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Content archived on 2022-12-23

Advanced computational chemistry of increasingly complex systems

Objective


A.Background

A1.Why a COST Action for this topic?

The term Advanced Computational Chemistry is used in the following in order to describe a technology, wherein computational methods are used for the prediction of structural, dynamical and thermodynamical properties of chemical systems. Examples for increasingly complex systems are molecules in interaction with their environment (solvent, surface, catalyst, etc.) or with radiation, reactive systems with several degrees of freedom, guest-host interactions in solution, energy surfaces with many local minima, liquid crystals, polymers and clusters etc.

Traditionally, Computational Chemistry is considered as a natural outgrowth of Theoretical Chemistry, the role of which should involve the creation and dissemination of penetrating conceptual infrastructure for the chemical sciences. As far as atomic and molecular levels are concerned, this infrastructure could be well established. There are numerous methodologies (at all levels of complexity) available for the treatment of quantum chemical problems as well as for molecular

dynamics and Monte Carlo type simulations. The applications of these methods in computational chemistry have led to the solution of many problems in real chemical systems, especially when these systems are of limited complexity. At present, for systems of larger complexity, the traditional tools can be applied only for very special cases because of the dramatical increase in the computational effort with the size of the molecules (or number of electrons). Therefore, the main goal of the action will be the extension of these methods to a rational design of drugs, to the prediction of properties of new compounds and proposals for their synthesis, to the support of catalysts design and simulation of physical and chemical processes in the environment. In this case, significant progress can be made by taking advantage of the innovative features of modern computers. Furthermore, new concepts and new tools are needed in this field. For example, there are only a few attempts to extend the set of computational chemistry toolkits which root back to mathematical statistics, data bank analysis, fuzzy logic, artificial intelligence and theoretical biology. In this case, efforts have to be directed to make them applicable to real systems in an effective manner.

The aim of the new COST action is to bring under a common umbrella European researchers, who either work on the extension of standard methods or have already started to develop (and apply) non-standard strategies and to bring them together with colleagues from other fields (mathematics, computer science, database handling, bioinformatics, etc.) and boost future developments.

A2.Status of Research in the Field

At present, the main emphasis of computational chemistry has been on solving the many-body electronic structure problem and on using the resulting potential energy surfaces to investigate nuclear motion. This has led to a collection of programmes based on classical, semiclassical, and quantum techniques. Since 1980, use of these programmes has become a key tool for modelling molecules and gas-phase chemical reactions of relatively small molecules. The list of achievements is long and only typical ones are reported below. Structural determination can be performed with so-called chemical accuracy (+ 0.01 _ on bond lengths, + 1? on angles) using computational methods, not only for gas-phase systems but also for crystalline materials. The fingerprint of most molecules provided by the vibrational spectra, and the Infrared and Raman spectroscopy can be reproduced rapidly and reliably with computational techniques. Molecular dynamics is easily providing accurate prediction on the density of states and Infrared and Raman spectra at different temperatures. Scattering experiments from electrons or from neutrons can be simulated with notable accuracy from trajectories analyses, in primary output from molecular dynamics. The availability of molecular trajectories coupled with computer graphics and visualization allows to represent important aspects of molecular aggregation previously totally inaccessible. Virtual reality is expected to bring these techniques to higher and higher resolution. Thermodynamic data and dissociation energies, once a most difficult prediction for theoretical and computational chemistry, are now accessible with an error no longer measured in a few eV but in a few Kcal/mole or even better. Relativistic effects very important for heavy atom molecules can now be computationally predicted. For large molecules simple methods have been used by chemists for a long time to estimate

the energy near their equilibrium geometry. In the molecular mechanics approach the total energy of a chemical system is approximated by a sum of simple terms involving distances between atoms, bond angles, and dihedral angles. These terms involve parameters estimated by assuming that they have the same value as those fitted to properties of simpler molecules. (Chemists have since long known that many structural and energetic features of molecules are nearly transferable among similar sub-fragments of molecules). This representation of the energy has made possible the modelling of biological systems and a rational design of drugs. The application of molecular dynamics and Monte Carlo methods to proteins and other biomolecules in the 1970s has led to their widespread use by the theoretical and experimental chemical community. The need for efficiency in designing molecular dynamics algorithms and Monte Carlo simulation to address relevant questions like those about protein folding is also prompting a renewed contact of computational chemists with the numerical mathematics and physics community.

Molecular quantum mechanics was extended to the treatment of chemical reactions rates of large molecules by modelling the reactive event as a passage over the barriers to reaction of a multidimensional potential energy surface. In its simplest form the model corresponds to splitting the reactive process into a first step of reactants moving towards transition states (the critical configurations), and a second step of transition states evolving towards reaction product.

Search for new drugs of pesticides typically involves the investigation of thousands of compounds, whose biological properties can be correctly forecast using computational methods. Intelligent data base retrievals play also an important role within the strategy for searches for new drugs or pesticides. There are well-documented cases of the use of computer methods, particularly quantitative

structure-activity relationship methods, as an integral part of the design of compounds presently marketed as drugs or agrochemicals. Usually in QSAR methods the relationships are examined using multiple linear or nonlinear regression, classical multivariate statistical techniques. However, discriminant analysis, principal components regression, factor analysis, and neural networks have also been applied to these problems. In the last 10 years Molecular Quantum Similarity techniques have emerged as a comprehensive tool for drug design.

A need for a merge of fluid dynamics with either classical micro-dynamics or cellular automata as well as the use of computed process rates, constitutes the scientific base to develop chemistry jointly with chemical engineering, with a great effect on chemistry and industry productivity.

Topology and artificial intelligence techniques are coupled to describe molecular transformations such as reactions and conformation changes.

A3.Relationship with other European Programmes

There is, presently, no organization in Europe with the mission of coordinating the design and the methodological development of "new and pioneering" software for European computational chemistry; this contrasts the trend whereby the USA Science Foundation and the USA Department of Energy (and other agencies) are financing American computational chemistry at the American Universities. The Esprit III programme, with EUROPORT, likely has been the most direct and comprehensive programme for computational chemistry, but it is now in its last phase. Therefore, despite the widespread research work in this field there is no official engagement from Europe in developing collaborative efforts. The relevance of the topic has been recognized by the CERC3 (Chairmen of the European Research Council Chemistry Committee), who organized a "European Young Chemists Workshop" on "Advanced computational studies of increasingly complex chemical systems" (Wien, 17-21 March 1996). Therefore, a coordination of this research is needed through the COST Action.

B.Objectives and benefits

The main objective of the new COST Action is to enlarge the scope of computational chemistry techniques so as to perform a realistic modelling of chemical systems. This means that computational chemistry tools should be considerably improved to gain efficiency and friendliness. Efficiency improvement will be gained by extensive design of algorithms for innovative parallel architectures. It will also be improved by using alternative non-directive approaches typical of artificial intelligence end data mining techniques. On the other hand, friendliness will be improved by boosting graphical tools and interactive approaches.

This means also that both the systems investigated and the models used should reflect chemical conditions in a realistic way. This requires the proper and simultaneous treatment of different species and phases involved as well as the adequate control of relevant parameters such as time, temperature, etc. Such simulations will then be applicable to problems of paramount importance in chemistry like rational drug design, prediction of properties of new materials and proposals for their synthesis, design of new catalysts, and modelling of physical and chemical processes in the environment. New methodological developments and synergistic combinations of different theoretical methods have to be introduced.

The objective of the new action is therefore to efficiently and accurately model systems and processes such as: Reactions of complex chemical systems such as those of environmental and biological relevance. Molecural systems and aggregates exhibiting special optical, electric and magnetic properties. Structural and electronic phenomena such as those occurring at surfaces and interfaces. Condensed phase materials simulated under non-equilibrium conditions over the nanosecond time scale with inclusion of polarisabilities. Potential drugs de novo designed with the aid of Molecular Quantum Similarity 3D-QSAR and artificial intelligence techniques.

These are selected applications of advanced computational chemistry techniques. The technology could also be applied to other fields like materials science, catalysis and supramolecular chemistry.

C.Scientific programme

The new Action should focus on methodological developments for the increasingly complex systems, in particular by taking into account the needs of advanced experiments, along the following lines:

1.Combine different approaches in order to obtain the synergetic effect of the individual methods. A relevant example of this is the embedding of quantum mechanics techniques into molecular mechanics approaches. Another example of interest for this action is the coupling of fluid dynamics codes with scattering and molecular dynamics methods.

2.Generalize the description of molecular processes by improving the algorithms treating dynamical aspects. This is the case of techniques based on cell-multipole and multiple time-step methods. Other relevant examples are the use of simplectic integrators and N-scaling methods for quantum molecular dynamics.

3.Develop efficient techniques and algorithms ex novo designed for parallel architectures to boost the performance of computational chemistry codes when considering large systems. Interesting developments are expected in fields like adaptive multi-grids techniques for treating electrostatic problems, domain decomposition for integrating dynamical differential equations, multi-level farm organization for approaches consisting of computational grains of different size.

4.Design efficient methods to treat electron correlation and relativistic effects. This may occur by adopting new exchange-correlation functionals in Density Functional Theory, by designing procedures to account for localized correlation, by improving coupled-cluster and perturbation theory methods, by taking into account correlation in semi-empirical schemes or by compact configuration interaction schemes.

5.Develop techniques to deal with the interaction of electronic and nuclear motions (going beyond the "Born-Oppenheimer Approximation"). This is important for transition states in reactions, in photochemical processes and in the spectroscopy of electronically excited states. It will be very important in modelling atmospheric and environmental processes and in the modelling of materials with unusual properties.

D.Organization and timetable

D1.Organization

Research projects fitting in the sub-topics described in section C will be submitted by scientists to the Management Committee members. This Committee will establish contacts between scientists.

The Management Committee has responsibilities for:

1.Drawing up the inventory during the first year, organization of workshops and start of the activity; existing contacts will be used which should greatly facilitate this task.

2.The coordination of the joint activities with other COST Actions, joint meetings are likely to result from this activity.

3.Exploration of wider participation and exchange of information with EC-specific programmes, ESF, etc.

4.The planning of the intermediate report, the final report, and the concluding symposium.

Progress in each of the projects will also be reported by the respective participants in their own countries within the framework of existing programmes.

D2.Reports

The progress of the programme will be monitored by brief annual reports from each of the participating scientists which will describe the results of research obtained through concertation. A mile-stone report will be prepared by the Management Committee after 3 years of joint activities. The report will be presented to the COST Technical Committee for Chemistry for their review.

A final report will be published to inform non-participating scientists and research workers interested in the results about the scientific achievements of the Action. It is expected that some reviews by participants which describe the progress made and state of the field will be published in International Journals. To conclude the COST Action, a symposium will be held after 5 years which will be accessible to other scientists.

D3.Timetable

The Action will have a duration of five years and comprise the following four stages:

Stage 1:After the first meeting of the Management Committee a detailed inventory of on-going research and existing plans of the participating groups to begin joint projects will be made. This will result in a discussion document which will allow further planning to occur.

Stage 2:It will be evident which projects are closely related and would benefit from joint activities. Researchers (and co-workers) will set up (and continue) joint collaborative projects, and exchange their recent research results. It may be appropriate to explore wider collaboration with other European countries during this stage.

Stage 3:An intermediate progress report will be prepared after 3 years for review by the COST Technical Committee for Chemistry and by the COST Senior Officials Committee.

Stage 4: This final phase will begin after 4 years and will involve the evaluation of the results obtained. It may include the organization of a symposium for all the participants and co-workers.

E.Economic Dimensions

During the preparation of this Action, interest to participate was shown by researchers from all COST countries except Luxembourg and Iceland.

The economic dimension of the Action can be estimated as follows: personnel costs + operational + running costs + coordination costs.

Activities in at least some sub-topics of the Action are already on-going in most of the COST member countries. The total human effort that can be ascribed to the Action is: 80 scientists (400 man-years, 40 MECU), 110 technicians (550 man-years, 30 MECU), 75 postdoctorals (370 man-years, 35 MECU), 200 graduate students (200 man-years, 30 MECU), 200 undergraduates (200 man-years, 22 MECU).

Total: 157 MECU.

E1.Personnel costs

Estimates of personnel costs (research + administration) 60 KECU/scientist, 40 KECU/technician/25 KECU/PhD, secretary, etc.

E2.Operational and running costs

Estimated operational/running costs of instruments/materials (5 MECU).

E3.Coordination costs

The costs for coordination to be covered by the COST budget are estimated to be 60 KECU per year.

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