Cage Hydrocarbons Research Articles

The structure of tricyclo[3.3.2.0 2.8]decane (hexahydrobullvalene) – A gas-phase electron diffraction (GED) study

The molecular structure of tricyclo[3.3.2.0 2.8]decane (hexahydrobullvalene) has been determined experimentally by gas-phase electron diffraction as well as by quantum chemical calculations. The bond lengths (twofold standard deviations in parentheses) in the skeleton [1.496(7) in the cyclopropane ring, 1.527(10) adjacent to it, 1.550(22) for the central bonds in the bridges and 1.548(16) Å for the bonds originating from the singular bridgehead] all can be explained in terms of the features of this cage hydrocarbon. All three C C C valence angles [113.0(8)° at the singular bridgehead, 112.8(12) adjacent to it and 122.3(20) adjacent to the skeletal cyclopropane ring] are larger than the regular tetrahedral angle on an sp 3-hybridized carbon atom. The two-carbon bridges between the skeletal cyclopropane ring and the opposite bridgehead are twisted with a dihedral angle of 43(2)°, i.e. significantly less than the approximately 60° in n-butane in its synclinal ( gauche) conformation.

Theoretical Study of the Fragmentation Pathways of Norbornane in Its Doubly Ionized Ground State

The potential energy surface of norbornane in its dicationic singlet ground state has been investigated in detail using density functional theory along with the nonlocal hybrid and gradient-corrected Becke three-parameter Lee-Yang-Parr functional (B3LYP) and the cc-pVDZ basis set. For the sake of more quantitative insight into the chemical reactions induced by double ionization of norbornane, this study was supplemented by a calculation of basic thermodynamic state functions coupled to a focal point analysis of energy differences obtained using correlation treatments and basis sets of improving quality, enabling an extrapolation of these energy differences at the CCSD(T) level in the limit of an asymptotically complete (cc-pV infinity Z) basis set. Our results demonstrate the likelihood of an ultrafast intramolecular rearrangement of the saturated hydrocarbon cage after a sudden removal of two electrons into a kinetically metastable five-membered cyclic C5H8+-CH+-CH3 intermediate, prior to a Coulomb explosion into C5H7+=CH2 and CH3+ fragments, which might explain a tremendous rise of electron-impact (e, 2e) ionization cross sections at electron binding energies around the double-ionization threshold. The first step is straightforward and strongly exothermic (DeltaH298 = -114.0 kcal mol-1). The second step is also exothermic (DeltaH298 = -10.2 kcal mol-1) but requires an activation enthalpy (DeltaH298) of 39.7 kcal/mol. The various factors governing the structure of this intermediate, such as electrostatic interactions, inductive effects, cyclic strains, and methylenic hyperconjugation interactions, are discussed in detail.

The abundance and distribution of diamondoids in biodegraded oils from the San Joaquin Valley: Implications for biodegradation of diamondoids in petroleum reservoirs

The biodegradability of diamondoids was investigated using a collection of crude oil samples from the San Joaquin Valley, California, that had been biodegraded to varying extent in the reservoir. Our results show that diamondoids are subjected to biodegradation, which is selective as well as stepwise. Adamantanes are generally more susceptible to biodegradation than other diamondoids, such as diamantanes and triamantanes. We report a possible pathway for the microbial degradation of adamantane. This cage hydrocarbon possibly breaks down to a metabolic intermediate through the action of microbes at higher levels of biodegradation in petroleum reservoirs. Microbial alteration has only a minor effect on diamondoid abundance in oil at low levels of biodegradation. Our results suggest that most diamondoids (with the exception of adamantane) are resistant to biodegradation, like the polycyclic terpanes (e.g. C 19–C 24 tricyclic terpanes, hopanes, gammacerane, oleananes, Ts, Tm, C 29 Ts), steranes and diasteranes. Microbial alteration of diamondoids has a negligible impact on the quantification of oil cracking achieved using the diamondoid–biomarker method.

Structures of the 2:1 adducts of benzyne with 2-methylanisole and benzene

The 2:1 adduct of benzyne with 2-methylanisole is shown to have the bisbenzotricyclic structure 6,6a,11,11a-tetrahydro-5-methoxy-6-methyl-5,6,11-metheno-5H-benzo[a]fluorene by a single-crystal X-ray diffraction study (C20H18O: Pca21, a = 15.0497(17), b = 9.87783(11), c = 9.6846(11); Z = 4; 1672 data points, R1 = 0.0325). This structure is compared to an unpublished crystal structure of the parent hydrocarbon 6,6a,11,11a-tetrahydro-5,6,11-metheno-5H-benzo[a]fluorene, C18H14. Both structures have also been computed by DFT methods at the B3LYP/6-311(d,p) level of theory. Bond distances and angles between the solid-state measurements and gas-phase calculations are found to agree well; average deviations are well below 1%. The 1H NMR spectra show surprisingly small 3JHH couplings in the central tricyclic cage, but can be assigned using 2D spectroscopy.Key words: Hydrocarbon cages, strained rings, cyclopropane, X-ray crystallography, NMR.

Oxidation of some cage hydrocarbons by dioxiranes. Nature of the transition structure for the reaction of C–H bonds with dimethyldioxirane: a comparison of B3PW91 density functional theory with experiment

Dimethyl- (DMD) and methyl(trifluoromethyl)-dioxiranes were used for oxyfunctionalization of spiro{1',7-cyclopropan-(E)-2-methylbicyclo[2.2.1]heptane} (), tricyclo[3.2.2.0(2,4)]nonane (), exo-endo-endo- () and exo-exo-exo- () heptacyclo[9.3.1.0(2,10).0(3,8).0(4,6).0(5,9).0(12,14)]pentadecane, yielding tertiary alcohols as the main products. The rate constants for oxidation of by DMD were measured and the Arrhenius parameters determined. The DFT theory (B3LYP and B3PW91) using restricted and unrestricted methods was employed to study the oxidation reaction of the C-H bond of cage hydrocarbons , adamantane, and acetone with DMD. The kinetic isotopic effect calculated using unrestricted methods agreed with experiment. The reaction mechanism in terms of the concerted oxygen insertion vs. the radical part is discussed.

Green's function study of the one‐electron and shake‐up ionization spectra of unsaturated hydrocarbon cage compounds

The valence one-electron and shake-up ionization spectra of stella-2,6-diene, stella-2,6-dione, bicyclo-[2.2.2]-octane-2,5-dione, and bicyclo-[2.2.1]-heptane-2,5-dione have been exhaustively studied, up to the double ionization threshold and beyond, by means of one-particle Green's function theory. This study is based on calculations employing the outer-valence Green's function and the third-order algebraic diagrammatic construction schemes, along with a variety of basis sets. A comparison is made with available ultraviolet (He I) photoelectron and (e, 2e) electron-impact ionization spectra, with main focus on the identification of spectral fingerprints for cyclic strains and through-bond pi-conjugation. As a byproduct, our results demonstrate that it is impossible to reliably assign complex (e, 2e) ionization spectra by resorting only to Hartree-Fock or Kohn-Sham orbital energies and to the related electron momentum distributions.

Formation and Structure of Cyclopentanethiol Self-Assembled Monolayers on Au(111)

Organic self-assembled monolayers (SAMs) prepared by the spontaneous adsorption of organosulfur compounds on gold have drawn much attention because they provide an excellent means to tailor the physical and chemical properties of surfaces for various technological applications in biosensing, nanopatterning, corrosion inhibition, and molecular electronic devices. To date, alkanethiol SAMs on gold surfaces have been the most thoroughly studied for understanding self-assembly phenomena of organic molecules. In addition, many studies have reported the structures and properties of aromatic thiol SAMs on gold surfaces, which are desirable due to their high electronic conductivity. It has been generally considered that the structures of the SAMs are determined by a balance of the chemical interactions between the sulfur headgroups and gold as well as van der Waals interactions between alkyl chains or aromatic groups. The contribution of van der Waals interactions plays a major role in determining the final SAM structure, and such interactions would be easily controlled by changing the alkyl groups or aromatic groups. As one of new classes in the SAM system, SAMs formed by thiols with spherical hydrocarbon cage or bulky alkyl groups on gold were prepared and characterized. Scanning tunneling microscopy (STM) studies reveals that sulfur compounds with bulky bicyclo[2.2.2]octane moieties can form unique ordered SAMs having a nearest neighbor spacing of 5.9 A, which is larger than that the ( × )R30 hexagonal structure for alkanethiol SAMs. From these STM studies, it is considered that van der Waals interactions between bulky alkyl groups is a dominant factor in the formation of ordered SAMs because alkanethiols with similar molecular lengths are rather difficult to form twodimensional (2D) ordered SAMs. The high-resolution STM study also revealed that cyclohexanethiol (CHT) containing a flexible six-membered aliphatic ring on Au(111) can form long-range 2D ordered SAMs, which can be described as a (5 × 2 )R48 superstructure. This unique superstructure can be ascribed to two geometrical isomers of the CHT molecule, the equatorial and axial chair isomers. In this study, the effect of the size of aliphatic cyclic ring on the structure of the SAMs formed by cyclopentanethiol (C5H9SH, CPT) with a five-membered aliphatic ring on the Au(111) surface was examined. To the best of my knowledge, there has been no study on the adsorption behavior of CPT molecules on gold surfaces thus far. To extend SAMbased applications, it is very important to understand the nature of the self-assembly processes of the molecules and the structure of SAMs. In this paper, the first molecularly resolved STM results of CPT SAMs with a ( × )R25 structure are reported.

Hexa‐ and Octacoordinate Carbon in Hydrocarbon Cages: Theoretical Design and Characterization

A new series of hydrocarbon cages containing hexa- and octacoordinate carbon centers were designed theoretically by performing DFT calculations at the B3 LYP/6-311+G** level. Among these non-classical structures that were found to still obey the 8e rule, the two tetracations with octacoordinate carbons may be the first examples found in pure hydrocarbons. Structural characteristics, as well as thermodynamic and kinetic stabilities, were also investigated theoretically for these two octacoordinate tetracations. These hydrocarbon compounds containing hypercoordinate carbon centers provide a challenge for synthetic organic chemists.

Long-lived phosphorescence of arenes in complexes with cyclodextrins 2. Room-temperature phosphorescence of ternary complexes of naphthalene and phenanthrene with β-cyclodextrin and adamantane derivatives in the presence of oxygen

Long-lived room-temperature phosphorescence (RTP) of arene—β-cyclodextrin (β-CD)— cage hydrocarbon complexes in the presence of oxygen was studied. Naphthalene-d8, phenanthrene, and fluorene were used as arenes and adamantane, 1,3-dimethyladamantane, diamantane, and diadamantyl were used as the cage hydrocarbons (according to PM3 quantum chemical calculations, the use of these compounds might cause the appearance of long-lived RTP). The RTP lifetime of the naphthalene-d8—β-CD—diadamantyl complex is 11.9 s at 20 °C.

Preparation and Reactivity of [D3d]‐Octahedrane: The Most Stable (CH)12 Hydrocarbon

The synthesis of the (CH)12 hydrocarbon [D(3d)]-octahedrane (heptacyclo[6.4.0.0(2,4).0(3,7).0(5,12).0(6,10).0(9,11)]dodecane) 1 and its selective functionalization retaining the hydrocarbon cage is described. The B3LYP/6-311+G* strain energy of 1 is 83.7 kcal mol(-1) (4.7 kcal mol(-1) per C-C bond) which is significantly higher than that of the structurally related (CH)16 [D(4d)]-decahedrane 2 (75.4 kcal mol(-1); 3.1 kcal mol(-1) per C-C bond) and (CH)20 [I(h)]-dodecahedrane 3 (51.5 kcal mol(-1); 1.7 kcal mol(-1) per C-C bond); the heats of formation for 1-3 computed according to homodesmotic equations are 52, 35, and 4 kcal mol(-1). Catalytic hydrogenation of 1 leads to consecutive opening of the two cyclopropane rings to give C2-bisseco-octahedrane (pentacyclo[6.4.0.0(2,6).0(3,11).0(4,9)]dodecane) 16 as the major product. Although 1 is highly strained, its carbon skeleton is kinetically quite stable: Upon heating, 1 does not decompose until above 180 degrees C. The B3LYP/6-31G* barriers for the S(R)2 attack of the tBuO. and Br3C. radicals on a carbon atom of one of the cyclopropane fragments (Delta(298) = 27-28 kcal mol(-1)) are higher than those for hydrogen atom abstraction. The latter barriers are virtually identical for the abstraction from the C1-H and C2-H positions with the tBuO. radical (DeltaG(298) = 17.4 and 17.9 kcal mol(-1), respectively), but significantly different for the reaction at these positions with the Br3C. radical (DeltaG(298) = 18.8 and 21.0 kcal mol(-1)). These computational results agree well with experiments, in which the chlorination of 1 with tert-butyl hypochlorite gave a mixture of 1- and 2-chlorooctahedranes (ratio 3:2). The bromination with carbon tetrabromide under phase-transfer catalytic (PTC) conditions (nBu4NBr/NaOH) selectively gave 1-bromooctahedrane in 43 % isolated yield. For comparison, the PTC bromination was also applied to 2,4-dehydroadamantane yielding 54 % 7-bromo-2,4-dehydroadamantane.

Bonding Patterns in a Strong 3c2e C−H···C Hydrogen Bond

Analysis of the topology of the electron density and underlying local orbital interactions of the fully optimized structure of the molecular cage of the in-bicyclo[4.4.4]-1-tetradecyl cation reveals that the inside 3c2e C-H...C hydrogen bond is not only unusual but also strong. The inside C-H bond of the unsaturated, neutral precursor bicyclo[4.4.4]-1-tetradecene is involved in an intramolecular C-H/pi interaction with the transannular double bond. Known and calculated (1)H and (13)C NMR properties, including diamagnetic and paramagnetic contributions to shielding tensors, are accounted for in terms of electron density redistributions and the unusual electronic environment within these hydrocarbon cages.

On the Viability of Small Endohedral Hydrocarbon Cage Complexes: X@C4H4, X@C8H8, X@C8H14, X@C10H16, X@C12H12, and X@C16H16

Small hydrocarbon complexes (X@cage) incorporating cage-centered endohedral atoms and ions (X = H(+), H, He, Ne, Ar, Li(0,+), Be(0,+,2+), Na(0,+), Mg(0,+,2+)) have been studied at the B3LYP/6-31G(d) hybrid HF/DFT level of theory. No tetrahedrane (C(4)H(4), T(d)()) endohedral complexes are minima, not even with the very small hydrogen atom or beryllium dication. Cubane (C(8)H(8), O(h)()) and bicyclo[2.2.2]octane (C(8)H(14), D(3)(h)()) minima are limited to encapsulating species smaller than Ne and Na(+). Despite its intermediate size, adamantane (C(10)H(16), T(d)()) can enclose a wide variety of endohedral atoms and ions including H, He, Ne, Li(0,+), Be(0,+,2+), Na(0,+), and Mg(2+). In contrast, the truncated tetrahedrane (C(12)H(12), T(d)()) encapsulates fewer species, while the D(4)(d)() symmetric C(16)H(16) hydrocarbon cage (see Table of Contents graphic) encapsulates all but the larger Be, Mg, and Mg(+) species. The host cages have more compact geometries when metal atoms, rather than cations, are inside. This is due to electron donation from the endohedral metals into C-C bonding and C-H antibonding cage molecular orbitals. The relative stabilities of endohedral minima are evaluated by comparing their energies (E(endo)) to the sum of their isolated components (E(inc) = E(endo) - E(cage) - E(x)) and to their exohedral isomer energies (E(isom) = E(endo) - E(exo)). Although exohedral binding is preferred to endohedral encapsulation without exception (i.e., E(isom) is always exothermic), Be(2+)@C(10)H(16) (T(d)(); -235.5 kcal/mol), Li(+)@C(12)H(12) (T(d)(); 50.2 kcal/mol), Be(2+)@C(12)H(12) (T(d)(); -181.2 kcal/mol), Mg(2+)@C(12)H(12) (T(d)(); -45.0 kcal/mol), Li(+)@C(16)H(16) (D(4)(d)(); 13.3 kcal/mol), Be(+)@C(16)H(16) (C(4)(v)(); 31.8 kcal/mol), Be(2+)@C(16)H(16) (D(4)(d)(); -239.2 kcal/mol), and Mg(2+)@C(16)H(16) (D(4)(d)(); -37.7 kcal/mol) are relatively stable as compared to experimentally known He@C(20)H(20) (I(h)()), which has an E(inc) = 37.9 kcal/mol and E(isom) = -35.4 kcal/mol. Overall, endohedral cage complexes with low parent cage strain energies, large cage internal cavity volumes, and a small, highly charged guest species are the most viable synthetic targets.

Sigma-antiaromaticity in cyclobutane, cubane, and other molecules with saturated four-membered rings.

Dissected nucleus-independent chemical shift (NICS) analyses of cycloalkanes and cage hydrocarbons reveal contrasting ring current effects, diatropic in three- and five-membered and paratropic in four-membered ring systems. The large shielding effects of the C-C bonds of the archetypal sigma-aromatic, cyclopropane, are magnified in tetrahedrane and related structures. The remarkable deshielding effect of the cyclobutane C-C(sigma) bonds is general: cubane and cages with four-membered rings are strongly deshielding (i.e., sigma-antiaromatic).[structure--see text]

Geometry for self-assembling of spherical hydrocarbon cages with methane thiolates on au(111).

An organodisulfide with a pair of adamantane moieties was synthesized, and its self-assembled monolayer (SAM) was formed on Au(111). The adamantane moieties are almost spherical and much bulkier than alkyl chains. The structure was characterized by scanning tunneling microscopy. Two-dimensional crystals of the SAM were found to be four orientationally different hexagonals with almost the same lattice constant with 4 radical 3a/3 and 7a/3 (a = 0.2884 nm, the Au lattice constant). The structure is assigned to four of the high-order commensurate adlayers. The present study of geometry and energetics for self-assembling of such an organosulfur compound with spherical cages provides a new insight into the probable SAM structure of various thiolate derivatives on Au(111).

Coalescence of C20 fullerenes

Coalescence of C20(H)n fullerenes with n=0–4 was studied by laser desorption and ionization in a time-of-flight mass spectrometer (337 nm N2 excimer laser). The fullerenes were produced by elimination of bromine from extensively brominated dodecahedranes (mixture, mean composition [C20H1Br13]≡Y, and mixtures with somewhat higher hydrogen content [C20H2Br12]≡X) accessible by photobromination of the C20H20 cage hydrocarbon. For Y probes at 80 mJ/cm2 laser fluence, coalescence of the generated C20 fullerenes was identified as the dominant process providing a series of (C20)k+ oligomers (k=1–13); there is evidence for the formation of C60+ from C20. At lower fluences (30 mJ/cm2) in the mass spectra measured near the desorption threshold or in the low ion velocity regime, the bromine substituents were not (totally) eliminated, the original degree of bromination has even been raised. High laser fluences (1500 mJ/cm2) primarily effect the bromine content, generating C20HnBrm ions with m ranging from 0 to 18, fullerene coalescence is suppressed. For X probes the only slightly higher hydrogen content inhibits C20 coalescence; a C36H4+ ion is interpreted as fullerene.

Classics in Hydrocarbon Chemistry. By Henning Hopf

Carbon and Hydrogen: the two basic building units can be combined in a million different ways to give a plethora of fascinating organic compounds.[...]

Thermodynamic properties of adamantane and the energy states of molecules in plastic crystals for some cage hydrocarbons

Thermodynamic properties of adamantane (I) were investigated in this paper. Heat capacities of I in the condensed state between 340 and 600 K were measured by a scanning calorimeter of triple heat bridge type, and characteristics of the fusion of I were determined. The measurements of the enthalpy of sublimation and the saturated vapor pressure for I were made. Thermodynamic functions of I in the ideal gas state were calculated by the statistical thermodynamics methods. The energy states of molecules in the plastic crystals for some cage hydrocarbons (adamantane, bicyclo[2.2.2]octane, pentacycloundecane, heptacyclotetradecane and diamantane) are discussed.

Planar-Tetracoordinate Carbon in a Neutral Saturated Hydrocarbon: Theoretical Design and Characterization.

Exact planarity at the central carbon atom is achieved, according to molecular orbital calculations, in the strained polycyclic cage hydrocarbon dimethanospiro[2.2]octaplane (see structure). There are no glaringly long C-C bonds, which might have reflected inherent instability in this molecule that is yet to be synthesized.

Common Radical Cation Intermediates in Cage Hydrocarbon Activations

The oxidation of 3,6-dehydrohomoadamantane (1) was achieved under chemical (NO+BF4–/EtOAc, NO+OAc–/Ac2O, and NO+BF4–/CH3CN), photochemical (photoexcited 1,2,4,5-tetracyanobenzene), and electrochemical (Pt anode, CH3CN, NH4BF4) conditions. Supporting ab initio [density functional theory (BLYP) and Møller–Plesset perturbation theory (MP2)] computations utilizing standard basis sets, 6–31G* (optimizations) and 6–311+G* (single-point energy evaluations), agree with the experimental results implicating the involvement of the same radical cation intermediates in the activation processes. Isomeric radical cations formed from different precursors can equilibrate with low barriers (2.0–11.7 kcal mol–1) and lead to common products. The computed and experimental adiabatic ionization potential of adamantane shows that activation with NO+BF4– is also likely to occur through the adamantyl radical cation. Hence, the bonds need not be attacked directly by the electrophile in the C–H or C–C activation of alkanes with relatively low ionization potentials.

Physico-Chemical Properties and Combustion Characteristics of New High-Energy-Density Caged Hydrocarbon Compounds

A new class of pentacyclic hydrocarbon compounds with high-energy/high density have been synthesized to be used as fuels or fuel additives, with the expectation that their inclusion in the fuel mixture will result in a net increase in volumetric efficiency of the current generation of powerplants. These compounds exhibit high density and contain a moderate amount of strain energy which contributes to the energy output during combustion. Through direct measurements, melting and boiling points, specific heats and latent heats of fusion were determined. Droplet combustion experiments with binary solutions of solid high-energy fuels in kerosene indicated increased effervescence and higher heat output. The liquid high-energy-density formulations exhibited microexplosive combustion behavior.