Acceleration of convergence in Monte Carlo simulations of aqueous solutions using the metropolis algorithm. Hydrophobic hydration of methane

Convergence problems encountered in the computer simulations of aqueous solutions are discussed. Solute–solvent radial distribution functions are shown to converge very poorly when the standard Metropolis Monte Carlo procedure is applied. To overcome this difficulty, several modifications are made in the Metropolis method. Optimum maximum step sizes are determined for simulations of liquid water. A scheme is employed for preferential sampling of both the solvent and the solute molecules. To test these modifications, a simulation is carried out for pure liquid water, treating a single water molecule as a “solute.” The convergence of the radial distribution functions is found to be accelerated significantly. A further test is made by simulating an aqueous solution of methane, consisting of one methane molecule (using the EPEN /2 potential for methane–water interactions) and 124 water molecules (using the MCY potential for water–water interactions). Again, the convergence of solute–solvent radial distribution functions is found to be accelerated. The computation of partial molar thermodynamic quantities, however, still suffers from convergence difficulties. This problem is discussed in detail. The EPEN /2 potential is found to yield structural and thermodynamic features of hydrophobic hydration that are consistent with available experimental and theoretical results for aqueous solutions of methane.     

Preparation of 5-substituted benzylbarburituric acids and investigation of the effect of the benzyl and substituted benzyl groups on the acidity of barbituric acid

The acidity of 5-benzylbarbituric acid and a series of 5-substituted benzylbarbituric acids has been determined in 50% ethanol/water and they were found to be more acidic than barbituric acid. The pK_as of these derivatives obey Hammett's equation indicating that their acidity is affected by substituents in the same manner as the benzoic acid ionization constants. A synthesis of these acids is described.     

Synthetic enantiopure aziridinomitosenes: preparation, reactivity, and DNA alkylation studies

An enantiocontrolled route to aziridinomitosenes had been developed from l-serine methyl ester hydrochloride. The tetracyclic target ring system was assembled by an internal azomethine ylide cycloaddition reaction based on silver ion-assisted intramolecular oxazole alkylation and cyanide-induced ylide generation via a labile oxazoline intermediate (62 to 66). Other key steps include reductive detritylation of 26, methylation of the N-H aziridine 56, oxidation of the sensitive cyclohexenedione 68 to quinone 70, and carbamoylation using Fmoc-NCO. Although the aziridinomitosene tetracycle is sensitive, a range of protecting group manipulations and redox chemistry can be performed if suitable precautions are taken. A study of DNA alkylation by the first C-6,C-7-unsubstituted aziridinomitosene 11a has been carried out, and evidence for DNA cross-link formation involving nucleophilic addition to the quinone subunit is described.     

An efficient synthesis of the novel triazoloquinazoline adenosine antagonist,CGS 15943

An efficient synthesis of the novel triazoloquinazoline adenosine antagonist, CGS 15943, is reported in five steps in approximately 50% overall yield. A key reaction in the synthetic sequence is the double cyclization of an N-(substituted-2-cyanophenyl)carbamate with a carboxylic acid hydrazide to afford a [1,2,4]triazolo-[1,5-c]quinazolin-5(6H)-one in high yield without either a Dimroth or “translocative” rearrangement occurring. Another key reaction is the condensation of a 2-(1H-1,2,4-triazol-5-yl)benzenamine with cyanamide under acidic conditions to prepare a guanidine.     

An HPLC and EPR investigation on the stability of DMPO and DMPO spin adducts in vivo

Application of the spin trapping technique in intact animals requires an understanding of the stability and distribution of the spin traps and their spin adducts in vivo. We studied the stability of DMPO in vivo in mice using HPLC and the stability of spin adducts of DMPO by EPR in plasma, whole blood, peritoneal fluid, and homogenized heart tissue of the rat. At 15 minutes after intraperitoneal injection DMPO had similar concentrations in the liver, heart, and blood of the mice and 40% remained in the organs 2 hours after the injection. In contrast, the spin adduct DMPO-OH was short lived, with a half-life of 3.0 minutes in plasma, and was not detectable 1 minute after formation in whole blood and homogenized heart tissue. The carbon centered spin adduct DMPO-CH(OH)CH₃ was more stable, having half-lives of 16, 11, 3.6, and 0.79 minutes in plasma, peritoneal fluid, whole blood, and homogenized heart tissue, respectively. The spin adduct DMPO-SO₃ was sufficiently stable for the adduct to be observed directly from living mice.     

Scaling of the energy gap withT c in Bi2Sr2CaCu2O8+δ

The results of a high-resolution photoemission study using synchrotron radiation of two single crystals of Bi₂Sr₂CaCu₂O₈₊, with different critical temperaturesT _c due to a variation in oxygen stoichiometry are reported. Within experimental accuracy, the energy gap 2 is found to scale withT _c , amounting to a reduced gap parameter of 2/k _BT_c7.4. Employing resonant photoemission at the O–2s and Cu–3p thresholds, two spectral peaks at binding energies of 180 meV and 320 meV were identified as predominantly O–2p-and Cu–3d 4s-derived states, respectively.     

A spectrophotometric assay for solid phase primary amino groups

A rapid, sensitive, and convenient spectrophotometric assay was developed for the measurement of amino groups on solid supports. This method is based on the reaction of amino groups of solids with an excess ofo-phthaldialdehyde (OPA) and subsequent quantitative determination of unreacted OPA by reaction with glycine. Four solids possessing variable quantities of amino groups were examined. Results indicate that about 70% of the total surface amino concentration (determined by the microKjeldahl method) are available for ligand attachment. Unlike the spectrophotometric 2,4,6-trinitrobenzenesulfonic acid method, the OPA spectrophotometric assay is more rapid, sensitive, and convenient, and unlike the spectrofluorimetric OPA, it does not require sophisticated instrumentation.     

Another look at complete positivity in generalized quantum dynamics: Reply to Raggio and Primas

In this rejoinder to a critique by Raggio and Primas of our paper, On Completely Positive Maps in Generalized Quantum Dynamics, we acknowledge that, contrary to our original assertion, the Bloch equations are indeed completely positive. We then explain briefly why this modification of our analysis does not alter its main conclusions.     

A comparative study on methods of optimal sample preparation for the analysis of oligonucleotides by matrix-assisted laser desorption/ionization mass spectrometry

Metal adducts (e.g., Na+ and K+) significantly hinder the analysis of oligonucleotides by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS). Although a number of sample purification methods exist, to date no comparative study exists to determine the most efficient method for purifying oligonucleotides. The objective of this work was to perform such a study. Several different oligonucleotide samples were synthesized. Aliquots of these samples were then purposely contaminated with sodium acetate to generate representative contaminated (salted) oligonucleotide samples. A number of popular oligonucleotide purification techniques were then tested as to their effectiveness at removing Na+ from the salted samples. The effectiveness of Na+ removal was qualitatively assessed by comparing the MALDI mass spectra of the original sample, the salted sample, and the salted sample after purification. Micropipet tips packed with C18 reversed-phase packing material (e.g., Zip Tips) appear to be the most effective means of purifying the oligonucleotides investigated. Minidialysis was found to be an effective alternative for purifying higher molecular weight oligonucleotides (> 10,000 u).