Catalina Achim

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Name: Achim, Catalina
Organization: St. Petersburg State Chemical Pharmaceutical Academy , USA
Department: Department of Pharmaceutical Engineering
Title: Professor(PhD)

TOPICS

Co-reporter:Toby J. Woods, Heather D. Stout, Brian S. Dolinar, Kuduva R. Vignesh, Maria F. Ballesteros-Rivas, Catalina Achim, and Kim R. Dunbar
Inorganic Chemistry October 16, 2017 Volume 56(Issue 20) pp:12094-12094
Publication Date(Web):September 25, 2017
DOI:10.1021/acs.inorgchem.7b01812
The radical bridged compound [(Ni(TPMA))2-μ-bmtz•–](BF4)3·3CH3CN (bmtz = 3,6-bis(2′-pyrimidyl)-1,2,4,5-tetrazine, TPMA = tris(2-pyridylmethyl)amine) exhibits strong ferromagnetic exchange between the S = 1 NiII centers and the bridging S = 1/2 bmtz radical with J = 96 ± 5 cm–1 (−2JNi-radSNiSrad). DFT calculations support the existence of strong ferromagnetic exchange.
Co-reporter:Edward Beall, Selma Ulku, Chaoren Liu, Emil Wierzbinski, Yuqi Zhang, Yookyung Bae, Peng Zhang, Catalina Achim, David N. Beratan, and David H. Waldeck
Journal of the American Chemical Society May 17, 2017 Volume 139(Issue 19) pp:6726-6726
Publication Date(Web):April 23, 2017
DOI:10.1021/jacs.7b02260
Scanning tunneling microscope break junction measurements are used to examine how the molecular conductance of nucleic acids depends on the composition of their backbone and the linker group to the electrodes. Molecular conductances of 10 base pair long homoduplexes of DNA, aeg-PNA, γ-PNA, and a heteroduplex of DNA/aeg-PNA with identical nucleobase sequence were measured. The molecular conductance was found to vary by 12 to 13 times with the change in backbone. Computational studies show that the molecular conductance differences between nucleic acids of different backbones correlate with differences in backbone structural flexibility. The molecular conductance was also measured for duplexes connected to the electrode through two different linkers, one directly to the backbone and one directly to the nucleobase stack. While the linker causes an order-of-magnitude increase in the overall conductance for a particular duplex, the differences in the electrical conductance with backbone composition are preserved. The highest molecular conductance value, 0.06G0, was measured for aeg-PNA duplexes with a base stack linker. These findings reveal an important new strategy for creating longer and more complex electroactive, nucleic acid assemblies.
Co-reporter:Emil Wierzbinski, Ravindra Venkatramani, Kathryn L. Davis, Silvia Bezer, Jing Kong, Yangjun Xing, Eric Borguet, Catalina Achim, David N. Beratan, and David H. Waldeck
ACS Nano 2013 Volume 7(Issue 6) pp:5391
Publication Date(Web):May 21, 2013
DOI:10.1021/nn401321k
This study examines quantitative correlations between molecular conductances and standard electrochemical rate constants for alkanes and peptide nucleic acid (PNA) oligomers as a function of the length, structure, and charge transport mechanism. The experimental data show a power-law relationship between conductances and charge transfer rates within a given class of molecules with the same bridge chemistry, and a lack of correlation when a more diverse group of molecules is compared, in contrast with some theoretical predictions. Surprisingly, the PNA duplexes exhibit the lowest charge-transfer rates and the highest molecular conductances. The nonlinear rate–conductance relationships for structures with the same bridging chemistries are attributed to differences in the charge-mediation characteristics of the molecular bridge, energy barrier shifts and electronic dephasing, in the two different experimental settings.Keywords: break junction; charge transport; dephasing; molecular bridge; nucleic acids
Co-reporter:Emil Wierzbinski ; Arnie de Leon ; Xing Yin ; Alexander Balaeff ; Kathryn L. Davis ; Srinivas Reppireddy ; Ravindra Venkatramani ; Shahar Keinan ; Danith H. Ly ; Marcela Madrid ; David N. Beratan ; Catalina Achim ;David H. Waldeck
Journal of the American Chemical Society 2012 Volume 134(Issue 22) pp:9335-9342
Publication Date(Web):April 30, 2012
DOI:10.1021/ja301677z
Charge transfer (CT) properties are compared between peptide nucleic acid structures with an aminoethylglycine backbone (aeg-PNA) and those with a γ-methylated backbone (γ-PNA). The common aeg-PNA is an achiral molecule with a flexible structure, whereas γ-PNA is a chiral molecule with a significantly more rigid structure than aeg-PNA. Electrochemical measurements show that the CT rate constant through an aeg-PNA bridging unit is twice the CT rate constant through a γ-PNA bridging unit. Theoretical calculations of PNA electronic properties, which are based on a molecular dynamics structural ensemble, reveal that the difference in the CT rate constant results from the difference in the extent of backbone fluctuations of aeg- and γ-PNA. In particular, fluctuations of the backbone affect the local electric field that broadens the energy levels of the PNA nucleobases. The greater flexibility of the aeg-PNA gives rise to more broadening, and a more frequent appearance of high-CT rate conformations than in γ-PNA.
Co-reporter:Arnie R. de Leon, Abiola O. Olatunde, Janet R. Morrow, and Catalina Achim
Inorganic Chemistry 2012 Volume 51(Issue 23) pp:12597-12599
Publication Date(Web):November 13, 2012
DOI:10.1021/ic301790v
Substitution of a nucleobase pair with a pair of 1,2-hydroxypyridinone (1,2-HOPO) ligands in the center of a 10-base-pair peptide nucleic acid (PNA) duplex provides a strong binding site for EuIII as evidenced by UV thermal melting curves, UV titrations, and luminescence spectroscopy. EuIII excitation spectra and luminescence lifetime data are consistent with EuIII bound to both 1,2 HOPO ligands in a PNA-HOPO duplex as the major species present in solution.
Co-reporter:Hoa V. Phan;Pradip Chakraborty;Meimei Chen;Yitzi M. Calm;Dr. Kirill Kovnir;Lawrence K. Keniley Jr.;Jordan M. Hoyt;Elisabeth S. Knowles;Dr. Céline Besnard; Mark W. Meisel; Andreas Hauser; Catalina Achim; Michael Shatruk
Chemistry - A European Journal 2012 Volume 18( Issue 49) pp:15805-15815
Publication Date(Web):
DOI:10.1002/chem.201202045

Abstract

Three iron(II) complexes, [Fe(TPMA)(BIM)](ClO4)2⋅0.5H2O (1), [Fe(TPMA)(XBIM)](ClO4)2 (2), and [Fe(TPMA)(XBBIM)](ClO4)2 ⋅0.75CH3OH (3), were prepared by reactions of FeII perchlorate and the corresponding ligands (TPMA=tris(2-pyridylmethyl)amine, BIM=2,2′-biimidazole, XBIM=1,1′-(α,α′-o-xylyl)-2,2′-biimidazole, XBBIM=1,1′-(α,α′-o-xylyl)-2,2′-bibenzimidazole). The compounds were investigated by a combination of X-ray crystallography, magnetic and photomagnetic measurements, and Mössbauer and optical absorption spectroscopy. Complex 1 exhibits a gradual spin crossover (SCO) with T1/2=190 K, whereas 2 exhibits an abrupt SCO with approximately 7 K thermal hysteresis (T1/2=196 K on cooling and 203 K on heating). Complex 3 is in the high-spin state in the 2–300 K range. The difference in the magnetic behavior was traced to differences between the inter- and intramolecular interactions in 1 and 2. The crystal packing of 2 features a hierarchy of intermolecular interactions that result in increased cooperativity and abruptness of the spin transition. In 3, steric repulsion between H atoms of one of the pyridyl substituents of TPMA and one of the benzene rings of XBBIM results in a strong distortion of the FeII coordination environment, which stabilizes the high-spin state of the complex. Both 1 and 2 exhibit a photoinduced low-spin to high-spin transition (LIESST effect) at 5 K. The difference in the character of intermolecular interactions of 1 and 2 also manifests in the kinetics of the decay of the photoinduced high-spin state. For 1, the decay rate constant follows the single-exponential law, whereas for 2 it is a stretched exponential, reflecting the hierarchical nature of intermolecular contacts. The structural parameters of the photoinduced high-spin state at 50 K are similar to those determined for the high-spin state at 295 K. This study shows that N-alkylation of BIM has a negligible effect on the ligand field strength. Therefore, the combination of TPMA and BIM offers a promising ligand platform for the design of functionalized SCO complexes.

Co-reporter:Emil Wierzbinski, Arnie de Leon, Kathryn L. Davis, Silvia Bezer, Matthäus A. Wolak, Matthew J. Kofke, Rudy Schlaf, Catalina Achim, and David H. Waldeck
Langmuir 2012 Volume 28(Issue 4) pp:1971-1981
Publication Date(Web):January 4, 2012
DOI:10.1021/la204445u
We studied the charge transfer properties of bipyridine-modified peptide nucleic acid (PNA) in the absence and presence of Zn(II). Characterization of the PNA in solution showed that Zn(II) interacts with the bipyridine ligands, but the stability of the duplexes was not affected significantly by the binding of Zn(II). The charge transfer properties of these molecules were examined by electrochemistry for self-assembled monolayers of ferrocene-terminated PNAs and by conductive probe atomic force microscopy for cysteine-terminated PNAs. Both electrochemical and single molecular studies showed that the bipyridine modification and Zn(II) binding do not affect significantly the charge transfer of the PNA duplexes.
Co-reporter:Silvia Bezer ; Srinivas Rapireddy ; Yury A. Skorik ; Danith H. Ly
Inorganic Chemistry 2011 Volume 50(Issue 23) pp:11929-11937
Publication Date(Web):November 7, 2011
DOI:10.1021/ic200855p
Peptide nucleic acid (PNA) is a synthetic analogue of DNA, which has the same nucleobases as DNA but typically has a backbone based on aminoethyl glycine (Aeg). PNA forms duplexes by Watson Crick hybridization. The Aeg-based PNA duplexes adopt a chiral helical structure but do not have a preferred handedness because they do not contain a chiral center. An l-lysine situated at the C-end of one or both strands of a PNA duplex causes the duplex to preferably adopt a left-handed structure. We have introduced into the PNA duplexes both a C-terminal l-lysine and one or two PNA monomers that have a γ-(S)-methyl-aminoethyl glycine backbone, which is known to induce a preference for a right-handed structure. Indeed, we found that in these duplexes the γ-methyl monomer exerts the dominant chiral induction effect causing the duplexes to adopt a right-handed structure. The chiral PNA monomer had a 2,2′:6′,2″-terpyridine (Tpy) ligand instead of a nucleobase and PNA duplexes that contained one or two Tpys formed [Cu(Tpy)2]2+ complexes in the presence of Cu2+. The CD spectroscopy studies showed that these metal-coordinated duplexes were right-handed due to the chiral induction effect exerted by the S-Tpy PNA monomer(s) except for the cases when the [Cu(Tpy)2]2+ complex was formed with Tpy ligands from two different PNA duplexes. In the latter case, the metal complex bridged the two PNA duplexes and the duplexes were left-handed. The results of this study show that the preferred handedness of a ligand-modified PNA can be switched as a consequence of metal coordination to the ligand. This finding could be used as a tool in the design of functional nucleic-acid based nanostructures.
Co-reporter:Zhijie Ma, Frank Olechnowicz, Yury A. Skorik, and Catalina Achim
Inorganic Chemistry 2011 Volume 50(Issue 13) pp:6083-6092
Publication Date(Web):June 2, 2011
DOI:10.1021/ic200138b
The substitution of nucleobases in nucleic acid duplexes with ligands that have high affinity for transition metal ions creates metal-binding sites at specific locations within the duplexes. Several studies on the incorporation of metal ions into DNA and peptide nucleic acid (PNA) duplexes have suggested that the stability constant of the metal complex formed within the duplexes is a primary determinant of the thermal stability of the duplexes. To understand this relationship, we have synthesized two PNA monomers that carry the same ligand, namely 8-hydroxyquinoline, but have this ligand attached differently to the PNA backbone. The PNA monomers have been incorporated into PNA duplexes. UV and CD spectroscopy and calorimetric studies of the 8-hydroxyquinoline–PNA duplexes showed that the effect of the stability of the metal complex on the PNA duplexes was significantly modulated by the steric relationship between the complex and the duplex. This information is useful for the construction of hybrid inorganic–nucleic acid nanostructures.
Co-reporter:Wei He, Matthew J. Crawford, Srinivas Rapireddy, Marcela Madrid, Roberto R. Gil, Danith H. Ly and Catalina Achim  
Molecular BioSystems 2010 vol. 6(Issue 9) pp:1619-1629
Publication Date(Web):13 Apr 2010
DOI:10.1039/C002254C
This paper presents the results of an NMR spectroscopy and distance-restrained molecular dynamics (MD) study of a γ-methylated, palindromic, 8-base pair peptide nucleic acid (γ-PNA) duplex. The goal of this study was to examine the impact of the γ-backbone modification on the structure of the PNA duplex. The 2D NMR information involving the backbone methyl group, especially the NOEs between the methyl protons and those of the amide and methylene groups of the backbone, led to distance restraints useful in the elucidation of the structure of the backbone of γ-PNA. Integration of the NOE peaks resulted in 138 inter-proton distance restraints, which were used in ten independent simulated annealing followed by 2 ns restrained MD runs. These simulations led to the conclusion that the γ-PNA duplex adopts a general P-form helical structure similar to that observed for non-modified PNA but with a smaller base pair rise, which is an A-like helical feature, and a slight helical bending towards the major groove (PDB ID 2KVJ). These properties of the γ-PNA duplex may be induced by the γ-methyl group. A similar effect of the methyl group was revealed by a previous NMR study of single stranded γ-PNA [A. Dragulescu-Andrasi, S. Rapireddy, B. M. Frezza, C. Gayathri, R. R. Gil and D. H. Ly, J. Am. Chem. Soc., 2006, 128, 10258–10267]. It appears that the steric constraint exerted by the γ-methyl on the backbone orientation is relatively independent of the base pairing and stacking and thus is likely to manifest when other substituents are introduced at the γ-position of the PNA.
Co-reporter: Joanne I. Yeh;Dr. Ehmke Pohl;Daphne Truan;Dr. Wei He; George M. Sheldrick;Dr. Shoucheng Du; Catalina Achim
Chemistry - A European Journal 2010 Volume 16( Issue 39) pp:11867-11875
Publication Date(Web):
DOI:10.1002/chem.201000392

Abstract

Peptide nucleic acid (PNA) is a synthetic analogue of DNA that commonly has an N-aminoethyl glycine backbone. The crystal structures of two PNA duplexes, one containing eight standard nucleobase pairs (GGCATGCC)2, and the other containing the same nucleobase pairs and a central pair of bipyridine ligands, have been solved with a resolution of 1.22 and 1.10 Å, respectively. The non-modified PNA duplex adopts a P-type helical structure similar to that of previously characterized PNAs. The atomic-level resolution of the structures allowed us to observe for the first time specific modes of interaction between the terminal lysines of the PNA and the backbone and the nucleobases situated in the vicinity of the lysines, which are considered an important factor in the induction of a preferred handedness in PNA duplexes. Our results support the notion that whereas PNA typically adopts a P-type helical structure, its flexibility is relatively high. For example, the base-pair rise in the bipyridine-containing PNA is the largest measured to date in a PNA homoduplex. The two bipyridines bulge out of the duplex and are aligned parallel to the major groove of the PNA. In addition, two bipyridines from adjacent PNA duplexes form a π-stacked pair that relates the duplexes within the crystal. The bulging out of the bipyridines causes bending of the PNA duplex, which is in contrast to the structure previously reported for biphenyl-modified DNA duplexes in solution, where the biphenyls are π stacked with adjacent nucleobase pairs and adopt an intrahelical geometry. This difference shows that relatively small perturbations can significantly impact the relative position of nucleobase analogues in nucleic acid duplexes.

Co-reporter:MatthewG. Hilfiger;Meimei Chen;TatianaV. Brinzari;TanyaM. Nocera;Michael Shatruk;DorosT. Petasis ;JaniceL. Musfeldt ;KimR. Dunbar
Angewandte Chemie International Edition 2010 Volume 49( Issue 8) pp:1410-1413
Publication Date(Web):
DOI:10.1002/anie.200906264
Co-reporter:MatthewG. Hilfiger;Meimei Chen;TatianaV. Brinzari;TanyaM. Nocera;Michael Shatruk;DorosT. Petasis ;JaniceL. Musfeldt ;KimR. Dunbar
Angewandte Chemie 2010 Volume 122( Issue 8) pp:1452-1455
Publication Date(Web):
DOI:10.1002/ange.200906264
Co-reporter:Amit Paul ; Silvia Bezer ; Ravindra Venkatramani ; Laura Kocsis ; Emil Wierzbinski ; Alexander Balaeff ; Shahar Keinan ; David N. Beratan ; Catalina Achim ;David H. Waldeck
Journal of the American Chemical Society 2009 Volume 131(Issue 18) pp:6498-6507
Publication Date(Web):April 21, 2009
DOI:10.1021/ja9000163
Self-assembled monolayers of single-stranded (ss) peptide nucleic acids (PNAs) containing seven nucleotides (TTTXTTT), a C-terminus cysteine, and an N-terminus ferrocene redox group were formed on gold electrodes. The PNA monomer group (X) was selected to be either cytosine (C), thymine (T), adenine (A), guanine (G), or a methyl group (Bk). The charge transfer rate through the oligonucleotides was found to correlate with the oxidation potential of X. Kinetic measurements and computational studies of the ss-PNA fragments show that a nucleobase mediated charge transport mechanism in the deep tunneling superexchange regime can explain the observed dependence of the kinetics of charge transfer on the PNA sequence. Theoretical analysis suggests that the charge transport is dominantly hole-mediated and takes place through the filled bridge orbitals. The strongest contribution to conductance comes from the highest filled orbitals (HOMO, HOMO-1, and HOMO-2) of individual bases, with a rapid drop off in contributions from lower lying filled orbitals. Our studies further suggest that the linear correlation observed between the experimental charge transfer rates and the oxidation potential of base X arises from weak average interbase couplings and similar stacking geometries for the four TTTXTTT systems.