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We investigate the vertical electron attachment energy (VAE) of 1-methyl-4-nitroimidazole, a model radiosensitizer, employing quantum mechanics/molecular mechanics (QM/MM) and QM/polarized continuum (QM/PCM) solvation models. We considered the solvent-excluded surface (QM/PCM-SES) and Van der Waals (QM/PCM-VDW) cavities within the PCM framework, the electrostatic embedding QM/MM (EE-QM/MM) model, and the self-consistent sequential QM/MM polarizable electrostatic embedding (scPEE-S-QM/MM) model. Due to slow VAE convergence concerning the number of QM solvent molecules, full QM calculations prove inefficient. Ensemble averages in these calculations do not align with VAEs computed for the representative solute-solvent configuration. QM/MM and QM/PCM calculations show agreement with each other for sufficiently large QM regions, although the QM/PCM-VDW model exhibits artifacts linked to the cavity. QM/MM models demonstrate good agreement between ensemble averages and VAEs calculated with the representative configuration. Notably, the VAE computed with the scPEE-S-QM/MM model achieves faster convergence concerning the number of QM water molecules compared to the EE-QM/MM model, attributed to enhanced efficiency from MM charge polarization in the scPEE-S-QM/MM approach. This emphasizes the importance of QM/classical models with accurate solute-solvent and solvent-solvent mutual polarization for obtaining converged VAEs at a reasonable computational cost. The full-QM approach is very inefficient, while the microsolvation model is inaccurate. Computational savings in QM/MM models result from electrostatic embedding and the representative configuration, with the scPEE-S-QM/MM approach emerging as an efficient tool for describing bulk-solvated anions within the QM/MM framework. Its potential extends to improving transient anion state descriptions in biomolecules and radiosensitizers, especially given the frequent employment of microsolvation models.
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8-oxo-Guanine is a mutagenic lesion produced by reactions involving reactive oxygen species and guanine in DNA. Its production induces mispairing between the canonical nucleobases during DNA replication such that various types of cancers are associated with the DNA lesion. Since radiation therapy is used in some cases, the interaction of low-energy electrons with 8-oxo-guanine can in turn produce other reactive species, which in principle could have either a detrimental or protective effect on the organism. Motivated by these facts, we report a comparative experimental study of electron-induced fragmentation of guanine and 8-oxo-guanine, along with a theoretical study of the π* shape resonances and bound anion states, which may trigger those dissociation reactions. The electron-induced fragmentation of 8-oxo-guanine is remarkably distinct from the native form. More complex reactions were observed for the oxidized species, which may produce several anion fragments at very low energies (â¼0 eV). The dehydrogenated parent anion, which is already a minor fragment in guanine, was completely suppressed in 8-oxo-guanine. The calculated thermodynamical thresholds also suggest that NH2 elimination in guanine, at sub-excitation energies, proceeds via a complex reaction involving rearrangement steps.
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DNA , Elétrons , Guanina , Mutagênese , Espécies Reativas de OxigênioRESUMO
Electron induced dissociation reactions are relevant to many fields, ranging from prebiotic chemistry to cancer treatments. However, the simulation of dissociation electron attachment (DEA) dynamics is very challenging because the auto-ionization widths of the transient negative ions must be accounted for. We propose an adaptation of the ab initio multiple spawning (AIMS) method for complex-valued potential energy surfaces, along the lines of recent developments based on surface hopping dynamics. Our approach combines models for the energy dependence of the auto-ionization widths, obtained from scattering calculations, with survival probabilities computed for the trajectory basis functions employed in the AIMS dynamics. The method is applied to simulate the DEA dynamics of 5-bromo-uracil in full dimensionality, i.e., taking all the vibrational modes into consideration. The propagation starts on the resonance state and describes the formation of Br- anions mediated by non-adiabatic couplings. The potential energies, gradients and non-adiabatic couplings were computed with the fractional-occupancy molecular orbital complete-active-space configuration-interaction method, and the calculated DEA cross section are consistent with the observed DEA intensities.
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Elétrons , Uracila , Ânions , Íons , Conformação Molecular , Uracila/químicaRESUMO
We report a computational study of the anion states of the resveratrol (RV) and resorcinol (RS) molecules, also investigating dissociative electron attachment (DEA) pathways. RV has well-known beneficial effects in human health, and its antioxidant activity was previously associated with DEA reactions producing H2. Our calculations indicate a valence bound state (π1*) and four resonances (π2* to π5*) for that system. While the computed thermodynamic thresholds are compatible with DEA reactions producing H2 at 0 eV, the well-known mechanism involving vibrational Feshbach resonances built on a dipole bound state should not be present in RV. Our results suggest that the shallow π1* valence bound state is expected to account for H2 elimination, probably involving π1*/σOH* couplings along the vibration dynamics. The RS molecule is also an oxidant and a subunit of RV. Because two close-lying hydroxyl groups are found in the RS moiety, the H2-elimination reaction in RV should take place at the RS site. Our calculations point out a correspondence between the anion states of RV and RS and even between the thresholds. Nevertheless, the absence of bound anion states in RS, indicated by our calculations, is expected to suppress the H2-formation channel at 0 eV. One is led to conclude that the ethene and phenol subunits in RV stabilize the π1* state, thus switching on the DEA mechanism producing H2.
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Antioxidantes , Elétrons , Humanos , Resveratrol , Ânions , Resorcinóis , OxidantesRESUMO
Recent measurements of spin-polarized electron collisions with halocamphor molecules have observed intriguing trends in their dissociative electron attachment (DEA) chiral asymmetries. While the differences between the DEA asymmetries of 3-bromocamphor (3BrC) and 3-iodocamphor (3IC) were consistent with the larger atomic number of iodine, the even higher chiral asymmetry reported for 10-iodocamphor (10IC) was unexpected. In fact, the helicity densities and the distances from the iodine atoms to the closest chiral centers would suggest smaller asymmetries for 10IC compared to 3IC. To better understand the observed trends, we performed electron scattering and bound state calculations, as well as Born-Oppenheimer molecular dynamics simulations for the three halocamphors. Our results indicate that the DEA signals stem exclusively from halide ions produced by the fast dissociation of low-lying σ* anion states. While we also found dipole bound states and higher-lying shape resonances, we do not expect those states to significantly contribute to the observed yields. Despite the fact that we do not account for the spin-orbit interactions or reaction dynamics, the energies and autoionization lifetimes of the σ* resonances strongly support larger DEA yields for 10IC than 3BrC. The more efficient dissociation could explain the fourfold difference between the maximum DEA chiral asymmetries, since the difference in the atomic numbers of iodine and bromine only accounts for a factor of two. Additionally, our calculations suggest that the twofold difference between the DEA asymmetries of the iodocamphor isomers could be related to the partial suppression of the cross section for electron attachment to 3IC, compared to 10IC.
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We report sufficient theoretical evidence of the energy stability of the e+ â H22- molecule, formed by two H- anions and one positron. Analysis of the electronic and positronic densities of the latter compound undoubtedly points out the formation of a positronic covalent bond between the otherwise repelling hydride anions. The lower limit for the bonding energy of the e+ â H22- molecule is 74â kJ mol-1 (0.77â eV), accounting for the zero-point vibrational correction. The formation of a non electronic covalent bond is fundamentally distinct from positron attachment to stable molecules, as the latter process is characterized by a positron affinity, analogous to the electron affinity.
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In this work, we report theoretical and experimental cross sections for elastic scattering of electrons by chlorobenzene (ClB). The theoretical integral and differential cross sections (DCSs) were obtained with the Schwinger multichannel method implemented with pseudopotentials (SMCPP) and the independent atom method with screening corrected additivity rule (IAM-SCAR). The calculations with the SMCPP method were done in the static-exchange (SE) approximation, for energies above 12 eV, and in the static-exchange plus polarization approximation, for energies up to 12 eV. The calculations with the IAM-SCAR method covered energies up to 500 eV. The experimental differential cross sections were obtained in the high resolution electron energy loss spectrometer VG-SEELS 400, in Lisbon, for electron energies from 8.0 eV to 50 eV and angular range from 7(∘) to 110(∘). From the present theoretical integral cross section (ICS) we discuss the low-energy shape-resonances present in chlorobenzene and compare our computed resonance spectra with available electron transmission spectroscopy data present in the literature. Since there is no other work in the literature reporting differential cross sections for this molecule, we compare our theoretical and experimental DCSs with experimental data available for the parent molecule benzene.
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We report theoretical and experimental total cross sections for electron scattering by phenol (C6H5OH). The experimental data were obtained with an apparatus based in Madrid and the calculated cross sections with two different methodologies, the independent atom method with screening corrected additivity rule (IAM-SCAR), and the Schwinger multichannel method with pseudopotentials (SMCPP). The SMCPP method in the Nopen-channel coupling scheme, at the static-exchange-plus-polarization approximation, is employed to calculate the scattering amplitudes at impact energies ranging from 5.0 eV to 50 eV. We discuss the multichannel coupling effects in the calculated cross sections, in particular how the number of excited states included in the open-channel space impacts upon the convergence of the elastic cross sections at higher collision energies. The IAM-SCAR approach was also used to obtain the elastic differential cross sections (DCSs) and for correcting the experimental total cross sections for the so-called forward angle scattering effect. We found a very good agreement between our SMCPP theoretical differential, integral, and momentum transfer cross sections and experimental data for benzene (a molecule differing from phenol by replacing a hydrogen atom in benzene with a hydroxyl group). Although some discrepancies were found for lower energies, the agreement between the SMCPP data and the DCSs obtained with the IAM-SCAR method improves, as expected, as the impact energy increases. We also have a good agreement among the present SMCPP calculated total cross section (which includes elastic, 32 inelastic electronic excitation processes and ionization contributions, the latter estimated with the binary-encounter-Bethe model), the IAM-SCAR total cross section, and the experimental data when the latter is corrected for the forward angle scattering effect [Fuss et al., Phys. Rev. A 88, 042702 (2013)].
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We recently extended the electron propagator theory to any type of quantum species based in the framework of the Any-Particle Molecular Orbital (APMO) approach [J. Romero, E. Posada, R. Flores-Moreno, and A. Reyes, J. Chem. Phys. 137, 074105 (2012)]. The generalized any particle molecular orbital propagator theory (APMO/PT) was implemented in its quasiparticle second order version in the LOWDIN code and was applied to calculate nuclear quantum effects in electron binding energies and proton binding energies in molecular systems [M. Díaz-Tinoco, J. Romero, J. V. Ortiz, A. Reyes, and R. Flores-Moreno, J. Chem. Phys. 138, 194108 (2013)]. In this work, we present the derivation of third order quasiparticle APMO/PT methods and we apply them to calculate positron binding energies (PBEs) of atoms and molecules. We calculated the PBEs of anions and some diatomic molecules using the second order, third order, and renormalized third order quasiparticle APMO/PT approaches and compared our results with those previously calculated employing configuration interaction (CI), explicitly correlated and quantum Montecarlo methodologies. We found that renormalized APMO/PT methods can achieve accuracies of ~0.35 eV for anionic systems, compared to Full-CI results, and provide a quantitative description of positron binding to anionic and highly polar species. Third order APMO/PT approaches display considerable potential to study positron binding to large molecules because of the fifth power scaling with respect to the number of basis sets. In this regard, we present additional PBE calculations of some small polar organic molecules, amino acids and DNA nucleobases. We complement our numerical assessment with formal and numerical analyses of the treatment of electron-positron correlation within the quasiparticle propagator approach.
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We report on the shape resonance spectra of phenol-water clusters, as obtained from elastic electron scattering calculations. Our results, along with virtual orbital analysis, indicate that the well-known indirect mechanism for hydrogen elimination in the gas phase is significantly impacted on by microsolvation, due to the competition between vibronic couplings on the solute and solvent molecules. This fact suggests how relevant the solvation effects could be for the electron-driven damage of biomolecules and the biomass delignification [E. M. de Oliveira et al., Phys. Rev. A 86, 020701(R) (2012)]. We also discuss microsolvation signatures in the differential cross sections that could help to identify the solvated complexes and access the composition of gaseous admixtures of these species.
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Gases/química , Hidrogênio/química , Modelos Químicos , Modelos Moleculares , Fenol/química , Solventes/química , Água/química , Ânions/química , Sítios de Ligação , Simulação por Computador , Ligação de HidrogênioRESUMO
When low-energy electrons interact with molecules, they can give rise to transient anion states commonly known as resonances. These states are formed through vertical electron attachment processes and have the potential to induce various forms of DNA lesions, including base damage, single- and double-strand breaks, cross-links, and clustered lesions that are challenging to repair. So far, most experimental and theoretical studies have investigated the formation of resonances of (bio)molecules in the gas phase or in microsolvated environments. Since cellular environments are mainly composed of water molecules, it is crucial to understand how bulk water affects the resonances of (bio)molecules. Given the existing gap in studies on resonances of bulk-solvated molecules, we propose a novel theoretical-computational approach to address this void. Our approach combines the multibasis-set (time-dependent-)density functional theory and self-consistent sequential quantum mechanics/molecular mechanics polarizable electrostatic embedding methods. We apply this combined methodology to predict the vertical electron attachment energies of 1-methyl-5-nitroimidazole (1M5NI), a well-known radiosensitizer model, in bulk water. In addition, we analyze the rapid mutual polarization between the resonances (both shape- and core-excited) of 1M5NI and the surrounding bulk water environment. For comparison, we also studied the isolated and microsolvated 1M5NI. Overall, while the polarization of the environment is clearly sensitive to the solute charge, causing a significant impact on the vertical electron affinity and consequently on the attachment electron energies, it does not have a significant impact on the excitation energies of the anion.
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We performed a computational study of positron attachment to hydrated amino acids, namely glycine, alanine, and proline in the zwitterionic form. We combined the sequential quantum mechanics/molecular mechanics (s-QM/MM) method with various levels of any particle molecular orbital (APMO) calculations. Consistent with previous studies, our calculations indicate the formation of energetically stable states for the isolated and microsolvated amino acids, in which the positron localizes around the carboxylate group. However, for the larger clusters, composed of 7 to 40 water molecules, hydrogen bonding between the solute and solvent molecules disfavors positron attachment to the amino acids, giving rise to surface states in which the positron is located around the water-vacuum interface. The analysis of positron binding energies, positronic orbitals, radial probability distributions, and annihilation rates consistently pointed out the change from positron-solute to positron-solvent states. Even with the inclusion of an electrostatic embedding around the aggregates, the positrons did not localize around the solute. Positron attachment to molecules in the gas phase is a well-established fact. The existence of hydrated positronic molecules could also be expected from the analogy with transient anion states, which are believed to participate in radiation damage. Our results indicate that positron attachment to hydrated biomolecules, even to zwitterions with negatively charged carboxylated groups, would not take place. For the larger clusters, in which positron-water interactions are favored, the calculations indicate an unexpectedly large contribution of the core orbitals to the annihilation rates, between 15 and 20%. Finally, we explored correlations between positron binding energies (PBEs) and dipole moments, as well as annihilation rates and PBEs, consistent with previous studies for smaller clusters.
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We report elastic integral, differential and momentum transfer cross sections for low-energy electron scattering by the cellulose components ß-D-glucose and cellobiose (ß(1 â 4) linked glucose dimer), and the hemicellulose component ß-D-xylose. For comparison with the ß forms, we also obtain results for the amylose subunits α-D-glucose and maltose (α(1 â 4) linked glucose dimer). The integral cross sections show double peaked broad structures between 8 eV and 20 eV similar to previously reported results for tetrahydrofuran and 2-deoxyribose, suggesting a general feature of molecules containing furanose and pyranose rings. These broad structures would reflect OH, CO and/or CC σ* resonances, where inspection of low-lying virtual orbitals suggests significant contribution from anion states. Though we do not examine dissociation pathways, these anion states could play a role in dissociative electron attachment mechanisms, in case they were coupled to the long-lived π* anions found in lignin subunits [de Oliveira et al., Phys. Rev. A, 2012, 86, 020701(R)]. Altogether, the resonance spectra of lignin, cellulose and hemicellulose components establish a physical-chemical basis for electron-induced biomass pretreatment that could be applied to biofuel production.
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Celulose/química , Polissacarídeos/química , Biomassa , Desoxirribose/química , Elétrons , Furanos/química , Modelos QuímicosRESUMO
We report cross sections for elastic electron scattering by gas phase glycine (neutral form), obtained with the Schwinger multichannel method. The present results are the first obtained with a new implementation that combines parallelization with OpenMP directives and pseudopotentials. The position of the well known π* shape resonance ranged from 2.3 eV to 2.8 eV depending on the polarization model and conformer. For the most stable isomer, the present result (2.4 eV) is in fair agreement with electron transmission spectroscopy assignments (1.93 ± 0.05 eV) and available calculations. Our results also point out a shape resonance around 9.5 eV in the A' symmetry that would be weakly coupled to vibrations of the hydroxyl group. Since electron attachment to a broad and lower lying σ* orbital located on the OH bond has been suggested the underlying mechanism leading to dissociative electron attachment at low energies, we sought for a shape resonance around ~4 eV. Though we obtained cross sections with the target molecule at the equilibrium geometry and with stretched OH bond lengths, least-squares fits to the calculated eigenphase sums did not point out signatures of this anion state (though, in principle, it could be hidden in the large background). The low energy (~1 eV) integral cross section strongly scales as the bond length is stretched, and this could indicate a virtual state pole, since dipole supported bound states are not expected at the geometries addressed here.
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Elétrons , Gases/química , Glicina/química , Ânions/química , Simulação por Computador , Isomerismo , Modelos Químicos , Análise EspectralRESUMO
Computational studies have shown that one or more positrons can stabilize two repelling atomic anions through the formation of two-center positronic bonds. In the present work, we study the energetic stability of a system containing two positrons and three hydride anions, namely 2e+[H3 3-]. To this aim, we performed a preliminary scan of the potential energy surface of the system with both electrons and positrons in a spin singlet state, with a multi-component MP2 method, that was further refined with variational and diffusion Monte Carlo calculations, and confirmed an equilibrium geometry with D 3h symmetry. The local stability of 2e+[H3 3-] is demonstrated by analyzing the vertical detachment and adiabatic energy dissociation channels. Bonding properties of the positronic compound, such as the equilibrium interatomic distances, force constants, dissociation energies, and bonding densities are compared with those of the purely electronic H3 + and Li3 + systems. Through this analysis, we find compelling similarities between the 2e+[H3 3-] compound and the trilithium cation. Our results strongly point out the formation of a non-electronic three-center two-positron bond, analogous to the well-known three-center two-electron counterparts, which is fundamentally distinct from the two-center two-positron bond [D. Bressanini, J. Chem. Phys., 2021, 155, 054306], thus extending the concept of positron bonded molecules.
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Low-energy electrons (LEEs) can very efficiently induce bond breaking via dissociative electron attachment (DEA). While DEA is ubiquitous, the importance of other reactions initiated by LEEs remains much more elusive. Here, we looked into this question by measuring highly accurate total cross sections for electron scattering from 1-methyl-5-nitroimidazole (1M5NI), a model radiosensitizer. The small uncertainty and high energy resolution allow us to identify many resonant features related to the formation of transient anions. In addition to novel insights about DEA reactions through the lower-lying resonances, our key finding is that the higher-lying resonances do not undergo DEA, implying alternative decay channels with significant cross sections. In particular, dissociation into two neutral fragments is probably involved in the case of 1M5NI. This finding has direct implications for the understanding of LEE-induced chemistry, particularly in the fundamental processes underlying the radiosensitization activity.
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Elétrons , Nitroimidazóis , Ânions , Nitroimidazóis/químicaRESUMO
We propose a model for solvated positronium (Ps) atoms in water, based on the sequential quantum mechanics/molecular mechanics (s-QM/MM) protocol. We developed a Lennard-Jones force field to account for Ps-water interactions in the MM step. The repulsive term was obtained from a previously reported model for the solvated electron, while the dispersion constant was derived from the Slater-Kirkwood formula. The force field was employed in classical Monte Carlo (MC) simulations to generate Ps-solvent configurations in the NpT ensemble, while the quantum properties were computed with the any-particle molecular orbital method in the subsequent QM step. Our approach is general, as it can be applied to other liquids and materials. One basically needs to describe the solvated electron in the environment of interest to obtain the Ps solvation model. The thermodynamical properties computed from the MC simulations point out similarities between the solvation of Ps and noble gas atoms, hydrophobic solutes that form clathrate structures. We performed convergence tests for the QM step, with particular attention to the choice of basis set and expansion centers for the positronic and electronic subsystems. Our largest model was composed of the Ps atom and 22 water molecules in the QM region, corresponding to the first solvation shell, surrounded by 128 molecules described as point charges. The mean electronic and positronic vertical detachment energies were (4.73 ± 0.04) eV and (5.33 ± 0.04) eV, respectively. The latter estimates were computed with Koopmans' theorem corrected by second-order self-energies, for a set of statistically uncorrelated MC configurations. While the Hartree-Fock wave functions do not properly account for the annihilation rates, they were useful for numerical tests, pointing out that annihilation is more sensitive to the choice of basis sets and expansion centers than the detachment energies. We further explored a model with reduced solute cavity size by changing the Ps-solvent force field. Although the pick-off annihilation lifetimes were affected by the cavity size, essentially the same conclusions were drawn from both models.
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The mechanisms for multimode vibrational couplings in resonant positron annihilation are not well understood. We show that these resonances can arise from positron-induced distortions of the potential energy surface (target response to the positron field). Though these distortions can transfer energy into single- and multiquantum vibrations, they have so far been disregarded as a pathway to resonant annihilation. We also compare the existing annihilation theories and show that the currently accepted model can be cast as a special case of the Feshbach annihilation theory.
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In the search for alternatives to chlorine-containing gases, tetrafluoroethane, CF3CH2F (R134a), a widely used refrigerant gas, has been recognized as a promising substitute for dichlorodifluoromethane, CCl2F2 (R12). When R12 is replaced by R134a, the global warming potential drops from 8100 to 1430, the ozone depletion potential changes from 1 to 0, and the atmospheric lifetime decreases from 100 to 14 years. Electron interactions in the gas phase play a fundamental role in the atmospheric sciences. Here, we present a detailed study on electron-driven fragmentation pathways of CF3CH2F, in which we have investigated processes induced by both electron ionization and electron attachment. The measurements allow us to report the ion efficiency curves for ion formation in the energy range of 0 up to 25 eV. For positive ion formation, R134a dissociates into a wide assortment of ions, in which CF3+ is observed as the most abundant out of seven ions with a relative intensity above 2%. The results are supported by quantum chemical calculations based on bound state techniques, electron-impact ionization models, and electron-molecule scattering simulations, showing a good agreement. Moreover, the experimental first ionization potential was found at 13.10 ± 0.17 eV and the second at around 14.25 eV. For negative ion formation, C2F3- was detected as the only anion formed, above 8.3 eV. This study demonstrates the role of electrons in the dissociation of R134a, which is relevant for an improvement of the refrigeration processes as well as in atmospheric chemistry and plasma sciences.
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The development of new alternative routes for production of second generation ethanol from sugarcane biomass poses a challenge to the scientific community. Current research in this field addresses the use of a plasma-based pretreatment of the lignocellulosic raw material. With the aim to provide a theoretical background for this experimental technique we investigate the role of low-energy electrons from the plasma in the rupture of the matrix of cellulosic chains. In this paper, we report calculated cross sections for elastic scattering of low-energy electrons by the alpha- and beta-D-glucose monomers. The calculations employed the Schwinger multichannel method with pseudopotentials and were carried out at the static-exchange and static-exchange plus polarization levels of approximation. Through the comparison of the results obtained with inclusion of polarization effects we discuss the influence of the different conformations of the hydroxyl group linked to the anomeric carbon on the resonance spectra of these molecules. Resonant structures appearing at different energies for alpha- and beta-glucose at the low-energy regime of impact energies can be understood as a fingerprint of an "isomeric effect" and suggest that distinct fragmentation mechanisms proceeding via sigma* shape resonances may become operative depending on the glucose anomer under consideration. For energies above 15 eV the integral elastic cross sections are very similar for both monomers. Differential cross sections for the glucopyranose anomers considered in this work are typically dominated by a strong forward scattering due to the molecules' large electric dipole moments and, for energies close to the resonances' positions, they display particular features at the intermediate angular region, notably a pronounced f-wave scattering pattern, that are probably associated with the presence of those structures.