Inelastic interactions of protons and electrons with biologically relevant molecules

Ionization and fragmentation of water and uracil molecules was studied both by electron and proton impact. A special coincidence technique allows on an event by event basis the investigation of product ions formed upon the collision of protons with neutral molecules including the identification of the charge state of the projectile. This enables the characterization of the ionization processes occurring, i.e. direct ionization, single electron capture or double electron capture for 0, 1 or 2 electrons that are transferred from the target to the projectile, respectively. For uracil the fragmentation patterns obtained by electron and proton impact ionization reveal close similarities and indicate a comparable amount of excitation for the two different ionization mechanisms at high enough projectile energies. Received 25 February 2002 Published online 13 September 2002     

Theoretical investigation of the ultrafast dissociation of core-ionized water and uracil molecules immersed in liquid water

We present a series of ab initio density functional based calculations of the fragmentation dynamics of core-ionized biomolecules. The computations are performed for pure liquid water, aqueous and isolated Uracil. Core ionization is described by replacing the 1s ² pseudopotential of one atom of the target molecule (C, N or O) with a pseudopotential for a 1s ¹ core-hole state. Our results predict that the dissociation of core-ionized water molecules may be reached during the lifetime of inner-shell vacancy (less than 10 fs), leading to OH bond breakage as a primary outcome. We also observe a second fragmentation channel in which total Coulomb explosion of the ionized water molecule occurs. Fragmentation pathways are found similar for pure water or when the water molecule is in the primary hydration shell of the uracil molecule. In the latter case, the proton may be transferred towards the uracil oxygen atoms. When the core hole is located on the uracil molecule, ultrafast dissociation is only observed in the aqueous environment and for nitrogen-K vacancies, resulting in proton transfers towards the hydrogen-bonded water molecule.     

Ultrafast nonadiabatic fragmentation dynamics of doubly charged uracil in a gas phase

A combination of time-dependent density functional theory and Born-Oppenheimer molecular dynamics methods is used to investigate fragmentation of doubly charged gas-phase uracil in collisions with 100 keV protons. The results are in good agreement with ion-ion coincidence measurements. Orbitals of similar energy and/or localized in similar bonds lead to very different fragmentation patterns, thus showing the importance of intramolecular chemical environment. In general, the observed fragments do not correspond to the energetically most favorable dissociation path, which is due to dynamical effects occurring in the first few femtoseconds after electron removal.     

Laser-induced nonthermal fragmentation of C60 studied by semiclassical dynamics simulation

Photofragmentation of the C₆₀ fullerene induced by ultrafast laser pulses is studied by semiclassical dynamics simulation. The simulation study is focused on the excitation below the continuum levels. A laser pulse of 40 fs (FWHM) with an effective photon energy of 2.0 eV and different intensities was selected to interact with the C₆₀ fullerene. The simulation results show that averaged fragmentation size distribution over groups of initial geometries selected at random exhibits a power law pattern with the peak at C₂ at high laser pulse intensities. The threshold for the C₆₀ fragmentation was determined. The simulation finds that as many as 55 electrons are excited from the occupied molecular orbitals to unoccupied molecular orbitals upon the laser irradiation and that the number of the fragments significantly depends on the number of electrons excited. Finally, the temperature examination seems to suggest that the nonthermal effect may play a significant role in laser fragmentation of the C₆₀ fullerene.     

Response of polyatomic molecules to ultrastrong laser- and ion-induced fields

The exposure of molecules to short, ultrastrong electric fields leads to multiple ionization and a subsequent Coulomb explosion. We present a comparative study where uracil molecules are exposed to fields generated by high-power laser pulses (tau approximately 75 fs, I > 10(16) W/cm2) or swift highly charged ions (0.5 MeV Xe25+) representing a half-cycle pulse of less than 10 fs duration. Molecular dynamics and structural information contained in the fragmentation pathways can be assessed separately. Despite the similar field strengths large differences in fragment kinetic energies are found which are related to field shape and duration with the aid of molecular dynamics simulations.     

Effects of molecular structure on ion disintegration patterns in ionization of O2 and N2 by short laser pulses

We demonstrate that the structure of the outermost orbitals of oxygen and nitrogen can be observed in the angular distribution of coincident ion pairs generated by the double ionization of these molecules by 8 fs laser pulses. We do this by establishing that these ions emerge from well defined excited electronic states of O2+2 and N2+2 respectively and that they are produced dominantly through a process which involves electron rescattering. The angular distributions of the ions from the two targets are very different, reflecting the different structures of the outermost orbitals of the two molecules.     

Selective action on nucleic acids components by picosecond light pulses

We report on first attempts for selective action on nucleic acid components, namely uracil and adenine, using picosecond light pulses. Selective action was achieved both in the case of irradiation of mixtures of bases and in the case of irradiation of mixtures of different nucleic acids components, which contain uracil and adenine.     

Orbital density reconstruction for molecules

The experimental imaging of electronic orbitals has allowed one to gain a fascinating picture of quantum effects. We here show that the energetically high-lying orbitals that are accessible to experimental visualization in general differ, depending on which approach is used to calculate the orbitals. Therefore, orbital imaging faces the fundamental question of which orbitals are the ones that are visualized. Combining angular-resolved photoemission experiments with first-principles calculations, we show that the orbitals from self-interaction-free Kohn-Sham density functional theory are the ones best suited for the orbital-based interpretation of photoemission.     

Fast fragmentation in core-excited molecules

Symmetry breaking is an important phenomenon connected to the excitation of core electrons in molecules. The fundamental question of whether inner-shell electronic-state orbitals are delocalized, and what the underlying mechanism for breaking the symmetry of a molecule upon dissociation are the subject of much debate, especially for the case of diatomic molecules. One method for studying molecular fragmentation, which is based upon a symmetry picture, is multicoincidence ion spectroscopy. Here we give a brief presentation of some of the applications of this technique, where symmetry, nuclear motion and the temporal signature are of importance.     

Charge self-trapping in two strand biomolecules: Adiabatic polaron approach

We investigate the properties of the excess charge (electron, hole) introduced into a two-strand biomolecule. We consider the possibility that the stable soliton excitation can be formed due to interaction of excess charge with the phonon subsystem. The influence of overlap of the molecular orbitals between adjacent structure elements of the macromolecular chain on the soliton properties is discussed. Special attention is paid to the influence of the overlapping of the molecular orbitals between structure elements placed on the different chains. Using the literature values of the basic energy parameters of the two-chain biomolecular structures, possible types of soliton solutions are discussed.     

Characteristic features of charge transfer in the interaction between sensitizer molecules and AgCl(I) molecules

We have used flash luminescence stimulation and photoinduced emission methods to study deep impurity states of AgCl(I) microcrystals with adsorbed organic cationic and anionic dye molecules. We have observed that when these molecules interact with the crystal, charge transfer occurs simultaneously from different orbitals and the transfer occurs differently from each orbital: some orbitals of the molecule pick up a negative charge, others at the same time give up a negative charge. We hypothesize that the type of transfer is determined by the overall charge.     

Unexpected deviation from diene behaviour of uracil amidine: towards synthesis of some pyrido[2,3-<Emphasis Type="Italic">d</Emphasis>]pyrimidine derivatives

Condensation products obtained from the treatment of uracil amidine with preformed or in situ generated suitably substituted olefins unexpectedly undergo intramolecular cyclisation during silica gel chromatography to generate pyrido[2,3-d]pyrimidines. Various reaction conditions are studied and the altered nature of the uracil amidine molecule is further explored by reacting it with different suitably substituted alkenes.     

Gaussian-type functions for the 3d Rydberg and 3d correlation orbitals in B to Ne and Al to Ar

Gaussian-type basis sets for the 3d Rydberg orbitals and 3d correlation orbitals are developed for the first- and second-row main group elements. The numbers of the Gaussian-type functions (GTFs) used for the 3d orbitals are 1–3 for the former elements and 1–4 for the latter elements. The 3d Rydberg orbitals for the first-row main group elements are close to the hydrogen (H) 3d orbitals, but those of the second-row main group elements are very different from H 3d except for Al. A two d or three d GTF set suffices to model the first-row main group elements, but at least four d GTFs are necessary for the second-row main group elements. The Rydberg GTF orbitals, consisting of three GTFs, are converted into correlating orbitals by introducing a single scaling factor. The correlation energies (CEs) calculated using these correlating orbitals cover 99.4–100% of those calculated using Dunning's three primitive GTFs for the first-row main group elements, and 94.9–99.7% of the CEs of Woon and Dunning's d's for the second-row main group elements. The resulting correlating 3d orbitals were tested by picking out F₂ and Cl₂, yielding spectroscopic constants close to or more accurate than those calculated by Dunning's 3d orbitals and Woon and Dunning's 3d orbitals.     

Particular type of a gap in the spectrum of multiband superconductors

We show that in contrast to the free electron model (standard BCS model), a particular gap in the spectrum of multiband superconductors opens at some distance from the Fermi energy, if conduction band is composed of hybridized atomic orbitals of different symmetries. This gap has composite superconducting-hybridization origin, because it exists only if both the superconductivity and the hybridization between different kinds of orbitals are present. Therefore, for many classes of superconductors with multiorbital structure such spectrum changes should take place. These particular changes in the spectrum at some distance from the Fermi level result in slow convergence of the spectral weight of the optical conductivity even in quite conventional superconductors with isotropic s-wave pairing mechanism.     

探测二茂铁外价轨道(e,2e)反应中的扭曲波效应

利用第三代高效率电子动量谱仪,分别在600和1500 eV两种不同入射电子能量下获得了二茂铁(ferrocene)分子外价轨道的电离能谱和电子动量谱的相关实验结果.并利用非相对论与标量相对论密度泛函方法计算出了二茂铁的重叠型和交错型两种不同构象的理论动量谱.两种构象的外价轨道一一对应,理论电子动量谱基本一样.对二茂铁的外价轨道,在低动量区观测到了强烈的扭曲波效应,这与这些轨道主要由铁原子的3d轨道构成有关.通过相对论和非相对论计算结果的比较,表明相对论效应对于二茂铁的外轨道动量分布几乎没有影响. 关键词： 二茂铁分子 电子动量谱 相对论效应 扭曲波效应     

Weak interactions between tetraphenylporphyrin dimers: A Wannier orbitals study

We investigate the weak interactions taking place in the tetraphenylporphyrin dimers by using Wannier orbitals and DFT. The Van der Waals interaction energies for various geometric configurations of the dimers are then compared to the differences between the total DFT energies of dimers and those of sums over the energies of monomers. The comparison allows us to estimate the weight of the Van der Waals contribution to the total interaction energy since the DFT values include all contributions such as weak chemical interaction or Pauli repulsion to the binding energy. We show that the interaction energy computed with vdW-DF-cx exchange-correlation functional is almost identical with the one computed using Wannier orbitals. By analyzing the properties of Wannier orbitals in monomer and dimer structures, we check the fact the Van der Waals energy can be accurately calculated by using only the orbitals corresponding to the single molecule, which is useful from a practical perspective.     

分子近阈结构的理论研究

本文利用多重散射方法研究了分子的近阈结构,阐明了:1)激发电子与分子离子实的相互作用动力学特征;2)势形共振的物理起源。并与实验比较,标识了NO₂内壳层激发的实验谱。 关键词：     

Unified treatment of one-range addition theorems for integer and non-integer n-STO, -GTO and -generalized exponential type orbitals with hyperbolic cosine in position, momentum and four-dimensional spaces

Simpler formulas are derived for one-range addition theorems for the integer and noninteger n generalized exponential type orbitals, momentum space orbitals, and hyperspherical harmonics with hyperbolic cosine (GETO HC, GMSO HC, and GHSH HC) in position, momentum and four-dimensional spaces, respectively. The final results are expressed in terms of one-range addition theorems of complete orthonormal sets of ψα -exponential type orbitals, α - momentum space orbitals and z α -hyperspherical harmonics. We notice that the one-range addition theorems for integer and noninteger n-Slater type orbitals and Gaussian type orbitals in position, momentum and four dimensional spaces are special cases of GETO HC, GMSO HC, and GHSH HC. The theorems presented can be useful in the accurate study of the electronic structure of atomic and molecular systems.     

A new approach to bonding in transition metal clusters

The idea that the molecular orbitals of a cluster of atoms can be usefully classified according to their nodal structure, so that the energy increases with the number of nodes, is quantified and shown to apply in its usual form only to molecular orbitals constructed from atomic σ orbitals. The method is extended to deal with atomic π and δ orbitals by the use of vector and tensor surface harmonics respectively. In all cases the orbitals can be classified approximately in terms of angular momentum quantum numbers l and m, but in the π and δ cases there are two orbitals, with different parity, for each lm, and the energy is determined primarily by the parity. The method provides a classification scheme and an approximate energy ordering which does not depend on any point-group symmetry that the cluster may have, and therefore provides a useful framework for discussion of the bonding in cluster compounds such as the boron hydrides and the transition metal cluster carbonyls.