The Photophysics of β-Tyrosine and Its Simple Derivatives

Synthesis and photophysical studies of (O-methyl)--tyrosine (-tyrosine; an analogue of tyrosine, in which the amino group is moved from the - to the -carbon, closer to the phenol ring) and its derivatives with a blocked amino and/or carboxyl group were performed to explain the nature of the fluorescence of tyrosine derived analogues. All -tyrosine derivatives, except Ac-Tyr(Me), displayed the monoexponential fluorescence decay. The biexponential fluorescence decay observed for Ac-Tyr(Me) is assumed to be the result of the presence of two low-energy conformations (extended and with an intramolecular hydrogen bond). Higher quenching of the fluorescence of -tyrosine derivatives by the N-acetyl group than by the N-methylamide group moved farther was found, contrary to the data found for the respective derivatives of natural tyrosine. The obtained photophysical data are discussed with theoretical calculations (AMBER, AM1) on the basis of the rotamer model.     

The effect of β-CD polymers structure on the efficiency of copper(II) ion flotation

β-Cyclodextrin (β-CD) polymers were prepared by cross-linking of β-CD with phtalic and 3-nitrophtalic anhydride in anhydrous N,N-dimethylformamide (DMF) in the presence of NaH. The weight-average molecular weight (M _W) and the chemical structure of the polymers were determined using high performance size exclusion chromatography (HPSEC) with refractive index (RI) detector, and ¹H NMR spectroscopy. The molecular weight of the polymer increased with molar ratio of substrates and reaction temperature. ¹H NMR spectra revealed that the β-CD polymers contained both mono- and diesters of phtalic and 3-nitrophtalic acids. In the case of phtalic moieties about four or five diester moieties groups and for 3-nitrophtalic moieties about to or three diester moieties are linkages for β-CD molecule, respectively. Results of copper(II) flotation obtained with the use of nonylphenol polyoxyethyl glycol ether as an non-anionic surfactant and β-CD polymers as complexation collector agent, show␣that the removal of Cu²⁺ decreases with increase of molecular mass of β-CD polymers linked by phtalic or␣3-nitrophtalic anhydrides. For both derivatives with pH increase the copper(II) removal increase. The highest flotation removal, i.e. 93%, was found for β-CD polymers synthesized at 100 °C with molar ratio CD:NaH:3-nitrophtalic anhydride equal to 1:7:7.     

Molecular origin of anticooperativity in hydrophobic association

The structuring of water molecules in the vicinity of nonpolar solutes is responsible for hydrophobic hydration and association thermodynamics in aqueous solutions. Here, we studied the potential of mean force (PMF) for the formation of a dimer and trimers of methane molecules in three specific configurations in explicit water to explain multibody effects in hydrophobic association on a molecular level. We analyzed the packing and orientation of water molecules in the vicinity of the solute to explain the effect of ordering of the water around nonpolar solutes on many-body interactions. Consistent with previous theoretical studies, we observed cooperativity, manifested as a reduction of the height of the desolvation barrier for the trimer in an isosceles triangle geometry, but for linear trimers, we observed only anticooperativity. A simple mechanistic picture of hydrophobic association is drawn. The free energy of hydrophobic association depends primarily on the difference in the number of water molecules in the first solvation shell of a cluster and that in the monomers of a cluster; this can be approximated by the molecular surface area. However, there are unfavorable electrostatic interactions between the water molecules from different parts of the solvation shell of a trimer because of their increased orientation induced by the nonpolar solute. These electrostatic interactions make an anticooperative contribution to the PMF, which is clearly manifested for the linear trimer where the multibody contribution due to changes in the molecular surface area is equal to zero. The information theory model of hydrophobic interactions of Hummer et al. also explains the anticooperativity of hydrophobic association of the linear trimers; however, it predicts anticooperativity with a qualitatively identical distance dependence for nonlinear trimers, which disagrees with the results of simulations.     

Charge loss in gas-phase multiply negatively charged oligonucleotides

In an attempt to shed light on the mechanism by which gaseous samples of negatively charged oligonucleotides undergo extremely slow (i.e., over 1-1000 s) charge loss, we have carried out molecular dynamics simulations on an oligonucleotide anion, T(5)(3-), containing five thymine, deoxyribose, and phosphate units in which the first, third, and fifth phosphates are negatively charged. The study is aimed at determining the rate at which an electron is detached from such a trianion by way of an internal Coulomb repulsion induced event. In this process, the intrinsic 5.0-5.1 eV electron binding strength of each phosphate site is reduced by the repulsive Coulomb potentials of the other two negative sites. As geometrical fluctuations cause the distances among the three negative phosphate sites to change, this causes the Coulomb repulsion energies at these sites to fluctuate. Once the Coulomb potential at any phosphate site exceeds ca. 5 eV, the electron on that site is able to undergo autodetachment. Although such an electron must tunnel through a barrier to escape, it is shown that the tunneling rate is not the rate-limiting step in electron loss; instead, it is the rate at which geometrical fluctuations cause the Coulomb potentials to exceed 5 eV that determines the rate of electron loss. Because these rates are extremely slow, special techniques had to be introduced to allow results of dynamics simulations on more flexible models of T(5)(3-) to be extrapolated to predict the behavior of the actual T(5)(3-).     

Protein structure prediction with the UNRES force-field using Replica-Exchange Monte Carlo-with-Minimization; Comparison with MCM, CSA, and CFMC

Two current methods of global optimization are coupled to produce the Replica-Exchange method together with Monte Carlo-with-Minimization (REMCM). Its performance is compared with each separate component and with other global optimization techniques. REMCM was applied to search the conformational space of coarse grain protein systems described by the UNRES force field. The method consists of several noninteracting copies of Monte Carlo simulation, and minimization was used after every perturbation to enhance the sampling of low-energy conformations. REMCM was applied to five proteins of different topology, and the results were compared to those from other optimization methods, namely Monte Carlo-with-Minimization (MCM), Conformational Space Annealing (CSA), and Conformational Family Monte Carlo (CFMC). REMCM located global minima for four proteins faster and more consistently than either MCM or CFMC, and it converged faster than CSA for three of the five proteins tested. A performance comparison was also carried out between REMCM and the traditional Replica Exchange method (REM) for one protein, with REMCM showing a significant improvement. Moreover, because of its simplicity, REMCM was easy to implement, thereby offering an alternative to other global optimization methods used in protein structure prediction.     

Excess molar volumes and deviations of the relative permittivity of the binary mixtures of 2-propoxyethanol with diethylene,triethylene, and tetraethylene glycols at various temperatures

Densities and relative permittivities at T = (293.15, 298.15, and 303.15) K in the binary liquid mixtures of 2-propoxyethanol with diethylene glycol, triethylene glycol, and tetraethylene glycol have been measured over the entire mixture compositions. These data have been used to compute the excess molar volumes and deviations of the relative permittivity. The results are discussed in terms of intermolecular interactions in the bulk of studied the binary mixtures.     

Reduced hybrid model of moving and rotating continua

The paper introduces the method of the model reduction of systems that experience a Coriolis acceleration or gyroscopic effect component. In such causes that corresponding system equations are non-self-adjoined. Modal reduced model is built up for the system without Coriolis or gyroscopic effect terms. These phenomena are next included by application of any lumping technique. Hence, the final reduced model is a hybrid one, obtained by both lumping and modal methods of modeling. (© 2009 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim)     

Speeds of sound and isentropic compressibilities of (2-ethoxyethanol + ethylene glycol, diethylene glycol, triethylene glycol, and tetraethylene glycol) binary mixtures at 298.15 K

The speed of sound (u) has been obtained at a frequency of 8.3 MHz in {CH₃CH₂OCH₂CH₂OH + HOCH₂CH₂(OCH₂CH₂)_nOH}for n = 0, 1, 2, and 3 over the whole composition range of studied binary liquid mixtures, at T = 298.15 K. The speed of sound values were combined with those of our previous results for densities and viscosities to obtain isentropic compressibility (κ_s), free volume (V_f), and intermolecular free length (L_f). From all these data excess isentropic compressibility (κ_s^E), excess free volume (V_f^E) and excess intermolecular free length (L_f^E) as well as the deviations of the speed of sound (Δu) were obtained. The results are interpreted in terms of molecular interactions occurring in the solutions.     

Simple physics-based analytical formulas for the potentials of mean force for the interaction of amino acid side chains in water. 3. Calculation and parameterization of the potentials of mean force of pairs of identical hydrophobic side chains

The potentials of mean force of homodimers of the molecules modeling hydrophobic amino acid side chains (ethane (for alanine), propane (for proline), isobutane (for valine), isopentane (for leucine and isoleucine), ethylbenzene (for phenylalanine), and methyl propyl sulfide (for methionine)) were determined by umbrella-sampling molecular dynamics simulations in explicit water as functions of distance and orientation. Analytical expressions consisting of the Gay-Berne term to represent effective van der Waals interactions and the cavity term derived in paper 1 of this series were fitted to the potentials of mean force. The positions and depths of the contact minima and the positions and heights of the desolvation maxima, including their dependence on the orientation of the molecules, were well represented by the analytical expressions for all systems, which justifies use of such potentials in coarse-grain protein-folding simulations.     

Nature and importance of three-body interactions in the (H2O)2HCl trimer

 The nature and importance of nonadditive three-body interactions in the (H₂O)₂HCl cluster have been studied by the supermolecule coupled-cluster method and by symmetry-adapted perturbation theory (SAPT). The convergence of the SAPT expansion was tested by comparison with the results obtained from the supermolecule coupled-cluster calculations including single, double, and noniterative triple excitations [CCSD(T)]. It is shown that the SAPT results reproduce the converged CCSD(T) results within 3% at worst. The SAPT method has been used to analyze the three-body interactions for various geometries of the (H₂O)₂HCl cluster. It is shown that the induction nonadditivity is dominant, but it is partly quenched by the first-order Heitler–London-type exchange and higher-order exchange–induction/deformation terms. This implies that the classical induction term alone is not a reliable approximation to the nonadditive energy and that it will be difficult to approximate the three-body potential for (H₂O)₂HCl by a simple analytical expression. The three-body energy represents as much as 21–27% of the pair CCSD(T) intermolecular energy. Received: 15 September 1999 / Accepted: 3 February 2000 / Published online: 2 May 2000