A density functional theory study of a concerted mechanism for proton exchange between amino acid side chains and water

 A concerted mechanism for proton exchange between water and the amino acid side chains of cysteine, serine, arginine and glutamic acid has been investigated with hybrid density functional theory. The models used include, besides the amino acid side chain, a number of water molecules ranging from one to five in some cases. The modeling of the amino acids without their backbones is shown to be an excellent approximation. Long-range polarization effects were incorporated through a dielectric cavity method allowing a better comparison to existing measurements for free amino acids in water. The barriers converge rather fast with the number of water molecules for all the present amino acids and the converged values are in reasonable agreement with experiments with discrepancies in the range 2–6 kcal/mol. The dielectric effects were found to be small for all systems except cysteine, where there is a lowering of the barrier by 3–5 kcal/mol. The transition states for these concerted pathways form rings in which the separated charges can be stabilized. Received: 25 October 1999 / Accepted: 5 April 2000 / Published online: 21 June 2000     

Generation of alkoxide anions from a series of aliphatic diols and alcohols and their ion-molecule reactions with carbon dioxide in the gas phase

Alkoxide anions, [M-H](-) from a series of aliphatic diols and alcohols are generated in the source under negative ion electrospray ionisation conditions by cone-voltage fragmentation of the corresponding [M + F](-) ions. The collision-induced dissociation (CID) spectra of [M-H](-) ions consist of [M-H-2H](-) ions, in addition to the other characteristic fragment ions, and the relative abundance of [M-H-2H(-) ions among the series of diols varies as a function of chain length that could be explained based on their stabilities through intramolecular hydrogen bonding. The reactivity of alkoxide anions is studied through ion-molecule reactions with CO(2) in the collision cell of a triple quadrupole mass spectrometer. All the alkoxide anions reacted with CO(2) and formed corresponding carbonate anions, [M-H + CO(2)](-) ions. The reactivity of alkoxide anions within the series of diols also reflected the stability of their [M-H](-) ions.     

Influence of substrate nature on the growth of copper oxide thin films

Cu thin films were deposited on Si(111), glass, and quartz substrates by magnetron sputtering. X‐ray diffraction, SEM, and photoemission electron microscope studies were carried out to characterize the films. An influence of the nature of substrate on the Cu₂O and CuO phases formed was observed. Copper silicide formation in case of silicon substrates aided in formation of Cu₂O rather than CuO unlike glass and quartz substrates. Formation of nanocrystallites was observed by SEM and X‐ray diffraction. Copyright © 2016 John Wiley & Sons, Ltd.     

A Decomposition Method for Solving Coupled Multi–Species Reactive Transport Problems

Concerns over the problems associated with mixed waste groundwater contamination have created a need for more complex models that can represent reactive contaminant fate and transport in the subsurface. In the literature, partial differential equations describing solute transport in porous media are solved either for a single reactive species in one, two or three dimensions, or for a limited number of reactive species in one dimension. Those solutions are constrained by many simplifying assumptions. Often, it is desirable to simulate transport in two or three dimensions for a more practical system that might have multiple reactive species. This paper presents a decomposition method to solve the partial differential equations of multi–dimensional, multi–species transport problems that are coupled by linear reactions. A matrix method is suggested as a tool for describing the reaction network. In this way, the level of complexity required to solve the multi–species reactive transport problem is significantly reduced.     

Mass spectral study on O,O-dialkyl N,N-dialkyl phosphoramidates under electron impact conditions

A series of O,O-dialkyl N,N-dialkyl phosphoramidates (1-25) were analyzed under GC-EIMS conditions. Clear-cut differences are found in the fragmentation of O,O-dialkyl N,N-dimethyl phosphoramidates (Series 1) and O,O-dimethyl N,N-dialkyl phosphoramidates (Series 2). The phosphoramidates comprising of mixed/crossed alkyl groups on nitrogen and oxygen (Series 3) showed mixed fragmentation pattern corresponding to both Series 1 and 2 depending on the nature of alkyl groups. All the possible isomers among the studied compounds showed distinguishable EI mass spectra. Although the major ions in the EI mass spectra for the isomers containing O-n-propyl or O-isopropyl and N,N-diethyl or N-isopropyl N-methyl are similar, the isomers could be distinguished by characteristic ions of low abundance at low mass region. The differences are prominent in the metastable ion spectra of characteristic ions.     

Natural abundance nitrogen-15 nuclear magnetic resonance spectral studies on selected donors

The natural abundance 15N-NMR chemical shifts of selected aliphatic amines, 2-substituted pyridine type compounds, bialicyclic tertiary amines have been measured as a function of the nature of the solvent. In the case of cyclic aliphatic amines, like piperidine, morpholine, piperazine, thiomorpholine, the nitrogen is more shielded in concentrated solution compared to that in dilute solution whereas in the hydrogen bonding and protonating solvents there is a prominent deshielding. 2-Substituted pyridines studied can be further divided into four sub groups. The site of hydrogen bonding and protonation in 2-amino, 2-hydroxy and 2-mercapto pyridines have been conclusively proved from the 15N-NMR chemical shifts and the well-known tautomeric forms of the above compounds. Similarly in the case of 2-(2-thienyl)pyridine and 2-(3-thienyl)pyridine, the site of donation has been proved as the nitrogen of the pyridine ring in both the compounds. In a similar manner, the site of hydrogen bonding and protonation in two individual compounds 2-anilinopyridine and 2-(2-pyridyl)benzimidazole have also been established. Among the bialicyclic amines, 1,2-diazabicyclo[2.2.2]octane (DABCO) behaved differently from the other two compounds. In both 1,8-diazabicyclo[5.4.0]undec-7-ene (DBU) and 1,5-diazabicyclo[4.3.0]non-5-ene (DBN), it was possible to show that N1-nitrogen in both the compounds is the site of donation. The effect of the second donor site on the 15N-NMR chemical shift, the site of donation in the selected compounds and some typical compounds reported in literature have been presented and discussed.     

An efficient aldol-based approach for the synthesis of dihydrokawain-5-ol

An efficient and simple aldol-based convergent approach toward the total synthesis of (+)- and (?)-dihydrokawain-5-ol is described. The key features of this synthetic strategy include Evans’ aldol reaction and an ethyl acetate addition reaction for the formation of the six-membered ring.     

Total synthesis of aculeatins A and B from (S)-malic acid

A simple convergent approach towards the total synthesis of bioactive spiroacetals aculeatins A and B is described. The key features of the synthetic strategy include a syn-stereoselective 1,3-asymmetric reduction, epoxide ring opening and oxidative spirocyclization reaction by employing (S)-malic acid as the starting material.