Reduced variable molecular dynamics

This article describes an extension to previously developed constraint techniques. These enhanced constraint methods will enable the study of large computational chemistry problems that cannot be easily handled with current constrained molecular dynamics (MD) methods. These methods are based on an O(N) solution to the constrained equations of motion. The benefits of this approach are that (1) the system constraints are solved exactly at each time step, (2) the solution algorithm is noniterative, (3) the algorithm is recursive and scales as O(N), (4) the algorithm is numerically stable, (5) the algorithm is highly amenable to parallel processing, and (6) potentially greater integration step sizes are possible. It is anticipated that application of this methodology will provide a 10- to 100-improvement in the speed of a large molecular trajectory as compared with the time required to run a conventional atomistic unconstrained simulation. It is, therefore, anticipated that this methodology will provide an enabling capacity for pursuing the drug discovery process for large molecular systems. © 1995 John Wiley & Sons, Inc.     

Reduced Arene Complexes of Scandium

Alkali metal naphthalenide or anthracenide reacted with scandium(III) anilides [Sc(X){N(tBu)Xy}₂(thf)] (X=N(tBu)Xy ( 1 ); X=Cl ( 2 ); Xy=C₆H₃-3,5-Me₂) to give scandium complexes [M(thf)_n][Sc{N(tBu)Xy}₂(RA)] (M=Li–K; n=1–6; RA=C₁₀H₈²⁻ ( 3-Naph-K ) and C₁₄H₁₀²⁻ ( 3-Anth-M )) containing a reduced arene ligand. Single-crystal X-ray diffraction revealed the scandium(III) center bonded to the naphthalene dianion in a σ²:π-coordination mode, whereas the anthracene dianion is symmetrically attached to the scandium(III) center in a σ²-fashion. All compounds have been characterized by multinuclear, including ⁴⁵Sc NMR spectroscopy. Quantum chemical calculations of these intensely colored arene complexes confirm scandium to be in the oxidation state +3. The intense absorptions observed in the UV/Vis spectra are due to ligand-to-metal charge transfers. Whereas nitriles underwent C−C coupling reaction with the reduced arene ligand, the reaction with one equivalent of [NEt₃H][BPh₄] led to the mono-protonation of the reduced arene ligand.     

Reduced protein adsorption by osmolytes

Osmolytes are substances that affect osmosis and are used by cells to adapt to environmental stress. Here, we report a neutron reflectivity study on the influence of some osmolytes on protein adsorption at solid-liquid interfaces. Bovine ribonuclease A (RNase) and bovine insulin were used as model proteins adsorbing at a hydrophilic silica and at a hydrophobic polystyrene surface. From the neutron reflectivity data, the adsorbed protein layers were characterized in terms of layer thickness, protein packing density, and adsorbed protein mass in the absence and presence of urea, trehalose, sucrose, and glycerol. All data point to the clear effect of these nonionic cosolvents on the degree of protein adsorption. For example, 1 M sucrose leads to a reduction of the adsorbed amount of RNase by 39% on a silica surface and by 71% on a polystyrene surface. Trehalose was found to exhibit activity similar to that of sucrose. The changes in adsorbed protein mass can be attributed to a decreased packing density of the proteins in the adsorbed layers. Moreover, we investigated insulin adsorption at a hydrophobic surface in the absence and presence of glycerol. The degree of insulin adsorption is decreased by even 80% in the presence of 4 M of glycerol. The results of this study demonstrate that nonionic cosolvents can be used to tune and control nonspecific protein adsorption at aqueous-solid interfaces, which might be relevant for biomedical applications.     

Alcohol Oxidations Using Reduced Polyoxovanadates

A full account of our recently communicated room temperature alcohol oxidation using reduced polyoxovanadates (r‐POV s) is presented. Extensive optimizations revealed optimal conditions employing 0.02 equiv. of r‐POV catalyst Cs₅(V₁₄As₈O₄₂Cl), 5 equiv. tert‐butyl hydrogen peroxide (^t BuOOH ) as the terminal co‐oxidant, in an acetone solvent for the quantitative oxidation of aryl‐substituted secondary alcohols to their ketone products. The substrate scope tolerates most aryl substituted secondary alcohols in good to quantitative yields while alkyl secondary and primary activated alcohols were sluggish in comparison under similar conditions. Catalyst recyclability was successful on a 1.0 mmol scale of starting alcohol 1‐phenylethanol. The oxidation was also successfully promoted by the V^IV /V^V mixed valent polyoxovanadate (POV ) Cs₁₁Na₃Cl₅(V₁₅O₃₆Cl). Finally, a third POV , Cs_2.64(V₅O₉)(AsO₄)₂, was investigated for catalytic activity using our established reaction protocol, but proved ineffective as compared to the other two r‐POV catalysts. This study expands the field of POM ‐mediated alcohol oxidations to include underexplored r‐POV catalysts. While our catalysts do not supplant the best catalysts known for the transformation, their study may inform the development of other novel oxidative transformations mediated by r‐POV s.     

Reduced parabolic model for radical addition reactions

The transition state of addition of free radicals and atoms to multiple bonds is considered as a result of intersecting of two parabolic potential curves. One of them characterizes the stretching vibration of the attacked multiple bond, and another curve characterizes the stretching vibration of the bond formed in the transition state. The force constant of the latter is calculated by an empirical equation that correlates the force constant with the bond dissociation energy. In the framework of this model, the thermally neutral activation energy (E _e0) and the elongation of the attacked and formed bonds (r _e) in the transition state were calculated from the experimental data (activation energy (E _e) and enthalpy of reaction (H _e)) for the addition of an H atom and methyl, alkoxyl, aminyl, triethylsilyl, and peroxyl radicals to the C=C bond and the addition of H and CH₃ to the C=O and CC bonds. Analysis of the data obtained showed that E _e0 depends linearly on the |H _e| + E_e sum, i.e., E_e0/kJ mol^–1 = 14.2 + 0.61 · (E_e – H _e), and the bond elongation in the transition state for addition of the most part of radicals to ethylene and acetylene vary within (0.65–0.87)·10_–10 m. The factors affecting the activation energy of the radical addition reactions are discussed.Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 8, pp. 1542–August, 2004.     

Reduced Overlap Population Analysis for Triosmium Clusters

The use of reduced overlap population (ROP) analysis from EHMO calculations as a means to gauge the presence of metal–metal bonds in triosmium clusters is examined. A number of triosmium clusters containing bridging ligands have been used as test cases, including the bis-ethoxy bridged cluster Os₃(μ-OEt)₂(CO)₁₀, 1b, and some of its group 15 derivatives Os₃(μ-OEt)₂(CO)₉(EPh₃), 2. These latter clusters are newly synthesized and have been characterized completely, including by single-crystal X-ray crystallographic studies. In honour of Professor Dieter Fenske on his 65th birthday.     

Reduced metabolites of 18-hydroxy-11-deoxycorticosterone

Conditions are described for the preparation of the dihydro (2 and 6) and tetrahydro derivatives (3, 5 and 7) of 18-hydroxy-11-deoxycortisterone (1a) by microbial transformations using Clostridium parapurificum and chemical methods. The products were fully characterized and degraded into their respective 20 → 18 etiolactones. Microbial and chemical reductions of the Δ⁴-3-ketolactone 8 are presented.     

Macrocyclic Protease Inhibitors with Reduced Peptide Character

There is a real need for simple structures that define a β‐strand conformation, a secondary structure that is central to peptide–protein interactions. For example, protease substrates and inhibitors almost universally adopt this geometry on active site binding. A planar pyrrole is used to replace two amino acids of a peptide backbone to generate a simple macrocycle that retains the required geometry for active site binding. The resulting β‐strand templates have reduced peptide character and provide potent protease inhibitors with the attachment of an appropriate amino aldehyde to the C‐terminus. Picomolar inhibitors of cathepsin L and S are reported and the mode of binding of one example to the model protease chymotrypsin is defined by X‐ray crystallography.     

A Reduced SNARE Model for Membrane Fusion

Let's get together : A minimal model system was developed to mimic the SNARE‐protein‐mediated fusion of biological membranes (see picture). Fusion between two populations of liposomes is controlled by a pair of complementary lipidated oligopeptides that form noncovalent coiled‐coil complexes and thereby force the membranes into close proximity to promote fusion. The model system displays the key characteristics of in vivo fusion events.

     

Reduced fluorescence quenching of cyclodextrin-acetylene dye rotaxanes

An acetylene dye rotaxane with alpha-CD has been synthesized using the Heck-Cassar-Sonogashira-Hagihara-type reaction in aqueous solution. Free dye with tetracarboxylic acids is found to be highly sensitive to various metal ions, showing high Stern-Volmer constants, KSV. As CD encapsulation protects and stabilizes the threaded chromophore against an outside quencher, metal-insensitive biological tags are an obvious application for this class of molecules.     

Reduced OFF-axis haze in polymer-dispersed liquid crystals

Polymer-dispersed liquid crystals (PDLCs) are composite materials formed by micron-sized droplets of liquid crystals (LCs) dispersed in a polymer matrix, which can be turned from an opaque state to a transparent one by application of a suitable electric field. PDLCs have been proposed in applications related to the control of light transmittance on large surfaces (light shutters, displays, rear mirrors). Despite several advantages, PDLCs’ main drawback is haze, i.e. the fast decay of transmission at large viewing angles. In this paper, a method for achieving highly transparent PDLC devices over a wide range of viewing angles is proposed. The method is based on the use of PDLCs with tilted elongated LC droplets and driven by opportune electric fields, which are experimentally calculated and able to ensure an almost constant value for OFF-axis transmittance.     

Reduced zirconium halide clusters in aqueous solution

Reduced hexazirconium halide cluster compounds have good solubility and stability in strongly acidic and/or halide-rich aqueous solutions. Cyclic voltammetric (CV) measurements in aqueous media established that [(Zr6BCl12)(H2O)6]2+/+ and [(Zr6BBr12)(H2O)6]2+/+ exhibited positive half-wave potentials (E1/2 = 0.059V and 0.160 V, respectively) vs the SHE, indicating that these clusters are only modestly reducing. Several new crystalline cluster compounds have been isolated from cold 12 M HCl solutions; the structures of each contain extended hydrogen-bonding water networks. Crystallographic data for these compounds are reported as follows: [Rb0.44(H3O)4.56][(Zr6BCl12)Cl6].19.44H2O (3), cubic, Im3m, a = 13.8962(3) A, Z = 2; (H3O)5[(Zr6BeCl12)Cl6].19H2O (4), cubic, Im3m, a = 13.8956(4) A, Z = 2; (H3O)5[(Zr6MnCl12)Cl6].19H2O (5), cubic, Im3m, a = 14.029(3) A, Z = 2; (H3O)4[(Zr6BCl12)Cl6].12.97H2O (6), tetragonal, P4(2)/mnm, a = 11.5373(2) A, c = 15.7169(4) A, Z = 2; (H3O)4[(Zr6BCl2)Br6].13.13H2O (7), tetragonal, P4(2)/mnm, a = 11.7288(6) A, c = 15.931(1) A, Z = 2.     

RedMD—Reduced molecular dynamics package

We developed a software package (RedMD) to perform molecular dynamics simulations and normal mode analysis of reduced models of proteins, nucleic acids, and their complexes. With RedMD one can perform molecular dynamics simulations in a microcanonical ensemble, with Berendsen and Langevin thermostats, and with Brownian dynamics. We provide force field and topology generators which are based on the one‐bead per residue/nucleotide elastic network model and its extensions. The user can change the force field parameters with the command line options that are passed to generators. Also, the generators can be modified, for example, to add new potential energy functions. Normal mode analysis tool is available for elastic or anisotropic network models. The program is written in C and C++ languages and the structure/topology of a molecule is based on an XML format. OpenMP technology for shared‐memory architectures was used for code parallelization. The code is distributed under GNU public licence and available at http://bionano.icm.edu.pl/software/ . © 2009 Wiley Periodicals, Inc. J Comput Chem, 2009     

Determination of Explosives Using Electrochemically Reduced Graphene

A graphene‐based electrochemical sensing platform for sensitive determination of explosive nitroaromatic compounds (NACs) was constructed by means of electrochemical reduction of graphene oxide (GO) on a glassy carbon electrode (GCE). The electrochemically reduced graphene (ER‐GO) adhered strongly onto the GCE surface with a wrinkled morphology that showed a large active surface area. 2,4‐Dinitrotoluene (2,4‐DNT), as a model analyte, was detected by using stripping voltammetry, which gave a low detection limit of 42 nmol L⁻¹ (signal‐to‐noise ratio=3) and a wide linear range from 5.49×10⁻⁷ to 1.1×10⁻⁵ M . Further characterizations by electrochemistry, IR, and Raman spectra confirmed that the greatly improved electrochemical reduction signal of DNT on the ER‐GO‐modified GC electrode could be ascribed to the excellent electrocatalytic activity and high surface‐area‐to‐volume ratio of graphene, and the strong π–π stacking interactions between 2,4‐DNT and the graphene surface. Other explosive nitroaromatic compounds including 1,3‐dinitrobenzene (1,3‐DNB), 2,4,6‐trinitrotoluene (TNT), and 1,3,5‐trinitrobenzene (TNB) could also be detected on the ER‐GO‐modified GC electrode at the nM level. Experimental results showed that electrochemical reduction of GO on the GC electrode was a fast, simple, and controllable method for the construction of a graphene‐modified electrode for sensing NACs and other sensing applications.     

Reduced density operators and the N-particle problem

An historical review of the theory of reduced density operators is given emphasizing the key role of the second order reduced matrix and related new concepts for understanding systems of many interacting fermions.     

Reduced percolation thresholds of immiscible conductive blends

The DC conductivity of polymer blends composed of poly(ethylene‐co‐vinyl acetate) (EVA) and high density polyethylene (HDPE), where a conductive carbon black (CB) had been preferentially blended into the HDPE, were investigated to establish the percolation characteristics. The blends exhibited reduced percolation thresholds and enhanced conductivities above that of the individually carbon filled HDPE and EVA. The percolation threshold of the EVA/HDPE/CB composites was between 3.6 and 4.2 wt % carbon black, where the volume resistivity changed by 8 orders of magnitude. This threshold is at a significantly lower carbon content than the individually filled HDPE or EVA. At a carbon black loading of 4.8 wt %, the EVA/HDPE/CB composite exhibits a volume resistivity which is approximately 14 and 11 orders of magnitude lower than the HDPE/CB and EVA/CB systems, respectively, at the same level of incorporated carbon black. The dielectric response of the ternary composites, at a temperature of 23°C and frequency of 1 kHz, exhibited an abrupt increase of ca. 252% at a carbon concentration of 4.8 wt %, suggesting that the percolation threshold is somewhat higher than the range predicted from DC conductivity measurements. Percolating composites with increasing levels of carbon black exhibit significantly greater relative permittivity and dielectric loss factors, with the composite containing 6 wt % of carbon black having a value of ϵ′ ≈ 79 and ϵ″ ≈ 14. © 1999 John Wiley & Sons, Inc. J Polym Sci B: Polym Phys 37: 1899–1910, 1999     

热动力学对比参量法 --简单级数反应

根据化学反应动力学和热动力学基本理论, 建立了简单级数反应的热动力学对比参量方程, 提出了一种新的热动力学研究法--对比参量法. 利用该法可以从一张热谱图上同时解析出化学反应的速率常数、半衰期和热动力学体系的冷却常数. 实验结果验证了方法的正确性.     

约化密度矩阵中的N表示问题

利用准自旋-辛群对称性基函数及Kummer提出的构造暴露算子法研究了量子化学中密度矩阵N表示理论的端点问题,找出了更多的二阶约化密度矩阵凸集的端点.