Classical Molecular Simulations Research Articles

Molecular dynamics simulations for the prediction of thermophysical properties of plutonium-based molten salts

Molten salt nuclear reactors are promising technologies for sustainable energy sources. In this context, understanding the physicochemical properties of molten salts is essential to the development, usage, and maintenance of reactors. Classical molecular simulations allow estimating the macroscopic properties of molten salts at a relatively low computational cost. In this work, we develop a new force field for plutonium-based molten salts. We validate our classical model by comparing molecular dynamics results with experimental measurements, obtaining a quantitative agreement. Our work demonstrates the reliability and transferability of classical force fields to represent the physicochemical properties of molten salts.

Electrochemical rewiring through quantum conductance effects in single metallic memristive nanowires.

Memristive devices have been demonstrated to exhibit quantum conductance effects at room temperature. In these devices, a detailed understanding of the relationship between electrochemical processes and ionic dynamic underlying the formation of atomic-sized conductive filaments and corresponding electronic transport properties in the quantum regime still represents a challenge. In this work, we report on quantum conductance effects in single memristive Ag nanowires (NWs) through a combined experimental and simulation approach that combines advanced classical molecular dynamics (MD) algorithms and quantum transport simulations (DFT). This approach provides new insights on quantum conductance effects in memristive devices by unravelling the intrinsic relationship between electronic transport and atomic dynamic reconfiguration of the nanofilment, by shedding light on deviations from integer multiples of the fundamental quantum of conductance depending on peculiar dynamic trajectories of nanofilament reconfiguration and on conductance fluctuations relying on atomic rearrangement due to thermal fluctuations.

Accessible Molecular System Creator: Building Molecular Configurations Based on the Inaccessible Molecular Volume and Accessible Molecular Surface via Static Monte Carlo Sampling.

Monte Carlo (MC) stochastic sampling is a powerful tool in classical molecular simulations that directly connects the observable macroscopic properties of matter and the underlying atomistic interactions. This connection operates within the framework of the statistical mechanics proposed by Gibbs. Most MC simulations are "dynamic," creating statistical ensembles of microstates via a Markovian chain, where each microstate in the ensemble depends only on its previous microstate. Herein, we re-examine an alternative form of MC that generates ensemble members through a "static" approach, building molecular systems stepwise. The basic theory for such an approach traces back to Rosenbluth and Rosenbluth, who proposed "static" stepwise sampling of a polymeric chain. It is almost as old as the Metropolis importance sampling approach used in dynamic MC, although the latter has been considerably more popular than the former. Herein, we address the main obstacle in static MC that has hindered the widespread adoption of Rosenbluth-based approaches in atomistic simulations. The obstacle lies in mapping the molecular accessible volume for adding a molecule in a Rosenbluth-like static sampling of atomistic configurations. We demonstrate a breakthrough by leveraging the ability to analytically map the inaccessible molecular volume and the accessible molecular surface owing to interatomically excluded volume interactions. This advance substantially enhances the ability to create molecular samples using a Rosenbluth-like static building process. The proposed approach can be used as a tool for creating initial configurations in MC or molecular dynamics simulations─a field where Rosenbluth-like static building has been applied. Additionally, this approach can be used as the first step in a perturbation scheme that accurately estimates free energy differences by estimating the chemical work related to molecule addition, removal, or reinsertion within the context of free energy perturbation schemes employed in molecular simulations.

MBX: A many-body energy and force calculator for data-driven many-body simulations.

Many-Body eXpansion (MBX) is a C++ library that implements many-body potential energy functions (PEFs) within the "many-body energy" (MB-nrg) formalism. MB-nrg PEFs integrate an underlying polarizable model with explicit machine-learned representations of many-body interactions to achieve chemical accuracy from the gas to the condensed phases. MBX can be employed either as a stand-alone package or as an energy/force engine that can be integrated with generic software for molecular dynamics and Monte Carlo simulations. MBX is parallelized internally using Open Multi-Processing and can utilize Message Passing Interface when available in interfaced molecular simulation software. MBX enables classical and quantum molecular simulations with MB-nrg PEFs, as well as hybrid simulations that combine conventional force fields and MB-nrg PEFs, for diverse systems ranging from small gas-phase clusters to aqueous solutions and molecular fluids to biomolecular systems and metal-organic frameworks.

Interaction of Nitrite Ions with Hydrated Portlandite Surfaces: Atomistic Computer Simulation Study.

The nitrite admixtures in cement and concrete are used as corrosion inhibitors for steel reinforcement and also as anti-freezing agents. The characterization of the protective properties should account for the decrease in the concentration of free NO2- ions in the pores of cement concretes due to their adsorption. Here we applied the classical molecular dynamics computer simulation approach to quantitatively study the molecular scale mechanisms of nitrite adsorption from NaNO2 aqueous solution on a portlandite surface. We used a new parameterization to model the hydrated NO2- ions in combination with the recently upgraded ClayFF force field (ClayFF-MOH) for the structure of portlandite. The new NO2- parameterization makes it possible to reproduce the properties of hydrated NO2- ions in good agreement with experimental data. In addition, the ClayFF-MOH model improves the description of the portlandite structure by explicitly taking into account the bending of Ca-O-H angles in the crystal and on its surface. The simulations showed that despite the formation of a well-structured water layer on the portlandite (001) crystal surface, NO2- ions can be strongly adsorbed. The nitrite adsorption is primarily due to the formation of hydrogen bonds between the structural hydroxyls on the portlandite surface and both the nitrogen and oxygen atoms of the NO2- ions. Due to that, the ions do not form surface adsorption complexes with a single well-defined structure but can assume various local coordinations. However, in all cases, the adsorbed ions did not show significant surface diffusional mobility. Moreover, we demonstrated that the nitrite ions can be adsorbed both near the previously-adsorbed hydrated Na+ ions as surface ion pairs, but also separately from the cations.

Molecular simulations of alkali metal halide hydrates

It has been known that classical molecular simulations of concentrated aqueous electrolyte solutions are limited by the ability of microscopic models (force fields) to predict the correct values of salt solubility, which also requires their ability to faithfully model crystalline salts. Previous simulation studies have often focused on the solubility of anhydrous crystalline salts, but virtually never on crystalline hydrates, except for hydrohalite, NaCl⋅2H2O, despite there are at least 23 experimentally known different hydrates that can precipitate from alkali-halide solutions. This work attempts to fill this gap in hydrate simulation studies by systematically investigating the ability of the best force fields selected to qualitatively capture the stability of the individual phases of various alkali-halide hydrates and to quantitatively predict their lattice parameters. First, we show that the nonpolarizable force fields studied often fail to model hydrates containing the Li+ cations, whereas the polarizable force fields recently refined by us are able to model all the hydrates except for LiCl⋅H2O. Second, we further refine our FFs for Li+ to yield stable LiCl⋅H2O. Third, our simulations clarify the positions of the Li+ cations in the β phases of LiBr⋅H2O and LiI⋅H2O, whose distributions were previously described only as stochastic. As a byproduct, a simple and reliable simulation methodology suitable also for complex polarizable models and nonorthorhombic crystal lattices is proposed and tested, based on simulations of finite crystals floating in vacuum.

Disulfide bond reduction and exchange in C4 domain of von Willebrand factor undermines platelet binding

BackgroundThe von Willebrand factor (VWF) is a key player in regulating hemostasis through adhesion of platelets to sites of vascular injury. It is a large, multi-domain, mechano-sensitive protein that is stabilized by a net of disulfide bridges. Binding to platelet integrin is achieved by the VWF-C4 domain, which exhibits a fixed fold, even under conditions of severe mechanical stress, but only if critical internal disulfide bonds are closed. ObjectiveTo determine the oxidation state of disulfide bridges in the C4 domain of VWF and implications for VWF’s platelet binding function. MethodsWe combined classical molecular dynamics and quantum mechanical simulations, mass spectrometry, site-directed mutagenesis, and platelet binding assays. ResultsWe show that 2 disulfide bonds in the VWF-C4 domain, namely the 2 major force-bearing ones, are partially reduced in human blood. Reduction leads to pronounced conformational changes within C4 that considerably affect the accessibility of the integrin-binding motif, and thereby impair integrin-mediated platelet binding. We also reveal that reduced species in the C4 domain undergo specific thiol/disulfide exchanges with the remaining disulfide bridges, in a process in which mechanical force may increase the proximity of specific reactant cysteines, further trapping C4 in a state of low integrin-binding propensity. We identify a multitude of redox states in all 6 VWF-C domains, suggesting disulfide bond reduction and swapping to be a general theme. ConclusionsOur data suggests a mechanism in which disulfide bonds dynamically swap cysteine partners and control the interaction of VWF with integrin and potentially other partners, thereby critically influencing its hemostatic function.

Gmak: A Parameter-Space Mapping Strategy for Force-Field Calibration.

In the context of classical molecular simulations, the accuracy of a force field is highly influenced by the values of the relevant simulation parameters. In this work, a parameter-space mapping (PSM) workflow is proposed to aid in the calibration of force-field parameters, based mainly on the following features: (i) regular-grid discretization of the search space; (ii) partial sampling of the search-space grid; (iii) training of surrogate models to predict the estimates of the target properties for nonsampled parameter sets; (iv) post hoc interpretation of the results in terms of multiobjective optimization concepts; (v) attenuation of statistical errors achieved via empiric extension of the duration of the simulations; (vi) iterative search-space translation according to a user-defined scalar objective function that measures the accuracy of the force field (e.g., the weighted root-mean-square deviation of the target properties relative to the reference data). This combination of features results in a hybrid of a single- and a multiobjective optimization strategy, allowing for the approximate determination of both a local minimum of the chosen objective function and its neighboring Pareto efficient points. The PSM workflow is implemented in the extensible Python program gmak, which is made available in the Git repository at http://github.com/mssm-labmmol/gmak. Using this implementation, the PSM workflow was tested in a proof-of-concept fashion in the recalibration of the Lennard-Jones parameters of the 3-point Optimal Point Charge (OPC3) water model for compatibility with the GROMOS treatment of nonbonded interactions. The recalibrated model reproduces typical pure-liquid properties with an accuracy similar to the original OPC3 model and represents a significant improvement relative to the Simple Point Charge (SPC) model, which is the official recommendation for simulations using GROMOS force fields.

Investigation of the Second Harmonic Generation at the Water-Vacuum Interface by Using Multi-Scale Modeling Methods.

Invited for this month's cover picture are Dr. Tárcius N. Ramos and Prof. Benoît Champagne at the University of Namur (Belgium). The cover picture shows the interfacial selectivity of second harmonic generation at the water-vacuum interface, which is targeted in this work. In more details, the molecular first hyperpolarizability responses have been calculated by combining classical molecular dynamics and quantum chemistry simulations, and our model was able to distinguish between the bulk and the interfacial contributions. Read the full text of their Research Article at 10.1002/open.202200045.

Collaborative Assessment of Molecular Geometries and Energies from the Open Force Field.

Force fields form the basis for classical molecular simulations, and their accuracy is crucial for the quality of, for instance, protein-ligand binding simulations in drug discovery. The huge diversity of small-molecule chemistry makes it a challenge to build and parameterize a suitable force field. The Open Force Field Initiative is a combined industry and academic consortium developing a state-of-the-art small-molecule force field. In this report, industry members of the consortium worked together to objectively evaluate the performance of the force fields (referred to here as OpenFF) produced by the initiative on a combined public and proprietary dataset of 19,653 relevant molecules selected from their internal research and compound collections. This evaluation was important because it was completely blind; at most partners, none of the molecules or data were used in force field development or testing prior to this work. We compare the Open Force Field "Sage" version 2.0.0 and "Parsley" version 1.3.0 with GAFF-2.11-AM1BCC, OPLS4, and SMIRNOFF99Frosst. We analyzed force-field-optimized geometries and conformer energies compared to reference quantum mechanical data. We show that OPLS4 performs best, and the latest Open Force Field release shows a clear improvement compared to its predecessors. The performance of established force fields such as GAFF-2.11 was generally worse. While OpenFF researchers were involved in building the benchmarking infrastructure used in this work, benchmarking was done entirely in-house within industrial organizations and the resulting assessment is reported here. This work assesses the force field performance using separate benchmarking steps, external datasets, and involving external research groups. This effort may also be unique in terms of the number of different industrial partners involved, with 10 different companies participating in the benchmark efforts.

Prenucleation at the Liquid/Substrate Interface: An Overview

Prenucleation refers to the phenomenon of substrate-induced atomic ordering in the liquid adjacent to the liquid/substrate interface at temperatures above the nucleation temperature. We investigated the effects of the physical and chemical properties of the substrate on prenucleation, using the classical molecular dynamics (MD) and ab initio MD simulations. We found that the physical origin of prenucleation is structural templating, which is affected significantly by the lattice misfit between the solid and the substrate, chemical interaction between the solid and the substrate, and the substrate surface roughness at the atomic level. Prenucleation ultimately determines the nucleation potency of a substrate and provides a precursor for heterogeneous nucleation at the nucleation temperature. In this paper, we provide an overview of the recent advances in the understanding of prenucleation made by the LiME Research Hub. After a brief review of the historical research on atomic ordering at the liquid/substrate interface in the literature, we present an overview of the recent advances in understanding prenucleation, covering the concept of prenucleation, the effect of temperature, lattice misfit and substrate chemistry, and substrate surface roughness at the atomic level. Our discussions will be focused on the effect of prenucleation on heterogeneous nucleation and its consequences on grain refinement.

Atomistic Mismatch Defines Energy-Structure Relationships during Oriented Attachment of Nanoparticles.

Oriented attachment is an important crystal growth pathway in nature and has been extensively exploited to develop hierarchically structured crystalline materials. Atomistic mismatch in the crystal structure of two particles in the solvent-separated state creates forces that drive particle motions enabling solvent expulsion and coalescence, but the relative magnitudes of the energy barriers for approach, rotation, and translation are not well-known. Here we use classical molecular simulations to calculate the potential of mean force for these three different motions for basal surface encounters of gibbsite nanoplatelets separated by one water layer. In all cases, the highest energy barrier is associated with removing this last water layer to enable jump to contact, even when coaligned. Mutual rotation is more probable than sliding motion, which are both much more probable than jump to contact. This work provides the first comparison on an equal footing of the energy-structure relationships for multiple alignment paths between solvent-separated particles in bulk aqueous solution.

Novel Spiro-pyrrolizidine-Oxindole and Spiropyrrolidine-Oxindoles: Green synthesis under Classical, Ultrasonic, and microwave conditions and Molecular docking simulation for antitumor and type 2 diabetes

Novel spiropyrrolizine / pyrrolidineoxindole moieties were synthesized chemo-, and regio-selectively in high yields from knoevenagel reaction of bis[arylmethylidene]piperidin-4-ones, isatin and L-proline or sarcosine under classical, ultrasonic, and microwave conditions. Seven derivatives of the synthesized dispiro-pyrrolizidine-oxindole and spiropyrrolidine were screened for their antitumor activity against two cell lines MCF-7 (breast cancer) and HEPG2 (liver cancer). The results of biological activity indicated that the tested derivatives showed potent activity against breast cancer cell MCF-7. Molecular docking simulation screening studies of the synthesized products with each of the receptors of (3hb5) for breast cancer and (4k9g) for liver cancer and their interaction with 1H5U of glycogen phosphorylase B, type 2 diabetes drug were examined. The docking study of dispiro-pyrrolizidine-oxindole and spiropyrrolidine showed promising results with several derivatives.

VOC Mixture Sensing with a MOF Film Sensor Array: Detection and Discrimination of Xylene Isomers and Their Ternary Blends.

Detection and recognition of volatile organic compounds (VOCs) are crucial in many applications. While pure VOCs can be detected by various sensors, the discrimination of VOCs in mixtures, especially of similar molecules, is hindered by cross-sensitivities. Isomer identification in mixtures is even harder. Metal-organic frameworks (MOFs) with their well-defined, nanoporous, and versatile structures have the potential to improve the VOC sensing performance by tailoring the adsorption affinities. Here, we detect and identify ternary xylene isomer mixtures by using an array of six gravimetric, quartz crystal microbalance (QCM)-based sensors coated with selected MOF films with different isomer affinities. We use classical molecular simulations to provide insights into the sensing mechanism. In addition to the attractive interaction between the analytes and the MOF film, the isomer discrimination is caused by the rigid crystalline framework sterically controlling the access of the isomers to different adsorption sites in the MOFs. The sensor array has a very low limit of detection of 1 ppm for each pure isomer and allows the isomer discrimination in mixtures. At 100 ppm, 16 different ternary o-p-m-xylene mixtures were identified with high classification accuracy (96.5%). This work shows the unprecedented performance of MOF-sensor arrays, also referred to as MOF-electronic nose (MOF-e-nose), for sensing VOC mixtures. Based on the study, guidelines for detecting and discriminating complex mixtures of volatile molecules are also provided.

Never Cared for What They Do: High Structural Stability of Guanine-Quadruplexes in the Presence of Strand-Break Damage.

DNA integrity is an important factor that assures genome stability and, more generally, the viability of cells and organisms. In the presence of DNA damage, the normal cell cycle is perturbed when cells activate their repair processes. Although efficient, the repair system is not always able to ensure complete restoration of gene integrity. In these cases, mutations not only may occur, but the accumulation of lesions can either lead to carcinogenesis or reach a threshold that induces apoptosis and programmed cell death. Among the different types of DNA lesions, strand breaks produced by ionizing radiation are the most toxic due to the inherent difficultly of repair, which may lead to genomic instability. In this article we show, by using classical molecular simulation techniques, that compared to canonical double-helical B-DNA, guanine-quadruplex (G4) arrangements show remarkable structural stability, even in the presence of two strand breaks. Since G4-DNA is recognized for its regulatory roles in cell senescence and gene expression, including oncogenes, this stability may be related to an evolutionary cellular response aimed at minimizing the effects of ionizing radiation.

Effects of structure relaxation and surface oxidation on nanoscopic wear behaviors of metallic glass

Both structure relaxation and oxidation of surface layer induced by thermal treatment or friction heat play significant roles in reducing wear of metallic glasses (MGs). To distinguish the effects of structure relaxation and surface oxidation, we prepared Zr-based MGs at different states, i.e., as-cast MG; the annealed MGs under argon atmosphere (referred to as structure-relaxed MG) and oxygen atmosphere (referred to as oxidized MG). Nano-wear tests were carried out by atomic force microscope (AFM) to quantitatively clarify these two effects on the wear performance. Compared with the as-cast MG, the structure-relaxed MG shows an increased adhesive but slightly decreased ploughing friction. While, the oxidized MG shows the best anti-wear performance with dramatic reductions in both adhesive and ploughing friction. Classic molecular dynamics (MD) and ab initio MD simulations revealed that the introduction of O hinders the MG atoms from forming interfacial bonds with diamond, and reduces significantly the adhesion between the diamond tip and passivated MG. In addition, the synergistic effect of high hardness and elastic recovery associated with oxidization reduces ploughing friction and enhances wear resistance. This finding clarifies the importance of surface chemistry over structure modification during wear, and offers a generic pathway for tailoring ultra-wear resistant MGs.

Influence of partial fluorination on growth modes of organic molecules on amorphous silicon dioxide

We study the influence of fluorination on nucleation and growth of the organic parasexiphenyl molecule ($p$-6P) on amorphous silicon dioxide ($a\text{\ensuremath{-}}\mathrm{Si}{\mathrm{O}}_{2}$) by means of atomistically resolved classical molecular dynamics computer simulations. We use a simulation model that mimics the experimental deposition from the vapor and subsequent self-assembly onto the underlying surface. Our model reproduces the experimentally observed orientational changes from lying to upright standing configurations of the grown layers. We demonstrate that the increase in the number of fluorinated groups inside the $p$-6P leads to a smoother, layer-by-layer growth on the $a\text{\ensuremath{-}}\mathrm{Si}{\mathrm{O}}_{2}$ surface: We observe that in the first layers, due to strong molecule-substrate interactions the molecules first grow in chiral (fan-like) structures, where each consecutive molecule has a higher angle, supported by molecules lying underneath. Subsequently deposited molecules bind to the already standing molecules of the chiral structures until all molecules are standing. The growth of chiral islands is the main mechanism for growth of the fluorinated $p$-6P derivative, while the $p$-6P, due to the lower interaction with the underlying substrate, forms less chiral structures. The higher degree of chirality leads to a lower-energy barrier for step-edge crossing for the fluorinated molecules. We find that partial fluorination of the $p$-6P molecule can, in this way, significantly alter its growth behavior by modifying rough, three-dimensional growth into smooth, layer-by-layer growth. This has implications for the rational design of molecules and their functionalized forms, which could be tailored for a desired growth behavior and structure formation.

Simulation Models for Prediction of Bioavailability of Medicinal Drugs-the Interface Between Experiment and Computation.

The oral drug bioavailability (BA) problems have remained inevitable over the years, impairing drug efficacy and indirectly leading to eventual human morbidity and mortality. However, some conventional lab-based methods improve drug absorption leading to enhanced BA, and the recent experimental techniques are up-and-coming. Nevertheless, some have inherent drawbacks in improving the efficacy of poorly insoluble and low impermeable drugs. Drug BA and strategies to overcome these challenges were briefly highlighted. This review has significantly unravelled the different computational models for studying and predicting drug bioavailability. Several computational approaches provide mechanistic insights into the oral drug delivery system simulation of descriptors like solubility, permeability, transport protein-ligand interactions, and molecular structures. The in silico techniques have long been known still are just being applied to unravel drug bioavailability issues. Many publications have reported novel applications of the computational models towards achieving improved drug BA, including predicting gastrointestinal tract (GIT) drug absorption properties and passive intestinal membrane permeability, thus maximizing time and resources. Also, the classical molecular simulation models for free solvation energies of soluble-related processes such as solubilization, dissolutions, supersaturation, and precipitation have been used in virtual screening studies. A few of the tools are GastroPlusTM that supports biowaiver for drugs, mainly BCS class III and predicts drug compounds' absorption and pharmacokinetic process; SimCyp® simulator for mechanistic modelling and simulation of drug formulation processes; pharmacodynamics analysis on non-linear mixed-effects modelling; and mathematical models, predicting absorption potential/maximum absorption dose. This review provides in silico-experiment annexation in the drug bioavailability enhancement, possible insights that lead to critical opinion on the applications and reliability of the various in silico models as a growing tool for drug development and discovery, thus accelerating drug development processes.

Wigner energy in irradiated graphite: A first-principles study

First-principles calculations were performed to examine the defect-induced energy storage in graphite. The accumulation of energy resulting from inducing defects in graphite is a well-known phenomenon. Given the recent interest in exploiting this process for energy-storing purposes, more careful investigation is necessary. Some of the earliest studies of damaged graphite, and the stored energy associated with that, were motivated by the associated technological issues in nuclear reactor operation. A large number of excited state defects, for example Frenkel pairs, can be generated in graphite through bombardment of high-energy neutrons. The sudden release of this energy (also called Wigner energy) poses a serious concern to the safe operation of nuclear reactors. At the same time, controlled defect generation in graphite using neutron/ion irradiation might represent a potential energy storage mechanism. In recently published papers, the design of an integrated energy system that couples a nuclear reactor with a Wigner effect-based energy storing system was proposed. To accurately estimate the performance that can be achieved in terms of stored energy density through defect generation, density functional theory (DFT) based first-principles calculations were performed. In this work, stored energy accumulation was modeled in two ways - by Frenkel pair accumulation and overlapping collision cascade methods. The former was done with ab initio molecular dynamics (AIMD) simulations, and the latter was done with combined classical molecular dynamics (MD) and AIMD simulations. The agreement between the calculated and experimental results for how stored energy changes with dosage suggests that this model could be useful for the on-going research into damaged graphite as an energy storage medium.

Thermodynamic integration combined with molecular dynamic simulations to explore the cross-resistance mechanism of isoniazid and ethionamide.

Tuberculosis is an ancient disease of mankind, and its causative bacterium is Mycobacterium tuberculosis. Isoniazid is one of the most effective first-line antituberculosis drugs. As prodrugs, it and its derivative ethionamide act on enoyl-acyl carrier protein reductase (InhA) after being oxidized in bacteria, and kill the bacteria by inhibiting the formation of M. tuberculosis cell walls. However, the S94A mutation of InhA causes M. tuberculosis to develop cross-resistance to isoniazid and ethionamide. This work is dedicated to studying the cross-resistance mechanism of isoniazid and ethionamide through theoretical calculations. First, thermodynamic integral simulations are used to accurately calculate the relative binding energy of two drugs in the mutant and wild-type system. Furthermore, through classic molecular dynamic simulations and molecular mechanics generalized-Born surface area calculation, some key residues are identified and the binding affinity of isoniazid and ethionamide reduced by 9-13 kcal/mol due to S94A mutation. The hydrogen bond between Ala94 and isoniazid (ethionamide) disappeared and the energy contribution of Ala94 decreased after the mutation. In addition, the dynamic network analysis indicated that the mutation of Ser94 also indirectly affected the conformation of key residues such as Met147, Thr196, and Leu97, resulting in a reduction in the energy contribution of these residues. Finally, the binding conformation of isoniazid and ethionamide has also undergone major changes. The obtained results could provide valuable information for the future molecular design to overcome the drug resistance.