Parameterization of a reactive force field using a Monte Carlo algorithm

Parameterization of a molecular dynamics force field is essential in realistically modeling the physicochemical processes involved in a molecular system. This step is often challenging when the equations involved in describing the force field are complicated as well as when the parameters are mostly empirical. ReaxFF is one such reactive force field which uses hundreds of parameters to describe the interactions between atoms. The optimization of the parameters in ReaxFF is done such that the properties predicted by ReaxFF matches with a set of quantum chemical or experimental data. Usually, the optimization of the parameters is done by an inefficient single‐parameter parabolic‐search algorithm. In this study, we use a robust metropolis Monte‐Carlo algorithm with simulated annealing to search for the optimum parameters for the ReaxFF force field in a high‐dimensional parameter space. The optimization is done against a set of quantum chemical data for MgSO₄ hydrates. The optimized force field reproduced the chemical structures, the equations of state, and the water binding curves of MgSO₄ hydrates. The transferability test of the ReaxFF force field shows the extend of transferability for a particular molecular system. This study points out that the ReaxFF force field is not indefinitely transferable. © 2013 Wiley Periodicals, Inc.     

Development of glycyl radical parameters for the OPLS-AA/L force field

On the basis of quantum chemical calculations C(alpha)-glycyl radical parameters have been developed for the OPLS-AA/L force field. The molecular mechanics hypersurface was fitted to the calculated quantum chemical surface by minimizing their molecular mechanics parameter dependent sum-of-squares deviations. To do this, a computer program in which the molecular mechanics energy derivatives with respect to the parameters were calculated analytically was developed, implementing the general method of Lifson and Warshel (J Chem Phys 1968, 49, 5116) for force field parameter optimization. This program, in principle, can determine the optimal parameter set in one calculation if enough representative value points on the quantum chemical potential energy surface are available and there is no linear dependency between the parameters. Some of the parameters in quantum calculations, including several new torsion types around a bond as well as angle parameters at a new central atom type, are not completely separable. Consequently, some restrictions and/or presumptions were necessary during parameter optimization. The relative OPLS-AA energies reproduced those calculated quantum chemically almost perfectly.     

Optical diffusers based on uniform nano-sized polymer balls/nematic liquid crystals composite films

ABSTRACT

Optical diffusers are promising diffusing materials in the optical devices such as monitors, projectors, fibre optics, light-emitting diode (LED) systems and liquid crystal displays (LCDs). We report optical diffusers comprising uniformly distributed nano-sized polymer balls/nematic liquid crystals (LCs) by ultraviolet (UV) click reaction of ene monomer and thiol monomer. By optimising the mass ratio 1:1 of ene and thiol, of which the average diameter of the corresponding nano-sized polymer balls is about 900 nm, relatively high optical transmission and haze with 88.99% and 94.49% are yielded, respectively. Furthermore, by controlling the curing time, the average diameter of nano-sized polymer balls can be reduced to 810 nm, and the developed film exhibits high transmission (98.49%) without sacrificing the high haze (91.77%). This paper demonstrates that UV click reaction is an economical approach to fabricate optical diffusers in a controllable manner.     

Automatic polarographic elucidation of electrode mechanisms by means of a knowledge-based system : Part 1. Sampled d.c. polarography

A knowledge-based system has been developed for the automatic elucidation of electrochemical mechanisms. The system is based on sampled direct current (or Tast) polarography at a dropping mercury electrode as a technique for collecting experimental information and consists of a general expert system shell for the reasoning process, the specific set of rules and experimental modules. The set of rules allows the elucidation of eight relatively simple electrode reaction mechanisms fully atomatically. The computer system has been validated with chemical systems the electrochemical behaviour of which is well established. All parts of the program are written in FORTH language for Apple II microcomputers. This expert system has an open character and new rules can be added to extend the set of mechanisms that can be determined.     

Probabilistic assessment of biodegradability based on metabolic pathways: CATABOL System

A novel mechanistic modeling approach has been developed that assesses chemical biodegradability in a quantitative manner. It is an expert system predicting biotransformation pathway working together with a probabilistic model that calculates probabilities of the individual transformations. The expert system contains a library of hierarchically ordered individual transformations and matching substructure engine. The hierarchy in the expert system was set according to the descending order of the individual transformation probabilities. The integrated principal catabolic steps are derived from set of metabolic pathways predicted for each chemical from the training set and encompass more than one real biodegradation step to improve the speed of predictions. In the current work, we modeled O 2 yield during OECD 302 C (MITI I) test. MITI-I database of 532 chemicals was used as a training set. To make biodegradability predictions, the model only needs structure of a chemical. The output is given as percentage of theoretical biological oxygen demand (BOD). The model allows for identifying potentially persistent catabolic intermediates and their molar amounts. The data in the training set agreed well with the calculated BODs ( r 2 =0.90) in the entire range i.e. a good fit was observed for readily, intermediate and difficult to degrade chemicals. After introducing 60% ThOD as a cut off value the model predicted correctly 98% ready biodegradable structures and 96% not ready biodegradable structures. Crossvalidation by four times leaving 25% of data resulted in Q 2 =0.88 between observed and predicted values. Presented approach and obtained results were used to develop computer software for biodegradability prediction CATABOL.     

Molecular modeling approaches for the prediction of the nonspecific binding of drugs to hepatic microsomes

Molecular modeling approaches for the prediction of the nonspecific binding of drugs to hepatic microsomes were examined using a published database of 56 compounds. Models generated were evaluated using an independent test set of 13 compounds. A pharmacophore approach identified structural features of drugs associated with nonspecific binding. A side-chain amino group and complementary hydrophobic domain were the principal features noted. The use of shape overlays, based on the pharmacophore, in conjunction with a chemical force field in the program ROCS, yielded discrimination between molecules classified as strong binders (experimental fraction unbound in microsomes<0.50) and those with a lower degree of binding (experimental fraction unbound in microsomes>0.50). In the initial data set of 56 molecules, 18 were classified as strong binders (on the basis of the above criteria), and all of those were recovered in the top 22 molecular hits from ROCS. Additionally, computationally generated values of log P were shown to provide a reasonable estimate of the fraction unbound in microsomes, providing the compounds were in their basic form at physiological pH.     

Synthesis and LPG sensing properties of nano-sized cadmium oxide

This paper reports the synthesis and liquid petroleum gas (LPG) sensing properties of nano-sized cadmium oxide (CdO). The nano-sized CdO powder was successfully synthesized by using a chemical co-precipitation method using cadmium acetate and the ammonium hydroxide, as starting materials and water as a carrier. The resulting nano-sized powder was characterized by X-ray diffraction (XRD) measurements and the transmission electron microscopy (TEM). The LPG sensing properties of the synthesized nano-sized CdO were investigated at different operating temperatures and LPG concentrations. It was found that the calcination temperature and the operating temperature significantly affect the sensitivity of the nano-sized CdO powder to the LPG. The sensitivity is found to be maximum when the calcination temperature was 400 °C. The sensitivity to 75 ppm of LPG is maximum at an operating temperature 450 °C and it was found to be ∼341%. The response and recovery times were found to be nearly 3-5 s and 8-10 s, respectively. The synthesized nano-sized CdO powder is able to detect up to 25 ppm for LPG with reasonable sensitivity at an operating temperature 450 °C and it can be reliably used to monitor the concentration of LPG over the range (25-75 ppm). The experimental results of the LPG sensing studies reveal that the nano-sized CdO powder synthesized by a simple co-precipitation method is a suitable material for the fabrication of the LPG sensor.     

The development of real-time RI imaging system for plant under light environment

We present the real-time RI imaging and analyzing system to study the kinetics of nutrient uptake manner in a living plant. The system allowed light condition for the up-ground part of the plant and continuous dark condition for the root part, therefore, light/dark cycles was set as 16/8 h. There was 9,000 lx of LED lights in an aluminum container where the plant was set. The container was shielded well so that there was no light leakage to damage highly sensitive CCD camera which detected beta-rays from the sample. With this system, RI imaging was able to perform for 6 days without damaging the activity of the plant.     

Remote Actuation of a Light-Emitting Device Based on Magnetic Stirring and Wireless Electrochemistry

We propose a straightforward access to a rotating light-emitting device powered by wireless electrochemistry. A magnetic stirrer is used to rotate a light-emitting diode (LED) due to the intrinsic magnetic properties of the tips that contain iron. At the same time, the LED is submitted to an electric field and acts as a bipolar electrode. The electrochemical processes that are coupled on both extremities of the LED drive an electron flow across the device, resulting in light emission. The variation of the LED alignment in time enables an alternating light emission that is directly controlled by the rotation rate. The stirring also enables a continuous mixing of the electrolyte that improves the stability of the output signal. Finally, the LED brightness can readily reveal a change of chemical composition in the electrolyte solution.     

Synthesis and electrorheological response of nano-sized laponite stabilized poly(methyl methacrylate) spheres

Poly(methyl methacrylate) (PMMA) nanospheres were fabricated via surfactant-free Pickering emulsion polymerization, in which hydrophilic laponite clay was used to stabilize the emulsions of methyl methacrylate dispersed in distilled water. These synthesized PMMA nanoparticles, of which the surface is compactly wrapped by laponite clay, are observed, as confirmed by scanning electron microscopy and transmission electron microscope images. Fourier-transform infrared spectra and thermogravimetry analysis confirm the chemical composition, thermal property, and mass percent of the laponite located on the surface of PMMA particles. Finally, laponite-wrapped nano-sized PMMA spheres were adopted as an electrorheological material. By using an optical microscope, the chain-like structure was observed when an external electric field was applied. In addition, the ER performance was also examined via a rotational rheometer equipped with a high voltage generator.     

An inexpensive, portable and microcontrolled near infrared LED-photometer for screening analysis of gasoline

A microcontrolled, portable and inexpensive photometer is proposed. It uses a near infrared light emitting diode (NIR LED) as radiation source, a PbSe photoresistor as infrared detector and a programmable interrupt controller (PIC) microcontroller as control unit. The detector system presents a thermoresistor and a thermoelectric cooling to control the detector temperature and keep the noise at low levels. The microcontroller incorporated total autonomy on the proposed photometer. As its components are inexpensive and of easy acquisition, the proposed NIR LED-photometer is an economical alternative for chemical analyses in small routine, research and/or teaching laboratories. By being portable and microcontrolled, it also allows carrying out field chemical analyses. The instrument was successfully applied on the screening analysis to verify adulteration in gasoline samples.     

Atmospheric Pressure Ion Source Development: Experimental Validation of Simulated Ion Trajectories within Complex Flow and Electrical Fields

Three-dimensionally (3D) resolved ion trajectory calculations within the complex viscous flow field of an atmospheric pressure ion source are presented. The model calculations are validated with spatially resolved measurements of the relative sensitivity distribution within the source enclosure, referred to as the distribution of ion acceptance (DIA) of the mass analyzer. In previous work, we have shown that the DIA shapes as well as the maximum signal strengths strongly depend on ion source operational parameters such as gas flows and temperatures, as well as electrical field gradients established by various source electrode potentials (e.g., capillary inlet port potential and spray shield potential). In all cases studied, distinct, reproducible, and, to some extent, surprising DIA patterns were observed. We have thus attempted to model selected experimental operational source modes (called operational points) using a validated computational flow dynamics derived 3D-velocity field as an input parameter set for SIMION/SDS, along with a suite of custom software for data analysis and parameter set processing. Despite the complexity of the system, the modeling results reproduce the experimentally derived DIA unexpectedly well. It is concluded that SIMION/SDS in combination with accurate computational fluid dynamics (CFD) input data and adequate analysis software is capable of successfully modeling operational points of an atmospheric pressure ion (API) source. This approach should be very useful in the computer-aided design of future API sources.

Quantum chemical cluster modeling of boundary conditions for metal azides

An approach to crystal field modeling for solids with a predominantly ionic type of bond is suggested. The approach uses Evjen 's method of iteratively selecting point charges in such a way that the net charge on the crystal fragment be close to zero. The MNDO quantum chemical program is modified to include electron interactions of a point charge system in the Fock operator. The approach is tested on potassium azide. The calculated charges on potassium atoms agree well with the results of band structure calculations. Translated fromZhurnal Strukturnoi Khimii, Vol. 41, No. 3, pp. 605-608, May-June, 2000.     

Development of Miniaturized Electrochemiluminescence Instrument using Multi‐pixel Photon Counter as the Optical Detector

We developed a miniaturized electrochemiluminescence (ECL) instrument coupled with a light‐emitting diode‐based bipolar electrochemical sensor (LED‐BPES). This instrument composes of a microcontroller circuit, a power supply circuit, a potentiostat, an optical detecting circuit, and a communication circuit. The multi‐pixel photon counter (MPPC), which is low‐cost, small‐size, and wide‐range in optical measurements, is chosen as the optical detector. The LED‐BPES composes of a disposable screen‐printed carbon electrode (SPCE) and a surface‐mount red LED. Depended on the closed bipolar electrode (C‐BPE) structure, the LED‐BPES not only avoids the employment of unstable and complex ECL reactions but also offers a cost‐effective alternative for the over‐priced ECL reagents by using a mini‐size commercial LED as the luminescent producer. The combination of MPPC and LED‐BPES helps to set up the simplified and downsized instrument system with low price and high efficiency. The presented instrument coupled with LED‐BPES works excellent in electroactive molecules detection and has great potential in the application of heavy metal ions detection.     

Hybrid classical quantum force field for modeling very large molecules

A coherent computational scheme on a very large molecule in which the subsystem that undergoes the most important electronic changes is treated by a semiempirical quantum chemical method, though the rest of the molecule is described by a classical force field, has been proposed recently. The continuity between the two subsystems is obtained by a strictly localized bond orbital, which is assumed to have transferable properties determined on model molecules. The computation of the forces acting on the atoms is now operating, giving rise to a hybrid classical quantum force field (CQFF ) which allows full energy minimization and modeling chemical changes in large biomolecules. As an illustrative example, we study the short hydrogen bonds and the proton-exchange process in the histidine-aspartic acid system of the catalytic triad of human neutrophil elastase. The CQFF approach reproduces the crystallographic data quite well, in opposition to a classical force field. The method also offers the possibility of switching off the electrostatic interaction between the quantum and the classical subsystems, allowing us to analyze the various components of the perturbation exerted by the macromolecule in the reactive part. Molecular dynamics confirm a fast proton exchange between the three possible energy wells. The method appears to be quite powerful and applicable to other cases of chemical interest such as surface reactivity of nonmetallic solids. © 1996 John Wiley & Sons, Inc.     

Probabilistic assessment of biodegradability based on metabolic pathways: catabol system

A novel mechanistic modeling approach has been developed that assesses chemical biodegradability in a quantitative manner. It is an expert system predicting biotransformation pathway working together with a probabilistic model that calculates probabilities of the individual transformations. The expert system contains a library of hierarchically ordered individual transformations and matching substructure engine. The hierarchy in the expert system was set according to the descending order of the individual transformation probabilities. The integrated principal catabolic steps are derived from set of metabolic pathways predicted for each chemical from the training set and encompass more than one real biodegradation step to improve the speed of predictions. In the current work, we modeled O2 yield during OECD 302 C (MITI I) test. MITI-I database of 532 chemicals was used as a training set. To make biodegradability predictions, the model only needs structure of a chemical. The output is given as percentage of theoretical biological oxygen demand (BOD). The model allows for identifying potentially persistent catabolic intermediates and their molar amounts. The data in the training set agreed well with the calculated BODs (r2 = 0.90) in the entire range i.e. a good fit was observed for readily, intermediate and difficult to degrade chemicals. After introducing 60% ThOD as a cut off value the model predicted correctly 98% ready biodegradable structures and 96% not ready biodegradable structures. Crossvalidation by four times leaving 25% of data resulted in Q2 = 0.88 between observed and predicted values. Presented approach and obtained results were used to develop computer software for biodegradability prediction CATABOL.     

Construction of a light-emitting diode fluorescence detector for high-performance liquid chromatography and its application to fluorometric determination of L-3-hydroxybutyrate

This study employed a new light source, a light-emitting diode (LED), for fluorescence detection of high-performance liquid chromatography to measure the concentration of trace constituents in biological fluids. Using l-3-hydroxybutyrate ( l-3HB) as a tested trace compound, the function of the new system was compared with that of the current commercially available model. A detailed schematic diagram of the path of the detection rays in the LED detector is given. A voltage-stabilizer for the drive circuit was designed with an input of 10 V and an output of 8 V, and another voltage regulator was used to maintain a constant 8 V. Then the regulator was used to set the output voltage for the LED at 2.8 V by two external resistors. Replacing the xenon lamp with LED, this system provided higher photon density and a narrow spectrum at a wavelength of 491 nm. At room temperature (22.1°C), the average temperature of six places in the chamber of LED detector was 22.1°C compared with 51.1°C in the xenon detector. The spectra of the excitation light sources were measured. Compared with the xenon lamp, approximately 1.32 times higher excitation intensity was obtained by the LED source. The accuracy of detection of l-3HB in 50 μL of rat serum was 99.85-100.85%, and the intra-day and inter-day precision values were within 8.99 and 13.90%, respectively. The limit of detection of l-3HB was approximately 0.73 μM (signal-to-noise ratio 3). The sensitivity of the proposed LED detector was comparable to that of traditional fluorescence detectors using xenon arc lamps; however, the cost and operating temperature of LED lamps were far lower. This assay system could be further used to detect trace constituents in various samples.     

Semicontinuous GC analysis and receptor modelling for source apportionment of ozone precursor hydrocarbons in Bresso, Milan, 2003

The European Ozone Directive 2002/3/EC specifies the analysis of 30 individual C2-C9 hydrocarbons in urban air with the attribution of emission sources to pollution concentrations as a major objective. In the present study, we investigate an approach for source apportionment of these ozone precursor hydrocarbons in urban air based on reliable semi continuous volatile organic compound (VOC) analysis in the field and in vehicle emission laboratory combined with multivariate receptor modeling. The GC system relies on an hourly analytical cycle based on a trap sample enrichment phase followed by a dual column gas chromatographic flame ionisation detector (FID) analysis and has successfully been tested during an air monitoring campaign at an urban site (Milan, Italy, September 2003) and in the vehicle laboratory performing exhaust emission measurements while running driving cycles on a chassis dynamometer (mopeds, gasoline and diesel cars). The receptor modeling relies on two complementary principles. The chemical mass balance (CMB) modeling apportions well characterized source profiles for the 30 individual C2-C9 hydrocarbons in the Ozone Directive to the concentrations in ambient air and produces source contribution estimates (SCE) as output. The positive matrix factorization (PMF) analyses variability in the ambient air concentration data and searches for latent variables consisting of co-varying hydrocarbons and produces profiles as output, which in this study could be attributed to known emission sources. Both CMB and PMF rely on an estimated uncertainty for each input data. A new approach is presented, by which the uncertainty is allowed to float as function of the photochemical reactivity of the atmosphere and the stability of each individual compound.