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.

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.

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.

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.

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.

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.

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.

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.

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.

A new isomer of C20 and a way to a new C240.

Here we show that the dynamic simulation of a molecular collision can give insight into new molecular species. In this way, a new stable isomer of C(20) (IV) has been found. It is planar with pentagonal form. This isomer is high in energy compared to the three most stable previously known isomers of C(20): cage (I), bowl (II) and ring (III). Most interestingly, we show that using this new isomer it is possible to construct a macrobucky C(240) (V) that is also stable. The electronic structure of this new isomer of C(240) is very different from properties of the C(240) fullerene. Contrary to the C(240) fullerene, in the new isomer the π electrons are localized.

The Fukui potential and the capacity of charge and the global hardness of atoms.

In the course of a reaction it is the shape of the Fukui potential that guides a distant reagent toward the site where an electrophile/nucleophile is willing to accept/donate charge. In this paper we explore the mathematical characteristics of the Fukui potential and demonstrate its relationship to the hardness and the ability of an atom in a molecule to change its charge. The Fukui potential not only determines the active site for electron transfer, but it also approximates the distribution of hardness of a molecule: it is the Coulomb contribution to the frontier local hardness. The Fukui potential at the position of the nuclei is equal to the variation of the chemical potential with the nuclear charge and therefore measures the sensitivity of the system to changes in atom type. In the specific case of atoms and slightly charged ions, the Fukui potential at the nucleus measures the hardness. The strong correlation between the hardness and the Fukui potential at the nucleus suggests that the Fukui potential at the nucleus is an alternative definition for the chemical hardness.

A computationally efficient and reliable bond order measure.

Bond order indexes are useful measures that connect quantum mechanical results with chemical understanding. One of these measures, the natural bond order index, based on the natural resonance theory procedure and part of the natural bond orbital analysis tools, has been proved to yield reliable results for many systems. The procedure's computational requirements, nevertheless, scales so highly with the number of functions in the basis set and the delocalization of the system, that the calculation of this bond order is limited to small or medium size molecules. We present in this work a bond order index, the first order perturbation theory bond order (fopBO), which is based on and strongly connected to the natural bond orbital analysis tools. We present the methodology for the calculation of the fopBO index and a number of test calculations that shows that it is as reliable as the natural bond orbital index, with the same weak sensitivity to variations among commonly used basis sets and, as opposed to the natural bond order index, suitable for the study of large systems, such as most of those of biological interest.

Solvent effects on global reactivity properties for neutral and charged systems using the sequential Monte Carlo quantum mechanics model.

The energy of the frontier molecular orbitals and reactivity indices such as chemical potential, hardness, and electrophilicity of neutral and charged molecules have been investigated in aqueous solution using explicit model for the solvent with the sequential Monte Carlo/quantum mechanics methodology. The supermolecular structures of the solute-solvent system were generated by Monte Carlo simulation. Statistically uncorrelated structures have been extracted for quantum mechanical calculations of the solute surrounded by the first solvation shell, using explicit water molecules, and the second and third shells as atomic point charges. The supermolecular calculations treating both the solute and the solvent explicitly were performed within density functional theory. The solvent dependence of the frontier molecular orbital energies was analyzed and used to calculate the reactivity indices in solution. The dependence of the results with respect to the number of explicit solvent molecules is also analyzed. It is seen that for the systems considered here, the energies of the highest occupied molecular orbital and the lowest unoccupied molecular orbital show a strong dependence with the number of solvent molecules. However, the properties derived from these are relatively stable. In particular, the results reported here for the reactivity indices obtained using the first solvation shell are similar to those obtained for the limit bulk value. For comparison, the reactivity indices were also calculated in the gas phase and using the polarizable continuum model (PCM). As frequently reported in the literature, neutral molecules do not show significant changes in the reactivity indices between gas phase and the PCM model. However, with the explicit solvent model some important changes were observed: a larger negative chemical potential, a smaller hardness, and a larger electrophilicity. The stabilization of an anion corresponding to a negative chemical potential is obtained only by using explicit solvent molecules. In general, the solvent effect was well treated by using the first solvation shell, and the calculated results are in agreement with the experimental trends. The delocalization of the solute orbitals over the solvent region is analyzed, and its consequence to the reactivity indices are discussed. The importance of including explicit solvent molecules and adopting a statistical approach for the liquid is emphasized.

On the nucleophilicity of boryllithium compounds. A theoretical study.

Boron compounds are widely used in synthetic chemistry. The synthesis of the compounds is relatively easy, presenting thermodynamic stability and synthetic versatility. Almost all of them show electrophilic reactivity. Recently, some boryllithium species have been reported as a base or a nucleophile in reaction with organic electrophiles in S(N)2 reactions. In the present work, the proton affinity (PA) of boryllithium compounds was calculated. These values can be useful as theoretical reference values and to provide valuable complementary information for the interpretation and discussion of the basicity of these compounds. The proton affinity was calculated using a theoretical method based on density functional theory and high-level theoretical methods through MP2 and G2MP2 levels of theory. In addition, some global and local reactivity indexes based on density functional theory (DFT) on boryllithium compounds were studied. In order to compare and discuss the chemical reactivity of these compounds, some analogues and electrophilic boron compounds were also studied. Our results showed a local and global nucleophilic reactivity of the boryllithium molecules in agreement with the experimental reactivity. The boryllithium compounds revealed to be strong bases in comparison to other analogue compounds studied in this work.

Endohedral cluster of Li(10)O with T(d) symmetry.

A detailed numerical study of several isomers of the Li(10) cluster has been done. The analysis of the electronic localization function and the analysis of energy diagrams revealed the existence of one cluster with an inner space capable to suit a heteroatom. The perfect candidate is the Li(10)O cluster due to the experimental evidence of the [Li(6)O](4+) core, the same core present in Li(10)O. In order to check the thermodynamic stability of this cluster, an analysis of its dissociation channels has been done. The IR and UV-vis spectra have been calculated to help in the further identification of this new cluster.

Chemical reactivity descriptors for ambiphilic reagents: dual descriptor, local hypersoftness, and electrostatic potential.

The second-order response of the electron density with respect to changes in electron number, known as the dual descriptor, has been established as a key reactivity indicator for reactions like pericyclic reactions, where reagents accept and donate electrons concurrently. Here we establish that the dual descriptor is also the key reactivity indicator for ambiphilic reagents: reagents that can act either as electrophiles or as nucleophiles, depending on the reaction partner. Specifically, we study dual atoms (which are proposed to act, simultaneously, as an electron acceptor and an electron donor), dual molecules (which react with both electrophiles and nucleophiles, generally at different sites), and dual ion-molecule complexes (which react with both cations and anions). On the basis of our analysis, the dual atom (an Al(I) that has been purported to be dual in the literature) is actually pseudodual in the sense that it does not truly accept electrons from a nucleophiles; rather, it serves as a conduit through which an electrophile can donate electrons to the attached aromatic ring. For understanding dual ion-molecule complexes, it helps to understand that the dual descriptor makes a key contribution to the long-range portion of the quadratic hyperpolarization. In all cases, a complete description of the reactivity of the ambiphilic reagent requires considering both an orbital-based descriptor of electron transfer (the dual descriptor or the local hypersoftness) and the electrostatic potential. The local hypersoftness strongly resembles the dual descriptor.

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.