Computational study of matrix-peptide interactions in MALDI mass spectrometry: Interactions of 2,5- and 3,5-dihydroxybenzoic acid with the tripeptide valine-proline-leucine

The mechanism of matrix-to-analyte proton transfer in matrix-assisted laser desorption and ionization mass spectrometry (MALDI-MS) has been investigated computationally by modeling the matrix-analyte interaction of potential MALDI matrixes such as 2,5-dihydroxybenzoic acid (2,5-DHB) and 3,5-DHB with the tripeptide valine-proline-leucine (VPL). A combination of molecular dynamics/simulated annealing calculations followed by density functional theory geometry optimization using a reasonably large basis set has been done on a large number of clusters in an attempt to study the ionization energy of each matrix in the cluster environment and the intracluster proton transfer from the matrix to the tripeptide. The calculations show a substantial reduction in the IP for both matrixes in their cluster environments. In the 2,5-system, proton transfer can sometimes occur in the neutral clusters (preformed ions), whereas proton transfer in the cationic clusters, which is actually a double proton transfer, is spontaneous and exoergic. Even though it is more acidic from a thermodynamic perspective, the radical cation of 3,5-DHB is a less efficient proton donor to VPL. The thermodynamics of proton transfer in the cationic clusters is discussed in detail.     

Tropospheric multiphase chemistry of 2,5- and 2,6-dimethylphenols: determination of the mass accommodation coefficients and the Henry's law constants

The uptake of 2,5-dimethylphenol and 2,6-dimethylphenol on aqueous surfaces was measured between 279 and 293 K, using the wetted-wall flow tube technique coupled with UV absorption spectroscopic detection. For both compounds, the uptake coefficients gamma were found to be independent of the KOH scavenger concentration in the range of 0.01 to 1 M (pH > pK(a)) and of the liquid-gas contact times. In addition, the uptake coefficients and the derived mass accommodation coefficients alpha show a negative temperature dependence in the investigated temperature range. The mass accommodation coefficients decrease from 1.1 x 10(-3) to 1.1 x 10(-4), and from 5.4 x 10(-4) to 6.4 x 10(-5) for 2,5-dimethylphenol and 2,6-dimethylphenol, respectively. These results are used to discuss the incorporation of these species into the liquid using the nucleation theory. Henry's law constants (HLC) of both compounds were directly measured using a dynamic equilibrium system based on the water/air equilibrium at the interface within the length of a microporous tube. The measurements were conducted over the range 278-293 K in both deionized water and 35 g L(-1) solution of NaCl. At 293 K and in pure water, HLC were found to be equal to (in units of M atm(-1)): 2,5-dimethylphenol, HLC = (1270 +/- 240); 2,6-dimethylphenol, HLC = (250 +/- 80). All of the values for HLC in 35 g L(-1) salt solution were 5-55% lower than the corresponding values in deionized water, depending on the compound and the temperature. These data (mass accommodation coefficients and Henry's law constants) were then used to estimate the partitioning of these phenolic compounds between gaseous and aqueous phases and the corresponding atmospheric lifetimes under clear sky (tau(gas)) and cloudy conditions (tau(multiphase)) have then been derived. The calculated multiphase lifetimes (in units of hours) are lower than those in gas phase at a cumulus temperature of 283 K (in parentheses): 2,5-dimethylphenol, 2.2 (3.5); 2,6-dimethylphenol, 3.8 (4.2).     

Interactions of aminomethylphosphonic acid and sarcosine with montmorillonite interlayer surfaces

The smectite clay, montmorillonite, can be found in many soils throughout the world. In addition to its importance in agriculture and soil remediation, montmorillonite has extensive applications in industry both in its natural form and as a component of composite materials. The adsorptive properties of montmorillonite have been explored in relation to its interactions with the common herbicide glyphosate. This herbicide, when exposed to microorganisms in the soil is degraded, forming two products: aminomethylphosphonic acid (AMPA) and sarcosine. The atomic‐level interactions of these compounds with the montmorillonite interlayer surfaces are studied here using molecular mechanics. The final outcomes of these calculations are analyzed in terms of the proximity of the montmorillonite surface to the moieties of the degradation products. The phosphonate moiety was found to be the most important source of interactions for AMPA, while for sarcosine there was an even distribution between the amino and carboxylic moieties, and Na⁺ ion mediated surface complexes. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2008     

Interactions of different heterocyclic compounds with monoionic forms of montmorillonite

Interactions of 3-R-and 2-R pyridine (R=CH₃, Cl, NH₂) with Ni(II)-exchanged montmorillonite have been studied. Thermal and X-ray analyses indicate that pyridine derivatives are intercalated into the interlayer spaces of montmorillonite. Infrared spectral data shown that the Lewis and/or Brönsted type of interactions of pyridine derivatives is connected with different steric and inductive effects of the substituents (R) on the pyridine ring. The alkylpyridines increase the electron density on the donor nitrogen atom and support the coordination to the central atom. The halogen substituents have a negative inductive effect (–I), so that those ligands show a lower basicity and weaker σ-bonding properties than pyridine and also the lower possibility of the coordination.     

The crystal and molecular structure of 3,5-Di-(t-butyl)-1-phenylphosphoryl-4-aza-2,5-cyclohexadiene

The crystal and molecular structure of the title compound (C₁₈H₂₆NOP) has been determined by a single crystal, x-ray diffraction study using Cu-Kα. radiation. The compound was found to crystallize in the orthorhombic space group Pnma with unit cell constants a = 12.686 ± .001 Å, b = 14.776 ± .001 Å, and c = 9.540 ± .001 Å. The structure was solved by the heavy atom method and refined by block-diagonal least-squares to a final R = 0.09₉ for the 696 statistically significant reflections. The compound exhibits orientational disorder in the crystalline state. Nevertheless, the planarity of this ring; the lengthening of the diene carbon-carbon bond to 1.41 Å the resultant shortening of both the carbon-nitrogen bond (1.43 Å) and the carbon-phosphorus bond (1.74 Å), and the CNC bond angle of 121° all strongly support the assumption of delocalization of the diene π-electrons within the heterocyclic ring system.     

The protonation and dimerization of 2,4-, 2,5-, 2,6-and 3,5-dihydroxybenzoic acids in 0.5M sodium perchlorate medium

The protonation equilibria of 2,4-, 2,5-, 2,6- and 3,5-dihydroxybenzoic acids were studied by means of potentiometric titrations at I = 0.5 (NaClO(4)) and 25 degrees . The dimeric species H(6)L(2) and H(5)L(2) were found to form as well as the monomeric species H(p)L in the acidic solutions of 2,4- and 3,5-dihydroxybenzoic acids under the conditions studied. For the other two acids, the protonation scheme can be expressed exclusively in terms of the species H(p)L (p = 1, 2 or 3).     

Absolute configuration and conformational stability of (+)-2,5-dimethylthiolane and (-)-2,5-dimethylsulfolane

Enantiopure (+)-2,5-dimethylthiolane and (-)-2,5-dimethylsulfolane were prepared using literature procedures and investigated using vibrational circular dichroism (VCD). Experimental absorption and VCD spectra of (+)-2,5-dimethylthiolane and (-)-2,5-dimethylsulfolane in CCl(4) solution in the 2000-900 cm(-)(1) region were compared with the ab initio predictions of absorption and VCD spectra obtained with density functional theory using the B3LYP/6-311G(2d, 2p) basis set for different conformers of (2R,5R)-2,5-dimethylthiolane and (2R,5R)-2,5-dimethylsulfolane. This comparison indicates that (+)-2,5-dimethylthiolane is of the (2R,5R)-configuration and has two predominant conformations in CCl(4) solution. In addition, (-)-2,5-dimethylsulfolane is of (2R,5R)-configuration and has only one predominant conformation. The stereochemical assignment is in agreement with literature.     

Total chemical synthesis of 2-ethenyl-3,5-dimethylpyrazine and 3-ethenyl-2,5-dimethylpyrazine

The aroma compounds 2-ethenyl-3,5-dimethylpyrazine 1 and 3-ethenyl-2,5-dimethylpyrazine 2 were synthesized via a new chemical route. The key steps of the synthesis involve cyclocondenzation of 1-[bicyclo[2.2.1]5-hepten-2-yl]-1,2-propanedione and 1,2-propanediamine, aromatization of the resulting 5,6-dihydropyrazines, and subsequent Retro-Diels-Alder reaction to generate pyrazines 1 and 2. Pyrazine 1, a powerful odorant, was obtained in large excess (8:2) when endo-1-[bicyclo[2.2.1]5-hepten-2-yl]-1,2-propanedione was used as intermediate substrate.     

Synthesis of 1,3-bis[(3,5-di-tert-butyl-4-oxocyclohexa-2,5-dienylidene)(dimethoxyphosphoryl)methyl]-4,6-dimethoxybenzene

A reaction of 1,3-dimethoxybenzene with dimethyl (3,5-di-tert-butyl-4-oxocyclohexa-2,5-dienylidenemethyl)phosphonate gave rise to 1,3-bis[(3,5-di-tert-butyl-4-hydroxyphenyl)-(dimethoxyphosphoryl)methyl]-4,6-dimethoxybenzene, which was oxidized to 1,3-bis[(3,5-di-tert-butyl-4-oxocyclohexa-2,5-dienylidene)(dimethoxyphosphoryl)methyl]-4,6-dimethoxy-benzene.     

Study on the equilibria of the complex formation of molybdenum(VI) with 3,5-dinitrocatehol and 3-(2-naphthyl)-2,5-diphenyl-2H-tetrazolium chloride

The formation of an ion-associated complex between the anionic chelate of Mo(VI)–3,5-dinitrocatehol (3,5-DNC) and the cation of 3-(2-naphthyl)-2,5-diphenyl-2H-tetrazolium chloride (TV) in the liquid–liquid extraction system Mo(VI)–3,5-DNC–TV–H₂O–CHCl₃ was studied by spectrophotometry. The optimum conditions for the complex formation and extraction of the ion-associated complex were established. The effect of co-existing ions and reagents on the process of complex formation was investigated under optimum extraction conditions. The validity of Beer’s law was checked and some analytical characteristics were calculated. The association process in aqueous phase and the extraction equilibria were investigated and quantitatively characterized. The following key constants of the processes were calculated: association constant, distribution constant, extraction constant and recovery factor. The molar ratio of the reagents was determined by independent methods. Based on this, a reaction scheme, a general formula and a structure of the complex were suggested.     

新型2,5-双(3,5-二取代吡唑基-1-羰基)噻吩的合成

β-二酮与水合肼环化制得3,5-二取代吡唑(2a～2d); 2与2,5-噻吩二甲酰氯反应合成了4个新的2,5-双(3,5-二取代吡唑基-1-羰基)噻吩,其结构经1H NMR, 13C NMR, IR, MS和元素分析表征.