INSTITUTE OF BIOLOGY, MEDICINAL CHEMISTRY & BIOTECHNOLOGY
 
  Drug Discovery
  Computational Chemistry
  Molecular Analysis
  Organic and Organometallic Chemistry
  Medicinal Chemistry
  Structural Biology & Chemistry
  Molecular Endocrinology
  Signal Mediated Gene Expression
  Molecular & Cellular Ageing
  Biomedical Applications
  Holistic Approaches in Health
  Chemical Carcinogenesis and Genetic Toxicology
  Metabolic Engineering-Bioinformatics
  Biotechnology
  Enzyme and Synthetic Biotechnology
  Biomimetics & Nanobiotechnology

Computational Chemistry

 

The Computational Chemistry Team develops and implements methods for:

. The computation of the linear and non-linear optical (L&NLO) properties of materials
. The design of NLO materials for photonic applications and
. The design and study of bioactive compounds, in cooperation with the other members of the Department.

Research Τeam

Manthos Papadopoulos, Ph.D.  -  Researcher A'
Heribert Reis, PhD - Scientific Personnel

Postdoctoral Researchers
Aggelos Avramopoulos, PhD.  
Γεώργιος Λεώνης, PhD Research Fellow-FP7-ARCADE

Ph.D. Students
Haralampos Tzoupis, M.Sc. 

Research Projects

A. Gas phase (atoms and molecules)

We are developing and implementing ab initio methods for taking into account the correlation and vibrational contributions to the L&NLO properties. The effect of the relativistic corrections to the properties of interest is also taken into account, where it is appropriate.

Vibrational conrtibutions
These include the pure vibrational contribution (pv) and the zero-point vibrational averaging (zpva). The following methods have been employed in order to take into account these contributions:

. The Bishop and Kirtman perturbation theory. This has been applied to small and medium size molecules (e.g. several azabenzenes) [JCP, 112, 6301 (2000)].
. A semi-numerical method based on Numerov-Cooley (NC) integration. The approach exploits the Born-Oppenheimer energy and property functions, utilizing susch information in the NC integration of the field-dependent vibrational equation, in a way which exposes separate contributions to the total electronic property [CPL, 316, 541 (2000)].
. We proposed a method for computing the vibrational contributions to any static electric property with respect to an arbitrary reference geometry which, at a given level of electronic structure theory, need not correspond to the associated minimum energy geometry [JCP, 112, 1645 (2000)].

Relativistic contributions
These has been taken into account by employing the Douglas-Kroll approximation. We note the following significant applications:
. The correlation, relativistic and vibrational contribution to the dipole moment, polarizabilities and first hyperpolarizabilities of ZnS, CdS and HgS [JCP, 111, 7904 (1999)].
. Vibrational corrections to electric properties of relativistic molecules: The coinage metal hydrides [JCP, 114, 198 (2001)].
. Relativistic effects on interaction induced electric properties of weakly interacting systems: The HF...AuH dimer [JCP, 117, 10026 (2002)].

Applications
We have employed state-of-the-art methods to study a number of interesting problems, for example:

. The dipole moment, polarizabilities and first hyperpolarizabilities of HArF. A computational and comparative study [JACS, 126, 6179 920040].
. Electronic spectrum of the confined auride ion [PCCP, 5, 1096 (2003)].
. Strong interactions through the X...Au-Y bridge: the Au bond? [CPL, 370, 765 (2003)].

B. Condensed phases

In our work on condensed phases (molecular crystals and liquids) we have studied the effect of environmental interactions on the molecules, using various approximations. We explore how the polarizabilities and hyperpolarizabilities of a molecule change, relative to those in the gas phase, when it is part of a crystalline solid or liquid. A detailed analysis of the local field s experienced by various molecules (e.g. urea, nitrobenzene) has been conducted. Hence we have shown how to solve many of the problems encountered in making the transition from the microscopic to macroscopic properties, needed in designing NLO devices. Some of our contributions in this area involve:

. Calculation of the macroscopic first-and third-order optical susceptibilities for the benzene molecule [TCA, 99, 384 (1998)].
. Computer simulation of the linear and nonlinear optical properties of liquid benzene: Its local fields, refractive index and second nonlinear susceptibility [JCP, 110, 6463 (1999)].
. Electrostatic calculation of linear and nonlinear optical properties of ice Ih, II. IX and VIII [Chem. Phys., 263, 301 (2001)].
. Calculation of refractive indices and third-harmonic generation susceptibilities of liquid benzene and water: Comparison of continuum and discrete local field theories [JCP, 114, 876 (2001)].

Organic and polymeric systems are now being intensively studied, because of their potential applications in optoelectronic and all optical computing devices. These systems posssess many advantages over inorganic systems. Our contribution in this area involves:

. Molecular dynamics simulations of electric field poled nonlinear optical chromophores incorporated in a polymer matrix [JPC B, 108, 588 (2004)].
. Nonlinear optical susceptibilities of poled guest-host systems: A computational approach [JPC B, 108, 8931 (2004)].

C. Design of NLO materials for photonic applications

There is currently a great demand for faster data processing. It is considered that photonic technologies, which use the light as carrier of the information instead of electrons, may provide the solution. One of the main problems in this area is to develop materials with large NLO properties. We have selected and/or designed several; derivatives with very large NLO properties:

. Some organic and organometallic molecules with remarkably large second hyperpolarizabilities [TCA, 99, 124 (1998)].
. The polarizability and the second hyperpolarizability of tetrakis(phenylethenyl) ethene and several of its lithiated derivatives [IJQC, 72, 177 (1999)].
. Hexalithiobenzene: A molecule with exceptionally high second hyperpolarizability [PCCP, 2, 3393 (2000)].

D. Design and study of bio-active compounds

We have participated in several projects, which have been
coordinated by members of the Department, for example:

. Novel 17β-substituted conformationally constrained neurosteroids that modulate GABAA receptors [J. Med. Chem. 2005, in press]. Scientist in charge: Dr T. Calogeropoulou.
. Computation of the bond-dissociation energy for the phenolic O-H bond. Scientist in charge: Dr M.Koufaki.

Cooperation with other research teams

Prof. A. D. Buckingham (Cambridge, UK), Prof. N. C. Handy (Cambridge, UK), Prof. A. J. Sadlej (N. Copernicus U., Poland), Prof. M. Barysz (N. Copernicus U., Poland), Prof. R. Wortmann (U. of Kaiseslautern, Germany), Prof. K. Jug (U. Hannover, Germany), Prof. R. W. Munn (UMIST, UK), Prof. P. Calaminici (CINVESTAV, Mexico), Prof. A. E. Underhill (U. of North Wales, UK), Prof. I. Boustani (U. of Wuppertal, Germany), Dr C. Hattig (Forschungszentrum Karlsruhe, Germany), Prof. J. G. Angyan (U. Henri Poincare, France).
Prof. D. N. Theodorou (National Technical University of Athens, Greece), Dr I. G. Economou (National Research Center for Physical Sciences, "Demokritos, Greece), Prof. I. N. Demetropoulos (U. of Ionnina, Greece), Prof. O. Igglessi-Markopoulou, National Technical University of Athens, Greece).

MGP has joint publications with the above researchers.

Current projects

We are involved in:

  • The computation of the L&NLO properties of nano-particles. We note, among the applications we are currently considering, the metal clusters (e.g. Mn, where M=Zn, Cd, Au) and the design of novel fullerene derivatives.
  • The development of a refined model for the description of the local field on a molecule in solution. This will allow us to describe more accurately the macroscopic L&NLO properties of solutions.
  • The design of novel bio-active compounds.

Infrastructure

The following facilities are available:

. 6 Intel-PCs and 3 DECs-workstations with adequate memory and disc space.
. A linux cluster with 8 dual-processor PCs; Memory:768 MB RAM X 8; Disc:40GBX7 and 50GBX1
. A linux cluster with 8 single-processor PCs
Memory: 1GB RAM X 8; Disc:40GBX6, 120GBX1 and 80GBX1
. Free access to an SMP Hewlett-Packard computer with 48 processors
Memory:36GB RAM; Disc: There are 86 discs, the capacity of each one of them is 36 GB.

Funding

Several of the projects of the CCG team have been funded by the European Union and the GSRT. Currently the team has a Marie Curie Host Development Fellowship (HPMD-CT-2001-00091), entitled: "Computation of non-linear optical properties of condensed phases". The Fellowship has budget 114000 euro. It expires 16/12/2005.

 
 

 

 

 

 
 

 

   
       

 

 

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