Saturated Molecules Research Articles

Large Interstellar and Cometary Biomolecules

AbstractThe relevance of hot molecular cores (HMCs) to the solar nebula has been strengthened as evidence emerges for a hot core phase in low mass star formation regions. Consequently, interferometric studies of large highly saturated molecules of biological interest (biomolecules) in HMCs have been extended to comets. A key goal is the interferometric detection and mapping of large biomolecules, which could be formed along chemical pathways similar to those for HMC species.

Do coupling constants and chemical shifts provide evidence for the existence of resonance-assisted hydrogen bonds?

Equation-of-motion coupled cluster singles and doubles (EOM-CCSD) calculations have been performed to determine two-bond 17O–17O and 15N–15N spin–spin coupling constants (2h J O–O and 2h J N–N) for ten neutral structures which may exhibit intramolecular O–H–O or N–H–N hydrogen bonds. MP2 chemical shifts of hydrogen-bonded protons have also been evaluated. The molecules include malonaldehyde and its diaza counterpart, and the corresponding saturated analogues. The aim of this study is to investigate whether the magnetic properties of the two-bond spin–spin coupling constants and the chemical shifts of the hydrogen-bonded protons provide evidence for the existence of resonance-assisted hydrogen bonds (RAHBs). The two-bond coupling constant for the equilibrium structures is greater for the hydrogen-bonded unsaturated molecule than for the saturated molecule, a result of the shorter O–O distance and stronger hydrogen bond in the former. However, when the O–O or N–N distances are forced to be the same in corresponding saturated and unsaturated structures, the coupling constants are similar. There is a significant increase in coupling constants when the intramolecular hydrogen bond (IMHB) changes from asymmetric to symmetric, due to much shorter O–O or N–N distances. Symmetrization effects also significantly affect the value of the proton chemical shift. For hydrogen-bonded conformers the trends in chemical shifts and coupling constants are similar. A detailed analysis of the NMR properties of oxygen-containing systems leads to the conclusion that neither the coupling constants nor the proton chemical shifts provide any evidence for the existence of RAHBs. Furthermore, the strength of the O–H···O IMHBs, investigated through the use of appropriate homodesmotic reactions, indicates that the enhanced stability of the IMHB in the unsaturated compound is associated with the σ skeleton of the molecule that allows the oxygen atoms to be in closer proximity than in the saturated analogue.

The assignment of dissociative electron attachment bands in compounds containing hydroxyl and amino groups

Dissociative electron attachment (DEA) spectra were recorded for methanol, phenol, diethylamine, tetramethylhydrazine, piperazine, pyrrole and N,N-dimethylaniline. Comparison with He I photoelectron spectra permitted the assignment of virtually all DEA bands in the saturated compounds to core excited Feshbach resonances with double occupation of Rydberg-like orbitals and various Koopmans' states of the positive ion as a core. These resonances shift to lower energies with alkyl substitution, in contrast to the shape resonances, and are found at surprisingly low energies in the amines. The DEA spectra in the unsaturated compounds show no or only weak evidence for the Rydberg-type Feshbach resonances. It is proposed that DEA in saturated polyatomic molecules containing hydroxyl and amino groups is in general dominated by this type of resonance.

Quantitative Structure-Property Relationship: XVII. Properties of Branched Hydrocarbon Molecules

A simple approach to estimating properties of branched molecules is suggested: A property of any nonlinear molecule is considered as a sum of the property of the corresponding linear molecule and correction "for branching,"] determined by the interaction of atoms of the substituting group with atoms of the main chain. The potential of this approach is demonstrated by the calculation of the melting points, heat capacities, entropies, and enthalpies and free energies of formation for 117 saturated hydrocarbon molecules, including all the linear C1-C20 molecules and branched C4-C10 molecules with methyl substituents; also the heats of vaporization are calculated for 72 molecules including all linear C1-C20 molecules and branched C4-C9 molecules with methyl substituents. The accuracy of all the estimates is high. When the linear contribution is taken into account more accurately, with correction for nonlinear variation of properties of linear molecules, it becomes possible to highly accurately in estimate various properties of both linear and branched molecules, using the molecular connectivity indices.

No Barrier for the Gas-Phase C2H + NH3 Reaction

The absolute rate constant of the reaction C2H + NH3 → products has been experimentally determined over the temperature range 295−765 K at a pressure of 10 Torr (He) and over the pressure range 5−30 Torr at 295 K. The concentration of C2H radicals was monitored in real time using the CH chemiluminescence method following their production by pulsed laser photolysis of C2H2 at 193 nm in a slow-flow reaction vessel. The pressure-independent rate constant is large and exhibits a pronounced negative temperature dependence: k1(T) = (1.2 ± 0.2) × 10-11 exp[(370 ± 40) K/T] cm3 s-1, both unusual for reaction of a radical with a saturated molecule. This may be rationalized by strong dipole−dipole and dipole − quadrupole interactions, as have been put forward for the isoelectronic CN + NH3 reaction. The C2H + NH3 reaction is somewhat faster than CN + NH3, even though ab initio calculations predict the CCH dipole moment to be smaller than that for CN. However the opposite sign of the dipole moment of C2H implies an initial HCC- - -HNH2 alignment, favorable for subsequent H-abstraction. The (extrapolated) high rate constant both at combustion temperatures and at interstellar temperatures should make this reaction very important in those environments.

Mono-unsaturated fatty acids protect against β-cell apoptosis induced by saturated fatty acids, serum withdrawal or cytokine exposure

Long-chain saturated fatty acids are cytotoxic to pancreatic β-cells while shorter-chain saturated and long-chain unsaturated molecules are better tolerated. Mono-unsaturated fatty acids are not, however, inert since they inhibit the pro-apoptotic effects of saturated molecules. In the present work we show that the mono-unsaturates palmitoleate (C16:1) or oleate (C18:1) also cause marked inhibition of apoptosis induced by exposure of clonal BRIN-BD11 β-cells to serum withdrawal or a combination of interleukin-1β plus interferon-γ. This response was dose-dependent and not accompanied by changes in NO formation. Taken together, the results suggest that mono-unsaturated fatty acids regulate a distal step common to several apoptotic pathways in pancreatic β-cells.

Room Temperature Negative Differential Resistance through Individual Organic Molecules on Silicon Surfaces

Room temperature negative differential resistance (NDR) has been measured through individual organic molecules on degenerately doped Si(100) surfaces using ultrahigh vacuum scanning tunneling microscopy (STM). For styrene molecules on n-type Si(100), NDR is observed only for negative sample bias because positive sample bias leads to electron stimulated desorption. By replacing styrene with a saturated organic molecule (2,2,6,6-tetramethyl-1-piperidinyloxy), electron stimulated desorption is not observed at either bias polarity. In this case, NDR is observed only for negative sample bias on n-type Si(100) and for positive sample bias on p-type Si(100). This unique behavior is consistent with a resonant tunneling mechanism via molecular orbitals and opens new possibilities for silicon-based molecular electronic devices and chemical identification with STM at the single-molecule level.

“Spectroscopic” Calculations of CH Bond Dissociation Energies for Ethane, Propane, Butane, Isobutane, Pentane, Hexane, and Neopentane Using Fundamental Vibration Frequencies

The fundamental spectrum and the parameters of the potential function of a number of saturated hydrocarbon molecules are calculated in an anharmonic approximation. The calculation is performed by the variational technique using a minimal Morse-harmonic basis. The potential function is taken as the sum of the Morse function for CH bonds and the harmonic function for the skeletal and deformation vibrations. The initial approximation for the potential function is found by ab initio calculations in a 6-31G basis and refined by solving the inverse problem. The calculated CH bond dissociation energies depend significantly on the molecular structure and on the position of CH bonds in the molecule. These energies correlate well with the experimental cleavage energies of these bonds. The changes in the dipole moment of the molecule induced by vibrations were found by ab initio calculations in a 6-31G basis. The calculated IR transmission curves are in good agreement with the experimental curves.

The Hot Core around the Low-Mass Protostar IRAS 16293-2422: Scoundrels Rule!

While warm dense gas is prevalent around low-mass protostars, the presence of complex saturated molecules—the chemical inventory characteristic of hot cores—has remained elusive in such environments. Here we report the results of an IRAM 30 m study of the molecular composition associated with the low-mass protostar IRAS 16293-2422. Our observations highlight an extremely rich organic inventory in this source with abundant amounts of complex O- and N-bearing molecules such as formic acid, HCOOH, acetaldehyde, CH3CHO, methyl formate, CH3OCHO, dimethyl ether, CH3OCH3, acetic acid, CH3COOH, methyl cyanide, CH3CN, ethyl cyanide, C2H5CN, and propyne, CH3CCH. We compare the composition of the hot core around this low-mass young stellar object with those around massive protostars and address the chemical processes involved in molecular complexity in regions of star formation.

Proton affinity of some radicals of alcohols, ethers and amines

Calculated proton affinities (PA) of the CH 3 CHX (X=OH, OCH 3, and NH 2) α-radicals and of four β-radicals CH 2CH 2X (X=OH, OCH 3, OCH 2CH 3, and NH 2) confirm that PA of α-radicals lie far below those of the corresponding saturated molecules and indicate, as a first and rough evaluation, that a radical in the β-position, has a negligible influence on the PA at the heteroatom. Experiments were performed to measure the PA of β-radicals both by measuring the rates of deprotonation of the corresponding β-distonic ions in a FT-ICR cell and by determining the Δ H f[ CH 2CH 2XH +], itself obtained by appearance energy (AE) measurements, using synchrotron radiation. From these results and those of literature, the following values are proposed: PA[ CH 2CH 2OH]=185.8±0.5 kcal/mol, PA[ CH 2CH 2OCH 3]=193.3±0.5 kcal/mol and PA[ CH 2CH 2NH 2]=116±1 kcal/mol.

Catalytic conversion of hydrocarbons over zeolites from first principles

Conversion of hydrocarbons over zeolites is an important industrial process. In the presence of zeolites, hydrocarbons are converted either to smaller molecules (cracking), or they recombine to branched compounds (isomerization). The microscopic steps of the conversion, however, are still not fully understood. This work brings together our previously published as well as new data into a coherent picture of hydrocarbon catalysis. We perform static and molecular dynamics DFT calculations on gmelinite zeolite with adsorbed linear saturated and unsaturated hydrocarbon molecules. Our simulations indicate that the conversion of olefins can proceed through the chemisorption inside the zeolite because species chemisorbed at specific sites are more stable than physisorbed molecules. Desorption at increased temperatures (400–700 K) produces unstable protonated molecules. These are found to be relatively long-lived, being stabilized in the zeolite surroundings. The collapse of protonated molecules then produces branched isomers. Protonation of saturated molecules leads to cracking. The calculated activation energies of both isomerization and cracking are in reasonable agreement with experimental data.

Theoretical justification of empirical additivity schemes for conformational energies

AbstractAdditivity of conformational energy of saturated molecules has been studied using the perturbation theory for density matrix. Analytical expressions for both total and conformational energies have been obtained and analyzed up to the third‐order members. It is shown that the conformational energy of compounds under investigation can be presented as a sum of transferable increments corresponding to the energies of separate conformational segments and their sequences. The role of end groups in determination of energies of conformational segments is revealed. The influence of substitution has been investigated. The dependence of subtle conformational effects on common structural peculiarities of Hamiltonians of saturated molecules has been concluded. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2003

Synthesis, X-ray structure, and properties of a tetrabenzannelated 1,2,4,5-cyclophane.

Parylene is the most frequently used material in the protective encapsulation of modern electronic components and medical implants.[1] This high-performance polymer is produced by the pyrolytic decomposition of [2.2]paracyclophane.[1c] Another high-performance organic material with even stronger C C bonds would be produced if another highly strained, all-aromatic cyclophane could be pyrolyzed, thus resulting in a TMsuperparylene∫. However, contrary to the mode of pyrolytic decomposition of [2.2]paracyclophane, where scission of the Csp3 Csp3 bond is the important first step leading to a p-xylylene monomer, in the case of a molecule such as 1 (Scheme 2), cleavage of a biaryl bond would produce a very reactive diradical monomer. Angle and bond strain in organic molecules and their effect on properties also continue to be an active field of research.[2] Over the last five decades, a substantial number of chemists have prepared many fascinating, strained saturated and unsaturated molecules.[2,3] The most notable of the strained unsaturated molecules are those of the fullerene C60 and the cyclophane families.[5] In the former, the hexagons are essentially cyclohexatrienes[6] and in the latter, the hexagons, while considerably distorted, still retain their benzenoid character. Since the first synthesis of [2.2]paracyclophane diene by Dewhirst and Cram,[7] a variety of [2.2]paracyclophanes with unsaturated or benzannelated bridges have been synthesized.[8] The influence of the bridges on the transannular benzene interactions and the geometry of the strained cyclophanes has been widely investigated.[9] To date, only a few unsaturated bridged and benzannelated cyclophanes are known,[9] but no benzannelated [2n]cyclophane with more than two bridges (n> 2) has been reported.[10] One would expect that, as the number of o-phenylene bridges increased, the total strain would also increase. To prepare a superparylene and to test the effect of benzo bridges in place of the alkyl bridges of cyclophanes one needs a rapid, reasonably high-yield synthetic entry. A priori, based on existing cyclophane synthetic methodology, the preparation of a symmetrical tetrabenzannelated [2n]cyclophane tetraene would appear to be rather difficult and lengthy. However, careful consideration of the molecular symmetry of the target revealed that the synthesis could be easily achieved. Herein, we describe the synthesis, X-ray structure, and some of the properties of the symmetrically benzannelated [24]cyclophane tetraene 1. In future publications we will report on the results of its pyrolytic decomposition. In Scheme 1 we depict the retrosynthetic analysis with a rather unusual disconnection leading to two dibenzocyclooctadiene-diynes and four methine units. As shown, the latter can originate from a meso-ionic precursor.

Diplatinum-Center-Mediated Transformation of a Substituted Benzene to a Cyclohexadienyl Dianion and the Breaking of C−Cl Bonds: Syntheses and Structures of Pt2R4(ttab) and Pt2(CH3)4(ttab)Cl2

Two novel dinuclear platinum(II) complexes, Pt2(CH3)4(ttab), 1, and Pt2Ph4(ttab), 2, have been synthesized from the reaction of 1,2,4,5-tetrakis(1-N-7-azaindolyl)benzene (ttab) with Pt2(CH3)4(SMe2)2 and [PtPh2(SMe2)]n (n = 2, 3), respectively. The Pt(II) centers in both complexes are within van der Waals contact distances with the central benzene ring of the ttab ligand. Compound 1 was found to react readily with saturated chlorinated molecules such as CFCl3, CCl4, CHCl3, and CH2Cl2 at ambient temperature to yield a dinuclear platinum(IV) complex, Pt2(CH3)4(ttab)Cl2, 3, quantitatively. The central benzene ring of the ttab ligand in 1 was transformed to a 1,4-cyclohexadiene dianion in 3, accompanied by the formation of two internal Pt−C bonds. The structures of 1, 2, and 3 are determined by X-ray diffraction analyses.

Pentagon Stability in Cycloarsanes

The orbital phase theory leads to the prediction that the saturated arsenic cyclic molecules prefer pentagons, which is substantiated by the negative strain energy of cyclic As 5 H 5 . The puckered five-membered arsenic ring is an important structural unit for the pentagon stability. Possible structures and conformers of polycycloarsanes As 8 H 4 , As 11 H 3 , "roof-like" and "cage-like" As 12 H 4 , As 13 H 3 , As 14 H 2 , and As 15 H 3 with relatively low strain energies were predicted due to many puckered pentagon units in them. The low stability of the dodecahedron As 20 with 12 planar pentagon units was suggested by the high strain energy.

Pentagon stability: cyclic delocalization of lone pairs through sigma conjugation and design of polycyclophosphanes.

The orbital-phase theory was applied to propose pentagon stability in a well-defined manner. Cyclic delocalization of the lone pair electrons on the five-membered ring atoms through the vicinal sigma bonds was shown to be favored by the orbital-phase properties. The pentagon stability was found to be outstanding in saturated phosphorus five-membered rings in the puckered conformation, and was substantiated by the negative strain energy of cyclopentaphosphane, P(5)H(5) (3). The relative increments of the remarkable increase in the strain energies of protonation on the different atoms in the most stable conformers supported the significance of the cyclic delocalization of the lone pairs. Pentagon stability led to the design of three novel polycyclic phosphanes, P(12)H(4) (18), P(13)H(3) (19), and P(14)H(2) (20), with low strain energies due to many puckered pentagon units in them. The low stability of the dodecahedron P(20) (22) was suggested by the high strain energy due to its planar pentagon units. The pentagon stability is less significant in the saturated nitrogen ring molecules due to the greater energy gap between the n and sigma orbitals.

Distance Dependence of Electron Tunneling through Self-Assembled Monolayers Measured by Conducting Probe Atomic Force Microscopy: Unsaturated versus Saturated Molecular Junctions

Electron tunneling through self-assembled monolayers (SAMs) composed of either unsaturated or saturated molecules was investigated using conducting probe atomic force microscopy (CP-AFM). SAMs of unsaturated oligophenylene thiolates or saturated alkanethiolates were assembled on Au substrates and contacted with a Au-coated AFM tip at constant applied load. The current−voltage (I−V) characteristics of both types of SAMs were linear over ±0.3 V. Resistance (R) increased exponentially with molecular length (s) in both cases according to the expected relationship, R = R0 exp(βs), but the rate of increase, as quantified by the structure-dependent factor β, was much less for the unsaturated SAMs than for the saturated alkanethiolate SAMs. Average β values were 0.42 ± 0.07 A-1 for the oligophenylene thiolate SAMs and 0.94 ± 0.06 A-1 for the alkanethiolate SAMs. Extrapolation of semilog plots of resistance versus molecular length to zero length yielded an estimate of the metal−molecule contact resistance, which w...

Ab Initio Topological Analysis of the Electronic Density inn-Butonium Cations and Their van der Waals Complexes

In this work, the topology of the ab initio electronic density charge, using the theory of atoms in molecules (AIM), developed by Bader, is studied for the n-C4H11+ species, the protonated n-butane. The electronic delocalization that operates through the σ bonds in saturated molecules and specifically in protonated alkanes is studied by means of analysis of the charge density and the bond critical points. This analysis is used in order to establish a relationship among the parameters that determine the stability order found for the different species and relate them with the carbonium ions structure. Comparing these results with the i-C4H11+ allow us to study the nature of the 3c−2e bonds in alkanes in greater detail, permitting the description on the σ basicity and reactivity scales in terms of structural parameters of the carbonium ions.

The effect of molecular composition on the oxidative behaviour of group I base oils in the presence of an antioxidant additive

AbstractThe response of base oil hydrocarbons to additive molecules is fundamental to any lubricant formulation. To have this understanding it is important to have complete knowledge of the base oil hydrocarbon composition. The work reported here is a study of a series of API Group I base oils showing the effect of various structural parameters during oxidation with an antioxidant additive (zinc dialkyldithiophosphate, ZDDP). To understand this complex base oil‐additive interaction pattern, a combination of chromatographic and spectroscopic methods has been adopted. The results show that certain NMR‐derived base oil structural parameters can be used as an index of the additive response in conjunction with column chromatographic and FTIR absorption data. It is also observed that saturated molecules, i.e., iso‐ and normal paraffins and naphthenes, behave differently towards an antioxidant additive, and the total additive response is the result of all the interactions in the system.

Thermo-oxidative stability studies on some new generation API group II and III base oils

Due to the increasing demand for highly saturated (group II and III) base oils for use in specialty lubricant application, it is necessary to obtain a clear picture of the base oil molecular distribution. These oils are more stable to oxidation and exhibit superior performance-based characteristics as compared with group I type base oils. With the aromatic content reaching a minimum value, saturated molecules control most of the physical properties in these oils. Molecular structure based characterization developed for conventionally refined base oils will be inadequate to address all the structural diversities of these base fluids. In this study, results from thin film micro oxidation (TFMO) and pressure differential scanning calorimetry (PDSC) were discussed in terms of the quantitative 13C NMR (inverse gated, CSE, GASPE) data. Correlations obtained with physical properties (e.g. viscosity), oxidation (evaporation, insoluble deposit) and structural data indicate the significance of base oil's saturate hydrocarbon structures in influencing most of the performance properties.