ItemThermally reversible and irreversible interstrand photocrosslinking of 5-chloro-2′-deoxy-4-thiouridine modified DNA oligonucleotides(Royal Society of Chemistry, 2021) Nowak-Karnowska, Joanna; Zielińska, Karolina; Milecki, Jan; Skalski, BohdanW artykule opisano wysoce wydajne międzyniciowe fotozszywanie dupleksu DNA zawierającego 5-chloro-2′-deoksy-4-tiourydynę (ClSdU) w jednej nici, przebiegające w dwuetapowej kaskadzie fotochemicznej, polegające na tworzeniu w pierwszym etapie reakcji odwracalnego termicznie wiązania kowalencyjnego pomiędzy ClSdU i tymidyną w nici docelowej i późniejszą konwersję do stabilnego termicznie fluorescencyjnego międzyniciowego crosslinku. Wyniki te pokazują, że ClSdU ma ogromny potencjał, aby stać się cennym czynnikiem fotosieciującym DNA. ItemFT-TR, UV-VISIBLE AND X-RAY STUDIES OF COMPLEXES OF PYRIDINE N-OXIDES WITH PENTACHLOROPHENOL(1995-11-01) Dega-Szafran, Zofia; Grunwald-Wyspianska, Monika; Kania, Anna; Kosturkiewicz, Zofia; Tykarska, Ewa; Szafran, MirosławThe crystal structure of the 4-methoxy-2,6-dimethylpyridine N-oxide pentachlorophenol complex has been determined by X-ray analysis. The O ... O distance is 2.439(6) Angstrom, the OHO angle is 152.3 degrees and the hydrogen-bonded proton is close to the phenol molecule. The FT-IR spectra of pentachlorophenol complexes with some substituted pyridine N-oxides in the solid state and seven aprotic solvents of different polarity (epsilon from 2.27 to 37.5) show a broad absorption. The broad absorption shows weak dependence upon solvent polarity and is classified as type (ii). UV spectra show that in the investigated complexes protons are not transferred from the phenol to the N-oxides. Formamide (epsilon = 111) is a much stronger proton acceptor than the pyridine N-oxides. Pentachlorophenol in formamide is converted to the phenolate ion. ItemStructural, spectroscopic and theoretical studies of dimethylphenyl betaine complex with two molecules of 2,6-dichloro-4-nitro-phenol(2015-02-05) Szafran, Mirosław; Komasa, Anna; Ostrowska, Kinga; Katrusiak, Andrzej; Dega-Szafran, ZofiaThe 1:2 complex (1) of dimethylphenyl betaine (DMPB) with two molecules of 2,6-dichloro-4-nitro-phenol (DCNP) was prepared and characterized by X-ray diffraction, B3LYP/6-311++G(d,p) and B3LYP-D3/6-311++G(d,p)calculations, FTIR and NMR spectroscopies. The crystal is monoclinic, space group P2(1)/c with Z = 4. The protons at the oxygen atoms of phenols are bonded to each oxygen atoms of the DMPB carboxylate group by two nonequivalent H-bonds with the O-H center dot center dot center dot O distances of 2.473(5) and 2.688(4) angstrom. Both H-bonds in the optimized structures 2 (in vacuum), 3 (in DMSO solution) and dispersion-correlated functional (D3) 4 (in vacuum) are comparable and are slightly shorter than O(6)-H(O6)center dot center dot center dot O(2) in the crystal. The FOR spectrum of 1 shows a broad absorption in the 3400-2000 cm(-1) region corresponding to a longer hydrogen bond and a broad absorption in the 1800-500 cm(-1) region caused by the shorter H-bond. The relations between the experimental C-13 and H-1 chemical shifts (delta(exp)) of the investigated compound 1 in DMSO solution and GIAO/B3LYP/6-311++G(d,p) magnetic isotropic shielding constants (sigma(calc)) obtained by using the screening solvation model (COSMO) for 3 are linear and reproduce well the experimental chemical shifts described by the equation: delta(exp) = a + b sigma(calc). ItemMolecular structure of 8-hydroxy-1-methylquinolinium iodide hydrate in crystal and solution(2006-06-29) Barczyński, Piotr; Komasa, Anna; Ratajczak-Sitarz, Małgorzata; Katrusiak, Andrzej; Brzezinski, Bogumil8-Hydroxy-1-methylquinolinium iodide monohydrate [(C10H10NO)I-+(-) H2O] has been studied by X-ray diffraction, FF-IR, H-1 and C-13 NMR spectroscopy. In the crystalline state, the iodide anion is hydrogen-bonded to the water molecule, which in turn is hydrogen bonded to the 8-OH group of the 8-hydroxyquinolinium ring, forming of a symmetric dimer. In acetonitrile and DMSO-d(6) the hydrate assumes a new structure due to almost complete dissociation of the water molecule from the complex structure. In acetonitrile the 8-OH group is hydrogen-bonded to the iodide anion, whereas in DMSO-d(6) it forms the hydrogen bond with the solvent molecules. This 8-OH... O(DMSO-d(6)) hydrogen bond is the strongest within the structure of the hydrate. ItemMolecular structure, hydrogen bonding and spectroscopic properties of the complex of piperidine-4-carboxylic acid with chloroacetic acid(2008-10-29) Komasa, Anna; Katrusiak, Andrzej; Szafran, Mirosław; Barczyński, Piotr; Dega-Szafran, ZofiaComplex of piperidine-4-carboxylic acid with chloroacetic acid has been studied by X-ray diffraction, FTIR, Raman, H-1 and C-13 NMR spectroscopy and B3LYP/6-31G(d,p) calculations. In crystal the piperidine ring is protonated and adopts a chair conformation with the COOH group in the equatorial position. The COO- group of chloroacetate unit is engaged in three hydrogen bonds: O(1)-H(1)center dot center dot center dot O(3) of 2.604(2) angstrom, N(1)-H(12)center dot center dot center dot O(3) of 2.753(2) angstrom and N(1)-H(11)center dot center dot center dot O(4) of 2.760(2) angstrom. According to the B3LYP calculations the isolated complexes both in vacuum and H2O solution have cyclic structures. In vacuum the molecules are connected by two H-bonds: the COOH group of chloroacetic acid is engaged with piperidine-4-carboxylic acid, one with the nitrogen atom, O(4)-H center dot center dot center dot N(1) of 2.658 angstrom and the second with carboxyl group, O(1)-H center dot center dot center dot O(3) of 2.860 angstrom. In water solution piperidine-4-carboxylic acid is protonated and forms two hydrogen bonds with the chloroacetate unit: N(1)-H center dot center dot center dot O(4) of 2.690 angstrom and O(1)-H center dot center dot center dot O(3) of 2.611 angstrom. Powder FTIR spectra of the complex and its deuterated analogue are consistent with the X-ray structure. Correlations between the experimental H-1 and C-13 chemical shifts of the complex investigated and the GIAO/B3LYP/6-31G(d,p) calculated magnetic isotropic shielding tensors (sigma(calc)) in vacuum and within the conductor-like screening continuum solvation model (COSMO) in H2O, delta(exp) = a + b sigma(calc), are reported. ItemSupramolecular structure of the 1:2 complex of 1,4-dimethylpiperazine mono-betaine with squaric acid(2013-07-01) Dega-Szafran, Zofia; Katrusiak, Andrzej; Komasa, Anna; Szafran, MirosławThe 1: 2 complex of 1,4-dimethylpiperazine mono-betaine (MBPZ) with squaric acid (H(2)SQ) has been characterised by single-crystal X-ray analysis, FTIR and NMR spectroscopies, and by DFT calculations. The crystals are monoclinic, space group P2(1)/c. Two MBPZ cations and four hydrogen squarate anions (HSQ(-)) are linked by strong O(1)=H center dot center dot center dot O(13) (2.525(4) angstrom), O(14)-H center dot center dot center dot O(21) (2.511(4) angstrom) and N(4)-H center dot center dot center dot O(23) (2.607(3)angstrom) hydrogen bonds into a cyclamer R-6(6)(38). In turn, the cyclamers are linked into a helix C-4(4)(20) through two O(24)-H center dot center dot center dot O(11) hydrogen bonds of 2.516(4)angstrom. The piperazinium ring has a chair conformation with N(4)-CH3 and N(1)-CH2COOH substituents in the equatorial positions, and N(1)-CH3 in the axial position. The FTIR spectrum is consistent with the crystal data. Two models of the 1: 2 complex of MBPZ with H(2)SQ have been optimised at the B3LYP/6-311++G(d,p) level of theory and have been used to calculate harmonic IR frequencies. One of the models (2) is dominated by electrostatic attraction between NH(4)(+) and HSQ(-), whereas in the other (3) squaric acid interacts with a zwitterionic MBPZ through the O-H center dot center dot center dot O and O-H center dot center dot center dot N hydrogen bonds. ItemExcitation energy of 9Be(American Physical Society, 2006-05) Pachucki, Krzysztof; Komasa, JacekThe high precision relativistic and radiative corrections to the energy of the excited 3 S-1 state of the beryllium atom are obtained. The nonrelativistic wave function, expanded in a basis of exponentially correlated Gaussian functions, yields the lowest upper bounds to the energy of 2 S-1 and 3 S-1 states. By means of the integral representation, a reference-quality Bethe logarithm has been obtained. The resulting theoretical 2 S-1-3 S-1 transition energy amounts to 54 677.78(45) cm(-1) and differs from the known experimental value by about 0.5 cm(-1). ItemDealing with communicative problems in English as a lingua franca(Vilnius University Publishing House, 2008) Nowicka, AgnieszkaThese days English happens to be one of the most widely used languages of international communication. Speakers communicating in English as a lingua franca have a diverse linguistic command of it. However, these are not only the problems of linguistic (structural) origin that speakers need to deal with while interacting in English. In the article, I aim to discuss, first, how the differences in socio-cultural interaction styles can influence communication, second, what is interaction participants’ orientation to the problems originating in those differing styles and, finally, how such problems are negotiated in communication. Ethnomethodological conversation analysis is used to analyze illustrative excerpt of interaction in English. ItemRovibrational levels of HD(ROYAL SOCIETY OF CHEMISTRY, 2010) Pachucki, Krzysztof; Komasa, JacekThe dissociation energies of all rotation-vibrational states of the molecular HD in the ground electronic state are calculated to a high accuracy by including nonadiabatic, relativistic alpha(2), and quantum electrodynamic alpha(3) effects, with approximate treatment of small higher order alpha(4), and finite nuclear size corrections. The obtained result for the ground molecular state of 36 405.7828(10) cm(-1) is in a small disagreement with the latest most precise experimental value. ItemThe ground state of (He-H-He)(+) from correlated ab initio calculations(POLISH CHEMICAL SOCIETY, 1998-07) Komasa, Jacek; Rychlewski, JacekHe2H+ ion in its ground state is studied by means of ab initio methods taking into account the electron correlation. Geometry optimization at the CCSD(T)/cc-pV5Z level of theory has been performed and the potential energy hypersurface scan is presented. The optimum conformation is linear and symmetric with the proton at the He-He midpoint and the He-H distance equal to 1.75 bohr. Stabilization energy with respect to the He2H+ --> HeH+ + He dissociation channel has been computed. Additionally, a single point variational calculations with the use of the Exponentially Correlated Gaussian wave functions have been performed. They supply an upper bound to both the total electronic energy (-5.903505 hartree) and the stabilization energy (-13.224 kcal/mol). A comparison of the results from both the perturbational coupled cluster and variational methods is presented. ItemTHE NUCLEAR MAGNETIC SHIELDING AND SPIN-ROTATION CONSTANTS OF THE HYDROGEN MOLECULE(Elsevier, 1995-04-07) Komasa, Jacek; Rychlewski, Jacek; Raynes, William T.The variation-perturbation method, employing an explicitly correlated basis set in the form of Gaussian functions with exponential correlation factors, has been used to calculate the paramagnetic component of the nuclear magnetic shielding and the electronic contribution to the spin-rotation constant for the hydrogen molecule in its ground state. The diamagnetic components of the shielding tensor have also been computed. The computations have been performed for three internuclear distances in the vicinity of equilibrium. A comparison of the calculated quantities, which are of high accuracy, with the experimental data reveals a small but significant discrepancy between theory and experiment. ItemBethe logarithm for the lithium atom from exponentially correlated Gaussian functions(AMERICAN PHYSICAL SOCIETY, 2003-10-27) Pachucki, Krzysztof; Komasa, JacekThe calculation of Bethe logarithm for the ground state of the lithium atom is presented. The Bethe logarithm is the main QED effect coming from the electron self-interaction, which has not been obtained yet. Both results for the infinite nuclear mass, ln k = 5.178 17(3), and the mass polarization correction, Delta ln k = 0.114(3), significantly improve the hitherto theoretical values for the lithium ground-state energy. They allow from one side to test the theory against precise measurements of transition frequencies and from the other side, to improve the accuracy of determination of the difference in the square of nuclear charge radii from the isotope-shift measurements. The applied calculational method is based on the well adapted explicitly correlated Gaussian basis set and can be extended to other few-electron atoms and molecules. ItemOn the acceleration of the convergence of singular operators in Gaussian basis sets(AMERICAN INSTITUTE OF PHYSICS, 2005-05-08) Pachucki, Krzysztof; Cencek, Wojciech; Komasa, JacekGaussian type wave functions do not reproduce the interparticle cusps which result in a slow convergence of the expectation values of the operators involved in calculations of the relativistic and QED energy corrections. Methods correcting this deficiency are the main topic discussed in this paper. Benchmark expectation values of the singular operators for several few-electron systems are presented. ItemA new approach to Kołos-Wolniewicz wave functions(Polish Chemical Society, 2004) Kubacki, Tomasz; Komasa, JacekThe Kołos-Wolniewicz (KW) wave functions are well known in quantum chemistry. In this work we study a possibility of generalization of KW functions towards greater flexibility and compactness. We report on a new approach to evaluation of integrals which allows numerical integration to be avoided. Some preliminary results illustrating an acceleration in energy convergence are reported. ItemExponentially correlated Gaussian functions in variational calculations. The EF singlet-Sigma-g-+ state of hydrogen molecule(scientific Publishers OWN, 2004) Komasa, Jacek; Cencek, WojciechThe Born-Oppenheimer (BO) potential energy curve, the adiabatic and the relativistic corrections for the EF state of the hydrogen molecule are calculated for the internuclear distances ranging from 0.01 to 20 bohr. 600-term variational expansions of exponentially correlated Gaussian (ECG) functions are used. The BO energies and the adiabatic corrections are more accurate than previously reported and the relativistic calculations confirm existing literature values. ItemThe Sigma- states of the molecular hydrogen(The Royal Society of Chemistry, 2008-05-08) Komasa, JacekA class of doubly excited electronic states of the hydrogen molecule is reported. The states are of Sigma− symmetry and are located ca. 200000 cm−1 above the ground state and about 75000 cm−1 above the ionization threshold. The electronic wave functions employed to described these states have been expanded in the basis of exponentially correlated Gaussian (ECG) functions with the nonlinear parameters variationally optimized. The lowest triplet-Sigma−g and singlet-Sigma−u states dissociate into hydrogen atoms in the n = 2 state, whereas the lowest triplet-Sigma−u and singlet-Sigma−g states have H(n = 2) and H(n = 3) as the dissociation products. All the four states are attractive and accommodate vibrational levels. The location of the vibrational energy levels has been determined by solving the radial Schrödinger equation within the Born–Oppenheimer approximation. ItemExponentially correlated Gaussian functions in variational calculations. Momentum space properties of the ground state helium dimer(American Institute of Physics, 2001-07-01) Komasa, JacekMicrohartree accuracy wave functions composed of exponentially correlated Gaussians were transformed in closed form to momentum space representation and applied to compute various isotropic momentum space properties of helium dimer in the ground state. The set of properties includes electron momentum density distribution, expectation values of powers of the electronic momentum operator, and the Compton profile. Calculations were performed at many internuclear separations R including the united atom (beryllium) and the separated atoms (helium) limits. ItemOrtho-para transition in molecular hydrogen(American Physical Society, 2008-03-14) Pachucki, Krzysztof; Komasa, JacekThe radiative ortho-para transition in molecular hydrogen is studied. This highly forbidden transition is very sensitive to relativistic and subtle nonadiabatic effects. Our result for the transition rate in the ground vibrational level Γ(J=1→J=0)=6.20(62)×10−14 yr−1 is significantly lower in comparison to all the previous approximate calculations. Experimental detection of such a weak line by observation of, for example, cold interstellar molecular hydrogen is at present unlikely. ItemDipole and quadrupole polarizabilities and shielding factors of beryllium from exponentially correlated Gaussian functions(American Physical Society, 2001-12-14) Komasa, JacekDynamic dipole and quadrupole polarizabilities as well as shielding factors of the beryllium atom in the ground state were computed at real frequencies by using the variation-perturbation method. The zeroth- and the first-order wave functions were expanded in many-electron basis of exponentially correlated Gaussian functions. The 1600-term expansion of the unperturbed wave function yielded the ground-state energy accurate to 1 cm-1. The first-order wave functions were expanded in very large bases (4800 and 4400 terms). The nonlinear parameters of the first-order correction functions were optimized with respect to both the static and dynamic polarizabilities, and with respect to the excited-state energies. The procedure employed ensures a high accuracy of determination of dynamic properties in a wide range of frequencies and correct positions of the transition poles. Test calculations, performed on He and Li, confirmed the ability of this method to obtain the atomic properties with very high accuracy. The final values of the static properties of Be were 37.755 e2a02EH-1 and 300.96 e2a04EH-1 for the dipole and quadrupole polarizabilities, respectively, and 1.4769 for the quadrupole shielding factor. The convergence of the atomic properties with the size of the expansion of both the zeroth- and first-order functions was checked. Thanks to very high accuracy of the unperturbed wave function and the efficient method of construction of the first-order wave functions, the dynamic polarizability results presented in this work are of benchmark quality. As a by-product of this project, a set of the most accurate upper bounds to the energies of 1P and 1D states of Be was obtained. ItemNonadiabatic corrections to rovibrational levels of H2(American Institute of Physics, 2009) Pachucki, Krzysztof; Komasa, JacekThe leading nonadiabatic corrections to rovibrational levels of a diatomic molecule are expressed in terms of three functions of internuclear distance: corrections to the adiabatic potential, the effective nuclear mass, and the effective moment of inertia. The resulting radial Schrödinger equation for nuclear motion is solved numerically yielding accurate nonadiabatic energies for all rovibrational levels of the H2 molecule. Results for states with J ≤ 10 are in excellent agreement with previous calculations by Wolniewicz, and for states with J>10 are new.