ‘double chair’ (CC) conformer as optimal for all of them, dominating over the ‘boat–chair’ (BC) form. Conformational effects of several substitution types involving positions 1, 5 and 9 are quantified, and their values are found rather transferable.     

The Cyclohexasilanes Si6H11X and Si6Me11X with X=F,Cl, Br and I: A Quantum Chemical and Raman Spectroscopic Investigation of a Multiple Conformer Problem

The conformers of the monohalocyclohexasilanes, Si₆H₁₁X (X=F, Cl, Br or I) and the haloundecamethylcyclohexasilanes, Si₆Me₁₁X (X=F, Cl, Br or I) are investigated by DFT calculations employing the B3LYP density functional and 6‐31+G* basis sets for elements up to the third row, and SDD basis sets for heavier elements. Five minima are found for Si₆H₁₁X—the axial and equatorial chair conformers, with the substituent X either in an axial or equatorial position—and another three twisted structures. The equatorial chair conformer is the global minimum for the X=Cl, Br and I, the axial chair for X=F. The barrier for the ring inversion is ～13 kJ mol^?1 for all four compounds. Five minima closely related to those of Si₆H₁₁X are found for Si₆Me₁₁X. Again, the equatorial chair is the global minimum for X=Cl, Br and I, and the axial chair for X=F. Additionally, two symmetrical boat conformers are found as local minima on the potential energy surfaces for X=F, Cl and Br, but not for X=I. The barrier for the ring inversion is ～14–16 kJ mol^?1 for all compounds. The conformational equilibria for Si₆Me₁₁X in toluene solution are investigated using temperature dependent Raman spectroscopy. The wavenumber range of the stretching vibrations of the heavy atoms X and Si from 270–370 cm^?1 is analyzed. Using the van′t Hoff relationship, the enthalpy differences between axial and equatorial chair conformers (H_ax?H_eq.) are 1.1 kJ mol^?1 for X=F, and 1.8 to 2.8 kJ mol^?1 for X=Cl, Br and I. Due to rapid interconversion, only a single Raman band originating from the “averaged” twist and boat conformers could be observed. Generally, reasonable agreement between the calculated relative energies and the experimentally determined values is found.     

Stereochemistry and opioid receptor affinity of 2,4‐dipyridine‐3,7‐diazabicyclo[3.3.1]nonanones ‐ influence of the substituent in position N7

The stereochemistry the 2,4‐di‐arene substituted 3,7‐diazabicyclo[3.3.1]nonan‐9‐one 1,5‐dicarboxylate skeleton was found to be regulated by the kind of substituents attached to the arene rings as well as to the nitrogens N3 and N7. Conformational isomers, i.e., chair/chair, boat/chair and chair/boat, in addition to cis/trans conflgurational isomerism with respect to the arene rings were reported. Since the analgesic potency of the diazabicyclononanones, which is related to their affinity toward the κ‐opioid receptor, is governed by the stereochemistry of the molecules, the influence of the substituents at nitrogen N7 was studied herein. The various differently N7 substituted diazabicyclononanones were found to crystallise in a highly symmetrical chair/chair conformation. However, beside HZ2 none of the compounds exhibits high affinity to the κ receptor. In contrast, some compounds with affinity to the μ receptor could be identified. In addition, the N7‐(4‐carboxybenzyl) substituted compound was found to have affinity to the δ receptor in the submi‐cromolar range of concentration.     

Strain‐Accelerated Formation of Chiral,Optically Active Buta‐1,3‐dienes

The formal [2+2] cycloaddition–retroelectrocyclization (CA–RE) reactions between tetracyanoethylene (TCNE) and strained, electron‐rich dibenzo‐fused cyclooctynes were studied. The effect of ring strain on the reaction kinetics was quantified, revealing that the rates of cycloaddition using strained, cyclic alkynes are up to 5500 times greater at 298 K than those of reactions using unstrained alkynes. Cyclobutene reaction intermediates, as well as buta‐1,3‐diene products, were isolated and their structures were studied crystallographically. Isolation of a rare example of a chiral buta‐1,3‐diene that is optically active and configurationally stable at room temperature is reported. Computational studies on the enantiomerization pathway of the buta‐1,3‐diene products showed that the eight‐membered ring inverts via a boat conformer in a ring‐flip mechanism. In agreement with computed values, experimentally measured activation barriers of racemization in these compounds were found to be up to 26 kcal mol^?1.     

Conformational analysis of some 1R,4S‐2‐arylidene‐p‐menthan‐3‐ones by 1H NMR spectroscopy and molecular simulation

Based on ¹H NMR spectral analysis combined with molecular simulation, conformational states of the cyclohexanone ring were studied for some 1R,4S‐2‐(4‐X‐benzylidene)‐p‐menthan‐3‐ones (X = COOCH₃ or C₆H₅) in CDCl₃ and C₆D₆. The co‐existence of chair conformers with an axial orientation of both alkyl substituents and twist‐boat forms was established for the compounds studied at room temperature (22–23° C). The substituent X does not influence appreciably the ratio of these conformers, but the fraction of twist‐boat forms increases noticeably in benzene solutions as compared with CDCl₃ solutions. Rotameric states of the isopropyl fragment were also characterised for the compounds studied. Distinctions in conformational states for the 1R,4S‐2‐arylidene‐p‐menthan‐3‐ones and (?)‐menthone were revealed and are discussed. Copyright © 2002 John Wiley & Sons, Ltd.     

Ab initio molecular orbital study of energies and conformers of 3,4-dihydro-1,2-dithiin, 3,6-dihydro-1,2-dithiin, 4H-1,3-dithiin,and 2,3-dihydro-1,4-dithiin

Optimized geometries and energies for 3,4-dihydro-1,2-dithiin ( 1 ), 3,6-dihydro-1,2-dithiin ( 2 ), 4H-1,3-dithiin ( 3 ), and 2,3-dihydro-1,4-dithiin ( 4 ) were calculated using ab initio 6-31G* and MP2/6-31G*//6-31G* methods. At the MP2/6-31G*//6-31G* level, the half-chair conformer of 4 is more stable than those of 1 , 2 , and 3 by 2.5, 3.5, and 3.6 kcal/mol, respectively. The half-chair conformers of 1 , 2 , 3 , and 4 are 2.9, 7.1, 2.0, and 5.6 kcal/mol, respectively, more stable than their boat conformers. The calculated half-chair structures of 1 – 4 are compared with the calculated chair conformer of cyclohexane and the half-chair structures for cyclohexene, 3,4-dihydro-1,2-dioxin ( 5 ), 3,6-dihydro-1,2-dioxin ( 6 ), 4H-1,3-dioxin ( 7 ), and 2,3-dihydro-1,4-dioxin ( 8 ). © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 1064–1071, 1998     

Photoisomerization of cis‐1,2‐di(1‐Methyl‐2‐naphthyl)ethene at 77 K in Glassy Media

cis‐1,2‐Di(1‐methyl‐2‐naphthyl)ethene, c‐ 1,1 , undergoes photoisomerization in methylcyclohexane, isopentane and diethyl ether/isopentane/ethanol glasses at 77 K. On 313 nm excitation the fluorescence of c‐ 1,1 is replaced by fluorescence from t‐ 1,1 . Singular value decomposition reveals that the spectral matrices behave as two component systems suggesting conversion of a stable c‐ 1,1 conformer to a stable t‐ 1,1 conformer. However, the fluorescence spectra are λ_exc dependent. Analysis of global spectral matrices shows that c‐ 1,1 is a mixture of two conformers, each of which gives one of four known t‐ 1,1 conformers. The λ_exc dependence of the c‐ 1,1 fluorescence spectrum is barely discernible. Structure assignments to the resolved fluorescence spectra are based on the principle of least motion and on calculated geometries, energy differences and spectra of the conformers. The relative shift of the c‐ 1,1 conformer spectra is consistent with the shift of the calculated absorption spectra. The calculated structure of the most stable conformer of c‐ 1,1 agrees well with the X‐ray crystal structure. Due to large deviations of the naphthyl groups from the ethenic plane in the conformers of both c‐ and t‐ 1,1 isomers, minimal motion of these bulky substituents accomplishes cis → trans interconversion by rotation about the central bond.     

IR Low‐Temperature Matrix and ab Initio Study on β‐Alanine Conformers

For the first time the argon‐matrix low‐temperature FTIR spectra of β‐alanine are recorded. They reveal a quite complicated spectral pattern which suggests the presence of several β‐alanine conformers in the matrix. To interpret the spectra, the eighteen β‐alanine conformers, stable in the gas phase, are estimated at the B3LYP and MP2 levels combined with the aug‐cc‐pVDZ. Ten low‐energy structures are reoptimized at the QCISD/aug‐cc‐pVDZ and B3LYP and MP2 levels by using the aug‐cc‐pVTZ basis sets. Assignment of the experimental spectra is undertaken on the basis of the calculated B3LYP/aug‐cc‐pVDZ anharmonic IR frequencies as well as careful estimation of the conformer population. The presence of at least three β‐alanine conformers is demonstrated. The detailed analysis of IR spectra points to the possible presence of five additional β‐alanine conformers.