Quantum Mechanical Calculations Research Articles

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.

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.

Computational Insights into Cyclodextrin Inclusion Complexes with the Organophosphorus Flame Retardant DOPO.

Cyclodextrins (CDs) were used as green char promoters in the formulation of organophosphorus flame retardants (OPFRs) for polymeric materials, and they could reduce the amount of usage of OPFRs and their release into the environment by forming [host:guest] inclusion complexes with them. Here, we report a systematic study on the inclusion complexes of natural CDs (α-, β-, and γ-CD) with a representative OPFR of DOPO using computational methods of molecular docking, molecular dynamics (MD) simulations, and quantum mechanical (QM) calculations. The binding modes and energetics of [host:guest] inclusion complexes were analyzed in details. α-CD was not able to form a complete inclusion complex with DOPO, and the center of mass distance [host:guest] distance amounted to 4-5 Å. β-CD and γ-CD allowed for a deep insertion of DOPO into their hydrophobic cavities, and DOPO was able to frequently change its orientation within the γ-CD cavity. The energy decomposition analysis based on the dispersion-corrected density functional theory (sobEDAw) indicated that electrostatic, orbital, and dispersion contributions favored [host:guest] complexation, while the exchange-repulsion term showed the opposite. This work provides an in-depth understanding of using CD inclusion complexes in OPFRs formulations.

Darobactin Substrate Engineering and Computation Show Radical Stability Governs Ether versus C-C Bond Formation.

The Gram-negative selective antibiotic darobactin A has attracted interest owing to its intriguing fused bicyclic structure and unique targeting of the outer membrane protein BamA. Darobactin, a ribosomally synthesized and post-translationally modified peptide (RiPP), is produced by a radical S-adenosyl methionine (rSAM)-dependent enzyme (DarE) and contains one ether and one C-C cross-link. Herein, we analyze the substrate tolerance of DarE and describe an underlying catalytic principle of the enzyme. These efforts produced 51 enzymatically modified darobactin variants, revealing that DarE can install the ether and C-C cross-links independently and in different locations on the substrate. Notable variants with fused bicyclic structures were characterized, including darobactin W3Y, with a non-Trp residue at the twice-modified central position, and darobactin K5F, which displays a fused diether ring pattern. While lacking antibiotic activity, quantum mechanical modeling of darobactins W3Y and K5F aided in the elucidation of the requisite features for high-affinity BamA engagement. We also provide experimental evidence for β-oxo modification, which adds support for a proposed DarE mechanism. Based on these results, ether and C-C cross-link formation was investigated computationally, and it was determined that more stable and longer-lived aromatic Cβ radicals correlated with ether formation. Further, molecular docking and transition state structures based on high-level quantum mechanical calculations support the different indole connectivity observed for ether (Trp-C7) and C-C (Trp-C6) cross-links. Finally, mutational analysis and protein structural predictions identified substrate residues that govern engagement to DarE. Our work informs on darobactin scaffold engineering and further unveils the underlying principles of rSAM catalysis.

Gallic acid improves color quality and stability of red wine via physico-chemical interaction and chemical transformation as revealed by thermodynamics, real wine dynamics and benchmark quantum mechanical calculations

The aim of this study was to explore the copigmentation effect of gallic acid on red wine color and to dissect its mechanism at the molecular level. Three-dimensional studies, e.g., in model wine, in real wine and in silico, and multiple indicators, e.g., color, spectrum, thermodynamics and phenolic dynamics, were employed. The results showed that gallic acid significantly enhanced the color quality and stability of red wine. Physico-chemical interactions and chemical transformations should be the most likely mechanism, and physico-chemical interactions are also a prerequisite for chemical transformations. QM calculations of the physico-chemical interactions proved that the binding between gallic acid and malvidin-3-O-glucoside is a spontaneous exothermic reaction driven by hydrogen bonding and dispersion forces. The sugar moiety of malvidin-3-O-glucoside and the phenolic hydroxyl groups of gallic acid affect the formation of hydrogen bonds, while the dispersion interaction was related to the stacking of the molecular skeleton.

Copper(II) coordination to the intrinsically disordered region of SARS-CoV-2 Nsp1

The intrinsically disordered C-terminal peptide region of severe acute respiratory syndrome coronavirus 2 nonstructural protein-1 (Nsp1-CT) inhibits host protein synthesis by blocking messenger RNA (mRNA) access to the 40S ribosome entrance tunnel. Aqueous copper(II) ions bind to the disordered peptide with micromolar affinity, creating a possible strategy to restore protein synthesis during host infection. Electron paramagnetic resonance (EPR) and tryptophan fluorescence measurements on a 10-residue model of the disordered protein region (Nsp1-CT10), combined with advanced quantum mechanics calculations, suggest that the peptide binds to copper(II) as a multidentate ligand. Two optimized computational models of the copper(II)-peptide complexes were derived: One corresponding to pH 6.5 and the other describing the complex at pH 7.5 to 8.5. Simulated EPR spectra based on the calculated model structures are in good agreement with experimental spectra.

The polyelectrolyte as corrosion inhibitor for the aluminum anode in alkaline-based primary battery: A comparative study with its monomer

In this work, the corrosion inhibition effect of the polyelectrolyte, poly(diallyl dimethylammonium chloride) (PDDA), as an additive in the alkaline Al-air battery is described and compared with the monomer dimethyl diallyl ammonium chloride (DMDAAC). Electrochemical measurement and morphology analysis are employed to characterize the inhibition effects of the additives. Additionally, the discharge characteristics of the battery are explored, and the capacity density is derived. These results demonstrate that the polymer additive suppresses Al samples' corrosion process more effectively than DMDAAC. The adsorption mechanism is proposed based on the Freundlich adsorption isotherm theory and quantum mechanical calculation.

Detecting Moisture in Building Materials and Commercial Food adducts by 2-Hydroxy-naphthaldehyde Derived Chromo-Fluorogenic Chemosensor.

A great deal of effort has been put into developing a novel and cost-effective molecular probe for selective and sensitive recognition of trace amounts of water in organic solvents due to their tremendous advantages in industrial, pharmaceutical, and laboratory-scale chemistry. Herein, a cost-effective chemosensor L has been designed and studied for the detection of trace amounts of water. The addition of water to the DMSO solution of L exhibited an enhancement of fluorescence emission at 460nm along with a color change from green to colorless. The spectral and color changes occurred due to the self-aggregation of L. The interaction between water and L was performed by dynamic light scattering (DLS), scanning electron microscope (SEM) and finally complemented by quantum mechanical calculation. The detection limit was found to be 0.0093 wt% in DMSO. The L also exhibits a fast visual response and is effectively applied to detect trace amounts of moisture in various food materials (salt, sugar, wheat and honey) and building materials (cement, fly ash, limestone and sand).

Quantum Monte Carlo Simulations of the Vibrational Wavefunction of the Aromatic Cyclo[10]carbon Using a Full Dimensional Permutationally Invariant Potential Energy Surface.

New experimental measurements [Sun et al., Nature 2023, 623, 972] of the cyclic C10 reveal a cumulenic pentagon-like D5h structure at ∼5 K. However, the long-standing presumption that a large zero-point vibrational energy combined with an extremely flat D5h ↔ D10h ↔ D5h isomerization pathway washes out the pentagonal D5h structure and yields a symmetric D10h decagon remains at odds with the experiment. We resolve this issue with our fitting approach based on a bond-order charge-density matrix expressed in permutationally invariant polynomials. We train the model on τHCTH/cc-pVQZ data morphed to reproduce a relativistic all-electron CCSDT(Q)/CBS D5h-D10h potential energy barrier (benchmarked previously by others). Large scale diffusion Monte Carlo simulations in full dimensionality show that the vibrational ground state of C10 has compositional character of more than 96% D5h, fully reflecting the experimental imaging data. Quantum mechanical variational calculations in 1-D further suggest persistence of the D5h symmetry structure at higher temperatures.

FFParam-v2.0: A Comprehensive Tool for CHARMM Additive and Drude Polarizable Force-Field Parameter Optimization and Validation.

Developing production quality CHARMM force-field (FF) parameters is a very detailed process involving a variety of calculations, many of which are specific for the molecule of interest. The first version of FFParam was developed as a standalone Python package designed for the optimization of electrostatic and bonded parameters of the CHARMM additive and polarizable Drude FFs by using quantum mechanical (QM) target data. The new version of FFParam has multiple new capabilities for FF parameter optimization and validation, with an emphasis on the ability to use condensed-phase target data in optimization. FFParam-v2 allows optimization of Lennard-Jones (LJ) parameters using potential energy scans of interactions between selected atoms in a molecule and noble gases, viz., He and Ne, and through condensed-phase calculations, from which experimental observables such as heats of vaporization and free energies of solvation may be obtained. This functionality serves as a gold standard for both optimizing parameters and validating the performance of the final parameters. A new bonded parameter optimization algorithm has been introduced to account for simultaneously optimizing multiple molecules sharing parameters. FFParam-v2 also supports the comparison of normal modes and the potential energy distribution of internal coordinates towards each normal mode obtained from QM and molecular mechanics calculations. Such comparison capability is vital to validate the balance among various bonded parameters that contribute to the complex normal modes of molecules. User interaction has been extended beyond the original graphical user interface to include command-line interface capabilities that allow for integration of FFParam in workflows, thereby facilitating the automation of parameter optimization. With these new functionalities, FFParam is a more comprehensive parameter optimization tool for both beginners and advanced users.