Methanol, model structure

Tapia, O., Cardenas, R., Andres. J. and Colonna-Cesari, F. Transition structure for hydride transfer to pyridinium cation from methanolate. Modeling of LADH catalyzed reaction, J. Am. Chem. Soc., 110 (1988), 4046-4047... 

Moreover, a new structure of passive DMFC with two methanol reservoirs separated by a porous medium layer was designed and a corresponding mathematical model was presented by Cai et al. [185], This type of DMFC can be directly fed with highly concentrated methanol solution or neat methanol. Modeling and experiments are used by the authors to optimize the porosity of the components. It was found that the new designed DMFC can be continuously operated for about 4.5 times longer than a conventional passive DMFC with the optimum parameters. 

The mechanism of liver alcohol dehydrogenase (LADH) has been extensively studied. For a recent overview the reader is referred to Ref [93]. Reaction field effects on the transition structure of model hydride transfer systems have been calculated at ab initio 4-3IG basis set level [93, 94]. The active site of enzymes are usually assumed to be designed to receive molecules in the transition state for the reaction they catalyze. This special sort of surrounding medium effects has been computationally documented recently [95]. From the reaction geodesic passing through the transition state for hybride transfer in the pyridium cation/methanolate model system, only the TS-structure could be fitted into the LADH active site. The normal mode analysis carried out on the TS showed an excellent agreement with isotopic substitution experiments [95]. Reaction field calculations on this model systems have also been performed. For an overview of biomolecular interactions the reader is referred to Ref [96]. 

The Tg-based octa-anion TglO lg can be seen as a model for the well-known D4R found in inorganic structures such as zeolite A. Synthesis of TglO Jg can be achieved more readily than many other POSS species and it can be obtained in quantitative yield from the reaction of a tetra-alkoxysilane with H2O (10 equiv./Si) in the presence of Me4NOH (1 equiv./Si) in methanol at room temperature for 1 day (Figure Alcoholysis of T8[OSiMe2H]g causes terminal Si-O bond... 

A peptoid pentamer of five poro-substituted (S)-N-(l-phenylethyl)glycine monomers, which exhibits the characteristic a-helix-like CD spectrum described above, was further analyzed by 2D-NMR [42]. Although this pentamer has a dynamic structure and adopts a family of conformations in methanol solution, 50-60% of the population exists as a right-handed helical conformer, containing all cis-amide bonds (in agreement with modeling studies [3]), with about three residues per turn and a pitch of 6 A. Minor families of conformational isomers arise from cis/trans-amide bond isomerization. Since many peptoid sequences with chiral aromatic side chains share similar CD characteristics with this helical pentamer, the type of CD spectrum described above can be considered to be indicative of the formation of this class of peptoid helix in general. 

PEMFC)/direct methanol fuel cell (DMFC) cathode limit the available sites for reduction of molecular oxygen. Alternatively, at the anode of a PEMFC or DMFC, the oxidation of water is necessary to produce hydroxyl or oxygen species that participate in oxidation of strongly bound carbon monoxide species. Taylor and co-workers [Taylor et ah, 2007b] have recently reported on a systematic study that examined the potential dependence of water redox reactions over a series of different metal electrode surfaces. For comparison purposes, we will start with a brief discussion of electronic structure studies of water activity with consideration of UHV model systems. 

Hosier H, Iwasita T, Baumgartner H, Vielstich W. 2001b. Pt-Ru model catalysts for anodic methanol oxdiation Influence of structure and composition on the reactivity. Phys Chem Chem Phys 3 337. 

Irreversible inhibition is probably due to the alkylation of a histidine residue.43 Chymotrypsin is selectively inactivated with no or poor inhibition of human leukocyte elastase (HLE) with a major difference the inactivation of HLE is transient.42,43 The calculated intrinsic reactivity of the coumarin derivatives, using a model of a nucleophilic reaction between the ligand and the methanol-water pair, indicates that the inhibitor potency cannot be explained solely by differences in the reactivity of the lactonic carbonyl group toward the nucleophilic attack 43 Studies on pyridyl esters of 6-(chloromethyl)-2-oxo-2//-1 -benzopyran-3-carboxylic acid (5 and 6, Fig. 11.5) and related structures having various substituents at the 6-position (7, Fig. 11.5) revealed that compounds 5 and 6 are powerful inhibitors of human leukocyte elastase and a-chymotrypsin thrombin is inhibited in some cases whereas trypsin is not inhibited.21... 

Zhong Y, Warren GL, Patel S (2008) Thermodynamic and structural properties of methanol-water solutions using nonadditive interaction models. J Comput Chem 29(7) 1142-1152... 

X-ray diffraction studies on gramicidin commenced as early as 1949 218-219> and this early work pointed to a helical structure 220). Recent work by Koeppe et al. 221) on gramicidin A crystallised from methanol (/%) and ethanol (.P212121) has shown that the helical channel has a diameter of about 5 A and a length of about 32 A in both cases. The inclusion complexes of gramicidin A with CsSCN and KSCN (P212121) have channels that are wider (6-8 A) and shorter (26 A) than the uncomplexed dimer 221 222). Furthermore there are two cation binding sites per channel situated either 2.5 A from either end of the channel or 2.5 A on each side of its centre 222) Unfortunately these data do not permit a choice to be made from the helical models (i)—(iv) and it is not certain if the helical canals studied are the same as those involved in membrane ion transport. 

Manganese nitrosyl porphyrins [215] are considered good models for the iron-nitric oxide analogs, which are relatively unstable but very vital to many biological operations. A six-coordinate manganese nitrosyl porphyrin of the form (por)Mn(NO)(L), where por can be TTP (TTP = tetra(4-methylphenyl)porphine) and L = piperidine, methanol, 1-methyhmidazole, has been prepared [216] in moderate yields by the reductive nitrosylation of the (por)MnCl complex with NO in piperidine. The crystal structures of these compounds give indication of a linear Mn-NO bond [215]. 

From a structural point of view the OPLS results for liquids have also shown to be in accord with available experimental data, including vibrational spectroscopy and diffraction data on, for Instance, formamide, dimethylformamide, methanol, ethanol, 1-propanol, 2-methyl-2-propanol, methane, ethane and neopentane. The hydrogen bonding in alcohols, thiols and amides is well represented by the OPLS potential functions. The average root-mean-square deviation from the X-ray structures of the crystals for four cyclic hexapeptides and a cyclic pentapeptide optimized with the OPLS/AMBER model, was only 0.17 A for the atomic positions and 3% for the unit cell volumes. 

M. M. Pires and V. F. DeTuri, Structural, energetic, and infrared spectra insights into methanol clusters iT HiOH ,. for n 2 12, 16, 20. ONIOM as an efficient method of modeling large methanol clusters. J. Chem. Theory Comput. 3, 1073 1082 (2007). 

U. Buck, J. G. Siebers, and R. J. Wheatley, Structure and vibrational spectra of methanol clusters from a new potential model. J. Chem. Phys. 108, 20 32 (1998). 

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