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J Leszczynski

Publications and source records attributed to J Leszczynski.

At least 19 recordsLinked to original sources
PubMed2006

Theoretical study of adsorption of sarin and soman on tetrahedral edge clay mineral fragments.

This study provides details of the structure and interactions of Sarin and Soman with edge tetrahedral fragments of clay minerals. The adsorption mechanism of Sarin and Soman on these mineral fragments containing the Si(4+) and Al(3+) central cations was investigated. The calculations were performed using the B3LYP and MP2 levels of theory in conjunction with the 6-31G(d) basis set. The studied systems were fully optimized. Optimized geometries, adsorption energies, and Gibbs free energies of Sarin and Soman adsorption complexes were computed. The number and strength of formed intermolecular interactions have been analyzed using the AIM theory. The charge of the systems and a termination of the mineral fragment are the main contributing factors on the formation of intermolecular interactions in the studied systems. In the neutral complexes, Sarin and Soman is physisorbed on these mineral fragments due to the formation of C-H...O, and O-H...O hydrogen bonds. The chemical bond is formed between a phosphorus atom of Sarin and Soman and an oxygen atom of the -2 charged clusters containing an Al(3+) central cation and -1 charged complex containing a Si(4+) central cation (chemisorption). Sarin and Soman interact mostly in the same way with the same terminated edge mineral fragments containing different central cations. However, the interaction energies of the complexes with an Al(3+) central cation are larger than these values for the Si(4+) complexes. The interaction enthalpies of all studied systems corrected for the basis set superposition error were found to be negative. However, on the basis of the Gibbs free energy values, only strongly interacting complexes containing a charged edge mineral fragment with an Al(3+) central cation are stable at room temperature. We can conclude that Sarin and Soman will be adsorbed preferably on this type of edge mineral surfaces. Moreover, on the basis of the character of these edge surfaces, a tetrahedral edge mineral fragment can provide effective centers for the dissociation.

Journal Article↗
PubMed2006

Effect of conjugation path length on quadratic nonlinear optical properties of monomer and aggregates of zwitterionic merocyanine dyes.

We present a quantum-chemical analysis of the conjugation path length effect on first hyperpolarizabilities of a series of zwitterionic merocyanine dyes whose synthesis has been reported earlier (J. Am. Chem. Soc.2002, 124, 9431, J. Am. Chem. Soc. 1997, 119, 3144). The effect of the conjugation path lengths is evaluated to demonstrate the engineering guidelines for enhancing molecular optical nonlinearity. The first hyperpolarizabilities are calculated for extended conjugated monomer and H and J type aggregates of merocyanine dyes, to provide insight into the intermolecular interactions and the relationship between structural and collective nonlinear optical properties. The molecular geometries for monomers are obtained via B3LYP/6-31G(d,p) level optimization including the SCRF/PCM approach, and the dynamic nonlinear optical (NLO) properties for monomer and aggregates are calculated with the ZINDO/CV method, including solvent effects. It is found that the chain length dependence of the first nonlinearity peaks at n = 6 and then it starts changing slowly for monomer and aggregates of zwitterionic merocyanine dyes. It is concluded that an excellent NLO response in solution might vanish when the active chromophore forms higher H aggregates. The importance of our results on the design of electrooptic materials has been discussed.

Journal Article↗
PubMed2005

Ionization energies of argon clusters: a combined experimental and theoretical study.

We have measured appearance energies of Ar(n)+, n<or=30, by electron impact of gas phase clusters. Quantum-chemical calculations have been performed to determine the adiabatic and vertical ionization energies of argon clusters up to n=4 and 6, respectively. The experimental appearance energy of the dimer ion approaches, under suitable cluster source conditions, the adiabatic ionization energy. The agreement with values obtained by photoionization and threshold photoelectron-photoion coincidence (TPEPICO) spectra demonstrates that autoionizing Rydberg states are accessible by electron impact. Appearance energies of larger clusters, though, exceed the TPEPICO values by about 0.5 eV.

Journal Article↗
PubMed2005

The dimerization of SnCl2(g): mass spectrometric and theoretical studies.

The vaporization of SnCl2(s) was investigated in the temperature range between 382 and 504 K by the use of Knudsen effusion mass spectrometry. The Sn+, SnCl+, SnCl2+, Sn2Cl3+, and Sn2Cl4+ ions were detected in the mass spectrum of the equilibrium vapor. The SnCl2(g) and Sn2Cl4(g) gaseous species were identified, and their partial pressures were determined. The structure and vibrational properties of both species and corresponding fragmentation products were studied applying density functional theory and second-order Møller-Plesset perturbation theoretical approaches. Molecular parameters yielded thermodynamic functions by the use of statistical thermodynamics. The sublimation enthalpies of SnCl2(g) and Sn2Cl4(g) at 298 K resulting from the second- and third-law methods are evaluated as 130.9 +/- 6.2 kJ mol(-1) and 155.8 +/- 7.3 kJ mol(-1), respectively. The enthalpy changes of the dissociation reactions Sn2Cl4(g) = 2 SnCl2(g) were obtained as delta(d)H degrees(298) = 106.8 +/- 6.2 kJ mol(-1). The corresponding theoretical value amounts to 103.4 kJ mol(-1). The change of monomer properties due to the dimerization reaction is also discussed.

Journal Article↗
PubMed2005

Carotid clamping time as a risk factor for early restenosis after carotid endarterectomy.

OBJECTIVE: The aim of our study was to identify risk factors for early restenosis after carotid endarterectomy (CEA). METHODS: Prospective follow-up of 497 primary CEAs was performed at 3, 6, 12 and 24 months by clinical assessment and duplex ultrasound to identify > or = 50% restenosis. RESULTS: Early restenosis occurred in 71 (14.3%) patients. By univariate analysis high carotid clamping time (CCT) (p = 0.002) and absence of shunt use (p = 0.03) were related to early restenosis. High CCT was the only independent predictor of early restenosis in a forward stepwise logistic regression model (OR = 2.25; CI 1.2-4.1; p = 0.008). CONCLUSIONS: Carotid clamping time may be a novel risk factor for early restenosis.

Adult↗
PubMed2005

Prediction of CL-20 chemical degradation pathways, theoretical and experimental evidence for dependence on competing modes of reaction.

Highest occupied and lowest unoccupied molecular orbital energies, formation energies, bond lengths and FTIR spectra all suggest competing CL-20 degradation mechanisms. This second of two studies investigates recalcitrant, toxic, aromatic CL-20 intermediates that absorb from 370 to 430 nm. Our earlier study (Struct. Chem., 15, 2004) revealed that these intermediates were formed at high OH(-) concentrations via the chemically preferred pathway of breaking the C-C bond between the two cyclopentanes, thereby eliminating nitro groups, forming conjugated pi bonds, and resulting in a pyrazine three-ring aromatic intermediate. In attempting to find and make dominant a more benign CL-20 transformation pathway, this current research validates hydroxylation results from both studies and examines CL-20 transformations via photo-induced free radical reactions. This article discusses CL-20 competing modes of degradation revealed through: computational calculation; UV/VIS and SF spectroscopy following alkaline hydrolysis; and photochemical irradiation to degrade CL-20 and its byproducts at their respective wavelengths of maximum absorption.

Aza Compounds↗
PubMed2004

Principles of magnetodynamic chemotherapy.

Basic principles of a novel method of cancer treatment are explained. Method is based on the thermal activation of an inactive prodrug encapsulated in magnetoliposomes via Neél and Brown effects of inductive heating of subdomain superparamagnetic particles to sufficiently high temperatures. This principle may be combined with targeted drug delivery (using constant magnetic field) and controlled release (using high-frequency magnetic field) of an activated drug entrapped in magnetoliposomes. Using this method drug may be applied very selectively in the particular site of organism and this procedure may be repeated several times using e.g. stealth magnetoliposomes which are circulating in a blood-stream for several days. Moreover the magnetoliposomes concentrated by external constant magnetic field in tumor vasculature may lead to embolic lesions and necrosis of a tumor body and further the heat produced for thermal activation of a drug enhances the effect of chemotherapy by local hyperthermic treatment of neoplastic cells.

Antineoplastic Combined Chemotherapy Protocols↗
PubMed2003

Localized basis orbitals: minimization of 2-electron integrals array and orthonormality of basis set.

A new scheme for deriving localized basis orbitals (LBOs) and for obtaining integral transformations from the basis orbitals (BOs) to the LBOs has been introduced. The scheme was tested at the ab initio Hartree-Fock level using the STO-3G basis set. It has been revealed that it provides results that are close to the conventional ab initio approximations for various physical-chemical properties. At the same time, both the number of differential overlaps and the number of electron repulsion integrals (ERIs) grow with the system size notably slower than those calculated for the usual BOs. The power exponent for ERI/LBO is typically smaller by 0.3-0.6 than that for ERI/BO. The exponent reaches the value of 1.69 even for triglycine (24 atoms only), which represents a relatively small molecular model. Thus, the localization of the BOs (using LBOs) may result in additional improvements in efficiency even for electronically delocalized systems. It was shown that ERI/LBO is particularly efficient for systems with complex spatial structures (including conjugated species). The obtained results indicate that the proposed scheme could be included in computational methods targeted at calculating large molecular systems (which achieve linear scaling for more distant interactions). Neglecting ERI/LBO does not depend on the delocalization of the localized MO using ERI/LBO. The orthogonality and locality of the LBOs should make them useful in methods based on dividing the system into orthogonal subsystems.

Journal Article↗
PubMed2001

Protonation of platinated adenine nucleobases. Gas phase vs condensed phase picture.

Protonation of adenine carrying a Pt(II) moiety either at N7, N3, or N1 is possible in solution, but the site of protonation is influenced by the location of the Pt(II) electrophile and to some extent also by the overall charge of the metal entity (+2, +1, 0, -1), hence the other ligands (NH(3), Cl(-), OH(-)) bound to Pt(II). Quantum chemical calculations based on density functional theory (DFT) have been carried out for intrinsic protonation energies of adenine complexes carrying the following Pt(II) species at either of the three ring N atoms: [Pt(NH(3))(3)](2+) (1), trans- [Pt(NH(3))(2)Cl](+) (2a), cis-[Pt(NH(3))(2)Cl](+) (2b), trans-[Pt(NH(3))(2)Cl(2)] (3a), cis-[Pt(NH(3))Cl(2)] (3b), [PtCl(3)](-) (4), trans-[Pt(NH(3))(2)OH](+) (5a), cis-[Pt(NH(3))(2)(OH)](+) (5b), trans-[Pt(NH(3))(OH)(2)] (6a), cis-[Pt(NH(3))(OH)(2)] (6b), and [Pt(OH)(3)](-) (7). The data have been compared with results derived from solution studies (water) and X-ray crystallography, whenever available. The electrostatic effects associated with the charge of the metal entity have the major influence on the calculated intrinsic (gas phase) proton affinities, unlike the condensed phase data. Nevertheless, the relative gas phase trends correlate surprisingly well with condensed phase data; i.e., variation of the pK(a) values measured in solution is consistent with the calculated gas phase protonation energies. In addition to a systematic study of the ring proton affinities, proton transfer processes within the platinated adenine species were often observed when investigating Pt adducts with OH(-) ligands, and they are discussed in more detail. To the best of our knowledge, this is the first study attempting to find a systematic correlation between gas phase and condensed phase data on protonation of metalated nucleobases. The gas phase data provide a very useful complement to the condensed phase and X-ray experiments, showing that the gas phase studies are capable of valuable predictions and contribute to our understanding of the solvent and counterion effects on metal-assisted proton shift processes.

Adenine Nucleotides↗
PubMed2001

The molecular structure and electronic spectrum of the C@C60 endohedral complex: an ab initio study.

We performed ab initio quantum-chemical studies at the HF and B3LYP levels of theory to determine the geometry and electronic spectra of the C@C60 complex. The STO-3G and 6-31G(d) basis sets were employed. Two different types of stable conformations for the endohedral atom related to the centers of five- and six-member rings were found. The estimated potential barrier between those conformations is small; under certain conditions, the endohedral atom can transfer from one location in the molecular cage to another. The influence of the location of endohedral carbon atom on the electronic spectrum of C60 is discussed.

Carbon↗
PubMed2001

Tautomerism and infrared spectra of 2-thiopurine: an experimental matrix isolation and theoretical ab initio and density functional theory study.

Infrared spectra of 2-thiopurine (2-mercaptopurine, 2-purinethiol ) isolated in low-temperature Ar and N2 matrixes are reported. These spectra indicate that the compound adopts exclusively the thiol N9H tautomeric form. The theoretical calculations of relative energies of 2-thiopurine tautomers have been carried out at the MP4(SDTQ)//HF level using the 6-31G(d,p) basis set. The thiol N9H tautomer was predicted to be the most stable of all isomers of 2-thiopurine. The infrared spectra of the tautomers of 2-thiopurine have been calculated at the DFT(B3LYP)/6-31G(d,p) level. Good agreement between the experimental spectra and the spectra calculated for thiol N9H tautomer supported the identification of the dominant tautomer. It has also allowed for the reliable assignment of the bands observed in the experimental IR spectrum.

Mercaptopurine↗
PubMed2001

An ab initio theoretical study of the stereoisomers of tetrahydrocannabinols.

An extensive theoretical study of the stereoisomers of tetrahydrocannabinols has been performed at the ab initio HF/6-31G* and B3LYP/6-31G* levels. Effects of solvation were calculated with the Onsager model (with full geometry optimization), SCRF with Tomasi's PCM, and isodensity polarization continuum models. Single-point MP2//HF/6-31G* calculations were carried out. Frequency calculations for all the isomers at the HF/6-31G* level and for two natural isomers delta1-THC-RR and delta6-THC-RR at the B3LYP/6-31G* level were performed. Our results support the findings of the previous AM1 studies that the orientation of the carbocyclic ring and its C1 substituent with respect to the phenyl group hydroxyl oxygen play the major role in the activity. The calculated values of the LUMO energy (lowest unoccupied molecular orbital) and the hardness of the stereoisomers show that for the trans isomers it is easier to remove one electron from its HOMO (highest occupied molecular orbital) to the LUMO and easier to accept an electron from the receptor binding site than for the cis isomers. Combining geometric features (the orientation of the carbocyclic ring and its C1 substituent with respect to the phenyl group hydroxyl oxygen) with electronic features (LUMO and hardness), we explain the activity differences among the stereoisomers.

Computer Simulation↗
PubMed2000

The interactions of square platinum(II) complexes with guanine and adenine: a quantum-chemical ab initio study of metalated tautomeric forms.

The influence of binding of square planar platinum complexes on tautomeric equilibria of the DNA bases guanine and adenine was investigated using the density functional B3LYP method. Neutral trans-dichloro(amine)-, +1 charged chloro(diamine)-, and +2 charged triamine-platinum(II) species were chosen for coordination to bases. Only the N7 interaction site of the bases was considered. The calculations demonstrate that the neutral platinum adduct does not change the tautomeric equilibria of the bases. Furthermore, N7 binding of the neutral Pt adduct moderately reduces the probability of protonation of the N1 position of adenine. Larger effects can be observed for +1 and mainly +2 adducts, but these can be rationalized by electrostatic effects. Since the electrostatic effects are expected to be efficiently compensated for by a charged backbone of DNA and counterions in a polar solvent, no dramatic increase in mispair formation is predicted for Pt(II) adducts, which is in agreement with experiment. The interaction energies between Pt adducts and the nucleobases were also evaluated. These interaction energies range from ca. 210 kJ/mol for neutral adducts, interacting with both bases and their tautomers, up to 500 kJ/mol for the +2 charged adducts, interacting with the keto-guanine tautomer and the anti-imino-adenine tautomer. The surprisingly large interaction energy for the latter structure is due to the strong H-bond between the NH3 ligand group of the metal adduct and the N6 nitrogen atom of the base.

Adenine↗
PubMed2000

Molecular structure and vibrational raman and infrared spectra of bromochlorofluoromethane and its silicon and germanium analogs: quantum-mechanical DFT and MP2 calculations.

DFT(B3LYP) and MP2 calculations with the 6-311G(2d, 2p)-type basis set have been carried out for the prediction of molecular parameters (bond distances, bond angles, rotational constants, and dipole moments) and vibrational Raman and infrared spectra (harmonic wavenumbers, absolute intensities, Raman scattering activities, and depolarization ratios) of bromochlorofluoromethane (HCBrCIF) and its silicon and germanium analogs (HSiBrClF and HGeBrCIF). The predicted geometry and vibrational Raman and infrared spectra of HCBrClF agree well with the available experimental data for this molecule and their deuterated derivatives. This agreement allows one to believe that the predicted molecular parameters and vibrational spectra of HSiBrClF, HGeBrClF, and their deuterated derivatives will guide their future experimental studies.

Germanium↗
PubMed2000

Cation-pi and amino-acceptor interactions between hydrated metal cations and DNA bases. A quantum-chemical view.

Cation-pi interactions between cytosine and hexahydrated cations have been characterized using ab initio method with inclusion of electron correlation effects, assuming idealized and crystal geometries of the interacting species. Hydrated metal cations can interact with nucleobases in a cation-pi manner. The stabilization energy of such complexes would be large and comparable to the one for cation-pi complex with benzene. Further, polarized water molecules belonging to the hydration shell of the cation are capable to form a strong hydrogen bond interaction with the nitrogen lone electron pair of the amino groups of bases and enforce a pronounced sp3 pyramidalization of the nucleobase amino groups. However, in contrast to the benzene-cation complexes, the cation-pi configurations are highly unstable for a nucleobase since the conventional in plane binding of hydrated cations to the acceptor sites on the nucleobase is strongly preferred. Thus, a cation-pi interaction with a nucleobase can occur only if the position of the cation is locked above the nucleobase plane by another strong interaction. This indeed can occur in biopolymers and may have an effect on the local DNA architecture. Nevertheless, nucleobases have no intrinsic propensity to form cation-pi interactions.

Cations↗
PubMed1999

Metal ions in non-complementary DNA base pairs: an ab initio study of Cu(I), Ag(I), and Au(I) complexes with the cytosine-adenine base pair.

Ab initio calculations have been carried out to characterize the structure and energetics of a silver(I) complex with the cytosine-adenine DNA base pair and an aqua ligand in the coordination sphere of Ag. In addition, we have also studied analogous complexes with Cu(I) and Au(I), and structures in which adenine has been replaced by purine in order to investigate the structural role of the adenine amino group. The calculations revealed that all metal-modified structures are dominated by the metal-base interactions, while the water-metal ion interaction and many-body interligand repulsion are less important contributions. Nevertheless, the structural role of the water molecule in the complex is quite apparent and in agreement with an earlier crystallographic study. The metal-modified base pairs exhibit large conformational flexibility toward out-of-plane motions (propeller twist and buckle), comparable or, in some cases, even larger than that observed in the base pairs without metal ions. All structures have been optimized within the Hartree-Fock approximation, while interaction energies were evaluated with the inclusion of electron correlation.

Adenine↗
PubMed1998

Tautomeric equilibria in 8-oxopurines: implications for mutagenicity.

Free-radical-induced DNA damage by ionizing radiation leads to a number of oxidized purines, of which 7H-8-oxoguanine (8OG) and 7H-8-oxoadenine (8OA) are predominant and known to cause an appreciable amount of cellular damage. A detailed quantum mechanical study at various levels of theory in both the gas phase and in an aqueous solution has been carried out in order to assess the tautomeric preferences of the bases. The calculated energies of various plausible tautomers suggest that at higher levels of ab initio theory with inclusion of electron correlation, the 8-keto-6-enolic form of 8-oxoguanine (8OG2) would predominate over the 6,8-diketo form (8OG1) in the gas phase whereas the 6-amino-8-keto form (8OA1) predominates over the other possible tautomers of 8-oxoadenine. Aqueous solvation, however, changes the gas-phase order for 8-oxoguanine, 8OG1 turning out to be the major tautomeric species in an aqueous medium. The estimated free energies of hydration by polarized continuum models are indicative that the mutagenically significant amounts of minor tautomeric forms of 8-oxoguanine and 8-oxoadenine exist in the aqueous phase and might be held responsible for inducing transversional as well as transitional mutations.

Computer Simulation↗