Quantum Mechanical Calculations Research Articles

ScaleLat: A chemical structure matching algorithm for mapping atomic structure of multi-phase system and high entropy alloys

ScaleLat (Scale Lattice) is a computer program written in C for performing the atomic structure analysis of multi-phase system or high entropy alloys (HEAs). The program implements an atomic cluster cell extraction algorithm to obtain all symmetry independent characteristic atomic cluster cells for the complex atomic configurations which are usually obtained from molecular dynamics or kinetic Monte-Carlo simulations at nanoscale or mesoscopic scale. ScaleLat implements an efficient and unique chemical structure matching algorithm to match all extracted atomic clusters from a large supercell (>104 atoms) to a representative small one (∼ 103 or less), providing the possibility to directly use the highly accurate quantum mechanical methods to study the electronic, magnetic, and mechanical properties of multi-component alloys for complex microstructures. We demonstrate the capability of ScaleLat code by conducting both the atomic structure matching analysis for Fe-12.8 at.% Cr binary alloy and equiatomic CrFeCoNiCu high entropy alloy, successfully obtaining the representative supercells containing 102∼103 atoms for two systems. The reliability of the proposed chemical structure matching scheme is tested and confirmed by calculating the electronic structures of both examples using trial supercells with various sizes. Overall, ScaleLat program provides a universal platform to efficiently map all essential chemical structures of large complex atomic structures to a relatively easy-handling small supercell for quantum mechanical calculations of various user interested properties. Program SummaryProgram Title: ScaleLatCPC Library link to program files: https://doi.org/10.17632/cv6wsxy938.1Developer's repository link: https://github.com/NanLi-xjtu/ScaleLat.gitLicensing provisions: MITProgramming language: CNature of Problem: Very large supercells containing more than 104 atoms must be used to describe the atomic structure of multi-phase materials or high entropy alloys, and their electronic and mechanical properties are almost not possible to be investigated using quantum mechanical calculations within conventional computational hardware. Decreasing the total number of atoms in a smaller representative supercell which preserves all essential chemical structures of the original large supercell is the key to tackling the problem.Solution to the Problem: An atomic cluster cell extraction algorithm is realized to thoroughly obtain all symmetry independent characteristic chemical structures of multi-phase system or high entropy alloys. Utilizing the direct atom swapping method, the efficient chemical structure matching procedure is developed to map all extracted characteristic atomic cluster cells of benchmark structure to the small supercell by minimizing their differences in both the types and relative fractions of atomic cluster cell sets.

Separation of isotopologues of amphetamine with various degree of deuteration on achiral and polysaccharide-based chiral columns in high-performance liquid chromatography

Hydrogen/deuterium (H/D) isotope effects are not unusual in chromatography and such phenomena have been observed in both gas- and liquid-phase separations. Despite the numerous reports on this topic, the understanding of mechanisms and the underlying noncovalent interactions at play remains rather challenging. In our recent study, we reported baseline separation of isotopologoues of some amphetamine (AMP) derivatives on achiral and polysaccharide-based chiral columns, as well as some correlations between the degree of separation of enantiomers and isotopologues on (the same) polysaccharide-based chiral column(s). Following our previous findings on isotope effects in high-performance liquid chromatography, we report herein a comparative study on the isotope effects observed with AMP and methamphetamine (MET). The impact of some pivotal factors such as the number of deuterium atoms part of AMP isotopologues, the structure of its isotopomers, the chemical structure of the achiral and chiral stationary phases used in this study, and the use of methanol- vs acetonitrile-containing mobile phases on the isotope effects was examined and discussed. Quantitative correlations between the observed isotope effects and the enantioselectivity of the chiral columns used are also shortly discussed. Furthermore, considering the chromatographic results as benchmark experimental data, we attempted to elucidate the molecular bases of the observed phenomena using quantum mechanics calculations.

Synergistic Machine Learning Accelerated Discovery of Nanoporous Inorganic Crystals as Non-Absorbable Oral Drugs.

Machine learning (ML) has taken drug discovery to new heights, where effective ML training requires vast quantities of high-quality experimental data as input. Non-absorbable oral drugs (NODs) have unique safety advantage for chronic diseases due to their zero systemic exposure, but their empirical discovery is still time-consuming and costly. Here, a synergistic ML method, integrating small data-driven multi-layer unsupervised learning, in silico quantum-mechanical computations, and minimal wet-lab experiments is devised to identify the finest NODs from massive inorganic materials to achieve multi-objective function (high selectivity, large capacity, and stability). Based on this method, a NH4-form nanoporous zeolite with merlinoite (MER) framework (NH4-MER) is discovered for the treatment of hyperkalemia. In three different animal models, NH4-MER shows a superior safety and efficacy profile in reducing blood K+ without Na+ release, which is an unmet clinical need in chronic kidney disease and Gordon's syndrome. This work provides a synergistic ML method to accelerate the discovery of NODs and other shape-selective materials.

Substitution-Induced Mechanistic Switching in SNAr-Warheads for Cysteine Proteases.

The aim of this study was to investigate the transition from non-covalent reversible over covalent reversible to covalent irreversible inhibition of cysteine proteases by making delicate structural changes to the warhead scaffold. To this end, dipeptidic rhodesain inhibitors with different N-terminal electrophilic arenes as warheads relying on the SNAr mechanism were synthesized and investigated. Strong structure-activity relationships of the inhibition potency, the degree of covalency, and the reversibility of binding on the arene substitution pattern were found. The studies were complemented and substantiated by molecular docking and quantum-mechanical calculations of model systems. Furthermore, the improvement in the membrane permeability of peptide esters in comparison to their corresponding carboxylic acids was exemplified.

Agglomeration in dimethyl sulfoxide and water binary System: A comprehensive study through thermodynamics, vibrational spectroscopy, quantum mechanical calculations and morphology

Some nano- or micro-sized agglomerates with different morphologies in the dimethyl sulfoxide (DMSO) and water binary system at different molar fractions were characterized using Scanning Electron Microscope (SEM) and Dynamic Light Scattering (DLS) for the first time. Four fundamental clusters with the composition of [(DMSO)2], [(DMSO)3], [(DMSO)2∙ H2O] and [(DMSO)3∙ H2O] were identified through the combination of quantum mechanical calculations and vibrational spectroscopy. These clusters act as seeds for the growth of agglomerates both in pure DMSO and in DMSO-water binary mixtures. According to SEM images, the morphology of the agglomerates varies with the molar fraction, wherein two main kinds were observed, viz. one growing from the center and spreading out to the surrounding, and the other growing into a chain-like structure. Inter-cluster and/or inter-agglomerate interactions are responsible for the molar fraction dependence of density, viscosity and other related thermodynamic properties. The present work is the first to study the morphology of agglomerates in the DMSO-water binary system and the first to propose the essential roles played by four dominant clusters in the agglomerating process.

Synthesis of isoprene from 1-butanol and from diethyl ether in the presence of 3d-metal oxides nano-clusters acting as catalysts

The conformational equilibria of 1-butanol (1-BuOH) and diethyl ether (DEE) molecules were investigated in gas and liquid phases. The geometry of the molecules of all stable isomers of 1-BuOH and DEE was fully optimised and the thermochemical quantities’ values (ΔH, ΔG and ΔS) were computed in the temperature range from close to 0 K to 1000 K at the Density Functional Theory (DFT) level. DEE shows two rotamers (namely, Tt and Tg), whereas five different rotamers were identified for 1-BuOH (namely, Tt, Tg, Gt, Gg and Gg’) with different stability, due to the presence of intramolecular interactions. Electrostatic properties of 1-BuOH, ethanol (EtOH), and DEE were also evaluated. Calculated vibration spectra of 1-BuOH and DEE were compared with the experimental FT-IR and Raman spectra recorded in neat phase and diluted in cyclohexane (CHX). The experimental vibrational spectra found the best match with the sum of calculated spectra using the Boltzmann coefficients based on the thermal stability of each conformer. The frequency shift observed for some peaks as a function of the concentration of 1-BuOH in CHX reveals the impact of hydrogen bonds between 1-BuOH molecules, in particular in the case of conformer Gg’. In contrast, very weak interactions among molecules of DEE were spectroscopically detected. The transformation reactions of {1-BuOH+EtOH} and {DEE+EtOH} mixtures at different temperatures were studied using the method of quantum mechanical calculations. The mechanism of isoprene formation from these mixtures was determined taking into account the chemisorption of 1-BuOH and DEE onto metal oxide nano-clusters M4O4 (M = Sc to Zn) and its effect on the vibrations of BuOH and DEE at the interface for M = Zn, Cu and Ti using Raman microscopic spectroscopy.

Exploratory data science on supercomputers for quantum mechanical calculations

Literate programming—the bringing together of program code and natural language narratives—has become a ubiquitous approach in the realm of data science. This methodology is appealing as well for the domain of Density Functional Theory (DFT) calculations, particularly for interactively developing new methodologies and workflows. However, effective use of literate programming is hampered by old programming paradigms and the difficulties associated with using high performance computing (HPC) resources. Here we present two Python libraries that aim to remove these hurdles. First, we describe the PyBigDFT library, which can be used to setup materials or molecular systems and provides high-level access to the wavelet based BigDFT code. We then present the related remotemanager library, which is able to serialize and execute arbitrary Python functions on remote supercomputers. We show how together these libraries enable transparent access to HPC based DFT calculations and can serve as building blocks for rapid prototyping and data exploration.

Crystal violet degradation by visible light-driven AgNP/TiO2 hybrid photocatalyst tracked by SERRS spectroscopy

Dyes are important concerns regarding aquatic environmental contamination given their extensive industrial use and the occurrence of highly toxic and carcinogenic effects on the biota. In this work, photodegradation processes of the organic dye crystal violet (CV) by a hybrid plasmonic photocatalyst involving titanium dioxide (TiO2) and silver nanoparticles (AgNP), through irradiation with low-power visible light were studied, and the experiments were tracked by ultraviolet-visible absorption (UV–VIS) and surface-enhanced resonance Raman scattering (SERRS) spectroscopies. Enhanced photocatalytic activity was observed, reaching about 71, 80 and 87 % of CV removal with only 100 minutes of irradiation, depending on the Ag loading used. The high photocatalytic efficiency is further highlighted by the low energy consumption in the process, requiring only ca. 1.46 kW h L-1 in the best reaction condition. Quantum-mechanical calculations were used to the assignment of electronic spectra, as well as to the prediction of frontier molecular orbitals and atomic charges, aiming to propose mechanisms for radical attacks. Such results allow suggesting degradation processes involved mainly N-demethylation and bond breaking of central carbon. The presence of CV protonated species was also supported through Density Functional Theory (DFT) investigation. The integration of theoretical and experimental results allows proposing the formation of pararosaniline, phenol and benzophenone derivatives, which may have highest ecotoxicity than the original contaminant, outstanding the remarkable relevance of SERRS spectroscopy in monitoring such recalcitrant substances.

17-β-Estradiol—β-Cyclodextrin complex as an aqueous solution: Structural and physicochemical characterization supported by MM and QM calculations

17-β-estradiol (EST) is an Active Pharmaceutical Ingredient characterized by a low water solubility. Complexation with β-cyclodextrin (βCD) enhances its bioavailability, hence such complex is an interesting research object from pharmaceutical point of view. However, basic facts like description of complex's structure and definition of its molar ratio, were debatable already for decades. This work for the first time justifies the EST:βCD molar ratio as 1:2 using the HRMS (high-resolution mass spectrometry) and phase solubility studies. The latter are used to define complex stability constant, as well. The structure and stability is analyzed using a variety of computational approaches: Quantum Mechanics (QM) based methods (DFT, semiempirical approaches) and MD/MMGBSA approach. In case of the QM, for the first time in the computational analysis of cyclodextrin complexes, a thorough benchmarking test is presented. Different computational parameters (solvent model, presence/absence of dispersion correction etc.) are used. Obtained results are compared with the experimental data.

A Combined Experimental, DFT and Molecular Dynamics Simulation Study of Binary Mixture of Ethylbenzene and Aniline

AbstractDensity and viscosity values of the binary mixture of ethylbenzene and aniline have been experimentally measured in different mole fractions at temperatures of 293.15 to 313.15 K and at an absolute pressure of 86.7 kPa. Based on the obtained experimental data, the excess molar volume and viscosity deviations have been reported, which can interpret the interactions in this mixture. The obtained data were fitted with the Redlich‐Kister equation. In addition, the viscosity results are discussed using the equation proposed by Gruenberg‐Nissan. After experimental studies, in order to investigate the interactions of these two components and their mixture, quantum mechanical calculations and molecular dynamics simulation have been used. In this way, the structures of the desired molecules have been optimized. Then Atoms in Molecules (AIM) and frontier molecular orbital (FMO) techniques have been used for a more detailed investigation. Finally, by plotting radial distribution functions (RDFs) obtained from molecular dynamics, these interactions have been investigated in a more comprehensive way. In addition, the simulated densities at 298.15 K have been reported. At the end, clear pictures of the interactions of molecules in mixtures were obtained by comparing the achievements of experimental measurements, quantum chemical and calculations MD simulation.

Reaction mechanisms for methyl isocyanate (CH3NCO) gas-phase degradation

Methyl isocyanate (MIC) is a toxic chemical found in many commercial, industrial, and agricultural processes, and was the primary chemical involved in the Bhopal, India disaster of 1984. The atmospheric environmental chemical reactivity of MIC is relatively unknown with only proposed reaction channels, mainly involving OH-initiated reactions. The gas-phase degradation reaction pathways of MIC and its primary product, formyl isocyanate (FIC), were investigated with quantum mechanical (QM) calculations to assess the fate of the toxic chemical and its primary transformation products. Transition state energy barriers and reaction energetics were evaluated for thermolysis/pyrolysis-like reactions and bimolecular reactions initiated by relevant radicals (•OH and Cl•) to evaluate the potential energy surfaces and identify the primary reaction pathways and products. Thermolysis/pyrolysis of MIC requires high energy to initiate N-CH3 and C-H bond dissociation and is unlikely to dissociate except under extreme conditions. Bimolecular radical addition and H-abstraction reaction pathways are deemed the most kinetically and thermodynamically favorable mechanisms. The primary transformation products of MIC were identified as FIC, methylcarbamic acid, isocyanic acid (isocyanate radical), and carbon dioxide. The results of this work inform the gas-phase reaction channels of MIC and FIC reactivity and identify transformation products under various reaction conditions.

Rhodium(I)-Catalyzed Annulation of Bicyclo[1.1.0]butyl-Substituted Dihydroquinolines and Dihydropyridines.

Bicyclo[1.1.0]butane-containing compounds feature a unique chemical reactivity, trigger "strain-release" reaction cascades, and provide novel scaffolds with considerable utility in the drug discovery field. We report the synthesis of new bicyclo[1.1.0]butane-linked heterocycles by a nucleophilic addition of bicyclo[1.1.0]butyl anions to 8-isocyanatoquinoline, or, alternatively, iminium cations derived from quinolines and pyridines. The resulting bicyclo[1.1.0]butanes are converted with high regioselectivity to unprecedented bridged heterocycles in a rhodium(I)-catalyzed annulative rearrangement. The addition/rearrangement process tolerates a surprisingly large range of functional groups. Subsequent chemo- and stereoselective synthetic transformations of urea, alkene, cyclopropane, and aniline moieties of the 1-methylene-5-azacyclopropa[cd]indene scaffolds provide several additional new heterocyclic building blocks. X-ray structure-validated quantum mechanical DFT calculations of the reaction pathway indicate the intermediacy of rhodium carbenoid and metallocyclobutane species.

Mechanistic insights into the role of cyclodextrin in the regioselective radical CH trifluoromethylation of aromatic compounds.

The regioselective radical CH trifluoromethylation of aromatic compounds have been shown to proceed in good yield and high regioselectivity when cyclodextrin (CD) is present. Yet, the reaction mechanism and the role of CD during the reaction have remained obscure. To this end, here we performed density functional theory (DFT) calculations to the conformations obtained by semiempirical quantum mechanical molecular dynamics calculations to reveal the reaction mechanism and the role of CD in controlling regioselectivity. The results show that metal salt increases the yield but do not affect the regioselectivity, which we further confirmed by an experiment. In contrast, multiple CD-substrate complex conformations and reaction pathways were obtained, and CD was shown to contribute to improving the regioselectivity by stabilizing the intermediate state via encapsulation. The present study indicates that CDs can increase the regioselectivity by stabilizing the intermediate and product states while only marginally affecting the transition state.

Computational Modeling Oriented Substructure Splicing Application in the Identification of Thiazolidine Derivatives as Potential Low Honeybee Toxic Neonicotinoids.

With the aim of identifying novel neonicotinoid insecticides with low bee toxicity, a series of compounds bearing thiazolidine moiety, which has been shown to be low bee toxic, were rationally designed through substructure splicing strategy and evaluated insecticidal activities. The optimal compounds A24 and A29 exhibited LC50 values of 30.01 and 17.08 mg/L against Aphis craccivora, respectively. Electrophysiological studies performed on Xenopus oocytes indicated that compound A29 acted on insect nAChR, with EC50 value of 50.11 μM. Docking binding mode analysis demonstrated that A29 bound to Lymnaea stagnalis acetylcholine binding protein through H-bonds with the residues of D_Arg55, D_Leu102, and D_Val114. Quantum mechanics calculation showed that A29 had a higher highest occupied molecular orbit (HOMO) energy and lower vertical ionization potential (IP) value compared to the high bee toxic imidacloprid, showing potentially low bee toxicity. Bee toxicity predictive model also indicated that A29 was nontoxic to honeybees. Our present work identified an innovative insecticidal scaffold and might facilitate the further exploration of low bee toxic neonicotinoid insecticides.

Toward Accurate Quantum Mechanical Thermochemistry: (1) Extensible Implementation and Comparison of Bond Additivity Corrections and Isodesmic Reactions.

Obtaining accurate enthalpies of formation of chemical species, ΔHf, often requires empirical corrections that connect the results of quantum mechanical (QM) calculations with the experimental enthalpies of elements in their standard state. One approach is to use atomization energy corrections followed by bond additivity corrections (BACs), such as those defined by Petersson et al. or Anantharaman and Melius. Another approach is to utilize isodesmic reactions (IDRs) as shown by Buerger et al. We implement both approaches in Arkane, an open-source software that can calculate species thermochemistry using results from various QM software packages. In this work, we collect 421 reference species from the literature to derive ΔHf corrections and fit atomization energy corrections and BACs for 15 commonly used model chemistries. We find that both types of BACs yield similar accuracy, although Anantharaman- and Melius-type BACs appear to generalize better. Furthermore, BACs tend to achieve better accuracy than IDRs for commonly used model chemistries, and IDRs can be less robust because of the sensitivity to the chosen reference species and reactions. Overall, Anantharaman- and Melius-type BACs are our recommended approach for achieving accurate QM corrections for enthalpies.

The Partition of Unity Finite Element Method for the Schrödinger Equation

Abstract A Schrödinger equation for the system’s wavefunctions in a parallelepiped unit cell subject to Bloch-periodic boundary conditions must be solved repeatedly in quantum mechanical computations to derive the materials’ properties. Recent studies have demonstrated how enriched finite element type Galerkin methods can substantially lower the number of degrees of freedom necessary to produce accurate solutions with respect to the standard plane-waves method. In particular, the flat-top partition of unity finite element method enriched with the radial eigenfunctions of the one-dimensional Schrödinger equation offers a very effective way of solving the three-dimensional Schrödinger eigenvalue problem. We investigate the theoretical properties of this approximation method, its well-posedness and stability, we prove its convergence and derive suitable bound for the ℎ- and 𝑝-refinement in the L 2 L^{2} and energy norm for both the eigenvalues and the eigenfunctions. Finally, we confirm these theoretical results by applying this method to the eigenvalue problem of the one-electron Schrödinger equation with the harmonic potential, for which the exact solution is known.

Lignin and Pluronic-based nanomicelles as promising amiodarone nanocarriers: Synthesis, physical characterization, biological, and in silico evaluations

Lignin, a major component of herbaceous plants, is one of the most abundant natural poly-mers that has lipophilic character and antipathogenic properties. Another biocompatible polymer is Pluronic F127, that can cross the blood brain barrier (BBB). Herein, novel drug delivery nanosystems based on oil-in-water microemulsions made of these two biocompatible polymers were developed to load amiodarone (AM), a cationic amphipathic drug used for treating cardiac arrhythmia that displays antifungal and antibacterial properties. The use of drug delivery nanocarriers enhances the solubilization and controlled release of this medication, thus reducing its therapeutic dosage and associated side effects. The morphology, size and surface charge of the nanomiceles was characterized via scanning and transmission electron microscopy (SEM and TEM), dynamic light scattering (DLS) and zeta potential measurements, respectively, which demonstrated their spherical shape, with an average diameter of 27 nm and a zeta potential of −25 mV. Very high entrapment efficiencies were attained for both types of nanomicelles (79.1% and 83.1% for lignin and F127, respectively). Furthermore, both types of AM-loaded nanomicelles exhibited a slower release profile compared to the free drug. Cytotoxicity assay with morphological examination of NIH/3T3 fibroblast cells confirmed a reduction in drug toxicity upon loading onto the nanocarriers. Blood cultures in a chocolate agar medium corroborated that the antibacterial properties of AM are preserved after nanomicelle encapsulation. The interactions of AM with F127 and lignin monomers were investigated via quantum mechanical computations, which revealed the formation of strong hydrogen bonds, the most intense being between AM and lignin. Overall, these novel formulations exhibit great potential for the sustained and targeted AM delivery.

Quantum mechanics insights into melatonin and analogs binding to melatonin MT1 and MT2 receptors

Melatonin receptors MT1 and MT2 are G protein-coupled receptors that mediate the effects of melatonin, a hormone involved in circadian rhythms and other physiological functions. Understanding the molecular interactions between these receptors and their ligands is crucial for developing novel therapeutic agents. In this study, we used molecular docking, molecular dynamics simulations, and quantum mechanics calculation to investigate the binding modes and affinities of three ligands: melatonin (MLT), ramelteon (RMT), and 2-phenylmelatonin (2-PMT) with both receptors. Based on the results, we identified key amino acids that contributed to the receptor-ligand interactions, such as Gln181/194, Phe179/192, and Asn162/175, which are conserved in both receptors. Additionally, we described new meaningful interactions with Gly108/Gly121, Val111/Val124, and Val191/Val204. Our results provide insights into receptor-ligand recognition’s structural and energetic determinants and suggest potential strategies for designing more optimized molecules. This study enhances our understanding of receptor-ligand interactions and offers implications for future drug development.

Development of a ReaxFF reactive force field for ternary phosphate-based bioactive glasses.

Phosphate-based glasses (PBGs) in the CaO-Na2O-P2O5 system have diverse applications as biomaterials due to their unique dissolution properties. A reactive force field (ReaxFF) has been developed to simulate these materials at the atomic level. The ReaxFF parameters of PBGs, including the interaction between phosphorus and calcium atoms, have been developed using a published code based on genetic algorithms. The training data, including the atomic charges, atomic forces, bond and angle parameters, and different differential energies, are chosen and measured from static quantum-mechanical calculations and abinitio molecular dynamics of PBGs. We did different short- and medium-range structural analyses on the bulk simulated PBGs with different compositions to validate the developed potential. Radial and angular distribution functions and coordination numbers of network formers and modifiers, as well as the network connectivity of the glass, are in agreement with experimental and previous simulations using both shell-model classical force fields and abinitio simulated data; for example, the coordination number of phosphorus is 4.0. This successful development of ReaxFF parameters being able to describe the bulk PBGs enables us to work on the dissolution behavior of the glasses, including the interaction of water molecules with PBGs, in future works.

Strong Angular Oscillation of Rotationally Resolved Differential Cross Section in the H + HD → H2 + D Reaction at the Collision Energy of 2.07 eV: Evidence of Geometric Phase Effects.

Geometric phase (GP) effects in chemical reactions are subtle quantum phenomena that are challenging to identify. In this work, we report a joint experimental and theoretical study of the H + HD → H2 + D reaction at a collision energy of 2.07 eV, which is far below the energy of the conical intersection of 2.53 eV. The rotationally state-resolved differential cross sections were measured by a crossed-beam experiment with the scheme of D-atom Rydberg tagging time-of-flight detection. Experimental angular distributions of three rotational states of H2 products exhibit notable variation near the backward scattering direction. Time-dependent quantum mechanics calculations (TDQMs) were carried out at the same collision energy, with and without the inclusion of GP. The experimental angular distributions are in good agreement with TDQM results with the inclusion of GP but do not agree with TDQM results without the inclusion of GP. This work demonstrates the existence of GP effects at energy far below the conical intersection.