Quantum Mechanical Calculations Research Articles

Capturing Differential Quality of Experimental Evidence in a Predictive Quantum-Mechanical Model for Respiratory Sensitization.

Asthma is of concern in occupational toxicology with significant public-health and economic costs. In the absence of benchmark in vivo and in vitro tests, the use of mechanistically sound in silico models is critical to inform hazard and to protect workers from exposure to potentially harmful substances. We recently reported on the computer-aided discovery and REdesign (CADRE) model for respiratory sensitization, which relies on a tiered structure of expert rules, molecular simulations, quantum-mechanics calculations and advanced statistics to accurately identify respiratory sensitizers from first principles. Here, we present an update to this model based on two years of testing in the pharmaceutical space, where we captured the heterogeneity of the underlying experimental evidence in two predictive tiers, thus allowing the practitioner to select an outcome based on their expert assessment of the data reliability and relevance. This user-based tuning of predictive models is critical for end points that lack consensus on what constitutes satisfactory evidence to support a decision in the handling of chemicals for occupational safety.

Pyrene Based Schiff Base for Cascade Fluorescent "On-Off" Detection of Aluminium(III) and Fluoride Ions and its Applications in Live Cells Imaging.

An easy-to-prepare pyrene-based Schiff base PNZ was synthesized by condensing equimolar amount of 1-pyrenebutyric hydrazide with 2-hydroxy-naphthaldehyde, and employed as a fluorescent chemosensor for in-situ cascade detection of aluminium (Al3+) and fluoride (F-) ions. In DMSO:H2O (1 : 1, v/v), the weakly emissive PNZ showed a significant fluorescence enhancement at 455 nm selectively upon the addition of Al3+ due to the complexation-induced formation of a pyrene excimer. Schiff base PNZ and Al3+ formed a complex in 2 : 1 binding ratio with the estimated binding constants of K1:1=9826.01 M-1 and K2:1=3188.49 M-1. The sensing mechanism was explored by performing quantum mechanical calculations and 1H-NMR titration of PNZ with Al3+. The in-situ formed PNZ-Al3+ complex species enabled the fluorescent turn-off detection of F-. Using PNZ and PNZ-Al3+, the concentrations of Al3+ and F- ions can be detected down to 2.89×10-7 M and 1.88×10-7 M, respectively. The cytotoxicity of the PNZ and its ability to bioimage Al3+ and F- ions was examined in the human cervical cancer cell line. Finally, the receptor PNZ was applied for the quantification of Al3+ and F- ions in various real samples, such as tap water, river water, rainwater, mouthwash, and toothpaste.

Molecular models of PM6 for non-fullerene acceptor organic solar cells: How DAD and ADA structures impact charge separation and charge recombination.

The quadrupole moment of a non-fullerene acceptor (NFA) generated by the constituent electron donor (D) and acceptor (A) units is a significant factor that affects the charge separation (CS) and charge recombination (CR) processes in organic photovoltaics (OPVs). However, its impact on p-type polymer domains remains unclear. In this study, we synthesized p-type molecules, namely acceptor-donor-acceptor (ADA) and donor-acceptor-donor (DAD), which are components of the benchmark PM6 polymer (D: benzodithiophene and A: dioxobenzodithiophene). Planar heterojunction films, a model of bulk heterojunction, were prepared using ADA, DAD, and PM6 as the bottom p-type layers and Y6 NFA as the top n-type layer. Flash-photolysis time-resolved microwave conductivity, femtosecond transient absorption spectroscopy, and quantum mechanical calculations were employed to probe the charge carrier dynamics. Our findings reveal that while the subtle difference in quadrupole moment and energy gradient of the p-type materials has a minimal influence on CS, the molecular type (ADA or DAD) significantly affects the bulk CR. This study expands the understanding of how the p-type component and its conformation at the p/n interface impact the CS and CR in OPVs, highlighting the critical role of molecular donors in optimizing device performance.

Vanadium incorporation in 2D-layered MoSe2

Recent advances in experimental techniques have made it possible to manipulate the structural and electronic properties of two-dimensional layered materials (2DM) through interaction with foreign atoms. Using quantum mechanics calculations based on the density functional theory, we explored the dependency of the structural, energetic, electronic, and magnetic properties of the interaction between Vanadium (V) atoms and monolayer and bilayer MoSe2. Spin-polarized metallic behavior was observed for high V concentration, and a semiconductor/metal interface emerged due to V adsorption on top of BL MoSe2. Our research demonstrated that the functionalization of 2D materials makes an important contribution to the design of spintronic devices based on a 2D-layered materials platform.

Efficient quantum mechanical minimum free energy path calculation by combining path integral hybrid Monte Carlo and climbing image nudged elastic band methods, and its application to the addition reaction of hydrogen isocyanide to formaldehyde.

We propose an efficient algorithm for a minimum free energy path calculation based on the path integral hybrid Monte Carlo (PIHMC) method by combining the climbing image-nudged elastic band (CI-NEB) and the thermodynamic integration (TI) methods. Here, the CI-NEB and the TI methods are used to find a transition state along the reaction path and evaluate the free energy path, respectively. Our algorithm is applied to the Walden inversion reaction of the hydronium ions (H3O+). The numerical results show that the computational effort by our algorithm is significantly reduced compared to that of the previously proposed algorithm combining PIHMC without losing accuracy. We also demonstrate the importance of temperature and isotope effects on the addition reaction of hydrogen isocyanide to formaldehyde. In this reaction, the nuclear quantum effect causes the structural change at the TS and decreases the energy barrier.

Photocatalytic degradation of methylene blue dye by ZnO nanoparticle thin films, using Sol–gel technique and UV laser irradiation

The focus of the current work is the study of the effect of the photo-catalytic activity of ZnO nanoparticles. The photocatalytic destruction of methylene blue dye, a common water contaminant, was used to assess the photocatalytic efficiency of the ZnO nanoparticles from its aqueous solution by using ZnO nanoparticles thin film under UV light and laser irradiation. Sol–gel methods prepared ZnO nanoparticle thin films. X-ray diffraction and a field-emitted scanning electron microscope were utilized to examine the structure of the produced ZnO nanoparticles. An extended characterization by laser-based fluorescence and UV–visible spectroscopic techniques. The effects of operational parameters such as photo-catalyst load and contact time on photocatalytic degradation of methylene blue were investigated. The recent study’s findings showed that irradiation with a UV laser increases with power density 25 µW/cm2, the photo-catalytic rate. The UV spectra show decay for the band at 664nm decreased and the concentration of M.B. in monomer form decayed to 26% of the original concentration in 24 h, while the band at 612 which is related to the dimer M.B. molecules was not affected. The laser irradiation did the same for monomer M.B. molecules in only 3 h, while the dimer decreased to 28% of its original concentration. The reaction mechanism has been discussed by molecular modelling. Quantum mechanical calculations at B3LYP/6-311g(d,p) level indicated that methylene blue changed from dimers to monomers in the existence of ZnO. The current results present a method for degrading M.B. not only in wastewater but also in the industrial waste scale.

2-Halomethyleneoxetanes from 2-Methyleneoxetanes by Reaction with N-Halosuccinimides: Reactant Influences on Stereochemical Outcomes and Reaction Pathways.

The first general synthesis of 2-halomethyleneoxetanes, realized by the reaction of 2-methyleneoxetanes with N-halosuccinimides (NXS), is reported. The relative diastereoselectivities of the transformations were dependent on the halogen of NXS, while alternative reaction outcomes were influenced by substituents on the oxetane. Quantum mechanical calculations and molecular dynamics simulations exploring the basis of the observed diastereoselectivities are described. These highly strained heterocycles underwent standard cross-coupling reactions, demonstrating their utility as synthetic intermediates.

Molecular quantum chemical data sets and databases for machine learning potentials

Abstract The field of computational chemistry is increasingly leveraging machine learning (ML) potentials to predict molecular properties with high accuracy and efficiency, providing a viable alternative to traditional quantum mechanical (QM) methods, which are often computationally intensive. Central to the success of ML models is the quality and comprehensiveness of the data sets on which they are trained. Quantum chemistry data sets and databases, comprising extensive information on molecular structures, energies, forces, and other properties derived from QM calculations, are crucial for developing robust and generalizable ML potentials.
In this review, we provide an overview of the current landscape of quantum chemical data sets and databases. We examine key characteristics and functionalities of prominent resources, including the types of information they store, the level of electronic structure theory employed, the diversity of chemical space covered, and the methodologies used for data creation. Additionally, an updatable resource is provided to track new data sets and databases at https://github.com/Arif-PhyChem/datasets_and_databases_4_MLPs. This resource also has the overview in a machine-readable database format with the Jupyter notebook example for analysis.
Looking forward, we discuss the challenges associated with the rapid growth of quantum chemical data sets and databases, emphasizing the need for updatable and accessible resources to ensure the long-term utility of them. We also address the importance of data format standardization and the ongoing efforts to align with the FAIR principles to enhance data interoperability and reusability. Drawing inspiration from established materials databases, we advocate for the development of user-friendly and sustainable platforms for these data sets and databases.

First principles investigation of structural, electronic, optical, transport properties of double perovskites X2TaTbO6 (X= Ca, Sr, Ba) for optoelectronic and energy harvesting applications

Structural, electrical, optical, thermoelectric response of X2TaTbO6 (X = Ca, Sr, Ba) double perovskites oxides are studied by using WIEN2k that is based on quantum mechanical calculations employing PBE-GGA approximation under the framework of DFT. We present electronic attributes including band gaps and density of states, and explain the electronic properties of all three oxide double perovskite materials which proved that they belong to directly forbidden band gap materials family. The cubic compounds Ba2TaTbO6, Sr2TaTbO6, and Ca2TaTbO6 have respective direct band gaps of 2.35 eV, 2.15eV, and 2.25 eV. Optical conductivity σ(ω), reflection R(ω), complex dielectric constants, refractive index ƞ(ω), absorbance α(ω), loss parameter L(ω) and extinction coefficient K(ω) are all utilized to explore light dependent characteristics of studied compounds. Thermoelectric parameter like, Number of Seebeck effect (S), charge carrier (n), magnetic susceptibility, power factor (PF), electrical conductivity (σ/t), thermal conductivity K/t, and heat capacity are key characteristics for materials to study its ability of thermal behavior. These thermoelectric parameters were determined by using BoltzTraP code. By studying the numbers on various material properties, scientists are uncovering new possibilities for creating sustainable materials for sustainable gadgets.

Integrating theoretical and experimental insights into nanoporous gold electrochemistry for enhanced baicalein sensing performance

We introduce an innovative electrochemical sensing method for the sensitive detection of Baicalein (BAI), emphasizing a simple surface modification process. The study encompasses both practical and theoretical investigations into the electrochemical behavior of nanoporous gold. Our theoretical analysis, based on advanced quantum-mechanical calculations, demonstrates that the adsorption of BAI molecule on gold-based substrates is energetically favorable, with adsorption energy increasing from an unmodified surface to a more porous substrate. BAI physisorbs on unmodified regions in a horizontal alignment, while it chemisorbs more strongly on nanoporous regions by penetrating the pores. On less modified surfaces, interaction energy predominates, whereas on heavily modified surfaces, distortion energies become more significant due to increased substrate reactivity. These results align with physicochemical characterizations, which reveal that nanoscale modifications, induced by different anodization times, explain the variations in electrode performance. Experimentally, cyclic voltammetry (CV) and differential pulse voltammetry (DPV) were employed using both a gold electrode (GE) and a nanoporous gold electrode (NPGE). The GE was subjected to surface treatment by immersion in H2SO4 and potential control at ca. +2.0 V for 40 seconds, resulting in a nanoporous configuration. Following optimizations, Adsorptive Stripping Voltammetry (AdSV) was used to determine BAI. The method achieved detection (LOD) and quantification (LOQ) limits of 0.015 µmol L-1 and 0.045 µmol L-1, respectively (Edeposition=-0.25 V; tdeposition=50 s). Additionally, the standard addition method was applied to the NPGE for recovering BAI from spiked synthetic human plasma and urine, with success rates ranging from 93.4% to 106%. This approach exhibited excellent stability, precision, and accuracy, with minimal interference from other substances. Moreover, the theoretical findings provided deeper insights into the selective electrochemical detection of BAI on nanoporous gold surfaces, offering new perspectives on this field.

Coherent dynamics in an optical quantum dot with phonons and photons

Genuine quantum-mechanical effects are readily observable in modern optomechanical systems comprising “classical” (bosonic) optical resonators. Unique features and advantages of optical two-level systems (qubits) for optomechanics, however, have not been so thoroughly explored. We experimentally demonstrate these advantages using charge-controlled InAs quantum dots (QDs) in surface-acoustic-wave resonators. We coherently control QD population dynamics using engineered optical pulses and mechanical motion, i.e., using both phonons and photons. As a first example, at moderate acoustic drive strengths, we demonstrate the potential of this technique to maximize fidelity in quantum microwave-to-optical transduction. Specifically, the scheme is tailored to enhance mechanically assisted photon scattering over the direct detuned photon scattering from the QD. Spectral analysis reveals distinct scattering channels related to Rayleigh scattering and luminescence in our pulsed excitation measurements, which lead to time-dependent scattering spectra. Quantum-mechanical calculations show good agreement with our experimental results, together providing a comprehensive description of excitation, scattering, and emission in a coupled QD-phonon system. These results highlight unique opportunities to expand the functionality of quantum optomechanical systems.

Evidence of conformational changes and self-aggregation of 1,2-Bis(4-pyridyl)ethylene in solutions with ethanol

In this work, we report on a concentration and temperature dependent study of the 1,2-Bis(4-pyridyl)ethylene (BPE) – ethanol solutions by means of ultrasonic relaxation spectroscopy. The results revealed two distinct relaxation processes that follow Debye-type frequency dependence. Despite the presence of both processes in the full concentration range studied, the low-frequency relaxation process, related to conformational change between the trans- and gauche-BPE conformers, dominates the acoustic spectra in the low-concentration range, while diminishes at higher concentrations with a parallel enhancement of the high-frequency relaxation process, which is attributed to the self-association of BPE molecules. Quantum mechanical calculations were performed to investigate the energetics of the trans- and gauche-conformers. The trans-species was found more thermodynamically stable than the gauche-conformer. By applying the Synchronous Transit-Guided Quasi-Newton (STQN) methodology, we confirmed the presence of a single transition structure. From the temperature dependence of the acoustic properties, we estimated the activation enthalpy and the enthalpy difference between the two conformers. Density Functional Theory (DFT) calculations have been applied to attain the corresponding enthalpies that were found close to the experimental values. Molecular docking calculations established the self-aggregation mechanism between BPE monomers forming three types of dimeric units, namely the trans-trans, the gauche-gauche and the trans-gauche dimer species with the latter found to be the most thermodynamically favorable. The concentration dependence of the sound velocity, mass density and shear viscosity evidenced the formation of BPE aggregates. From the temperature dependence of the acoustic spectra, the thermodynamic properties of the self-aggregation mechanism of BPE were also determined. Based on the vibrational spectroscopic data, the population of the gauche conformers was found to increase with concentration at the expense of the population of the trans conformers. From the study of the vibrational properties of the system in the short-rage order, we cannot exclude the presence of a specific dimer type in the overall structure. Nevertheless, regarding to the binding score of the trans-gauche dimer (-1.25 kcal/mol), this species is the most thermodynamically stable and most likely its population is higher in dense solutions relative to the other two dimer species.

Unveiling the intermolecular forces and unique properties of [EMIM][EtSO4] + [EMIM][MeSO3]

This study delves into the intricate interplay of intermolecular forces governing the archetypal ionic liquid mixture [EMIM][EtSO4] + [EMIM][MeSO3] through a synergistic integration of experimental and computational techniques. High-precision measurements of density, viscosity, and thermal conductivity across a temperature and compositional landscape unveil the system’s phase behavior and miscibility. Complementary insights into the microscopic interactions, including hydrogen bonding and ion-specific effects, are gleaned from molecular dynamics simulations and quantum mechanical calculations. This multipronged approach fosters a comprehensive understanding of the underlying forces dictating the observed thermophysical properties, propelling fundamental knowledge in the realm of ionic liquid mixtures and paving the way for the rational design of tailor-made ionic liquids with targeted properties for diverse fields, ranging from chemical engineering to energy storage.

A QSPR Model for Henry's Law Constants of Organic Compounds in Water and Ethanol for Distilled Spirits.

Henry's law describes the vapor-liquid equilibrium for dilute gases dissolved in a liquid solvent phase. Descriptions of vapor-liquid equilibrium allow the design of improved separations in the food and beverage industry. The consumer experience of taste and odor are greatly affected by the liquid and vapor phase behavior of organic compounds. This study presents a machine learning (ML) based model that allows quick, accurate predictions of Henry's law constants (kH) for many common organic compounds. Users input only a Simplified Molecular-Input Line-Entry System (SMILES) string or a common English name, and the model returns Henry's law estimates for compounds in water and ethanol. Training was performed on 5,690 compounds. Training data were gathered from an existing database and were supplemented with quantum mechanical (QM) calculations. An extra trees regression model was generated that predicts kH with a mean absolute error of 1.3 in log space and an R2 of 0.98. The model is applied to common flavor and odor compounds in bourbon whiskey as a test case for food and beverage applications.

Macrocyclic anti-inflammatory diterpenes from the South China Sea soft coral Sinularia erecta and their isolation by combined column chromatography

Eleven new macrocyclic casbane-type diterpenes, namely sinueracasbanones E–O (1–11), have been isolated from the South China Sea soft coral Sinularia erecta using combined column chromatography. The structures of new compounds were elucidated by extensive spectroscopic data analysis, the modified Mosher's method, X-ray diffraction analysis and quantum mechanical calculation methods. In bioassay, compounds 2, 5, 10 and 11 displayed interesting anti-inflammatory activities by the inhibition of lipopolysaccharide (LPS)-induced tumor necrosis factor (TNF)-α protein release with half maximal inhibitory concentration (IC50) values of 15.6, 7.1, 13.7 and 6.6 µM, respectively.

Pharmacoinformatics, Molecular Dynamics Simulation, and Quantum Mechanics Calculation Based Phytochemical Screening of Croton bonplandianum Against Breast Cancer by Targeting Estrogen Receptor-α (ERα)

Breast cancer progression is strongly influenced by estrogen receptor-α (ERα), a ligand-activated transcription factor that regulates hormone binding, DNA interaction, and transcriptional activation. ERα plays a key role in promoting cell proliferation in breast tissue, and its overexpression is associated with the advancement of breast cancer through estrogen-mediated signaling pathways. Targeting ERα is, therefore, a promising therapeutic strategy for breast cancer. However, there are currently no phytochemical-based drug candidates approved for effectively inhibiting breast cancer progression driven by elevated ERα expression. This study aims to identify phytochemical inhibitors from Croton bonplandianum against ERα using pharmacoinformatics approaches. Eighty-three bioactive compounds from C. bonplandianum were retrieved from the IMPPAT (Indian Medicinal Plants, Phytochemistry, and Therapeutics) database and screened through molecular docking for their binding affinity to ERα. The top candidates were further evaluated through molecular dynamics simulations, ADME analysis, toxicity assessment, and quantum mechanics-based DFT calculations. The thermodynamic properties and HOMO-LUMO energy gap values indicated that the selected compounds were both stable and active. Among them, 2,3-oxidosqualene (CID-5366020) and 5,8,11-eicosatriynoic acid, trimethylsilyl ester (CID-91696396) demonstrated the most potent inhibitory activity against ERα. These findings suggest that these compounds have significant potential as therapeutic agents for breast cancer treatment by targeting ERα.

Computational and experimental analysis of Luteolin-β-cyclodextrin supramolecular complexes: Insights into conformational dynamics and phase solubility

Investigating the structural stability of poorly-soluble luteolin (LuT) after encapsulation within cyclodextrins (CDs) is crucial for unlocking the therapeutic potential of LuT bioactive molecule. Herein, native and modified β-CD were employed to investigate LuT inclusion complex formation. Molecular mechanics (MM) and quantum mechanics (QM) were utilized for structural dynamics analysis. Microsecond timescale MD simulations yielded insights into LuT-CD interactions. The binding affinity between LuT and selected β-CDs was assessed by calculating the binding free energy using MM-PBSA and umbrella sampling simulations. The MM-PBSA results indicated that Heptakis-O-(2-hydroxypropyl)-β-CD (HP-β-CD) (−82.59+/-11.67 kJ/mol) and Di-O-methyl-β-CD (DM-β-CD) (−54.01+/-11.07 kJ/mol) exhibited good binding affinity for LuT. Subsequently, derivative screening of HP-β-CD revealed that only 2-HP-β-CD (HP-β-CD-1)/LuT (−21.38 kJ/mol) displayed a superior binding free energy (obtained from umbrella sampling) than HP-β-CD/LuT (−16.55 kJ/mol) inclusion complex. We conducted QM calculations on the top three inclusion complexes namelly HP-β-CD, DM-β-CD, and HP-β-CD-1 employing wB97X-D/6–311 + G(d,p) model chemistry to strengthen the MM results. The computational analysis aligns with experimental findings (phase solubility analysis), validating HP-β-CD-1 as most effective cavitand molecule for improving the solubility of LuT. This study offers critical structural insights for developing novel HP-β-CD derivatives with enhanced host capacity to encapsulate guest molecules efficiently.

Quantum mechanics/molecular mechanics (QM/MM) methods in drug design: a comprehensive review of development and applications

The integration of quantum mechanics (QM) and molecular mechanics (MM) methods, known as QM/MM, has emerged as a powerful computational approach in drug design. This hybrid technique combines the accuracy of QM calculations for the reactive region with the computational efficiency of MM methods for the surrounding environment. QM/MM methods have proven invaluable in studying chemical reactions, exploring enzyme mechanisms, and investigating ligand-protein interactions, all of which are crucial for rational drug design. This review provides a comprehensive overview of the QM/MM methodology, its theoretical foundations, and its applications in various aspects of drug design. We discussed the key components, such as QM and MM region partitioning, link atom schemes, and boundary treatments. Additionally, we highlight recent advancements and challenges in QM/MM methods, including polarizable force fields, implicit solvation models, and enhanced sampling techniques. Furthermore, we present illustrative examples showcasing the successful application of QM/MM methods in lead optimization, virtual screening, and the elucidation of biochemical mechanisms relevant to drug targets. Finally, we provide perspectives on future developments and the potential impact of QM/MM methods on the drug discovery pipeline.

A Quantum Mechanical Approach to The Mechanism of Asymmetric Synthesis of Chiral Amine by Imine Reductase from Stackebrandtia Nassauensis.

The asymmetric synthesis of tetrahydroisoquinolines (THIQs) has gained importance in recent years due to their significant potential in drug development studies. In this study, the conversion of 1-methyl-3,4-dihydroisoquinoline substrate to a chiral amine, 1-methyl-1,2,3,4-tetrahydroisoquinoline, under the catalysis of the stereoselective imine reductase enzyme from Stackebrandtia nassauensis (SnIR) was investigated in detail to elucidate the mechanism and explain the experimental enantioselectivity. The results were found to be in agreement with the experimental data. To elucidate the reaction mechanism, quantum mechanical calculations were performed by considering a large cluster of the active site of the enzyme. In this regard, possible reaction pathways leading to both R- and S-products with the corresponding intermediates and the transition states for the hydride transfer from the cofactor to the substrate were considered by density functional theory (DFT) calculations, and the factors contributing to the observed stereoselectivity were sought. The calculations supported a stepwise mechanism rather than the concerted protonation and the hydride transfer steps. The stereoselectivity in the hydride transfer was found to be due not only to the stability of the enzyme-subtrate complex but also to the corresponding reaction barriers. The calculations were performed at the wB97XD/6-311+G(2df,2p)//B3LYP/6-31G(d,p) level of theory using the PCM approach.

Albumins constrainting the conformation of mitochondria-targeted photosensitizers for tumor-specific photodynamic therapy

Tumor ablation Preclinical organelle-targeted phototherapies have effectively achieved tumor photoablation for regenerative biomedical applications in cancer therapies. However, engineering effective phototherapy drugs with precise tumor-localization targeting and organelle direction remains challenging. Herein, we report a albumins constrainting mitochondrial-targeted photosensitizer nanoparticles (PSs@BSAs) for tumor-specific photodynamic therapy. X-ray crystallography elucidates the two-stage assembly mechanism of PSs@BSAs. Femtosecond transient absorption spectroscopy and quantum mechanical calculations reveal the implications of conformational dynamics at the excited state. PSs@BSAs can efficiently disable mitochondrial activity, and further disrupt tumor angiogenesis based on the photodynamic effect. This triggers a metabolic and oxidative stress crisis to facilitate photoablation of solid tumor and antitumor metastasis. The study fully elucidates the interdisciplinary issues of chemistry, physics, and biological interfaces, thereby opening new horizons to inspire the engineering of organelle-targeted tumor-specific photosensitizers for biomedical applications.