Interaction of chromophore, 11-<Emphasis Type="Italic">cis</Emphasis>-retinal,with amino acid residues of the visual pigment rhodopsin in the region of protonated Schiff base: A molecular dynamics study

A molecular dynamics study of the dark adapted visual pigment rhodopsin molecule was carried out. The interaction of the chromophore group, 11-cis-retinal, with the nearest amino acid residues in the chromophore center of the molecule, namely, in the region of the protonated Schiff base linkage, was analyzed. Most likely, the interaction of the CH=NH bond with the negatively charged amino acid residue Glu113 cannot be described as a simple electrostatic interaction of two oppositely charged groups. One can propose that not only Glu113 but also Glu181 and Ser186 are involved in stabilization of the protonated Schiff base linkage. Accord-ing to calculations, Glu181 interacts, as the counter-ion, with the Schiff base indirectly via Ser186. The intramolecular mechanisms of protonated Schiff base stabilization in rhodopsin are discussed. Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 1, pp. 19–27, January, 2007.     

Studies on synthesis and molecular dynamics simulation of dendrimers containing amino acids and peptides

A series of poly(ether-amide) dendrimers with amino acids and peptides as the peripheral functional groups was synthesized, and their structures were confirmed by nuclear magnetic resonance (NMR) and electrospray ionization-mass spectrometry (ESI-MS) spectrometry. Molecular dynamics simulation of the peptide dendrimers in solution was performed, indicating that, the prior conformations of the dendrimers were atom number dependent, i.e., with the increases of the atom number, the prior conformations were more spherical. Also, the amino acid α-C atom radial distribution indicated that, with larger peripheral groups, more back-folding of the dendrimers occurred. __________ Translated from Acta Chimica Sinica, 2007, 65(1): 21–26 [译自: 化学 通报]     

Protein dynamics tightly connected to the dynamics of surrounding and internal water molecules.

Proteins are key components of biological cells. For example, enzymes catalyze biochemical reactions, membrane transporters are responsible for uptake and release of critical and superfluous components from the cell environment, and structural proteins are responsible for the stability of the cell wall and cytoskeleton. Many of the diverse protein functions involve dynamic transitions ranging from small local atomic displacements up to large allosteric conformational changes. In any conformation, proteins are in contact with the universal solvent medium of cells, water. Water not only surrounds proteins but is often an integral part of proteins and also is involved in key mechanistic steps. This Minireview discusses recent experimental and theoretical results on the role of water for protein dynamics and function.     

Preparation, characterization and properties studies of quinine-imprinted polymer in the aqueous phase

The uniform-sized spherical molecularly imprinted polymers were successfully prepared through molecular imprinting technology by two-step seed swelling and mini-emulsion polymerization in the aqueous condition using quinine as template molecules and methacrylic acid (MAA) as functional monomer. The polymers were characterized by IR spectra, thermal-weight analysis, scanning electron microscope and laser particle size analysis. The properties of imprinted polymers were investigated in different organic phases and aqueous media. In the organic media, results suggested that polar interactions (hydrogen bonding, ionic interactions) between acidic monomer/polymer and template molecules are mainly responsible for the binding and recognition; whereas in the aqueous medium, a considerable recognition effect was also obtained where the ionic (electrostatic) interaction and hydrophobic interaction play an important role. The experiments of binding different substrates indicated that the MIPs possessed an excellent rebinding ability and inherent selectivity to quinine. __________ Translated from Zhongshan Dcocue Xuebao/Acta Scientianum Natralium University Sunyatseni, 2005, 44(3)(in Chinese)     

Spectroscopic constants and molecular properties of CN−, SiH−, PO−, SO−, SF−, and SiS−: Density functional study

Spectroscopic constants and molecular properties of selected diatomic anions namely CN^?, SiH^?, PO^?, SO^?, SF^?, and SiS^? in their ground states have been studied in detail using the hybrid HF/DF B3LYP method. The consistency of the calculated values has been verified with four different basis sets, with improved quality. The spectroscopic constants and molecular properties calculated with the aug‐cc‐pVTZ basis set agree very well with the experimental and theoretical values wherever available. Most of the spectroscopic constants and molecular properties of the selected diatomic anions, particularly the spectroscopic constants and molecular properties of SO^? and SiS^? are reported for the first time. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2004     

Molecular structures of benzoylbenzo-12-crown-4 and diphenylacetylbenzo-12-crown-4 and possible reasons for different conformational states of their macrocycles

The molecular structures of (benzoyl)benzo-12-crown-4 (a=22.387,b=4.503,c=16.167 Å,d _calc=1.34 g cm^–3,Z=4, space groupP2₁ nc, DAR-UM, Cu-K,R=0.056) and (diphenylacetyl)benzo-12-crown-4 (a=8.866,b=23.337,c=10.737 Å;d _calc=1.25 g cm^–3,Z=4, space groupP2₁2₁2₁, DAR-UM, Cu-K, R=0.056) have been investigated. The differences in the conformations of the macrocycles and the degree of conjugation between the benzene ring orbitals and the lone pairs on the adjacent oxygen atoms in the macrocycle are discussed.Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 11, pp. 1906–1911, November, 1993.     

Synthesis and characterization of MCM-48 tubular membranes

MCM-48 membranes have been prepared on alumina supports of different pore sizes. A battery of characterization techniques has been used to study the physical properties and the quality of the membranes prepared. The highest quality membranes were prepared on supports with pore size of up to 60 nm. The MCM-48 membranes were tested in the separation of gas phase mixtures and a cyclohexane/O₂ selectivity higher than 270 was obtained. The selective separation of organic compounds from inert components is a result of the cooperative effects of capillary condensation in MCM-48 pores and of the specific interactions of the permeating compounds and the membrane material.     

Cathodic materials for lithium-ion batteries based on spinels Li x Mn2−y Me y O4: Synthesis, phase composition, and structure of Li x Mn2−y Cr y O4 at x = 1.0−1.2 and y = 0−0.5

Extralithiated chromium-doped finely divided lithium-manganese spinels are synthesized as a result of a two-step solid-phase process with use made of the fusion-saturation method. The spinels are intended for application as cathodic materials in lithium-ion batteries. The phase composition and structural characteristics of samples of cathodic materials of the type Li _x Mn_2?y Cr _y O₄ are studied. The samples with x = 1.0?1.2 and y = 0?0.5 are characterized by phase purity and cubic syngony with parameter a = 0.817?0.823 nm and a disperseness equal to 1–2 nm. The maximum content of chromium and lithium in Li _x Mn_2?y Cr _y O₄ that does not lead to violation of cubic syngony is determined. Lithium excess in the cathodic material that does not exceed 0.2 formula units may be used for compensating the irreversible capacity. Replacing some manganese atoms by chromium may facilitate retention of the structures’s integrity in the course of cycling.     

Complete graph conjecture for inner-core electrons: homogeneous index case

The complete graph conjecture that encodes the inner-core electrons of atoms with principal quantum number n >or= 2 with complete graphs, and especially with odd complete graphs, is discussed. This conjecture is used to derive new values for the molecular connectivity and pseudoconnectivity basis indices of hydrogen-suppressed chemical pseudographs. For atoms with n = 2 the new values derived with this conjecture are coincident with the old ones. The modeling ability of the new homogeneous basis indices, and of the higher-order terms, is tested and compared with previous modeling studies, which are centered on basis indices that are either based on quantum concepts or partially based on this new conjecture for the inner-core electrons. Two similar algorithms have been proposed with this conjecture, and they parallel the two "quantum" algorithms put forward by molecular connectivity for atoms with n > 2. Nine properties of five classes of compounds have been tested: the molecular polarizabilities of a class of organic compounds, the dipole moment, molar refraction, boiling points, ionization energies, and parachor of a series of halomethanes, the lattice enthalpy of metal halides, the rates of hydrogen abstraction of chlorofluorocarbons, and the pED(50) of phenylalkylamines. The two tested algorithms based on the odd complete graph conjecture give rise to a highly interesting model of the nine properties, and three of them can even be modeled by the same set of basis indices. Interesting is the role of some basis indices all along the model.