Quantum Mechanical Simulations Research Articles

Using Label-Free Raman Spectroscopy Integrated with Microfluidic Chips to Probe Ferroptosis Networks in Cells.

Ferroptosis, a regulated form of cell death driven by oxidative stress and lipid peroxidation, has emerged as a pivotal research focus with implications across various cellular contexts. In this study, we employed a multifaceted approach, integrating label-free Raman spectroscopy and microfluidics to study the mechanisms underpinning ferroptosis. Our investigations included the ferroptosis initiation based on the changes in the lipid Raman band at 1436 cm-1 under different cellular states, the generation of reactive oxygen species (ROS), lipid peroxidation, DNA damage/repair, and mitochondrial dysfunction. Importantly, our work highlighted the dynamic role of vital cellular components, such as nicotinamide adenine dinucleotide phosphate hydrogen (NADPH), ferredoxin clusters, and other key factors such as glutathione peroxidase 4 and nuclear factor erythroid 2, which collectively influenced cellular responses to redox imbalance and oxidative stress. Quantum mechanical (QM) and molecular docking simulations (MD) provided further evidence of interactions between the ferredoxin (containing 4Fe-4S clusters), NADPH, and ROS, which led to the production of reactive Fe species in the cells. As such, our approach not only offered a real-time, multidimensional perspective on ferroptosis but also provided valuable methods and insights for therapeutic interventions in diverse biomedical contexts.

Adsorptive Characteristic Analysis of Graphene Oxide for Hydrogen Sulfide using Quantum Mechanical Simulation

Adsorptive Characteristic Analysis of Graphene Oxide for Hydrogen Sulfide using Quantum Mechanical Simulation

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.

Bending-induced enhanced spatial separation of dopants and long-lived conventional nanoribbon p-n junctions.

The spatial separation of dopants is crucial in extending the lifetime of nanoribbon p-n junctions, which is traditionally realized via van der Waals heterostructures at a high cost. In this study, we employ atomistic quantum mechanical simulations to demonstrate that a simple in-plane bending deformation can lead to an enhanced doping preference in conventional nanoribbons. Dopants with larger atomic sizes than those of host atoms tend to reside on the tensile side close to the outermost edge of the bent nanoribbons, while dopants with smaller atomic sizes than those of host atoms tend to reside on the compressive side close to the innermost edge of the bent nanoribbons. We also show that this doping preference induces an enhanced spatial separation of n-type and p-type dopants with different atomic sizes. As conventional nanoribbons are easier to synthesize and cost-effective, our results provide a pathway for modulating dopant distribution and designing long-lived nanoribbon p-n junctions via inhomogeneous strain engineering.

Vibronic coupling in the energetically six lowest electronic states of oxirane radical cation.

Multi-dimensional quantum mechanical simulations are carried out to understand the multi-state and multi-mode vibronic interactions in the first six low-lying viz., X̃2B1, Ã2A1, B̃2B2, C̃2A2, D̃2A1, and Ẽ2B1 electronic states of c-C2H4O·+. Vibronic coupling theory is applied to study interactions among electronic states using symmetry selection rules. A model 6 × 6 diabatic electronic Hamiltonian is constructed. The parameters of the diabatic Hamiltonian are estimated by performing extensive abinitio electronic structure calculations, using the EOM-IP-CCSD method. The nuclear dynamics calculations are performed with both time-independent and time-dependent quantum mechanical methods. The calculated vibronic structures of six electronic states are found to be in excellent agreement with the available experimental findings. Progressions found in the theoretical spectrum are assigned in terms of vibrational modes. It is found that extremely strong vibronic interactions among the X̃2B1-Ã2A1, B̃2B2-C̃2A2, and D̃2A1-Ẽ2B1 electronic states results into highly overlapping vibronic bands due to multiple multi-state conical intersections. The impact of associated nonadiabatic effects on the vibronic structure and dynamics of the mentioned electronic states is examined at length. Interesting comparison is made with the results obtained for the isomeric acetaldehyde radical cation.

Ionic conduction and cathodic properties of CaMO3 (M=Fe and Mn) electrode materials via molecular dynamics and first-principles simulations

Calcium-ion(Ca-ion) batteries are gaining ever-increasing attention for next-generation energy storage systems due to affordability, highly abundant, high energy density, high theoretical capacity, and low redox potential close to Li-ion. In this work, we deployed the first-principles and classical molecular dynamics simulations to investigate the electronic and diffusive properties of isostructural ternary perovskite CaMO3 (M= Fe and Mn). The transport properties at various temperatures from ion dynamics and electronic properties of CaMO3 perovskites are examined using classical molecular dynamics and quantum mechanical simulations, respectively. We present the microscopic origin of the diffusion of multivalent ions like Ca2+ within the crystal structure of perovskite material and the effects of two transition metals, manganese and iron. Dynamic studies of Ca-ions were performed using molecular dynamic simulation, which depicts the diffusivity and conductivity of Ca-ion in CaMO3 material. We find that the diffusivity in both the crystals increases with temperature; as a result, conductivity increases. Among both the crystals, CaFeO3 requires less activation energy for diffusion and ionic conduction than CaMnO3. Using density functional theory, we calculated specific capacity, electronic density of states, phase stability and equilibrium cell voltage, and charge transfer process during intercalation-deintercalation from first-principles calculations. The electronic behavior of these materials shows that CaFeO3 has better electronic and transport properties than CaMnO3.

Neural net analysis of NMR spectra from strongly-coupled spin systems

Extracting parameters such as chemical shifts and coupling constants from proton NMR spectra is often a first step in using spectra for compound identification and structure determination. This can become challenging when scalar couplings between protons are comparable in size to chemical shift differences (strongly coupled), as is often the case with low-field (bench top) spectrometers. Here we explore the potential utility of AI methods, in particular neural networks, for extracting parameters from low-field spectra. Rather than seeking large experimental sets of spectra for training a network, we chose quantum mechanical simulation of sets, something that is possible with modern software packages and computer resources. We show that application of a network trained on 2-D J-resolved spectra and applied to a spectrum of iduronic acid, shows some promise, but also meets with some obstacles. We suggest that these may be overcome with improved pulse sequences and more extensive simulations.

Investigating structural, optoelectronic, and mechanical properties of novel Tungsten-based oxides double-perovskites compounds Sr2XWO6 (X= Mn, Fe): A DFT approach

We employ PF-LAPW (full-potential linear augmented plane-wave) integrated within DFT (density functional theory) for a comprehensive exploration of the structural, optoelectronic, and mechanical properties of novel Tungsten-based oxides double-perovskites compounds Sr2XWO6 (X= Mn, Fe) through the quantum mechanical WIEN2K simulation package. All the computations are done by considering TB-mBJ (Tran-Blaha modified Becke-Johnson potential) and GGA (generalized gradient approximation) as the exchange-correlation potential. The stability and formation of the Sr2XWO6 (X= Mn, Fe) compounds in a cubic structure are validated through structural optimization and the tolerance factor. The analysis of elastic constants and Born-Huang stability criteria predict that the interested oxide double perovskites are ductile, mechanically stable, hard to scratch, anisotropic, and possess a dominant covalent bonding. Both Sr2MnWO6 and Sr2FeWO6 materials are indirect semiconductors with a band gap of 2.05 eV for Sr2FeWO6 and 1.98 eV for Sr2MnWO6 from W-L symmetry points within the 1st Brillouin zone. The small values of band gap and various parameters of optical properties, specifically the broad monotonically increasing absorption spectra, reveal that novel Tungsten-based oxides double-perovskites compounds Sr2XWO6 (X= Mn, Fe) exhibit great potential for optoelectronic properties.

Preparation of red mud derived eggshell coupling adsorbent and study on carbon dioxide capture performance based on experiment and density functional theory simulation

Preparing advanced CO2 capture materials is crucial for mitigating carbon emissions and alleviating global warming. Calcium-based adsorbents have attracted much attention due to their excellent environmental performance and high theoretical CO2 adsorption capacity. However, its poor cycling stability limits its widespread application. In this study, a red mud derived eggshell coupled CO2 adsorbent (RM/CaO) was prepared using solid waste RM and eggshell. The structure, CO2 capture performance, and micro-mechanism of the adsorbent were evaluated through macro micro-experiments combined with quantum mechanics simulations, to improve the adsorption performance of calcium-based adsorbents and achieve waste resource utilisation—an active, open area of research. The 1-1RM/CaO adsorbent had a specific surface area of 10.62 m2/g and a spatial structure with fused cross-linking layers. Its CO2 saturation adsorption capacity was 0.481 g/g; 171.43 % that of pure CaO. High level cycling stability can still be maintained after 15 cycles of CO2 adsorption desorption. Quantum mechanics simulations revealed that the CO2 adsorption energy on the RM/CaO (200) crystal plane can be enhanced to −8.25 eV. This indicates that the interaction between RM/CaO atoms is stronger, which is enhances the CO2 adsorption. This study optimized environmental and economic benefits by utilizing waste resources, deepened understanding of the interaction mechanism between CO2 adsorbents, and provided theoretical guidance for designing as well as optimizing future adsorbents.

Monte Carlo QM/MM simulation studies of the Cannizzaro reaction in ionic liquids for improved biofuel production.

The conversion of biomass to 5-hydroxymethylfurfural (HMF) holds substantial promise as a renewable energy source. Notably, HMF can be transformed into 2,5-bis(hydroxymethyl)furan (BHMF), a crucial reactant in biofuel production, but requires harsh operating conditions, H2, and precious metal catalysts. A recently reported Cannizzaro reaction of HMF to BHMF, characterized by its efficiency, mild conditions, and eco-friendliness, instead employed ionic liquids (ILs) to achieve high yields. In this study, combined quantum mechanical and molecular mechanical (QM/MM) simulations in conjunction with Metropolis Monte Carlo statistical mechanics and free-energy perturbation theory utilized M06-2X/6-31+G(d), PDDG/PM3, and the OPLS-VSIL force field to uncover important solute-solvent interactions present in the HMF to BHMF reaction pathway. The Cannizzaro reaction was examined in water and in five ILs composed of the 1-butyl-3-methylimidazolium [BMIM] cation coupled to hexafluorophosphate, tetrafluoroborate, thiocyanate, chloride, and bromide. Energetic and structural analysis of the rate-determining hydride transfer between HMF and the hydride-donor anion HMFOH- attributed the enhanced reactivity to highly organized solvent interactions featuring (1) hydrogen bonding between the ring protons of [BMIM] and the negatively charged carbonyl oxygen atoms on the transition structure, (2) favorable electrostatic interactions between the IL anions and solute hydroxyl groups, and (3) beneficial π-π stacking interactions between [BMIM] and the two aromatic rings present in HMF and HMFOH-.

Mechanism of Rejuvenation in Aged SBS-Modified Asphalt by Density Functional Theory

As a large area of SBS-modified asphalt pavement entered the maintenance period, the aging and rejuvenation of SBS-modified asphalt have attracted attention in recent years. In order to further study the rejuvenation of aged SBS-modified asphalt, both rheological experiments and quantum mechanical simulations were used. Complex shear modulus (G*) and phase angle (δ) were used to analyze the rejuvenation effect of aged SBS-modified asphalt. Electron density, binding energy (Ebinding), and charge transfer number (Qtransfer) were used to observe the process of rejuvenation in aged SBS-modified asphalt. The results show that compared to asphalt components, SBS polymer was the least stable and most susceptible to breaking. After oxidative aging, SBS polymer with its aging products could impair the rejuvenation in aged asphalt. The interaction between aromatic components in rejuvenator and asphaltenes in aged asphalt was unstable and could be influenced by asphalt aging level. The interaction between heavy component molecules in aged asphalt with saturate component molecules in rejuvenator are closer than those with aromatic components molecules. The binding energies between saturate components in rejuvenator and asphaltenes in aged asphalt could be served as an evaluation indicator of rejuvenation.

Quantum-Mechanics Calculations Elucidate Skin-Sensitizing Pharmaceutical Compounds.

Skin sensitization is a critical end point in occupational toxicology that necessitates the use of fast, accurate, and affordable models to aid in establishing handling guidance for worker protection. While many in silico models have been developed, the scarcity of reliable data for active pharmaceutical ingredients (APIs) and their intermediates (together regarded as pharmaceutical compounds) brings into question the reliability of these tools, which are largely constructed using publicly available nonspecialty chemicals. Here, we present the quantum-mechanical (QM) Computer-Aided Discovery and REdesign (CADRE) model, which was developed with the bioactive and structurally complex chemical space in mind by relying on the fundamentals of chemical interactions in key events (versus structural attributes of training-set data). Validated in this study on 345 APIs and intermediates, CADRE achieved 95% accuracy, sensitivity, and specificity and a combined 79% accuracy in assigning potency categories compared to the mouse local lymph node assay data. We show how historical outcomes from CADRE testing in the pharmaceutical space, generated over the past 10 years on ca. 2500 chemicals, can be used to probe the relationships between sensitization mechanisms (or the underlying chemical classes) and the probability of eliciting a sensitization response in mice of a given potency. We believe this information to be of value to both practitioners, who can use it to quickly screen and triage their data sets, as well as to model developers to fine-tune their structure-based tools. Lastly, we leverage our experimentally validated subset of APIs and intermediates to show the importance of dermal permeability on the sensitization potential and potency. We demonstrate that common physicochemical properties used to assess permeation, such as the octanol-water partition coefficient and molecular weight, are poor proxies for the more accurate energy-pair distributions that can be computed from mixed QM and classical simulations using model representations of the stratum corneum.

Efficient Mixed-Precision Matrix Factorization of the Inverse Overlap Matrix in Electronic Structure Calculations with AI-Hardware and GPUs.

In recent years, a new kind of accelerated hardware has gained popularity in the artificial intelligence (AI) community which enables extremely high-performance tensor contractions in reduced precision for deep neural network calculations. In this article, we exploit Nvidia Tensor cores, a prototypical example of such AI-hardware, to develop a mixed precision approach for computing a dense matrix factorization of the inverse overlap matrix in electronic structure theory, S-1. This factorization of S-1, written as ZZT = S-1, is used to transform the general matrix eigenvalue problem into a standard matrix eigenvalue problem. Here we present a mixed precision iterative refinement algorithm where Z is given recursively using matrix-matrix multiplications and can be computed with high performance on Tensor cores. To understand the performance and accuracy of Tensor cores, comparisons are made to GPU-only implementations in single and double precision. Additionally, we propose a nonparametric stopping criteria which is robust in the face of lower precision floating point operations. The algorithm is particularly useful when we have a good initial guess to Z, for example, from previous time steps in quantum-mechanical molecular dynamics simulations or from a previous iteration in a geometry optimization.

Quantum nature of reactivity modification in vibrational polariton chemistry.

In this work, we present a mixed quantum-classical open quantum system dynamics method for studying rate modifications of ground-state chemical reactions in an optical cavity under vibrational strong-coupling conditions. In this approach, the cavity radiation mode is treated classically with a mean-field nuclear force averaging over the remaining degrees of freedom, both within the system and the environment, which are handled quantum mechanically within the hierarchical equations of motion framework. Using this approach, we conduct a comparative analysis by juxtaposing the mixed quantum-classical results with fully quantum-mechanical simulations. After eliminating spurious peaks that can occur when not using the rigorous definition of the rate constant, we confirm the crucial role of the quantum nature of the cavity radiation mode in reproducing the resonant peak observed in the cavity frequency-dependent rate profile. In other words, it appears necessary to explicitly consider the quantized photonic states in studying reactivity modification in vibrational polariton chemistry (at least for the model systems studied in this work), as these phenomena stem from cavity-induced reaction pathways involving resonant energy exchanges between photons and molecular vibrational transitions.

Molecular Docking, Quantum Mechanics and Molecular Dynamics Simulation of Anti-CAD Drugs Against High-Risk Xanthine Dehydrogenase Variants Associated with Oxidative Stress Pathways

Xanthine dehydrogenase (XDH) contributes significantly to generating reactive oxygen species in coronary artery disease (CAD). XDH has been proposed as a therapeutic target, but its genetic variants could affect protein structure and drug response. We aimed to assess protein structure modification occur due to genetic variants and to screen 215 CAD drugs for their utility in personalized CAD treatment against the XDH variants. A series of computational methods were implemented to identify pathogenic variants that cause XDH structure instability localized at the conserved regions contributing to functional significance. Then, the XDH structures with the pathogenic variants were modeled using two different approaches to select the best models for docking with the CAD drugs. Finally, the stability of the docked complexes and their ability to transfer electrons were evaluated using molecular dynamics (MD) simulations and quantum mechanics/molecular mechanics (QM/MM) calculation. Among 751 variants examined; R149C and Q919R showed high pathogenicity, localized in conserved regions could alter protein structure and function. Further, docking of CAD drugs against XDH (native, R149C and Q919R) showed vericiguat with higher affinity, ranging from -7.95 kcal/mol to -10.41 kcal/mol, than the well-known XDH inhibitor (febuxostat, -5.73 kcal/mol to -8.35 kcal/mol). This indicates that vericiguat will be effective in CAD treatment, regardless of the XDH variants. Additionally, MD simulation and QM/MM confirmed vericiguat stability and electron transfer ability to form hydrogen bonds with the XDH protein. In conclusion, vericiguat will be beneficial for the personalized treatment of CAD by inhibiting XDH variants. Additional clinical studies are necessary to confirm our findings.

Application of Cr2Si2Te6 saturable absorber in Er-doped fiber laser for generating dual-wavelength mode-locked pulse

As a typical two-dimensional (2D) ferromagnetic insulator (FI), the Cr2Si2Te6 (CST) has performance ferromagnetic properties. The previous investigation has shown that quantum mechanical simulation can get structure and electronic properties of CST, and the indirect gap value of CST is 0.6 eV by establishing its layered calculation. It implies that the CST is an excellent optical modulator due to larger infrared radiation absorption interval. Based on that, some groups conducted the research of fiber laser based on CST saturable absorber (SA). However, the exploration and application of 2D CST in optics is still in the early stage. In this investigation, the CST was utilized as a SA in an Er-doped fiber laser. The dual-wavelength mode-locked pulse could be observed when the pump power was adjusted from 25 to 140 mW. The CST was applied in Er-doped fiber as SA for generating dual-wavelength mode-locked pulse for the first time. It exhibits performance optical properties that provide a significant reference for exploring the application of 2D materials in ultrafast laser.

Consideration of the effect of nanoscale porosity on mass transport phenomena in PECVD coatings

Here we show a novel approach to characterize the gas transfer behavior of silicon-oxide (SiO x ) coatings and explain the underlying dynamics. For this, we investigate the coating on a nm-scale both by measurement and simulation. Positron annihilation spectroscopy (PAS) and quantum mechanical electronic structure-based molecular dynamics simulations are combined to characterize the porous landscape of SiO x coatings. This approach analyses the influence of micropores smaller than 2 nm in diameter on gas permeation which are difficult to study with conventional methods. We lay out the main pore diameter ranges and their associated porosity estimates. An influence of layer growth on pore size and porosity was found, with an increased energy input during layer deposition leading to smaller pore sizes and a reduced porosity. The molecular dynamics simulations quantify the self-diffusion of oxygen and water vapor through those PAS deducted micropore ranges for hydrophilic and hydrophobic systems. The theoretical pore size ranges are fitting to our PAS results and complete them by giving diffusion coefficients. This approach enables detailed analysis of pore morphology on mass transport through thin film coatings and characterization of their barrier or membrane performance. This is a crucial prerequisite for the development of an exhaustive model of pore dominated mass transports in PECVD coatings.

Bartender: Martini 3 Bonded Terms via Quantum Mechanics-Based Molecular Dynamics.

Coarse-grained (CG) molecular dynamics (MD) simulations have grown in applicability over the years. The recently released version of the Martini CG force field (Martini 3) has been successfully applied to simulate many processes, including protein-ligand binding. However, the current ligand parametrization scheme is manual and requires an a priori reference all-atom (AA) simulation for benchmarking. For systems with suboptimal AA parameters, which are often unknown, this translates into a CG model that does not reproduce the true dynamical behavior of the underlying molecule. Here, we present Bartender, a quantum mechanics (QM)/MD-based parametrization tool written in Go. Bartender harnesses the power of QM simulations and produces reasonable bonded terms for Martini 3 CG models of small molecules in an efficient and user-friendly manner. For small, ring-like molecules, Bartender generates models whose properties are indistinguishable from the human-made models. For more complex, drug-like ligands, it is able to fit functional forms beyond simple harmonic dihedrals and thus better captures their dynamical behavior. Bartender has the power to both increase the efficiency and the accuracy of Martini 3-based high-throughput applications by producing numerically stable and physically realistic CG models.

Conformational Analysis of 1,3-Difluorinated Alkanes.

Fluorine substitution can have a profound impact on molecular conformation. Here, we present a detailed conformational analysis of how the 1,3-difluoropropylene motif (-CHF-CH2-CHF-) determines the conformational profiles of 1,3-difluoropropane, anti- and syn-2,4-difluoropentane, and anti- and syn-3,5-difluoroheptane. It is shown that the 1,3-difluoropropylene motif strongly influences alkane chain conformation, with a significant dependence on the polarity of the medium. The conformational effect of 1,3-fluorination is magnified upon chain extension, which contrasts with vicinal difluorination. Experimental evidence was obtained from NMR analysis, where polynomial complexity scaling simulation algorithms were necessary to enable J-coupling extraction from the strong second-order spectra, particularly for the large 16-spin systems of the difluorinated heptanes. These results improve our understanding of the conformational control toolkit for aliphatic chains, yield simple rules for conformation population analysis, and demonstrate quantum mechanical time-domain NMR simulations for liquid state systems with large numbers of strongly coupled spins.

The effect of hypo‐sulfonamide accelerators on the induction period of rubber vulcanization based on experiments and molecular simulations

AbstractAccelerators are indispensable additives in rubber vulcanization reactions. Hypo‐sulfonamide accelerators are widely used due to their fast vulcanization speed. However, the short vulcanization induction period compromises the processing safety of rubber. In this paper, we incorporated experiments with molecular simulations to investigate the underlying reasons for the different effects of various hypo‐sulfonamide accelerators The vulcanization induction period of each accelerator was investigated according to the vulcanization curves. Furthermore, the corresponding reaction mechanism was explored from the molecular scale through quantum mechanical and molecular dynamics simulations. Subsequently, the research focus was discussed in depth. The compatibility relationship between the accelerators and the rubber materials was verified through the crosslinking density test, and a coincidence between the experimental and simulation results was found. This study guides the selection and improvement of hypo‐sulfonamide accelerators and corroborates the factors influencing the vulcanization induction period of natural rubber by accelerators.Highlights Reactivity of accelerators calculated by quantum mechanical simulations. Difference in solubility parameter characterizes accelerator/NR compatibility. Mobility and diffusion coefficient reflect the diffusion ability of the promoter. Molecular simulation results are consistent with experimental results.