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.

Child psychiatric emergency visits during the COVID-19 pandemic

Introduction

Paediatric and adult psychiatric emergency department (ED) visits decreased during the initial COVID-19 pandemic outbreak. Long-term consequences of the pandemic will include increases in mental healthcare needs especially among especially vulnerable groups such as children and adolescents.

Objectives

This study examined changes in the number of overall and diagnosis-specific mental health ED visits among patients aged <18 years following onset of the COVID-19 pandemic in Madrid, Spain.

Methods

We used electronic health records to extract the monthly numbers of total and diagnosis-specific mental health ED visits among patients aged <18 years, between October 2018 and April 2021, to La Paz University Hospital. We conducted interrupted time-series analyses and compared trends before and after the day of the first ED COVID-19 case (1^st March 2020).

Results

In March 2020, there was a marked initial decrease of -12.8 (95%CI -21.9, -7.9) less monthly mental health ED visits. After April 2020, there was a subsequent increasing trend of 3.4 (95%CI 2.6, 4.2) additional monthly mental health ED visits.

Conclusions

After onset of the COVID-19 pandemic, there was an increase in paediatric psychiatric ED visits, especially due to suicide-related reasons. These data reinforce the crucial role of the ED in the management of acute mental health problems among youth and highlight the need for renovated efforts to enhance access to care outside of and during acute crises during the pandemic and its aftermath.

Disclosure

No significant relationships.

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.

Polypeptide formation in clusters of β-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 β-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.

Hydrogenated polycyclic aromatic hydrocarbons: isomerism and aromaticity

A simple model based on adjacency matrices is introduced to study the stability of hydrogenated polycyclic aromatic hydrocarbons. Aromaticity governs their relative stability having the most stable isomers the higher number of non-hydrogenated rings.

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, C_nH_m, C_nN, and C_n clusters for which experimental fragmentation branching ratios are available in the literature. We show that the constrained statistical model describes fairly well fragmentation of C_nH_m clusters in contrast with the poor description provided by the fully statistical model. The latter model, however, works pretty well for both C_n and C_nN 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?

Three different models for endohedral metallofullerene structure prediction are compared, revealing the physical origin of the stability of these compounds.

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.

XUV/X-ray light and fast ions for ultrafast chemistry

The deposition of large amounts of energy in a molecule by XUV/X-ray photon absorption or fast-ion collision, triggers a set of complex ultrafast electronic and nuclear dynamics that allow a deep understanding and control of chemical reactivity. This themed issue showcases the research performed in the understanding, monitoring and control of these processes.

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

A systematic study of Diels–Alder cycloadditions to empty fullerenes reveals that π effects control site preference. Simple Hückel calculation allows to obtain quantitative descriptors and to understand why addition occurs preferentially at certain types of bonds. A couple of simple rules are proposed as a visual guide for a rapid prediction of Diels–Alder reactivity.

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.

M3C: A Computational Approach To Describe Statistical Fragmentation of Excited Molecules and Clusters

The Microcanonical Metropolis Monte Carlo method, based on a random sampling of the density of states, is revisited for the study of molecular fragmentation in the gas phase (isolated molecules, atomic and molecular clusters, complex biomolecules, etc.). A random walk or uniform random sampling in the configurational space (atomic positions) and a uniform random sampling of the relative orientation, vibrational energy, and chemical composition of the fragments is used to estimate the density of states of the system, which is continuously updated as the random sampling populates individual states. The validity and usefulness of the method is demonstrated by applying it to evaluate the caloric curve of a weakly bound rare gas cluster (Ar₁₃), to interpret the fragmentation of highly excited small neutral and singly positively charged carbon clusters (C_n, n = 5,7,9 and C_n⁺, n = 4,5) and to simulate the mass spectrum of the acetylene molecule (C₂H₂).

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.

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 (GABA^z+,z= 2, 3) in the gas phase.

Generalized structural motif model for studying the thermodynamic stability of fullerenes: from C60to graphene passing through giant fullerenes

A generalized motif model to describe the stability of neutral fullerenes, covering the full range of cage sizes, starting from C₆₀, going through giant fullerenes, and ultimately leading to graphene.

Determination of Energy-Transfer Distributions in Ionizing Ion-Molecule Collisions

The ionization and fragmentation of the nucleoside thymidine in the gas phase has been investigated by combining ion collision with state-selected photoionization experiments and quantum chemistry calculations. The comparison between the mass spectra measured in both types of experiments allows us to accurately determine the distribution of the energy deposited in the ionized molecule as a result of the collision. The relation of two experimental techniques and theory shows a strong correlation between the excited states of the ionized molecule with the computed dissociation pathways, as well as with charge localization or delocalization.

Adsorption of Hydrogen Molecules on Carbon Nanotubes Using Quantum Chemistry and Molecular Dynamics

Physisorption and storage of molecular hydrogen on single-walled carbon nanotube (SWCNT) of various diameters and chiralities are studied by means of classical molecular dynamics (MD) simulations and a force field validated using DFT-D2 and CCSD(T) calculations. A nonrigid carbon nanotube model is implemented with stretching (C-C) and valence angle potentials (C-C-C) formulated as Morse and Harmonic cosine potentials, respectively. Our results evidence that the standard Lennard-Jones potential fails to describe the H2-H2 binding energies. Therefore, our simulations make use of a potential that contains two-body term with parameters obtained from fitting CCSD(T)/CBS binding energies. From our MD simulations, we have analyzed the interaction energies, radial distribution functions, gravimetric densities (% wt), and the distances of the adsorbed H2 layers to the three zigzag type of nanotubes (5,0), (10,0), and (15,0) at 100 and 300 K.

Mechanical Isolation of Highly Stable Antimonene under Ambient Conditions

Antimonene fabricated by mechanical exfoliation is highly stable under atmospheric conditions over periods of months and even when immersed in water. Density functional theory confirms the experiments and predicts an electronic gap of ≈1 eV. These results highlight the use of antimonene for optoelectronics applications.

Antimonene: Mechanical Isolation of Highly Stable Antimonene under Ambient Conditions (Adv. Mater. 30/2016)

On page 6332, J. Gómez-Herrero, F. Zamora, and co-workers describe the isolation of antimonene, a new allotrope of antimony that consists of a single layer of atoms. They obtain antimonene flakes by the scotch tape method; these flakes are highly stable in ambient conditions and even when immersed in water. The 1.2 eV gap calculated in this study suggests potential applications in optoelectronics.

Understanding the self-assembly of TCNQ on Cu(111): a combined study based on scanning tunnelling microscopy experiments and density functional theory simulations

Two polymorphic structures of TCNQ on Cu(111) can be formed by varying the deposition conditions.

Is C50 a superaromat? Evidence from electronic structure and ring current calculations

Of the three lowest isomers of C₅₀ fullerene, the minimal energy D₃ isomer comes closest to a spherical aromat or superaromat.

Theoretical study of the interaction between molecular hydrogen and [MC60]+ complexes

In this work we present a density functional theory study of the interaction between a positively charged exohedral metallofullerene and several hydrogen molecules.

Surface-Supported Robust 2D Lanthanide-Carboxylate Coordination Networks

Lanthanide-based metal-organic compounds and architectures are promising systems for sensing, heterogeneous catalysis, photoluminescence, and magnetism. Herein, the fabrication of interfacial 2D lanthanide-carboxylate networks is introduced. This study combines low- and variable-temperature scanning tunneling microscopy (STM) and X-ray photoemission spectroscopy (XPS) experiments, and density functional theory (DFT) calculations addressing their design and electronic properties. The bonding of ditopic linear linkers to Gd centers on a Cu(111) surface gives rise to extended nanoporous grids, comprising mononuclear nodes featuring eightfold lateral coordination. XPS and DFT elucidate the nature of the bond, indicating ionic characteristics, which is also manifest in appreciable thermal stability. This study introduces a new generation of robust low-dimensional metallosupramolecular systems incorporating the functionalities of the f-block elements.

N-Acetylglycine Cation Tautomerization Enabled by the Peptide Bond

We present a combined experimental and theoretical study of the ionization of N-acetylglycine molecules by 48 keV O(6+) ions. We focus on the single ionization channel of this interaction. In addition to the prompt fragmentation of the N-acetylglycine cation, we also observe the formation of metastable parent ions with lifetimes in the microsecond range. On the basis of density functional theory calculations, we assign these metastable ions to the diol tautomer of N-acetylglycine. In comparison with the simple amino acids, the tautomerization rate is higher because of the presence of the peptide bond. The study of a simple biologically relevant molecule containing a peptide bond allows us to demonstrate how increasing the complexity of the structure influences the behavior of the ionized molecule.

Molecular Growth Inside of Polycyclic Aromatic Hydrocarbon Clusters Induced by Ion Collisions

The present work combines experimental and theoretical studies of the collision between keV ion projectiles and clusters of pyrene, one of the simplest polycyclic aromatic hydrocarbons (PAHs). Intracluster growth processes induced by ion collisions lead to the formation of a wide range of new molecules with masses larger than that of the pyrene molecule. The efficiency of these processes is found to strongly depend on the mass and velocity of the incoming projectile. Classical molecular dynamics simulations of the entire collision process-from the ion impact (nuclear scattering) to the formation of new molecular species-reproduce the essential features of the measured molecular growth process and also yield estimates of the related absolute cross sections. More elaborate density functional tight binding calculations yield the same growth products as the classical simulations. The present results could be relevant to understand the physical chemistry of the PAH-rich upper atmosphere of Saturn's moon Titan.

Unusual hydroxyl migration in the fragmentation of β-alanine dication in the gas phase

Experimental and theoretical investigations show that hydroxyl migration leads to unexpected fragmentation dynamics of β-alanine dication in the gas phase.

Controlling the spatial arrangement of organic magnetic anions adsorbed on epitaxial graphene on Ru(0001)

Achieving control over the self-organization of functional molecules on graphene is critical for the development of graphene technology in organic electronic and spintronic. Here, by using a scanning tunneling microscope (STM), we show that the electron acceptor molecule 7,7',8,8'-tetracyano-p-quinodimethane (TCNQ) and its fluorinated derivative 2,3,5,6-tetrafluoro-7,7',8,8'-tetracyano-p-quinodimethane (F4-TCNQ), co-deposited on the surface of epitaxial graphene on Ru(0001), transform spontaneously into their corresponding magnetic anions and self-organize in two remarkably different structures. TCNQ forms densely packed linear magnetic arrays, while F4-TCNQ molecules remain as isolated non interacting magnets. With the help of density functional theory (DFT) calculations, we trace back the origin of this behavior in the competition between the intermolecular repulsion experienced by the individual charged anions, which tends to separate the molecules, and the delocalization of the electrons transferred from the surface to the molecules, which promotes the formation of molecular oligomers. Our results demonstrate that it is possible to control the spatial arrangement of organic magnetic anions co-adsorbed on a surface by means of chemical substitution, paving the way for the design of two-dimensional fully organic magnetic structures on graphene and on other surfaces.

Charge transfer-assisted self-limited decyanation reaction of TCNQ-type electron acceptors on Cu(100)

TCNQ derivatives adsorbed on a metal surface undergo a self-limited decyanation reaction that only affects two out of the four cyano groups in the molecule. Combined Scanning Tunneling Microscopy/X-ray Photoelectron Spectroscopy experiments and Density Functional Theory calculations relate the self-limiting behavior to the transfer of electrons from the metal to the molecule.

Probing the site-dependent Kondo response of nanostructured graphene with organic molecules

TCNQ molecules are used as a sensitive probe for the Kondo response of the electron gas of a nanostructured graphene grown on Ru(0001) presenting a moiré pattern. All adsorbed molecules acquired an extra electron by charge transfer from the substrate, but only those adsorbed in the FCC-Top areas of the moiré show magnetic moment and Kondo resonance in the STS spectra. DFT calculations trace back this behavior to the existence of a surface resonance in the low areas of the graphene moiré, whose density distribution strongly depends on the stacking sequence of the moiré area and effectively quenches the magnetic moment for HCP-Top sites.

Fragmentation dynamics of doubly charged methionine in the gas phase

The dependence of the fragmentation of doubly charged gas-phase methionine (C5H11NO2S) on the electronic-state character of the parent ion is studied experimentally by energy-resolved electron ion-ion coincidence spectroscopy. The parent dication electronic states are populated by Auger transitions following site-specific sulfur 2p core ionization. Two fragmentation channels are observed to be strongly dependent on the electronic states with vacancies in weakly bound molecular orbitals. All-electron calculations are applied to assign doubly charged final states of sulfur 2p core ionized methionine. In addition, the Car-Parrinello method is applied to model fragmentation dynamics of doubly charged methionine molecules with various initial temperatures to understand the typical characteristics of the molecular dissociation and partly to support the interpretation of experimental data.

Ordered arrays of metal-organic magnets at surfaces

We report here on the molecular self-assembly of 7, 7', 8, 8' tetracyanoquinodimethane (TCNQ) (schematic representation of the molecule on figure 1(b)) on a single-crystal Cu(111) surface, followed by deposition of Fe and Mn, and on the formation of an ordered metal–organic coordination network of Fe (or Mn)–TCNQ units, which contains magnetic ions separated by 0.9 nm.

Onset of chiral adenine surface growth

The structure and stability of adenine crystals and thin layers has been studied by using scanning tunneling microscopy, X-ray diffraction, and density functional theory calculations. We have found that adenine crystals can be grown in two phases that are energetically quasi-degenerate, the structure of which can be described as a pile-up of 2D adenine planes. In each plane, the structure can be described as an aggregation of adenine dimers. Under certain conditions, kinetic effects can favor the growth of the less stable phase. These results have been used to understand the growth of adenine thin films on gold under ultra-high vacuum conditions. We have found that the grown phase corresponds to the α-phase, which is composed of stacked prochiral planes. In this way, the adenine nanocrystals exhibit a surface that is enantiopure. These results could open new insight into the applications of adenine in biological, medical, and enantioselective or pharmaceutical fields.