Proton affinity of β-oxalylaminoalanine (BOAA): Incorporation of direct entropy correction into the single-reference kinetic method

A new version of the single-reference-extended kinetic method is presented in which direct entropy correction is incorporated. Results of calibration experiments with the monodentate base pyridine and the bidentate base ethylenediamine are presented for which the method provides proton affinities in excellent agreement with published values and reasonable predictions for the protonation entropies. The method is then used to determine the proton affinity and protonation entropy of the non-protein amino acid beta-oxalylaminoalanine (BOAA). The PA of BOAA is found to be 933.1 +/- 7.8 kJ/mol and a prediction for the protonation entropy of -39 J mol(-1) K(-1) is also obtained, indicating a significant degree of intramolecular hydrogen bonding in the protonated form. These results are supported by hybrid density functional theory calculations at the B3LYP/6-311++G**//B3LYP/6-31+G* level. They indicate that the preferred site of protonation is the alpha-nitrogen atom (PA = 935.0 kJ/mol) and that protonated BOAA has a strong hydrogen bond between the hydrogen on the alpha-amino group and one of the carbonyl oxygen atoms on the side chain.     

Structure of a de novo designed protein model of radical enzymes

The use of side chains as catalytic cofactors for protein mediated redox chemistry raises significant mechanistic issues as to how these amino acids are activated toward radical chemistry in a controlled manner. De novo protein design has been used to examine the structural basis for the creation and maintenance of a tryptophanyl radical in a three-helix bundle protein maquette. Here we report the detailed structural analysis of the protein by multidimensional NMR methods. An interesting feature of the structure is an apparent pi-cation interaction involving the sole tryptophan and a lysine side chain. Hybrid density functional calculations support the notion that this interaction raises the reduction potential of the W degrees /WH redox pair and helps explain the redox characteristics of the protein. This model protein system therefore provides a powerful model for exploring the structural basis for controlled radical chemistry in protein.     

Dissociation constants of the ampholyte glycine in 50 mass % methanol-water from 5 to 55°C,with related thermodynamic quantities

The two thermodynamic dissociation constants of glycine at 11 temperatures from 5 to 55°C in 50 mass % methanol-water mixed solvent have been determined from precise emf measurements with hydrogen-silver bromide electrodes in cells without liquid junction. The first acidic dissociation constant (K ₁)for the process HG⁺H⁺+G^± is expressed as a function ofT(^oK) by the equation pK ₁ = 2043.5/T – 9.6504 + 0.019308T. At 25°C, pK ₁is 2.961 in the mixed solvent, as compared with 2.350 in water, with H°=1497 cal-mole^–1, G°=4038 cal-mole^–1, S°=–8.52 cal-°K^–1-mole^–1, and C _p ^o =–53 cal-°K^–1-mole^–1. The second acidic dissociation constant (K ₂)for the process G^±H⁺+G^– over the temperature range studied is given by the equation pK ₂ = 3627.1/T – 7.2371 + 0.015587T. At 25°C, pK ₂is 9.578 in MeOH–H₂O as compared with 9.780 in water, whereas H° is 10,257 cal-mole^–1, G° is 13,063 cal-mole^–1, S° is –9.41 cal-°K^–1-mole^–1, and C _p ^o is –43 cal-°K^–1-mole^–1. The protonated glycine becomes weaker in 50 mass % methanol-water, whereas the second dissociation process becomes stronger despite the lower dielectric constant of the mixed solvent (=56.3 at 25°C).     

Use of coupled-cluster based linear response theory and multireference hermitian MBPT to IP calculations of HF

We report in this paper the results of outer and inner valence IP calculations for the HF molecule using two different many-body methods for the direct evaluation of energy differences. The first is the nonperturbative coupled-cluster based linear response theory (LRT) and the second is the hermitian open-shell many-body perturbation theory (MBPT). A Huzinaga-Dunning (9s5p→ 5s3p/3s) basis has been used. LRT uses an “ionization operator” S as in the equation of motion method (EOM) to generate the ionized states from a coupled-cluster type of ground state. S is chosen to consist of single ionization and ionization-cum-shake-up operators, thus treating the Koopmans as well as the shake-up states on equal footing. LRT would thus be capable of computing both the outer and the inner valence regions with equal facility. This is borne out by the results. For the open-shell MBPT, the model space is chosen to be spanned by the singly ionized determinants. The convergence of the results for the inner valence region is slow, and the results obtained from the [2, 1] Pade' approximants are presented. Unlike the LRT, the inner valence region is not reproduced with full complexity in MBPT, indicating that it is essential to modify the theory by way of expanding the model space to contain the shake-up determinants also.     

Studies on the substrate specificity of Escherichia coli galactokinase

In vitro glycorandomization (IVG) technology is dependent upon the ability to rapidly synthesize sugar phosphates. Compared with chemical synthesis, enzymatic (kinase) routes to sugar phosphates would be attractive for this application. This work focuses upon the development of a high-throughput colorimetric galactokinase (GalK) assay and its application toward probing the substrate specificity and kinetic parameters of Escherichia coli GalK. The demonstrated dinitrosalicylic assay should also be generally applicable to a variety of sugar-processing enzymes. [reaction: see text]     

Relationship between side chain structure and 14-helix stability of beta3-peptides in water

Folded polymers are used in Nature for virtually every vital process. Nonnatural folded polymers, or foldamers, have the potential for similar versatility, and the design and refinement of such molecules is of considerable current interest. Here we report a complete and systematic analysis of the relationship between side chain structure and the 14-helicity of a well-studied class of foldamers, beta(3)-peptides, in water. Our experimental results (1) verify the importance of macrodipole stabilization for maintaining 14-helix structure, (2) provide comprehensive evidence that beta(3)-amino acids branched at the first side chain carbon are 14-helix-stabilizing, (3) suggest a novel role for side chain hydrogen bonding as an additional stabilizing force in beta(3)-peptides containing beta(3)-homoserine or beta(3)-homothreonine, and (4) demonstrate that diverse functionality can be incorporated into a stable 14-helix. Gas- and solution-phase calculations and Monte Carlo simulations recapitulate the experimental trends only in the context of oligomers, yielding insight into the mechanisms behind 14-helix folding. The 14-helix propensities of beta(3)-amino acids differ starkly from the alpha-helix propensities of analogous alpha-amino acids. This contrast informs current models for alpha-helix folding, and suggests that 14-helix folding is governed by different biophysical forces than is alpha-helix folding. The ability to modulate 14-helix structure through side chain choice will assist rational design of 14-helical beta-peptide ligands for macromolecular targets.     

Micro-Raman investigations of myelins in aerosol-OT/water system

Surfactant outgrowth during dissolution as myelin figures, which happens on contact with water, is of prime importance in emulsification and detergency. Micro-Raman investigation of different lyotropic phases formed during dissolution of aerosol-OT (bis 2-ethylhexyl sulfosuccinate) in water during myelin formation reveals the flexible arrangement of the surfactant bilayers in myelin. The conformation around CC-CS bond and the hydrocarbon chains of aerosol-OT in the different liquid crystalline phases were identified from the fingerprints of CC-CS stretching, C-C stretching, C-H bending, and stretching frequencies. Existence of mixture of trans and gauche conformations around CC-CS bond and that of the hydrocarbon chains in myelin supports the fluid nature of bilayers by which it is made. Similar conformations of hydrocarbon chains in lamellar phase and in myelin support the concept of myelins being rolled up lamella. The observations are in line with the disorderness of the hydrocarbon chains in the bilayers of phospholipids that has been reported earlier. From the C-C stretching frequencies at the root of myelins, the kinked structure of the hydrocarbon chain is identified, and loose packing of molecules which would facilitate water transport across membranes is evident.     

Highly efficient water promoted allylation and propargylation of arylepoxides via rearrangement-carbonyl addition

A simple and highly efficient one-pot procedure for allylation and propargylation of arylepoxides has been developed. A combination of SnCl₂ and catalytic Pd(0) or Pd(II) promotes the reaction of organic halides and epoxides in DMSO with controlled water addition, leading to the regioselective formation of the corresponding homoallyl and homopropargyl alcohols in good yields.