One-Electron Oxidation Potentials and Hole Delocalization in Heterogeneous Single-Stranded DNA.

The study of DNA processes is essential to understand not only its intrinsic biological functions but also its role in many innovative applications. The use of DNA as a nanowire or electrochemical biosensor leads to the need for a deep investigation of the charge transfer process along the strand as well as of the redox properties. In this contribution, the one-electron oxidation potential and the charge delocalization of the hole formed after oxidation are computationally investigated for different heterogeneous single-stranded DNA strands. We have established a two-step protocol: (i) molecular dynamics simulations in the frame of quantum mechanics/molecular mechanics (QM/MM) were performed to sample the conformational space; (ii) energetic properties were then obtained within a QM1/QM2/continuum approach in combination with the Marcus theory over an ensemble of selected geometries. The results reveal that the one-electron oxidation potential in the heterogeneous strands can be seen as a linear combination of that property within the homogeneous strands. In addition, the hole delocalization between different nucleobases is, in general, small, supporting the conclusion of a hopping mechanism for charge transport along the strands. However, charge delocalization becomes more important, and so does the tunneling mechanism contribution, when the reducing power of the nucleobases forming the strand is similar. Moreover, charge delocalization is slightly enhanced when there is a correlation between pairs of some of the interbase coordinates of the strand: twist/shift, twist/slide, shift/slide, and rise/tilt. However, the internal structure of the strand is not the predominant factor for hole delocalization but the specific sequence of nucleotides that compose the strand.

Controlling the diversity of ion-induced fragmentation pathways by N-methylation of amino acids.

We present a combined experimental and theoretical study of the fragmentation of singly and doubly N-methylated glycine (sarcosine and N,N-dimethyl glycine, respectively) induced by low-energy (keV) O6+ ions. Multicoincidence mass spectrometry techniques and quantum chemistry simulations (ab initio molecular dynamics and density functional theory) allow us to characterise different fragmentation pathways as well as the associated mechanisms. We focus on the fragmentation of doubly ionised species, for which coincidence measurements provide unambiguous information on the origin of the various charged fragments. We have found that single N-methylation leads to a larger variety of fragmentation channels than in no methylation of glycine, while double N-methylation effectively closes many of these fragmentation channels, including some of those appearing in pristine glycine. Importantly, the closure of fragmentation channels in the latter case does not imply a protective effect by the methyl group.

Timing of charge migration in betaine by impact of fast atomic ions.

The way molecules break after ion bombardment is intimately related to the early electron dynamics generated in the system, in particular, charge (or electron) migration. We exploit the natural positive-negative charge splitting in the zwitterionic molecule betaine to selectively induce double electron removal from its negatively charged side by impact of fast O6+ ions. The loss of two electrons in this localized region of the molecular skeleton triggers a competition between direct Coulomb explosion and charge migration that is examined to obtain temporal information from ion-ion coincident measurements and nonadiabatic molecular dynamics calculations. We find a charge migration time, from one end of the molecule to the other, of approximately 20 to 40 femtoseconds. This migration time is longer than that observed in molecules irradiated by ultrashort light pulses and is the consequence of charge migration being driven by adiabatic nuclear dynamics in the ground state of the molecular dication.

Hydrogenation of C24 Carbon Clusters: Structural Diversity and Energetic Properties.

This work aims at exploring the potential energy surfaces of C24Hn=0,6,12,18,24 using the genetic algorithm in combination with the density functional based tight binding potential. The structural diversity was analyzed using order parameters, in particular the sum of the numbers of 5- and 6-carbon rings R5/6. The most abundant and lowest energy population was designated as the flake population (isomers of variable shapes, large R5/6 values), characterized by an increasing number of spherical isomers when nH/nC increases. Simultaneously, the fraction of the pretzel population (spherical isomers, smaller R5/6 values) increases. The fraction of the cage population (largest R5/6 values) remains extremely minor while the branched population (smallest R5/6 values) remains the highest energy population for all nH/nC ratios. For all C24Hn=0,6,12,18,24 clusters, the evolution of the carbon ring size distribution with energy clearly shows the correlation between the stability and the number of 6-carbon rings. The average values of the ionization potentials of all populations were found to decrease when nH/nC increases, ranging from 7.9 down to 6.4 eV. This trend was correlated to geometric and electronic factors, in particular to carbon hybridization. These results are of astrophysical interest, especially regarding the role of carbon species in the gas ionization.

A general approach to study molecular fragmentation and energy redistribution after an ionizing event.

We propose to combine quantum chemical calculations, statistical mechanical methods, and photoionization and particle collision experiments to unravel the redistribution of internal energy of the furan cation and its dissociation pathways. This approach successfully reproduces the relative intensity of the different fragments as a function of the internal energy of the system in photoelectron-photoion coincidence experiments and the different mass spectra obtained when ions ranging from Ar+ to Xe25+ or electrons are used in collision experiments. It provides deep insights into the redistribution of the internal energy in the ionized molecule and its influence on the dissociation pathways and resulting charged fragments. The present pilot study demonstrates the efficiency of a statistical exchange of excitation energy among various degrees of freedom of the molecule and proves that the proposed approach is mature to be extended to more complex systems.

Hydrogenated polycyclic aromatic hydrocarbons: isomerism and aromaticity.

A simple model, based on connectivity (adjacency) matrices, is introduced to study the relative stability of hydrogenated polycyclic aromatic hydrocarbons (HPAHs). The model allows us to consider a very large number of isomeric structures for HPAHs of variable size and degree of hydrogenation, by taking into account the different positions available in each hydrogenation step. The validity of our approach is demonstrated by comparing, for a few selected cases, with the predictions of Density Functional Theory calculations. We have found that aromaticity is the main factor governing the relative stability of HPAH isomers and that the most stable structures are in general those containing the maximum possible number of non-hydrogenated rings.

Polypeptide formation in clusters of ß-alanine amino acids by single ion impact.

The formation of peptide bonds by energetic processing of amino acids is an important step towards the formation of biologically relevant molecules. As amino acids are present in space, scenarios have been developed to identify the roots of life on Earth, either by processes occurring in outer space or on Earth itself. We study the formation of peptide bonds in single collisions of low-energy He2+ ions (α-particles) with loosely bound clusters of ß-alanine molecules at impact energies typical for solar wind. Experimental fragmentation mass spectra produced by collisions are compared with results of molecular dynamics simulations and an exhaustive exploration of potential energy surfaces. We show that peptide bonds are efficiently formed by water molecule emission, leading to the formation of up to tetrapeptide. The present results show that a plausible route to polypeptides formation in space is the collision of energetic ions with small clusters of amino acids.

When is the Bell-Evans-Polanyi principle fulfilled in Diels-Alder reactions of fullerenes?

We present a theoretical study on the thermodynamic and kinetic reactivity of Diels-Alder cycloadditions to several empty fullerenes in order to investigate the relationship between reaction energies and energy barriers. The results show that fullerenes with large HOMO-LUMO gaps present good correlation coefficients. In all other cases, two factors are responsible for the lack of correlation. First, the formation of unexpected adducts which are not the ones resulting from a [4+2] addition and second the change in the electronic structure of some adducts due to the mixing of the ground state with excited states close in energy.

Fully versus constrained statistical fragmentation of carbon clusters and their heteronuclear derivatives.

The Microcanonical Metropolis Monte Carlo (MMMC) method has been shown to describe reasonably well fragmentation of clusters composed of identical atomic species. However, this is not so clear in the case of heteronuclear clusters as some regions of phase space might be inaccessible due to the different mobility of the different atomic species, the existence of large isomerization barriers, or the quite different chemical nature of the possible intermediate species. In this paper, we introduce a constrained statistical model that extends the range of applicability of the MMMC method to such mixed clusters. The method is applied to describe fragmentation of isolated clusters with high, moderate, and no heteronuclear character, namely, CnHm, CnN, and Cn clusters for which experimental fragmentation branching ratios are available in the literature. We show that the constrained statistical model describes fairly well fragmentation of CnHm clusters in contrast with the poor description provided by the fully statistical model. The latter model, however, works pretty well for both Cn and CnN clusters, thus showing that the ultimate reason for this discrepancy is the inability of the MMMC method to selectively explore the whole phase space. This conclusion has driven us to predict the fragmentation patterns of the C4N cluster for which experiments are not yet available.

Aromaticity, Coulomb repulsion, π delocalization or strain: who is who in endohedral metallofullerene stability?

Endohedral metallofullerenes (EMFs) synthetized in the laboratory are known to often violate the isolated pentagon and pentagon adjacency penalty rules that successfully describe the relative stability of pristine fullerene isomers. To explain these anomalies, several models have been proposed. In this work, we have systematically investigated the performance of the widely used IPSI (inverse pentagon separation index), ALA (additive local aromaticity) and CSI (charge stabilization index) models in predicting the relative stability of a large number of EMF isomers with cages ranging from C28 to C104 and charge states of 4- and 6-. By explicitly comparing with existing experiments and quantum chemistry calculations, we show that the predictive power of the ALA and CSI models is similarly good, with CSI being slightly superior though computationally much less involved. IPSI's performance is generally worse though still acceptable in a wide range of cage sizes, except for the higher charge states in the C62 to C82 size interval. From our analysis, we conclude that neither Coulomb electronic repulsion (IPSI) nor aromaticity (ALA) are the sole parameters governing the relative stability of EMF isomers. Electron delocalization in the π shell in combination with minimum strain (CSI) provides a more realistic description of the relative stabilities observed experimentally, as the former can compensate an unfavorable Coulomb repulsion and account for stabilizing binding effects that do not necessarily translate into aromaticity.

Simple bond patterns predict the stability of Diels-Alder adducts of empty fullerenes.

We present an extensive and systematic study on the regioselectivity of Diels-Alder (DA) cycloadditions to empty fullerenes, covering the whole range of cage sizes from C60 to C180. Reaction energies obtained from DFT calculations, which correlate with activation barriers, can be well reproduced by using a simple Hückel model, indicating that π electronic effect is the key factor determining the relative stability of DA adducts. Based on these results, we propose a couple of simple rules of thumb, in terms of a set of bond patterns, as a visual guide for approximate prediction of DA reactive sites. Moreover, we suggest two quantitative descriptors for the stability of DA regioadducts of empty fullerenes; one combines the π free valences and bond orders involved in the DA addition, and the other characterizes the local π aromaticity around the addition site. The latter criterion allows us to easily rationalize the proposed rules.

Furan Fragmentation in the Gas Phase: New Insights from Statistical and Molecular Dynamics Calculations.

We present a complete exploration of the different fragmentation mechanisms of furan (C4H4O) operating at low and high energies. Three different theoretical approaches are combined to determine the structure of all possible reaction intermediates, many of them not described in previous studies, and a large number of pathways involving three types of fundamental elementary mechanisms: isomerization, fragmentation, and H/H2 loss processes (this last one was not yet explored). Our results are compared with the existing experimental and theoretical investigations for furan fragmentation. At low energies the first processes to appear are isomerization, which always implies the breaking of one C-O bond and one or several hydrogen transfers; at intermediate energies the fragmentation of the molecular skeleton becomes the most relevant mechanism; and H/H2 loss is the dominant processes at high energy. However, the three mechanisms are active in very wide energy ranges and, therefore, at most energies there is a competition among them.

Computational Study of the Structure and Degradation Products of Alloxydim Herbicide.

Density functional theory calculations allowed us to study alloxydim herbicide and to identify the most stable conformers, the factors that governs their stability, and the interconversion mechanisms among the most relevant conformers. The degradation chain involves, as a first step, the cleavage of the N-O bond and the formation of a stable intermediate difficult to characterize experimentally. The study performed also allowed us to identify the properties of this elusive intermediate and to determine that the dominant fragmentation process in the gas phase is the homolytic fragmentation. Stability of alloxydim conformers and homolytic fragments were also assessed in the water phase. Computed IR spectra were consistent with those observed experimentally.

Topology-Based Approach to Predict Relative Stabilities of Charged and Functionalized Fullerenes.

Understanding the relationship between structure and stability is one of the fundamental aspects of fullerene chemistry, as the number of possible cage isomers is very large and complexity increases by orders of magnitude when chemical groups are attached to the fullerene cage. The well-established stability rules valid for neutral fullerenes do not apply to many charged or functionalized fullerenes. Here we present the theory, implementation, and applications of two simple topology-based models that allow one to predict the relative stability of charged and functionalized fullerenes without the need for quantum chemistry calculations: (i) the charge stabilization index (CSI) model, based on the concepts of cage connectivity and frontier π orbitals, which offers a general framework for the relative stability of both positively and negatively charged fullerenes, as well as endohedral metallofullerenes, and (ii) the exohedral fullerene stabilization index (XSI) model, which incorporates all key factors governing the stability of exohedral fullerenes, namely, π delocalization, σ strain, and steric hindrance between addends. Based exclusively on topological information, both models are powerful prescreening tools for predicting the most stable structures of a large number of charged and functionalized fullerenes. For easy use by fullerene chemists, both models have been implemented in the FullFun (for Fullerene Functionalization) software package, whose effectiveness and efficiency are demonstrated by some illustrative examples.

Quantum chemistry in environmental pesticide risk assessment.

The scientific community and regulatory bodies worldwide, currently promote the development of non-experimental tests that produce reliable data for pesticide risk assessment. The use of standard quantum chemistry methods could allow the development of tools to perform a first screening of compounds to be considered for the experimental studies, improving the risk assessment. This fact results in a better distribution of resources and in better planning, allowing a more exhaustive study of the pesticides and their metabolic products. The current paper explores the potential of quantum chemistry in modelling toxicity and environmental behaviour of pesticides and their by-products by using electronic descriptors obtained computationally. Quantum chemistry has potential to estimate the physico-chemical properties of pesticides, including certain chemical reaction mechanisms and their degradation pathways, allowing modelling of the environmental behaviour of both pesticides and their by-products. In this sense, theoretical methods can contribute to performing a more focused risk assessment of pesticides used in the market, and may lead to higher quality and safer agricultural products. © 2017 Society of Chemical Industry.

Generalized structural motif model for studying the thermodynamic stability of fullerenes: from C60 to graphene passing through giant fullerenes.

We present an extension of the structural motif model [Cioslowski et al., J. Am. Chem. Soc., 2000, 122, 8265], originally proposed to predict the relative stability of medium-sized neutral fullerenes (C60-C102), to account for the correct graphene limit, thus widening its range of applicability to giant and supergiant icosahedral fullerenes. The new model has been parameterized using the density functional theory (DFT) energies of 426 distinct fullerenes ranging from C60 to C180, most of which correspond to the lowest-energy isomers of each cage size. While the original model is inapplicable for fullerenes larger than C150, the new model performs very well for these systems, with typical deviations of 3.4 kcal mol-1 from the DFT energies. Based on the optimized parameters, we have obtained the actual energy contributions for all motifs, which we show are closely related to the number and separation of pentagonal rings, in contrast to the original version of the model. We also point out that, in general, motif models result in large deviations for largely aspherical fullerenes and propose a way to correct the errors.

Production of doubly-charged highly reactive species from the long-chain amino acid GABA initiated by Ar9+ ionization.

We present a combined experimental and theoretical study of the fragmentation of multiply-charged γ-aminobutyric acid molecules (GABAz+, z = 2, 3) in the gas phase. The combination of ab initio molecular dynamics simulations with multiple-coincidence mass spectrometry techniques allows us to observe and identify doubly-charged fragments in coincidence with another charged moiety. The present results indicate that double and triple electron capture lead to the formation of doubly-charged reactive nitrogen and oxygen species (RNS and ROS) with different probabilities due to the different charge localisation and fragmentation behaviour of GABA2+ and GABA3+. The MD simulations unravel the fast (femtosecond) formation of large doubly charged species, observed on the experimental microsecond timescale. The excess of positive charge is stabilised by the presence of cyclic X-member (X = 3-5) ring structures. 5-Member cyclic molecules can sequentially evaporate neutral moieties, such as H2, H2O and CO2, leading to smaller doubly charged fragments as those observed in the experiments.

Relative Stability of Empty Exohedral Fullerenes: π Delocalization versus Strain and Steric Hindrance.

Predicting and understanding the relative stability of exohedral fullerenes is an important aspect of fullerene chemistry, since the experimentally formed structures do not generally follow the rules that govern addition reactions or the making of pristine fullerenes. First-principles theoretical calculations are of limited applicability due to the large number of possible isomeric forms, for example, more than 50 billion for C60X8. Here we propose a simple model, exclusively based on topological arguments, that allows one to predict the relative stability of exohedral fullerenes without the need for electronic structure calculations or geometry optimizations. The model incorporates the effects of π delocalization, cage strain, and steric hindrance. We show that the subtle interplay between these three factors is responsible for (i) the formation of non-IPR (isolated pentagon rule) exohedral fullerenes in contrast with their pristine fullerene counterparts, (ii) the appearance of more pentagon-pentagon adjacencies than predicted by the PAPR (pentagon-adjacency penalty rule), (iii) the changes in regioisomer stability due to the chemical nature of the addends, and (iv) the variations in fullerene cage stability with the progressive addition of chemical species.