Electron scattering from molecules and molecular aggregates of biological relevance

TL;DR: The methods and techniques used in the investigation of low energy electron collisions with biologically relevant molecules and molecular clusters are described and the results obtained so far for DNA constituents and their model compounds, amino acids, peptides and other biomolecules are summarized.

Abstract: In this Topical Review we survey the current state of the art in the study of low energy electron collisions with biologically relevant molecules and molecular clusters. We briefly describe the methods and techniques used in the investigation of these processes and summarise the results obtained so far for DNA constituents and their model compounds, amino acids, peptides and other biomolecules. The applications of the data obtained is briefly described as well as future required developments.

Summary

1. Introduction

• These days, treatments are highly sophisticated, using several types of ionisation radiation (photons, alpha particles, ions, etc.) and a variety of methods to ensure dose is maximized for the cancer cells while protecting healthy tissue.
• Any type of ionising radiation interacting with a medium will produce large number of secondary electrons, the product of enough energy being transferred between projectile and target to ionise the latter.
• This work marked the beginning of intense experimental and theoretical interest in electron interactions with biologically relevant molecules, particularly DNA components, as well as DNA strands.
• A lot of the work has been performed in the gas phase (or, the computational equivalent, isolated molecules).

1.1. Targets and processes of interest

• The work described in this Topical Review corresponds to low-energy collisions.
• These resonances can be seen as the incoming electron being trapped in one of the unoccupied orbitals of the molecule.
• Cross sections can be presented as an integrated (over all parameters) quantity or as differential cross sections.
• It is much more usual for experimental work to provide ion yields as a function of scattering energy, given the difficulty in turning these into absolute values and thus cross sections.

2. Isolated targets: methods

• As already mentioned, most of the work done so far on electron collisions with biologically relevant targets has involved gas-phase molecules (and the corresponding theoretical equivalent, single isolated molecules).
• These studies can provide a level of detail and understanding that collisions with more complex targets cannot: theoretical calculations are generally more accurate due to their reduced size and complexity.
• Experimentally, for example, the increased number dissociation pathways and the difficulty in detecting some of the products of DEA makes it hard to interpret anion spectroscopy data for condensed targets.
• The authors review briefly the computational and experimental techniques most often applied to the study of electron scattering from biologically relevant targets.

2.1. Computational methods

• The methods applied to biologically relevant targets are standard scattering methods, developed to treat general electron collisions with any molecular target (Huo & Gianturco 1995).
• The quality of the calculations is dependent on the wavefunctions used to describe the electronic states of the target.
• The electron-molecule interaction potential is built as a sum of three terms: a static contribution, an exchange contribution (that can be local or nonlocal depending on the target) and a correlation-polarization contribution that describes the response of the target electrons to the scattering one.
• The radial functions fΓlh(rN+1) are represented on a numerical grid.
• Again, method is more easily applicable to larger target molecules than the R-matrix technique as the work described below demonstrates.

2.2. Experimental methods

• Below the authors describe the experimental techniques most usually applied to the study of electron scattering from biological molecules.
• The authors note that many of the biomolecules of interest are powder at room temperature and that this entails additional experimental difficulties (some of which are discussed below) and make it particularly difficult to provide absolute experimental cross sections.
• Therefore, the various peaks detected in the energy loss obtained at the electron energy of a temporary anion, provide evidence of vibrational states in the low energy range (Abouaf et al. 2008).
• Various types of electron devices (e.g., trochoidal or hemispherical electron monochromators) are used for high resolution DEA studies, and a hot filament or a commercial electron gun are used for lower resolution studies.

3. Isolated targets: results

• The authors present here a summary of current data available for elastic, electron and vibrational excitation cross sections, as well as DEA.
• Results for TCS are mentioned in Section 3.1, because at low energies it is sometimes customary to compare experimental TCS with calculated elastic integral cross sections as the inelastic contribution to the TCS can be, in this energy range, significantly smaller.
• As the energy increases, electronic excitation becomes more important and, above 20-30 eV, the ionization cross section becomes significant too.
• Neither theoretical nor experimental cross section for electroninduced rotational excitation of biomolecules have been reported in the literature.
• One of the experimental limitations of performing this type of investigation is that the energy spacing of the lowest rotational states is much lower than meV (∼ 10−5 eV for the rotational energy levels for isolated nucleobases, see Franz & Gianturco 2014), which is difficult to resolve by current experimental techniques.

3.1. Elastic cross sections

• Elastic integral (ECS) and differential (DCS) cross sections are among the most widely studied.
• It is now understood, for example, that the current method used in R-matrix calculations to ’correct’ in this way the cross sections overestimates the very small angle contribution to the DCS and therefore the ECS (see Regeta, Allan, Winstead, McKoy, Maš́ın & Gorfinkiel 2016).
• Calculations have also been performed on ribose and 2- deoxyribose (Winstead & McKoy 2006a, Baccarelli et al. 2007, Baccarelli et al. 2009); β-D-ribose and β-D-deoxyribose in the latter publication.

3.2. Vibrational excitation cross sections

• Only a handful of reports have examined the vibrational excitations of gas-phase biomolecules and provided cross sections.
• Similarly, investigations of glycine and alanine at excitation energy of 2 eV, the energy at which transmission experiments in gas-phase demonstrated the presence of resonances (Aflatooni et al. 2001), showed that vibrational excitation primarily concerns the COOH group and CH stretch modes, which indicates that the carboxylic group plays a major role in the formation of the resonance.
• Therefore, research designed to obtain precise cross sections in a wide range of energies for liquid samples that can act as models of biomolecules has increased over the past few years.
• Electron-impact vibrational excitation for both furan and THF have been experimentally investigated very recently.

3.3. Electronic excitation

• Fewer results are available for electronic excitation of biologically relevant targets.
• The experiments are also more difficult, requiring more convoluted ’post-processing’ of the data to identify which states are being excited.
• No experiments are available for these targets.
• Both experiments and R-matrix calculations have been performed for pyridimine (Maš́ın et al. 2012, Regeta, Allan, Maš́ın & Gorfinkiel 2016), with excellent agreement between the cross section (for excitation of a group of states; the experiment can only differentiate ’bands’) in the latter work .
• Tashiro (2008) presented integral cross sections for excitation into the lowest four excited states of glycine as well as angular differential cross sections for these same states at 10 eV.

3.4. Dissociative electron attachment and resonance parameters

• Dissociative electron attachment (DEA) is experimentally one of the most widely studied processes in electron-biomolecule scattering due to its centrality to radiation damage.
• These DEA studies of nucleobases and their related compounds show a remarkable feature that can be recognised as a common phenomenon, site selectivity (Abdoul-Carime et al.
• Based on a comparison with resonance of their analogues [MX]− for amino acid esters, it was proposed that the dehydrogenated anions are produced at the lower adiabatic state via hydrogen-atom tunnelling through the barrier that separates a dipole-supported minimum and repulsive valence state.
• Accurate mass measurements of anionic fragments showed that N- and C-terminal anions resulting from DEA to amino acids that have the same masses exhibit resonances at different electron energies (Shchukin et al. 2010).
• 4.1. Resonance characterization Computational work has focused on the study of resonances, their energy and lifetime and their link to DEA products.

4. Aggregates

• Early on in the study of electron scattering from biologically relevant molecules, it was recognised that gas-phase/isolated molecule studies, in neglecting the influence of the environment in the collision, may not be providing a wholly accurate picture.
• Biological matter is condensed matter, and all electron interactions with it will be influenced by the environment ∗.
• Work was also performed on dimers of non-biological molecules (Gianturco et al.
• More recently, work is being carried out for neutral clusters containing a biomolecule and one or several water molecules.
• Caron et al. (2009) and Caron et al. (2008) used a multiple-scattering approach to combine R-matrix eigenchannel scattering data for DNA constituents and investigate this effect in electron attachment to a DNA base-pair decamer (including structural water). ∗.

4.1. Theoretical approaches

• Ab initio calculations of electron scattering from small clusters containing a biologically relevant molecule are difficult due to the size of the calculation.
• Some work, however, has been performed using the R-matrix method.
• Work has also been performed to understand DEA in microhydrated nucleobases.
• The methodology applied here is based on using a combination of techniques: the non-local complex potential method mentioned in section 3.4.2 and the multiple scattering approach, standard quantum chemistry techniques to determine the vertical attachment energies of the resonance of interest and standard scattering techniques to generate the T-matrices needed for the multiple scattering approach.
• The approach is currently limited to 1-dimensional DEA.

4.2. Experimental approaches

• Electron scattering experiments using biomolecular clusters as a target system have been performed using crossed electron-molecular beam setups coupled to a mass spectrometer as described in Section 2.2 for DEA studies.
• The biomolecule reservoir is typically heated more than the water reservoir and the clusters are formed in a conical-shaped nozzle.
• In another design, a mixture of humidied buffer gas (helium or argon, Kočǐsek, Pysanenko, Fárńık & Fedor 2016, Kočǐsek, Grygoryeva, Lengyel, Fárńık & Fedor 2016) and nucleobase vapour expand into the vacuum, where they collide with a tunable-energy electron beam, resulting in negatively charged ions that are detected by a reflectron timeof-flight mass spectrometer.
• The humidified buffer gas passes through a reservoir filled with a sample powder.

4.3. Aggregates: results

• The authors highlight two recent experimental works that look at DEA measurements in molecular clusters.
• Figure 9 shows results for two different ’amounts’ of microhydration obtained performing the experiments under two different sets of conditions.
• The authors’ hypothesis is that the quenching is due to the presence of water preventing the H atom from detaching (rather than changes to the electron attachment process itself), an effect not included in the calculations of Smyth et al. (2014).
• In the second experiment, DEA to pure and hydrated clusters of pyrimidine was investigated (Neustetter et al. 2015).

5. Applications

• The authors now turn their attention to the use of the data and insight into electron scattering described in Sections 3 and 4.3 (Section 5.1.1).
• The authors also discuss calculations and experiments geared towards understanding radiosensitisers (Section 5.1.2).
• The authors then describe briefly other (non-medical) areas where electron scattering from biological molecules is relevant: biofules and electron transport linked to metabolical processes.
• Finally, the authors include a brief summary of the (very much related) research on positron scattering from biological molecules.

5.1. Biomedical applications

• 1.1. Track structure modelling Track structure simulations model the propagation of a radiation particle along a medium, its interactions with it, and the secondary particles that this interaction produces.
• The simulations require as input integral and differential cross sections for all of the possible processes that can take place in the medium for a broad range of electron scattering energies.
• Very recently, the recommended gas-phase cross section data set of analogues of DNA constituents, i.e., pyrimidine, purine, THF, and trimethyl phosphate for electron scattering in the energy range between about 10 eV and 1 keV were reported (Bug et al. 2017).
• Several gas-phase experimental and theoretical studies of a variety of halogenated pyrimidines, such as 5-bromouracil (Abdoul-Carime et al.
• Gas-phase DEA studies have also been initiated on halogenated purines, such as chloroadenine (Kossoski et al. 2015), fluoroadenine (Rackwitz et al. 2016), and fluorinated nucleoside (2-deoxy-5-uorocytidine and 2,2-diuorocytidine (gemcitabine) Kopyra et al. 2014) to test their properties as potential radiosensitising drugs.

5.2. Biofuels

• Biofuels are a renewable source of energy that has been given significant attention in recent years.
• One potential source is lignocellulosic biomass (made of cellulose, hemicellulose and lignin) from which ethanol can be obtained.
• The process requires the removal of lignin and hemicellulose and plasmas have been tested for this purpose.

5.3. Electron transport and other metabolites

• The authors briefly mention here experimental studies of resonance formation in various other biological molecules.
• Herbicides (Scheer et al. 2014), ascorbic acid (electron exchange is thought to play a role in its cellular chemistry, Pshenichnyuk et al. 2016) and pesticides (Pshenichnyuk & Modelli 2013) where the products of DEA may be dangerous for mitochondrial functionalities as well as interfere with cellular signalling pathways, have also been studied with the same techniques.
• Similarly, resonance formation in 1,4-benzoquinone has been studied theoretically (see references in Cheng & Huang 2014, Kunitsa & Bravaya 2016) and experimentally by ETS and EELS (Modelli & Burrow 1984, Allan 1983).
• Quinones are involved in biological electron transfer reactions like photosynthesis and some synthetic quinones are known for their antitumoral effect.
• DEA experiments have been performed for biotin, a vitamin involved in the cellular response to DNA damage and other biological processes, both in the gas phase and in the condensed phase using DNA origami nanostructures (Keller et al. 2013).

5.4. Positron scattering

• The study of positron collisions with biologically relevant molecules has been stimulated by the medical uses of positrons, in particular positron emission tomography (PET).
• From a theoretical perspective, below the positronium formation threshold (determined by the difference between the molecule’s ionisation potential and the ground state energy of positronium), the same methods can be used to study positron and electron scattering.
• The authors refer the reader to a few reviews (Surko et al. 2005, Gribakin et al. 2010, Danielson et al. 2015) that summarise the techniques and methods applied.
• Total, elastic, and inelastic cross sections for collisions with THF have been determined theoretically (using the IAM-SCAR method) and experimentally over a range of higher energies (Chiari, Anderson, Tattersall, Machacek, Palihawadana, Makochekanwa, Sullivan, Garćıa, Blanco, McEachran, Brunger & Buckman 2013) as have those of 3-hydroxy-tetrahydrofuran (Chiari, Palihawadana, Machacek, Makochekanwa, Garćıa, Blanco, Brunger, Buckman & Sullivan 2013).
• Finally, ECS have been determined for scattering from glycine and alanine (Nunes et al. 2016).

6.1. Experimental developments

• In order to study the dynamics of electron induced dissociation, velocity map imaging (VMI) of fragment ions from DEA was developed a decade ago (Nandi et al. 2005, Nandi et al. 2006).
• While a significant amount of details about chemical dynamics was revealed for small polyatomic systems, the only study relevant to biological molecules was reported for uracil (Kawarai et al. 2014).
• The challenges of detecting neutrals from DEA have been overcome by developing a novel two-step electron ionisation technique, which will significantly enhance their understanding of DEA processes.
• No such investigations have been performed for biomolecules.
• Performing experiments with selected clusters (i.e., those containing a specific number of molecules) would simplify their interpretation as well as facilitate the comparison with theoretical results.

6.2. Theoretical developments

• An improved description of the effect of electron scattering on biomolecules and their clusters requires two ingredients: highly efficient software that enables the study of larger targets with increased accuracy.
• Improving and optimizing the description of the electronically excited states of the target in the scattering software would also be of benefit.
• Methodological developments that will improve their ability to describe some of the processes taking place.
• The application of adapted quantum chemistry techniques to the description of resonances described in Section 3.4.1 may also provide useful information for the modelling and understanding of DEA.
• It is worth mentioning that another push towards better computational description of electron-biomolecule interactions comes from the study of molecular processes induced by ultrashort laser pulses (e.g., high-harmonic generation in biomolecules (Marangos 2016), charge migration (Calegari et al. 2016)).

6.3. Data requirements

• This includes not only the processes discussed in this Topical Review, but others too.
• Thus, determining electron impact cross sections for excited targets is important for radiation therapy research and other fields.
• The task is not a trivial one: incorporating reliable values in the databases requires a critical compilation of available data, both experimental and theoretical: few quantitative comparisons of this data have been performed in the literature, where in many cases the results are just presented in graphical form.
• In addition, many of the cross sections published (including the vast majority of theoretical ones) do not come accompanied by uncertainty bars.

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Electron scattering from molecules and molecular
aggregates of biological relevance
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Electron scattering from molecules and molecular
aggregates of biological relevance
Jimena D. Gorfinkiel
School of Physical Sciences, The Open University, Walton Hall, Milton Keynes,
United Kingdom
E-mail: Jimena.Gorfinkiel@open.ac.uk
Sylwia Ptasinska
Radiation Laboratory and Department of Physics, University of Notre Dame, Notre
Dame, Indiana 46556, USA
E-mail: sptasins@nd.edu
Abstract.
In this Topical Review we survey the current state of the art in the study of low
energy electron collisions with biologically relevant molecules and molecular clusters.
We briefly describe the methods and techniques used in the investigation of these
processes and summarise the results obtained so far for DNA constituents and their
model compounds, amino acids, peptide and other biomolecules. The applications of
the data obtained is briefly described as well as future required developments.
PACS numbers: 34.80.-i, 36.40.Qv, 87.14.ef, 87.14.gf, 87.53.-j
Keywords: Submitted to: J. Phys. B: At. Mol. Phys.
1. Introduction
One of the main challenges of the XXI century is to respond to the medical needs of
a growing and ageing population. Over 20 million new cancers are predicted for 2030
(Ferlay et al. 2013). The improvement and development of current and new cancer
treatments is therefore a major scientific concern. Radiation therapy, that is, the
use of highly energetic, ionising radiation, is employed to treat around 50% of cancer
patients (Baskar & Itahana 2017). Its relative low cost compared to other treatments
makes it particularly appropriate for use in developing countries, where cancer-survival
rates require improvement. In addition, radiation is also used for medical imaging
and understanding of its interaction with biological material is important for radiation
protection (not only on Earth but also during space missions).

Electron scattering from biological targets 2
The first medical use of radiation was in imaging (X-rays) and the treatment of skin
conditions (UV light). By the 1930’s protocols for the use of radiation to treat some
cancers had been developed. These days, treatments are highly sophisticated, using
several types of ionisation radiation (photons, alpha particles, ions, etc.) and a variety
of methods to ensure dose is maximized for the cancer cells while protecting healthy
tissue. Overall, radiotherapy developments have been based on experimental knowledge
and empirical methods. Nowadays, however, efforts are being made to develop a deeper
understanding of the underlying molecular processes in order to design models and
software to aid these developments.
Any type of ionising radiation interacting with a medium will produce large
number of secondary electrons, the product of enough energy being transferred between
projectile and target to ionise the latter. Around 10
4
electrons with energies below 30 eV
are generated per MeV of deposited radiation (Pimblott & LaVerne 2007, Alizadeh &
Sanche 2012). The experiments of Bouda¨ıffa et al. (2000) confirmed that subionisation
electrons can produce single and double-strand breaks (SSBs and DSBs, respectively)
in DNA via the process known as dissociative electron attachment (DEA). This work
marked the beginning of intense experimental and theoretical interest in electron
interactions with biologically relevant molecules, particularly DNA components, as
well as DNA strands. The aim of this research is to provide an understanding of the
mechanisms of electron induced damage, as well as quantitative data to be used in its
modelling. A lot of the work has been performed in the gas phase (or, the computational
equivalent, isolated molecules). Researchers recognise, however, that radiation damage
in the cell occurs in a condensed medium and that the environment (fundamentally, the
water that surrounds cell constituents) will modify the electron-molecule interaction and
its outcome. For this reason, studies in the condensed phase (mostly films) and, more
recently, in pure and hydrated clusters have been performed.
It should be pointed out that an understanding of radiation effects at the molecular
level is only a small part of the knowledge needed to accurately describe (and predict)
biological radiation damage. A number of other effects (dose deposition, repair
mechanisms, indirect mechanisms like the bystander effect, etc.) contribute to the
complex biological process and must be taken into account (Hall & Giaccia 2012). We
should also mention that many exciting developments in the field of cancer treatment are
currently taking place (from the concurrent use of radio and chemotherapy to genetics-
based approaches) not all of which involve the use of radiation. It is the case however,
that radiation will remain a highly used tool both for treatment and imaging.
The aim of this Topical Review is to provide an overview of the research performed
so far on electron collisions with biological targets, summarising the main finds and
how this information is relevant, both from an applied perspective and a fundamental
one. A prior review (Baccarelli et al. 2011) described the work performed up to 2011,
particularly on resonance formation and DEA. We also refer the reader to two recent
reviews of DEA (Fabrikant et al. 2017) and DEA to biomolecules (Bald et al. 2017)
for more details regarding this process. In this Topical Review, we will concentrate on

Electron scattering from biological targets 3
more recent work and include all electron-induced processes as well as widen the range
of targets including aggregates. Results from aggregates can bridge our understanding
of electron-induced processes in the gas and condensed biomolecules, including DNA
and its constituents. A comparison of results from different states of matter has
already revealed the basics mechanisms initiated by electron scattering and how they are
modified under conditions more related to those in the cell (Alizadeh & Sanche 2012).
These mechanisms can assist in a better interpretation of the role of secondary electrons
in radiation-induced damage as well as in potential applications to radiotherapy
(Sanche 2016). We will also describe some electron-biomolecule interactions not related
to biological radiation damage.
1.1. Targets and processes of interest
The work described in this Topical Review corresponds to low-energy collisions. We
define these as collisions happening below ≈20 eV (i.e., not much above the ionisation
threshold). Low energy electrons (LEEs) can scatter elastically or lead to the excita-
tion (rotational, vibrational and/or electronic) of the target molecule. This excitation
can lead to (neutral) dissociation. In addition, DEA can take place. This is a reso-
nant process that involves electron capture by a molecule, AB, to produce a temporary
molecular anion (also called a transient negative ion, TNI, or resonance), (AB)
∗−
that
can then dissociate into an anion, A
−
, and a neutral radical or radicals, B·, according
to the following reaction:
e + AB −→ (AB)
∗
−→ A + B·
where A and B· are atoms and/or molecular fragments. DEA can lead to both simple,
single bond cleavage or a more complex decomposition into a number of fragments;
it is also extremely effective at selectively breaking specific molecular bonds. The
experiments of Bouda¨ıffa et al. (2000) demonstrated clearly the presence of resonant
features in the occurrence of SSBs and DSBs as a function of electron kinetic energy;
that is, they showed that DEA played a major role in DNA damage.
Resonances are classified according to whether they involve fundamentally the
electronic states of the target or they involve nuclear (vibrational) degrees of freedom.
The electronic resonances are classified into shape, when the electron attaches to the
molecule in its ground state (the ground state is then described as the parent state of the
resonance) and core-excited, when the electron attaches to the molecule an electronic
excited state (Schulz 1973a, Schulz 1973b). In shape resonances the incoming electron
is trapped by the potential resulting from a combination of short-range attractive and
long-range repulsive forces (the latter are caused by the angular-momentum barrier of
the incoming electron). These resonances can be seen as the incoming electron being
trapped in one of the unoccupied orbitals of the molecule. In core-excited resonances
the incoming electron can be seen as electronically exciting the target molecule to a

Electron scattering from biological targets 4
state (the parent state) and then being trapped into one of the empty spin-orbitals.
Core-excited resonances are further classified as Feshbach (also known as Type I) or
core-excited-shape (known as Type II) . In the latter the resonance is energetically
above its parent state and can therefore decay (via autoionisation) to it and in the
former it lies below (Herbert 2015)‡. Feshbach resonances have lifetimes much larger
than shape or core-excited shape resonances and, consequently, very narrow widths.
Vibrational Feshbach resonances (VFR) involve nuclear motion and usually occur at
very low energies when the electron is trapped into a diffuse (dipole-bound) state and its
energy transferred to the molecular vibrations (since the anion state is weakly bound,
it tends to lie slightly below the ground state of the neutral target and therefore its
vibrational levels are very close, but slightly below the corresponding vibrational states
of the neutral target). VFRs are likely to occur in molecules with large polarizability
and/or a very large dipole moment that leads to a long-range attractive interaction
(large dipole moments can also lead to the very-low energy formation of scattering-type
dipole states that might lead to anion stabilization as an alternative route to DEA
(Carelli & Gianturco 2016)). VFRs are found just below the thresholds for vibrational
excitation of the target molecule.
At higher energies (≈10 eV for most of the molecules discussed here) ionisation
becomes energetically possible and so does ion pair formation/dipolar dissociation. Data
(cross sections) for a broad energy range are needed for the description of radiation
interaction with matter, for example using Monte Carlo-based techniques. In addition,
the computational description of DEA requires information on the temporary anions
formed (energy and lifetime). In this Topical Review, we will summarise work available
on most of the relevant low-energy cross sections (neutral dissociation and rotational
excitation are excluded because of the very little available data) as well as theoretical
work on resonance characteristics.
In principle, all biological molecules present in the cell are of potential relevance
to understanding the effects of radiation. In addition, electron scattering data for some
inorganic molecules is also highly relevant. The most significant of all is water, the main
constituent of most living organisms. Other molecules used in track structure modelling
(see Section 5.1.1 for more details) are N
2
, CH
4
and CO
2
(these are employed to produce
tissue equivalent gas). We will not review work on these inorganic targets here, so we
refer the reader to earlier reviews: Itikawa & Mason (2005) for water, Anzai et al. (2012)
for water and CO
2
, etc..
DNA (and RNA) constituents have been the focus of a lot of the experimental
work: not only the bases and sugar, but also nucleosides and nucleotides as well as
as short DNA strands. Collisions with substituted DNA bases (in particular halo-
substituted) have been studied as these substitutions can render the molecules more
prone to radiation-induced break-up, in other words, these molecules have the potential
‡ We note that this classification is somewhat over-simplifying: resonances that have a mixed shape
and core-excited character have been identified (e.g. Nenner & Schulz 1975, Winstead & McKoy 2007)
as well as other resonances that have more than one parent state.

Frequently asked questions

Q1. What are the contributions in "Electron scattering from molecules and molecular aggregates of biological relevance" ?

In this Topical Review the authors survey the current state of the art in the study of low energy electron collisions with biologically relevant molecules and molecular clusters. The authors briefly describe the methods and techniques used in the investigation of these processes and summarise the results obtained so far for DNA constituents and their model compounds, amino acids, peptide and other biomolecules. 

Q2. What is the widely studied process in electron-biomolecule scattering?

Dissociative electron attachment (DEA) is experimentally one of the most widely studied processes in electron-biomolecule scattering due to its centrality to radiation damage. 

Q3. Why are absolute DEA cross sections still challenging?

due to the low precision of pressure measurements of the effusive molecularbeam, particularly in the case of powder samples, absolute DEA cross sections for most biomolecules still remain challenging. 

Q4. What is the probability of a biomolecule decomposing during heating?

Since most biomolecules (e.g., nucleobases, amino acids, and peptides) exist as solids at room temperature, there is a probability that they will decompose during heating, as was reported for thymidine (Ptasinska et al. 2006). 

Q5. What is the main reason for the improvement of the computational description of the effects of the laser?

The provision of accurate photoionisation data (that involves determining similar quantities to those needed in electron scattering studies and therefore can be done using the same software) is an essential step to improve the computational description of the effects induced by the laser field. 

Q6. What are the sources of uncertainty in low energy calculations of electron-molecule collisions?

There are three sources of uncertainty in low-energy calculations of electron-molecule collisions: the description of the (non-interacting target (i.e. the model that is used to describe its internal states), the approximation used to describe the scattering processes (e.g. how the continuum is modelled, whether polarization is included) and the theoretical method (and the computational implementation) used to perform the scattering calculations. 

Q7. What is the common technique used to study electron scattering from gas-phase targets?

One of the earliest experimental techniques used to study electron scattering from gas-phase targets is Electron Transmission Spectroscopy (ETS). 

Q8. What is the main difficulty in evaluating elastic cross sections for biologically relevant molecules?

The main difficulty in evaluating elastic cross sections for most biologically relevantmolecules arises from their permanent dipole moment. 

Q9. What is the peculiar observation in the resonance formation of dehydrogenated amino acids?

Another peculiar observation in the resonance formation of dehydrogenated amino acids is that the ion yield alters significantly depending on the position of the amino group in the molecule, as was shown by comparing DEA processes to α- and β-isomers alanine (Vizcaino et al. 2011). 

Q10. How was the breakage of the N-C bond in the tripeptide proposed?

This peptide breakage was proposed to be energetically possible only via a complex reaction, including a subsequent proton transfer, as was also suggested for dipeptides (Muftakhov & Shchukin 2011a). 

Q11. What is the simplest way to study the motion of a nuclear wave packet?

The 2D spectra provide both state-to-state information and insight into the dynamics of nuclear motion in resonances: information about the motion of a nuclear wave packet on a resonant potential surface is possible since this wave packet (of the resonant state) follows one of two competing pathways: molecular dissociation (DEA) or electron detachment. 

Q12. What type of molecules are considered as the elementary prototype of deoxyribose?

Targets of these type are, for example, tetrahydrofuran (THF) a five-membered heterocyclic compound which may be considered a hydrogenated form of furan and is regarded as the elementary prototype of deoxyribose, and pyrimidine. 

Q13. Why are the positions of the shape resonances higher than those determined experimentally?

The calculated positions tend to be higher than those determined experimentally (Aflatooni et al. 1998) for well known reasons: in general, the polarization effects are not fully described, or (particularly for the third resonance) the character of the resonance is partially core-excited so elastic calculations do not describe it very well. 

Q14. Why is it important to compare experimental TCS with calculated elastic integral cross sections?

Results for TCS are mentioned in Section 3.1, because at low energies it is sometimes customary to compare experimental TCS with calculated elastic integral cross sections as the inelastic contribution to the TCS can be,in this energy range, significantly smaller. 

Q15. What are the types of cross sections that are provided for a specific energy?

The latter, in the energy range of interest to this Topical Review, are normally angular differential cross section that are provided for a specific scattering energy as a function of the scattering angle (these cross sections can also be provided for a specific scattering angle as a function of scattering energy; these are normally referred to as excitation functions). 

Q16. What is the main reason for the push towards better computational description of electron-biomolecule interactions?

It is worth mentioning that another push towards better computational descriptionof electron-biomolecule interactions comes from the study of molecular processes induced by ultrashort laser pulses (e.g., high-harmonic generation in biomolecules (Marangos 2016), charge migration (Calegari et al. 2016)). 

Q17. Why is the phosphate group in the gas phase not investigated?

due to experimental difficulties, the phosphate group in the gas phase has not been investigated but several compounds involving phosphoric acid derivatives, e.g., dibutylphosphate and triethylphosphate (König et al. 2006), have been examined.