Modeling of recognition sites of nucleic acid bases aaand amide side chains of amino acids. Combination of experimental and theoretical approaches

A combined experimental-theoretical approach to modeling of building blocks of recognition complexes formed by nucleic acid bases and the amino-acids side-chain amino group is reviewed. The approach includes the temperature dependent field-ionization mass spectrometry and ab initio quantum chemical calculations. The mass spectrometric technique allows determination of interaction enthalpies of biomolecules in the gas phase, and the results it produces are directly comparable to the results obtained through theoretical modeling. In our works we have analyzed both thermodynamic and structural aspects of the recognition complexes of four canonical nucleic acid bases and acrylamide, which models the side chain of asparagine and glutamine. It has been shown that all bases can interact with amide group of the amino acids via their Watson-Crick sites when being incorporated into a single strand DNA or RNA. Stability of the complexes studied, expressed as - ΔH (kJ mole^-1) decreases as: m⁹Gua (- 59.5) > m ¹Cyt (- 57.0) > m ⁹Ade (- 52.0) ≫m ¹Ura (- 40.6). We have determined that in the double stranded DNA only purine bases can be recognized. Received 5 February 2002 and Received in final form 14 March 2002 Published online 13 September 2002     

The role of enhanced aromatic -electron donating aptitude of the tyrosyl sidechain with respect to that of phenylalanyl in intramolecular interactions

An exhaustive ab initio and DFT search for energetically stable conformers from the topologically possible set was undertaken on the N-acetyl-phenylalanyl-N-methylamide and N-acetyl-tyrosyl-N-methylamide systems. The geometries of all 81 phenylalanyl and 162 tyrosyl possible rotamers, described under the rules outlined by Multi-Dimensional Conformational Analysis (MDCA), were attempted at each of the RHF/3-21G, RHF/6-31G(d) and B3LYP/6-31G(d) levels of theory. A total of 32 and 66 stable conformational minima were found for the phenylalanyl and tyrosyl amino acid diamides, respectively, at the B3LYP/6-31G(d) level. From the tyrosyl set, 33 unique conformers emerge when the orientation of the A _i ³ dihedral angle (p-OH orientation) is disregarded. A total of 31 conformers were common to both sets and showed nearly identical geometries. The comparison of the optimized DFT geometries of the two systems showed near by perfect linear fits with R² values of 0.9997, 0.9994, 0.9997, and 0.9996 for the φ _i , ψ _i , A _i ¹ , and A _i ² dihedral angles, respectively. Relative energies of the matching 31 conformers also fitted to a linear plot with an R² value of 0.9985. The geometric centroid of the aromatic ring in the sidechain of both systems was found to be within 4.1 ?of the H and O atoms of the peptide groups, in 21 and 2 of the conformers, respectively. None of the non-matching conformers showed any such interaction distance ≤4.1 ?. Received 1st February 2002 / Received in final form 28 May 2002 Published online 13 September 2002     

The “island of inversion" from a nuclear moments perspective and the g factor of 35Si

This paper reviews recent results from electromagnetic moment measurements on isotopes in the island of inversion around N=20. The obtained moments on neutron rich Na, Mg, Al and Si isotopes allow to draw conclusions on the amount of intruder components in their ground state wave function, demonstrating a gradual transition from the normal sd-shell region into the island of inversion, starting at N=18 for Na, N=19 for Mg and N=20 for Al isotopes. A measurement of the ground state g factor of ³⁵Si (N=21), using a polarized fragment beam at GANIL, is discussed in more detail. The magnetic moment μ(³⁵Si, I^π= 7/2^-) = (-)1.638(4) μ_N is consistent with a normal ground state structure, dominated by a νf_7/2 neutron.     

Evolution of the N = 20 and N = 28 shell closures in neutron-rich nuclei

The isospin dependence of shell closure phenomena is studied for light neutron-rich nuclei within a microscopic self-consistent approach using the Gogny force. Introducing configuration mixing, ³²Mg is found to be dynamically deformed, although the N = 20 spherical shell closure persists at the mean-field level for all N = 20 isotones. In contrast, the N = 28 spherical shell closure is found to disappear for N - Z≥ 10 whereas deformed shell closures are preserved and lead to shape coexistence in ⁴⁴ S. Configuration mixing shows that the ground state of this nucleus is triaxially deformed. The first 2⁺ excitation energy E_x = 1.46 MeV and the reduced transition probability B(E2;0⁺ _gs→ 2⁺ ₁)= 420 e ² fm ⁴ obtained with our approach are in good agreement with experimental data. Received: 26 July 2000 / Accepted: 30 August 2000     

The first excited states of 9Be and 9B

It is found here that the 1/2⁺ first excited state of ⁹Be is a virtual state with the energy of −23.5 KeV. The line shape for the excitation of the state is approximated with a simple analytic form based on the effective range expansion. The partner in ⁹B of this state is found to be a resonance with a maximum in the peak at about 1.1 MeV, FWHM of 1.5 MeV, and complex energy of 0.6 −i0.75 MeV. The line shape for its excitation is calculated in terms of the p−⁸Be phase shift. The phase shifts are obtained from N−⁸Be effective potentials deduced from the data on the photodisintegration of ⁹Be. A possibility for direct extraction of the energy of the resonant state from experimental data is also discussed, and an expression for a residue at a virtual state pole in terms of a quadrature taken over the virtual state eigenfunction is given. Received: 23 March 1998 / Revised version: 3 September 1998     

Tautomer contributions to the near UV spectrum of guanine: towards a refined picture for the spectroscopy of purine molecules

By using depopulation laser techniques, like IR-UV population labeling coupled to mass-selected R2PI detection, we confirm that four tautomers are responsible for the near UV spectroscopy (310-280 nm) of guanine: two enol and two keto forms, each pair having a 7NH and a 9NH form. Besides the UV spectroscopy of each tautomer, additional information on the excited state nature and dynamics is obtained from fluorescence studies. In particular, the quenching of fluorescence beyond 285 nm, the existence of a background absorption, as well as the existence of a strongly red-shifted component in the fluorescence emission provides evidence for a strong electronic mixing in the excited state together with an efficient non-radiative process. The details of these features are found to be tautomer-dependent. Comparison of the present results with literature data on other purine molecules, like adenine or 9-substituted guanines, enables us to propose a new insight on the spectroscopy and dynamics of the purine molecules. First, a large variability of the tautomer distribution in the gas phase is found within the purine family, in particular a molecular change, as simple as a 9-methylation on guanine, can reduce the tautomer distribution to a single species (enol form). Since the absorption spectrum is tautomer-dependent as well as substituent-dependent, it turns out that the tautomer population is one of the major parameters that control the overall shape of the UV spectrum. Second, the excited state model, often evoked in the literature, which involves electronic coupling between excited states of different natures, namely ππ^* and nπ^* states, might account for the present fluorescence measurements on guanine, providing an extensive excited state electronic mixing is assumed for these systems. Received 24 June 2002 Published online 13 September 2002     

IR Vibrational spectra of H-bonded complexes of adenine, 2-aminopurine and 2-aminopurine<Superscript>+</Superscript> with cytosine and thymine: Quantum-chemical study

Using theoretical study on the B3LYP/6-311++G(d,p) level of theory, we have compared vibrational spectra of 2-aminopurine (as neutral or protonated at N1 atom species) with adenine and H-bonded complexes of 2-aminopurine (as neutral or protoned at N1 atom species) · cytosine or 2-aminopurine · thymine with adenine · cytosine and adenine · thymine base pairs. The nature of the base pairing between adenine, 2-aminopurine, 2-aminopurine⁺ and cytosine or thymine have been investigated by means of quantum-mechanical calculations. We have investigated the effect of the hydrogen bond formation on the vibrational spectra of the investigated base pairs. The main differences in the vibrational spectra as for bases so for base pairs have been observed in the high-frequency region.     

Interaction between aromatic amine cations and nonpolar solvents: Infrared spectra of isomeric aniline -Ar n ( ) complexes

Infrared (IR) photodissociation spectra of the aniline⁺-Ar_n cations, An ⁺ - Ar _n (n = 1, 2), are analyzed in the vicinity of the N-H stretch fundamentals. The complexes are produced in an electron impact (EI) ion source which produces predominantly the most stable cluster isomers. Two isomers of An⁺-Ar are identified by their characteristic N-H stretch frequencies: the planar proton-bound global minimum, in which the Ar ligand forms a nearly linear H-bond to the amino group, and the less stable π-bound local minimum, in which the Ar atom is attached to the π-electron system of the aromatic ring. This result is the first unambiguous detection of the most stable H-bound An⁺-Ar dimer. All previous spectroscopic studies of An⁺-Ar employed resonance enhanced multiphoton ionization (REMPI) of neutral An-Ar and identified only the less stable π-bound cation due to restrictions arising from the Franck-Condon principle. The EI-IR spectrum of An⁺-Ar₂ shows that the most stable structure of this trimer features two equivalent H-bonds (C_2v symmetry). The interpretation of the experimental data is supported by quantum chemical calculations. The ab initio potential of An⁺-Ar calculated at the UMP2/6-311G(2df, 2pd) level features H-bound global minima ( D _e = 513 cm^-1) and π-bound local minima ( D _e = 454 cm^-1), with a barrier of V _b ≈ 140 cm^-1 for isomerization from the π-bound toward the H-bound minimum. Received 4 February 2002 Published online 13 September 2002     

Properties of N=84, even-even nuclei populated in the spontaneous fission of 248Cm

Excited states in the neutron-rich, N=84 nuclei ¹³⁴Sn, ¹³⁶Te and ¹³⁸Xe, populated in the spontaneous fission of ²⁴⁸Cm, were studied to medium spins using the EUROGAM2 array. OXBASH code calculations support the experimental identification of maximum aligned configurations in these isotopes. Empirical shell model calculations agree with the proposed excitation energy of the neutron h_9/2 excitation in the ¹³²Sn region. A discrepancy between the observed and calculated excitation energy of the I^π= 12⁺ level in ¹³⁶Te indicates possible admixtures of collective excitations in this nucleus. Clear signs of collective excitations are observed in ¹³⁸Xe. Received: 10 November 1999 / Revised version: 22 December 1999     

High-spin structure of the neutron-rich odd-odd 106, 108 45Rh and 110, 112 47Ag isotopes

The ^{106, 108}Rh and ^{110, 112}Ag nuclei have been produced as fission fragments following the fusion reaction ²⁸Si + ¹⁷⁶Yb at 145 MeV bombarding energy and studied with the Eurogam2 array. The yrast high-spin states of these four odd-odd nuclei, which are observed for the first time, consist of rotational bands in which the odd proton occupies the πg _9/2 subshell and the odd neutron the νh _11/2 subshell. Their behaviour as a function of spin values does not vary with the number of neutrons: as observed in the odd-N neighbouring nuclei, the motion of the odd neutron remains decoupled from the motion of the core, from N = 61 to N = 65. Moreover, the staggering observed in the yrast bands of odd-odd isotopes is strongly reduced as compared to the large values displayed by the rotational bands built on the πg _9/2 subshell in the odd-A Rh and Ag isotopes. The results of particle-rotor calculations indicate that this reduction is related to a change of the core deformation. Received: 1 June 2001 / Accepted: 23 July 2002 / Published online: 10 December 2002 RID="a" ID="a"e-mail: porquet@csnsm.in2p3.fr RID="b" ID="b"Present address: CSNSM IN2P3-CNRS and Université Paris-Sud 91405 Orsay, France. RID="c" ID="c"Present address: NAC, Faure, ZA 7131, South Africa. RID="d" ID="d"Present address: Department of Nuclear Physics, ANU, Canberra ACT 0200, Australia. Communicated by D. Schwalm     

Development of magnetic rotation in light Gd nuclei; study of 142Gd

High-spin states in ¹⁴²Gd have been populated by means of the ⁹⁹Ru(⁴⁸Ti, 2p3n) reaction at 240 MeV and investigated with the γ-spectrometer EUROBALL III and the charged-particle detector array ISIS. The features of four dipole bands have been determined and compared with tilted-axis cranking model calculations indicating that they are magnetic rotational bands. A transition from regular to irregular bands has been found approaching N = 82 demonstrating that this is a general phenomenon in nuclei near a double-shell closure. Received: 9 December 2001 / Accepted: 9 January 2002     

Quadrupole collectivity of neutron-rich neon isotopes

The Angular Momentum Projected Generator Coordinate Method, with the quadrupole moment as collective coordinate and the Gogny force (D1S) as the effective interaction, is used to describe the properties of the ground state and low-lying excited states of the even-even neon isotopes ^20-34Ne, that is, from the stability valley up to the drip line. It is found that the ground state of the N = 20 nucleus ³⁰Ne is deformed but to a lesser extent than the N = 20 isotope of the magnesium. In the calculations, the isotope ³²Ne is at the drip line in good agreement with other theoretical predictions. On the other hand, rather good agreement with experimental data for many observables is obtained. Received: 19 Novemeber 2002 / Accepted: 24 January 2003 / Published online: 8 April 2003     

Nuclear magnetic moment of 57Cu ground state

The nuclear magnetic moment of the ground state of ⁵⁷Cu(I^π = 3/2^-, T_1/2 = 196.3 ms) has been measured to be |μ(⁵⁷Cu)| = (2.00 ±0.05) μ_N using the β-NMR technique. Together with the known magnetic moment of the mirror partner ⁵⁷Ni, the spin expectation value was extracted as = -0.78 ± 0.13. Discrepancy between present results and shell model calculations in the full fp shell implies significant shell breaking at ⁵⁶Ni with the neutron number N = 28.     

Landau fragmentation and deformation effects in dipoSe response of sodium clusters

Recent experimental data on the dipole plasmon in axial sodium clusters Na _N ⁺ with 11 ≤ N ≤ 57 are analyzed within a self-consistent separable random-phase approximation (SRPA) based on the deformed Konh-Sham functional. Good agreement with the data is achieved. The calculations show that, while in light clusters plasmon properties (gross structure and width) are determined mainly by deformation splitting, in medium clusters with N τ 50 the Landau fragmentation becomes decisive. Moreover, in medium clusters shape isomers come to play with contributions to the plasmon comparable with the ground state one. As a result, commonly used methods of the experimental analysis of cluster deformation become useless and correct treatment of cluster shape requires microscopic calculations.     

ωN final state interactions and ω-meson production from heavy-ion collisions

We calculate the elastic and inelastic ωN→ωN, →πN, →ρN, →ρπN, →ππN, →σN reactions within a boson exchange approximation where the ωρπ coupling constant and form factor are fixed by the reaction πN→ωN in comparison to the experimental data. We find rather large ωN cross sections at low relative momenta of the ω-meson which leads to a substantial broadening of the ω-meson width in nuclear matter. The implications of the ωN final state interactions are studied for ω production in ¹²C +¹²C, ⁴⁰Ca +⁴⁰Ca and ⁵⁸Ni +⁵⁸Ni reactions at about 2 · A GeV within the HSD transport approach; the drastic changes of the transverse mass spectra relative to a general m _T-scaling (for π⁰ and η mesons) might be controlled experimentally by the TAPS Collaboration. Received: 28 April 1999 / Revised version: 7 June 1999     

Shell model structures in the N = 46 isotones 86Zr, 87Nb, 88Mo, 89Tc, 90Ru and 91Rh

The known level energies, electromagnetic moments and decay probabilities of high-spin states in the N = 46 isotones ⁸⁶Zr, ⁸⁷Nb, ⁸⁸Mo, ⁸⁹Tc, and ⁹⁰Ru are interpreted within the shell model. The single-particle space was truncated to the p _1/2 and g _9/2 orbits (relative to the ⁸⁸Sr core) and the single-particle energies and empirical two-body matrix elements derived by Gross and Frenkel were used in the calculations. Based on the generally good success of this approach, energies and decay properties of the yrast spectra in ⁹⁰Ru and ⁹¹Rh are predicted. Received: 31 July 2000 / Accepted: 18 December 2000     

K<Superscript>+</Superscript> production in proton-nucleus reactions and the role of momentum-dependent potentials

The production of K⁺-mesons in proton-nucleus collisions from 1.0 to 2.5GeV is analyzed with respect to one-step nucleon-nucleon ( NN → NYK ⁺) and two-step Δ-nucleon ( ΔN → K ⁺ YN) or pion-nucleon ( πN → K ⁺ Y) production channels on the basis of a coupled-channel transport approach (CBUU) including the kaon final-state interactions. The influence of momentum-dependent potentials for the nucleon, hyperon and kaon in the final state are studied as well as the importance of K⁺ elastic rescattering in the target nucleus. The transport calculations are compared to the experimental K⁺ spectra taken at LBL Berkeley, SATURNE, CELSIUS, GSI and COSY-Jülich. It is found that the momentum-dependent baryon potentials affect the excitation function of the K⁺ cross-section; at low bombarding energies of ∼ 1.0GeV the attractive baryon potentials in the final state lead to a relative enhancement of the kaon yield, whereas the net repulsive potential at bombarding energies ∼ 2GeV causes a decrease of the K⁺ cross-section. Furthermore, it is pointed out that especially the K⁺ spectra at low momenta (or kinetic energy T _K) allow to determine the in-medium K⁺ potential almost model independently due to a relative shift of the K⁺ spectra in kinetic energy that arises from the acceleration of the kaons when propagating out of the nuclear medium to free space, i.e. converting the potential energy to the kinetic energy of the free kaon. Received: 28 January 2002 / Accepted: 3 June 2002 / Published online: 19 November 2002 RID="a" ID="a"e-mail: Wolfgang.Cassing@theo.physik.uni-giessen.de Communicated by P. Schuck     

Sensitive detection of methane and nitrous oxide isotopomers using a continuous wave quantum cascade laser

A continuous wave quantum cascade laser (QCL), operating near 8.1 μm, was used for wavelength modulation spectroscopy of methane (CH₄) and nitrous oxide (N₂O) stable isotopes. Several rotational transitions of ¹⁴N₂ ¹⁶O, ¹⁵N¹⁴N¹⁶O, ¹⁴N₂ ¹⁸O, ¹⁴N₂ ¹⁷O, ¹³CH₄ and ¹²CH₄ fundamental bands were detected. The noise-equivalent absorbance was measured to be less than 10^-5 in a 1-Hz bandwidth. A characterization of the laser source was also performed. The use of a QCL spectrometer for high-precision isotope ratio measurements is discussed. Received 14 March 2002     

Three-valence-particle fission product 51 135Sb84

By analysis of fission product γ-ray data measured at Eurogam II using a ₂₄₈Cm source, yrast levels up to about 2 MeV in the N=84 three-particle nucleus ₁₃₅Sb have been identified. These levels are interpreted as π g^7/2ν f^7/2 ₂ and π g^7/2ν f^7/2h^9/2 states with the help of shell model calculations using empirical nucleon-nucleon interactions. Received: 30 July 1998     

Probing shell structure in neutron-rich nuclei with in-beam γ-spectroscopy

The structure of neutron-rich light nuclei around N = 20 and 28 has been investigated at GANIL by means of in-beam gamma-spectroscopy using fragmentation reactions of ³⁶S and ⁴⁸Ca beams on a Be target. Gamma-decay of relatively high-lying excited states have been measured for the first time in nuclei around ³²Mg and ⁴⁴S. Level schemes are proposed and discussed for a large number of these neutron-rich nuclei around N = 20 and N = 28. Received: 21 March 2002 / Accepted: 16 May 2002 / Published online: 31 October 2002 RID="a" ID="a"e-mail: azaiez@ipno.in2p3.fr