Clustering Methods for Vibro-Acoustic Sensing Features as a Potential Approach to Tissue Characterisation in Robot-Assisted Interventions.

This article provides a comprehensive analysis of the feature extraction methods applied to vibro-acoustic signals (VA signals) in the context of robot-assisted interventions. The primary objective is to extract valuable information from these signals to understand tissue behaviour better and build upon prior research. This study is divided into three key stages: feature extraction using the Cepstrum Transform (CT), Mel-Frequency Cepstral Coefficients (MFCCs), and Fast Chirplet Transform (FCT); dimensionality reduction employing techniques such as Principal Component Analysis (PCA), t-Distributed Stochastic Neighbour Embedding (t-SNE), and Uniform Manifold Approximation and Projection (UMAP); and, finally, classification using a nearest neighbours classifier. The results demonstrate that using feature extraction techniques, especially the combination of CT and MFCC with dimensionality reduction algorithms, yields highly efficient outcomes. The classification metrics (Accuracy, Recall, and F1-score) approach 99%, and the clustering metric is 0.61. The performance of the CT-UMAP combination stands out in the evaluation metrics.

DFT exchange: sharing perspectives on the workhorse of quantum chemistry and materials science.

In this paper, the history, present status, and future of density-functional theory (DFT) is informally reviewed and discussed by 70 workers in the field, including molecular scientists, materials scientists, method developers and practitioners. The format of the paper is that of a roundtable discussion, in which the participants express and exchange views on DFT in the form of 302 individual contributions, formulated as responses to a preset list of 26 questions. Supported by a bibliography of 777 entries, the paper represents a broad snapshot of DFT, anno 2022.

Electronegativity under Confinement.

The electronegativity concept was first formulated by Pauling in the first half of the 20th century to explain quantitatively the properties of chemical bonds between different types of atoms. Today, it is widely known that, in high-pressure regimes, the reactivity properties of atoms can change, and, thus, the bond patterns in molecules and solids are affected. In this work, we studied the effects of high pressure modeled by a confining potential on different definitions of electronegativity and, additionally, tested the accuracy of first-order perturbation theory in the context of density functional theory for confined atoms of the second row at the Hartree-Fock level. As expected, the electronegativity of atoms at high confinement is very different than that of their free counterparts since it depends on the electronic configuration of the atom, and, thus, its periodicity is modified at higher pressures.

Vascular Auscultation of Carotid Artery: Towards Biometric Identification and Verification of Individuals.

BACKGROUND: Biometric sensing is a security method for protecting information and property. State-of-the-art biometric traits are behavioral and physiological in nature. However, they are vulnerable to tampering and forgery. METHODS: The proposed approach uses blood flow sounds in the carotid artery as a source of biometric information. A handheld sensing device and an associated desktop application were built. Between 80 and 160 carotid recordings of 11 s in length were acquired from seven individuals each. Wavelet-based signal analysis was performed to assess the potential for biometric applications. RESULTS: The acquired signals per individual proved to be consistent within one carotid sound recording and between multiple recordings spaced by several weeks. The averaged continuous wavelet transform spectra for all cardiac cycles of one recording showed specific spectral characteristics in the time-frequency domain, allowing for the discrimination of individuals, which could potentially serve as an individual fingerprint of the carotid sound. This is also supported by the quantitative analysis consisting of a small convolutional neural network, which was able to differentiate between different users with over 95% accuracy. CONCLUSION: The proposed approach and processing pipeline appeared promising for the discrimination of individuals. The biometrical recognition could clinically be used to obtain and highlight differences from a previously established personalized audio profile and subsequently could provide information on the source of the deviation as well as on its effects on the individual's health. The limited number of individuals and recordings require a study in a larger population along with an investigation of the long-term spectral stability of carotid sounds to assess its potential as a biometric marker. Nevertheless, the approach opens the perspective for automatic feature extraction and classification.

Links among the Fukui potential, the alchemical hardness and the local hardness of an atom in a molecule.

This paper presents a brief summary of the difficulty that resides in the definition of the elusive concept of local chemical hardness. We argue that a definition of local hardness should be useful to a reactivity principle and not just as a mere definition. We then continue with a formal discussion about the benefits and difficulties of using the Fukui potential, which is interpreted as an alchemical derivative (alchemical hardness), as descriptor of local hardness of molecules. Computational evidence shows that the alchemical hardness is at least as good a descriptor as the combination of other two well-stabilized descriptors of local hardness, such as the Fukui function and grand canonical local hardness. Although our results are auspicious for the alchemical hardness as descriptor of local hardness, we finish by calling the attention of the community on the importance of discussing the raison d'être of a local hardness function and its main characteristics. We suggest that an axiomatic construction of local hardness could be they way of constructing a local hardness which is both useful and free of arbitrariness.

Coulomb Explosion of Multi-charged Atomic Alkaline Metal Clusters.

In the present work, a computational study of the Coulomb explosions of atomic metal clusters of the type X82+ was carried out, X = (Li-Cs). The work was done within the Kohn-Sham methodology using the Born-Oppenheimer molecular dynamics approximation. The dominant fission channels were established and the electron bonding patterns were analyzed with the help of the Electron Localization Function (ELF). A simple theoretical model was developed to understand and describe, in a qualitatively way, the main physical mechanism involved in the fission of these multicharged clusters. It has been found that the most possible fragments after explosion are the same considering the dynamics or the thermodynamics results. The bonds breaking and formation are well depicted by the ELF, and the main physical effects are well described by the developed model.

Predicting Deprotonation Sites Using Alchemical Derivatives.

An alchemical transformation is any process, physical or fictitious, that connects two points in the chemical space. A particularly important transformation is the vanishing of a proton, whose energy can be linked to the proton dissociation enthalpy of acids. In this work we assess the reliability of alchemical derivatives in predicting the proton dissociation enthalpy of a diverse series of mono- and polyprotic molecules. Alchemical derivatives perform remarkably well in ranking the proton affinity of all molecules. Additionally, alchemical derivatives could be use also as a predictive tool because their predictions correlate quite well with calculations based on energy differences and experimental values. Although second-order alchemical derivatives underestimate the dissociation enthalpy, the deviation seems to be almost constant. This makes alchemical derivatives extremely accurate to evaluate the difference in proton affinity between two acid sites of polyprotic molecule. Finally, we show that the reason for the underestimation of the dissociation enthalpy is most likely the contribution of higher-order derivatives.

Electron Localization Function in Excited States: The Case of the Ultrafast Proton Transfer of the Salicylidene Methylamine.

The physical characterization of the chemical bond in the ground state has been a central theme to theoretical chemistry. Among many techniques, quantum chemical topology (QCT) has emerged as a robust technique to understand the features of the chemical bond and electron organization within molecules. One consolidate tool within QCT is the topological analysis of the electron localization function (ELF). Most research on ELF and chemical bond has focused either on singlet ground states or the first excited triplet. However, most photochemical reactions and photophysical processes occur in excited states with the same spin-symmetry as the ground state. In this work, we develop a proposal on how to compute the ELF in excited states of any symmetry within linear-response time-dependent density functional theory. Then, we study the evolution of the chemical bonds in the ground- and excited-state intramolecular proton transfer (ESIPT) of a prototypal Schiff base (the salicylidene methylamine). We found that the topological analysis of the ELF along reaction paths explains the presence of a barrier for the proton transfer in the ground state and the absence of it in the excited state. Briefly, in the ground state, the cleavage of the O-H bond results in a structure with high electrostatic potential energy due to an excess of electron lone-pairs (3) in the oxygen atom, which explains the barrier. In the excited state, the electronic transition promotes an enhancement of the basicity of nitrogen by allocating three nonbonding electrons in the basin of its lone-pair. This excess of electrons in the N exerts an electrostatic attraction of the proton, which we suggest as the primary driven-force of the barrierless reaction. Because in excited states the molecule can develop more vibrational kinetic energy than in the ground state, we performed an ab initio molecular dynamics of the proton transfer in the excited state and corroborate that our conclusions on the topology of the ELF do not change due to dynamic effects.

The Pauli principle and the confinement of electron pairs in a double well: Aspects of electronic bonding under pressure.

It has become recently clear that chemical bonding under pressure is still lacking guiding principles for understanding the way electrons reorganize when their volume is constrained. As an example, it has recently been shown that simple metals can become insulators (aka electrides) when submitted to high enough pressures. This has lead to the general believe that "a fundamental yet empirically useful understanding of how pressure alters the chemistry of the elements is lacking" [R. J. Hemley, High Pressure Res. 30, 581 (2010)]. In this paper, we are interested in studying the role that the Pauli principle plays on the localization/delocalization of confined noninteracting electrons. To this end, we have considered the simple case of a 1-dimensional (1-D) double well as a confining potential, and the Electron Localization Function (ELF) has been used to characterize the degree localization/delocalization of the systems of noninteracting electrons. Then, we have systematically studied the topology of the ELF as a function of the double well parameters (barrier eight and wells distance) and of the number of electrons. We have found that the evolution of the ELF distributions has a good correspondence with the evolution of chemical bonding of atomic solids under pressure.

Cardiotocograph Data Classification Improvement by Using Empirical Mode Decomposition.

This work proposes to study the fetal heart rate (FHR) signal based on information about its dynamics as a signal resulting from the modulation by the autonomic nervous system. The analysis is performed using the complete ensemble empirical mode decomposition with adaptive noise (CEEMDAN) technique. The main idea is to extract a set of signal features based on that technique and also conventional time-domain features proposed in the literature in order to study their performance by using a support vector machine (SVM) as a classifier. As a hypothesis, we postulate that by including CEEMDAN based features, the classification performance should improve compared with the performance achieved by conventional features. The proposed method has been evaluated using real FHR data extracted from the open access CTU-UHB database. Results show that the classification performance improved from 67, 6% using only conventional features, to 71, 7% by incorporating CEEMDAN based features.

Local electrophilicity.

In this work some possibilities for deriving a local electrophilicity are studied. First, we consider the original definition proposed by Chattaraj, Maiti, and Sarkar (J Phys Chem A 107:4973, 2003), in which the local electrophilicity is given by the product of the global electrophilicity, and the Fukui function for charge acceptance is derived by two different approaches, making use of the chain rule for functional derivatives. We also modify the proposals based on the electron density so as to have a definition with the same units of the original definition, which also introduces a dependence in the Fukui function for charge donation. Additionally, we also explore other possibilities using the tools of information theory and the temperature dependent reactivity indices of the density functional theory of chemical reactivity. The poor results obtained from the last two approaches lead us to conjecture that this is due to the fact that the global electrophilicity is not a derivative, like most of the other reactivity indices. The conclusion is that Chattaraj's suggestion seems to be the simplest, but at the same time a very reliable approach to this important property.

Proposal of a simple and effective local reactivity descriptor through a topological analysis of an orbital-weighted fukui function.

The prediction of reactivity is one of the long-standing objectives of chemistry, contributing to enforce the link between theory and experiment. In particular, the regioselectivity of aromatic molecules has motivated the proposal of different reactivity descriptors based on foundational theories, like Frontier Molecular Orbital (FMO) theory and density functional theory, to predict and rationalize such regioselectivity. This article examines cases where reactivity descriptors, based on FMO theories, are known to have failed, specifically on electrophilic aromatic substitution reactions, through a simple but effective new reactivity model: the Orbital-weighted Fukui function ( fw-(r)) and its topological analysis. Interestingly, this descriptor proves to be effective in adequately predicting regioselectivities where other approximations failed. © 2017 Wiley Periodicals, Inc.

Ferromagnetic bond of Li10 cluster: An alternative approach in terms of effective ferromagnetic sites.

In this work, a model to explain the unusual stability of atomic lithium clusters in their highest spin multiplicity is presented and used to describe the ferromagnetic bonding of high-spin Li10 and Li8 clusters. The model associates the (lack of-)fitness of Heisenberg Hamiltonian with the degree of (de-)localization of the valence electrons in the cluster. It is shown that a regular Heisenberg Hamiltonian with four coupling constants cannot fully explain the energy of the different spin states. However, a more simple model in which electrons are located not at the position of the nuclei but at the position of the attractors of the electron localization function succeeds in explaining the energy spectrum and, at the same time, explains the ferromagnetic bond found by Shaik using arguments of valence bond theory. In this way, two different points of view, one more often used in physics, the Heisenberg model, and the other in chemistry, valence bond, come to the same answer to explain those atypical bonds.

Lewis Acidity/Basicity Changes in Imidazolium Based Ionic Liquids Brought About by Impurities.

We herein report on the effect that water molecules, present as impurities, in the vicinity of an ionic liquid model structure, may induce on the Lewis acidity/basicity patterns normally observed in these materials. Depending on the position and orientation of water, the Lewis acidity/basicity pattern changes from "normal distribution" (i.e., the basicity located at the anion moiety and the acidity located at the cation fragment) to "bifunctional distribution" (i.e., the acidity and basicity located at the cation moiety). In some specific cases, there appears a third Lewis acidity/basicity distribution, where water may bind both the cation and the anion of the ion pair; a response we tentatively call "amphoteric". These effects are clearly traced to the hydrogen bond formation ability of water to coordinate different regions of pure ionic liquids taken as references.

Regional electrophilic and nucleophilic Fukui functions efficiently highlight the Lewis acidic/basic regions in ionic liquids.

The origin of catalysis and selectivity induced by room temperature ionic liquids in several organic reactions has putatively been associated with the concept of cation effect (hydrogen bond donor ability of the ionic liquids) or anion effect (hydrogen bond accepting ability of the ionic liquids). We show that there may be cases where this a priori classification may not be correctly assigned. Cations may concentrate both Lewis acidity and basicity functions in one fragment of the ionic liquid: an effect we tentatively call bifunctional distribution of the molecular Lewis acidity/basicity. Bifunctionality on the cation is however anion dependent through electronic polarization effects. The molecular distribution of the Lewis acidity/basicity may simply be assessed by evaluating the regional Fukui function within a reference ion pair structure. The model is tested for a set of nine ionic liquids based on the 1-butyl-3-methylimidazolium cation commonly used as solvent to run organic reactions.

An information-theoretic resolution of the ambiguity in the local hardness.

The ambiguity of the local hardness is resolved by using information theory to select definitions of the local hardness that are as close as possible to a well-defined approximate formula for the local hardness. A condensed local hardness is derived by using the atomic hardnesses as a reference distribution; a pointwise local hardness is derived by using the uniform electron gas as a reference distribution. This information-theoretic condensed local hardness is tested by examining electrophilic attack on some substituted pyridines.

How to Compute the Fukui Matrix and Function for Systems with (Quasi-)Degenerate States.

A system in a spatially (quasi-)degenerate ground state responds in a qualitatively different way to a change in the external potential. Consequently, the usual method for computing the Fukui function, namely, taking the difference between the electron densities of the N- and N ± 1 electron systems, cannot be applied directly. It is shown how the Fukui matrix, and thus also the Fukui function, depends on the nature of the perturbation. One thus needs to use degenerate perturbation theory for the given perturbing potential to generate the density matrix whose change with respect to a change in the number of electrons equals the Fukui matrix. Accounting for the degeneracy in the case of nitrous oxide reveals that an average over the degenerate states differs significantly from using the proper density matrix. We further show the differences in Fukui functions depending on whether a Dirac delta perturbation is used or an interaction with a true point charge (leading to the Fukui potential).

Comment on "Going beyond the frozen core approximation: development of coordinate-dependent pseudopotentials and application to Na2(+)" [J. Chem. Phys. 138, 054110 (2013)].

The new coordinate-dependent pseudopotential for Na2(+) by Kahros and Schwartz [J. Chem. Phys. 138, 054110 (2013)] is assessed and compared to the pseudopotential approach by Fuentealba et al. [Chem. Phys. Lett. 89, 418 (1982)] which incorporates the coordinate-dependent core-polarization potential by Müller and Meyer [J. Chem. Phys. 80, 3311 (1984)]. In contrast to the latter approach, the one by Kahros and Schwartz does not reproduce the accurately known experimental data and∕or high level theoretical results for Na2(+). The treatment of core polarization by Kahros and Schwartz neglects the dynamic polarization of atomic cores which is much more important for Na2(+) than the static one. On the other hand, the Kahros and Schwartz method heavily overestimates frozen-core corrections at the Hartree-Fock level by compounding them with artifacts of a superposition of non-norm-conserving pseudopotentials.

Effect of unsaturation on the absorption of ethane and ethylene in imidazolium-based ionic liquids.

The influence of the presence of imidazolium side chain unsaturation on the solubility of ethane and ethylene was studied in three ionic liquids: 1-butyl-3-methylimidazolium bis(trifluoromethanesulfonyl)amide-saturated alkyl side-chain in the cation; 1-methyl-3-(buten-3-yl)imidazolium bis(trifluorosulfonyl)imide-double bond in the side-chain of the cation; and 1-methyl-3-benzylimidazolium bis(trifluorosulfonyl)imide-benzyl group in the side-chain of the cation. The solubility of both gases decreases when the side-chain of the cations is functionalized with an unsaturated group. This can be explained by a less favorable enthalpy of solvation. The difference of solubility between ethane and ethylene can be explained from a balance of enthalpic and entropic factors: for the ionic liquid with the saturated alkyl side-chain and the benzyl-substituted side-chain, it is the favorable entropy of solvation that explains the larger ethylene solubility, whereas in the case of the saturated side-chain, it is the more favorable enthalpy of solvation. Molecular simulation allowed the identification of the mechanisms of solvation and the preferential solvation sites for each gas in the different ionic liquids. Simulations have shown that the entropy of solvation is more favorable when the presence of the gas weakens the cation-anion interactions or when the gas can be solvated near different sites of the ionic liquid.

Atomic Charges and the Electrostatic Potential Are Ill-Defined in Degenerate Ground States.

A system in a spatially degenerate ground state responds in a qualitatively different way to positive and negative point charges. This means that the molecular electrostatic potential is ill-defined for degenerate ground states due to the ill-defined nature of the electron density. It also means that it is impossible, in practice, to define fixed atomic charges for molecular mechanics simulations of molecules with (quasi-)degenerate ground states. Atomic-polarizability-based models and electronegativity-equalization-type models for molecular polarization also fail to capture this effect. We demonstrate the ambiguity in the electrostatic potential using several molecules of different degree of degeneracy, quasi-degeneracy, and symmetry.