Research directions

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Institute of Organic Chemistry with Centre of Phytochemistry (IOCCP) –BAS

Main directions of research at the affiliation Institute IOCCP-BAS that necessitate the utilization of modern computational chemistry methods and powerful computational resources are as follows:

-Conformational analysis. Conformational and co-conformational dynamics and energetics of supramolecular functional systems and large rings with potential useful applications (modified and large-ring cyclodextrins, cyclodextrinic dimers, macrolide antibiotics, chiral solvating agents, pseudorotaxanes, [2]-, [3]rotaxanes and catenanes). Modelling of molecular crystals.

-Computational studies of reaction mechanisms and stereochemistry. Molecular design – drugs and photoelectronic materials. Biomolecular and supramolecular complexes and mechanisms. Kinetics and thermodynamics of reactions in solution, general acid-base catalysis. Mechanism of bioorganic reactions by means of sterically strained substrates. Quantitative correlation of reactivity, steric effects in particular.

-Mechanism of proton transfer reactions in ground and excited state. Isotope effects. Tautomerism of organic compounds. Theoretical studies of structure and nonlinear optical properties of organic compounds: undoped and doped conjugated systems. Optical and chirooptical properties of helicenes. Structure of coordination compounds. Theoretical chemometrics.

-Non-empirical quantum-chemical studies on medicines, food additives, strong poisons etc., including isotope labeled ones, their hydrogen-bonded complexes as well as anions-intermediates in important chemical reactions. Monitoring of the spectral and structural variations, caused by the conversion of organic molecules into complexes and anions.
-Theoretical study on the mechanism of ribosome action in the biosynthesis of proteins, with the purposes for the design of new inhibitors of the protein synthesis that may have useful application in medicine.

-Quantum-chemical calculations of NMR parameters. Computer programs for: automatic multiplets analysis; signal to noise enhancement in NMR spectra; determination of correlation times and activation energies of the overall and internal molecular reorientation; 13С chemical shifts prediction for natural compounds using spectral databases.

-Quantum chemical studies aimed at elucidation of the relationship of the chemical and electronic structure of conjugated organic compounds containing heteroatom with the processes of radiative and nonradiative deactivation of their singlet and triplet electronically excited states. The research is directed to potential application of the studied compounds as fluorescent laser dyes, pH sensors, fluorescent markers for polymers, biopolymers and nanoparticles, OLEDs, photosensibillizators for photodynamic therapy of cancer or cleaning of waste waters and structural characterization of biomolecules as well.

-Infrared ellipsometric studies of thin films and self-assembled monolayers on metallic and silicon surfaces.

-Vibrational circular dichroism studies of DNA oligonucleotides. Influence of different factors: base sequence, pH, salt concentration and interactions with drugs on the DNA structure and conformation.

-Composite materials with specific reduction, magnetic, adsorption and catalytic properties, that combine the properties of nano particles of transition metals and their oxides and the ordered nano-structure of different micro-, meso- and mixed micro-mesoporous supports with regulated size and architecture of the pores.

-Elucidation of the dependencies of the activity of different natural antioxidants on their structure, on the type of the lipid system, on the presence of biologically important microcomponents and on temperature. Computer modelling of the kinetics of lipid oxidation in the presence of various antioxidants.

Institute of Physical Chemistry “Acad. Rostislav Kaishev” (IPC) – BAS

Main fields of interests in IPC-BAS requiring computational power:

– Discrete and continuum models (in 1D and 2D) of step bunching on vicinal crystal surface caused by electromigration of the adatoms, Ehrich-Schwoebel effect and step permeability. Size and time scaling of the bunches.

– Growth instabilities of electrochemical systems far from equilibrium – diffusion limited aggregation and growth instabilities on lattice and off lattice. Cluster – cluster aggregation, ballistic deposition and sedimentation, and scaling properties of growing surfaces.

– Transfer matrix approach to different statistical physics problems (bottom – up approach): phase transitions, diffusion, conductivity, etc.

– Investigations on the structure, the dynamic properties and the phase transitions of polymers, membranes, micelles. Self-avoiding tethered (polymerized) membranes, embedded in three-dimensional space, by means of Monte Carlo computer simulations. Thermodynamic behavior of tethered membranes and systematic finite size scaling analysis at different phases of the observed sequence of temperature-driven folding phase transitions. Anomalous diffusion dynamics of a self-avoiding tethered membrane.

Institute of General and Inorganic Chemisrty (IGIC) – BAS:

The Institute of General and Inorganic chemistry is one of the leading chemical institutes of the Bulgarian Academy of Sciences in the field of inorganic materials science. It was recently recognized by the European Commission as a Centre of New Functional materials and New Processes with Environmental impact (Project INCO 016414 “MISSION”, within the frame of FP6-2004-ACC-SSA-2). The Project covers many fields of the fundamental and performance-oriented inorganic chemistry, e.g., design of materials with preset magnetic, optical, electrical and biological properties, as well as superhard materials and coatings. The environmental aspect of the institute’s activities comprises studies on the preparation of novel adsorbents and catalysts for low-temperature removal of harmful and toxic emissions by industry and transport. Highly sensitive and selective methods of determination of trace and major components as well as impurities in the bulk or on the surface of the solids and natural products are developed and validated.
The theoretical investigations (preferentially by ab initio MO and DFT methods) in the field of the molecular design, new materials and nanotechnology are focused on inorganic materials with electric, magnetic, photophysical and biological properties in the following thematic areas:

– First-principles modelling of periodical structures, cluster systems and adsorption processes. Elucidation of the type of the Co2+-nitrosyl complexes in different zeolites.

– Studies of electronic structures and properties of inorganic systems in solid state, gas phase and in solution in the ground- and in excited states.

– Simulation of electronic and vibrational spectra of inorganic systems.

– Modelling of molecular geometries of coordination compounds; investigation of the ligand binding mode to different transition metal and lanthanide ions; calculations of the metal-ligand binding energy, energetic contributions to the metal-ligand interaction (electrostatic, covalent, and repulsion energy).

– Estimation of the thermodynamic stability of inorganic systems by estimating the reaction formation energy.

– Prediction of reactive sites for electrofilic interactions in gas phase and in solution based on calculations of molecular electrostatic potential, Fukui functions, reactive indexes and basicity.

– TDDFT simulation of excited state proton transfer reaction in solution.

– Investigation of intra- and intermolecular interactions in inorganic compounds, evaluation of the character, the strength and the stabilizing effect of intramolecular hydrogen bonds.

– Investigation of solvatochromic and ionochromic phenomena in inorganic systems.

Institute of Catalysis (IC) – BAS

The research in IC-BAS focuses on the understanding of atomic-scale processes at surfaces by applying quantum mechanical methods with a strong emphasis on processes which are of large importance for the society, either today or in the near future. A special focus area of the research is the systematic analysis of trends in heterogeneous catalysis. These are some of the reactions, processes and materials currently studied:

– Reactivity trends for reactions over transition metals, oxides, sulfides, and nitrides: quantum chemical investigation of the structure, electronic properties and catalytic activity of layered sulfides; theoretical investigation on the influence of the morphology, the electron structure and the acid-basic properties of γ-Al2O3 and TiO2 surfaces on the formation of the catalytic site; theoretical study of the electronic, magnetic and catalytic properties of clusters, complexes and systems of low dimensionality; quantum chemical modelling of geometrical and spectral structure of adsorbed molecules on well defined surfaces; investigation of hydrocarbon interactions with Si(100)-(2×1) surface from the structural properties and vibrational spectra, computed within the Density Functional Theory.

– Hydro-treating (HDS): quantum chemical simulation of surface reactions on edge structures of promoted molybdenum disulfide.

– Environmental catalysis (NO decomposition, CO oxidation): theoretical investigation of СО+NО reaction over pure supported on MgO catalysts.

– Methodological developments: Elaboration of effective method to describe Wan der Waals interactions within the framework of Density Functional Theory: application towards self-assembly processes, governing the formation of hybrid nano-objects.

Institute of Polymers (IP) – BAS

In recent years the synthesis of α-aminophosphonates has received an increasing attention because they are considered as structural analogues of the corresponding α-amino acids and transition state mimics of peptide hydrolysis. These so-called „phosphorus analogues“ of the amino acids or phospha amino acids, in which the carboxylic acid group is replaced by a phosphonic group, P(O)(OH)2, have attracted particular interests and have reached a position of prominence in fields of research directed to the discovery, understanding, and modification of physiological processes in living organisms.

It has been demonstrated that N-phosphonomethyl glycine is effective in inhibiting test-tube growth of Plasmodium falciparum, the parasite that causes malaria. It has the same effect on related types of single-celled parasites such as Toxoplasma and Cryptosporidium that give rise to opportunistic infections in AIDS patients. Research teams from Procter& Gamble have found that modified N-phosphonomethyl glycines are especially effective in suppressing the growth of cancer, tumors, viruses, or bacteria. Structure activity relationship (SAR) studies are very important for effective research along these lines.

Institute of Chemical Engineering (IChE) – BAS

The Institute of Chemical Engineering is a basic scientific organization for chemical engineering at the Bulgarian Academy of Sciences and a principal national research centre for chemical engineering and bioengineering science. The IChE is involved both in fundamental and applied research in the priority fields like “new technologies”, “economy of energy”, “environmental protection”. The principal areas of the research activity are:

•hydrodynamics, heat and mass transfer processes in multiphase systems
•development of strategies for examining nano-filtration
• methods for optimal use and storage of energy
• chemical engineering problems in catalysis
• practical aspects of biochemical processes (studies on micro- and nano-properties of biocatalysts)
• computer simulation and control of chemical systems.

The main achievements are in the development of new industrial processes, novel equipment and process technologies, creation of methods for optimized industrial design, control and renovation of chemical engineering systems. The Institute has developed and applied in industrial scale more than 20 new processes, equipment and systems with environmental or energy saving effects: contact economisers for utilization of heat from flue gases of heat power stations; technologies and apparatuses for removal of toxic contamination from gas fluxes; new concepts for heterogeneous catalytic reactors; extraction technologies for producing and recovery of valuable or toxic substances from waste waters. The scientific staff of the Institute is recognized at the international level for contributions in the development of liquid membrane methods for simultaneous extraction and concentration of valuable solutes or toxic substances from waste waters and natural sources.

The studies in the field of biotechnology concern the kinetics of various fermentation and enzyme processes, practically applied for biological treatment of waste waters, and in the pharmaceutical industry. New methods are developed for optimal energy use in batch chemical and biochemical processes as well as for modelling of multicomponent liquid-vapour equilibrium. Scientific teams from the Institute participate in projects of the European programmes COST, TEMPUS, BIOSAP etc. Informational networks and education programs are elaborated in collaboration with scientists from many European countries. Projects with the European Commission are also currently developed.

Centre of Biomedical Engineering “Prof. Ivan Daskalov” (CBE) – BAS

The CBE carries out theoretical and applied studies in the field of pharmacology and toxicology related to development of quantitative structure-activity relationships (QSARs) and molecular models for predicting pharmacological activity and toxicity and elucidating the molecular mechanisms of action of bioactive compounds. The main goals are:

– Modelling of ligand-receptor interactions and rational drug design (classical QSARs, 3D QSARs, pharmacophore and homology modeling, docking and virtual screening).

– Assessment and prediction of ecotoxicity according to the requirements of the new European chemical legislation REACH (Registration, Evaluation, Authorization and Restriction of Chemicals) and support of the regulatory organizations in the assessment of chemical risk REACH calls for application of alternative to in vivo testing methods like QSAR aiming at reduction of the expenses and the number of laboratory animals used.
To achieve these goals the following particular tasks are performed:

– Development of QSAR and 3D QSAR models of different classes of bioactive compounds, including antitumour drugs, modulators of multidrug resistance (MDR) in tumour cells, compounds interacting with the transport P-glycoprotein (Pgp), compounds interacting with the enzymes cytochrome P450, UDP-glucoronyltransferase, cyclooxygenase (COX), inhibitors of the epidermal growth factor receptor (EGFR), antioxidant compounds, drugs interacting with the blood-brain barrier, etc.

– Development of pharmacophore models of drug compounds;

– Modelling of receptors and ligand – receptor interactions.

– Comparative analysis of virtual screening algorithms, compounds selection and selection of methods for docking and virtual screening; development of automated procedure for small molecules minimization and minimization of protein-ligand complexes when working with huge databases.

– Development and validation of QSAR models for predicting toxic effects, useful for regulators and chemical industry.

Central Laboratory of Optical Storage and Processing of Information (CLOSPI) – BAS

In the frame of the planned research tasks and under the contracts within the 6th FP of EC, CLOSPI-BAS focuses on methods and devices for digital holography, phase-stepping and speckle interferometry in real time. To fulfill these tasks CLOSPI is equipped with high resolution 2D photosensors, liquid crystal and DMD spatial-light modulators, diode and diode pumped solid state lasers. Implementation of digital holographic methods in a 3D case, however, as digital object reconstruction from a digitally recorded optical hologram or computer generation of digital holograms which are encoded on a fixed or dynamic medium for optical reconstruction requires a computational power which exceeds the power of the PCs in CLOSPI’s disposal. Additional computational power is required for utilization of the developed in CLOSPI coherent interferometric systems for precise micro/macro measurements in real time. The goal of these research activities is to realize a holographic microscopy of biological cells in vivo, as well as monitoring of transient processes. A primary task of CLOSPI is a real time 3D capture of objects and scenes with a multi-camera system for a 3D display. An increased computational power will facilitates also solution of inverse optical problems in characterization of thin nanolayers, Monte-Carlo simulation of photon migration in biomedical optics, as well as feature recognition of 2D objects from raw data arrays.

The University of Sofia “St. Kliment Ohridsky”

In the Faculty of Chemistry at the University of Sofia function three laboratories (as well as some independent scientists) doing theoretical research on various topics and targets related to modern technologies and Materials Science. They employ an assortment of Quantum Chemistry and Computational Chemistry methods and all of them need powerful computational facilities.
The Computational Chemistry based research activities at the Faculty may be summarized briefly as:

– Band structure, optical, conducting and magnetic properties of a variety of organic delocalized systems with an emphasis on extended or periodic (1-D and 2-D) molecular structures: conjugated polymers or/and stacks built of conjugated moieties, graphenes and nanotubes. Molecular design of new materials with tunable technical parameters for nanotechnological purposes, e.g., for molecular devices, data storage media, etc., is carried out.

– Modeling of supramolecular organization of conducting polymers – doping, counterions, solvent effects.

– Reactivity indices for mechanistic studies of organic reactions.

– Structure and properties of metal-organic high-spin complexes.

– Charge transport in DNA. DNA-chromophore complexes with enhanced hole transport for technical application.

– Structure, organization, electric, magnetic, dielectric, thermodynamic properties and nucleation behavior of insoluble (Langmuir) pure and mixed monolayers at the air-water interface to the end of modeling eco-media, membranes and Langmuir-Blodgett films precursors.

– Computational modeling of zeolites and porous materials at quantum mechanics and molecular mechanics levels. Theoretical simulation of the adsorption, spectral properties, and catalytic transformation of gases, organic molecules or intermediates in protonic and cation-exchanged zeolites.

– Structure, characterization, and mechanism of catalytic reactions on molecular sieves containing transition metal ions. Structure, stability, magnetism and reactivity of sub-nanosized transition metal particles in gas phase and on supports.

– Modeling the structure and reactivity of selected heterocyclic compounds.

– Molecular simulations of IR and Raman spectra with ab initio quantum mechanical methods.

– Theoretical investigation of reaction mechanisms, transition states, intermediates. Mechanism of solvolytic reactions, SN2 reactions and electrophilic substitutions in aromatics – reactivity of organic molecules.

– Electrostatic effects in organic reactions.

– Electrostatic effects in intermolecular interactions – hydrogen bonding.

– Conformational equilibria in organic molecules.

– Molecular modeling of bioactive compounds – quantitative structure-activity relationships (QSAR).

– Quantum chemistry of surface phenomena.

– Theory of scanning probe techniques.

– Quantum Nanodynamics.

– Mechanism of decoherence on solid surfaces.

In addition to scientific investigations, all researchers at the Faculty are keenly involved in teaching activities covering all (three) levels of higher education. Traditionally, the attendees of their courses are the most brilliant students who start working on research projects well before receiving their B.Sc. degree. Particularly active in this respect are the students in Chemistry&Informatics and in Computer Chemistry B.Sc. programs who have extended syllabus on theoretical methods and acquire professional computing skills at an early stage of their training accomplished at the expense of substantial machine time. At the M.Sc. level the Faculty offers a specialized master program in Computational Chemistry. All successful graduates from this program are sought team members of the most advanced Theoretical Chemistry research centers worldwide. The preparation of a master thesis in this program also requires considerable computing resources. The same applies for specific courses comprising molecular modeling and simulations as part of other B.Sc. and M.Sc. programs. A sizeable number of PhD students are trained in the theoretical laboratories as well and the access to adequate computing facilities is crucial for the satisfying outcome of their education. The expertise of the theorists at the Faculty demonstrated by the diversity of research topics and specialized courses offered is internationally acknowledged and the lack of a decent computational center is the major shortcoming that drives away our gifted students abroad and prevents international students from joining the Faculty programs.

South-West University “Neophit Rilski” – Blagoevgrad

A research group in the Department of Chemistry at the Faculty of Natural Sciences and Mathematic is involved intensively in the utilization of Computational chemistry methods.
Research problems on which the group is working are:

– The radical-trapping (scavenging) activity of thioamides;

– Antioxidant activity of phenolic compounds;

– Antioxidant activity of melatonin;

– Anticancer activity of spin-labeled nitrosoureas.

Besides, a compulsory lecture course on “Structure of Matter” is included in the bachelor program of the major “Chemistry.” The course elucidates the structure, the physical properties and the chemical behavior of atomic-molecular systems on quantum-mechanical grounds. The basic concepts needed for the interpretation of atomic structure, origin and type of chemical bonding, intra- and inter-molecular interactions, energy spectrum and reaction mechanisms are discussed. Each student works on an individual assignment. There is also an optional course “Computer-simulations of molecular structure and properties” in the bachelor program of majors “Chemistry” and “Chemistry and Physics” which extend the knowledge on the quantum chemical methods and molecular modeling.

The University of Plovdiv “Paisii Hilendarski”

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