Saturated Molecules Research Articles

High-Resolution Electronic Spectroscopy of the Doorway States to Intramolecular Charge Transfer

Reported here are several of the ground, first, and second excited state structures and dipole moments of three benchmark intramolecular charge transfer (ICT) systems; 4-(1H-pyrrol-1-yl)benzonitrile (PBN), 4,4'-dimethylaminobenzonitrile (DMABN), and 4-(1-pyrrolidinyl)benzonitrile (PYRBN), isolated in the gas phase and probed by rotationally resolved spectroscopy in a molecular beam. The related molecules 1-phenylpyrrole (PP) and 4-aminobenzonitrile (ABN) also are discussed. We find that the S1 electronic state is of B symmetry in all five molecules. In PBN, a second excited state (S2) of A symmetry is found only ~400 cm(-1) above the presumed origin of the S1 state. The change in dipole moment upon excitation to the A state is measured to be Δμ ≈ 3.0 D, significantly smaller than the value predicted by theory and also smaller than that observed for the "anomalous" ICT band of PBN in solution. The B state dipole moments of DMABN and PYRBN are large, ~10.6 D, slightly larger than those attributed to "normal" LE fluorescence in solution. In addition, we find the unsaturated donor molecules (PP, PBN) to be twisted in their ground states and to become more planar upon excitation, even in the A state, whereas the saturated donor molecules (ABN, DMABN, PYRBN), initially planar, either remain planar or become more twisted in their excited states. It thus appears that the model that is appropriate for describing ICT in these systems depends on the geometry of the ground state.

Improving the CHARMM Force Field for Polyunsaturated Fatty Acid Chains

CHARMM36 (C36) is the most up-to-date pairwise additive all-atom lipid force field and is able to accurately represent bilayer properties of saturated and monounsaturated lipid molecules in the natural constant particle, pressure, and temperature (NPT) ensemble. However, molecular dynamics (MD) simulations on 1-stearoyl-2-docosahexaenoyl-sn-glycerco-3-phosphocholine (SDPC) bilayers of the polyunsaturated fatty acid (PUFA) chains result in inaccuracies of the surface area per lipid (SA), deuterium order parameters (S(CD)), and X-ray form factors. Therefore, in this study, high-level quantum mechanical calculations are used to improve the dihedral potential of neighboring double bonds, and the corresponding force field is referred to as C36p. The SA for SDPC at 303 K increases from 63.2 ± 0.2 (C36) to 70.8 ± 0.2 (C36p) Å(2) and agrees favorably with X-ray diffraction results at 297 K. The resulting S(CD) are in excellent agreement with experimental values of both the sn-1 and sn-2 chains. Calculated NMR (13)C relaxation times and X-ray form factors from MD simulations of SDPC bilayers also agree with experiments. MD simulations of 1,2-diarachidonyl-phosphatidylcholine (DAPC) bilayers are used to further validate our force field parameters on a lipid with both chains containing PUFAs. As expected, the thickness of DAPC bilayers is reduced, and the SA is increased compared to the SDPC bilayers. This update in the PUFA force field should allow for accurate MD simulations of PUFA-containing bilayers in the NPT ensemble.

The explicit interactions of five-membered saturated heterocyclics containing one and two heteroatoms with single water molecule

In this article, the hydrogen bonding interaction between saturated five-membered heterocyclic molecules and water has been investigated. Molecular orbital and density functional theory methods have been used to evaluate the stabilization energies associated with the adduct formation between heterocyclic molecules and water. The hydrogen bond acceptor ability of O, S, Se, and N as members of five-membered ring has been analyzed. The effect of the presence of second heteroatom N in the ring on the hydrogen bond interaction has also been evaluated. Atoms in molecules theory calculations were carried out to characterize the hydrogen bond through the changes in electron density and Laplacian of electron density. A natural energy decomposition analysis and natural bond orbital analysis is also performed to understand the nature of hydrogen bonding interaction in monohydrated five-membered heterocyclic adducts.

Modelling the adsorption of short alkanes in protonated chabazite: The impact of dispersion forces and temperature

The adsorption of alkanes in a protonated zeolite has been investigated at different levels of theory. At the lowest level we use density-functional theory (DFT) based on semi-local (gradient-corrected) functionals which account only for the interaction of the molecule with the acid site. To describe the van der Waals (vdW) interactions between the saturated molecule and the inner wall of the zeolite we use (i) semi-empirical pair interactions, (ii) calculations using a non-local correlation functional designed to include vdW interactions, and (iii) an approach based on calculations of the dynamical response function within the random-phase approximation (RPA). The effect of finite temperature on the adsorption properties has been studied by performing molecular dynamics (MD) simulations based on forces derived from DFT plus semi-empirical vdW corrections. The simulations demonstrate that even at room temperature the binding of the molecule to the acid site is frequently broken such that only the vdW interaction between the alkane and the zeolite remains. The finite temperature adsorption energy is calculated as the ensemble average over a sufficiently long molecular dynamics run, it is significantly reduced compared to the T=0K limit. At a higher level of theory where MD simulations would be prohibitively expensive we propose a simple scheme based on the averaging over the adsorption energies in the acid and in the purely siliceous zeolite to account for temperature effects. With these corrections we find an excellent agreement between the RPA predictions and experiment.

Analysis of Saturated Hydrocarbons by Redox Reaction with Negative-Ion Electrospray Fourier Transform Ion Cyclotron Resonance Mass Spectrometry

A novel technique was developed for characterization of saturated hydrocarbons. Linear alkanes were selectively oxidized to ketones by ruthenium ion catalyzed oxidation (RICO). Branched and cyclic alkanes were oxidized to alcohols and ketones. The ketones were then reduced to alcohols by lithium aluminum hydride (LiAlH(4)). The monohydric alcohols (O(1)) in the products obtained from the RICO and RICO-LiAlH(4) reduction reactions were characterized using negative-ion electrospray ionization (ESI) Fourier transform ion cyclotron resonance mass spectrometry (FTICR MS) for identification of iso-paraffins, acyclic paraffins and cyclic paraffins. Various model saturated compounds were used to determine the RICO reaction and ionization selectivity. The results from the FTICR MS analysis on the petroleum distillates derived saturated fraction were in agreement with those from field ionization gas chromatography time-of-flight mass spectrometry (FI GC-TOF MS) analysis. The technique was also used to characterize a petroleum vacuum residue (VR) derived saturates. The results showed that the saturated molecules in the VR contained up to 11 cyclic rings, and the maximum carbon number was up to 92.

To Mix or Not To Mix: 2D Crystallization and Mixing Behavior of Saturated and Unsaturated Aliphatic Primary Amides

Physisorbed monolayers based on relatively weak noncovalent interactions can serve as excellent model systems for understanding crystallization of materials in reduced dimensionality. Here we employ a powerful combination of scanning tunneling microscopy (STM), differential scanning calorimetry (DSC), and computational modeling to reveal two-dimensional (2D) crystallization and mixing behavior of saturated and unsaturated (cis as well as trans) aliphatic primary amides. The foundation of the present work is laid by DSC measurements, which reveal characteristic adsorption and mixing behavior of aliphatic amides. These results are further supported by STM visualization of the adlayers. STM reveals, at submolecular resolution, the adsorption as well as the two-component 2D phase behavior of these molecules at the liquid-solid interface. The saturated and trans-unsaturated amides exhibit random mixing in view of their size and shape complementarity. Binary mixtures of saturated and cis-unsaturated amides, on the other hand, display unprecedented mixing behavior. The linear saturated and bent cis-unsaturated amide molecules are found to mix surprisingly better at the liquid-solid interface than might have been expected on account of the dissimilarity in their shapes. Strong, directional intermolecular hydrogen-bonding interactions as well as the relative stabilization energies of the adlayers are responsible for such unusual mixing behavior. Computational modeling provides additional insight into all the possible interactions in 2D assemblies and their impact on stabilization energies of the supramolecular networks. This study provides a model for understanding the effect of nanoscale cocrystallization on the thin film structure at interfaces and demonstrates the importance of molecular geometry and hydrogen bonding in determining the coadsorption behavior.

Hydrogenation of solid hydrogen cyanide HCN and methanimine CH2NH at low temperature

Context. Hydrogenation reactions dominate grain surface chemistry in dense molecular clouds and lead to the formation of complex saturated molecules in the interstellar medium.Aims. We investigate in the laboratory the hydrogenation reaction network of hydrogen cyanide HCN.Methods. Pure hydrogen cyanide HCN and methanimine CH2 NH ices are bombarded at room temperature by H-atoms in an ultra-high vacuum experiment. Warm H-atoms are generated in an H2 plasma source. The ices are monitored with Fourier-transform infrared spectroscopy in reflection absorption mode. The hydrogenation products are detected in the gas phase by mass spectroscopy during temperature-programmed desorption experiments.Results. HCN hydrogenation leads to the formation of methylamine CH3 NH2 , and CH2 NH hydrogenation leads to the formation of methylamine CH3 NH2 , suggesting that CH2 NH can be a hydrogenation-intermediate species between HCN and CH3 NH2 . Conclusions. In cold environments the HCN hydrogenation reaction can produce CH3 NH2 , which is known to be a glycine precursor, and to destroy solid-state HCN, preventing its observation in molecular clouds ices.

Experimental Study of Hydrocarbons Synthesis from Syngas by a Tip–Tip Electrical Discharge at Very High Pressure

This paper is dedicated to the study of hydrocarbons synthesis from a syngas using a plasma process based on the generation of a electrical discharge at very high pressure. We report experimental results performed using a He/H2/CO mixture with the ratio 40%/48%/12% at a pressure of 2.2 MPa, through three modes of treatment: one continuous mode and two intermittent modes including a relaxation time between two successive discharges. The study shows that significant quantities of C1, and saturated and unsaturated C2 molecules are synthesized at these experimental conditions. It also indicates the better efficiency of the intermittent treatment modes for the C2 molecules synthesis. Estimates of the chemical synthesis balance occurring in the reactor during an instantaneous treatment are also presented in the manuscript. In addition, the study indicates a preliminary scan of other synthesized molecules which have been identified by varying the operating pressure in the continuous treatment mode.

Analytical theory of the nuclear-spin-induced optical rotation in liquids

Based on the thought on the antisymmetric polarizability induced by nuclear magnetic moments and theory of the Faraday effect, an analytical theoretical expression is derived for the nuclear-spin-induced optical rotation (NSOR) of diamagnetic saturated molecules in a circular cylinder. That consists of two parts, ϕ ( I ) and ϕ ( B ) , induced by the intramolecular and intermolecular hyperfine interaction, respectively. By using them and the Verdet constants, NSOR for 1H in water, hexane, cyclohexane and methyl–alcohol in liquid and H 2 gas have been calculated. The calculated NSOR for water agrees with the experiment and for three hydrocarbons predicts the same order of magnitude as water. For the samples studied except H 2 gas, ϕ ( I ) and ϕ ( B ) are comparable in magnitude.

Ethene/ethane mixture diffusion in the MOF sieve ZIF-8 studied by MAS PFG NMR diffusometry

The adsorption and diffusion of ethene/ethane mixtures is explored by 1H and 13C MAS NMR spectroscopy and by the combination of PFG NMR with magic-angle spinning (MAS PFG NMR). Some indication for a preferential adsorption of the molecules close to the methyl-groups of the imidazole-rings was found, however no evidence for structural changes upon adsorption of an ethene/ethane mixture. MAS PFG NMR allows an individual but simultaneous observation of both molecules in adsorbed state and as well as in the gas phase. The intracrystalline MAS PFG NMR diffusivities are in consistent agreement with our previous data obtained by IR microscopy. Our consideration includes the loading dependence and the correlation of self-diffusion with transport diffusion by accounting for the influence of the thermodynamic factor. The diffusion selectivity is determined to D ethene: D ethane = 5.5 at a loading of four molecules per cavity. The higher mobility of ethene can be rationalized by its smaller size compared to ethane. This conclusion is validated by the measured activation energies for diffusion which are considerably higher for ethane. On the other hand, differences in the guest–host interaction between the saturated and non-saturated molecules can be excluded as possible reason for the different diffusivities.

Observations of Complex Molecules in Low-Mass Protostars

AbstractLow-mass star forming regions are rich inventories of complex organic molecules. Furthermore, they show significant chemical diversity even among sources in a similar physical evolutionary stage (i.e. Class 0 sources). One distinct case is the hot corino chemistry characterized by rich existence of saturated complex organic molecules such as HCOOCH3 and C2H5CN, whereas the other is the warm carbon-chain chemistry (WCCC) characterized by extraordinary richness of unsaturated complex organic molecules such as carbon-chain molecules. We here summarize these observational achievements during the last decade, and present a unified picture of carbon chemistry in low-mass protostellar cores. The chemical diversity most likely originates from the source-to-source difference in chemical compositions of grain mantles. In particular, the gas-phase abundance of CH4 evaporated from grain mantles is thought to be a key factor for appearance of WCCC. The origin of the diversity and its evolution to protopranetary disks are discussed.

Structure–activity relationships influencing lipid-induced changes in eIF2α phosphorylation and cell viability in BRIN-BD11 cells

Fatty acids influence the viability of eukaryotic cells differentially such that long chain saturated molecules are poorly tolerated, whereas unsaturated species are less detrimental and can be cytoprotective. The basis for these effects is unclear but studies in yeast imply that they reflect the spatial configuration of the molecules when incorporated into the ER membrane. Using BRIN-BD11 β-cells, we show that a wide range of unsaturated free fatty acids and their methyl-esters (having differing chain length and disposition of the double bonds) elicit cytoprotection and relief of protein kinase RNA-like endoplasmic reticulum kinase-dependent ER stress. Thus, both physical properties and specific signalling events may regulate fatty acid responses in β-cells.

Universal Scaling of the Charge Transport in Large‐Area Molecular Junctions

Charge transport through alkanes and para-phenylene oligomers is investigated in large-area molecular junctions. The molecules are self-assembled in a monolayer and contacted with a top electrode consisting of poly(3,4-ethylenedioxythiophene)-poly(4-styrenesulfonic acid) (PEDOT:PSS). The complete set of J(V,T) characteristics of both saturated and π-conjugated molecules can be described quantitatively by a single equation with only two fit parameters. The derived parameters, in combination with a variation of the bulk conductivity of PEDOT:PSS, demonstrate that the absolute junction resistance is factorized with that of PEDOT:PSS.

Unusual mechanism for H3+ formation from ethane as obtained by femtosecond laser pulse ionization and quantum chemical calculations

The formation of H(3)(+) from saturated hydrocarbon molecules represents a prototype of a complex chemical process, involving the breaking and the making of chemical bonds. We present a combined theoretical and experimental investigation providing for the first time an understanding of the mechanism of H(3)(+) formation at the molecular level. The experimental approach involves femtosecond laser pulse ionization of ethane leading to H(3)(+) ions with kinetic energies on the order of 4 to 6.5 eV. The theoretical approach involves high-level quantum chemical calculation of the complete reaction path. The calculations confirm that the process takes place on the potential energy surface of the ethane dication. A surprising result of the theoretical investigation is, that the transition state of the process can be formally regarded as a H(2) molecule attached to a C(2)H(4)(2+) entity but IRC calculations show that it belongs to the reaction channel yielding C(2)H(3)(+) + H(3)(+). Experimentally measured kinetic energies of the correlated H(3)(+) and C(2)H(3)(+) ions confirm the reaction path suggested by theory.

Single-molecule conductance measurement of self-assembled organic monolayers using scanning tunneling spectroscopy in combination with statistics analysis

Based on ambient atmosphere scanning tunneling microscope (STM) technique, scanning tunneling spectroscopy (STS) combined with statistics analysis was developed to investigate the single-molecule conductance of various kinds of molecules which were self-assembled on the Au (1 1 1). Conductance histograms obtained from current–voltage curves revealed well-defined peaks at integer multiples of a fundamental conductance and were used to identify the conductance of a single molecule. The conductances of saturated molecules like 1,8-octanedithol and hexanethiocyanate were found to be 0.072 × 10 −4G 0 and 0.06 × 10 −4G 0 respectively and 0.23 × 10 −4G 0 and 0.13 × 10 −4G 0 for unsaturated molecules like 5,5′-dithiol- 2,2′,5′,2″-terthiophene and 4,4′-dithio-tert(phenylene ethylene).

Monomolecular cracking of propane over acidic chabazite: An ab initio molecular dynamics and transition path sampling study

The monomolecular Haag–Dessau mechanism for propane cracking over acidic chabazite has been studied using dispersion-corrected periodic DFT calculations in combination with ab initio molecular dynamics (AIMD) simulations, transition path sampling (TPS), and free-energy integrations. The AIMD simulations show that due to the weak specific interaction of the saturated molecule with Brønsted acid sites, the adsorption energy is considerably reduced at elevated temperature and that only a fraction of the molecules adsorbed within the zeolite is sufficiently close to the acid site to form a reactant complex for protonation. TPS shows that the preferred reaction mechanism is the protonation of a terminal methyl group. The direct proton attack on the C–C bond between the methyl and methylene groups is not excluded but occurs with lower probability. The intrinsic reaction parameters such as free energy and entropy of activation are determined using thermodynamic integration based on constrained molecular dynamics simulations.

Reactive uptake kinetics of NO3 on multicomponent and multiphase organic mixtures containing unsaturated and saturated organics

We investigated the reactive uptake of NO(3) (an important night-time oxidant in the atmosphere) on binary mixtures containing an unsaturated organic (methyl oleate) and saturated molecules (diethyl sebacate, dioctyl sebacate, and squalane) which we call matrix molecules. These studies were carried out to better understand the reactivity of unsaturated organics in multicomponent and multiphase atmospheric particles. For liquid binary mixtures the reactivity of methyl oleate depended on the matrix molecule. Assuming a bulk reaction, H(matrix)√(D(matrix)k(oleate)) varied by a factor of 2.7, and assuming a surface reaction H(matrix)(S)K(matrix)(S)k(oleate)(S) varied by a factor of 3.6, where H(matrix)√(D(matrix)k(oleate) and H(matrix)(S)K(matrix)(S)k(oleate)(S) are constants extracted from the data using the resistor model. For solid-liquid mixtures, the reactive uptake coefficient depended on exposure time: the uptake decreased by a factor of 10 after exposure to NO(3) for approximately 90 min. By assuming either a bulk or surface reaction, the atmospheric lifetime of methyl oleate in different matrices was estimated for moderately polluted atmospheric conditions. For all liquid mixtures, the lifetime was in the order of a few minutes (with an upper limit of 35 min). These lifetimes can be used as lower limits to the lifetimes in semi-solid mixtures. Our studies emphasize that the lifetime of unsaturated organics (similar to methyl oleate) is likely short if the particle matrix is in a liquid state.

Potentially important nighttime heterogeneous chemistry: NO3 with aldehydes and N2O5 with alcohols

We report the first measurements of the reactive uptake of NO(3) with condensed-phase aldehydes. Specifically, we studied NO(3) uptake on solid tridecanal and the uptake on liquid binary mixtures containing tridecanal and saturated organic molecules (diethyl sebacate, dioctyl sebacate, and squalane) which we call matrix molecules. Uptake on the solid was shown to be efficient, where γ = (1.6 ± 0.8) × 10(-2). For liquid binary mixtures the reactivity of aldehyde depended on the matrix molecule. Assuming a bulk reaction, H(matrix)√(D(matrix)k(2°,aldehyde)) varied by a factor of 2.6, and assuming a surface reaction H(matrix)(S)K(matrix)(S)k(2°,aldehyde)(S) varied by a factor of 2.9, where H(matrix)√(D(matrix)k(2°,aldehyde)) and H(matrix)(S)K(matrix)(S)k(2°,aldehyde)(S) are constants extracted from the data using the resistor model. By assuming either a bulk or surface reaction, the atmospheric lifetimes for aldehydes were estimated to range from 1.9-7.5 h. We also carried out detailed studies of N(2)O(5) uptake kinetics on alcohols. We show that uptake coefficients of N(2)O(5) for five different organics at 293 K varied by more than 2 orders of magnitude, ranging from 3 × 10(-4) to 1.8 × 10(-2). We show that the uptake coefficients correlate with √(D(alcohol)(OH concentration)) but more work is needed with other alcohols to completely understand the dependence. Using this kinetic data we show that the atmospheric lifetime of alcohols with respect to N(2)O(5) heterogeneous chemistry can vary from 0.6-130 h, depending on the physical and chemical properties of the organic liquid.

C60-C70 2元系固溶体の作製（I）：揮発法を用いた場合

C60-C70 solids were prepared via volatilization of solutions of C60 and C70 in toluene as the solvent. During volatilization of the toluene, saturated fullerene molecules did not precipitate as a C60-C70 solid, but formed a single phase (C60)1−x(C70)x•C6H5CH3 solvate. The solvate was unstable in air when x was small and naturally decomposed into a C60-C70 solid. With heat-treatment in a vacuum, the solvate could also be converted into the C60-C70 solid even when x was large. The single solvate phase produced two phases of C60-C70 solids, indicating that the C60-C70 system possesses a miscibility gap.

Sedimentation in biodiesel and Ultra Low Sulfur Diesel Fuel blends

A biodiesel storage stability study was conducted on Ultra Low Sulfur Diesel Fuel (ULSDF) and three biodiesel fuels (B100), including a Tallow-based Methyl Ester (TME), a Canola-based Methyl Ester (CME), and, a Yellow Grease Methyl Ester (YGME), and fuel blends (B5 and B20). The stability study was conducted over ten months (Aug 07–Jun 08) and consisted of storing fuel samples in quarter filled plastic and steel 20L cans, in an unheated shed. Fuel cans were vented twice a week to ensure exposure of the fuel to air. Changes in Acid Number, kinematic viscosity and free water and sediments levels were monitored over the storage period. Temperature and relative humidity ranged from −25°C to 35°C and 25% to 100%, respectively. Acid Number and the viscosity did not increase beyond the uncertainty of the method used. Reference samples kept at 40°C were used for comparison. Free water and sediment levels were barely above the detection limit of 0.003mL/100mL of fuel for CME and YGME and their blends. TME and its B20 blend displayed free water and sediment levels up to 0.05mL/100mL of fuel in February, after six months of storage. These values decreased considerably after the warm Summer months back to below 0.01mL/100mL. All free water and sediment levels were measured after fuel samples came to equilibrium with room temperature. The TME B5 free water and sediment levels remained low throughout the storage period. Proton Nuclear Magnetic Resonance (NMR) spectroscopy performed on particulates from the sediments revealed a similar composition but a slightly lower concentration for protons in alkenyl groups. The presence of these sediments was attributed to more saturated molecules coming out of solution in colder weather and very slowly going back to solution at room temperature.