Fulton D.B., Hrabal R., Ni, F.
Gradient-enhanced TOCSY experiments with improved sensitivity and solvent suppression.
J. Biomolecular NMR, 8, 213-218 (1996) 
    Gradient-enhanced versions of the homonuclear TOCSY expt. are described, with solvent suppression and sensitivity superior to that of a conventional TOCSY expt.  The pulse sequences are constructed by appending a WATERGATE module to a z-filtered TOCSY expt.  Pulsed-field gradients and appropriately phased selective rf pulses are used to maintain precise control of the water magnetization vector.  Problems assocd. with radiation damping and spin-locking of the water magnetization are thus alleviated.  The water magnetization is returned to equil. prior to each acquisition, which improves water suppression and minimizes signal losses due to satn. transfer.
Veverka V., Hrabal R., Durchan M, Stys D.
Studies of phospholipid binding to N-terminal domain of membrane protein light-harvesting complex II
J. Mol. Str., 523/1-3, 281-287 (2000)
    The peptide fragment of the light harvesting complex II comprising the trimerisation site binds strongly and selectively to phosphatidylglycerol while the affinity to the other LHCII-bound lipid digalactosyldiacylglycerol is negligible. Upon its binding, large aggregates of the lipid are formed which do not occur in the presence of other peptides, in particular the peptide comprising the phosphorylation site. Our observation supports a hypothesis that the trimerisation site of LHCII is also the specific binding site for phosphatidylglycerol and favors another hypothesis that the phosphorylation site is directly involved in the control of trimerisation.
Blindauer C.A., Holý A., Dvořáková H., Sigel H. 
Solution properties of antiviral adenine-nucleotide analogues. The acid-base properties of 9-[2-(phosphonomethoxy)ethyl]adenine (PMEA) and its N1, N3, and N7 deaza derivatives in aqueous solution.
J. Chem. Soc., Perkin Trans. 2, 2353 - 2363 (1997).
   The pD dependence of the 1H NMR chem. shifts of the arom. and aliph. hydrogens of 9-[2-(phosphonomethoxy)ethyl]adenine (PMEA) and of its 1-, 3- and 7-deaza derivs. have been measured in D2O at 25 °C (I = 0.1 mol dm-3, NaNO3; at pD < 1 I increases to 0.3 mol dm-3) in order to det. the sites of protonation as well as the acidity consts.  The most basic site in all these PMEAs (=PM) is the phosphonate group, -PO32-, followed by N1 in PMEA, 3- and 7-deaza-PMEA.  As in various instances the buffer regions of two successive equil. are overlapping, a micro acidity const. scheme has been developed and the consts. for the various sites calcd.; it is concluded, e.g. that about 80 of the H(7-deaza-PMEA)- species carry the proton at the phosphonate residue and 20% at N1.  The 1H NMR data indicate that the PMEAs in the form PM2- occur to some extent in an orientation similar to the anti conformation of 5'-AMP2-; i.e. the phosph(on)ate group is close to H8.  For H(3-deaza-PMEA)- the monoprotonated phosphonate group is in the vicinity of H2 in a hydrophobic region and it is suggested that this is the reason for the relatively high pKa value of about 7.8 compared with pKa x 6.9 to 7.0 for HPM- of the other PMEAs.  Finally, the acid-base properties of the PMEAs are compared with those of 5'-AMP and of tubercidin 5'-monophosphate (= 7-deaza-5'-AMP).
Blindauer C.A., Emwas A.H., Holý A., Dvořáková H., Sletten E., Sigel H. 
Complex Formation of the Antiviral 9-[2-(Phosphonomethoxy)ethyl]adenine (PMEA) and Its N1, N3, and N7 Deaza Derivatives with Copper(II) in Aqueous Solution.
Chem.Eur. J. 3, 1526 - 1536 (1997).
    The stability consts. of the 1:1 complexes formed between Cu2+ and the anions of the N1, N3, and N7 deaza derivs. of 9-[2-(phosphonomethoxy)-ethyl]adenine (PA2-), Cu(H;PA)+ and Cu(PA), were detd. by potentiometric pH titrn. in aq. soln. (25°C; I = 0.1 M, NaNO3) and compared with previous results for 9-[2-(phosphonomethoxy)ethyl]adenine (PMEA2-) and (phosphonomethoxy)ethane (PME2-).  A microconstant scheme reveals that in Cu(H;PA)+ Cu2+ is coordinated to the nucleobase, H+ being at the phosphonate group, in about 90% of the Cu(H;PMEA)+ and Cu(H;1-deaza-PMEA)+ species, but only in about 37% and 12% of the corresponding complexes with H(3-deaza-PMEA)- and H(7-deaza-PMEA)-, resp.  Straight-line plots of log KCu(R - PO3)Cu vs. pKH(R - PO3)H for simple phosph(on)ate ligands show that all the Cu(PA) complexes, including those with PMEA2- and PME2-, are more stable than expected simply from the basicity of the -PO32- group; to some extent five-membered chelates (Cu(PA)clO) involving the ether oxygen of the -CH2-O-CH2-PO32- chain are formed, and in all complexes an addnl. nucleobase-metal-ion interaction occurs.  Based on 1HNMR line-broadening measurements and structural considerations it is concluded that in Cu(3-deaza-PMEA) the interaction occurs with N7 whereas in Cu(7-deaza-PMEA), Cu(1-deaza-PMEA), and Cu(PMEA) it occurs with N3.  The proof of a metal ion-N3 interaction is important (and also of relevance regarding DNA) because so far this interaction has received little attention.  In all Cu(PA) systems three major isomeric species are in equil.; for example, 17(±3)% of Cu(PMEA) exists as an isomer with a sole Cu2+ -phosphonate coordination, 34(±10)% as Cu(PMEA)cl/O, and in 49(±10)% the Cu2+ is bound to the phosphonate group, the ether O, and N3.  In contrast, 54(±8)% of Cu(5'-AMP) occurs as an isomer with sole Cu2+ -phosphate coordination and 46(±8)% as a macrochelate involving N7 too.
Pihera P., Dvořáková H., Svoboda J. 
Diels-Alder Reactions of Vinyl Derivatives of [1]Benzothieno[3,2-b]furan. 
Collect. Czech. Chem. Commun. 64, 389 - 407 (1999).
    2-Vinyl- (I) and 3-vinyl[1]benzothieno[3,2-b]furan react with di-Me acetylenedicarboxylate, Me propiolate, maleic anhydride, or acrylonitrile endo-selectively as dienes to afford new [1]benzothieno[3,2-b][1]benzofuran derivs.  E.g., Diels-Alder reaction of I with di-Me acetylenedicarboxylate gave di-Me [1]benzothieno[3,2-b][1]furan-8,9-dicarboxylate.  Some reactions, e.g., hydrolysis, aromatization, of the Diels-Alder products were investigated.
Hocková D., Hocek M., Dvořáková H., Votruba I. 
Synthesis and Cytostatic Activity of Nucleosides and Acyclic Nucleoside Analogues Derived from 6-(Trifluoromethyl)purines.
Tetrahedron 55, 11109 – 11118 (1999).
Glycosylation and alkylation of 6-(trifluoromethyl)purine by several protected halogenoses or hydroxyalkyl chlorides afforded regio- and stereoselectively the 9-b-nucleosides or 9-alkylated purine derivs. in good yields.  Deprotection of these intermediates gave a series of nucleoside (b-D-ribofuranosyl, 2-deoxy-b-D-ribofuranosyl and b-D-arabinofuranosyl) and acyclonucleoside (2,3-dihydroxypropyl and (2-hydroxyethyl)oxymethyl) derivs. of 6-(trifluoromethyl)purine.  While 9-(b-D-ribofuranosyl)-6-(trifluoromethyl)purine showed significant cytostatic activity, the other derivs. were inactive.
Štěpánek Josef, Kowalewski Jozef, Lang Jan, Mojzeš Peter
Spectroscopic investigation of nickel cation binding with adenine nucleotides: stability and structure of the 1:2 complex with adenosine 5'-monophosphate. 
J. Biol. Inorg. Chem. 3 (1998), 543-556.
    The interaction of Ni(II) ions with adenine mononucleotides (5’-AMP, 3’-AMP, 2’-AMP, 2’,3’-cAMP, 3’,5’-cAMP) was studied in aqueous solution using Raman spectroscopy and 13C and 31P NMR paramagnetic relaxation measurements. Macrochelate structures were observed to form for all non-cyclic AMPs, with increasing stability in the series: 3’-AMP < 2’-AMP < 5’-AMP. N7 of adenine was found to be the key site of Ni(II) - adenine interaction for all non-cyclic AMPs. For 2’-AMP, an alternative binding to the pyrimidine ring may also exist.
    The dependence of Raman spectra on AMP and Ni(II) concentration confirmed the existence of a stable 1:2 Ni(II) - 5’-AMP complex, besides the 1:1 complexes. In this complex, the adenine moieties of both 5’-AMP molecules are situated close to Ni(II), and their relative orientations with respect to the cation are very similar. The paramagnetic relaxation enhancements of carbons indicate that the nickel ion is not located in the plane of the adenine units, but that the line connecting Ni(II) and N7 deviates  strongly from the adenine planes. Phosphates are outer-sphere coordinated by the cation. Findings from both methods have led us to propose possible global architectures of the complex.
Lang Jan, Chmelová Kateřina, Štěpánek Josef, Kowalewski Jozef, Holý Antonín 
Applicability of spectroscopic methods in investigation of transition metal cation binding to adenine mononucleotides and their analogues.
J. Mol. Struct. 480-481 (1999), 363-367.
    NMR paramagnetic relaxation measurement and Raman spectroscopy were applied to obtain structural information on the macrochelate complexes of nickel(II) with adenine nucleotides: adenosine monophosphates and 9-[2-(phosphonomethoxy)ethyl]adenine (PMEA). The principles of the methodological approach used are described and its reliability is discussed in terms of the results obtained.
Lang Jan, Dvořáková Hana, Bartošová Ivana, Lhoták Pavel, Stibor Ivan, Hrabal Richard 
Conformational Flexibility of a Novel Tetraethylether of Thiacalix[4]arene. A Comparison with the "Classical" Methylene-Bridged Compounds. 
Tetrahedron Lett. 40 (1999), 373-376.
    Conformational analysis of a novel tetraethylether of thiacalix[4]arene by means of NMR spectroscopy is presented. Equilibrium between three dominant conformers paco, 1,3-alt and cone exists in CDCl3 solution at room temperature. Observed chemical exchange between conformers indicates higher internal flexibility of the title compound in comparison with similar methylene bridged analogues of tetraethylethers of calix[4]arene and p-tert-butylcalix[4]arene. The cone conformer experiences additional internal motions.
Czernek Jiří, Lang Jan, Sklenář Vladimír
Ab Initio Calculations of Spin-Spin Coupling Constants in Anhydrodeoxythymidines.
J. Phys. Chem. A 104 (2000), 2788 -2792.
   For relatively large organic molecules (containing 16 non-hydrogen atoms each), anhydrodeoxythymidines, three- (3JHH) and two-bond (2JHH) 1H-1H and one-bond 1H-13C (1JCH) spin-spin coupling constants (J-couplings) were determined both experimentally and theoretically using NMR spectroscopy and density functional theory (DFT). A very good agreement between DFT-predicted and measured values was obtained for 3JHH (rmsd = 0.4 Hz). 2JHH and 1JCH were underestimated relative to the experiment. For all J-couplings investigated, noncontact contributions were negligible or canceled each other out. In general, the level of agreement between DFT and experiment is very promising.