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.     

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     

2,8‐Di­hydroxy‐1,3,7,9‐tetra­methyl‐6,12‐di­hydro­dipyrido­[1,2‐a:1′,2′‐d]pyrazine­diyl­ium dichloride dihydrate

The 2,8‐di­hydroxy‐1,3,7,9‐tetra­methyl‐6,12‐di­hydro­di­pyrido[1,2‐a:1′,2′‐d]pyrazine­diyl­ium dication possesses 2/m symmetry and lies in the mirror plane together with a chloride anion and the water O atom. The dication also lies on an inversion centre, i.e. C₁₆H₂₀N₂O₂²⁺·2Cl^?·2H₂O. Due to these symmetry constrictions the dication adopts an unexpected planar conformation. Molecules are linked by O—H?O and O—H?Cl hydrogen bonds to form chains, which are cross‐connected by C—H?Cl attractive interactions forming a complex three‐dimensional hydrogen‐bond network.     

3‐Fluoro‐2,4‐dioxa‐7‐aza‐3‐phosphadecalin 3‐Oxides as Rigid Acetylcholine Mimetics: Conformational Analysis and Direct Evidence of the Anomeric Effect

Conformational analyses of the P(3)‐axially and P(3)‐equatorially F‐substituted (±)‐cis‐ and (±)‐trans‐2,4‐dioxa‐7‐aza‐3‐phosphadecalin 3‐oxides (3‐fluoro‐2,4‐dioxa‐7‐aza‐3‐phosphabicyclo[4.4.0]decane 3‐oxides) were performed. The results are based on independent studies in both solution and the solid state by ¹H‐ and ³¹P‐NMR experiments and computational and X‐ray crystallographic data. As expected, the axial epimers adopt neat double‐chair conformations in solution and in the crystal. Due to the anomeric effect of the electron withdrawing F‐substituent, the 2,4‐dioxa‐3‐phospha moiety in the equatorial epimers adopts a mixture of conformations in solution, mainly chair and twist‐boat; whereas a neat twist‐boat (trans‐isomer) and the unusual envelope conformation (cis‐isomer) were detected in the solid state. This is the first report of a straight visualization of these conformations and the impact of the anomeric effect in such systems.     

1,4‐Dimethyl‐1,4‐diazo­nia­bicyclo­[2.2.2]octane diiodide acetonitrile solvate

In the crystal structure of the title compound, C₈H₁₈N₂²⁺·2I⁻·CH₃CN, the dication lies on a mirror plane containing the mol­ecular dication threefold axis. The structure displays C—H⋯I inter­actions between H atoms of the 1,4‐dimethyl‐1,4‐diazo­nia­bicyclo­[2.2.2]octane dication and the iodide anions. The H⋯I distances are in the range 2.96–3.18 (4) Å. The dications pack forming channels along the b axis, which contain the iodide anions and acetonitrile solvent mol­ecules.     

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.     

Two isomeric cucurbitane derivatives

Two isomeric cucurbitane derivatives, 3β,7α,11β‐triacetoxycucurbit‐5(10)‐ene, (I), and 3β,7α,11β‐triacetoxy‐5α‐cucurbit‐1(10)‐ene, (II), both C₃₆H₅₈O₆, have their single endocyclic C=C double bonds in different positions. This results in differences in the conformation of the four‐ring system, which is close to a half‐chair/half‐chair/chair/half‐chair arrangement in (I) and to a half‐chair/twist‐boat/boat/half‐chair arrangement in (II). The orientation of some of the substituents is also different; the 3β‐acetoxy group is in an equatorial position in (I) but in an axial position in (II), while the 11β‐acetoxy group occupies an axial position in (I) and an equatorial position in (II). The asymmetric unit of (I) contains two symmetry‐independent molecules which do not differ significantly, being related by a pseudo‐twofold axis of symmetry. In both structures, the aliphatic chain fragments are disordered and the disorder persists at lower temperatures.     

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 of the rotational isomers of nitrosomethanol by semiempirical (AM1) and ab initio methods

The conformational potential energy surface as a function of the two internal torsion angles in C-nitrosomethanol has been obtained using the semiempirical AM1 method. Optimized geometries are reported for the local minima on this surface and also for the corresponding points on the HF/6-31G, 6-31G*, and 6-31G** surfaces. All methods predict cis and trans minima which occur in degenerate pairs, each pair being connected by a transition state of C_s symmetry. The AM1 structures are found to compare well with the corresponding ab initio structures. Ab initio HF/6-31G and HF/6-31G* harmonic vibrational frequencies are reported for the cis and trans forms of nitrosomethanol. When scaled appropriately the calculated frequencies are found to compare well with experimental frequencies. The ab initio calculations predict the energy barrier for cis → trans isomerization to be between 5.8 and 6.5 kcal/mol with the trans → cis isomerization barrier lying between 2.3 and 6.5 kcal/mol. The corresponding AM1 energy barriers are around 1 kcal/mol lower in energy. The ab initio calculations predict the barrier to conversion between the two cis rotamers to be very small with the AM1 value being around 1 kcal/mol. Both AM1 and ab initio calculations predict interconversion between trans rotamers to require between 1.2 and 1.4 kcal/mol.     

1,1′‐Methylenedipyridinium tetrachloridocuprate(II) and bis[tetrachloridoaurate(III)] hybrid salts by X‐ray powder diffraction

In order to explore the potential propensity of the 1,1′‐methylenedipyridinium dication to form organic–inorganic hybrid ionic compounds by reaction with the appropriate halide metal salt, the organic–inorganic hybrid salts 1,1′‐methylenedipyridinium tetrachloridocuprate(II), (C₁₁H₁₂N₂)[CuCl₄], (I), and 1,1′‐methylenedipyridinium bis[tetrachloridoaurate(III)], (C₁₁H₁₂N₂)[AuCl₄]₂, (II), were obtained by treatment of 1,1′‐methylenedipyridinium dichloride with CuCl₂ and Na[AuCl₄], respectively. Both hybrid salts were isolated as pure compounds, fully characterized by multinuclear NMR spectroscopy and their molecular structures confirmed by powder X‐ray diffraction studies. The crystal structures consist of discrete 1,1′‐methylenedipyridinium dications and [CuCl₄]²⁻ and [AuCl₄]⁻ anions for (I) and (II), respectively. As expected, the dications form a butterfly shape; the Cu^II centre of [CuCl₄]²⁻ has a distorted tetrahedral configuration and the Au^III centre of [AuCl₄]⁻ shows a square‐planar coordination. The ionic species of (I) and the dication of (II) each have twofold axial symmetry, while the two [AuCl₄]⁻ anions are located on a mirror‐plane site. Both crystal structures are stabilized by intermolecular C—H...Cl hydrogen bonds and also by Cl...π interactions. It is noteworthy that, while the average intermolecular centroid–centroid pyridinium ring distance in (I) is 3.643 (8) Å, giving strong evidence for noncovalent π–π ring interactions, for (II), the shortest centroid–centroid distance between pyridinium rings of 5.502 (9) Å is too long for any significant π–π ring interactions, which might be due to the bulk of the two [AuCl₄]⁻ anions.     

Single and Double Ionization of Corannulene and Coronene

Electron‐transfer processes that involve single and doubly charged cations of corannulene (C₂₀H₁₀) and coronene (C₂₄H₁₂) are examined by three different mass‐spectrometric techniques. Photoionization studies give first‐ionization energies of IE(C₂₀H₁₀)=7.83±0.02 eV and IE(C₂₄H₁₂)=7.21 ±0.02 eV. Photoionizations of the neutrals to the doubly charged cations occur at thresholds of 20.1±0.2 eV and 18.5±0.2 eV for corannulene and coronene, respectively. Energy‐resolved charge‐stripping mass spectrometry yields kinetic energy deficits of Q_min(C₂₀H=13.8±0.3 eV and Q_min(C₂₄H=12.8±0.3 eV for the transitions from the mono‐ to the corresponding dications in keV collisions. Reactivity studies of the C₂₀H and C₂₄H dications in a selected‐ion flow‐tube mass spectrometer are used to determine the onsets for the occurrence of single‐electron transfer from several neutral reagents to the dications, affording two different monocationic products. With decreasing IEs of the neutral reagents, electron transfer to doubly charged corannulene is first observed with hexafluorobenzene (IE=9.91 eV), while neutrals with lower IEs are required in the case of the coronene dication, e.g., NO₂ (IE=9.75 eV). Density‐functional theory is used to support the interpretation of the experimental data. The best estimates of the ionization energies evaluated are IE(C₂₀H₁₀)=7.83±0.02 eV and IE(C₂₄H₁₂)=7.21 ±0.02 eV for the neutral molecules, and IE(C₂₀H)=12.3±0.2 eV and IE(C₂₄H)=11.3±0.2 eV for the monocations.     

The crucial role of C—H...O and C=O...π interactions in the building of three‐dimensional structures of dicarboxylic acid–biimidazole compounds

The supramolecular architectures of three dicarboxylic acid–biimidazole compounds, namely, 2,2′‐biimidazolium malonate, C₆H₈N₄²⁺·C₃H₂O₄²⁻, (I), 2,2′‐bi(1H‐imidazole) succinic acid, C₆H₆N₄·C₄H₆O₄, (II), and 2,2′‐biimidazolium 2,2′‐iminiodiacetate chloride, C₆H₈N₄²⁺·C₄H₆NO₄⁻·Cl⁻, (III), are reported. The crystal structures are assembled by the same process, namely double conventional N—H...O or O—H...N hydrogen bonds link the dicarboxylates and biimidazoles to form tapes, which are stacked in parallel through lone‐pair–aromatic interactions between carbonyl O atoms and biimidazole groups and are further linked via weak C—H...O interactions. The C=O...π interactions involved in stacking the tapes in (II) and the C—H...O interactions involved in linking the tapes in (II) and (III) demonstrate the crucial role of these interactions in the crystal packing. There is crystallographically imposed symmetry in all three structures. In (I), two independent malonate anions have their central C atoms on twofold axes and two biimidazolium dications each lie about independent inversion centres; in (II), the components lie about inversion centres, while in (III), the unique cation lies about an inversion centre and the iminiodiacetate and chloride anions lie across and on a mirror plane, respectively.     

Hexane‐1,6‐diaminium chloride [hydrogen bis(chloroacetate)]

In the structure of the title compound, C₆H₁₈N₂²⁺·H(C₂H₂ClO₂)₂⁻·Cl⁻, the hexane‐1,6‐diaminium dication is disordered over two sets of positions, with almost equal occupancies. Both alternative positions of the dication are in the fully extended conformation, situated on an inversion centre at (, , ). Two chloroacetic acid moieties, related by another centre of symmetry at (, , ), are connected by a very short symmetrical O...H...O hydrogen bond [O...O = 2.452 (2) Å], with the H atom at the centre of inversion. These two fragments thus effectively form the hydrogen bis(chloroacetate) monoanion, and the overall charge is balanced by an additional chloride anion which resides on a twofold axis. The ions form a layer structure, with alternating layers of dications and anions running along the [101] direction, linked via hydrogen bonds. There are two N—H...O interactions and two N—H...Cl⁻ interactions.     

6,6′‐Dimethoxygossypolone

6,6′‐Dimethoxygossypolone (systematic name: 7,7′‐dihydroxy‐5,5′‐diisopropyl‐6,6′‐dimethoxy‐3,3′‐dimethyl‐1,1′,4,4′‐tetraoxo‐2,2′‐binaphthalene‐8,8′‐dicarbaldehyde), C₃₂H₃₀O₁₀, is a dimeric molecule formed by oxidation of 6,6′‐dimethoxygossypol. When crystallized from acetone, 6,6′‐dimethoxygossypolone has monoclinic (P2₁/c) symmetry, and there are two molecules within the asymmetric unit. Of the four independent quinoid rings, three display flattened boat conformations and one displays a flattened chair/half‐chair conformation. The angles between the planes of the two bridged naphthoquinone structures are fairly acute, with values of about 68 and 69°. The structure has several intramolecular O—H...O and C—H...O hydrogen bonds and several weak intermolecular C—H...O hydrogen bonds, but no intermolecular O—H...O hydrogen bonds.     

Verticine ethanol hydrate (2/1/1)

The two symmetry‐independent mol­ecules of the title compound, cevane‐3β,6α,20‐triol ethanol hydrate (2/1/1), 2C₂₇H₄₅NO₃·C₂H₆O·H₂O, have the same stereochemical assignments. The six‐membered rings A, B, E and F are in the chair conformation, while ring D is in a boat conformation. The ring fusions are A/Btrans, B/Ctrans, C/Dcis, D/Etrans and E/Ftrans. The verticine mol­ecules are bridged by water and ethanol mol­ecules via hydrogen bonds to form two‐dimensional layers, and the crystal structure is built up by stacking of these layers.     

Computational thermochemistry of glycolaldehyde

We use a variant of the focal point analysis to refine estimates of the relative energies of the four low‐energy torsional conformers of glycolaldehyde. The most stable form is the cis‐cis structure which enjoys a degree of H‐bonding from hydroxyl H to carbonyl O; here dihedral angles τ₁ (O?C? C? O) and τ₂ (C? C? O? H) both are zero. We optimized structures in both CCSD(T)/aug‐cc‐pVDZ and aug‐cc‐pVTZ; the structures agree within 0.01 Å for bond lengths and 1.0 degrees for valence angles, but the larger basis brings the rotational constants closer to experimental values. According to our extrapolation of CCSD(T) energies evaluated in basis sets ranging to aug‐cc‐pVQZ the trans‐trans form (180°, 180°) has a relative energy of 12.6 kJ/mol. The trans‐gauche conformer (160°, ±75°) is situated at 13.9 kJ/mol and the cis‐trans form (0°, 180°) at 18.9 kJ/mol. Values are corrected for zero point vibrational energy by MP2/aug‐cc‐pVTZ frequencies. Modeling the vibrational spectra is best accomplished by MP2/aug‐cc‐pVTZ with anharmonic corrections. We compute the Watsonian parameters that define the theoretical vibrational‐rotational spectra for the four stable conformers, to assist the search for these species in the interstellar medium. Six transition states are located by G4 and CBS‐QB3 methods as well as extrapolation using energies for structures optimized in CCSD(T)/aug‐cc‐pVDZ structures. We use two isodesmic reactions with two well‐established thermochemical computational schemes G4 and CBS‐QB3 to estimate energy enthalpy and Gibbs energy of formation as well as the entropy of the gas phase system. Our extrapolated electronic energies of species appearing in the isodesmic reactions produce independent values of thermodynamic quantities consistent with G4 and CBS‐QB3. © 2013 Wiley Periodicals, Inc.     

Imidazolium-Based Dicationic Cyclophanes. Solid-State Aggregates with Unconventional (C–H)+···Cl− Hydrogen Bonding Revealed by X-ray Diffraction

The first single-crystal X-ray crystallographic diffraction analysis of a dicationic heterophane showed a non-classic (C–H)⁺···Cl^?  hydrogen bond between the imidazolium rings and halide anions and the formation of unconventional charged assisted hydrogen bonds, which were the non-covalent forces driving the anion interactions shown by the dications 4·2X. Here is reported the halide-templated controlled synthesis and chemical response in basic media of 4·2X. Their structural properties were examined at the gas phase by electrospray ionization mass spectrometry in the negative-ion mode and in the solid-state by X-ray crystallography. Thus, the negative-ion ESI-MS response showed that the formation of non-covalent self-aggregates of macrocyclic dications is a consequence of hydrogen-bonded complexes with halide anions. Notably, X-ray diffraction of dication 4a·2Cl·2H₂O provides evidence for the H-bonding network, which has a crucial role in crystal packing. The solid-state aggregates showed that chloride anions and water molecules formed channels among dications 4a⁺.     

Benzo­[i]­naphtho­[c,d]­bi­cyclo­[5.4.1]dodecan‐12‐one

In the title compound, penta­cyclo­[11.8.1.1^3,11.0^7,23.0^15,20]­tricosa‐3,5,7,9,11(23),15,17,19‐octaen‐22‐one, C₂₃H₂₀O, the bi­cyclo­[5.4.1]­dodecan‐12‐one moiety takes a rigid conformation in which the seven‐ and eight‐membered rings take chair and boat–boat forms, respectively. The mol­ecule has a non‐crystallographic mirror symmetry perpendicular to the benzene and naphthalene planes.     

Triterpenoide. XIX. 3β‐Hydroxy‐11‐oxo‐18α‐olean‐12‐en‐28‐säure‐methyl­ester und 3,11‐Dioxo‐18α‐olean‐12‐en‐28‐säure‐methyl­ester

The X‐ray crystal structure analyses of 3β‐hydroxy‐11‐oxo‐18α‐olean‐12‐en‐28‐oic acid methyl ester ethanol solvate, C₃₁H₄₈O₄·C₂H₆O, (I), and 3,11‐dioxo‐18α‐olean‐12‐en‐28‐oic acid methyl ester, C₃₁H₄₆O₄, (II), are described. These two compounds differ only in the structure of ring A. In (I), ring A has a chair conformation, while in (II), it has a twisted boat conformation. In both compounds, ring C has a slightly distorted sofa conformation, rings B, D and E are in chair conformations, and rings D and E are trans‐fused. The asymmetric unit of (I) contains one mol­ecule of ethanol linked by hydrogen bonds with two different mol­ecules of (I).