I. Baccarelli

Ring-breaking electron attachment to uracil: Following bond dissociations via evolving resonances

Calculations are carried out at various distinct energies to obtain both elastic cross sections and S-matrix resonance indicators (poles) from a quantum treatment of the electron scattering from gas-phase uracil. The low-energy region confirms the presence of pi(*) resonances as revealed by earlier calculations and experiments which are compared with the present findings. They turn out to be little affected by bond deformation, while the transient negative ions (TNIs) associated with sigma(*) resonances in the higher energy region ( approximately 8 eV) indeed show that ring deformations which allow vibrational redistribution of the excess electron energy into the molecular target strongly affect these shape resonances: They therefore evolve along different dissociative pathways and stabilize different fragment anions. The calculations further show that the occurrence of conical intersections between sigma(*) and pi(*)-type potential energy surfaces (real parts) is a very likely mechanism responsible for energy transfers between different TNIs. The excess electron wavefunctions for such scattering states, once mapped over the molecular space, provide nanoscopic reasons for the selective breaking of different bonds in the ring region.

Bound-state energies in argon trimers via a variational expansion: The effects from many-body corrections

In this paper we study the bound-state energies and geometries of Ar(3) for J=0, using the distributed Gaussian functions method that provides a configurational description of the different structures contributing to these states. Atom-atom potentials are employed and three-body long-range effects are also included in the computational treatment by adding to the sum of potentials the Axilrod-Teller triple-dipole correction for the whole rotationless energy spectrum. An estimate of the total number of bound states for the Ar trimer is given. With respect to previous calculations, limited to the lower-lying states, our results show slightly larger nonadditive effects and are further able to predict the full range of the bound spectrum. Changes on the geometries of a large part of the vibrationally excited states of Ar(3) when the Axilrod-Teller term is included in the molecular potential are found by the present study.

A variational method to treat diffuse states in weakly bound trimers

Abstract A variational method based on the use of pair coordinates and distributed Gaussian functions (DGF) is applied to the study of weakly bound triatomic clusters. The approach is particularly well suited to treat very diffuse states as those presented by the 4 He 3 , and by 4 He 2 X systems, with X being also a very weakly bound atomic ‘impurity’. Several statistical properties such as radial and angular distributions, sizes and dominance of triangular configurations for the corresponding bound states are presented and discussed. The special nature of the Efimov effect is also analyzed in detail.

ELECTRON-DRIVEN REACTIONS IN PROTO-PLANETARY ATMOSPHERES: METASTABLE ANIONS OF GASEOUS o-BENZYNE

In this paper, we present an investigation into low-energy electron scattering (E < 15 eV) processes from a specific benzene-like polyatomic target such as ortho-benzyne, o-C6H4(1?), in order to gain a better understanding of the effects that possible low-lying metastable electron-attachment states could have on its nuclear fragmentation dynamics. The current importance of the dynamical evolution of this molecule lies in the fact that o-C6H4 is considered to be relevant for the circumstellar synthesis of large polycyclic aromatic hydrocarbons (PAHs), as a precursor for C6H6 production via ion-based ring closure reaction from C2H2. Our parameter-free scattering calculations are performed within the molecular reference frame, where we obtain the metastable anionic states for the nuclear equilibrium configuration and further characterize the properties of such transient anions with respect to those found earlier for the benzene molecule. Our quantum studies indicate that o-C6H4 is a more efficient producer of compact, fairly long-lived anionic intermediates than benzene itself; hence, this should more rapidly enter the chemical reaction cycles of PAHs formation, thereby disappearing from possible direct observation as a stable anion.

A theoretical investigation on the spectrum of the Ar trimer for high rotational excitations.

A detailed study of the rovibrational spectrum of the Ar trimer is performed by means of an exact hyperspherical coordinate (HC) method and a variational approach based on distributed Gaussian functions (DGFs) to describe the interparticle distances. The good agreement observed between the energy levels obtained with both procedures for high values of the total angular momentum (J=15 and 20) reveals the quality of the DGF method to describe the rotation of the title system. Rotational constants for the lowest bound states, obtained as averages for each vibrational state, have been obtained and compared to previous results. A detailed analysis of density probability functions obtained by means of the HC approach for rovibrational states at J=0 and 20 shows close similitudes thus supporting the vibration-rotation separation adopted within the DGF scheme for the Ar(3) system.

Electron-Driven Molecular Processes Induced in Biological Systems by Electromagnetic and Other Ionizing Sources

Abstract We describe, and analyse in some detail, a selection of the most recent theoretical and computational models which attempt to explain, at the molecular level, the dynamics of metastable negative ion formation from biological molecules in the gas-phase. Such Transient Negative Ions (TNIs) are related to the nanoscopic nuclear dynamics presiding over the occurrence of irreversible damage in the biosystems through the many possible pathways leading to dissociative attachment decay of the initial TNI. We will review the theoretical approach we adopted to study electron–molecule collision as applied to systems of biological interest. The connection between the spatial symmetry of the metastable anion and its role during the dissociative electron attachment event is also discussed and analysed through several examples.

SCELib3.0: The new revision of SCELib, the parallel computational library of molecular properties in the Single Center Approach☆

Abstract SCELib is a computer program which implements the Single Center Expansion (SCE) method to describe molecular electronic densities and the interaction potentials between a charged projectile (electron or positron) and a target molecular system. The first version (CPC Catalog identifier ADMG_v1_0) was submitted to the CPC Program Library in 2000, and version 2.0 (ADMG_v2_0) was submitted in 2004. We here announce the new release 3.0 which presents additional features with respect to the previous versions aiming at a significative enhance of its capabilities to deal with larger molecular systems. SCELib 3.0 allows for ab initio effective core potential (ECP) calculations of the molecular wavefunctions to be used in the SCE method in addition to the standard all-electron description of the molecule. The list of supported architectures has been updated and the code has been ported to platforms based on accelerating coprocessors, such as the NVIDIA GPGPU and the new parallel model adopted is able to efficiently run on a mixed many-core computing system. Program summary Program title: SCELib3.0 Catalogue identifier: ADMG_v3_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/ADMG_v3_0.html Program obtainable from: CPC Program Library, Queens University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 2 018 862 No. of bytes in distributed program, including test data, etc.: 4 955 014 Distribution format: tar.gz Programming language: C Compilers used: xlc V8.x, Intel C V10.x, Portland Group V7.x, nvcc V2.x Computer: All SMP platforms based on AIX, Linux and SUNOS operating systems over SPARC, POWER, Intel Itanium2, X86, em64t and Opteron processors Operating system: SUNOS, IBM AIX, Linux RedHat (Enterprise), Linux SuSE (SLES) Has the code been vectorized or parallelized?: Yes. 1 to 32 (CPU or GPU) used RAM: Up to 32 GB depending on the molecular system and runtime parameters Classification: 16.5 Catalogue identifier of previous version: ADMG_v2_0 Journal reference of previous version: Comput. Phys. Comm. 162 (2004) 51 External routines: CUDA libraries (SDK V2.x). Does the new version supersede the previous version?: Yes Nature of problem: In this set of codes an efficient procedure is implemented to describe the wavefunction and related molecular properties of a polyatomic molecular system within the Single Center of Expansion (SCE) approximation. The resulting SCE wavefunction, electron density, electrostatic and correlation/polarization potentials can then be used in a wide variety of applications, such as electron–molecule scattering calculations, quantum chemistry studies, biomodelling and drug design. Solution method: The polycentre Hartree–Fock solution for a molecule of arbitrary geometry, based on linear combination of Gaussian-Type Orbital (GTO), is expanded over a single center, typically the Center Of Mass (C.O.M.), by means of a Gauss Legendre/Chebyschev quadrature over the θ , φ angular coordinates. The resulting SCE numerical wavefunction is then used to calculate the one-particle electron density, the electrostatic potential and two different models for the correlation/polarization potentials induced by the impinging electron, which have the correct asymptotic behavior for the leading dipole molecular polarizabilities. Reasons for new version: The present release of SCELib allows the study of larger molecular systems with respect to the previous versions by means of theoretical and technological advances, with the first implementation of the code over a many-core computing system. Summary of revisions: The major features added with respect to SCELib Version 2.0 are 1. molecular wavefunctions obtained via the Los Alamos (Hay and Wadt) LAN ECP plus DZ description of the inner-shell electrons (on Na–La, Hf–Bi elements) [1] can now be single-center-expanded; the addition required modifications of: (i) the filtering code readgau, (ii) the main reading function setinp, (iii) the sphint code (including changes to the CalcMO code), (iv) the densty code, (v) the vst code; 2. the classes of platforms supported now include two more architectures based on accelerated coprocessors (Nvidia GSeries GPGPU and ClearSpeed e720 (ClearSpeed version, experimental; initial preliminary porting of the sphint() function not for production runs – see the code documentation for additional detail). A single-precision representation for real numbers in the SCE mapping of the GTOs (sphint code), has been implemented into the new code; 3. the Ih symmetry point group for the molecular systems has been added to those already allowed in the SCE procedure; 4. the orientation of the molecular axis system for the Cs (planar) symmetry has been changed in accord with the standard orientation adopted by the latest version of the quantum chemistry code (Gaussian C03 [2]), which is used to generate the input multi-centre molecular wavefunctions (z-axis perpendicular to the symmetry plane); 5. the abelian subgroup for the Cs point group has been changed from C1 to Cs; 6. atomic basis functions including g-type GTOs can now be single-center-expanded. Restrictions: Depending on the molecular system under study and on the operating conditions the program may or may not fit into available RAM memory. In this case a feature of the program is to memory map a disk file in order to efficiently access the memory data through a disk device. The parallel GP-GPU implementation limits the number of CPU threads to the number of GPU cores present. Running time: The execution time strongly depends on the molecular target description and on the hardware/OS chosen, it is directly proportional to the ( r , θ , φ ) grid size and to the number of angular basis functions used. Thus, from the program printout of the main arrays memory occupancy, the user can approximately derive the expected computer time needed for a given calculation executed in serial mode. For parallel executions the overall efficiency must be further taken into account, and this depends on the no. of processors used as well as on the parallel architecture chosen, so a simple general law is at present not determinable. References: [1] P.J. Hay, W.R. Wadt, J. Chem. Phys. 82 (1985) 270; W.R. Wadt, P.J. Hay, J. Chem. Phys. 284 (1985); P.J. Hay, W.R. Wadt, J. Chem. Phys. 299 (1985). [2] M.J. Frisch et al., Gaussian 03, revision C.02, Gaussian, Inc., Wallingford, CT, 2004.

Variational calculations of structures and energetics in very floppy trimers: A new computational implementation

Abstract Fully variational calculations which employ the Distributed Gaussian Functions (DGF) approach, and an overall potential within each trimer given as a sum of two-body potentials, have been implemented with a new computational scheme and used to verify the features of bound states in very weakly interacting systems. As test cases, the “half-neon” and the weakly bound bosonic He3, have been analyzed. The present, very extended expansions are discussed in detail and our findings are found to compare favorably with the existing results on these systems.

Competitive bond breaking in floppy molecular trimers: HeNeH and HeNeH− calculations

Calculations for the J=0 bound states associated with the two title molecular systems are carried out using distributed Gaussian function approach and using the sum of two-body potential approximation to describe the overall interactions. The results yield one bound state for the neutral trimer and three bound states for the anionic triatom. The relative values of dissociation energies place the first dissociation threshold at the H emission for the neutral complex and at the He emission for the corresponding anion. The general spatial properties of the various bound states are analyzed on both systems.

Searching for many-body effects and Efimov states in very weakly bound triatomics: HeNeH− and HeNeH

The rotationless, vibrational states of two weakly bound triatomic species are calculated using a variational expansion over multicentred Gaussian functions (the DGF method described in the main text) and corrections are introduced by using the three-body potentials vis à vis the sum-of-potentials approximation. The effects are seen to be very small and isotopic substitution is further introduced to evaluate changes on the vibrational structures of both systems, aiming at possibly detecting Efimov behaviour in such special trimers: no Efimov states are found with the available potentials and when the two-body potential strengths are varied. An additional study on the effects of isotopic substitutions for H atoms is also presented. 1 This paper is dedicated to Professor R.D. Levine, a great scientist and a dear friend, on the occasion of his 70th birthday.