Reaction mechanism - explored with the unified reaction valley approach.

One of the ultimate goals of chemistry is to understand and manipulate chemical reactions, which implies the ability to monitor the reaction and its underlying mechanism at an atomic scale. In this article, we introduce the Unified Reaction Valley Approach (URVA) as a tool for elucidating reaction mechanisms, complementing existing computational procedures. URVA combines the concept of the potential energy surface with vibrational spectroscopy and describes a chemical reaction via the reaction path and the surrounding reaction valley traced out by the reacting species on the potential energy surface on their way from the entrance to the exit channel, where the products are located. The key feature of URVA is the focus on the curving of the reaction path. Moving along the reaction path, any electronic structure change of the reacting species is registered by a change in the normal vibrational modes spanning the reaction valley and their coupling with the path, which recovers the curvature of the reaction path. This leads to a unique curvature profile for each chemical reaction, with curvature minima reflecting minimal change and curvature maxima indicating the location of important chemical events such as bond breaking/formation, charge polarization and transfer, rehybridization, etc. A decomposition of the path curvature into internal coordinate components or other coordinates of relevance for the reaction under consideration, provides comprehensive insight into the origin of the chemical changes taking place. After giving an overview of current experimental and computational efforts to gain insight into the mechanism of a chemical reaction and presenting the theoretical background of URVA, we illustrate how URVA works for three diverse processes, (i) [1,3] hydrogen transfer reactions; (ii) α-keto-amino inhibitor for SARS-CoV-2 Mpro; (iii) Rh-catalyzed cyanation. We hope that this article will inspire our computational colleagues to add URVA to their repertoire and will serve as an incubator for new reaction mechanisms to be studied in collaboration with our experimental experts in the field.

A High-Sensitivity Gravimetric Biosensor Based on S1 Mode Lamb Wave Resonator.

The development of MEMS acoustic resonators meets the increasing demand for in situ detection with a higher performance and smaller size. In this paper, a lithium niobate film-based S1 mode Lamb wave resonator (HF-LWR) for high-sensitivity gravimetric biosensing is proposed. The fabricated resonators, based on a 400-nm X-cut lithium niobate film, showed a resonance frequency over 8 GHz. Moreover, a PMMA layer was used as the mass-sensing layer, to study the performance of the biosensors based on HF-LWRs. Through optimizing the thickness of the lithium niobate film and the electrode configuration, the mass sensitivity of the biosensor could reach up to 74,000 Hz/(ng/cm2), and the maximum value of figure of merit (FOM) was 5.52 × 107, which shows great potential for pushing the performance boundaries of gravimetric-sensitive acoustic biosensors.

Piezoelectric Energy Harvesting from Low-Frequency Vibrations Based on Magnetic Plucking and Indirect Impacts.

This work proposes a mono-axial piezoelectric energy harvester based on the innovative combination of magnetic plucking and indirect impacts, e.g., impacts happening on the package of the harvester. The harvester exploits a permanent magnet placed on a non-magnetic mass, free to move within a predefined bounded region located in front of a piezoelectric bimorph cantilever equipped with a magnet as the tip mass. When the harvester is subjected to a low-frequency external acceleration, the moving mass induces an abrupt deflection and release of the cantilever by means of magnetic coupling, followed by impacts of the same mass against the harvester package. The combined effect of magnetic plucking and indirect impacts induces a frequency up-conversion. A prototype has been designed, fabricated, fastened to the wrist of a person by means of a wristband, and experimentally tested for different motion levels. By setting the magnets in a repulsive configuration, after 50 s of consecutive impacts induced by shaking, an energy of 253.41 µJ has been stored: this value is seven times higher compared to the case of harvester subjected to indirect impacts only, i.e., without magnetic coupling. This confirms that the combination of magnetic plucking and indirect impacts triggers the effective scavenging of electrical energy even from low-frequency non-periodical mechanical movements, such as human motion, while preserving the reliability of piezoelectric components.

Trajectory Control for Vibrating Screen with Magnetorheological Dampers.

The article presents a method of vibrating screen trajectory control based on MR (magnetorheological) dampers applied in a screen suspension. A mathematical description of the dynamic screen model was derived, and parameters of this model were estimated based on experimental data from a semi-industrial vibrating screen. The investigated screen included a single mechanical exciter with unbalanced masses, generating a circular vibration trajectory and operating with over-resonant frequency close to 19 Hz. It was experimentally tested in several phases of operation: start-up, nominal operation at a target vibration frequency and shutdown. The implemented screen model was further extended and included several MR dampers oriented horizontally and vertically in the form of Bouc-Wen models. The Bouc-Wen model was identified based on experiments carried out for an MR damper subjected to harmonic excitations generated by the MTS (material testing system). Dominant frequencies of excitation varied by up to 20 Hz during experiments. The main novelty of the reported solution is that according to the proposed control algorithm, the desired forces generated by MR dampers emulate an additional virtual mechanical exciter of the vibrating screen. In turn, it interacts with the available exciter, resulting in conversion of the trajectory from circular to linear, which was validated in the presented study. For the purpose of simulation accuracy, the desired control force was additionally limited within the simulator by MR damper dissipative domain, which maps the constraints of a semi-active damper. The presented approach allows one to obtain a close to linear trajectory with only one exciter and with semi-active control of suspension stiffness. The results were successfully repeated with different configurations of desired trajectory, indicating that the effectiveness of the desired linear trajectory generation depends on its orientation. The reported findings may lead to the design of new vibrating screen constructions, taking advantage of the semi-active control of a suspension in the attenuation of disturbance resulting from varying processed material parameters.

Influence of 40 Hz and 100 Hz Vibration on SH-SY5Y Cells Growth and Differentiation-A Preliminary Study.

(1) Background: A novel bioreactor platform of neuronal cell cultures using low-magnitude, low-frequency (LMLF) vibrational stimulation was designed to discover vibration influence and mimic the dynamic environment of the in vivo state. To better understand the impact of 40 Hz and 100 Hz vibration on cell differentiation, we join biotechnology and advanced medical technology to design the nano-vibration system. The influence of vibration on the development of nervous tissue on the selected cell line SH-SY5Y (experimental research model in Alzheimer's and Parkinson's) was investigated. (2) Methods: The vibration stimulation of cell differentiation and elongation of their neuritis were monitored. We measured how vibrations affect the morphology and differentiation of nerve cells in vitro. (3) Results: The highest average length of neurites was observed in response to the 40 Hz vibration on the collagen surface in the differentiating medium, but cells response did not increase with vibration frequency. Also, vibrations at a frequency of 40 Hz or 100 Hz did not affect the average density of neurites. 100 Hz vibration increased the neurites density significantly with time for cultures on collagen and non-collagen surfaces. The exposure of neuronal cells to 40 Hz and 100 Hz vibration enhanced cell differentiation. The 40 Hz vibration has the best impact on neuronal-like cell growth and differentiation. (4) Conclusions: The data demonstrated that exposure to neuronal cells to 40 Hz and 100 Hz vibration enhanced cell differentiation and proliferation. This positive impact of vibration can be used in tissue engineering and regenerative medicine. It is planned to optimize the processes and study its molecular mechanisms concerning carrying out the research.

Modeling the influence of COVID-19 protective measures on the mechanics of phonation.

In an effort to mitigate the 2019 novel coronavirus disease pandemic, mask wearing and social distancing have become standard practices. While effective in fighting the spread of the virus, these protective measures have been shown to deteriorate speech perception and sound intensity, which necessitates speaking louder to compensate. The goal of this paper is to investigate via numerical simulations how compensating for mask wearing and social distancing affects measures associated with vocal health. A three-mass body-cover model of the vocal folds (VFs) coupled with the sub- and supraglottal acoustic tracts is modified to incorporate mask and distance dependent acoustic pressure models. The results indicate that sustaining target levels of intelligibility and/or sound intensity while using these protective measures may necessitate increased subglottal pressure, leading to higher VF collision and, thus, potentially inducing a state of vocal hyperfunction, a progenitor to voice pathologies.

Study of optical-based speech acquisition system using vibration signals from speakers' medical masks.

Medical masks have become necessary of late because of the COVID-19 outbreak; however, they tend to attenuate the energy of speech signals and affect speech quality. Therefore, this study proposes an optical-based microphone approach to obtain speech signals from speakers' medical masks. Experimental results showed that the optical-based microphone approach achieved better performance (85.61%) than the two baseline approaches, namely, omnidirectional (24.17%) and directional microphones (31.65%), in the case of long-distance speech and background noise. The results suggest that the optical-based microphone method is a promising approach for acquiring speech from a medical mask.

Invariant in variants.

The coronavirus Covid-19 mutates quickly in the pandemic, leaves people struggling to verify and improve the effectiveness of the vaccine based on biochemistry. Is there any physical invariant in the variants of such kind of pathogen that could be taken advantage to ease the tensions? To this point, extensive numerical experiments based on continuity mechanics have been accomplished to discover the consistent vibration modes and the range of natural frequency of coronavirus Covid-19. Such invariant could help us in developing some flexible technique to deactivate the coronavirus, like as resonantly breaking the viral spike by ultrasound wave. The fundamental mechanisms governing such process are demonstrated via solving the coupled acoustic wave and elastic dynamic equations, after which the practical strategies are proposed to efficiently realize the technique concept.

Characterization of Covid-19 infected pregnant women sera using laboratory indexes, vibrational spectroscopy, and machine learning classifications.

Herein, we show differences in blood serum of asymptomatic and symptomatic pregnant women infected with COVID-19 and correlate them with laboratory indexes, ATR FTIR and multivariate machine learning methods. We collected the sera of COVID-19 diagnosed pregnant women, in the second trimester (n = 12), third-trimester (n = 7), and second-trimester with severe symptoms (n = 7) compared to the healthy pregnant (n = 11) women, which makes a total of 37 participants. To assign the accuracy of FTIR spectra regions where peak shifts occurred, the Random Forest algorithm, traditional C5.0 single decision tree algorithm and deep neural network approach were used. We verified the correspondence between the FTIR results and the laboratory indexes such as: the count of peripheral blood cells, biochemical parameters, and coagulation indicators of pregnant women. CH2 scissoring, amide II, amide I vibrations could be used to differentiate the groups. The accuracy calculated by machine learning methods was higher than 90%. We also developed a method based on the dynamics of the absorbance spectra allowing to determine the differences between the spectra of healthy and COVID-19 patients. Laboratory indexes of biochemical parameters associated with COVID-19 validate changes in the total amount of proteins, albumin and lipase.

Tuning the Computational Evaluation of Spectroscopic, ELF, LOL, NCI analysis and Molecular Docking of Novel Anti COVID-19 Molecule 4-Dimethylamino Pyridinium 3, 5-Dichlorosalicylate.

In this work novel antiviral compound 4-(Dimethylamino) Pyridinium 3, 5-dichlorosalicylate was synthesized and characterized by UV-vis, FT-IR, FT-Raman, 1H NMR and 13C NMR spectra. Quantum chemical computations were carried out by Density functional theory methods at B3LYP level. Electronic stability of the compound arising from hyper conjugative interactions and charge delocalization is investigated using natural bond orbital analysis. Assignments of vibrational spectra have been carried out with the aid of Normal coordinate analysis following the SQMFF methodology. TD-DFT approach was applied to assign the electronic transition observed in UV visible spectrum measured experimentally. Frontier molecular orbital energy gap affirms the bioactivity of the molecule and NCI analysis gives information about inter and intra non covalent interactions. ESP recognises the nucleophilic and electrophilic regions of molecule and the chemical implication of molecule was explained using ELF, LOL. The reactive sites of the compound were studied from the Fukui function calculations and chemical descriptors define the reactivity of the molecule. Molecular docking done with SARS and MERS proteins endorses the bioactivity of molecule and drug likeness factors were calculated to comprehend the biological assets of DADS.

Molecular structure, NBO analysis of the hydrogen-bonded interactions, spectroscopic (FT-IR, FT-Raman), drug likeness and molecular docking of the novel anti COVID-2 molecule (2E)-N-methyl-2-[(4-oxo-4H-chromen-3-yl)methylidene]-hydrazinecarbothioamide (Dimer) - quantum chemical approach.

Prospective antiviral molecule (2E)-N-methyl-2-[(4-oxo-4H-chromen-3-yl)methylidene]-hydrazinecarbothioamide has been probed using Fourier transform infrared (FTIR), FT-Raman and quantum chemical computations. The geometry equilibrium and natural bond orbital analysis have been carried out with density functional theory employing Becke, 3-parameter, Lee-Yang-Parr method with the 6-311G++(d,p) basis set. The vibrational assignments pertaining to different modes of vibrations have been augmented by normal coordinate analysis, force constant and potential energy distributions. Drug likeness and oral activity have been carried out based on Lipinski's rule of five. The inhibiting potency of 2(2E)-methyl-2-[(4-oxo-4H-chromen-3-yl)methylidene]-hydrazinecarbothioamide has been investigated by docking simulation against SARS-CoV-2 protein. The optimized geometry shows a planar structure between the chromone and the side chain. Differences in the geometries due to the substitution of the electronegative atom and intermolecular contacts due to the chromone and hydrazinecarbothioamide were analyzed. NBO analysis confirms the presence of two strong stable hydrogen bonded NH⋯O intermolecular interactions and two weak hydrogen bonded CH⋯O interactions. The red shift in NH stretching frequency exposed from IR substantiates the formation of NH⋯O intermolecular hydrogen bond and the blue shift in CH stretching frequency substantiates the formation of CH⋯O intermolecular hydrogen bond. Drug likeness, absorption, distribution, metabolism, excretion and toxicity property gives an idea about the pharmacokinetic properties of the title molecule. The binding energy of the nonbonding interaction with Histidine 41 and Cysteine 145, present a clear view that 2(2E)-methyl-2-[(4-oxo-4H-chromen-3-yl)methylidene]-hydrazinecarbothioamide can irreversibly interact with SARS-CoV-2 protease.

Quantum chemical insight into molecular structure, NBO analysis of the hydrogen-bonded interactions, spectroscopic (FT-IR, FT-Raman), drug likeness and molecular docking of the novel anti COVID-19 molecule 2-[(4,6-diaminopyrimidin-2-yl)sulfanyl]-N-(4-fluorophenyl)acetamide - dimer.

Novel antiviral active molecule 2- [(4,6-diaminopyrimidin-2-yl)sulfanyl]-N-(4-fluoro- phenyl)acetamide has been synthesised and characterized by FT-IR and FT-Raman spectra. The equilibrium geometry, natural bond orbital calculations and vibrational assignments have been carried out using density functional B3LYP method with the 6-311G++(d,p) basis set. The complete vibrational assignments for all the vibrational modes have been supported by normal coordinate analysis, force constants and potential energy distributions. A detailed analysis of the intermolecular interactions has been performed based on the Hirshfeld surfaces. Drug likeness has been carried out based on Lipinski's rule and the absorption, distribution, metabolism, excretion and toxicity of the title molecule has been calculated. Antiviral potency of 2- [(4,6-diaminopyrimidin-2-yl)sulfanyl]-N-(4-fluoro-phenyl) acetamide has been investigated by docking against SARS-CoV-2 protein. The optimized geometry shows near-planarity between the phenyl ring and the pyrimidine ring. Differences in the geometries due to the substitution of the most electronegative fluorine atom and intermolecular contacts due to amino pyrimidine were analyzed. NBO analysis reveals the formation of two strong stable hydrogen bonded N-H···N intermolecular interactions and weak intramolecular interactions C-H···O and N-H···O. The Hirshfeld surfaces and consequently the 2D-fingerprint confirm the nature of intermolecular interactions and their quantitative contributions towards the crystal packing. The red shift in N-H stretching frequency exposed from IR substantiate the formation of N-H···N intermolecular hydrogen bond. Drug likeness and absorption, distribution, metabolism, excretion and toxicity properties analysis gives an idea about the pharmacokinetic properties of the title molecule. The binding energy -8.7 kcal/mol of the nonbonding interaction present a clear view that 2- [(4,6-diaminopyrimidin-2-yl)sulfanyl]-N-(4-fluoro- phenyl) acetamide can irreversibly interact with SARS-CoV-2 protease.

Potential Application of Whole Body Vibration Exercise For Improving The Clinical Conditions of COVID-19 Infected Individuals: A Narrative Review From the World Association of Vibration Exercise Experts (WAVex) Panel.

COVID-19 is a highly infectious respiratory disease which leads to several clinical conditions related to the dysfunction of the respiratory system along with other physical and psychological complaints. Severely affected patients are referred to intensive care units (ICUs), limiting their possibilities for physical exercise. Whole body vibration (WBV) exercise is a non-invasive, physical therapy, that has been suggested as part of the procedures involved with pulmonary rehabilitation, even in ICU settings. Therefore, in the current review, the World Association of Vibration Exercise Experts (WAVEX) reviewed the potential of WBV exercise as a useful and safe intervention for the management of infected individuals with COVID-19 by mitigating the inactivity-related declines in physical condition and reducing the time in ICU. Recommendations regarding the reduction of fatigue and the risk of dyspnea, the improvement of the inflammatory and redox status favoring cellular homeostasis and the overall improvement in the quality of life are provided. Finally, practical applications for the use of this paradigm leading to a better prognosis in bed bound and ICU-bound subjects is proposed.