Construction of combustion models for rapeseed methyl ester bio-diesel fuel for internal combustion engine applications

Bio-diesel fuels are non-petroleum-based diesel fuels consisting of long chain alkyl esters produced by the transesterification of vegetable oils, that are intended for use (neat or blended with conventional fuels) in unmodified diesel engines. There have been few reports of studies proposing theoretical models for bio-diesel combustion simulations. In this study, we developed combustion models based on ones developed previously. We compiled the liquid fuel properties, and the existing detailed mechanism of methyl butanoate ester (MB, C₅H₁₀O₂) oxidation was supplemented by sub-mechanisms for two proposed fuel constituent components, C₇H₁₆ and C₇H₈O (and then, by mp2d, C₄H₆O₂ and propyne, C₃H₄) to represent the combustion model for rapeseed methyl ester described by the chemical formula, C₁₉H₃₄O₂ (or C₁₉H₃₆O₂). The main fuel vapor thermal properties were taken as those of methyl palmitate C₁₉H₃₆O₂ in the NASA polynomial form of the Burcat database. The special global reaction was introduced to “crack” the main fuel into its constituent components. This general reaction included 309 species and 1472 reactions, including soot and NO_x formation processes. The detailed combustion mechanism was validated using shock-tube ignition-delay data under diesel engine conditions. For constant volume and diesel engine (Volvo D12C) combustion modeling, this mechanism could be reduced to 88 species participating in 363 reactions.     

Evaluations of the accuracies of DMol3 density functionals for calculations of experimental binding enthalpies of N2, CO,H2, C2H2 at catalytic metal sites

The density functionals that can be used with numerical basis sets in the density functional methodology of the programme DMol3 are evaluated by comparison with experimental data. The objective is to identify and validate the most accurate and computationally efficient density functional to be used in DMol3 simulations that use large molecular models (many hundreds of atoms) of the reaction steps involved in the chemical mechanisms of metalloenzymes and synthetic metallocatalysts. The experimental systems focus on enthalpy data for reactions analogous to those involved in the chemical mechanism of nitrogenase, including coordination of N₂, CO, H₂ and C₂H₄ and hydrogen bonding. Some geometric and vibrational frequency data are included in the 19 test systems. The conclusion is that the gradient-corrected functionals PBE, PW91 and BP provide acceptably accurate results, with the best functional being PBE, which yields reaction energies within or very close the experimental error range. These functionals are also the most computationally efficient.     

Titanium(III) alkoxides. A new synthetic route and solid state properties (CP/MAS 13C NMR,X-ray and IR)

Ti(OR)₃ compounds (R=C₂H₅, C₄H₉ⁿ, C₆H₅) were prepared by reduction of titanium tetralkoxides with organosilicon compounds containing SiH bonds. The reaction mechanism probably involves a four membered cyclic intermediate. The tervalent alkoxides have been characterized by elemental analyses, X-ray powder diffraction, infrared spectroscopy and solid-state magic angle sample spinning ¹³C NMR.The compounds are polymeric owing to the presence of alkoxide bridges. They are diamagnetic, insoluble materials which decompose on melting. Previously reported results are critically discussed and compared with the experimental findings from both infrared and NMR spectroscopy.     

SPARTA+: a modest improvement in empirical NMR chemical shift prediction by means of an artificial neural network

NMR chemical shifts provide important local structural information for proteins and are key in recently described protein structure generation protocols. We describe a new chemical shift prediction program, SPARTA+, which is based on artificial neural networking. The neural network is trained on a large carefully pruned database, containing 580 proteins for which high-resolution X-ray structures and nearly complete backbone and ¹³C^β chemical shifts are available. The neural network is trained to establish quantitative relations between chemical shifts and protein structures, including backbone and side-chain conformation, H-bonding, electric fields and ring-current effects. The trained neural network yields rapid chemical shift prediction for backbone and ¹³C^β atoms, with standard deviations of 2.45, 1.09, 0.94, 1.14, 0.25 and 0.49 ppm for δ¹⁵N, δ¹³C’, δ¹³C^α, δ¹³C^β, δ¹H^α and δ¹H^N, respectively, between the SPARTA+ predicted and experimental shifts for a set of eleven validation proteins. These results represent a modest but consistent improvement (2–10%) over the best programs available to date, and appear to be approaching the limit at which empirical approaches can predict chemical shifts.     

A new visualization scheme of chemical energy density and bonds in molecules

Covalent bond describes electron pairing in between a pair of atoms and molecules. The space is partitioned in mutually disjoint regions by using a new concept of the electronic drop region R_D, atmosphere region R_A, and the interface S (Tachibana in J Chem Phys 115:3497–3518, 2001). The covalent bond formation is then characterized by a new concept of the spindle structure. The spindle structure is a geometrical object of a region where principal electronic stress is positive along a line of principal axis of the electronic stress that connects a pair of the R_Ds of atoms and molecules. A new energy density partitioning scheme is obtained using the Rigged quantum electrodynamics (QED). The spindle structure of the stress tensor of chemical bond has been disclosed in the course of the covalent bond formation. The chemical energy density visualization scheme is applied to demonstrate the spindle structures of chemical bonds in H₂, C₂H₆, C₂H₄ and C₂H₂ systems.Figure Field theory of the energy density.     

Uncovering symmetry-breaking vector and reliability order for assigning secondary structures of proteins from atomic NMR chemical shifts in amino acids

Unravelling the complex correlation between chemical shifts of ¹³ C ^α, ¹³ C ^β, ¹³ C′, ¹ H ^α, ¹⁵ N, ¹ H ^N atoms in amino acids of proteins from NMR experiment and local structural environments of amino acids facilitates the assignment of secondary structures of proteins. This is an important impetus for both determining the three-dimensional structure and understanding the biological function of proteins. The previous empirical correlation scores which relate chemical shifts of ¹³ C ^α, ¹³ C ^β, ¹³ C′, ¹ H ^α, ¹⁵ N, ¹ H ^N atoms to secondary structures resulted in progresses toward assigning secondary structures of proteins. However, the physical-mathematical framework for these was elusive partly due to both the limited and orthogonal exploration of higher-dimensional chemical shifts of hetero-nucleus and the lack of physical-mathematical understanding underlying those correlation scores. Here we present a simple multi-dimensional hetero-nuclear chemical shift score function (MDHN-CSSF) which captures systematically the salient feature of such complex correlations without any references to a random coil state of proteins. We uncover the symmetry-breaking vector and its reliability order not only for distinguishing different secondary structures of proteins but also for capturing the delicate sensitivity interplayed among chemical shifts of ¹³ C ^α, ¹³ C ^β, ¹³ C′, ¹ H ^α, ¹⁵ N, ¹ H ^N atoms simultaneously, which then provides a straightforward framework toward assigning secondary structures of proteins. MDHN-CSSF could correctly assign secondary structures of training (validating) proteins with the favourable (comparable) Q3 scores in comparison with those from the previous correlation scores. MDHN-CSSF provides a simple and robust strategy for the systematic assignment of secondary structures of proteins and would facilitate the de novo determination of three-dimensional structures of proteins.     

Synthesis and spectroscopic studies of platinum(II) complexes of N,N′-dicyclohexylethylenediamine

The platinum(II) complexes of the formula [Pt(DCHEDA)X₂], where DCHEDA is N,N′-dicyclohexylethylenediamine and X⁻ is CL⁻, Br⁻, I⁻, 0.5C₂O₄²⁻ (oxalate), 0.5C₃H₂O₄²⁻ (malonate), 0.5C₉H₄O₆²⁻ (4-carboxyphthalate), 0.5S₂O₃²⁻ or 0.5SO₄²⁻, have been synthesized and characterized by UVVis, IR, and ¹H NMR spectral techniques. All the above complexes are non-electrolytes in DMF/H₂O, except the sulphate complex which becomes a 1:1 electrolyte after incubation for 24 h at 28 °C. The halide complexes were also studied by X-ray photoelectron spectroscopy and these data suggest that there is π-bonding from platinum to halide in these complexes. The oxalate, malonate and sulphate bind in their complexes as bidentate ligands to platinum through two oxygen atoms whereas the thiosulphate in its complex binds as a bidentate ligand to platinum through one oxygen atom and one sulphur atom.     

Decomposition of toluene in a steady-state atmospheric-pressure glow discharge

Results are presented from experimental studies of decomposition of toluene (C₆H₅CH₃) in a polluted air flow by means of a steady-state atmospheric pressure glow discharge at different water vapor contents in the working gas. The experimental results on the degree of C₆H₅CH₃ removal are compared with the results of computer simulations conducted in the framework of the developed kinetic model of plasma chemical decomposition of toluene in the N₂: O₂: H₂O gas mixture. A substantial influence of the gas flow humidity on toluene decomposition in the atmospheric pressure glow discharge is demonstrated. The main mechanisms of the influence of humidity on C₆H₅CH₃ decomposition are determined. The existence of two stages in the process of toluene removal, which differ in their duration and the intensity of plasma chemical decomposition of C₆H₅CH₃ is established. Based on the results of computer simulations, the composition of the products of plasma chemical reactions at the output of the reactor is analyzed as a function of the specific energy deposition and gas flow humidity. The existence of a catalytic cycle in which hydroxyl radical OH acts a catalyst and which substantially accelerates the recombination of oxygen atoms and suppression of ozone generation when the plasma-forming gas contains water vapor is established.     

Protein modeling and molecular dynamics simulation of the two novel surfactant proteins SP-G and SP-H

The prospects of a control for a novel gallium nitride pseudo-halide vapor phase epitaxy (PHVPE) with HCN were thoroughly analyzed for hydrocarbons–NH₃–Ga gas phase on the basis of quantum chemical investigation with DFT (B3LYP, B3LYP with D3 empirical correction on dispersion interaction) and ab-initio (CASSCF, coupled clusters, and multireference configuration interaction including MRCI+Q) methods. The computational screening of reactions for different hydrocarbons (CH₄, C₂H₆, C₃H₈, C₂H₄, and C₂H₂) as readily available carbon precursors for HCN formation, potential chemical transport agents, and for controlled carbon doping of deposited GaN was carried out with the B3LYP method in conjunction with basis sets up to aug-cc-pVTZ. The gas phase intermediates for the reactions in the Ga-hydrocarbon systems were predicted at different theory levels. The located π-complexes Ga…C₂H₂ and Ga…C₂H₄ were studied to determine a probable catalytic activity in reactions with NH₃. A limited influence of the carbon-containing atmosphere was exhibited for the carbon doping of GaN crystal in the conventional GaN chemical vapor deposition (CVD) process with hydrocarbons injected in the gas phase. Our results provide a basis for experimental studies of GaN crystal growth with C₂H₄ and C₂H₂ as auxiliary carbon reagents for the Ga-NH₃ and Ga-C-NH₃ CVD systems and prerequisites for reactor design to enhance and control the PHVPE process through the HCN synthesis.     

Spontaneous resolution of a bis(η-methylcyclopentadienyl)zinc complex

Two crystalline complexes of bis(η¹-methylcyclopentadienyl)zinc, [Zn(C₅H₄Me)₂(py)₂] (1), where py is pyridine, and [Zn(C₅H₄Me)₂(teeda)], 2, where teeda is N,N,N′,N′-tetraethylethylenediamine have been isolated. The crystal structures of 1 and 2 are the first crystal structures for Zn(C₅H₄Me)₂ complexes reported in the literature; both structures display η¹-coordination of the methylcyclopentadienyl ring to zinc, and both compounds display chirogenic α-carbon atoms. While 1 forms racemic crystals, 2 undergoes spontaneous resolution and crystals of 2 are thus enantiomerically pure. ¹H NMR showed that Zn(C₅H₄Me)₂ is stereochemically labile in solution with only one signal for the Cp-protons. This fact opens up the possibility for total spontaneous resolution and absolute asymmetric synthesis.     

Structures of some botryococcenes: branched hydrocarbons from the b-race of the green alga Botryococcus braunii

Nine branched hydrocarbons of the botryococcene type (C_nH_2n-10 30 ? n ? 37) have been isolated from the green alga Botryococcus braunii. Hydrocarbon mixtures were recovered from wild algae collected in fresh water lakes or from the same strains growing in laboratory; they were further separated by reversed-phase, and in some cases by normal phase, HPLC. From chemical investigations, GC/MS analyses, ¹H and ¹³C NMR spectroscopy, the structures of four new botryococcenes (one C₃₃H₅₆, two C₃₄H₅₈ and one C₃₇H₆₄) were elucidated.     

Aromatic C20F20 cage and its endohedral complexes X@C20F20 (X = H-, F-, Cl-, Br-, H, He)

The structure and stability of endohedral X@C₂₀F₂₀ complexes (X = H⁻, F⁻, Cl⁻, Br⁻, H, He) have been computed at the B3LYP level of theory. All complexes in I _h symmetry were found to be energy minimum structures. H⁻@C₂₀F₂₀ and F⁻@C₂₀F₂₀ complexes have negative inclusion energies, while other complexes have positive inclusion energies. Similarity between C₂₀F₂₀ and C₂₀H₂₀ has been found for X = H and He. On the basis of the computed nucleus independent chemical shift values at the cage center, both C₂₀F₂₀ and C₂₀F₂₀ are aromatic. Figure Endohedral X@C₂₀F₂₀ complexes     

<Emphasis Type="Italic">Ab initio</Emphasis> calculations of ionic hydrocarbon compounds with heptacoordinate carbon

Ionic hydrocarbon compounds that contain hypercarbon atoms, which bond to five or more atoms, are important intermediates in chemical synthesis and may also find applications in hydrogen storage. Extensive investigations have identified hydrocarbon compounds that contain a five- or six-coordinated hypercarbon atom, such as the pentagonal-pyramidal hexamethylbenzene, C₆(CH₃)₆²⁺, in which a hexacoordinate carbon atom is involved. It remains challenging to search for further higher-coordinated carbon in ionic hydrocarbon compounds, such as seven- and eight-coordinated carbon. Here, we report ab initio density functional calculations that show a stable 3D hexagonal-pyramidal configuration of tropylium trication, (C₇H₇)³⁺, in which a heptacoordinate carbon atom is involved. We show that this tropylium trication is stable against deprotonation, dissociation, and structural deformation. In contrast, the pyramidal configurations of ionic C₈H₈ compounds, which would contain an octacoordinate carbon atom, are unstable. These results provide insights for developing new molecular structures containing hypercarbon atoms, which may have potential applications in chemical synthesis and in hydrogen storage.

Open image in new window

Graphical abstract Possible structural transformations of stable configurations of (C₇H₇)³⁺, which may result in the formation of the pyramidal structure that involves a heptacoordinate hypercarbon atom.

     

Isomer distribution and structure of (2,2′-biphenyldiolato)bis(β-diketonato)titanium(IV) complexes: A single crystal X-ray, solution NMR and computational study

Novel dichlorobis(β-diketonato)titanium(IV) Ti(C₆H₅COCHCOR)₂Cl₂ and (2,2′-biphenyldiolato)bis(β-diketonato)titanium(IV) Ti(C₆H₅COCHCOR)₂biphen complexes with R = CH₃, C₆H₅ and CF₃, are synthesized and characterized by X-ray crystallography and further physical methods. There is a good agreement between DFT calculated and experimental structural data. A configurational analysis gives a calculated isomer distribution that is in agreement with the experimental data derived from low temperature ¹H NMR spectroscopy. The Ti(C₆H₅COCHCOR)₂biphen complexes exhibit high hydrolytic stability.     

A tracked approach for automated NMR assignments in proteins (TATAPRO)

A novel automated approach for the sequence specific NMR assignments of ¹H^N, ¹³C, ¹³C, ¹³C/¹H and ¹⁵N spins in proteins, using triple resonance experimental data, is presented. The algorithm, TATAPRO (Tracked AuTomated Assignments in Proteins) utilizes the protein primary sequence and peak lists from a set of triple resonance spectra which correlate ¹H^N and ¹⁵N chemical shifts with those of ¹³C, ¹³C and ¹³C/¹H. The information derived from such correlations is used to create a `master_list' consisting of all possible sets of ¹H^N _i, ¹⁵N_i, ¹³C _i, ¹³C _i, ¹³C_i/¹H _i, ¹³C _i–1, ¹³C _i–1 and ¹³C_i–1/ ¹H _i–1 chemical shifts. On the basis of an extensive statistical analysis of ¹³C and ¹³C chemical shift data of proteins derived from the BioMagResBank (BMRB), it is shown that the 20 amino acid residues can be grouped into eight distinct categories, each of which is assigned a unique two-digit code. Such a code is used to tag individual sets of chemical shifts in the master_list and also to translate the protein primary sequence into an array called pps_array. The program then uses the master_list to search for neighbouring partners of a given amino acid residue along the polypeptide chain and sequentially assigns a maximum possible stretch of residues on either side. While doing so, each assigned residue is tracked in an array called assig_array, with the two-digit code assigned earlier. The assig_array is then mapped onto the pps_array for sequence specific resonance assignment. The program has been tested using experimental data on a calcium binding protein from Entamoeba histolytica (Eh-CaBP, 15 kDa) having substantial internal sequence homology and using published data on four other proteins in the molecular weight range of 18–42 kDa. In all the cases, nearly complete sequence specific resonance assignments (> 95%) are obtained. Furthermore, the reliability of the program has been tested by deleting sets of chemical shifts randomly from the master_list created for the test proteins.     

Hash: a program to accurately predict protein Hα shifts from neighboring backbone shifts

Chemical shifts provide not only peak identities for analyzing nuclear magnetic resonance (NMR) data, but also an important source of conformational information for studying protein structures. Current structural studies requiring H^α chemical shifts suffer from the following limitations. (1) For large proteins, the H^α chemical shifts can be difficult to assign using conventional NMR triple-resonance experiments, mainly due to the fast transverse relaxation rate of C^α that restricts the signal sensitivity. (2) Previous chemical shift prediction approaches either require homologous models with high sequence similarity or rely heavily on accurate backbone and side-chain structural coordinates. When neither sequence homologues nor structural coordinates are available, we must resort to other information to predict H^α chemical shifts. Predicting accurate H^α chemical shifts using other obtainable information, such as the chemical shifts of nearby backbone atoms (i.e., adjacent atoms in the sequence), can remedy the above dilemmas, and hence advance NMR-based structural studies of proteins. By specifically exploiting the dependencies on chemical shifts of nearby backbone atoms, we propose a novel machine learning algorithm, called Hash, to predict H^α chemical shifts. Hash combines a new fragment-based chemical shift search approach with a non-parametric regression model, called the generalized additive model, to effectively solve the prediction problem. We demonstrate that the chemical shifts of nearby backbone atoms provide a reliable source of information for predicting accurate H^α chemical shifts. Our testing results on different possible combinations of input data indicate that Hash has a wide rage of potential NMR applications in structural and biological studies of proteins.     

A tetrameric allyl complex of sodium, and computational modeling of the Na-allyl chemical shift

Transmetallation of Li[A′] (A′ = [1,3-(SiMe₃)₂C₃H₃]⁻) with sodium tert-butoxide produces the corresponding sodium salt, which crystallizes from THF/toluene in the form of a cyclic tetramer, {Na[A′](thf)}₄. The Na atoms are in a square planar arrangement, bridged with π-bound allyl ligands; the Na-C distances range from 2.591(3)-2.896(3) Å, with an average of 2.70 Å. The geometries of several model organosodium complexes containing cyclopentadienyl and allyl ligands were optimized with density functional theory methods. The optimized structures were used with the gauge-including atomic orbital (GIAO) method to calculate their ²³Na NMR magnetic shielding values. Unlike the case with NaCp, the chemical shift of unsubstituted Na(C₃H₅) is very sensitive to the presence of coordinated THF (causing a 20 ppm upfield shift); silyl substitution has an even larger effect (30 ppm upfield shift). The observed ²³Na shift of δ −3.3 ppm for Na[A′] in THF-d₈, however, cannot be reliably distinguished from that calculated for the [Na(thf)₄]⁺ cation alone.     

A Monte-Carlo step-by-step simulation code of the non-homogeneous chemistry of the radiolysis of water and aqueous solutions—Part II: calculation of radiolytic yields under different conditions of LET,pH, and temperature

The importance of the radiolysis of water in the initial events following irradiation of biological systems has motivated considerable theoretical and experimental work in the field of radiation chemistry of water and aqueous systems. These studies include Monte-Carlo simulations of the radiation track structure and of the non-homogeneous chemical stage, which have been successfully used to calculate the yields of radiolytic species (H^·, ^·OH, H₂, H₂O₂, e_aq⁻, …). Most techniques used for the simulation of the non-homogeneous chemical stage such as the independent reaction time (IRT) technique and diffusion kinetics methods do not calculate the time evolution of the positions of the radiolytic species. This is a major limitation to their extension to the simulation of the irradiation of radiobiological systems. Step-by-step (SBS) simulation programs provide such information, but they are very demanding in term of computer power and storage capacity. Recent improvements in computer performance now allow the regular use of the SBS method in radiation chemistry simulations. In the first of a series of two papers, the SBS method has been reviewed in details and the implementation of a SBS code has been discussed. In this second paper, the results of several studies are presented: (1) the time evolution of the radiolytic yields from the formation of the radiation track to 10⁻⁶ s; (2) the effect of pH on yields (pH ~ 0.4–7.0); (3) the effect of proton energy (and LET) on yields (300 MeV-0.1 MeV), and iv) the effect of the ion type (¹H⁺, ⁴He²⁺, ¹²C⁶⁺) on yields. Nonbiological applications, i.e., the study of the temperature on the yields (about 25–300°C) and the simulation of the time evolution of G(Fe³⁺) in the Fricke dosimeter are also discussed.     

Chemical speciation of oxalato complexes of indium(III)

Abstract

Chemical speciation of binary complexes of indium(III) with oxalic acid has been investigated pH metrically at 303 K and at an ionic strength of 0.2 mol dm^?3. The approximate formation constants have been calculated with the computer program SCPHD utilizing the experimental data obtained by monitoring H⁺ ion concentration. The formation constants thus obtained are refined with the computer program, MINIQUAD75 using primary alkalimetric data. The selection of the best-fit chemical model is based on the statistical parameters and residual analysis. The major complexes formed are In(C₂O₄)₂^?, In(C₂O₄)₃^3?, [In(C₂O₄)₂OH]^2? and [In(C₂O₄)₂ (OH)₂]^3?. The distribution patterns of the different species with the pH values showed that In(C₂O₄)₂^? is the predominant species.     

Synthesis and structural characterization of dimolybdenum(IV) and molybdenum(VI) complexes with trisbenzenethiolatophosphine ligands

The synthesis and crystal structures of two high valent molybdenum complexes containing trisbenzenethiolatophosphine ligands, [Mo₂(PS3)₂(PS3H)] (1) and [Mo(PS3″)₂] (2), where PS3 = [P(C₆H₄-2-S)₃]³⁻, PS3H = [P(C₆H₄-2-S)₂(C₆H₄-2-SH)]²⁻, and PS3″ = [P(C₆H₃-3-Me₃Si-2-S)₃]³⁻, are described. Compound 1 is a dimeric Mo(IV) species containing three PS3 ligands with an uncoordinated thiol group. An intramolecular hydrogen bonding S-H?S was found in the structure. Two molybdenum ions are bridged by three thiolates. The geometry can be described as two pentagonal bipyramids sharing a triangle face formed by three bridging S atoms. Compound 2 is a Mo(VI) species binding with two tetradentate PS3″ ligands. The eight-coordinate molybdenum center adopts a dodecahedral geometry.