Conserving energy during molecular dynamics simulations of water,proteins, and proteins in water

Molecular dynamics simulations have been carried out for a series of systems of increasing complexity including: pure water, a model polypeptide (α-helical decaglycine) in vacuo, a protein (Pancreatic Trypsin Inhibitor, PTI) in vacuo, and a fully solvated protein (PTI in water). The equations of motion were integrated using Andersen's velocity version of the Verlet algorithm with internal contraints (the RATTLE algorithm). The accuracy with which the equations of motion are integrated has been analyzed for several different simulation conditions. The effects of various nonbonded interaction truncation schemes on the conservation of energy have been examined, including the use of atomic cutoffs, and (neutral group) residue cutoffs. The use of a smoothing function to eliminate the discontinuities in the potential at the cutoff leads to a significant improvement in the accuracy of the integration for each of the systems studied. The accuracy with which the equations of motion are integrated using the RATTLE algorithm for pure water and for the solvated protein are found to be comparable when the nonbonded interactions are tapered with a smoothing function at the cutoff.     

PHOTOCHEMISTRY OF RETINOCHROME

Abstract— Retinochrome is a photopigment found in the visual cells of cephalopods. It has been considered to act as a supplier of the 11- cis -retinal required for synthesis of rhodopsin, because its all-trans chromophore is isomerized to 11- cis form in the light. Light and thermal reactions of squid retinochrome were investigated by low-temperature spectrophotometry.
On irradiation with green light at liquid-nitrogen temperature, retinochrome (λ_max 496 nm, – 190°C) is converted mainly to an intermediate lumiretinochrome (λ_max 475 nm, – 190°C), its chromophore being changed to 11- cis -retinal. On irradiation with blue light at - 190°C, retinochrome is changed to a photosteady–state mixture (λ_max 487 nm, – 190°C) composed mainly of retinochrome and lumiretinochrome, since lumiretinochrome is partially regenerated back to retinochrome. Similarly, irradiation of lumiretinochrome with blue light also results in the same photosteady-state mixture, which can be completely reverted to lumiretinochrome on re-irradiation with green light.
Lumiretinochrome is stable at a wide range of temperatures from – 190°C to about – 20°C. Above – 20°C, it is further converted, thermally, into metaretinochrome (λ_max 470 nm), which is the same bleached product as has been observed on irradiation of retinochrome at room temperatures. Thus, the light-bleaching process of retinochrome is rather simple compared with that of rhodopsin.     

Characteristics of Diffraction Gratings Fabricated by the Two-Beam Interference Method Using Photosensitive Hybrid Gel Films

Diffraction gratings of arbitrary periods have been fabricated by the two-beam interference method using photosensitive ZrO₂ gel films and characterized. The ZrO₂ gel films were formed on Si or silica glass substrates from sols that were derived from Zr-butoxide modified chemically with benzoylacetone. The gel films were irradiated with two interference beams from a He-Cd laser (325 nm) and then leached in ethyl alcohol. The above process gave uniform surface-relief gratings of periods ranging from 1.0 to 0.5 m, depending on the incidence angle of the interference beams. The diffraction efficiency, measured in the Littrow configuration using a He-Ne laser (633 nm), showed polarization dependence for the grating of 0.5 m period but not for the gratings of 1.0 m period. The maximum diffraction efficiency was 18% for the grating of 1.0 m period and 28% for that of 0.5 m period in the reflection mode. The present study has proved that the photosensitive gel films are versatile in fabrication of optical devices.     

N-Tosylaziridine, a new substrate for chemical fixation of carbon dioxide via ring expansion reaction under atmospheric pressure

N-Tosylaziridine was found to be a useful substrate for cycloaddition reaction with carbon dioxide. The reaction was successfully catalyzed by lithium bromide under atmospheric pressure to give the corresponding five-membered cyclic urethane, N-tosyl-1,3-oxazolidin-2-one, selectively. It was found that electron-donating nature of the substituent at 2-position of N-tosylaziridine accelerated the reaction, and this tendency allowed us to estimate the reaction mechanism.     

Volume changes accompanying the stepwise complex formation in aqueous solutions for the case of Cu2+ and Zn2+ with the ligand bipyridine and phenanthroline

The volume changes for each step in the successive complex formation between the metal ions Cu²⁺ and Zn²⁺ with the ligand L, where L is bpy = 2,2-bipyridine and phen = 1,10-phenanthroline, in water have been determined at 25°C in the following way: Aqueous solution of M(NO₃)₂ has been taken as solvent and the densities of solutions have been measured at various ratio of [ligand]/[M²⁺]. The partial molar volumes V ₂ ⁰ have been calculated for the nitrates of the complex ions [ML]²⁺, [ML₂]²⁺, and [ML₃]²⁺. The volume change V is given as V=V ₂ ⁰ ([ML _n+1](NO₃)₂)–V ₂ ⁰ ([ML _n ](NO₃)₂)–V ₂ ⁰ (L). Volume changes of the first coordination of L to M²⁺ are larger than the other two steps and the third step coordination leads to small or even negative values of V.     

Host-guest sensory system of sodium anthranilate-modifiedβ-cyclodextrin: Molecular recognition properties

Sodium anthranilate-modified-cyclodextrin (1) has been prepared as a sensor for detecting organic compounds including terpenoids and steroids.1 shows a pure monomer fluorescence whose intensity is increased or decreased upon addition of the guest species examined. In this system, the sodium anthranilate moiety acts either as a spacer, which enables the cyclodextrin to form a 11 guest complex by narrowing the-cyclodextrin cavity or acts as a hydrophobic cap.1 shows a higher sensitivity for terpenoids than for steroids, but has a higher selective molecular recognition ablity for steroids than for terpenoids.     

Inclusion compounds of N,N,N′,N′-tetracyclohexylfumaride with isomers of cresol and water

The crystal structures and thermal analyses of the host compound, N,N,N,N-tetracyclohexylfumaride, witho-cresol,p-cresol and water are reported and compared to that of them-cresol complex previously reported in an attempt to elucidate the reasons for host selectivity.     

Magnetic properties of R2Fe17−xGax (R=Y and Gd) compounds

The magnetic properties of Y₂Fe_17−xGa_x for 3≤x≤7 and Gd₂Fe_17−xGa_x for 5≤x≤7 have been investigated using ⁵⁷Fe Mössbauer spectroscopy. These compounds have the rhombohedral Th₂Zn₁₇ structure. X-ray diffraction analysis of aligned powders shows that the easy direction of magnetization is parallel to the c-axis in Y₂Fe₁₀Ga₇ and Gd₂Fe₁₀Ga₇ and is perpendicular to the c-axis in Y₂Fe₁₄Ga₃, Y₂Fe₁₂Ga₅, Gd₂Fe₁₂Ga₅ and Gd₂Fe₁₁Ga₆. Mössbauer studies indicate that those samples are ordered ferromagnetically. The ⁵⁷Fe hyperfine field decreases with increasing Ga content. This decrease results from the decreased magnetic exchange interactions resulting from Ga substitution. The average isomer shift, δ, for R₂Fe_17−xGa_x (R=Y and Gd) at room temperature is positive and the magnitude of δ increases with increasing Ga content.     

Synthesis and properties of conjugated polymers containing 3,9‐ and 2,9‐linked carbazole units in the main chain

Novel conjugated polymers containing 3,9‐ or 2,9‐linked carbazole units in the main chain were synthesized by the polycondensation of ethynyl‐ and iodo‐substituted 9‐arylenecarbazolylene monomers, and their optical and electrical properties were studied. Polymers with weight‐average molecular weights of 3400–12,000 were obtained in 76–99% yields by the Sonogashira coupling polycondensation in piperidine or tetrahydrofuran (THF)/piperidine at 30 °C for 48 h. All the 3,9‐linked polymers absorbed light around 300 nm. The para‐phenylene‐linked polymer also absorbed light around 350 nm, while meta‐phenylene‐linked one did not. The 3,9‐linked polymers absorbed light at a wavelength longer than the 2,9‐linked one. The polymers emitted blue fluorescence with high quantum yields (0.21–0.78) upon excitation at the absorption maxima. The polymers were oxidized around 0.6 V, and reduced around 0.5 V. Poly( 1 ) showed the dark conductivity of 3.7 × 10^?11 S/cm (10³ V/cm). © 2009 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 47: 3506–3517, 2009     

Effects of strain field in nitrogen-mediated Co film growth on Cu(0 0 1): Segregation and electronic structure change

Growth modes of Co thin films on the both N-saturated and partially N-adsorbed Cu(0 0 1) surfaces are studied in detail. From results of the STM and XPS measurements, segregation of N atoms depending on the Co island size is concluded. This new type of atom segregation is explained by means of a lattice strain of the substrate due to the small Co island formation. A novel core-level shift of N 1s during the Co film growth is also reported. A possible influence of the lattice strain to the electronic structure of the surfactant is discussed.