Free energy perturbation calculations on models of active sites: Applications to adenosine deaminase inhibitors

Free energy perturbation calculations were performed to determine the free energy of binding associated with the presence of perhaps an unusual hydroxyl group in the transition state analog of nebularine, an inhibitor of the enzyme adenosine deaminase. The presence of a single hydroxyl group in this inhibitor has been found to contribute ?9.8 kcal/mol to the free energy of binding, with a 10⁸-fold increase in the binding affinity by the enzyme. In this work, we calculate the difference in solvation free energy for the 1,6-dihydropurine complex versus that of the 6-hydroxyl-1,6-dihydropurine complex to determine if this marked increase in binding affinity is attributed to an unusually hydrophobic hydroxyl group. The calculated ΔG associated for the solvation free energy is ?11.8 kcal/mol. This large change in the solvation free energy suggests that this hydroxyl is instead unusually hydrophilic and that the difference in free energy of interaction for the two inhibitors to the enzyme must be at least ca. 20 kcal/mol. Although the crystal structure for adenosine deaminase is currently not known, we attempt to mimic the nature of the active site by constructing models which simulate the enzyme-inhibitor complex. We present a first attempt at determining the change in free energy of binding for a system in which structural data for the enzyme is incomplete. To do this, we construct what we believe is a minimal model of the binding between adenosine deaminase and an inhibitor. The active site is simulated as a single charged carboxyl group which can form a hydrogen bond with the hydroxyl group of the analog. Two different carboxyl anion models are used. In the first model, the association is modeled between an acetic acid anion and the modified inhibitor. The second model consists of a hydrophobic amino acid pocket with an interior Glu residue in the active site. From these models we calculate the change in free energy of association and the overall change in free energy of binding. We calculate the free energies of interaction both in the absence and presence of water. We conclude from this that the presence of a single suitably placed-CO^?₂ group probably cannot explain the binding effect of the-OH group and that additional interactions will be found in the adenosine deaminase active site.     

Die thermische Umlagerung von 2-(Buta-1′,3′-dienyl)-phenolen in 2-Alkyl-2H-chromene; Beispiele für aromatische [1,7a]- und [1,5s]sigmatropische Wasserstoffverschiebungen

2-(1′-cis,3′-cis-)- and 2-(1′-cis,3′-trans-Penta-1′,3′-dienyl)-phenol (cis, cis- 4 and cis, trans- 4 , cf. scheme 1) rearrange thermally at 85–110° via [1,7 a] hydrogen shifts to yield the o-quinomethide 2 (R ? CH₃) which rapidly cyclises to give 2-ethyl-2H-chromene ( 7 ). The trans formation of cis, cis- and cis, trans- 4 into 7 is accompanied by a thermal cis, trans isomerisation of the 3′ double bond in 4. The isomerisation indicates that [1,7 a] hydrogen shifts in 2 compete with the electrocyclic ring closure of 2 . The isomeric phenols, trans, trans- and trans, cis- 4 , are stable at 85–110° but at 190° rearrange also to form 7 . This rearrangement is induced by a thermal cis, trans isomerisation of the 1′ double bond which occurs via [1, 5s] hydrogen shifts. Deuterium labelling experiments show that the chromene 7 is in equilibrium with the o-quinomethide 2 (R ? CH₃), at 210°. Thus, when 2-benzyl-2H-chromene ( 9 ) or 2-(1′-trans,3′-trans,-4′-phenyl-buta1′,3′-dienyl)-phenol (trans, trans- 6 ) is heated in diglyme solution at >200°, an equilibrium mixture of both compounds (～ 55% 9 and 45% 6 ) is obtained.     

Produktintegration mit nicht-äquidistanten Stützstellen

Summary For the numerical evaluation of , 0<<1 andx smooth, product integration rules are applied. It is known that high-order rules, e.g. Gauss-Legendre quadrature, become normal-order rules in this case. In this paper it is shown that the high order is preserved by a nonequidistant spacing. Furthermore, the leading error terms of this product integration method and numerical examples are given.

     

On guaranteed stability of uncertain linear systems via linear control

This paper addresses the problem of stabilizing an uncertain linear system. The uncertaintyq(·) which enters the dynamics is nonstistical in nature. That is, noa priori statistics forq(·) are assumed; only boundsQ on the admissible variations ofq(·) are taken as given. The results given here applied to so-called matched systems differ from previous results in two ways. Firstly, the stabilizing control in this paper is linear; for this same class of problems, many of the existing results would require a nonlinear control. Furthermore, those results which do in fact yield linear controls are only valid when a certain matrix (q) (formed using the given data) is negative definite for allq Q. In contrast, the theory given here only requires compactness of the bounding setQ. Secondly, we show that the so-called matching conditions (used in earlier work) can be generalized so as to encompass a larger class of dynamical systems.This research was supported by the US Department of Energy under Contract No. ET-78-S-01-3390.     

A new ℋ -space formalism

The equations governing geometrical objects in ? space are written in terms of operators adapted to families of left shear-freeσ ⁰= 0) cross sections of complexified null infinity (C I ⁺). The concept of ?-conformai weight (HCW) is introduced, and a derivative operatorI _a ^′ , which is closely connected with the covariant derivative but which (unlike the covariant derivative) maps objects having well-defined HCW to other such objects, is defined. A function ?, derived from the Gaussian curvature of left shear-free slicings ofC I ⁺ and having a well-defined HCW, is shown to contain all the curvature information for ? space.     

A tensiometric study of diamond (111) and (110) faces

Tensiometric contact angle measurements of diamond surfaces in both the air:water and octane:water systems reveal moderate hydrophobicity, as might be expected of a surface with a minority of oxygen-containing groups. High-temperature reaction with oxygen or hydrogen leads to large changes in the contact angles. Spectroscopic methods show a “one-third” coverage by oxygen. The response to pH and adsorption of ferric ion suggests that the oxygen is present as an hydroxyl group. Steric resistance to higher oxide coverage, because of the small lattice constant of the crystal, may be an explanation for the natural hydrophobicity of the diamond surface.     

The formation of polymerizable tubules

We have been investigating the crystallization behavior of the phospholipid amphiphile, 1,2 bis (10, 12-tricosadiynol)-sn-glycero-3-phosphocholine, DC_8,9PC, which forms both vesicles and hollow tubules as well as Langmuir Blodgett monolayers and multilayers. This material has polymerizable diacetylene groups in equivalent positions on the two hydrocarbon tails. The direct crystallization from solution of this amphiphile has been studied using different solvent mixtures and temperatures. The Langmuir Blodgett technique was also used to compress and orient the tubules.     

An average-of-configuration method for using Kohn-Sham density functional theory in modeling ligand-field theory

The Amsterdam Density Functional (ADF) package has been used to constrain Kohn-Sham DFT in such a fashion that a transition from KS-DFT to ligand-field theory in the form of the parametrical d(q)() model is completely well-defined. A relationship is established between the strong-field approximation of the parametrical d(2) model for the tetrahedral complexes VCl(4)(-) and VBr(4)(-) and certain fixed-orbital ADF-computed energies. In this way values for all the parameters of the d(2)() model may be computed, thus allowing the ADF results to be expressed in terms of a KS-DFT energy matrix that can be diagonalized. This means that the KS-DFT deficiency with regard to computation of nondiagonal elements has been overcome and the KS-DFT eigenenergies have become available through the KS-DFT mimicking of the ligand-field plus repulsion model. By using mutually orthogonal strong-field energy matrices, the mimicking has been further elucidated. The computed values for the empirical parameters of VCl(4)(-) and VBr(4)(-) are in good agreement with experimental data. The spectrochemical and the nephelauxetic series have been computed by including the remaining halide complexes and the quantitatively special position of F(-)() among the halides corroborated for both series.     

Selectivity in microemulsion electrokinetic chromatography

Microemulsion electrokinetic chromatography (MEEKC) is a most promising separation technique providing good selectivity and high separation efficiency of anionic, cationic as well as neutral solutes. In MEEKC lipophilic organic solvents dispersed as tiny droplets in an aqueous buffer by the use of surfactants provide a pseudo-stationary phase to which the solutes may have an affinity either to the surface or they may even partition into the droplets. When the droplets are charged, typically negatively, they will migrate opposite to the electroosmotic flow and hence separation of neutral solutes may take place. In the present paper focus has been set on how to change selectivity in MEEKC. Changes in the nature of surfactant as well as in pH have been shown to be powerful tools in changing the selectivity. The type of lipophilic organic phase is of less importance for the separation of fairly lipophilic solutes. Also changes in the temperature surrounding the capillary may alter the selectivity.     

The determination of trace amounts of tin by flow-injection hydride generation atomic-absorption spectrometry with on-line ion-exchange separation and preconcentration

A hydride generation atomic-absorption spectrometric (AAS) method with flow-injection (FI), aimed at developing a practical routine assay for the determination of tin in food digests, is described. In order to modify the sample matrix and to achieve optimized and reproducible conditions for the hydride generation reaction, the analyte is initially converted into its chlorostannate-complex thereby allowing it to be separated and preconcentrated on-line on an incorporated micro-column packed with a strongly basic anion exchanger and subsequently to be eluted by diluted nitric acid under strictly controlled conditions. Optimum acidic conditions for the FI hydride generation AAS system was found to be 0.01-0.05M nitric acid. At a consumption of 2.7-ml sample volume, aspirated by time-based injection, the procedure resulted in an enrichment factor of 3.5 and yielded a detection limit of 0.08 microg/l. (3sigma) at a sampling frequency of 72/hr. The precision was 2.5% rsd at the 10 microg/l. level. Potential interferents, such as Ni(II), Co(II), Zn(II) and Fe(III) could, at a Sn level of 10 microg/l., be tolerated at an excess of 1000 times without impairing the assay, while a 100-1000-fold excess of Cu(II) decreased the signal by 10-15%. Recoveries in the range 94-102% were obtained for canned food sample digests spiked with 10 microg/l. Sn.