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Virtual simulations are a very useful educational resource to improve the teaching of chemistry. Their use makes it possible to facilitate the comprehension of concepts, promotes the development of scientific competences and even improves student attitudes toward chemistry. However, it is important to point out that a simulation by itself is not enough to improve student learning. Methodological design is a crucial aspect in order for its classroom use to be significant. Simulations must form part of an instructional sequence that promotes said learning, and thus the role of the instructor is key. This work conducts a systematic review with the aim of analyzing how to apply the use of simulations in the teaching of chemistry in secondary schools, delving deeper into the way in which simulations are used from a methodological perspective, in order to improve the learning processes and results. In this sense, it was found that there is an improvement in learning on both the level of content comprehension and in scientific competences. Guided research is also identified as the most effective methodology for the application of simulations in the classroom. With a look to the future, it is suggested that there is a need to conduct research on the continued use of simulations in the classroom, as well as their characteristics and the instructional methods used. [ABSTRACT FROM AUTHOR]

In this study we investigate the dissociative photoionization of molecular hydrogen H2, addressing the influence of autoionizing states and nuclear motion on the photoelectron dynamics. Experimental results are compared with ab initio calculations.

We present a theoretical study of vibrationally resolved photoelectron angular distributions for ammonia in both laboratory and molecular frames, in the photon energy range up to 70 eV, where only valence and inner-valence ionization is possible. We focus on the band resulting from ionization of the 3a1 HOMO orbital leading to NH3+ in the electronic ground state, , for which the dominant vibrational progression corresponds to the activation of the umbrella inversion mode. We show that, at room temperature, the photoelectron angular distributions for randomly oriented molecules or molecules whose principal C3 symmetry axis is aligned along the light polarization direction are perfectly symmetric with respect to the plane that contains the intermediate D3h conformation connecting the pyramidal structures associated with the double-well potential of the umbrella inversion mode. These distributions exhibit symmetric, nearly perfect two-lobe shapes in the whole range of investigated photon energies. In contrast, for molecules where the initial vibrational state is localized in one of the two wells, a situation that can experimentally be achieved by introducing an external electric field, the molecular-frame photoelectron angular distributions (MFPADs) are in general asymmetric, but the degree of asymmetry of the two lobes dramatically changes and oscillates with photoelectron energy. We also show that, at ultracold temperatures, where all aligned molecules initially lie in the delocalized ground vibrational state, the photoelectron angular distributions are perfectly symmetric, but the two-lobe shape is only observed when the final vibrational state of the resulting NH3+ cation has even parity. When the latter vibrational state has odd parity, the angular distributions are much more involved and, at photoelectron energies of ∼10 eV, they directly reflect the bi-pyramidal geometry of the molecule in its ground vibrational state. These results suggest that, in order to obtain structural information from MFPADs in ammonia and likely in other molecules containing a similar double-well potential, one could preferably work at ultracold temperatures, which is not the case for most molecules. [ABSTRACT FROM AUTHOR]

Recent experiments in gas-phase molecules have shown the versatility of using attosecond pulse trains combined with IR femtosecond pulses to track and control excitation and ionization yields on the attosecond timescale. The interplay between electron and nuclear motions drives the light-induced transitions favoring specific reaction paths, so that the time delay between the pulses can be used as the tracking parameter or as a control knob to manipulate the molecular dynamics. Here, we present ab initio simulations on the hydrogen molecule to demonstrate that by filtering the high harmonics in an attosecond pulse train one can quench or enhance specific quantum paths thus dictating the outcome of the reaction. It is then possible to discriminate the dominant sequential processes in two-photon ionization, as for example molecular excitation followed by ionization or the other way around. More interestingly, frequency filters can be employed to steer the one- and two-photon yields to favor electron emission in a specific direction. [ABSTRACT FROM AUTHOR]

We investigate different approximations in a polarization control scheme in two-color two-photon ionization by means of second-order time-dependent perturbation theory. Experiments revealed light-polarization dependencies in the above-threshold ionization of water molecules assisted by an IR field. These experiments were performed at photoelectron energies at which the soft-photon approximation exhibits discrepancies. We show that these discrepancies may be attributed to the coulombic nature of the scattering process for continuum–continuum transitions. [ABSTRACT FROM AUTHOR]

We present a theoretical study of the electron and nuclear dynamics that would arise in an attosecond two-color XUV-pump/XUV-probe experiment in glycine. In this scheme, the broadband pump pulse suddenly ionizes the molecule and creates an electronic wave packet that subsequently evolves under the influence of the nuclear motion until it is finally probed by the second XUV pulse. To describe the different steps of such an experiment, we have combined a multi-reference static-exchange scattering method with a trajectory surface hopping approach. We show that by changing the central frequency of the pump pulse, i.e., by engineering the initial electronic wave packet with the pump pulse, one can drive the cation dynamics into a specific fragmentation pathway. Reminiscence of this early electron dynamics can be observed in specific fragmentation channels (not all of them) as a function of the pump–probe delay and in time-resolved photoelectron spectra at specific photoelectron energies. The optimum conditions to visualize the initial electronic coherence in photoelectron and photo-ion spectra depend very much on the characteristics of the pump pulse as well as on the electronic structure of the molecule under study. [ABSTRACT FROM AUTHOR]

We investigate how attosecond XUV pump/IR probe schemes can be used to exert control on the ionization dynamics of the hydrogen molecule. The aim is to play with all available experimental parameters in the problem, namely the XUV pump–IR probe delay, the energy and emission direction of the produced photo-ions, as well as combinations of them, to uncover control strategies that can lead to preferential electron ejection directions. We do so by accurately solving the time-dependent Schrödinger equation, with inclusion of both electronic and nuclear motions, as well as the coupling between them. We show that both the IR pulse and the nuclear motion can be used to break the molecular inversion symmetry, thus leading to asymmetric molecular-frame photoelectron angular distributions. The preferential electron emission direction can thus be tuned by varying the pump–probe delay, by choosing specific ranges of proton kinetic energies, or both. We expect that similar control strategies could be used in more complex molecules containing light nuclei. [ABSTRACT FROM AUTHOR]

We propose a scheme to generate electric dipole moments in homonuclear molecular cations by creating, with an ultrashort pump pulse, a quantum superposition of vibrational states on electronic states strongly perturbed by very strong static electric fields. By field-induced molecular stabilization, the dipoles can reach values as large as 50 Debyes and oscillate on a time-scale comparable to that of the slow vibrational motion. We show that both the electric field and the pump pulse parameters can be used to control the amplitude and period of the oscillation, while preventing the molecule from ionizing or dissociating. [ABSTRACT FROM AUTHOR]

High-level ab initio calculations have been carried out to evaluate the lifetimes of complexes formed by the association of Cu2+ to water, ammonia, and hydrogen cyanide. The corresponding binding energies were evaluated at the CCSD(T)/6-311+G(3df,2pd) level of theory. The potential-energy curves corresponding to their dissociation into Cu++L+ (L=H2O, NH3, and HCN) were obtained at the CCSD(T)/6-311+G(3df,2p) level on BHLYP/6-311+G(d,p) optimized geometries. Lifetimes were calculated using the exterior complex scaling and the semiclassical WKB methods. Although all the complexes investigated are thermodynamically unstable with respect to their dissociation into Cu++L+ in a typical Coulomb explosion, the activation barrier is high enough to accommodate several vibrational resonances, with very large lifetimes. As a matter of fact, if the three complexes are produced in the lowest vibrational levels, they behave as totally bound (with almost infinite lifetime) species. [ABSTRACT FROM AUTHOR]

Abstract: A pump‐probe experiment in the tetrafluoro‐methane (CF4) molecule has been theoretically simulated, allowing one to access electron dynamics in its natural time scale: the attosecond. The chosen pump and probe pulses can be currently produced in most attosecond laboratories. In this scheme, CF4 is first ionized by an extreme UV (XUV) attosecond pulse and the charge dynamics induced in the corresponding cation is probed with a few‐femtosecond visible light (VIS) pulse. We demonstrate that modulations in the calculated photoelectron spectra with the pump‐probe delay reflect the dynamics of the XUV‐induced electronic wave packet. In particular, from the analysis of these modulations in the interval of time delays where the pump and probe pulses do not overlap any more, one has access to the amplitudes and phases of the different components of the electronic wave packet generated by the attosecond pulse. These reflect a complex dynamics that basically consists of very fast charge fluctuations occurring all over the molecule without any preference for a particular molecular site. [ABSTRACT FROM AUTHOR]

The combination of attosecond pump–probe techniques with mass spectrometry methods has recently led to the first experimental demonstration of ultrafast charge dynamics in a biomolecule, the amino acid phenylalanine [Calegari et al., Science, 2014, 346, 336]. Using an extension of the static-exchange density functional theory (DFT) method, the observed dynamics was explained as resulting from the coherent superposition of ionic states produced by the broadband attosecond pulse. Here, we have used the static-exchange DFT method to investigate charge migration induced by attosecond pulses in the glycine molecule. We show that the observed dynamics follows patterns similar to those previously found in phenylalanine, namely that charge fluctuations occur all over the molecule and that they can be explained in terms of a few typical frequencies of the system. We have checked the validity of our approach by explicitly comparing with the photoelectron spectra obtained in synchrotron radiation experiments and with the charge dynamics that follows the removal of an electron from a given molecular orbital, for which fully correlated ab initio results are available in the literature. From this comparison, we conclude that our method provides an accurate description of both the coherent superposition of cationic states generated by the attosecond pulse and its subsequent time evolution. Hence, we expect that the static-exchange DFT method should perform equally well for other medium-size and large molecules, for which the use of fully correlated ab initio methods is not possible. [ABSTRACT FROM AUTHOR]

The sudden ionization of a molecule by an attosecond pulse is followed by charge redistribution on a time scale from a few femtoseconds down to hundreds of attoseconds. This ultrafast redistribution is the result of the coherent superposition of electronic continua associated with the ionization thresholds that are reached by the broadband attosecond pulse. Thus, a correct theoretical description of the time evolution of the ensuing wave packet requires the knowledge of the actual ionization amplitudes associated with all open ionization channels, a real challenge for large and medium-size molecules. Recently, the first calculation of this kind has come to light, allowing for interpretation of ultrafast electron dynamics observed in attosecond pump–probe experiments performed on the amino acid phenylalanine [Calegari et al., Science 2014, 346, 336]. However, as in most previous theoretical works, the interpretation was based on various simplifying assumptions, namely, the ionized electron was not included in the description of the cation dynamics, the nuclei were fixed at their initial position during the hole migration process, and the effect of the IR probe pulse was ignored. Here we go a step further and discuss the consequences of including these effects in the photoionization of the glycine molecule. We show that (i) the ionized electron does not affect hole dynamics beyond the first femtosecond, and (ii) nuclear dynamics has only a significant effect after approximately 8 fs, but does not destroy the coherent motion of the electronic wave packet during at least few additional tens of fs. As a first step towards understanding the role of the probe pulse, we have considered an XUV probe pulse, instead of a strong IR one, and show that such an XUV probe does not introduce significant distortions in the pump-induced dynamics, suggesting that pump–probe strategies are suitable for imaging and manipulating charge migration in complex molecules. Furthermore, we show that hole dynamics can be changed by shaping the attosecond pump pulse, thus opening the door to the control of charge dynamics in biomolecules. [ABSTRACT FROM AUTHOR]

In the past few years, attosecond techniques have been implemented for the investigation of ultrafast dynamics in molecules. The generation of isolated attosecond pulses characterized by a relatively high photon flux has opened up new possibilities in the study of molecular dynamics. In this paper, we report on experimental and theoretical results of ultrafast charge dynamics in a biochemically relevant molecule, namely, the amino acid phenylalanine. The data represent the first experimental demonstration of the generation and observation of a charge migration process in a complex molecule, where electron dynamics precede nuclear motion. The application of attosecond technology to the investigation of electron dynamics in biologically relevant molecules represents a multidisciplinary work, which can open new research frontiers: those in which few-femtosecond and even subfemtosecond electron processes determine the fate of biomolecules. It can also open new perspectives for the development of new technologies, for example, in molecular electronics, where electron processes on an ultrafast temporal scale are essential to trigger and control the electron current on the scale of the molecule. [ABSTRACT FROM PUBLISHER]

We investigate the use of UV-pump-UV-probe schemes to trace the evolution of nuclear wave packets in excited molecular states by analyzing the asymmetry of the electron angular distributions resulting from dissociative ionization. The asymmetry results from the coherent superposition of gerade and ungerade states of the remaining molecular ion in the region where the nuclear wave packet launched by the pump pulse in the neutral molecule is located. Hence, the variation of this asymmetry with the time delay between the pump and the probe pulses parallels that of the moving wave packet and, consequently, can be used to clock its field-free evolution. The performance of this method is illustrated for the H2 molecule. [ABSTRACT FROM AUTHOR]

High-level single-reference CCSD(T) and multireference MS-CASPT2/CASSCF ab initiocalculations have been carried out to determine the electronic structure and the lifetimes of GaX2+(X = N, F) doubly charged diatomic systems. Lifetimes were evaluated using the Exterior Complex Scaling (ECS) method implemented with basis sets of B-spline functions. The results obtained led to the conclusion that both species GaN2+and GaF2+can be considered as bound systems in the gas phase. GaN2+is a kinetically stable dication, because although it is thermodynamically unstable with respect to its dissociation into Ga+(1S) + N+(3P) the barrier to be surmounted is rather high and wide, so that the lowest 14 vibrational states of this system are bound. GaF2+is found to be a thermodynamically stable species with respect to its dissociation into Ga+(1S) + F+(1D). With respect to its dissociation into Ga+(1S) + F+(3P), strictly speaking, it is metastable. However, the crossing between the attractive PEC and the repulsive one occurs at rather large internuclear distances, and therefore it can be only explored by highly vibrationally excited molecules. Thus, in practical terms GaF2+can be considered as a bound species. The behavior of GaN2+and GaF2+is in clear contrast with that predicted for GaO2+, which was found to be metastable with respect to its dissociation into Ga+(1S) + O+(4S), with lifetimes in the range of ns to seconds. This seems to indicate that the primary factor governing the stability and lifetimes of these doubly charged diatomic species is the ionization energy of the atom X bound to Ga. [ABSTRACT FROM AUTHOR]

The electronic structure, stability, and lifetime of GaO have been investigated using high-level ab initio calculations. The potential energy curves have been calculated at the CCSD(T)/aug-cc-pV5Z and at the MS-CASPT2/ANO-RCC levels of theory. Lifetimes were evaluated using the Exterior Complex Scaling (ECS) method and B-spline basis functions. Our calculations show that GaO is a metastable species in the gas phase, since the diatomic dication, in its ground state, lies 97.1 kcal/mol above the Ga (S) + O (S) dissociation limit. However, the energy barrier that has to be overcome to reach this limit is 3 kcal/mol high so that five vibrational resonances can be accommodated between the bottom of the well and the top of the barrier. The evaluated lifetimes vary from hundreds of femtoseconds to approximately 1 s, so at least two of them have long enough lifetimes (1 s and 91 μs) to be detected using mass spectrometry techniques, in agreement with the experimental evidence. In the experiment (Fiser et al. in Eur J Mass Spectrom 15:315-324, 2009), GaO was observed for an ion flight time of about ~12 μs through a magnetic-sector mass spectrometer and unambiguously identified by its isotopic abundance. Our results also show that isotopic effects on the resonances' energies and on their lifetimes, when Ga is replaced by Ga or Ga, are very small (~0.1 and ~1%, respectively), reflecting the large mass of the system. [ABSTRACT FROM AUTHOR]

Inhibitor of growth protein 4 (ING4) belongs to the ING family of tumour suppressors and is involved in chromatin remodelling, in growth arrest and, in cooperation with p53, in senescence and apoptosis. Whereas the structure and histone H3-binding properties of the C-terminal PHD domains of the ING proteins are known, no structural information is available for the N-terminal domains. This domain contains a putative oligomerization site rich in helical structure in the ING2-5 members of the family. The N-terminal domain of ING4 was overexpressed in Escherichia coli and purified to homogeneity. Crystallization experiments yielded crystals that were suitable for high-resolution X-ray diffraction analysis. The crystals belonged to the orthorhombic space group C222, with unit-cell parameters a = 129.7, b = 188.3, c = 62.7 Å. The self-rotation function and the Matthews coefficient suggested the presence of three protein dimers per asymmetric unit. The crystals diffracted to a resolution of 2.3 Å using synchrotron radiation at the Swiss Light Source (SLS) and the European Synchrotron Radiation Facility (ESRF). [ABSTRACT FROM AUTHOR]

Abstract: The INhibitor of Growth (ING) family of tumor suppressors regulates the transcriptional state of chromatin by recruiting remodeling complexes to sites with histone H3 trimethylated at position K4 (H3K4me3). This modification is recognized by the plant homeodomain (PHD) present at the C-terminus in the five members of the ING family. ING4 facilitates histone H3 acetylation by the HBO1 complex. Here, we show that ING4 forms homodimers through its N-terminal domain, which folds independently into an elongated coiled-coil structure. The central region of ING4, which contains the nuclear localization sequence, is disordered and flexible and does not directly interact with p53, or does it with very low affinity, in contrast to previous findings. The NMR analysis of the full-length protein reveals that the two PHD fingers of the dimer are chemically equivalent and independent of the rest of the molecule. The detailed NMR analysis of the full-length dimeric protein binding to histone H3K4me3 shows essentially the same binding site and affinity as the isolated PHD finger. Therefore, the ING4 dimer has two identical and independent binding sites for H3K4me3 tails, which, in the context of the chromatin, could belong to the same or to different nucleosomes. These results show that ING4 is a bivalent reader of the chromatin H3K4me3 modification and suggest a mechanism for enhanced targeting of the HBO1 complex to specific chromatin sites. This mechanism could be common to other ING-containing remodeling complexes. [Copyright &y& Elsevier]

The inhibitors of growth (ING) family of tumor suppressors consists of five homologous proteins involved in chromatin remodeling. They form part of different acetylation and deacetylation complexes and are thought to direct them to specific regions of the chromatin, through the recognition of H3K4me3 (trimethylated 1(4 in the histone 3 tail) by their conserved plant homeodomain (PHD). We have determined the crystal structure of ING4-PHD bound to H3K4me3, which reveals a tight complex stabilized by numerous interactions. NMR shows that there is a reduction in the backbone mobility on the regions of the PHD that participate in the peptide binding, and binding affinities differ depending on histone tail lengths Thermodynamic analysis reveals that the discrimination in favor of methylated lysine is entropy-driven, contrary to what has been described for chromodomains. The molecular basis of H3K4me3 recognition by ING4 differs from that of ING2, which is consistent with their different affinities for methylated histone tails. These differences suggest a distinct role in transcriptional regulation for these two ING family members because of the antagonistic effect of the complexes that they recruit onto chromatin. Our results illustrate the versatility of PHD fingers as readers of the histone code. [ABSTRACT FROM AUTHOR]

The five members of the family of tumor suppressors ING contain a Plant Homeodomain (PHD) that specifically recognizes histone H3 trimethylated at lysine 4 (H3K4me3) with an affinity in the low micromolar range. Here, we use NMR to show that in the presence of 15% Ficoll 70, an inert macromolecular crowding agent, the mode of binding does not change but the affinity increases by one order of magnitude. The affinity increases also for unmethylated histone H3 tail, but the difference with H3K4me3 is larger in the presence of Ficoll. These results indicate that in the cellular milieu, the affinity of the ING proteins for their chromatin target is larger than previously thought. [ABSTRACT FROM AUTHOR]

The aim of this research is to determine the impact of perceived Teachers' Digital Competence (TDC) on how well math teachers prepare the educational videos needed to put the flipped classroom model into practice. In preparing the videos, the teachers had to select pre-existing audiovisual material and then edit the content to adapt it to the flipped classroom. Described here is a non-experimental study of a sample of 50 teachers pursuing a Master's degree in Secondary School Math Education in Spain. This is a preliminary univariate descriptive study of the relationship between TDC and the quality of videos prepared. Possible correlations between these two variables and between the characteristics of the sample are also explored. In general, the teachers had an intermediate level of TDC and prepared satisfactory videos. Nevertheless, the videos were deficient in the sections related to their pedagogical and math instructional components. No correlation was observed between TDC and the quality of the videos prepared. These results indicate that the integration of technological, pedagogical, and math instructional components is more important for developing quality instructional videos than the technological component alone. Teacher training should incorporate elements which emphasize the application of technology to the pedagogical process of math instruction. [ABSTRACT FROM AUTHOR]

With the advent of attosecond light pulses at the beginning of this century, the possibility to perform real‐time observations of electron motion in molecules has spurred impressive theoretical developments aimed at providing support and guidance to numerous, but still incipient, experimental efforts devoted to understand chemistry at its ultimate temporal frontier: the attosecond. The first real‐time observation of electron dynamics in a relatively large molecule, phenylalanine, was reported in 2014. This would have been difficult without the help of theory, since observations in this emerging field, recently coined attochemistry, are still indirect. While standard Quantum Chemistry methods can describe excited bound‐state dynamics, new approaches incorporating scattering theory formalisms are needed to understand the interaction with attosecond pulses. Indeed, due to their short wavelengths, lying in the XUV and X‐ray spectral regions, the interaction of such pulses with any molecule inevitably leads to ionization, which requires describing the molecular ionization continuum. Also, because of their short duration (i.e., large bandwidth), ionization is accompanied by the formation of a molecular electronic wave packet (i.e., a coherent superposition of electronic states), which evolves in time and dictates the fate of the molecule at the longer time scales where chemistry shows up. Although much has already been done up to date, current bottlenecks in the field are to account for electron correlations during the ionization process and for the coupled electron and nuclear dynamics that follows. Past and ongoing theoretical efforts are described here along with experimental work towards the solid establishment of attochemistry. This article is categorized under: Electronic Structure Theory > Ab Initio Electronic Structure MethodsSoftware > Quantum ChemistryTheoretical and Physical Chemistry > Spectroscopy [ABSTRACT FROM AUTHOR]