Gas Phase Structures of Peroxides: Experiments and Computational Problems

Gas‐phase structures of several organic and inorganic peroxides X‐O‐O‐X and X‐O‐O‐X′, which have been determined experimentally by gas electron diffraction and/or microwave spectroscopy, are discussed. The O?O bond length in these peroxides varies from 1.481(8) Å in Me₃SiOOSiMe₃ to 1.214(2) Å in FOOF and the dihedral angle ?(XO‐OX) between 0° in HC(O)O‐OH and near 180° in Bu^tO‐OBu^t. Some of the peroxides cause problems for quantum chemistry, since several computational methods fail to reproduce the experimental structures. Extreme examples are MeO‐OMe and FO‐OF. In the case of MeO‐OMe only about half of the more than 100 computational methods reported in the literature reproduce the experimentally determined double‐minimum shape of the torsional potential around the O?O bond correctly. For FO‐OF only a small number of close to 200 computational methods reproduce the O?O and O?F bond lengths better than ±0.02 Å.     

Crystal structure of a liquid crystal non‐symmetric dimer: cholesteryl 4‐[4‐(4‐n‐butylphenylethynyl)phenoxy]butanoate

The crystal structure of cholesteryl 4‐[4‐(4‐n‐butylphenylethynyl)phenoxy]butanoate [phase sequence: Cr 155°C (46.1?J?g^?1) SmA 186.8°C (1.5?J?g^?1) TGB‐N* 204.7 (6?J?g^?1) I] has been solved from single crystal X‐ray diffraction data. The compound crystallizes in the monoclinic space group P2₁ with unit cell parameters: a?=?13.129(2), b?=?9.3904(10), c?=?17.4121(8)?Å, β?=?92.790(7)°, Z?=?2. The structure has been solved by direct methods and refined to R?=?0.0606 for 3?250 observed reflections. The bond distances and angles are in good agreement with the corresponding values for compounds containing phenyl and cholesterol moieties. The phenyl rings A and B are planar. The dihedral angle between the least‐squares planes of the two phenyl rings is 28°. The cholesterol moiety has the usual structure: the C and E rings have chair conformations, and the D and F rings adopt half‐chair conformations. The molecules in the unit cell are arranged in an antiparallel manner. The crystal structure is stabilized by an intermolecular C–H…O contact of 2.989(10)?Å.     

Configurational assignment in alkyl‐branched sugars via the geminal C,H coupling constants

The measurement of the magnitude and sign of ²J(C,H) couplings offers a reliable way to determine the absolute configuration at a carbon center in a fixed cyclic system. A decrease of the dihedral angle ? in the O—C_A—C_B—H fragment always leads to a change of the ²J(C_A,H_B) coupling to more negative values, independent of the type and position of substituents at the two carbon centers. The orientations of the two substituents at C‐3 of the epimeric pair 1 and 2 were determined unambiguously through the measurement of the geminal coupling constants between C‐3 and the hydrogen atoms at C‐2 and C‐4. In particular, ²J(C‐3,H‐2ax) with ?1.5 Hz, ? = 174° in 1 and ?6.6 Hz, ? = 47° in 2 , and ²J(C‐3,H‐4) with +1.5 Hz, ? = 175° in 1 and ?4.7 Hz, ? = 49° in 2 showed the greatest differences between the two epimers. Both couplings therefore allow the determination of the absolute configuration at C‐3. It should be noted, however, that the size of the coupling constants can be different for dihedral angles of nearly identical size, when there are different numbers of electronegative substituents on the two coupling pathways, i.e. no O‐substituent at C‐2, but one axial O‐substituent at C‐4. It becomes clear that it is not sufficient to measure the magnitude of ²J coupling constants only, but that the sign of the geminal coupling is needed to identify the absolute configuration at a chiral center. The coupling of C‐3 with H‐2eq is not useful for the determination of the configuration at C‐3, as the similarity of the dihedral angles ? (O—C‐3—C‐2—H‐2eq) (57° in 1 and 70° in 2 ) leads to identical coupling constants (?6.1 Hz) for both epimers. Copyright © 2003 John Wiley & Sons, Ltd.     

Hydrogen‐Bond Dynamics of C?H⋅⋅⋅O Interactions: The Chloroform⋅⋅⋅Acetone Case

Spectroscopic evidence for C? H ??? O hydrogen bonding in chloroform ??? acetone [Cl₃CH ??? O?C(CH₃)₂] mixtures was obtained from vibrational inelastic neutron scattering (INS) spectra. Comparison between the INS spectra of pure samples and their binary mixtures reveals the presence of new bands at about 82, 130 and 170 cm^?1. Assignment of the 82 cm^?1 band to the νO ??? H anti‐translational mode is considered and discussed. In addition, the βC? H mode of CHCl₃ at 1242 cm^?1 is split in the spectra of the mixtures, and the high‐wavenumber component is assigned to the hydrogen‐bonded complex. The plot of the integrated intensity of this component shows a maximum for x=0.5, in agreement with the 1:1 stoichiometry of the chloroform ??? acetone complex, with a calculated complexation constant of 0.15 dm³ mol^?1. Results also show that the complex behaves as an independent entity, that is, despite being weak, such interactions play a key role in supramolecular chemistry.     

Pairing of Isolated Nucleobases: Double Resonance Laser Spectroscopy of Adenine–Thymine

The vibronic spectrum of the adenine–thymine (A–T) base pair was obtained by one‐color resonant two‐photon ionization (R2PI) spectroscopy in a free jet of thermally evaporated A and T under conditions favorable for formation of small clusters. The onset of the spectrum at 35 064 cm^?1 exhibits a large red shift relative to the π–π* origin of 9H‐adenine at 36 105 cm^?1. The IR–UV spectrum was assigned to cluster structures with HNH???O?C/N???HN hydrogen bonding by comparison with the IR spectra of A and T monomers and with ab initio calculated vibrational spectra of the most stable A–T isomers. The Watson–Crick A–T base pair is not the most stable base‐pair structure at different levels of ab initio theory, and its vibrational spectrum is not in agreement with the observed experimental spectrum. Experiments with methylated A and T were performed to further support the structural assignment.     

Synthesis,properties and X‐ray structure of 5‐azido‐2‐methoxy‐1,3‐xylyl‐18‐crown‐5

5‐Azido‐2‐methoxy‐1,3‐xylyl‐18‐crown‐5 has been prepared by reacting p‐toluenesulfonyl azide with the carbanion generated from the reaction of 5‐bromo‐2‐methoxy‐1,3‐xylyl‐18‐crown‐5 with n‐butyl lithium. The asymmetric N₃ stretch of this product has been observed as a single band at 2110 cm^?1 in dichloromethane solution. Addition of solid NaSCN, KSCN and CsSCN shifts this band to 2115, 2113 and 2112 cm^?1, respectively. Computational studies of this azide at the B3LYP‐6‐31G* level in the presence and absence of Na⁺ predicted these bands to be at 2173 cm^?1 and 2184 cm^?1. For the salt‐containing solutions, additional bands were observed at 2066 cm^?1, 2056 cm^?1 and 2055 cm^?1, respectively, which are in the range expected for CN stretches. The X‐ray structure of this azide has been determined. The terminal and internal N? N bond lengths were found to be 1.127(2) and 1.245(2) Δ, respectively, which is the usual pattern for aromatic azides. The crown ether is looped over the face of the aromatic ring resulting in an angle of 38.94° between the plane defined by the aromatic ring and that defined by the five ring oxygen atoms. In addition, the CH₃ group is rotated out of the plane of the phenyl ring with C1‐C18‐O181‐C182 and C17‐C18‐O181‐C182 dihedral angles of 93.81(14)° and ‐90.54(14)°, respectively.     

Nearly Degenerate Isomers of C(BH)2: Cumulene,Carbene, or Carbone?

The ground electronic state of C(BH)₂ exhibits both a linear minimum and a peculiar angle‐deformation isomer with a central B‐C‐B angle near 90°. Definitive computations on these species and the intervening transition state have been executed by means of coupled‐cluster theory including single and double excitations (CCSD), perturbative triples (CCSD(T)), and full triples with perturbative quadruples (CCSDT(Q)), in concert with series of correlation‐consistent basis sets (cc‐pVXZ, X=D, T, Q, 5, 6; cc‐pCVXZ, X=T, Q). Final energies were pinpointed by focal‐point analyses (FPA) targeting the complete basis‐set limit of CCSDT(Q) theory with auxiliary core correlation, relativistic, and non‐Born–Oppenheimer corrections. Isomerization of the linear species to the bent form has a minuscule FPA reaction energy of 0.02 kcal mol^?1 and a corresponding barrier of only 1.89 kcal mol^?1. Quantum tunneling computations reveal interconversion of the two isomers on a timescale much less than 1 s even at 0 K. Highly accurate CCSD(T)/cc‐pVTZ and composite c～CCSDT(Q)/cc‐pCVQZ anharmonic vibrational frequencies confirm matrix‐isolation infrared bands previously assigned to linear C(BH)₂ and provide excellent predictions for the heretofore unobserved bent isomer. Chemical bonding in the C(BH)₂ species was exhaustively investigated by the atoms‐in‐molecules (AIM) approach, molecular orbital plots, various population analyses, local mode vibrations and force constants, unified reaction valley analysis (URVA), and other methods. Linear C(BH)₂ is a cumulene, whereas bent C(BH)₂ is best characterized as a carbene with little carbone character. Weak B–B attraction is clearly present in the unusual bent isomer, but its strength is insufficient to form a CB₂ ring with a genuine boron–boron bond and attendant AIM bond path.     

Trimethyl[3‐methyl‐1‐(o‐tolenesulfonyl)indol‐2‐ylmethyl]ammonium iodide and benzyl[3‐bromo‐1‐(phenylsulfonyl)indol‐2‐ylmethyl]tolylamine

The title compounds, C₂₀H₂₅N₂O₂S⁺·I^?, (I), and C₂₉H₂₅BrN₂O₂S, (II), respectively, both crystallize in space group P. The pyrrole ring subtends an angle with the sulfonyl group of 33.6° in (I) and 21.5° in (II). The phenyl ring of the sulfonyl substituent makes a dihedral angle with the best plane of the indole moiety of 81.6° in (I) and 67.2° in (II). The lengthening or shortening of the C—N bond distances in both compounds is due to the electron‐withdrawing character of the phenyl­sulfonyl group. The S atoms are in distorted tetrahedral configurations. The molecular structures are stabilized by C—H?O and C—H?I interactions in (I), and by C—H?O and C—H?N interactions in (II).     

Note: Helix or No Helix of β‐Peptides Containing β3hAla(αF) Residues?

A remote ⁴J(F,H) coupling (F? C(α)? C(O)? N? H) of up to 4.2 Hz in α‐fluoro amides with antiperiplanar arrangement of the C? F and the C?O bonds (dihedral angle F? C? C?O ca. 180°) confirms that previous NMR determinations, using the XPLOR‐NIH procedure, of the secondary structures of β‐peptides containing β³hAla(αF) and β³hAla(αF₂) residues were correct. In contrast, molecular‐dynamics (MD) simulations, using the GROMOS program with the 45A3 force field, led to an incorrect conclusion about the relative stability of secondary structures of these β‐peptides. The problems encountered in NMR analyses and computations of the structures of backbone‐F‐substituted peptides are briefly discussed.     

Strukturen ladungsgestörter oder räumlich überfüllter Moleküle. 15. Tetracyanethen-Natrium-Dimethoxyethan

Structures of Charge-Perturbed or Sterically Overcrowded Molecules. 16. Tetracyanoethylene Sodium Dimethoxyethane The Single crystal structure of [(NC)₂C? C(CN)₂?·Na⊕(H₃CO? CH₂CH₂? OCH₃)]∞ reveals two formula units within the triclinic (P1 ) unit cell. The tetracyanoethylene radical anions are arranged along parallel double layers, which are shifted relative to each other, and in between which are interspersed the sodium counter cations and their dimethoxyethane ligands. The distances within the double layers amount to 300 pm and the ones between them to 385 pm. The six-fold coordinated Na⊕ centers are surrounded by four radical anions with contact distances Na…?N between 250 and 254 pm as well as by a twofold solvent ligand with Na…?O of 238 and 241 pm. Due to the electron transfer to the acceptor molecule, its (NC)₂C-halves twist by 8° and the bond lengths of the N?C? C subunits, bent by each 3°, are shortened up to 2 pm. The structural parameters are compared to those of the analogous potassium salt [TCNE^?K^⊕DME], of the dianion , of the sodium salts [(NC)₃C^?Na^⊕]∞ as well as [(NC)₂C? C(CHCH)₂? C(CN)₂^?Na^⊕]_∞ and, in addition, are discussed based on geometry-optimized MNDO calculations.     

A PM3 study on intrinsic decarboxylation process of methyl–ethyl-α–pyridylacetic acid

To probe the decarboxylation process of methyl–ethyl–α pyridylacetic acid (MEPA), molecular orbital calculations on the optimized geometry, transition-state geometry, and intrinsic reaction coordinate were performed by the MNDO –PM 3 method. The salient features of the optimized structure of MEPA are that the carboxyl anion is nearly on the plane of the pyridine ring (the dihedral angle of C8? C7? C2? N1 is 14.7°) and that the interatomic distance

1 …? is used for a noncovalent bond, such as N⁺ 1 …? O^?9.

of O^?9 …? H1′ is 1.6 Å (exchange of electrons exists between their atoms). The transition-state geometry of the decarboxylation process has the following features: (1) the activation enthalpy is 6.0 kcal/mol, (2) the dihedral angle of C8? C7? C2? N1 is ?50.2°, and (3) the interatomic distance of O^?9? H1′ and C7? C8 increase by 111 and 124%, respectively, as compared with the optimized geometry. From the extreme beginning of the intrinsic decarboxylation process, the exchange of electrons between O^?9 …? H1′ begins to decrease. This decrease, which is considered to be induced by the rotation of C2? C7, seems to initiate the dissociation of C7? C8. © 1995 John Wiley & Sons, Inc.     

Probing the weakest bond and the cleavage of p‐chlorobenzaldehyde diperoxide energetic molecule via quantum chemical calculations and theoretical charge density analysis

A high‐level ab initio Hartree‐Fock/Møller‐Plesset 2 and density functional theory quantum chemical calculations were performed on p‐chlorobenzaldehyde diperoxide energetic molecule to understand its bond topological, electrostatic, and energetic properties. The optimized molecular geometry for the basis set 6‐311G** exhibit chair diperoxide ring and planar aromatic side rings. Although the diperoxide ring bear same type of side rings, surprisingly, both the rings are almost perpendicular to each other, and the dihedral angle is 96.1°. The MP2 method predicts the O? O bond distance as ～1.466 Å. The charge density calculation reveals that the C? C bonds of chlorobenzaldehyde ring have rich electron density and the value is ～2.14 e Å^?3. The maximum electron density of the O? O bonds does not lie along the internuclear axes; in view of this, a feeble density is noticed in the ring plane. The high negative values of laplacian of C? C bonds (approximately ?22.4 e Å^?5) indicate the solidarity of these bonds, whereas it is found too small (approximately ?1.8 e Å^?5 for MP2 calculation) in O? O bonds that shows the existence of high degree of bond charge depletion. The energy density in all the C? C bonds are found to be uniform. A high electronegative potential region is found at the diperoxide ring which is expected to be a nucleophilic attack area. Among the bonds, the O? O bond charge is highly depleted and it also has high bond kinetic energy density; in consequence of this, the molecular cleavage is expected to happen across these bonds when the material expose to any external stimuli such as heat or pressure treatment. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Secondary interactions in n‐(chloromethyl)pyridinium chlorides (n = 2, 3, 4)

In the isomeric title compounds, viz. 2‐, 3‐ and 4‐(chloro­methyl)pyridinium chloride, C₆H₇ClN⁺·Cl^?, the secondary interactions have been established as follows. Classical N—H?Cl^? hydrogen bonds are observed in the 2‐ and 3‐isomers, whereas the 4‐isomer forms inversion‐symmetric N—H(?Cl^??)₂H—N dimers involving three‐centre hydrogen bonds. Short Cl?Cl contacts are formed in both the 2‐isomer (C—Cl?Cl^?, approximately linear at the central Cl) and the 4‐isomer (C—Cl?Cl—C, angles at Cl of ca 75°). Additionally, each compound displays contacts of the form C—H?Cl, mainly to the Cl^? anion. The net effect is to create either a layer structure (3‐isomer) or a three‐dimensional packing with easily identifiable layer substructures (2‐ and 4‐isomers).     

The effect of molecular planarity on crystal non‐centrosymmetry in benzyl­idene–aniline derivatives

In the title compound, N‐(2‐methoxy­phenyl)‐4‐nitro­benzyli­deneamine, C₁₄H₁₂N₂O₃, the two phenyl rings make a dihedral angle of 48.0 (2)° and the nitro group is at an angle of 6.5 (1)° with respect to its attached phenyl ring. In the crystal structure, mol­ecules are related as centrosymmetric pairs through π–π interactions and are further connected through strong C—H?O hydrogen bonds [C?O 3.4259 (17) Å and C—H?O 167°], forming molecular stacks along [100]. These stacks associate further through longer C—H?O interactions, forming two‐dimensional networks. In the c direction, there are only weak van der Waals interactions. The relationship between the molecular planarity and its centrosymmetry is also briefly described.     

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.     

Cyclotridecanone 2,4‐dinitrophenylhydrazone

In cyclotridecanone 2,4‐dinitrophenylhydrazone, C₁₉H₂₈N₄O₄, the 13‐membered carbocycle exists in the triangular [337] conformation. The 2,4‐dinitrophenylhydrazone group is almost perpendicular to the 13‐membered ring, with a dihedral angle of 82.66 (2)° between the mean planes. The dinitrophenylhydrazone rings are packed parallel to each other and separated by 3.28 (1) Å. The NH group forms an intramolecular hydrogen bond to a nitro O atom, and there is a weaker C—H...O interaction between a cyclotridecane CH group and a symmetry‐related 4‐nitro O atom, with a C...O distance of 3.436 (2) Å and a 150° angle about the H atom. The structure, in combination with additional evidence, indicates that [337] is the preferred conformation of cyclotridecane and other simple 13‐membered rings.     

Vibrational Sum‐Frequency Generation Activity of a 2,4‐Dinitrophenyl Phospholipid Hybrid Bilayer: Retrieving Orientational Parameters from a DFT Analysis of Experimental Data

The vibrational nonlinear activity of films of 2,4‐dinitrophenyl phospholipid (DNP) at the solid interface is measured by sum‐frequency generation spectroscopy (SFG). Hybrid bilayers are formed by a Langmuir–Schaefer approach in which the lipid layer is physisorbed on top of a self‐assembled monolayer of dodecanethiol on Pt with the polar heads pointing out from the surface. The SFG response is investigated in two vibrational frequency domains, namely, 3050–2750 and 1375–1240 cm^?1. The first region probes the CH stretching modes of DNP films, and the latter explores the vibrational nonlinear activity of the 2,4‐dinitroaniline moiety of the polar head of the lipid. Analysis of the CH stretching vibrations suggests substantial conformational order of the aliphatic chains with only a few gauche defects. To reliably assign the detected SFG signals to specific molecular vibrations, DFT calculations of the IR and Raman activities of molecular models are performed and compared to experimental solid‐state spectra. This allows unambiguous assignment of the observed SFG vibrations to molecular modes localized on the 2,4‐dinitroaniline moiety of the polar head of DNP. Then, SFG spectra of DNP in the 1375–1240 cm^?1 frequency range are simulated and compared with experimental ones, and thus the 1,4‐axis of the 2,4‐dinitrophenyl head is estimated to have tilt and rotation angles of 45±5° and 0±30°, respectively.     

Strukturen sterisch überfüllter oder ladungsgestörter Moleküle. 9. Tetracyanethen-Kalium-Dimethoxyethan

Structures of Sterically Overcrowded or Charge Perturbed Molecules. 9. Tetracyanoethylene Potassium Dimethoxyethane The single crystal structure of [(NC)₂C?C(CN)₂ ^?K^⊕(H₃CO? CH₂CH₂? OCH₃)] reveals 4 formula units per monoclinic (P2₁/n) unit cell. The tetracyanoethylene radical anions are stapled within slightly undulated layers exhibiting alternating average intermolecular distances of 315 pm and 360 pm between their central C?C bonds. In- between the closer layers both are interspersed the eight-fold coordinated K^⊕ counter cations and the solvating dimethoxyethane molecules with contact distances K^⊕…?N of 282 to 306 pm and K^⊕…?O of 279 to 294 pm. The molecular halves of the radical anions (NC)₂C?C(CN)₂^? are twisted by 12° and the C?C, C? C and C?N bond length amount to 142, 142, and 114 pm, respectively. These structural features are discussed by comparison with those of analogous cyanohydrocarbon salts, with those of the neutral molecule, its largely interaction-free anion and its dianion as well as with results of geometry-optimized MNDO calculations.     

4‐[1‐(Phenylsulfonyl)indol‐3‐yl]‐3a,4,5,9b‐tetrahydro‐3H‐cyclopenta[c]quinoline

In the title compound, C₂₆H₂₂N₂O₂S, the tetra­hydro­pyridine ring has a conformation intermediate between half‐chair and sofa. The tetrahydroquinoline mean plane makes a dihedral angle of 73.3 (1)° with the cyclopentene ring, which adopts an envelope conformation, and an angle of 45.45 (4)° with the indole best plane. The dihedral angle between the benzene and pyrrole rings is 2.6 (1)°. The orientations of the phenyl ring on the sulfonyl group and of the indole are governed by weak C—H?O interactions. The packing of the mol­ecule in the solid state is stabilized by C—H?O and C—H?N hydrogen bonds.     

4‐[2‐(3‐Methoxyphenyl)ethenyl]‐N‐methylpyridinium tetraphenylborate

In the title compound, C₁₅H₁₆NO⁺·C₂₄H₂₀B⁻, the pyridinium ring of the cation makes a dihedral angle of 4.3 (2)° with the benzene ring. Each is rotated in the same direction with respect to the central C—CH=CH—C linkage, by 10.0 (2) and 7.8 (2)°, respectively. The anions have a slightly distorted tetrahedral geometry. The most interesting feature of the structure is that the anions form a honeycomb‐like hexagonal structure down the b axis through C—H...π interactions. The hexagon is constructed from six BPh₄⁻ anions. The cations interact in a head‐to‐tail fashion along [010], forming chains, and pack antiparallel inside the above honeycomb‐like structure through C—H...π interactions.