The technological and economic management of the environmental variable in the pharmaceutical–chemical industry

Industrial risks increate with technological progress. The study of potential risks is routine in the pharmaceutical–chemical industry. Here, like in other industrial activities, a risk coefficient is introduced that varies within space time limits.A control system of environmental safety and health monitoring processes should be based on the data obtained from Hazard and Operability Studies (HAZOP).The space variable influences the chemical risk coefficient that applies to the whole the production cycle (including waste recycling). For the sake of prevention, many enterprises have adopted the integrated management system, which is now moving to an additional required feature: environment and health protection and safety assurance inside and outside the industrial area (in compliance with UNI, ISO 14000 and OHSAS 18001standards).Our goal is to examine the technological–scientific–environmental changes in the pharmaceutical–chemical sector in order to asses the new extent of chemical regarding management systems.This will entail a cultural change that will call for the necessary economic strategies for industries to implement the appropriate environmental–technological programs.     

A new algorithm for the determination of protolytic constants from spectrophotometric data in multiwavelength mode: Calculations of acidity constants of 4-(2-pyridylazo)resorcinol (PAR) in mixed nonaqueous-water solvents

A new efficient, simple and versatile algorithm is presented for determination of the protolytic constants from spectrophotmetric data in multiwavelength mode based on the combining of hard and soft modeling. The algorithm was checked by determining the acidity constants of a triprotic acid from theoretical and real absorption-pH data. The real spectral data are obtained from photometric titration of different solutions of 4-(2-pyridylazo)resorcinol (PAR) by a standard base solution under an inert atmosphere. The algorithm starts the minimization process using an user supplied number of components and initial guesses of the unknown parameters and refined in a least squares manner. New algorithm is implemented in the new version of DATAN package (version 3.1). The validity of the obtained results was checked by some well known programs such as DATAN 2.1, SPECFIT/32, SQUAD, a modified version of difference spectra and a A-pH curve method. The comparison of the outputs of the DATAN 3.1 with the other programs reveals that there is a very good agreement between the obtained results and mentioned programs.     

An efficient and extensible format,library, and API for binary trajectory data from molecular simulations

Molecular dynamics simulations is an important application in theoretical chemistry, and with the large high‐performance computing resources available today the programs also generate huge amounts of output data. In particular in life sciences, with complex biomolecules such as proteins, simulation projects regularly deal with several terabytes of data. Apart from the need for more cost‐efficient storage, it is increasingly important to be able to archive data, secure the integrity against disk or file transfer errors, to provide rapid access, and facilitate exchange of data through open interfaces. There is already a whole range of different formats used, but few if any of them (including our previous ones) fulfill all these goals. To address these shortcomings, we present “Trajectory Next Generation” (TNG)—a flexible but highly optimized and efficient file format designed with interoperability in mind. TNG both provides state‐of‐the‐art multiframe compression as well as a container framework that will make it possible to extend it with new compression algorithms without modifications in programs using it. TNG will be the new file format in the next major release of the GROMACS package, but it has been implemented as a separate library and API with liberal licensing to enable wide adoption both in academic and commercial codes. © 2013 Wiley Periodicals, Inc.     

Software package for quantitative analysis of solid materials by energy-dispersive x-ray fluorescence spectrometry without absolute calibration

A software package for quantifying elements in solids from energy-dispersive x-ray fluorescence data is described. The algorithm is based on the fundamental parameter approach and facilitates the simultaneous determination of several elements at widely varying concentrations. The software comprises three programs. One program, for spectrometer control and data acquisition, resides in a dedicated microcomputer. The two other programs, for spectra deconvulution and data evaluation, reside in a larger central computer. On-line communication between the computers is feasible, and the system facilitates the implementation of new improved programs. The performance of the system was tested on standard reference materials, and satisfactory accuracy was obtained for up to 21 elements.     

HomologyPlot: Searching for homology to a family of proteins using a database of unique conserved patterns

Summary A new database of conserved amino acid residues is derived from the multiple sequence alignment of over 84 families of protein sequences that have been reported in the literature. This database contains sequences of conserved hydrophobic core patterns which are probably important for structure and function, since they are conserved for most sequences in that family. This database differs from other single-motif or signature databases reported previously, since it contains multiple patterns for each family. The new database is used to align a new sequence with the conserved regions of a family. This is analogous to reports in the literature where multiple sequence alignments are used to improve a sequence alignment. A program called Homology-Plot (suitable for IBM or compatible computers) uses this database to find homology of a new sequence to a family of protein sequences. There are several advantages to using multiple patterns. First, the program correctly identifies a new sequence as a member of a known family. Second, the search of the entire database is rapid and requires less than one minute. This is similar to performing a multiple sequence alignment of a new sequence to all of the known protein family sequences. Third, the alignment of a new sequence to family members is reliable and can reproduce the alignment of conserved regions already described in the literature. The speed and efficiency of this method is enhanced, since there is no need to score for insertions or deletions as is done in the more commonly used sequence alignment methods. In this method only the patterns are aligned. HomologyPlot also provides general information on each family, as well as a listing of patterns in a family.     

Examination of segmental average mass spectra from liquid chromatography–tandem mass spectrometric (LC–MS/MS) data enables screening of multiple types of protein modifications

It has been observed that a modified peptide and its non-modified counterpart, when analyzed with reverse phase liquid chromatography, usually share a very similar elution property [1–3]. Inasmuch as this property is common to many different types of protein modifications, we propose an informatics-based approach, featuring the generation of segmental average mass spectra (^saMS), that is capable of locating different types of modified peptides in two-dimensional liquid chromatography–mass spectrometric (LC–MS) data collected for regular protease digests from proteins in gels or solutions. To enable the localization of these peptides in the LC–MS map, we have implemented a set of computer programs, or the ^saMS package, that perform the needed functions, including generating a complete set of segmental average mass spectra, compiling the peptide inventory from the Sequest/TurboSequest results, searching modified peptide candidates and annotating a tandem mass spectrum for final verification. Using ROCK2 as an example, our programs were applied to identify multiple types of modified peptides, such as phosphorylated and hexosylated ones, which particularly include those peptides that could have been ignored due to their peculiar fragmentation patterns and consequent low search scores. Hence, we demonstrate that, when complemented with peptide search algorithms, our approach and the entailed computer programs can add the sequence information needed for bolstering the confidence of data interpretation by the present analytical platforms and facilitate the mining of protein modification information out of complicated LC–MS/MS data.     

The Amber biomolecular simulation programs

We describe the development, current features, and some directions for future development of the Amber package of computer programs. This package evolved from a program that was constructed in the late 1970s to do Assisted Model Building with Energy Refinement, and now contains a group of programs embodying a number of powerful tools of modern computational chemistry, focused on molecular dynamics and free energy calculations of proteins, nucleic acids, and carbohydrates.     

Evidence of an intermediate and parallel pathways in protein unfolding from single-molecule fluorescence

Determining how proteins fold into their native structures is a subject of great importance, since ultimately it will allow protein structure and function to be predicted from primary sequence data. In addition, there is now a clear link between protein unfolding and misfolding events and many disease states. However, since proteins fold over rugged, multidimensional energy landscapes, this is a challenging experimental and theoretical problem. Single-molecule fluorescence methods developed over the past decade have the potential to follow the unfolding/folding of individual molecules. Mapping out the landscape without ensemble averaging will enable the identification of intermediate states which may not be significantly populated, in addition to the presence of multiple pathways. To date, there have been only a limited number of single-molecule folding/unfolding studies under nonequilibrium conditions and no intermediates have been observed. Here, for the first time, we present a single-molecule study of the unfolding of a large autofluorescent protein, Citrine, a variant of green fluorescent protein. Single-molecule fluorescence techniques are used to directly detect an intermediate on the unfolding/folding pathway and the existence of parallel unfolding pathways. This work, and the novel methods used, shows that single-molecule fluorescence can now provide new, hitherto experimentally inaccessible, insights into the folding/unfolding of proteins.     

Computer-aided drug design platform using PyMOL

The understanding and optimization of protein-ligand interactions are instrumental to medicinal chemists investigating potential drug candidates. Over the past couple of decades, many powerful standalone tools for computer-aided drug discovery have been developed in academia providing insight into protein-ligand interactions. As programs are developed by various research groups, a consistent user-friendly graphical working environment combining computational techniques such as docking, scoring, molecular dynamics simulations, and free energy calculations is needed. Utilizing PyMOL we have developed such a graphical user interface incorporating individual academic packages designed for protein preparation (AMBER package and Reduce), molecular mechanics applications (AMBER package), and docking and scoring (AutoDock Vina and SLIDE). In addition to amassing several computational tools under one interface, the computational platform also provides a user-friendly combination of different programs. For example, utilizing a molecular dynamics (MD) simulation performed with AMBER as input for ensemble docking with AutoDock Vina. The overarching goal of this work was to provide a computational platform that facilitates medicinal chemists, many who are not experts in computational methodologies, to utilize several common computational techniques germane to drug discovery. Furthermore, our software is open source and is aimed to initiate collaborative efforts among computational researchers to combine other open source computational methods under a single, easily understandable graphical user interface.     

PCGAP: Application to analyze gamma-ray pulse-height spectra on a personal computer under Windows NT®

PCGAP is a software code, which was written to provide gamma-ray pulse height spectrum analysis on a personal computer platform. The code was specifically developed for Windows NT for either an Intel^® or DEC Alpha^® based processor. PCGAP includes programs which can be used to control data collection using a Canberra INSPECTOR^® multichannel pulse-height analyzer. With suitable spectrum conversion routines PCGAP can be used to analyze data from almost any multi-channel analyzer. Besides the normal functions associated with a robust spectrum analysis package, PCGAP can be used for radionuclide analysis for actinides via L-X and gamma-ray spectrometry. It can be used to control and analyze data from an INEEL developed pulse injection system for individual spectrum validation. The package includes programs for the manual analysis of spectra using displays which permit the spectroscopist to interactively define the spectral continuum and peak fitting limits, and display the resulting function fitting forms.     

Metrology of polymorph identification tests

Identification of polymorphs – compounds containing the same chemical entities, but differing by their solid state properties – is a challenge for analytical chemists, since the solid state characteristics of polymorphs sometimes have subtle differences in their infrared (IR) spectra. A method based on the evaluation of FTIR spectra by Principal Component Analysis and a Software Independent Modelling Class Analogy package is proposed for estimation of reliability of polymorph identification. It is demonstrated that by proper choice of the spectral region, the same approach can be used for identification of polymorphs in low dosage formulations.Presented at the Second International Conference on Metrology – Trends and Applications in Calibration and Testing Laboratories, November 4–6, 2003, Eilat, Israel.     

New antimalarial drugs

Approximately 40% of the world population live in areas with the risk of malaria. Each year, 300-500 million people suffer from acute malaria, and 0.5-2.5 million die from the disease. Although malaria has been widely eradicated in many parts of the world, the global number of cases continues to rise. The most important reason for this alarming situation is the rapid spread of malaria parasites that are resistant to antimalarial drugs, especially chloroquine, which is by far the most frequently used. The development of new antimalarial drugs has been neglected since the 1970s owing to the end colonialism, changes in the areas of military engagement, and the restricted market potential. Only in recent years, in part supported by public funding programs, has interest in the development of antimalarial drugs been renewed. New data available from the recently sequenced genome of the malaria parasite Plasmodium falciparum and the application of methods of modern drug design promise to bring significant development in the fight against this disease.     

Molecular constants of aluminum monohalides: caveats for computations of simple inorganic molecules

Quantum chemical calculations have become an everyday tool in chemistry. There are commercial program packages and downloadable basis sets for most needs. However, many chemists rarely go beyond the routine use of these programs, rarely, if ever, checking the original references for basis sets. In this letter, we point out some of the pitfalls of such an approach. Structural parameters of the aluminum-monohalides, AlF, AlCl, AlBr, and AlI, have been calculated using the Gaussian 03 program package and different basis set combinations.     

Technological applications of BINP industrial electron accelerators with focused beam extracted into atmosphere

Simultaneously with production of industrial accelerators BINP develops new EB technologies. For this purpose the set of equipment based on electron accelerators was installed. The accelerator has an energy range of 0.8–1.5 MeV and a maximum electron beam power of 100 kW. Electron beam is extracted into the atmosphere through the system of diaphragms with output holes about 1 mm in diameter. The operational vacuum in the accelerating tube is provided by a differential pumping system. The extraction device is equipped with additional scanning magnets. It allows the operator to change average beam power density in extra wide region from 10 to 10⁷ Wt/cm². The focused beam has many applications due to its unique properties.     

Calculation of phase diagrams of ternary M-Ga-Sb (M = In,Al) systems by convex hull approach

The ternary semiconductor phase diagrams of M-Ga-Sb (M = In, Al) are calculated by means of the convex hull approach. The software package TernAPI is tested as an effective tool for these purposes. The new facilities and advantages of this package are proven. It enables one to construct ternary phase diagrams based on thermodynamic properties of all phases existing in systems. The changes in phase region shapes and phase transformations with temperature can be studied by means of the TernAPI package. Selection of reliable thermodynamic models of solutions is of crucial importance for correct calculations of phase equilibria. It is shown that an adequate phase diagram can be constructed when a polynomial model of liquid solutions in the Al-Ga-Sb system is used.     

A generalized any particle propagator theory: Assessment of nuclear quantum effects on electron propagator calculations

In this work we propose an extended propagator theory for electrons and other types of quantum particles. This new approach has been implemented in the LOWDIN package and applied to sample calculations of atomic and small molecular systems to determine its accuracy and performance. As a first application of the method we have studied the nuclear quantum effects on electron ionization energies. We have observed that ionization energies of atoms are similar to those obtained with the electron propagator approach. However, for molecular systems containing hydrogen atoms there are improvements in the quality of the results with the inclusion of nuclear quantum effects. An energy term analysis has allowed us to conclude that nuclear quantum effects are important for zero order energies whereas propagator results correct the electron and electron-nuclear correlation terms. Results presented for a series of n-alkanes have revealed the potential of this method for the accurate calculation of ionization energies of a wide variety of molecular systems containing hydrogen nuclei. The proposed methodology will also be applicable to exotic molecular systems containing positrons or muons.     

Analysis of the electron density redistribution in the course of nucleophilic addition reactions of H− and F− to acetylene and methylacetylene molecules according toab initio calculations

Energy characteristics and peculiarities of variation of structural parameters along the minimum energy pathways (MEP) calculated earlier of six reactions of nucleophilic addition of H^– and F^– to acetylene and methylacetylene have been analyzed. The electronic mechanism of the reactions, the character of the electron density redistribution, and its relation with the changes in structural parameters have been discussed. It has been found for all six reactions that the structural reorganization of an alkyne + Nu system is completed before the barriers. However, the increase in the alkyne multiple bond length and changes in electronic characteristics for the reactions with F^– (endothermic reactions) take place before the barrier (late transition state) and for the reaction with H^– (exothermic reactions), after the barrier (early transition state).Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 12, pp. 2373–2377, December, 1995.     

Chip-based high-throughput screening of herbal medicines

At present, high-throughput screening (HTS) programs in drug discovery rely mainly on compound libraries from combinational chemistry. Similarly, natural flora has been used as a prominent origin for new and potent herbal drugs. Herbal medicines have been used worldwide for thousands of years to cure many diseases. As such, herbal secondary metabolites show a remarkable structural diversity that supplements chemically synthesized compound analogs in drug discovery screening. Unfortunately, there is often a considerable deterioration in the quality of herbal drugs in such screening programs as there are time-consuming manual processes involved in the isolation of active ingredients from the highly complex mixtures of herbal plant products. The quality and quantity of herbal samples are critical for the success of HTS programs. In the recent past, there have been substantial improvements in HTS due to the miniaturization and integration of microchip (e.g., Herbochip(?), DNA chip, protein chip, cell chip, etc.)-based technologies so as to design herbal drugs that compete with synthetic drug analogs. Here we will review various technologies used for HTS of herbal medicines. Finally, we will summarize our efforts to develop a novel chip-based HTS assay to explore the antioxidant and radioprotective properties of herbal plants.     

High power electron accelerators for flue gas treatment

Over 1000 accelerators based on different principles have been constructed and used in the field of radiation chemistry and radiation processing. One of the radiation processes which was successfully demonstrated in many laboratories and pilot plant facilities is the reduction of SO₂ and NO_x pollutants from flue gases emitted during fuel combustion in boilers for electrical power and heat production. The full scale industrial implementation of an electron beam process for flue gases treatment would require accelerator modules with a beam power of over 500 kW and electron energy in the range 1–1.5 MeV. The 500 MW power plant may require 5–8 MW of electron beam power deposited in the flue gas.