Combined Molecular Dynamics Research Articles

Phase-Controlled Synthesis of Monolayer Ternary Telluride with a Random Local Displacement of Tellurium Atoms.

Alloying 2D transition metal dichalcogenides has opened up new opportunities for bandgap engineering and phase control. Developing a simple and scalable synthetic route is therefore essential to explore the full potential of these alloys with tunable optical and electrical properties. Here, the direct synthesis of monolayer WTe2 x S2(1- x ) alloys via one-step chemical vapor deposition (CVD) is demonstrated. The WTe2 x S2(1- x ) alloys exhibit two distinct phases (1H semiconducting and 1T ' metallic) under different chemical compositions, which can be controlled by the ratio of chalcogen precursors as well as the H2 flow rate. Atomic-resolution scanning transmission electron microscopy-annular dark field (STEM-ADF) imaging reveals the atomic structure of as-formed 1H and 1T ' alloys. Unlike the commonly observed displacement of metal atoms in the 1T ' phase, local displacement of Te atoms from original 1H lattice sites is discovered by combined STEM-ADF imaging and ab initio molecular dynamics calculations. The structure distortion provides new insights into the structure formation of alloys. This generic synthetic approach is also demonstrated for other telluride-based ternary monolayers such as WTe2 x Se2(1- x ) single crystals.

Comparative analysis of plastocyanin–cytochrome f complex formation in higher plants, green algae and cyanobacteria

Mechanisms of the complex formation between plastocyanin and cytochrome f in higher plants (Spinacia oleracea and Brassica rapa), green microalgae Chlamydomonas reinhardtii and two species of cyanobacteria (Phormidium laminosum and Nostoc sp.) were investigated using combined Brownian and molecular dynamics simulations and hierarchical cluster analysis. In higher plants and green algae, electrostatic interactions force plastocyanin molecule close to the heme of cytochrome f. In the subsequent rotation of plastocyanin molecule around the point of electrostatic contact in the vicinity of cytochrome f, copper (Cu) atom approaches cytochrome heme forming a stable configuration where cytochrome f molecule behaves as a rather rigid body without conformational changes. In Nostoc plastocyanin molecule approaches cytochrome f in a different orientation (head-on) where the stabilization of the plastocyanin-cytochrome f complex is accompanied by the conformational changes of the G188E189D190 loop that stabilizes the whole complex. In cyanobacterium P. laminosum, electrostatic preorientation of the approaching molecules was not detected, thus indicating that random motions rather than long-range electrostatic interactions are responsible for the proper mutual orientation. We demonstrated that despite the structural similarity of the investigated electron transport proteins in different photosynthetic organisms, the complexity of molecular mechanisms of the complex formation increases in the following sequence: non-heterocystous cyanobacteria-heterocystous cyanobacteria-green algae-flowering plants.

Combined 3D-QSAR, molecular docking and molecular dynamics study on the benzimidazole inhibitors targeting HCV NS5B polymerase

The hepatitis C virus (HCV)-infected population has continued to grow during recent years, and novel HCV antiviral agents are urgently needed. In this work, a combined theoretical study was performed on the HCV non-structural 5B (NS5B) polymerase and 53 benzimidazole inhibitors. Comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) were carried out with ligand-based and receptor-based alignments. Ligand-based QSAR models (cross-validated q2 of 0.918 for CoMFA and 0.825 for CoMSIA) were found to be superior to receptor-based approaches (cross-validated q2 of 0.765 for CoMFA and 0.740 for CoMSIA). Based on the most predictive CoMFA and CoMSIA models, the structural features that were essential for the inhibitory activity of benzimidazoles were characterized. A molecular dynamics study revealed that the induced fit effect between NS5B and its substrate may be responsible for the inferiority of the receptor-based CoMFA and CoMSIA models. The binding-free energy calculated using the MM/PBSA method correlated well with the experimental results and revealed that the van der Waals and electrostatic interactions most contributed to the binding. In addition, energetically favorable NS5B residues were identified by the per-residue decomposition of binding-free energy. The results presented in this work provide meaningful information for the design of novel benzimidazole inhibitors targeting the NS5B polymerase.Communicated by Ramaswamy H. Sarma

Combined molecular dynamics and phase-field modelling of crack propagation in defective graphene

In this work, a combined modelling approach for crack propagation in defective graphene is presented. Molecular dynamics (MD) simulations are used to obtain material parameters (Young’s modulus and Poisson ratio) and to determine the energy contributions during the crack evolution. The elastic properties are then applied in phase-field continuum simulations which are based on the Griffith energy criterion for fracture. In particular, the influence of point defects on elastic properties and the fracture toughness are investigated. For the latter, we obtain values consistent with recent experimental findings. Further, we discuss alternative definitions of an effective fracture toughness, which accounts for the conditions of crack propagation and establishes a link between dynamic, discrete and continuous, quasi-static fracture processes on MD level and continuum level, respectively. It is demonstrated that the combination of MD and phase-field simulations is a well-founded approach to identify defect-dependent material parameters.

Making and breaking of small water clusters: A combined quantum chemical and molecular dynamics approach.

We present a combined quantum chemical and molecular dynamics study of cyclic and noncyclic water n-mers ([(H2 O]n , n = 2-6) at four different temperatures and showcase that the dynamics of small water clusters can reproduce the known properties of bulk water reasonably well. We investigate the making and breaking of the water clusters by computing the hydrogen bond strengths, average lifetimes, and relative stabilities, which are important to understand the complex solution dynamics. We compare the behavior of water clusters in the gas phase and in the solution phase as well as the variation in the properties as a function of cluster size and highlight the notably more interesting cluster dynamics of the water trimer when compared to the other water clusters. © 2019 Wiley Periodicals, Inc.

Precipitation, planar defects and dislocations in alloys: Simulations on Ni3Si and Ni3Al precipitates

We present simulations of the formation of Ni3Si precipitates using a combination of molecular dynamics (MD) and the Metropolis Monte Carlo (MMC) method. Applying this technique to a Ni-Si solid solution in Cu matrix leads to Ni3Si precipitates with L12 structure as observed in experiments. Since L12 structured precipitates are most relevant for precipitation strengthening of several alloys, we focus on planar defects and dislocations in Ni3Si and Ni3Al. Ab initio calculations of the generalised stacking fault energies of Ni3Si presented in our previous work [S. Hocker, H. Lipp, E. Eisfeld, S. Schmauder, J. Roth, J. Chem. Phys. 149, 024701 (2018)] revealed that the complex stacking fault is not stable and the inflection point as well as the minimum corresponding to the antiphase boundary is shifted. In this study it is shown that this behaviour can be understood from the analysis of charge densities. Furthermore, the consequences on dislocations in Ni3Si and Ni3Al are discussed and interactions of edge dislocations with Ni3Si and Ni3Al precipitates are simulated.

Understanding Hygroscopic Nucleation of Sulfate Aerosols: Combination of Molecular Dynamics Simulation with Classical Nucleation Theory.

We present a combined molecular dynamics (MD) and classical nucleation theory (CNT) approach to address many issues regarding the nucleation of inorganic aerosols. By taking parameters from MD simulations, we find the CNT predicts fairly reasonable free-energy profiles for the hygroscopic nucleation of aerosols. Moreover, we find that the ionization of sulfates can play a key role in stabilizing aqueous clusters and that both the size of the critical nucleus and the nucleation barrier can be significantly lowered by the H2SO4 and NH4HSO4, whereas the effect of NH3 on nucleation is negligible. NH4HSO4 provides stronger enhancement effect to aerosol formation than H2SO4. In view of the consistency between the theoretical prediction and experimental observation, the combination of MD simulation and CNT appears to be a valuable approach to gain deeper understanding of how aerosol nucleation is affected by different chemical species.

Extensional-shear coupled flow-induced morphology and phase evolution of polypropylene/ultrahigh molecular weight polyethylene blends: Dissipative particle dynamics simulations and experimental studies

The property of ultrahigh molecular weight polyethylene (UHMWPE)-based materials are significantly dependent on the morphology and phase behavior evolution subjected to extensional-shear coupled flow fields. In this study, we utilize polypropylene (PP)/UHMWPE blends as model and present a combination of numerical simulation and experimental study on their association behavior under extensional-shear coupled flow field. In terms of simulation, combined molecular dynamics (MD) and dissipative particle dynamics (DPD) method are applied, where two kinds of extensional-shear coupled flow fields are produced, named as coupledⅠand coupled Ⅱ. In response to coupled Ⅰ, shear-stretched alignment of PP chains is observed at shear rate of γ˙ = 0.01, followed by a quick disordering transition with increasing the shear rates and a final phase-separation at shear rate of γ˙ = 0.1. When subjected to coupled Ⅱ, the weak segregation start to connect with the adjacent ones, giving a homogeneous phase when further increasing the applied pressure. The presence of pressure-driven flow helps in bridging different chains, causing the percolating polymer network reinforcement. Besides, experimental studies by means of Raman spectroscopy, Raman mapping and rheological measurement are compared with the above simulations. It confirms that it is more efficiently broken for melted drops under an extensional dominated coupled flow than those under a shear dominated coupled flow, in which an effective lubricating phase forms, leading to the induced miscibility in polymer blends and reduction in storage modulus and viscosity. These experimental findings are consistent with simulation results.

Thermodynamic mechanism of selective cocrystallization explored by MD simulation and phase diagram analysis

AbstractThe thermodynamic mechanism of selective cocrystallization was investigated by combination of molecular dynamics (MD) simulations and phase diagram analysis, using system of urea and cresol isomers as model compounds. Hansen solubility parameters (HSPs) models were utilized to predict miscibility and cocrystal formation. Thermodynamic phase diagrams of cresol isomers and urea were measured with the help of process analysis technology. MD simulations were performed to investigate the intermolecular interactions between m‐ and/or p‐cresol and urea, by calculating the solvation free energies (SFEs) and analysing radial distribution functions (RDFs). The simulation and experimental results indicate that the solubility data of urea are apparently affected by the SFEs, which are linearly related with the concentration of urea. Moreover, it was also found that the type of O‐H···O=C hydrogen bond plays a critical role in the contribution of intermolecular interactions and is also a key factor for selective cocrystallization.

Hydrogen and deuterium adsorption on uranium decorated graphene nanosheets: A combined molecular dynamics and density functional theory study

In this study, the combined density functional theory (DFT) and molecular dynamics (MD) simulation methods were carried out to investigate the potential capability of uranium-decorated graphene (U–G) for the separation of deuterium from hydrogen gases. Graphene with hexagonal honeycomb lattice arrangement is suitable for adsorption of individual uranium atoms, with a high binding energy (−1.173 eV) and U-U distance longer than 7 Å. This U-G system has ability to hold up to six H2 (5.16% wt) or seven D2 (11.75% wt) molecules per U atoms. To gain further insights into these interactions, partial electronic density of states (PDOS) and the electron density distribution of the elements were analyzed. The MD results are in reasonable agreement with the results obtained by DFT method. Our calculated results indicate that at room temperature, D2 molecule has higher affinity for U-G system than the H2 molecule. In order to increase the D2 separation factor from H2, the effect of temperature was studied. The results indicated that adsorption ratio of D2 to H2 increases by decreasing the temperature.

Both Reactivity and Accessibility Are Important in Cytochrome P450 Metabolism: A Combined DFT and MD Study of Fenamic Acids in BM3 Mutants.

Cytochrome P450 102A1 from Bacillus megaterium (BM3) is a fatty acid hydroxylase that has one of the highest turnover rates of any mono-oxygenase. Recent studies have shown how mutants of BM3 can produce metabolites of known drug compounds similar to those observed in humans. Single-point mutations in the binding pocket change the regioselective metabolism of fenamic acids from aromatic hydroxylation to aliphatic hydroxylation. This study is concerned with the individual contribution from accessibility and reactivity for drug metabolism with a future goal to develop fast methods for prediction. For a BM3 M11 mutant as well as the M11 V87F and M11 V87I mutants, we studied the metabolism of the nonsteroidal anti-inflammatory drugs (NSAIDs) mefenamic acid, meclofenamic acid, tolfenamic acid, and diclofenac. Density functional theory (DFT; B3LYP and B3LYP-D3) calculations for all possible reactions were performed using a porphyrin model reacting with the four substrates. Molecular dynamics (MD) simulations were used to determine the potential sites of metabolism that are accessible. Finally, we combine reactivity and accessibility for each potential site to interpret the experimentally determined metabolism. Generally, the 3 and 5 positions (on the ring containing the acidic substituent) and the 2', 3', and 4' positions are most reactive, whereas 4, 5, 3', and 4' are most accessible. Combining reactivity and accessibility show that the 5, 3', and 4' positions are predicted to be most prone to be metabolized, in agreement with experimentally observed data. Reactivity seems to be the dominant factor in the CYP-mediated metabolism of these NSAIDs, which is consistent with previously published methods based solely on reactivity.

Vibrational Optical Activity of Intermolecular, Overtone, and Combination Bands: 2-Chloropropionitrile and α-Pinene.

Spectroscopy of vibrational optical activity has been established as a powerful tool to study molecular structures and interactions. In most cases, only fundamental molecular transitions are analyzed. In the present study, we analyze a broader range of vibrational frequencies (40-4000 cm-1), which could be measured on a new Raman optical activity (ROA) instrument. An unexpectedly strong vibrational Raman optical activity of 2-chloropropionitrile has been observed within the low-frequency region (40-150 cm-1). On the basis of combined molecular dynamics and density functional theory simulations, it could be assigned to intermolecular vibrations. A detailed analysis also revealed connection between spectral shapes and molecular structure and flexibility, such as bending of the CCN group. At the other edge of the scale, within ∼1500-4000 cm-1, for the first time, many combination and overtone ROA bands have been observed for 2-chloropropionitrile and α-pinene. These were also partially assigned, using quantum-chemical computations. The band assignment was confirmed by a comparison with Raman, absorption, and vibrational circular dichroism spectra. The measurement in the broader vibrational range thus significantly extends the information that can be obtained by optical spectroscopy, including intermolecular interactions of chiral molecules and liquids.

Understanding the interaction of single-walled carbon nanotube (SWCNT) on estrogen receptor: A combined molecular dynamics and experimental study

Considering the large-scale production of diversified nanomaterials, it is paramount importance to unravel the structural details of interactions between nanoparticles and biological systems, and thus to explore the potential adverse impacts of nanoparticles. Estrogen receptors (ER) is one of the most important receptor of human reproductive system and the binding of carbon nanotubes to estrogen receptors was the possible trigger leading to the reproductive toxicity of carbon nanotubes. Thus, with single-walled carbon nanotube (SWCNT) treated as model nanomaterials, a combination of in vivo experiments, spectroscopy assay and molecular dynamic modeling was applied to help us unravel some important issues on the binding characterization between SWCNT and the ligand binding domain (LBD) of ER alpha (ERα). The fluorescence assay and molecular dynamics simulations together validated the binding of SWCNT to ERα, suggesting the possible molecular initiating event. As a consequence, SWCNT binding led to a conformational change on tertiary structure levels and hydrophobic interaction was recognized as the driving force governing the binding behavior between SWCNT and LBD of ERα. A in vivo process presented that the exposure of SWCNT increased ERα expression from 26.43 pg/ml to 259.01 pg/ml, suggesting a potential estrogen interference effects of SWCNT. Our study offers insight on the binding of SWCNT and ERα LBD at atomic level, helpful to accurately evaluate the potential health risks of SWCNT.

An investigation into non-covalent functionalization of a single-walled carbon nanotube and a graphene sheet with protein G:A combined experimental and molecular dynamics study

Investigation of non-covalent interaction of hydrophobic surfaces with the protein G (PrG) is necessary due to their frequent utilization in immunosensors and ELISA. It has been confirmed that surfaces, including carbonous-nanostructures (CNS) could orient proteins for a better activation. Herein, PrG interaction with single-walled carbon nanotube (SWCNT) and graphene (Gra) nanostructures was studied by employing experimental and MD simulation techniques. It is confirmed that the PrG could adequately interact with both SWCNT and Gra and therefore fine dispersion for them was achieved in the media. Results indicated that even though SWCNT was loaded with more content of PrG in comparison with the Gra, the adsorption of the PrG on Gra did not induce significant changes in the IgG tendency. Several orientations of the PrG were adopted in the presence of SWCNT or Gra; however, SWCNT could block the PrG-FcR. Moreover, it was confirmed that SWCNT reduced the α-helical structure content in the PrG. Reduction of α-helical structure of the PrG and improper orientation of the PrG-SWCNT could remarkably decrease the PrG tendency to the Fc of the IgG. Importantly, the Gra could appropriately orient the PrG by both exposing the PrG-FcR and also by blocking the fragment of the PrG that had tendency to interact with Fab in IgG.

CO2 Capture via Crystalline Hydrogen-Bonded Bicarbonate Dimers

Summary Limiting global temperature rises is increasingly dependent on the development of energy-efficient carbon-capture methods. Here, we report a simple CO2-separation cycle using an aqueous bis(iminoguanidine) (BIG) sorbent that reacts with CO2 and crystallizes into an insoluble bicarbonate salt. X-ray diffraction analysis of the bicarbonate crystals revealed “anti-electrostatic” hydrogen-bonded (HCO3−)2 dimers, stabilized by guanidinium cations and water. Mild heating of the crystals releases the CO2 and regenerates the BIG sorbent quantitatively, thereby closing the CO2-separation cycle. Experimental and computational investigations support a CO2-release mechanism consisting of surface-initiated low-barrier proton transfer from guanidinium groups to bicarbonate anions with the formation of carbonic acid dimers, followed by CO2 and H2O release in the rate-limiting step, with a measured activation energy of 102 ± 12 kJ/mol. The minimum energy required for sorbent regeneration is 151.5 kJ/mol CO2, which is 24% lower than the regeneration energy of monoethanolamine, a benchmark industrial sorbent.

Strain‐Induced Structural Deformation Study of 2D MoxW(1‐x) S2

AbstractThe possibility of tuning properties and its potential applications in the fields of optoelectronics and/or flexible electronics, has increased the demand for 2D alloys in recent times. Understanding the mechanical performance of 2D materials under extreme conditions, such as strain, stress, and fracture is essential for the reliable electronic devices based on these structures. In this study, combined molecular dynamics (MD) simulations and in situ Raman spectroscopic techniques are used to study the mechanical performance of a 2D alloy system, MoxW(1‐x) S2. It is observed that W substitution in MoS2 causes solid‐solution strengthening and increase in the Young's modulus values. Higher W content decreases failure strain for MoS2. Based on spatially resolved Raman spectroscopy and MD simulations results, a detailed model to explain failure mechanisms in MoxW(1‐x) S2 alloys is proposed.

Prospecting and Structural Insight into the Binding of Novel Plant-Derived Molecules of Leea indica as Inhibitors of BACE1.

Alzheimer disease (AD) can be considered as the most common age related neurodegenerative disorder and also an important cause of death in elderly patients. A number of studies showed the correlation of this disease pathology with BACE1 inhibitor and it is also evident that BACE1 inhibitor can function as a very potent strategy in treating AD. In this present study, we aimed to prospect for novel plant-derived BACE1 inhibitors from Leea indica and to realise structural basis of their interactions and mechanisms using combined molecular docking and molecular dynamics based approaches. An extensive library of Leea indica plant derived molecule was compiled and computationally screened for inhibitory action against BACE1 by using virtual screening approaches. Furthermore, induced fit docking and classical molecular dynamics along with steered molecular dynamics simulations were employed to get insight of the binding mechanisms. Two triterpenoids, ursolic acid and lupeol were identified through virtual screening; wherein, lupeol showed better binding free energy in MM/GBSA, MM/PBSA and MM/GBVI approaches. Furthermore classical and steered dynamics revealed the favourable hydrophobic interactions between the lupeol and the residues of flap or catalytic dyadof BACE1; however, ursolic acid showed disfavorable interactions with the BACE1. This study therefore unveiled the potent BACE1 inhibitor from a manually curated dataset of Leea indica molecules, which may provide a novel dimension of designing novel BACE1 inhibitors for AD therapy.

Towards Understanding the Anticorrosive Mechanism of Novel Surfactant Based on Mentha pulegium Oil as Eco-friendly Bio-source of Mild Steel in Acid Medium: a Combined DFT and Molecular Dynamics Investigation

Today, due to the increasingly stringent European directives concerning the use of molecules with certain toxicities towards the environment or their users, the essential oils, extracts, and molecules derived from plants exhibiting the characteristic of being biodegradable can be considered as a source of green corrosion inhibitors instead of harmful synthetic chemicals. The present work was devoted to testing the essential oil extracted from Mentha pulegium leaves(M1) as a corrosion inhibitor for C-steel in 1 mol/L HCl solution using both electrochemical techniques and gravimetric measurements for the evaluation of the inhibition efficiencies at different temperatures. The results obtained showed that the inhibition efficiency increased with an increase in M1 concentration to reach a maximum value of 92.21%. We sought to determine the molecule responsible for this high efficiency, starting with the analysis of oil chemical composition by gas chromatography coupled with mass spectrometry. This analysis revealed that menthol(M2) and isomenthol(M3) were the principal constituents. In order to identify the molecule responsible for the inhibition and explain the protection mechanism involved, quantum chemical calculations and Monte Carlo simulations were used to explain the interaction of menthol, the major constituent of M1 with the Fe-surface. To practically confirm these results, we studied the action of 1 mol/L HCl on steel with and without the addition of M2 by both methods(gravimetric and electrochemical study). A very high efficiency was obtained, an efficiency of 94.90% at 10‒3 mol/L, which was retained for a long exposure time, and slightly decreased in function of temperature. Finally, a good correlation between the experimental data, theoretical calculations, and SEM studies was obtained, which denied that the M1 efficiency was only a result of a synergy effect and confirmed the high efficiency of Mentha oil and its main component(menthol) as a strong ecological inhibitor of corrosion.

Understanding the structural features of JAK2 inhibitors: a combined 3D-QSAR, DFT and molecular dynamics study.

JAK2 plays a critical role in JAK/STAT signaling pathway and in patho-mechanism of myeloproliferative disorders and autoimmune diseases. Thus, effective JAK2 inhibitors provide a promising opportunity for the pharmaceutical intervention of many diseases. In this work, 3D-QSAR study was performed on a series of 1-amino-5H-pyrido-indole-4-carboxamide derivatives as JAK2 inhibitors to obtain reliable comparative molecular field analysis (CoMFA) and comparative molecular similarity analysis (CoMSIA) models with three different alignment methods. Among the different alignment methods, ligand-based (CoMFA: q2 = 0.676, r2 = 0.979; CoMSIA: q2 = 0.700, r2 = 0.953) and pharmacophore-based alignment (CoMFA: q2 = 0.710, r2 = 0.982; CoMSIA: q2 = 0.686, r2 = 0.960) has produced better statistical results when compared to receptor-based alignment (CoMFA: q2 = 0.507, r2 = 0.979; CoMSIA: q2 = 0.544, r2 = 0.917). Statistical parameters indicated that data are well fitted and have high predictive ability. The presence of electrostatic and hydrophobic field is highly desirable for potent inhibitory activity, and the steric field plays a minor role in modulating the activity. The contour analysis indicates ARG980, ASN981, ASP939 and LEU937 have more possibility of interacting with bulky, hydrophobic groups in pyrido and positive and negative groups in pyrazole ring. Based on our findings, we have designed sixteen molecules and predicted its activity and drug-like properties. Subsequently, molecular docking, molecular dynamics and DFT calculations were performed to evaluate its potency.

Combination of coarse-grained molecular dynamics simulations and small-angle X-ray scattering experiments.

The combination of molecular dynamics (MD) simulations and small-angle X-ray scattering (SAXS), called the MD-SAXS method, is efficient for investigating protein dynamics. To overcome the time-scale limitation of all-atom MD simulations, coarse-grained (CG) representations are often utilized for biomolecular simulations. In this study, we propose a method to combine CG MD simulations with SAXS, termed the CG-MD-SAXS method. In the CG-MD-SAXS method, the scattering factors of CG particles for proteins and nucleic acids are evaluated using high-resolution structural data in the Protein Data Bank, and the excluded volume and the hydration shell are modeled using two adjustable parameters to incorporate solvent effects. To avoid overfitting, only the two parameters are adjusted for an entire structure ensemble. To verify the developed method, theoretical SAXS profiles for various proteins, DNA/RNA, and a protein-RNA complex are compared with both experimental profiles and theoretical profiles obtained by the all-atom representation. In the present study, we applied the CG-MD-SAXS method to the Swi5-Sfr1 complex and three types of nucleosomes to obtain reliable ensemble models consistent with the experimental SAXS data.