Laboratory of Theoretical Methods and Computations (PD)

Staff:

Supervisor: Professor Aleksander Paweł Mazurek,
phone: +48 022 851-43-85 ; +48 022 841-18-88 ext. 369
 e-mail:

Theoretical Methods Group
Professor Joanna Sadlej, phone: 851-52-30, 841-48-69 ext. 355,
Associate Professor Jan Czesław Dobrowolski, phone: 851-52-30, 841-48-69 ext. 355,
Ph.D. Małgorzata Jarończyk, phone: 851-52-30, 841-48-69 ext. 355,
M.Sc. Grażyna Karpińska, phone: 851-52-30, 841-48-69 ext. 355,
Ph.D. Wojciech Ozimiński, phone: 841-48-69 ext. 166,

Physicochemistry Group
Ph.D. Franciszek Pluciński, phone: 841-48-69 ext. 440,
M.Sc. Krzysztof Pawłowski, phone: 841-48-69 ext. 447,

PD Activity:

PD Scientific Activity:

The research carried out in the lab is based on quantum chemical and molecular modeling methods as well as other computational techniques.

The main research areas of the studies are as follows :

  • study on substances active against the histamine H1, H2, H3 receptors,
  • interaction of the serotonin receptors with agonists and antagonists,
  • hydrogen bonding of the pharmacologically active molecules,
  • isomerism of the biologically active molecules: including conformational isomerism, tautomerism, substitutional and constitutional isomerism,
  • spectroscopy of the pharmacologically active molecules,
  • topological isomerism,
  • cell multi-drug resistance mechanisms for the anticarcinogenic drugs with use of the quantum chemical methods
  • theoretical spectroscopy - in particular studies on hydrogen bonded systems of biologically active molecules
  • substituent influence on tautomerism of heterocyclic systems

PD Scientific Projects:

PD Participation in the NMI Scientific Projects in 2007
1.18 Chiral drug analysis by using the chromatography methods
2.14: Molecular basis for drug-receptor interactions
2.15: Quantum chemical studies on molecular mechanism of cell resistance to selected anticancer drugs
2.17: Theoretical studies on intermolecular interactions of biologically active compounds by means of vibrational circular dichroism VCD method
2.18: Structural studies of pharmacologically active substances
2.19: Theoretical studies on infuence of substituennt on tautomerism of benzodiazoles and their aza-analogs
2.56: Construction of substituent effect scale based on NBO (Natural Bond Orbitals) calculations
2.57: Theoretical investigations on tautomerism of guanazole and guanosine systems and their analogs

PD cooperates with:

  1. Scientific Institutions in Poland: Chemistry Dept. of Warsaw University, Industrial Chemistry Research Institute, Institute of Physical Chemistry Polish Academy of Sciences, Institute of Organic Chemistry Polish Academy of Sciences, Warsaw Agriculture University, Interdisciplinary Centre of Mathematical and Computer Modeling (ICM) Warsaw University, Institute of Nuclear Chemistry and Technology, Institute of Chemistry, Świętokrzyska Academy
  2. Scientific Institutions abroad Poland: University of Tromso in Norway; Hebrew University in Jerusalem.

PD can accept orders for:

Molecular modeling of the pharmacologically active molecules.

PD Equipment:

The lab is equipped with Silicon Graphics and PC net with the Gaussian, Mathematica, Amber, and Spartan programs implemented

PD Publications since 2004

  • J. Sadlej, J. Cz. Dobrowolski, J. E. Rode, M. H. Jamróz,
    Density Functional Theory Study on Vibrational Circular Dichroism as a Tool for Analysis of Intermolecular Systems: (1:1) Cysteine-Water Complex Conformations,
    J. Phys. Chem. A, 2007,111,10703-10711.
  • J. Cz. Dobrowolski, M. H. Jamróz, R. Kołos, J. E. Rode, J. Sadlej,
    Theoretical prediction and the first IR-matrix observation of several L-cysteine molecule conformers,
    ChemPhysChem., 2007,8, 1085-1094.
  • J. K Maurin, F. Pluciński, A. P Mazurek, Z. Fijałek
    The usefulness of simple X-ray powder diffraction analysis for counterfeit control-The Viagra((R)) example.
    J Pharm Biomed Anal. 2007, 43, 1514-1518
  • J. E. Rode, J. Cz. Dobrowolski,
    Variation of BCP ellipticities in the course of the pericyclic and pseudopericyclic [2 + 2] cycloaddition reactions of cumulenes,
    Chem. Phys. Lett., 2007,449, 240-245.
  • M. E. Jamróz, M. Jarosz, J. Witowska-Jarosz, E. Bednarek, W. Tęcza, M. H. Jamróz, J. Cz. Dobrowolski, J. Kijeński,
    Mono-, di-, and tri-tertbutyl ethers of glycerol. A molecular spectroscopic study,
    Spectrochim. Acta, A., 2007,67,980-988.
  • J. Cz. Dobrowolski, J. E. Rode, J. Sadlej,
    Cysteine conformations revisited,
    J. Mol. Struct. (Theochem), 2007,810,129-134.
  • W. P. Ozimiński, P. Garnuszek, E. Bednarek, J. Cz. Dobrowolski,
    The Pt(II) and Pt(IV) Complexes with Histamine,
    Inorg. Chim. Acta, 2007,360,1902-1914.
  • J. E. Rode, J. Cz. Dobrowolski,
    An ab Initio Study on the Allene-Isocyanic Acid and Ketene-Vinylimine [2+2] Cycloaddition Reactions Paths
    J. Phys. Chem., 2006, 110, 3723-3737.
  • J. Sadlej, J. Cz. Dobrowolski, J. E. Rode, M. H. Jamróz,
    DFT study of vibrational circular dichroism spectra of D-lactic acid-water complexes,
    Phys. Chem. Chem. Phys., 2006. 8,101-113.
  • J. E. Rode, J. Cz. Dobrowolski,
    The Reaction Paths of the [2+2] Cycloaddition of the X=C=Y Molecules (X, Y=S or O or CH2). An ab Initio Study,
    J. Phys. Chem., 2006, 110, 207-218.
  • M. Grudzień, F. Pluciński, A. P Mazurek
    Molecular properties of econazole and sulconazole relevant to bioavailability
    Acta Pol. Pharm., 2006, 63, 465-466.
  • W. P. Ozimiński, J. Cz. Dobrowolski,
    On tautomerism, planarity, and vibrations of phospholes,
    Chem. Phys., 2005, 313,123-132.
  • M. Jarończyk, J Cz. Dobrowolski, Aleksander P. Mazurek,
    Tautomerism of 1,3-diphospholes. A DFT study,
    Chem. Phys. Lett., 2005, 406,173-178.
  • J. Cz. Dobrowolski, J. E. Rode, R. Kołos, M. H. Jamróz, K. Bajdor, A. P. Mazurek,
    Ar-matrix IR Spectra of 5-Halouracils Interpreted by Means of DFT Calculations,
    J. Phys. Chem., 2005, 109, 2167-2182.
  • J. Cz. Dobrowolski, A. P. Mazurek,
    Model Carbyne vs. Ideal and DNA Catenanes,
    J. Chem. Inf. Model., 2005, 45,1030-1038.
  • J. Cz. Dobrowolski, J. Sadlej, A. P. Mazurek,
    An ab initio study on monocyclic ?-lactam antibiotics,
    J. Mol. Struct. (Theochem),684(2004)181-186.
  • J. E. Rode, E. D. Raczyńska, E. Górnicka, J. Cz. Dobrowolski,
    Low inversion energy barrier of cytisine NH group - an expanation for the FT-IR signals splitting,
    J. Mol. Struct., 2005, 749, 51-59.
  • J. Cz. Dobrowolski, R. Kawęcki,
    Interaction of sulfinimines with boron trifluoride. A theoretical study,
    J. Mol. Struct., 2005, 734, 235-239.
  • M. Jarończyk, J. Cz. Dobrowolski, A. P. Mazurek,
    Theoretical studies on tautomerism and IR spectra of pyrazole derivative,
    J. Mol. Struct. (Theochem),2004,673, 17-28
  • W. P. Ozimiński, J. Cz. Dobrowolski, A. P. Mazurek,
    DFT studies on tautomerism of C5-substituted 1,2,4-triazoles,
    J. Mol. Struct. (Theochem), 2004, 680, 107-115
  • J. Cz. Dobrowolski, J. Sadlej, A. P. Mazurek,
    An ab initio study on monocyclic ?-lactam antibiotics,
    J. Mol. Struct. (Theochem),2004, 684, 181-186.
  • A. A. Strzelczyk, M. Jarończyk, Z. Chilmonczyk, A. P. Mazurek, E. Chojnacka-Wójcik, I. Sylte,
    Intrinsic activity and comparative molecular dynamics of buspirone analogues at the 5-HT1A receptors
    Biochem. Pharmacol., 2004, 67, 2219-2230
  • E. Górnicka, J. E. Rode, E. D. Raczyńska, B. Dasiewicz, J. Cz. Dobrowolski,
    Experimental (FT-IR and Raman) and theoretical (DFT) studies on the vibrational dynamics in cytisine,
    Vibr. Spectr. 2004, 36, 105-115.