Independent Atom Model Research Articles

Elastic electron scattering by the CF3 radical in the 1–1000 eV energy range

Elastic scattering of electrons by a CF3 radical has been studied theoretically in a wide energy range of 1–1000 eV in the framework of an independent-atom model (IAM). The optical potential method is used for calculating the electron scattering amplitudes of the different atoms of the target molecule. The differential and integral cross sections are calculated for equilibrium internuclear distances of the ground state of the CF3 radical in two approaches—IAM and additivity rule (IAM-AR) approximations. The calculated cross sections are compared with the experimental data for e + CF3 and e + CF3H scattering and with other theoretical results. It is justified that the IAM performs slightly better for the differential cross sections, while the simpler IAM-AR approximation describes the integral cross sections better.

An experimental and theoretical investigation into the electronically excited states of para-benzoquinone

We report on a combination of experimental and theoretical investigations into the structure of electronically excited para-benzoquinone (pBQ). Here synchrotron photoabsorption measurements are reported over the 4.0–10.8 eV range. The higher resolution obtained reveals previously unresolved pBQ spectral features. Time-dependent density functional theory calculations are used to interpret the spectrum and resolve discrepancies relating to the interpretation of the Rydberg progressions. Electron-impact energy loss experiments are also reported. These are combined with elastic electron scattering cross section calculations performed within the framework of the independent atom model–screening corrected additivity rule plus interference (IAM-SCAR + I) method to derive differential cross sections for electronic excitation of key spectral bands. A generalized oscillator strength analysis is also performed, with the obtained results demonstrating that a cohesive and reliable quantum chemical structure and cross section framework has been established. Within this context, we also discuss some issues associated with the development of a minimal orbital basis for the single configuration interaction strategy to be used for our high-level low-energy electron scattering calculations that will be carried out as a subsequent step in this joint experimental and theoretical investigation.

Crystal structure and electrostatic properties of prednisolone acetate studied using a transferred multipolar atom model.

Prednisolone acetate {systematic name: 2-[(8S,9S,10R,13S,14S,17R)-11,17-dihydroxy-10,13-dimethyl-3-oxo-6,7,8,9,10,11,12,13,14,15,16,17-dodecahydro-3H-cyclopenta[a]phenanthren-17-yl]-2-oxoethyl acetate}, is an ophthalmic drug that belongs to the class of corticosteroids. Its crystal structure was refined using the classical independent atom model (IAM) and a transferred multipolar atom model using the ELMAM2 database. The results of both refinements have been compared. The ELMAM2 refinement was found to be superior in terms of the refinement statistics. It has been shown that certain electron-density-derived properties can be calculated on the basis of the transferred parameters for crystals which diffract to ordinary resolution. The procedure proves helpful in understanding the mode of action of the drug molecule.

Comparison of ultrafast electron and X-ray diffraction – A computational study

We compare ultrafast electron and X-ray diffraction using quantum molecular dynamics simulations in photoexcited ethylene. The simulations of ethylene are done using the ab-initio multiconfigurational Ehrenfest (AI-MCE) approach, with electronic structure calculations at the SA3-CASSCF(2,2)/cc-ppVDZ level. The diffraction signal is calculated using the independent atom model. We find that the electron diffraction is more sensitive to the nuclear wavepacket, and the dynamics of the hydrogen atoms in particular.

Dynamic quantum crystallography: lattice-dynamical models refined against diffraction data. II. Applications to L-alanine, naphthalene and xylitol.

In the first paper of this series [Hoser & Madsen (2016). Acta Cryst. A72, 206-214], a new approach was introduced which enables the refinement of frequencies of normal modes obtained from ab initio periodic computations against single-crystal diffraction data. In this contribution, the performance of this approach is tested by refinement against data in the temperature range from 23 to 205 K on the molecular crystals of L-alanine, naphthalene and xylitol. The models, which are lattice-dynamical models derived at the Γ point of the Brillouin zone, are able to describe the atomic vibrations of L-alanine and naphthalene to a level where the residual densities are similar to those obtained from the independent atom model. For the more flexible molecule xylitol, larger deviations are found. Hydrogen ADPs (anisotropic displacement parameters) derived from the models are in similar or better agreement with neutron diffraction results than ADPs obtained by other procedures. The heat capacity calculated after normal mode refinement for naphthalene is in reasonable agreement with the heat capacity obtained from calorimetric measurements (to less than 1 cal mol-1 K-1 below 300 K), with deviations at higher temperatures indicating anharmonicity. Standard uncertainties and correlation of the refined parameters have been derived based on a Monte Carlo procedure. The uncertainties are quite small and probably underestimated.

Imaging rotations and vibrations in polyatomic molecules with X-ray scattering.

An approach for calculating elastic X-ray scattering from polyatomic molecules in specific electronic, vibrational, and rotational states is presented, and is used to consider the characterization of specific states in polyatomic molecules using elastic X-ray scattering. Instead of the standard independent atom model (IAM) method, the X-ray scattering is calculated directly from ab initio wavefunctions. The role of molecular symmetry and Friedel's law is examined, with the molecules BF3, C5H5-, NF3, and 1,3-cyclohexadiene used as specific examples. The contributions to the elastic X-ray scattering from the electronic, vibrational, and rotational portions of the molecular wavefunction are examined in CS2. In particular, it is observed that the rotational states give rise to distinct signatures in the scattering signal.

Transferable aspherical atom model refinement of protein and DNA structures against ultrahigh-resolution X-ray data.

In contrast to the independent-atom model (IAM), in which all atoms are assumed to be spherical and neutral, the transferable aspherical atom model (TAAM) takes into account the deformed valence charge density resulting from chemical bond formation and the presence of lone electron pairs. Both models can be used to refine small and large molecules, e.g. proteins and nucleic acids, against ultrahigh-resolution X-ray diffraction data. The University at Buffalo theoretical databank of aspherical pseudo-atoms has been used in the refinement of an oligopeptide, of Z-DNA hexamer and dodecamer duplexes, and of bovine trypsin. The application of the TAAM to these data improves the quality of the electron-density maps and the visibility of H atoms. It also lowers the conventional R factors and improves the atomic displacement parameters and the results of the Hirshfeld rigid-bond test. An additional advantage is that the transferred charge density allows the estimation of Coulombic interaction energy and electrostatic potential.

Transferred multipolar atom model for 10β,17β-dihydroxy-17α-methylestr-4-en-3-one dihydrate obtained from the biotransformation of methyloestrenolone.

Biotransformation is the structural modification of compounds using enzymes as the catalysts and it plays a key role in the synthesis of pharmaceutically important compounds. 10β,17β-Dihydroxy-17α-methylestr-4-en-3-one dihydrate, C19H28O3·2H2O, was obtained from the fungal biotransformation of methyloestrenolone. The structure was refined using the classical independent atom model (IAM) and a transferred multipolar atom model using the ELMAM2 database. The results from the two refinements have been compared. The ELMAM2 refinement has been found to be superior in terms of the refinement statistics. It has been shown that certain electron-density-derived properties can be calculated on the basis of the transferred parameters for crystals which diffract to ordinary resolution.

Integral elastic, electronic-state, ionization, and total cross sections for electron scattering with furfural.

We report absolute experimental integral cross sections (ICSs) for electron impact excitation of bands of electronic-states in furfural, for incident electron energies in the range 20-250 eV. Wherever possible, those results are compared to corresponding excitation cross sections in the structurally similar species furan, as previously reported by da Costa et al. [Phys. Rev. A 85, 062706 (2012)] and Regeta and Allan [Phys. Rev. A 91, 012707 (2015)]. Generally, very good agreement is found. In addition, ICSs calculated with our independent atom model (IAM) with screening corrected additivity rule (SCAR) formalism, extended to account for interference (I) terms that arise due to the multi-centre nature of the scattering problem, are also reported. The sum of those ICSs gives the IAM-SCAR+I total cross section for electron-furfural scattering. Where possible, those calculated IAM-SCAR+I ICS results are compared against corresponding results from the present measurements with an acceptable level of accord being obtained. Similarly, but only for the band I and band II excited electronic states, we also present results from our Schwinger multichannel method with pseudopotentials calculations. Those results are found to be in good qualitative accord with the present experimental ICSs. Finally, with a view to assembling a complete cross section data base for furfural, some binary-encounter-Bethe-level total ionization cross sections for this collision system are presented.

Electron collisions with small esters: A joint experimental-theoretical investigation

A theoretical and experimental investigation on elastic electron scattering by two small esters, namely, methyl formate and ethyl acetate, is reported. Experimental differential, integral, and momentum-transfer cross sections are given in the 30--1000 eV and ${10}^{\ensuremath{\circ}}--{120}^{\ensuremath{\circ}}$ ranges. The relative-flow technique was used to determine such quantities. Particularly for methyl formate, a theoretical study was also carried out in the 1--500 eV range. A complex optical potential derived from a Hartree-Fock molecular wave function was used to represent the collision dynamics, whereas the Pad\'e approximation was used to solve the scattering equations. In addition, calculations based on the framework of the independent-atom model (IAM) were also performed for both targets. In general, there is good agreement between our experimental data and the present theoretical results calculated using the Pad\'e approximation. The theoretical results using the IAM also agree well with the experimental data at 200 eV and above. Moreover, for methyl formate, our calculations reveal a ${}^{2}{A}^{\ensuremath{'}\ensuremath{'}}$ $({\ensuremath{\pi}}^{*})$ resonance at about 3.0 eV and a ${\ensuremath{\sigma}}^{*}$-type resonance centered at about 8.0 eV in the ${}^{2}{A}^{\ensuremath{'}}$ scattering channel. The ${\ensuremath{\pi}}^{*}$ resonance is also seen in other targets containing a carbonyl group.

Experimental and theoretical cross sections for positron scattering from the pentane isomers.

Isomerism is ubiquitous in chemistry, physics, and biology. In atomic and molecular physics, in particular, isomer effects are well known in electron-impact phenomena; however, very little is known for positron collisions. Here we report on a set of experimental and theoretical cross sections for low-energy positron scattering from the three structural isomers of pentane: normal-pentane, isopentane, and neopentane. Total cross sections for positron scattering from normal-pentane and isopentane were measured at the University of Trento at incident energies between 0.1 and 50 eV. Calculations of the total cross sections, integral cross sections for elastic scattering, positronium formation, and electronic excitations plus direct ionization, as well as elastic differential cross sections were computed for all three isomers between 1 and 1000 eV using the independent atom model with screening corrected additivity rule. No definitive evidence of a significant isomer effect in positron scattering from the pentane isomers appears to be present.

Yes, one can obtain better quality structures from routine X-ray data collection.

Single-crystal X-ray diffraction structural results for benzidine dihydrochloride, hydrated and protonated N,N,N,N-peri(dimethylamino)naphthalene chloride, triptycene, dichlorodimethyltriptycene and decamethylferrocene have been analysed. A critical discussion of the dependence of structural and thermal parameters on resolution for these compounds is presented. Results of refinements against X-ray data, cut off to different resolutions from the high-resolution data files, are compared to structural models derived from neutron diffraction experiments. The Independent Atom Model (IAM) and the Transferable Aspherical Atom Model (TAAM) are tested. The average differences between the X-ray and neutron structural parameters (with the exception of valence angles defined by H atoms) decrease with the increasing 2θmax angle. The scale of differences between X-ray and neutron geometrical parameters can be significantly reduced when data are collected to the higher, than commonly used, 2θmax diffraction angles (for Mo Kα 2θmax > 65°). The final structural and thermal parameters obtained for the studied compounds using TAAM refinement are in better agreement with the neutron values than the IAM results for all resolutions and all compounds. By using TAAM, it is still possible to obtain accurate results even from low-resolution X-ray data. This is particularly important as TAAM is easy to apply and can routinely be used to improve the quality of structural investigations [Dominiak (2015 ▸). LSDB from UBDB. University of Buffalo, USA]. We can recommend that, in order to obtain more adequate (more accurate and precise) structural and displacement parameters during the IAM model refinement, data should be collected up to the larger diffraction angles, at least, for Mo Kα radiation to 2θmax = 65° (sin θmax/λ < 0.75 Å(-1)). The TAAM approach is a very good option to obtain more adequate results even using data collected to the lower 2θmax angles. Also the results of translation-libration-screw (TLS) analysis and vibrational entropy values are more reliable for 2θmax > 65°.

Low-energy positron scattering by pyrimidine.

This work reports elastic integral and differential cross sections for positron collisions with pyrimidine, for energies up to 20 eV. The cross sections were computed with the Schwinger multichannel method in the static plus polarization approximation. We also employed the Born closure procedure to account for the long range potential due to the permanent dipole moment of the molecule. Our results are compared with the experimental total cross section of Zecca et al. [J. Phys. B 43, 215204 (2010)], the experimental grand-total, quasi-elastic integral and differential cross section of Palihawadana et al. [Phys. Rev. A 88, 12717 (2013)]. We also compare our results with theoretical integral and differential cross sections obtained by Sanz et al. [Phys. Rev. A 88, 62704 (2013)] with the R-matrix and the independent atom model with screening-corrected additivity rule methods, and with the results computed by Franz and Gianturco [Phys. Rev. A 88, 042711 (2013)] using model correlation-polarization potentials. The agreement between the theory and the experiment is encouraging.

Screening corrections for the interference contributions to the electron and positron scattering cross sections from polyatomic molecules

An improvement of the screening-corrected Additivity Rule (SCAR) is proposed for calculating electron and positron scattering cross sections from polyatomic molecules within the independent atom model (IAM), following the analysis of numerical solutions to the three-dimensional Lippmann–Schwinger equation for multicenter potentials. Interference contributions affect all the considered energy range (1–300eV); the lower energies where the atomic screening is most effective and higher energies, where interatomic distances are large compared to total cross sections and electron wavelengths. This correction to the interference terms provides a significant improvement for both total and differential elastic cross sections at these energies.

Experimental and Theoretical Charge Density Studies of Chalcogen Bonding and Other Intermolecular Contacts in 4-[[4-(Methoxy)-3-quinolinyl]thio]-3-thiomethylquinoline

High-resolution diffraction data have been used for modeling the electron density distribution in the crystal structure of 4-[[4-(methoxy)-3-quinolinyl]thio]-3-thiomethylquinoline. The results confirm the presence of intermolecular, electron pairs−σ-holes S···S bonding. The calculated minimum energy distance is 3.33–3.34 A and agrees very well with the separation of 3.3300(11) A, observed in the crystal structure. A large spectrum of weak interactions, including C–H···O, C–H···S, and π···π has been analyzed by means of electron density distribution details and Atoms-In-Molecules approach. There is apparently a good agreement between the results obtained with the multipolar Hansen-Coppens model and theoretical study. At the same time, comparison with the results of the best independent atom model has revealed its deficiencies.

Crossed-beam experiment for the scattering of low- and intermediate-energy electrons from BF3: A comparative study with XF3 (X = C, N, and CH) molecules.

Absolute differential cross sections (DCSs) for electron interaction with BF3 molecules have been measured in the impact energy range of 1.5-200 eV and recorded over a scattering angle range of 15°-150°. These angular distributions have been normalized by reference to the elastic DCSs of the He atom and integrated by employing a modified phase shift analysis procedure to generate integral cross sections (ICSs) and momentum transfer cross sections (MTCSs). The calculations of DCSs and ICSs have been carried out using an independent atom model under the screening corrected additivity rule (IAM-SCAR). The present elastic DCSs have been found to agree well with the results of IAM-SCAR calculation above 20 eV, and also with a recent Schwinger multichannel calculation below 30 eV. Furthermore, in the comparison with the XF3 (X = B, C, N, and CH) molecules, the elastic DCSs reveal a similar angular distribution which are approximately equal in magnitude from 30 to 200 eV. This feature suggests that the elastic scattering is dominated virtually by the 3-outer fluorine atoms surrounding the XF3 molecules. The vibrational DCSs have also been obtained in the energy range of 1.5-15 eV and vibrational analysis based on the angular correlation theory has been carried out to explain the nature of the shape resonances. Limited experiments on vibrational inelastic scattering confirmed the existence of a shape resonance with a peak at 3.8 eV, which is also observed in the vibrational ICS. Finally, the estimated elastic ICSs, MTCSs, as well as total cross sections are compared with the previous cross section data available.

Interference effects in the electron and positron scattering from molecules at intermediate and high energies

The independent atom model representation (IAM) in combination with the additivity rule (AR) is customary accepted as a good approximation to describe electron and positron scattering processes with polyatomic molecules at intermediate and high energies (typically above 100eV). Within this approach, interference terms are not properly evaluated and are usually ignored in the cross section calculations. However, through a numerical solution of the Lippmann–Schwinger equation for three dimensional multicentre potentials we here demonstrate how interference terms can affect to the calculated differential and integral cross section values even at such relatively high energies. Practical corrections to the AR approach for both differential and integral electron and positron scattering cross section calculations from molecules are also proposed.

Electron capture and ionization processes in high velocity Cn+, C-Ar and Cn+, C-He collisions

SynopsisSingle and double electron capture as well as projectile single and multiple ionization processes occurring in 125keV/u Cn+-He, Ar collisions have been studied experimentally and theoretically for 1 ≤ n ≤ 5. The Independent atom and electron (IAE) model has been used to describe the cluster-atom collision. The ion/atom-atom probabilities required for the IAE simulations have been determined by classical trajectory Monte Carlo (CTMC) and semiclassical atomic orbital close coupling (SCAOCC) calculations for the Ar and He targets respectively. In general the agreement between experiment and IAE simulations was good, with the exception of double electron capture leading to anionic C−n species.

Integral cross sections for electron impact excitation of vibrational and electronic states in phenol.

We report on measurements of integral cross sections (ICSs) for electron impact excitation of a series of composite vibrational modes and electronic-states in phenol, where the energy range of those experiments was 15-250 eV. There are currently no other results against which we can directly compare those measured data. We also report results from our independent atom model with screened additivity rule correction computations, namely, for the inelastic ICS (all discrete electronic states and neutral dissociation) and the total ionisation ICS. In addition, for the relevant dipole-allowed excited electronic states, we also report f-scaled Born-level and energy-corrected and f-scaled Born-level (BEf-scaled) ICS. Where possible, our measured and calculated ICSs are compared against one another with the general level of accord between them being satisfactory to within the measurement uncertainties.

Electron capture and ionization processes in high-velocity Cn+ , C–Ar and Cn+ , C–He collisions

Single-electron and double-electron capture as well as projectile single-ionization and multiple-ionization processes in 125 keV u−1 C–He (n = 1–5) and C–Ar () collisions have been studied experimentally and theoretically. Helium target single-ionization and double-ionization cross sections are also reported for C–He (n = 1, 4) collisions in the 100–400 keV u−1 impact energy domain. These results are compared with predictions from the independent atom and electron (IAE) model developed for describing cluster–atom collisions. The ion/atom–atom probabilities required for the IAE simulations have been determined by classical trajectory Monte Carlo (CTMC) and semiclassical atomic orbital close coupling (SCAOCC) calculations for the Ar and He targets, respectively. For comparison, electron capture cross sections were also measured in C–He and C–Ar collisions. In general the agreement between experiment and IAE calculations has been found to be rather good, with the exception of double-electron capture leading to anionic C species.