Simulation studies of the protein-water interface. I. Properties at the molecular resolution

We report molecular dynamics simulations of three globular proteins: ubiquitin, apo-calbindin D(9K), and the C-terminal SH2 domain of phospholipase C-gamma1 in explicit water. The proteins differ in their overall charge and fold type and were chosen to represent to some degree the structural variability found in medium-sized proteins. The length of each simulation was at least 15 ns, and larger than usual solvent boxes were used. We computed radial distribution functions, as well as orientational correlation functions about the surface residues. Two solvent shells could be clearly discerned about charged and polar amino acids. Near apolar amino acids the water density near such residues was almost devoid of structure. The mean residence time of water molecules was determined for water shells about the full protein, as well as for water layers about individual amino acids. In the dynamic properties, two solvent shells could be characterized as well. However, by comparison to simulations of pure water it could be shown that the influence of the protein reaches beyond 6 A, i.e., beyond the first two shells. In the first shell (r < or =3.5 A), the structural and dynamical properties of solvent waters varied considerably and depended primarily on the physicochemical properties of the closest amino acid side chain, with which the waters interact. By contrast, the solvent properties seem not to depend on the specifics of the protein studied (such as the net charge) or on the secondary structure element in which an amino acid is located. While differing considerably from the neat liquid, the properties of waters in the second solvation shell (3.5< r < or =6 A) are rather uniform; a direct influence from surface amino acids are already mostly shielded.     

Towards the Expression of Sex Hormone Receptors in the Human Vocal Fold

BACKGROUND: The human larynx is assumed to be a steroid receptor target organ. There are only very limited data on the evidence of steroid receptors in the vocal folds, although voice alterations due to hormonal influence and treatment have been found. GOAL OF THE STUDY: To investigate the expression of estrogen alpha, progesterone, and androgen receptors in human vocal folds (vocalis muscle, glands, lamina propria, epithelium). METHODS: Immunohistochemically, vocal fold cadaver specimens of 15 autopsied patients (6 women, 9 men), which were taken approximately 4 to 8 hours postmortem were investigated. Furthermore, one (male) vocal fold biopsy obtained intraoperatively during a laryngectomy was tested. RESULTS: No specific immunohistochemical staining for the different types of steroid hormones investigated could be observed in either the postmortem taken biopsies nor the intraoperatively one. However, several unspecific staining patterns could be observed. CONCLUSION: The results of this study contradict recently published data and question the expression of sex hormone receptors in the vocal folds. Main causes of false interpretations of unspecific staining are discussed.     

On the collective network of ionic liquid/water mixtures. I. Orientational structure

In this work, the collective structure of aqueous solutions of ionic liquids was studied by means of molecular dynamics simulations. Various concentrations of 1-butyl-3-methyl-imidazolium tetrafluoroborate and TIP3P water were simulated at the very same size of the simulation box. For the analysis, the ternary system cation/anion/water was subdivided into binary networks. The local structure of each of these six networks is investigated by atom-atom radial distribution functions as well as by the so-called g coefficients, which reveal the mutual orientation of the network constituting partners. Furthermore, the collective structure of the whole samples was characterized by the contribution of each species to the static dielectric constant epsilon(omega=0) and to the Kirkwood G(K) factor. The combination of the analysis tools mentioned above provides knowledge about the cross-linking of the ionic species with the dipolar water. Thereby, the interplay between charge-charge and hydrogen bond networks is analyzed in detail.     

Relational models for contingency tables

The paper considers general multiplicative models for complete and incomplete contingency tables that generalize log-linear and several other models and are entirely coordinate free. Sufficient conditions for the existence of maximum likelihood estimates under these models are given, and it is shown that the usual equivalence between multinomial and Poisson likelihoods holds if and only if an overall effect is present in the model. If such an effect is not assumed, the model becomes a curved exponential family and a related mixed parameterization is given that relies on non-homogeneous odds ratios. Several examples are presented to illustrate the properties and use of such models.     

Rényi 100, Quantitative and qualitative (in)dependence

We discuss recent developments in the following important areas of Alfréd Rényi’s research interest: axiomatization of quantitative dependence measures, qualitative independence in combinatorics, conditional qualitative independence in statistics/data science and in measure theory/probability theory, and finally, prime gaps that are responsible for Rényi’s early career reputation. Most authors of this paper are main contributors to the new developments.

     

Cyclometalated Mono‐ and Dinuclear IrIII Complexes with “Click”‐Derived Triazoles and Mesoionic Carbenes

Orthometalation at Ir^III centers is usually facile, and such orthometalated complexes often display intriguing electronic and catalytic properties. By using a central phenyl ring as C?H activation sites, we present here mono‐ and dinuclear Ir^III complexes with “click”‐derived 1,2,3‐triazole and 1,2,3‐triazol‐5‐ylidene ligands, in which the wingtip phenyl groups in the aforementioned ligands are additionally orthometalated and bind as carbanionic donors to the Ir^III centers. Structural characterization of the complexes reveal a piano stool‐type of coordination around the metal centers with the “click”‐derived ligands bound either with C^N or C^C donor sets to the Ir^III centers. Furthermore, whereas bond localization is observed within the 1,2,3‐triazole ligands, a more delocalized situation is found in their 1,2,3‐triazol‐5‐ylidene counterparts. All complexes were subjected to catalytic tests for the transfer hydrogenation of benzaldehyde and acetophenone. The dinuclear complexes turned out to be more active than their mononuclear counterparts. We present here the first examples of stable, isomer‐pure, dinuclear cyclometalated Ir^III complexes with poly‐mesoionic‐carbene ligands.     

RuII,OsII, and IrIII Complexes with Chelating Pyridyl–Mesoionic Carbene Ligands: Structural Characterization and Applications in Transfer Hydrogenation Catalysis

Chelating ligands with one pyridine donor and one mesoionic carbene donor are fast establishing themselves as privileged ligands in homogeneous catalysis. The synthesis of several new Ir^III–Cp*‐ and Os^II–Cym complexes (Cp*=pentamethylcyclopentadienyl, Cym=p‐cymene=4‐isopropyl‐toluene) derived from chelating pyridyltriazolylidenes where the additional pyridine donor was incorporated via the azide part of the triazole is presented. Furthermore, different 4‐substituted phenylacetylene building blocks have been used to introduce electronic fine‐tuning in the ligands. The ligands thus can be generally described as 4‐(4‐R‐phenyl)‐3‐methyl‐1‐(pyridin‐2‐yl)‐1H‐1,2,3‐triazol‐5‐ylidene (with R being H (L¹), Me (L²), OMe (L³), CN (L⁴), CF₃ (L⁵), Br (L⁶) or NO₂ (L⁷)). The corresponding complexes (Ir‐ 1 to Ir‐ 7 and Os‐ 1 to Os‐ 7 ) were characterized by standard spectroscopic methods, and the expected three‐legged, piano‐stool type coordination was unambiguously confirmed by X‐ray diffraction analysis of selected compounds. Together with Ru^II analogues previously reported by us, a total of 21 complexes were tested as (pre)catalysts for the transfer hydrogenation of carbonyl groups, showing a remarkable reactivity even at very low catalyst loadings. The electronic effects of the ligands as well as different substrates were investigated. Some mechanistic elucidations are also presented.     

Random trees and general branching processes

We consider a tree that grows randomly in time. Each time a new vertex appears, it chooses exactly one of the existing vertices and attaches to it. The probability that the new vertex chooses vertex x is proportional to w(deg(x)), a weight function of the actual degree of x. The weight function w : ℕ → ℝ₊ is the parameter of the model. In 4 and 11 the authors derive the asymptotic degree distribution for a model that is equivalent to the special case, when the weight function is linear. The proof therein strongly relies on the linear choice of w. Using well‐established results from the theory of general branching processes we give the asymptotical degree distribution for a wide range of weight functions. Moreover, we provide the asymptotic distribution of the tree itself as seen from a randomly selected vertex. The latter approach gives greater insight to the limiting structure of the tree. Our proof is robust and we believe that the method may be used to answer several other questions related to the model. It relies on the fact that considering the evolution of the random tree in continuous time, the process may be viewed as a general branching process, this way classical results can be applied. © 2006 Wiley Periodicals, Inc. Random Struct. Alg., 2007     

Elektrometrie

Ohne Zusammenfassung     

Simulation studies of ionic liquids: orientational correlations and static dielectric properties

The ionic liquids BMIM+I-, BMIM+BF4-, and BMIM+PF6- were simulated by means of the molecular dynamics method over a time period of more than 100 ns. Besides the common structural analysis, e.g., radial distribution functions and three dimensional occupancy plots, a more sophisticated orientational analysis was performed. The angular correlation functions g(00)110(r) and g(00)101(r) are the first distance dependent coefficients of the pairwise orientational distribution function g(rij,Omega1,Omega2,Omega12). These functions help to interpret the three dimensional plot and reveal interesting insights into the local structure of the analyzed ionic liquids. Furthermore, the collective network of ionic liquids can be characterized by the Kirkwood factor Gkappa(r) [J. Chem. Phys. 7, 911 (1939)]. The short-range behavior (r<10 A) of this factor may be suitable to predict the water miscibility of the ionic liquid. The long-range limit of Gkinfinity is below 1 which demonstrates the strongly coupled nature of the ionic liquid networks. In addition, this factor relates the orientational structure and the dielectric properties of the ionic liquids. The static dielectric constant epsilon(omega=0) for the simulated system is 8.9-9.5. Since in ionic liquids the very same molecule contributes to the total dipole moment as well as carries a net charge, a small, but significant contribution of the cross term between the total dipole moment and the electric current to epsilon(omega=0) is observed.