Classical Molecular Dynamics Calculations Research Articles

From RNA sequence to its three-dimensional structure: geometrical structure, stability and dynamics of selected fragments of SARS-CoV-2 RNA.

In this computational study, we explore the folding of a particular sequence using various computational tools to produce two-dimensional structures, which are then transformed into three-dimensional structures. We then study the geometry, energetics and dynamics of these structures using full electron quantum-chemical and classical molecular dynamics calculations. Our study focuses on the SARS-CoV-2 RNA fragment GGaGGaGGuguugcaGG and its various structures, including a G-quadruplex and five different hairpins. We examine the impact of two types of counterions (K+ and Na+) and flanking nucleotides on their geometrical characteristics, relative stability and dynamic properties. Our results show that the G-quadruplex structure is the most stable among the constructed hairpins. We confirm its topological stability through molecular dynamics simulations. Furthermore, we observe that the nucleotide loop consisting of seven nucleotides is the most flexible part of the RNA fragment. Additionally, we find that RNA networks of intermolecular hydrogen bonds are highly sensitive to the surrounding environment. Our findings reveal the loss of 79 old hydrogen bonds and the formation of 91 new ones in the case when the G-quadruplex containing flanking nucleotides is additionally stabilized by Na+ counterions.

Water-Hydrocarbon Interactions in Anionic Pyrene Monohydrate.

Interactions between water and polycyclic aromatic hydrocarbons are essential in many aspects of chemistry, from interstellar and atmospheric processes to interfacial hydrophobicity and wetting phenomena. Despite their growing importance, the intermolecular potentials of the water-hydrocarbon interactions are underdeveloped compared to the water-water potentials, and there are similarly few experimental probes that are sensitive to the details of the water-hydrocarbon potential. We present a combined experimental and computational study of anionic pyrene monohydrate, one of the simplest water/hydrocarbon clusters. The action spectrum in the OH region of the mass-selected cluster ion provides a rigorous benchmark for intermolecular potentials and computational methodologies. We identify missing intermolecular interactions and shortcomings in conventional dynamics calculations by comparing experimental data to density functional theory and classical molecular dynamics calculations. Kinetic trapping is prevalent, even for one water molecule and one pyrene molecule, leading to slow equilibration in conventional molecular dynamics calculations, even on nanosecond time scales and at low temperatures (50 K). At constant energy, temperature fluctuations for the pair of molecules are substantial. Immersing the system in a bath of soft spheres and employing parallel tempering alleviates kinetic trapping and dampens temperature fluctuations, bringing the system closer to the thermodynamic limit. With such augmented sampling, a simple, flexible water model reproduces the line width and the asymmetric broadening of the symmetric OH stretching mode, which we assign to spectral diffusion. In the OH stretching region, dynamics calculations predict a more intense antisymmetric peak than experiments observe but do not predict the bimodal split symmetric peak that the experiments show. Our work suggests that electronic polarization, missing in the empirical force field, is responsible for the first discrepancy and that quantum nuclear effects, captured neither in density functional theory nor in classical dynamics, may be responsible for the second.

Miakhs carbon allotropes: Three novel two-dimensional carbon allotropes with sp2 + sp3 hybridized network

MIAKHs carbon allotropes with mixed sp2 + sp3 hybridized network have different properties. Here, three novel two-dimensional materials, namely the MIAKH20, MIAKH28, and MIAKH32 respectively, were predicted based on density functional theory (DFT). MIAKHs carbon allotropes belong to the P4mm (No. 99) space group and their structural properties, mechanical properties, mechanical and dynamical stability, and electronic properties are investigated in this work. The studies of mechanical properties indicate that these 2D materials are mechanically stable and also exhibit the isotropy behavior. In order to examine the thermal stability of these novel 2D materials, MD simulations with Tersoff potential are performed under a NVT ensemble. Our classical molecular dynamics calculations demonstrate that MIAKHs carbon allotropes are dynamically stable. The calculation of electronic band structure of MIAKH32 indicates that this structure is semiconductor with an indirect band gap of 0.53 eV, whereas band structure of MIAKH20, MIAKH28 structures indicates that both materials are metals. This research introduces new 2D polygon-like carbon allotropes and their excellent properties. The obtained results show that these three novel 2D materials can be candidate materials for applications in electromechanical systems and open a new viewpoint for the designs of novel 2D carbon allotropes based on highorder carbon rings.

Computational Modeling of the Neurofibromin-Stimulated Guanosine Triphosphate Hydrolysis by the KRas Protein

We report the results of computational studies of the guanosine triphosphate (GTP) hydrolysis in the active site of the KRas-NF1 protein complex, where KRas stands for the K-isoform of the Ras (ras sarcoma) protein and NF1 (neurofbromin-1) is the activating protein. The model system was constructed using coordinates of heavy atoms from the crystal structure PDB ID 6OB2 with the GTP analog GMPPNP. Large-scale classical molecular dynamics (MD) calculations were performed to analyze conformations of the enzyme-substrate complexes. The Gibbs energy profiles for the hydrolysis reaction were computed using MD simulations with quantum mechanics/molecular mechanics (QM/MM) interaction potentials. The density functional theory DFT(ωB97X-D3/6-31G**) approach was applied in QM and the CHARMM36 force field parameters in MM. The most likely scenario of the chemical step of the GTP hydrolysis in KRas-NF1 corresponds to the water-assisted mechanism of the formation of the inorganic phosphate coupled with the dissociation of GTP to GDP.

Validation of an MD simulation approach for electrical field responsive micelles and their application in drug delivery

In the current work, a new type of micelle is designed that has active connectivity in respond to exterior stimulus and the desired water solubility. Two end-ornamented homopolymers, polystyrene-beta-cyclodextrin (PS-β-CD) and polyethylene oxide-ferrocene (PE-FE), can aggregate as a supramolecular micelle (PS-β-CD/PE-FE) by the guest–host interactions. Our results showed that the Lennard–Jones and hydrophobic interactions are the main powerful forces for the micelle formation process. It was found that the electrical field plays a role as a driving force in the reversible assembly-disassembly of the micellar system. Moreover, for the first time, we examined the PS-β-CD/PE-FE micelle interaction as a drug delivery system with anastrozole (ANS) and mitomycin C (MIC) anti-cancer drugs. The investigation of the total energy between PS-β-CD/PE-FE micelle and drugs predicts the drug adsorption process as favorable (Etotal = − 638.67 and − 259.80 kJ/mol for the Micelle@ANS and Micelle@MIC complexes, respectively). Our results offer a deep understanding of the micelle formation process, the electrical field-respond, and drug adsorption behaviors of the micelle. This simulation study has been accomplished by employing classical molecular dynamics calculation.

First-principles redox energy estimates under the condition of satisfying the general form of Koopmans' theorem: An atomistic study of aqueous iron.

In this work, we explore the relative accuracy to which a hybrid functional, in the context of density functional theory, may predict redox properties under the constraint of satisfying the general form of Koopmans' theorem. Taking aqueous iron as our model system within the framework of first-principles molecular dynamics, direct comparison between computed single-particle energies and experimental ionization data is assessed by both (1) tuning the degree of hybrid exchange, to satisfy the general form of Koopmans' theorem, and (2) ensuring the application of finite-size corrections. These finite-size corrections are benchmarked through classical molecular dynamics calculations, extended to large atomic ensembles, for which good convergence is obtained in the large supercell limit. Our first-principles findings indicate that while precise quantitative agreement with experimental ionization data cannot always be attained for solvated systems, when satisfying the general form of Koopmans' theorem via hybrid functionals, theoretically robust estimates of single-particle redox energies are most often arrived at by employing a total energy difference approach. That is, when seeking to employ a value of exact exchange that does not satisfy the general form of Koopmans' theorem, but some other physical metric, the single-particle energy estimate that would most closely align with the general form of Koopmans' theorem is obtained from a total energy difference approach. In this respect, these findings provide important guidance for the more general comparison of redox energies computed via hybrid functionals with experimental data.

Broadband infrared absorption spectroscopy of low-frequency inter-molecular vibrations in crystalline poly(L-lactide)

The broadband vibrations of poly l-lactide (PLLA) were investigated by terahertz (THz) spectroscopy in the range of 2–16 THz, infrared (IR) spectroscopy, density functional theory (DFT), and classical molecular dynamics (MD) simulations. Characteristic functional group peaks were observed in the IR spectra, which were independent of the crystallinity. A simple model analysis utilizing DFT calculations with an isolated l-lactide monomer and MD simulations for nine polymer chains in a unit cell were performed to investigate the origin of intra-molecular vibrations between molecular chains. Experimentally observed peaks in the THz region were assigned to the inter- and intra-molecular vibration modes. Results showed that classical MD calculations are a particularly powerful tool for the vibrational-mode analysis of inter-molecular interactions.

Adsorption of imidazolium-based ionic liquids on the Fe(1 0 0) surface for corrosion inhibition: Physisorption or chemisorption?

The use of imidazolium-based ionic liquids (ILs) as corrosion inhibitors for iron was studied using both first-principles based density functional theory (DFT) calculations and ab initio molecular dynamics (AIMD), to understand their adsorption structure, stability, and mechanism. A total of 36 ionic liquids (ILs) were selected, with various anion type (Cl−, Br−, I−, N(CN)2−, BF4− and PF6−) and alkyl chain length (Cn, n = 0, 1, 2, 4 and 6). Our calculations revealed that the ILs exhibit strong adsorption on the metal surface and is classified as chemisorption under various different criteria. AIMD simulations including explicit solvation effects verified that these adsorption configurations calculated under vacuum are representative of the adsorption process in an aqueous environment. Furthermore, we showed that the basis of this chemisorption interaction is through net electron donation from the iron slab to the imidazolium ring. Employing dispersion corrected DFT methods (DFT-D3), we demonstrated that the alkyl chain length of the cation greatly influences adsorption energy. Finally, we showed that DFT calculations model the adsorption process much more accurately compared to classical molecular dynamics calculations. The results from this computational study agree with past experimental findings and demonstrate that DFT calculations can be used to provide insight into the nature of the adsorption process of the green and sustainable ILs involved in corrosion inhibition.

Computational Analyses of Plasmonics of a Silver Nanoparticle in a Vacuum and in a Water Solution by Classical Electronic and Molecular Dynamics Simulations.

We present basic optical responses of a silver nanoparticle (Ag309) in a vacuum and a water solution obtained by classical electronic and molecular dynamics (CEMD) calculations, where the CEMD is our previously developed force-field based molecular dynamics simulation method that incorporates the classical equation of motion for free electrons in metal and an interaction with the applied oscillating electric field (Yamada, A. J. Chem. Phys. 2021, 155, 174118)). The present work is the follow-up of the previous study. Calculated absorption spectra in the visible region with various conditions are reported together with parameter determination for realistic analyses as well as the verification of the method. Time-domain optical responses of Ag309 in water solvent are as well analyzed in terms of the plasmon resonance excitation under a subpicosecond light pulse and its thermal relaxation.

Computational Characterization of N-acetylaspartylglutamate Synthetase: From the Protein Primary Sequence to Plausible Catalytic Mechanism

The methods of supercomputer molecular modeling are applied to characterize structure and dynamics of one of the key human brain enzymes, N-acetylaspartylglutamate synthetase. The three-dimensional all-atom models of the enzyme with the reactants in the active site are constructed in several steps, starting from pilot protein structure in the apo-form obtained with the AlphaFold2 from the protein primary sequence. Deposition of reactant molecules into the protein cavity, construction of the reaction intermediate and relaxation of the complex are carried out with the help of large-scale classical molecular dynamics calculations. On the top of the construct, molecular dynamics simulations with the quantum mechanics/molecular mechanics interaction potentials are performed for the most promising conformations of the model system. Analysis of the latter allows us to propose plausible catalytic mechanisms of chemical reactions in the enzyme active site. The applied computational strategy opens the way towards ab initio enzymology using modern supercomputer simulations.

Modeling Liquid Water by Climbing up Jacob's Ladder in Density Functional Theory Facilitated by Using Deep Neural Network Potentials.

Within the framework of Kohn-Sham density functional theory (DFT), the ability to provide good predictions of water properties by employing a strongly constrained and appropriately normed (SCAN) functional has been extensively demonstrated in recent years. Here, we further advance the modeling of water by building a more accurate model on the fourth rung of Jacob's ladder with the hybrid functional, SCAN0. In particular, we carry out both classical and Feynman path-integral molecular dynamics calculations of water with the SCAN0 functional and the isobaric-isothermal ensemble. To generate the equilibrated structure of water, a deep neural network potential is trained from the atomic potential energy surface based on ab initio data obtained from SCAN0 DFT calculations. For the electronic properties of water, a separate deep neural network potential is trained by using the Deep Wannier method based on the maximally localized Wannier functions of the equilibrated trajectory at the SCAN0 level. The structural, dynamic, and electric properties of water were analyzed. The hydrogen-bond structures, density, infrared spectra, diffusion coefficients, and dielectric constants of water, in the electronic ground state, are computed by using a large simulation box and long simulation time. For the properties involving electronic excitations, we apply the GW approximation within many-body perturbation theory to calculate the quasiparticle density of states and bandgap of water. Compared to the SCAN functional, mixing exact exchange mitigates the self-interaction error in the meta-generalized-gradient approximation and further softens liquid water toward the experimental direction. For most of the water properties, the SCAN0 functional shows a systematic improvement over the SCAN functional. However, some important discrepancies remain. The H-bond network predicted by the SCAN0 functional is still slightly overstructured compared to the experimental results.

Toward Sustainable Li-Ion Battery Recycling: Green Metal–Organic Framework as a Molecular Sieve for the Selective Separation of Cobalt and Nickel

The growing demand for Li-ion batteries (LIBs) has made their postconsumer recycling an imperative need toward the recovery of valuable metals, such as cobalt and nickel. Nevertheless, their recovery and separation from active cathode materials in LIBs, via an efficient and environmentally friendly process, have remained a challenge. In this work, we approach a simple and green method for the selective separation of nickel ions from mixed cobalt–nickel aqueous solutions under mild conditions. We discovered that the bioinspired microporous metal−organic framework (MOF) SU-101 is a selective sorbent toward Ni2+ ions at pH 5–7 but does not adsorb Co2+ ions. According to the Freundlich isotherm, the adsorption capacity toward Ni2+ reached 100.9 mg·g–1, while a near-zero adsorption capacity was found for Co2+ ions. Ni2+ removal from aqueous solutions was performed under mild conditions (22 °C and pH 5), with a high yield up to 96%. The presence of Ni2+ ions adsorbed on the surface of the material has been proven by solid-state 1H nuclear magnetic resonance spectroscopy. Finally, the separation of Ni2+ from Co2+ from binary solutions was obtained with approximately 30% yield for Ni2+, with a near-zero adsorption of Co2+, which has been demonstrated by UV–vis spectroscopy. The ion adsorption process of Ni2+ and Co2+ ions was additionally studied by means of classical molecular dynamics calculations (force fields), which showed that the Ni2+ ions were more prone to enter the MOF canals by replacing some of their coordinated water molecules. These results offer a green pathway toward the recycling and separation of valuable metals from cobalt-containing LIBs while providing a sustainable route for waste valorization in a circular economy.

Modeling the mechanical properties of nanoparticles: a review

Nanoparticles are commonly used in various fields of applications such as electronics, catalysis or engineering where they can be subjected to a certain amount of stress leading to structural instabilities or irreversible damages. In contrast with bulk materials, nanoparticles can sustain extremely high stresses (in the GPa range) and ductility, even in the case of originally brittle materials. This review article focuses on the modeling of the mechanical properties of nanoparticles, with an emphasis on elementary deformation processes. Various simulation methods are described, from classical molecular dynamics calculations, the best suited method when applied to the modeling the mechanics of nanoparticles, to dislocation dynamics based hybrid methodologies. We detail the mechanical behaviour of nanoparticles for a large array of material classes (metals, semi-conductors, ceramics, etc.), as well as their deformation processes. Regular crystalline nanoparticles are addressed, as well as more complex systems such as nanoporous or core-shell particles. In addition to the exhaustive review on the recent works published on the topic, challenges and future trends are proposed, providing solid foundations for forthcoming investigations.

GPU-accelerated molecular dynamics: State-of-art software performance and porting from Nvidia CUDA to AMD HIP

Classical molecular dynamics (MD) calculations represent a significant part of the utilization time of high-performance computing systems. As usual, the efficiency of such calculations is based on an interplay of software and hardware that are nowadays moving to hybrid GPU-based technologies. Several well-developed open-source MD codes focused on GPUs differ both in their data management capabilities and in performance. In this work, we analyze the performance of LAMMPS, GROMACS and OpenMM MD packages with different GPU backends on Nvidia Volta and AMD Vega20 GPUs. We consider the efficiency of solving two identical MD models (generic for material science and biomolecular studies) using different software and hardware combinations. We describe our experience in porting the CUDA backend of LAMMPS to ROCm HIP that shows considerable benefits for AMD GPUs comparatively to the OpenCL backend.

Molecular dynamics simulations of zinc sulfide deposition on silver sulfide from aqueous solution

Classical molecular dynamics (CMD) simulation has been performed to study the ZnS deposition from aqueous solution on a surface of crystalline Ag2S. The initial configuration of the Ag2S + ZnS + H2O simulated system includes the surface of crystalline Ag2S silver sulfide with H2O molecules above this surface and Zn2+ and S2- ions located between water molecules. In Ag2S + ZnS + H2O system, sulfur ions are adsorbed originally from a solution on Ag2S surface. The part of deposited Zn atoms Zn is under the first deposited layer of S atoms S, and other Zn atoms Zn are located approximately level with surface S atoms. Performed CMD calculation has shown that the dependences of relative number of the deposited sulfur and zinc atoms on the deposition time are symbate, and formation of first surface ZnS layer occurs during deposition about 10 ns.In addition, the analytical model of ZnS deposition on Ag2S surface is proposed. The CMD simulation confirmed the adequacy of this analytical model.

Velocity of mixed dislocations in body centered cubic iron studied by classical molecular dynamics calculations

The velocity of mixed dislocations in the 11111-0 slip system in body centered cubic iron was investigated with classical molecular dynamics calculations. Local minimum points of the dislocation velocity as a function of the angle between the mixed dislocation line and Burgers vector at low temperatures are found. The local minimum points gradually disappear with the increase in temperature, and the function is smooth at 300 K. Mixed dislocations are modeled with a combination of two types of segments. The segment velocity is modeled based on kink formation and spreading below friction stress, while it is proportional to applied stress beyond friction stress. The dislocation velocity calculated by classical molecular dynamics calculations is reproduced by the model.

Interaction of cobalt and iron hydroperoxo bleomycin with deoxyribonucleic acid (DNA): Dynamic vs. electronic structure considerations

Classical molecular mechanics and quantum mechanical dynamics calculations of iron and cobalt hydroperoxo adducts of bleomycin with deoxyribonucleic acid (DNA) yield structures in reasonable agreement with the experimentally-known Co structures. The hydroxyl (OH) group of the metal-bound hydroperoxide is predicted to reside very close to a deoxyribose proton in the Co-hydroperoxo-DNA adduct (in agreement with experiment) as well as in the ferric counterpart (for which no structural data is available from experiments). According to density functional theory calculations, this sterical arrangement leads to facile insertion of the peroxide OH into the sugar within the Fe(III) but not in the Co(III)-hydroperoxo-bleomycin-DNA complex. However, experiments reveal that the peroxo oxygen is in fact not inserted into the product – at odds with the quantum mechanical calculations. On the other hand, the computed dynamics of the peroxide-sugar distance involve occasional movement of the peroxide ~1.5 Å further away from the CH bond, providing an opportunity for Fe(III)O-OH bond cleavage without immediately trapping the departing OH onto the deoxyribose. Also, while the peroxide moiety in the DNA-bleomycin complex is on average well shielded from the solvent, the dynamics calculations reveal occasional opening of this shielding on nanosecond timescales; individual snapshots are identified, where water molecules from the solvent are in direct contact with the iron-bound hydroperoxide in the bleomycin-DNA complex. Therefore, the general picture provided by molecular dynamics simulations is one where the oxygen–oxygen bond is initially cleaved to generate a high-valent intermediate, which can oxidize the deoxyribose in an outer-sphere manner

Thermal stability and electronic properties of boron nitride nanoflakes.

Nowadays, boron nitride has attracted a great deal of attention due to its physical (chemical) properties, facile synthesis, and experimental characterization, indicating great potential for industrial application. Based on this, we develop here a theoretical study on boron nitride nanoflakes built-up from hexagonal boron nitride nanosheets exhibiting hexagonal, rectangular, and triangular shapes. In order to investigate geometry effects such as those due to the presence of armchair and zigzag edges and distinct shapes, we analyzed their properties from both classical and quantum viewpoints. Using classical molecular dynamics calculations, we show that the nanosheets preserve their structural stability at high temperatures, while DFT calculations demonstrate HOMO-LUMO energy gap variation within the theoretical energy gaps of h-BN in bulk and 2D crystals. Besides that, we have also found that boron nitride nanoflakes structures have spatially symmetrical spin densities.

Surface Propensity of Aqueous Atmospheric Bromine at the Liquid-Gas Interface.

Multiphase reactions of halide ions in aqueous solutions exposed to the atmosphere initiate the formation of molecular halogen compounds in the gas phase. Their photolysis leads to halogen atoms, which are catalytic sinks for ozone, making these processes relevant for the regional and global tropospheric ozone budget. The affinity of halide ions in aqueous solution for the liquid-gas interface, which may influence their reactivity with gaseous species, has been debated. Our study focuses on the surface properties of the bromide ion and its oxidation products. In situ X-ray photoelectron spectroscopy carried out on a liquid jet combined with classical and first-principles molecular dynamics calculations was used to investigate the interfacial depth profile of bromide, hypobromite, hypobromous acid, and bromate. The simulated core electron binding energies support the experimentally observed values, which follow a correlation with bromine oxidation state for the anion series. Bromide ions are homogeneously distributed in the solution. Hypobromous acid, a key species in the multiphase cycling of bromine, is the only species showing surface propensity, which suggests a more important role of the interface in multiphase bromine chemistry than thought so far.

Adsorption of nucleotides on clay surfaces: Effects of mineral composition, pH and solution salts

In the context of the origin of life, clays have been proposed as possible materials to adsorb, protect and potentially foster the formation of complex bio molecules. In the present study, the adsorption of nucleotides onto clay surfaces has been tackled through classical molecular dynamics calculations. Various parameters have been varied by modelling the deoxyguanosine mono phosphate molecule at the basal surface of two clay minerals: montmorillonite and nontronite, at pH = 3 and 7, and in a 0.5 M NaCl solution in presence or absence of Ca2+ divalent cations. It has been firstly observed that counter cations in solution adopts a three-layers structure above the mineral basal surfaces which can be modified by the mineral composition, the location of the surface charge, and results in substantial effects on nucleotide adsorption. For montmorillonite, for which the charge is located in the octahedral (inner) layer, the two closest counter cations layers above the mineral surface are less populated while the third layer comprises the largest cations density. For nontronite, for which the negative charge is located on the surface oxygen atoms of the tetrahedral layer in contact with the aqueous solution, the first two counter cations layers are the most populated. The negative charge on the surface is thus screened by the first two layers above nontronite surface, and by only the third layer for montmorillonite. As a result, the negatively charged phosphate moiety of nucleotides can approach closer to the surface of nontronite by coordinating with the first two layers cations and the nucleobase adsorb on the surface in a parallel orientation maximizing Van der Walls interactions. On montmorillonite, the phosphate coordinates the cations of the third layer and thus remains rather far from the surface, which does not allow the nucleobase parallel binding. These theoretical results explain experimental results on the effect of mineral and solution composition on the adsorption of nucleotides on the surface of swelling clays.