On the role of the conserved aspartate in the hydrolysis of the phosphocysteine intermediate of the low molecular weight tyrosine phosphatase

The usual rate-determining step in the catalytic mechanism of the low molecular weight tyrosine phosphatases involves the hydrolysis of a phosphocysteine intermediate. To explain this hydrolysis, general base-catalyzed attack of water by the anion of a conserved aspartic acid has sometimes been invoked. However, experimental measurements of solvent deuterium kinetic isotope effects for this enzyme do not reveal a rate-limiting proton transfer accompanying dephosphorylation. Moreover, base activation of water is difficult to reconcile with the known gas-phase proton affinities and solution phase pK(a)'s of aspartic acid and water. Alternatively, hydrolysis could proceed by a direct nucleophilic attack by a water molecule. To understand the hydrolysis mechanism, we have used high-level density functional methods of quantum chemistry combined with continuum electrostatics models of the protein and the solvent. Our calculations do not support a catalytic activation of water by the aspartate. Instead, they indicate that the water oxygen directly attacks the phosphorus, with the aspartate residue acting as a H-bond acceptor. In the transition state, the water protons are still bound to the oxygen. Beyond the transition state, the barrier to proton transfer to the base is greatly diminished; the aspartate can abstract a proton only after the transition state, a result consistent with experimental solvent isotope effects for this enzyme and with established precedents for phosphomonoester hydrolysis.     

On the theory underlying the Car-Parrinello method and the role of the fictitious mass parameter

The theory underlying the Car-Parrinello extended-Lagrangian approach to ab initio molecular dynamics (CPMD) is reviewed and reexamined using "heavy" ice as a test system. It is emphasized that the adiabatic decoupling in CPMD is not a decoupling of electronic orbitals from the ions but only a decoupling of a subset of the orbital vibrational modes from the rest of the necessarily coupled system of orbitals and ions. Recent work [J. Chem. Phys. 116, 14 (2002)] has pointed out that, due to the orbital-ion coupling that remains once adiabatic decoupling has been achieved, a large value of the fictitious mass mu can lead to systematic errors in the computed forces in CPMD. These errors are further investigated in the present work with a focus on those parts of these errors that are not corrected simply by rescaling the masses of the ions. It is suggested that any comparison of the efficiencies of Born-Oppenheimer molecular dynamics (BOMD) and CPMD should be performed at a similar level of accuracy. If accuracy is judged according to the average magnitude of the systematic errors in the computed forces, the efficiency of BOMD compares more favorably to that of CPMD than previous comparisons have suggested.     

On the complexity of kinetics and the mechanism of the thiosulfate-periodate reaction

The thiosulfate-periodate reaction has been studied spectrophotometrically in a slightly acidic medium at 25.0 ± 0.1 °C in an acetate/acetic acid buffer by monitoring the absorbance in the 250-600 nm wavelength range at a constant ionic strength adjusted by the buffer component sodium acetate. In agreement with a previous study, we found that the reaction cannot be described by a single stoichiometric equation, tetrathionate and sulfate are simultaneously formed, and its ratio strongly depends on the pH. As expected at certain initial concentration ratios of the reactants, the reaction behaves as a clock reaction, but after its appearance, iodine is slowly consumed mainly because of the moderate tetrathionate-iodine reaction. It is also enlightened that the initial rate of the reaction is completely independent of the pH, which apparently contradicts a previous study, which postulates a "supercatalytic" behavior of the hydrogen ion on the title reaction. Significant buffer assistance that may change the absorbance-time profiles was also observed. On the basis of the kinetic data, a robust 28-step kinetic model with 22 fitted parameters is proposed and discussed to explain adequately all of the important characteristics of the kinetic curves.     

Koopmans-like approximation in the Kohn-Sham method and the impact of the frozen core approximation on the computation of the reactivity parameters of the density functional theory

A Koopmans-like approximation is introduced in the spin-polarized version of the Kohn-Sham (KS) density functional theory to obtain a relation between KS orbital energies and vertical ionization potential and electron affinity. Expressions for reactivity indexes (like electronegativity, hardness, electrophilicity, and excitation energies) include KS frontier orbital energies and additional contributions associated with the self-interaction correction. Those reactivity parameters were computed with different exchange-correlation functionals to test the approach for a set of small molecules. The results show that the present approximation provides a better way to estimate hardness, electronegativity, and electrophilicity than just the use of frontier orbital energy values. However KS HOMO and LUMO energy gap gives a better agreement with excitation energies.     

Studies toward the asymmetric synthesis of the right part of the mycalamides

Described herein is the asymmetric synthesis of a functionalized, trioxadecalin unit that comprises the right-hand part of the mycalamides and related natural products. The synthetic route involves a 16-step sequence that accomplishes the formation of two heterocyclic rings and the generation of five stereocenters. The synthesis commenced with a C2-symmetric starting material, diethyl D-tartrate, and took advantage of a relay of diastereoselective reactions to extend this four-carbon chain and introduce new chiral centers. Subsequent electrophile-mediated cyclization afforded the desired pyran ring, which was then transformed into the desired, functionalized trioxadecalin skeleton.     

From the Micro- to the Macro-: Managing the Conservation of the Warship,Vasa

Sweden's famous warship, Vasa, sank on her maiden voyage in August 1628, and remained on the bottom of Stockholm harbour for 333 years. Raised in 1961, she became the first large-scale wooden object to be treated with polyethylene glycol (PEG). In the summer of 2000 a number of acidic salt precipitations were noticed on the surface of the ship and on wooden artefacts in the storerooms. An international research project has been established to look into the causes of this problem and suggest possible re-treatments. Meanwhile projects are underway to monitor movements in the ship, to build a better support system, and to replace the thousands of iron bolts holding the structure together, while a sophisticated new climate system has recently been installed in the museum.     

Behavior of the Surface Tension and the Viscosity in the Eutecticregion of the Liquid Feb alloy

Abstract

Thermodynamic and transport properties of pure liquid metals show interesting correlations near the melting temperature. This is well known for the case of the surface tension σ and the shear viscosity η In this paper we investigate the possible extension of these correlations to binary alloys, taking the FeB alloy as a case study. Based on literature data we analyze the variation of σ and η as a function of temperature and concentration in a deep eutectic region of the phase diagram of this alloy, as well as the possible correlations between those two quantities. Substantial differences with respect to the behavior in pure metals are found.     

明朝迁都北京与多民族国家治理

明朝建立后,面对多民族国家治理的新格局,定都问题一直是困扰朱元璋君臣的一大难题。终洪武之世,朱元璋也未能解决迁都的问题。燕王朱棣称帝后,将北平改为北京,条件具备后迅速将京师从南京迁到北京。成祖去世之后,虽有短暂的反复,但英宗即位不久,宣布定都北京,从此北京成为明朝永久的都城。迁都北京是明朝主动适应唐以后多民族交融局面的具体表现,一方面可以有效应对元朝残余的侵扰,另一方面能够整合农耕和游牧两大区域,为中国多民族国家治理做出了积极的贡献,意义重大。     

Application of the chiral base desymmetrisation of imides to the synthesis of the alkaloid jamtine and the antidepressant paroxetine

The synthesis of the alkaloid jamtine and the antidepressant paroxetine have been addressed by a strategy involving asymmetric desymmetrisation of prochiral imides by a chiral lithium amide base. A short reaction sequence, starting with a cyclohexane fused succinimide, led to the structures originally reported for the alkaloid jamtine and its derived N-oxide. The structures synthesised are shown not to correspond with those originally reported. A second sequence involves desymmetrisation of a 4-arylglutarimide, and provides a short enantioselective synthesis of the drug substance paroxetine.     

On the Nature of the Temperature-Induced Transition From the Molten Globule to the Unfolded State of Globular Proteins

In this paper we try to perform a thermodynamic analysis of the temperature-induced transition from the molten globule to the unfolded state of globular proteins. A series of calorimetric investigations showed that this process is not associated with an excess heat capacity absorption peak, and cannot be regarded as a first-order phase transition. This result contrasts with the well-established conclusion that the thermal unfolding of the native tertiary structure of globular proteins is a first-order phase transition. First, the theoretical approach developed by Ikegami is outlined to emphasize that a second-order or gradual transition induced by temperature is expected for globular proteins when the various secondary structure elements do not interact cooperatively. Secondly, a simple thermodynamic model is presented which, taking into account the independence of the secondary structure elements among each other, is able to rationalize the shape of the experimental DSC profiles.This revised version was published online in November 2005 with corrections to the Cover Date.     

Influence of the errors made in the measurement of the extra-column volume on the accuracies of estimates of the column efficiency and the mass transfer kinetics parameters

The influences of the errors made in the measurement of the extra-column volume of an instrument on the accuracies of the estimates made of the column efficiency and of the parameters of the mass transfer kinetics were investigated from an experimental point of view. A standard HP1090 apparatus (extra-column volume, approximately 50 micro L) was used to measure the efficiency of a Sunfire-C(18) RPLC column (column hold-up volume, approximately 1.50 mL). The first and second moments of the peaks of phenol (a retained compound) and of thiourea (a practically non-retained compound) were measured at six different temperatures between 22 and 78 degrees C, for flow rates between 0.10 and 4.70 mL/min (i.e., for linear velocities between 0.025 and 1.179 cm/s). Each series of measurements was successively made with the instrument being fitted with and without the column. The experimental HETP data must be corrected for the solute dispersion in the connected tubes in order properly to assess the true column efficiency. Even with a modern, high performance instrument, the dispersion of a non-retained compound is essentially due to the band broadening phenomena that take place in the extra-column volumes, the sum of all these extra-column band broadening contributions accounting for more than 80% of the total band broadening measured. The contribution of the sampling device is particularly deleterious since, for a 2 mu L injection, the maximum solute concentration in the peak that enters into the column is nearly ten-fold lower than that of the sample. Nevertheless, the impact of the extra-column volumes on the estimates of the kinetic parameters (e.g., molecular diffusion coefficient D(m) and effective particle diffusivity D(e)) remains negligible. Obviously, the relative error made on the column efficiency of a retained compound depends much on its retention factor. It decreases from 8 to 1% when the retention factor increases from 5 to 17.     

Regarding the theory of the Zeno line

The line of thermodynamic states with a unit value of the compressibility factor was calculated for a Lennard-Jones system using four different approaches. We show that all four approaches give rise to a straight line on the density-temperature plane. Thus, we theoretically confirm that the Lennard-Jones system satisfies Zeno line regularity.     

Tracing the minimum-energy path on the free-energy surface

The free-energy profile of a reaction can be estimated in a molecular-dynamics approach by imposing a mechanical constraint along a reaction coordinate (RC). Many recent studies have shown that the temperature can greatly influence the path followed by the reactants. Here, we propose a practical way to construct the minimum-energy path directly on the free-energy surface at a given temperature. First, we follow the blue-moon ensemble method to derive the expression of the free-energy gradient for a given RC. These derivatives are then used to find the actual minimum-energy reaction path at finite temperature, in a way similar to the intrinsic reaction path of Fukui on the potential-energy surface. [K. Fukui, J. Phys. Chem. 74, 4161 (1970)]. Once the path is known, one can calculate the free-energy profile using thermodynamic integration. We also show that the mass-metric correction cancels for many types of constraints, making the procedure easy to use. Finally, the minimum-free-energy path at 300 K for the addition of CCl2 to ethylene is compared with a path based on a simple one-dimensional reaction coordinate. A comparison is also given with the reaction path at 0 K.     

On the scaling of the interface energy of the liquid clusters in the disordered nanoporous medium

Similarity of the extrusion curves of non-wetting liquid in a nanoporous medium with different initial fill volume fractions is observed experimentally. The similarity can be explained by the scaling of the interface energy and the self-similarity of the infinite percolation cluster of fluid-filled pores. Understanding the physical processes leading to the observed phenomena is a foundation for the development of high-performance devices for damping and energy storage on the basis of such heterogeneous systems.     

Quantum-chemical analysis of the nucleophilic substitution of the bromine atom by the cyano group at the sp-hybridized carbon atom in the methylbromoacetylene molecule

This paper reports on our quantum-chemical analysis of the nucleophilic substitution of the bromine atom by the cyano group in the reaction of methylbromoacetylene with copper cyanide. According to calculations, the reaction can form a four-membered ring containing a copper atom.     

Concerning the deprotonation of the trimethylsulfonium ion by the dimethylsulfinyl anion

As shown by deuterium labelling experiments, the deprotonation of the trimethylsulfonium ion (1) by the dimsyl anion (8) is accompanied by extensive hydrogen exchange. This cannot be explained by an acid-base equilibrium between the trimethylsulfonium ion (1) and the dimsyl anion (8) on one side and dimethylsulfonium methylide (2) and DMSO on the other side, because for thermodynamic reasons this process is irreversible due to the limited life-time of 2. Therefore, the isotopic exchange that accompanies the deprotonation is an indicator of a more complex deprotonation process. It is suggested that in a kinetically controlled reaction, a proton of 1 is transferred to the O-atom of 8 rather than to the carbanionic centre. This means that instead of DMSO, its tautomer, hydroxy-methylsulfonium methylide (10), is obtained in the deprotonation process. Similarly, in the acid-base interaction between DMSO and its conjugate base 8, the formation of the DMSO tautomer 10 is kinetically favoured. The intermediate 10 produced in this way transfers a DMSO-derived proton to 1 when it intervenes in the back reaction 10 + 2→8 + 1. An alternative mechanism based on methyl group exchange between 1 and 8 could be excluded by a (13)C-labelling experiment. The hydrogen exchange according to the suggested scenario is taking place in competition with the reaction of dimethylsulfonium methylide (2) with electrophilic substrates. This explains the different degrees of isotopic exchange when compounds of different electrophilicities are used to scavenge 2 from the deprotonation-hydrogen distribution equilibria.     

Influence of the Position of the Connecting Spacer of the Chromophore on the Nonlinear Optical Response

A new chromophore, C1 , based on a similar DπA‐structure as in the FTC ‐chromophore but with a hydroxyalkyl spacer perpendicular to the direction of the dipole moment was synthesized. Both chromophores and the CLD ‐chromophore were used to prepare high T_g nonlinear optical vinyl polymers. The influence of the position of the spacer on the DπA‐system on the NLO response of the resulting polymers was investigated.

     

Tandem electrostatic effect from the first to the third aglycon in the trimeric RNA owing to the nearest-neighbor interaction

We here show an electrostatic polar-pi interaction from the first to the third aglycon, via the second aglycon, in the ground state in two single stranded trimeric RNAs, 5'-GpA(1)pA(2)-3' (3) and 5'-GpApC-3' (4), as a result of intramolecular nearest neighbor offset-stacking. The experimental evidence in support of this conclusion has been obtained by comparing the pK(a)s of each aglycone in the two trimers with those of guanosine 3'-ethyl phosphate, GpEt (1) and 5'-GpA-3' (2): Thus, the pK(a) of N(1)-H of guanin-9-yl of 5'-GpA(1)pA(2)-3' (3) could be measured by pH titration (pH 7.3-11.6) of its own deltaH8G (pK(a) 9.75 +/- 0.02) as well as from deltaH8A(1) (pK(a) 9.72 +/- 0.02) and deltaH2A(1) (pK(a) 9.83 +/- 0.04) of the neighboring pA(1)p moiety and the deltaH8A(2) (pK(a) 9.83 +/- 0.02) of the terminal pA(2) moiety. Similarly, the pH titration of GpApC (4) shows the pK(a) of N(1)-H of guanin-9-yl from its own deltaH8G (pK(a) 9.88 +/- 0.03) as well as from deltaH8A (pK(a) 9.87 +/- 0.01) of the neighboring pAp moiety, and deltaH5/H6C (pK(a) 9.88 +/- 0.01 and 9.90 +/- 0.01 respectively) of the 3'-terminal cytosin-1-yl. This intramolecular nearest neighbor electrostatic interaction in the single-stranded RNA modulates the pseudoaromaticity of the nearest neighbors by almost total transmission of because they constitute an extended array of offset-stacked coupled aromatic heterocycles within a polyanionic sugar-phosphate backbone at the ground state. The enhanced basicity of Gp residue by ca. 0.6 pK(a) unit in the trimers compared to that of the dimer is a result of the change in the electrostatic microenvironment owing to the nearest neighbors in the former (the nucleobases as well as the phosphates). Thus, the from the 5'-guanylate ion to the 3'-end aglycon via the central adenin-9-yl is 55 to 56 kJ mol(-)(1) in each step through a distance spanning approximately 6.8 A in an unfolded state. As a result, the pK(a) of guanin-9-yl moiety has become 9.25 +/- 0.02 in GpEt (1), 9.17 +/- 0.02 in GpA (2), 9.75 +/- 0.02 in GpApA (3), and 9.88 +/- 0.03 in GpApC (4). This means that guanin-9-yl moiety of trimers 3 and 4 is more basic than in the monomer or the dimer. The net outcome of this electrostatic cross-talk between the two neighboring heterocycles is creation of new hybrid aglycones in an oligo or polynucleotide, whose physicochemical property and the pseudoaromatic character are completely dependent both upon the nearest neighbors, and whether they are stacked or unstacked. Thus, this tunable physicochemical property of an aglycon (an array of the extended genetic code) may have considerable implication in our understanding of the specific ligand binding ability of an aptamer, the pK(a) and the hydrogen bonding ability of nucleic acids in a microenvironment, or in the triplet usage by the anticodon-codon interaction in the protein biosynthesis in the ribosome.     

Features of the interactions between the methyl-CpG motif and the arginine residues on the surface of MBD proteins

Recognition of the methylated regions of the DNA plays an important role in the epigenetic processes. We analyze the interactions between the methylated DNA and the methyl-CpG-binding proteins using two models. The first model was built from a methylated or non-methylated cytosine, a guanine and an arginine residue in the experimental arrangement. We applied the M06L density functional method with a small, polarized double-ζ basis set for the geometry optimizations, and the MP2 method with polarized triple-ζ basis set for the energy calculations. The second model was built from two methylcytosines, guanines, guanidinium groups plus an additional carboxyl group in the experimental arrangement. We applied the B3LYP method with a small, polarized double-ζ basis set for the geometry optimizations and thermal corrections. The single-point energies were obtained from dual-hybrid dRPA75 and dRPA@PBE0 calculations supplemented by a moderately large polarized triple-ζ basis set. The hydration effects were modeled by adding explicit water molecules. These calculations revealed that the hydrophobic interaction has the largest contribution to the Gibbs interaction energy and turns the arginine side chains into hydrogen bonding position. Our results show that the translation of the protein along the DNA double helix is sterically hindered by the contact of its arginine side chains with the methyl groups of the methyl cytosines. This supports a hopping mechanism for the searching movement of the protein along the DNA.

     

Reconstruction of the free energy in the metastable region using the path ensemble

By quenching into the metastable region of the three-dimensional Ising model, we investigate the paths that the magnetization (energy) takes as a function of time. We accumulate the magnetization (energy) paths into time-dependent distributions from which we reconstruct the free energy as a function of the magnetic field, temperature, and system size. From the reconstructed free energy, we obtain the free-energy barrier that is associated with the transition from a metastable state to the stable equilibrium state. Although mean-field theory predicts a sharp transition between the metastable and the unstable region where the free-energy barrier is zero, the results for the nearest-neighbor Ising model show that the free-energy barrier does not go to zero.