DFT Molecular Dynamics Simulations Research Articles

First-Principles Simulation Study on the Weakening of Silane Coupling to Silica under Alkaline Conditions

Silane coupling is commonly used to connect organic polymers to inorganic substrates for surface modification and composite material fabrication. It is known that the covalent bonds that form between the silane coupling agent (SCA) and hydroxylated SiO2 weaken under alkaline conditions. In the present work, we theoretically investigated the microscopic mechanisms of this phenomenon by combining first-principles calculations of the deprotonation free energy with density functional theory (DFT), bond-breaking transition-state barrier energy calculations, and DFT-based molecular dynamics (MD) simulations. We found that the following occurs under alkaline conditions: (i) the terminal −OH of SiO2(001) is significantly deprotonated, while the −OH group of the SCA is hardly deprotonated; (ii) the transition-state barrier energy to break the Si–O bond between the SCA and SiO2(001) becomes less than 1 eV with the assistance of H2O dissociation when 50% of the terminal −OH groups on SiO2(001) is deprotonated; and (iii) the predicted Si–O bond-breaking reactions occurred in DFT–MD simulations with realistic settings.

Explicit solvent effects on (1 1 0) ruthenium oxide surface wettability: Structural, electronic and mechanical properties of rutile RuO2 by means of spin-polarized DFT-MD

The structural, electronic and mechanical properties of crystalline ruthenium dioxide RuO2 in its rutile structure have been calculated via forefront spin-polarized Density Functional Theory (DFT) and DFT-Molecular Dynamics (DFT-MD) simulations. Notwithstanding RuO2 is known as a highly active catalyst for a wide number of (photo) electrochemical reactions in aqueous/humid environments, the study of the interaction of RuO2 surfaces with water has been confined largely to (static) surface science and water adsorption calculations. Herein, an atomistic understanding of bulk rutile RuO2 and explicit solvent effects on (110)-RuO2 facet are provided. We especially focus on the comprehension of the mechanistic interplay between surface wettability, interfacial water dynamics and surface chemical activity.Analysis and characterization of the interfacial water and H-bond environment reveal how explicit liquid water and its dynamics play a role in the surface reconstruction and in the hydrophobic nature of the (110)-RuO2 facet with a prevailing H-bond acceptor character. Moreover, we provide a dependence of physical and chemical properties, such as surface electric field and work function, from different degrees of surface wettability of the (110)-RuO2 facet. Results on bulk properties of crystalline ruthenium dioxide RuO2 are in good agreement with the nowadays available experimental evidences and previous DFT studies.

Diketopyrrolopyrrole-based supramolecular nano-leveler for the enhancement of conformal copper electrodeposition

Diketopyrrolopyrrole (DPP) quaternary ammonium compound is an excellent leveler for the copper electrodeposition. Herein, we propose a supramolecular nano-leveler based on DPP molecule, which is composed of a symmetrical amphiphilic molecule of bipyridinium (Bpy) units grafted on DPP skeleton and assembled with cucurbit[7]uril (CB[7]). Compared with unassembled levelers, this supramolecular leveler shows significant advantages in achieving conformal copper electrodeposition. DFT calculations and molecular dynamics simulations demonstrate that the CB[7] assembled strategy can increase the charge density of nano-leveler and lead to the strong adsorption on the surface of substrate, thus efficiently regulating the copper deposition process. As a result, the solution implement of 2 μmol/L nano-leveler and other additives achieves excellent bottom-up filling performance, accompanying by a high filling efficiency of 97.7%. This supramolecular assembled strategy of leveler may open up a new avenue for the interfaces engineering of organics for semiconductor fabrication.

Thermodynamic and structural description of relative solubility of the flavonoid rutin by DFT calculations and molecular dynamics simulations

Understanding the solubility of flavonoids is of relevance in view of the broad application such as antioxidant and antitumor agents. The solubility of flavonoid rutin has been experimentally investigated in a homologous series of alcohols, acetone, n-heptane and water solvents. In this work theoretical evaluation of Gibbs free energy of solvation was performed at the Density Functional Theory (DFT) and Molecular Dynamics (MD) levels, with the ωB97x-D functional and multistate Bennett acceptance ratio (MBAR) method, respectively. The degree of solubility of a given solute among various solvents is dictated by solute-solvent interactions, which may be represented by the solvation energy. Our calculated relative energy values due to solvent effects, using quantum chemical methods (PCM and SMD solvent models) do not follow strictly the observed solubility trend. However, the PCM model including solute-solvent dispersion interaction, solute-solvent repulsion interaction and solute cavitation energy contribution to the total energy (named DIS,REP,CAV) yielded an overall agreement with experimental solubility profile, with exception of ethanol solvent. A similar satisfactory accordance with experiment was found for MBresults, with a discrepancy also found for 1-butanol, which deserve further investigation. Analysis of spatial and radial distribution functions (SDF and RDF) for pure solvents and the analysis of the contributions of vdW and electrostatic terms for the total free energy reveal that a balance between dispersive and electrostatic interactions between the rutin and the solvent is necessary to solubilize the flavonoid, which corroborates with the values of these energy contributions to the solvation-free energy calculated by the MBAR method. The use of explicit solvent molecules in DFT calculations is precluded due to the size, flexibility, and many sites for solvent interactions of rutin molecule. Our results indicate that in general DFT-PCM (DIS,REP,CAV) and MBAR levels of calculations can satisfactorily predict the solvation free energy and solubility trend for flavonoid rutin along a series of solvents, and also provide a reasonable estimate of relative solubilities of other flavonoids, information that can be relevant for further molecular modeling studies.

Quantum chemical exploration on the inhibition performance of indole and some of its derivatives against copper corrosion

The inhibitory behavior of indole and some of its derivatives and their conformers against copper corrosion was studied by density functional theory (DFT) and molecular dynamics simulations. The calculated reactivity parameters based on the values of EHOMO, ELUMO, energy gap (ΔEgap), hardness (η), softness (σ), electronegativity (χ), electrophilicity (ω), Fukui indices (fk), fraction of electron transferred (ΔN) and back-donation of electrons (ΔEback-d) between the inhibitors and the copper surface have been scrutinized. DFT-molecular dynamics simulations have been used to investigate the adsorption mechanism for neutral and deprotonated forms of inhibitors. It was established that the carbonyl and carboxylic groups of the indole derivatives have a great effect on the inhibition efficiency. The results of molecular reactivity indicate that the inhibition efficiency is ranked as follows: indole < IND3-C2 < IND3-C1 < IND5-C1 < IND2-C2 < IND2-C1 < IND5-C2 < isatin. Neutral inhibitors physisorb to the copper surface except for isatin, which is chemisorbed due to its higher binding energy and its increased amount of charge transfer. The deprotonated inhibitors are chemisorbed on Cu(111) surface by establishing strong covalent CuN bonds, as supported by charge density difference analysis.

Computational Design of Radical Recognition Assay with the Possible Application of Cyclopropyl Vinyl Sulfides as Tunable Sensors.

The processes involving the capture of free radicals were explored by performing DFT molecular dynamics simulations and modeling of reaction energy profiles. We describe the idea of a radical recognition assay, where not only the presence of a radical but also the nature/reactivity of a radical may be assessed. The idea is to utilize a set of radical-sensitive molecules as tunable sensors, followed by insight into the studied radical species based on the observed reactivity/selectivity. We utilize this approach for selective recognition of common radicals—alkyl, phenyl, and iodine. By matching quantum chemical calculations with experimental data, we show that components of a system react differently with the studied radicals. Possible radical generation processes were studied involving model reactions under UV light and metal-catalyzed conditions.

The structure of liquid perfluoro Tert-Butanol using Infrared, Raman and X-Ray scattering analyzed by quantum DFT calculations and molecular Dynamics

The state of aggregation of room temperature liquid perfluoro tert-butanol (TBF) has been assessed in comparison with that of its hydrogenated homologue (TBH). This study has been performed using vibrational spectroscopy (Raman scattering and infrared absorption) and X-ray diffraction, analyzed by quantum DFT calculations and Molecular Dynamics simulations. In contrast with TBH, in which large oligomers (aggregates of 4 to 6 molecules) predominate, TBF was found to mainly consist of monomers and dimers. The strongly acidic properties of this molecule, due to the electron-withdrawing effect of its CF3 groups, plays a relevant role in making it a poorly associated alcohol.

Measuring the structure and equation of state of polyethylene terephthalate at megabar pressures

We present structure and equation of state (EOS) measurements of biaxially orientated polyethylene terephthalate (PET, ({hbox {C}}_{10} {hbox {H}}_8 {hbox {O}}_4)_n, also called mylar) shock-compressed to (155 pm 20) GPa and (6000 pm 1000) K using in situ X-ray diffraction, Doppler velocimetry, and optical pyrometry. Comparing to density functional theory molecular dynamics (DFT-MD) simulations, we find a highly correlated liquid at conditions differing from predictions by some equations of state tables, which underlines the influence of complex chemical interactions in this regime. EOS calculations from ab initio DFT-MD simulations and shock Hugoniot measurements of density, pressure and temperature confirm the discrepancy to these tables and present an experimentally benchmarked correction to the description of PET as an exemplary material to represent the mixture of light elements at planetary interior conditions.

First-principles study of the liquid and amorphous phases of Sb2Te phase change memory material

We have investigated the local structure of liquid and amorphous phases of Sb2Te phase change memory material by the means of density functional theory-molecular dynamics simulations. The models of liquid and amorphous states were generated by quenching from the melt. The results show that the local environment of liquid Sb2Te is a mixed bonding geometry, where the average coordination numbers (CNs) of Sb and Te atoms are 4.93 and 4.23, respectively. Compared with crystalline state, there are more Sb–Sb bonds (∼53%) and less Sb–Te bonds (∼42%) with the presence of Te–Te bonds (∼5%) in liquid Sb2Te. Therefore, the formation of homopolar bonds and the breaking of heteropolar bonds are important structural transformations in melt process. For amorphous Sb2Te, the average CNs of Sb and Te atoms are 4.54 and 3.57, respectively. They are mostly in an octahedral environment, similar to the case in crystalline phase. The fractions of Sb–Sb, Te–Te, and Sb–Te bonds are ∼52%, ∼2%, and ∼46%, respectively. Thus, the increase in the fraction of octahedron accompanied with the decrease in average CN is the major structural changes in quenching process. Furthermore, the octahedral geometry in both the crystalline and amorphous Sb2Te increases the local structural similarity, facilitating the rapid low-energy crystallization.

Is the cytotoxic activity of phenanthriplatin dependent on the specific size of the phenanthridine ligand π system?

The monofunctional Pt(II) drug phenanthriplatin is a leading preclinical anticancer drug, whose main characteristic is the presence of the extended aromatic system of the phenanthridine ligand, which allows intercalation. Intercalation, in turn, induces DNA unwinding and facilitates DNA binding. Aiming at verifying to what extent the peculiar cytotoxic activity of phenanthriplatin depends on the specific size of the aromatic system, two phenanthriplatin derivatives have been designed increasing the number of the rings in the N-heterocyclic ligand, and their reactivity has been computationally investigated. Both quantum mechanical DFT computations and molecular dynamics (MD) simulations have been employed to investigate some of the aspects that are considered important for the activity of Pt(II) monofunctional complexes. In particular, the substitution of the chlorido ligand with water, subsequent interaction of the aquated complexes with guanine as a model, eventual deactivation by the model N-acetyl methionine as well as intercalation into, binding to and distortion of DNA have been examined. The outcomes of such analysis have been compared with the analogous ones for the phenanthriplatin complex in order to highlight how the addition of one more ring to the phenanthridine ligand and, eventually, its identity influence the reactivity and, consequently, the cytotoxic profile of the complexes.

Understanding the CO2 capture performance by MDEA-based deep eutectics solvents with excellent cyclic capacity

Solvents for CO2 capture with efficient regeneration are essential for industrial applications. Here, three methyldiethanolamine (MDEA) based deep eutectic solvents (DESs) were developed and their performance for CO2 uptake and regeneration was evaluated. Density functional theory (DFT) calculation and molecular dynamics (MD) simulations were performed to elucidate the features of DES and the DES interaction with CO2. The CO2 absorption performance is dependent on the hydrogen bond acceptor (HBA). [Monoethanolamine hydrochloride (MEAHCl)][MDEA] exhibits the best CO2 absorption performance, which is further enhanced by the addition of monoethanolamine (MEA), reaching 13.5 wt% after 6 h of absorption at 25 °C when the ratio of MEAHCl, MDEA, and MEA at 1:3:0.5. Both DFT calculation and MD simulations reveal that the CO2 interaction with [MEAHCl][MDEA] is via the –NH2 group in MEAH+ and the –OH group in MDEA, also confirmed by nuclear magnetic resonance (NMR) and Fourier transform infrared spectroscopy (FTIR) results. The ternary DES of [MEAHCl][MDEA][MEA] with low desorption activation energy exhibits excellent cyclic capacity after 5 cycles of regeneration, offering an efficient and low-cost CO2 capture system for industrial applications.

Synergistic inhibition effect of novel counterion-coupled surfactant based on rice bran oil and halide ion on the C-steel corrosion in molar sulphuric acid: Experimental and computational approaches

The counterion-coupled surfactant (RBOS-12) based on rice bran oil is synthesized, characterized, and evaluated as a new inhibitor for carbon steel corrosion. The inhibition, and synergistic effect performance of individual RBOS-12, and that is combined with chloride ions on the corrosion of carbon steel in a molar sulphuric acid medium at 30–60 ± 1 °C has been examined using open circuit potential-time, linear polarization resistance (LPR) corrosion rate, impedance spectroscopy (EIS), potentiodynamic polarization (PDP), surface topology (Field emission-scanning electron microscopy/Energy dispersive X-ray analysis (FE-SEM/EDS), X-ray diffraction (XRD) and UV–vis spectroscopic studies), density functional theory (DFT) and molecular dynamics (MD) simulations. Experimental findings exhibited that the inhibition capacity of individual RBOS-12 is 95.5% at the concentration of 1.0 × 10−3 M. Synergistic inhibition effect was observed between the RBOS-12 surfactant and the Cl- ion additives, with the maximum corrosion inhibition capacity as high as ~99.1% at 1 × 10–5 M RBOS-12 + 0.1 M Cl- ions. The individual RBOS-12 and RBOS-12/Cl− system get adsorbed onto the metal interface through mixed categories of adsorption mainly with the chemisorption. Meanwhile, the adsorption mode follows the Langmuir isotherm model. FE-SEM/EDS and XRD investigates approve the protective and adsorption capabilities of the individual RBOS-12 and RBOS-12/Cl− inhibitor systems. UV–vis spectroscopic analysis display that the additive interacts with metal in H2SO4 medium to form Fe-inhibitor complexes. DFT calculations and MD simulations further support the empirical outcomes. The findings exhibited that the prepared RBOS-12/Cl- system can be used as economic, eco-friendly, and efficient corrosion inhibitor with good anticorrosion properties for metals in acidic environments.

Experimental and theoretical explorations of S-alkylated mercaptobenzimidazole derivatives for use as corrosion inhibitors for carbon steel in HCl

Two mercaptobenzimidazole derivatives, namely the 1H-benzimidazol-2-thioyl hexane (MBI-C6) and the 1H-benzimidazol-2-thioyl dodecane (MBI-C12) were synthesized. The corrosion inhibiting potential of both compounds was studied in HCl solution (1.0 M HCl) for carbon steel. The investigation was conducted using gravimetric, electrochemical, Density Functional Theory (DFT), and molecular dynamics (MD) assessment methods. The carbon steel surfaces with or without the MBI-C6 and MBI-C12 were also assessed employing a Scanning Electron Microscope (SEM). The findings showed a high inhibition efficiency for both MBI-C6 and MBI-C12 at low concentrations, reaching 90% and 95.7% for MBI-C6 and MBI-C12 at 10−3 mol/L, respectively. Impedance results showed that the polarization resistance was greatly increased, from an initial value for the CS (in blank) of 12 up to 241 Ω cm2 for the inhibited solution (1.0 mol/L HCl with 10−3 mol/L of MBI-C12). Tested compounds inhibited CS corrosion through a physical-chemical adsorption mechanism that followed Langmuir adsorption isotherm model with a change in the free energy of adsorption from −35.97 to −38.63 kJ/mol. DFT calculations and MD simulations were used to check the effect of the molecular structure of MBI-C6 and MBI-C12 on their reactivity and, on the other hand, to explain their adsorption mode on the metal surface. By scanning electron microscopy (SEM), the adequate protection of carbon steel by the usage of MBI-C6 and MBI-C12 in 1.0 M HCl was confirmed. All the outcomes from experimental findings and theoretical calculations were in line.

Phenol adsorption mechanism on the zinc oxide surface: Experimental, cluster DFT calculations, and molecular dynamics simulations

Pollution by phenols is considered a major environmental issue. Therefore, their removal from wastewaters is of great practical significance and is directly related to human health. Herein, a porous zinc oxide (ZnO) was synthesized by a simple precipitation method and used as an adsorbent for the removal of phenol at different operating conditions. Besides experimental investigations, a comprehensive understanding of the mechanism of phenol adsorption on ZnO surface at the molecular level was achieved by using cluster Density Functional Theory (DFT) and molecular dynamics (MD) simulations. The prepared adsorbent was characterized using a variety of techniques, including X-ray diffraction (XRD), Fourier-transform infrared spectroscopy (FT-IR), as well as the Brunauer Emmett Teller (BET) method. The effects of different variables, such as pH, pHpzc (pH at the point of zero charge), initial concentration, and temperature, were investigated to optimize and understand the adsorption process. Possible controlling mechanism and the potential rate-limiting steps were analyzed using Lagergren's pseudo-first-order and pseudo-second-order models, and the data were found to follow the pseudo-second-order equation. The maximum removal of the phenol molecule was observed at pH = 4 with adsorption capacities of 3.61 and 4.51 mg/g at 30° and 50°, respectively. Furthermore, Cluster DFT calculations and molecular dynamics simulations were used to get deeper mechanistic insights on the adsorption behavior of the phenol molecule onto zinc oxide. DFT results confirmed the predominance of chemisorption while those from MD simulations indicated an increased interaction of ZnO with phenol in the presence of solvent due to water-bridged H-bonds.

Unveiling the novel characteristics of IGPD polymer and inhibitors binding affinities using 12-6-4 LJ-type nonbonded Mn2+ model

The metalloenzyme imidazole glycerophosphate dehydratase (IGPD) (EC 4.2.1.19) is essential in the histidine biosynthesis pathway in prokaryotes and eukaryotes, hence it has been identified as an attractive target with a majority of inhibitor studies focused on the development of broad-spectrum herbicides and bacteriostatic agent. However, due to the lack of work in structural biology, the reported inhibitors developed slowly with poor selectivity and diversity. To reveal the inhibitors binding affinities in ions centers of IGPD, we built point charge models based on a 12-6-4 type Lennard-Jones (LJ) potential, while combined DFT analyses, molecular docking and molecular dynamics (MD) simulations. This work introduced the interaction with surrounding solvent molecules and revealed a few undiscovered structural and kinetic characterizations of IGPD Mn2+ ions centers and ligand binding path, which revised some previous inexact assumptions inferred from crystal structures information. In addition, we also compared the dynamic binding characteristics of five IGPD inhibitors, and found that hydrogen bond interaction, spatial position and coordination stability with two Mn2+ ions can lead to the difference in potency. Overall, this work firstly unraveled the dynamic characteristics of IGPD polymer systems in explicit solvent and also provided a reference for the theoretical work of Mn2+-containing metalloenzyme, contributing for further target development.

Conformational Mobility and Efficiency in Supramolecular Catalysis. A Computational Approach to Evaluate the Performances of Enzyme Mimics

In the present study, we apply a computational approach, based on DFT calculations and molecular dynamics simulations, to investigate the catalytic behavior of four supramolecular catalysts active in the cleavage of phosphodiesters. The QM data indicate the operation of a synchronous associative mechanism with limited differences in the structures and energies of the transition states. The comparison with the experimental data, expressed in terms of effective molarity (EM), suggests that the difference in catalytic performance are not ascribable to a difference in the enthalpy of activation. On the other hand, the analysis of the Molecular Dynamics trajectories clearly indicates the conformational mobility, and therefore the conformational entropy, to be at the origin of the superior catalytic efficiency of the catalysts based on a more preorganized structure. Essentially, the combined method presented here provides, at a limited computational cost, a tool that is simple, general, and potentially suited for a large variety of catalytic systems to rationalize their performances and to predict those of enzyme mimics to be synthesized in a rational design process.

Fabrication of environmentally friendly Losartan potassium film for corrosion inhibition of mild steel in HCl medium

The present study aimed to find a suitable alternative for traditional and hazardous corrosion inhibitors. A green antihypertensive drug-Losartan potassium (LP) with superior corrosion protection ability was developed for the first time. Gravimetric method, potentiodynamic polarization, AC impedance, and scanning vibrating electrode technique (SVET) were combined to evaluate the corresponding inhibition performance towards Q235 steel in HCl medium. The results indicated that LP exhibited superior mixed-type corrosion protection to steel at different temperatures owing to the formation of compact and ordered LP-adsorption film on steel surface. Specifically, the inhibition performance values increased to 88.9%, 91.8%, and 92.0% for 5 mM LP at 298, 308, and 318 K, respectively. Meanwhile, N-Fe bond from X-ray photoelectronic spectroscopy (XPS) implied multiple anchoring interaction between steel and LP with nitrogen atoms as active sites. Based on DFT calculation and molecular dynamics (MD) simulation, the obtained low energy gap (ΔE) and high Ebinding values as well as radial distribution function (RDF) analysis represented strong chemisorption of LP on Fe substrate, which theoretically explained the favorable inhibition effectiveness of LP compound at molecular or atomic level.

Heuristics for chemical species identification in dense systems.

A new approach to identify chemical species from molecular dynamics (MD) simulations of reacting materials under extreme temperatures and pressures is presented. The approach is based on bond-distance and vibrational criteria, derived from the examination of atomic behavior during a density functional theory MD simulation of an overdriven shock of the explosive pentaerythritol tetranitrate. For comparison, the trajectory was analyzed using popular bonding criteria commonly used in analysis of reactive MD simulations, including distance, distance-time, and bond-order criteria. Cluster analyses using the new time-dependent bond definition approach presented here and a bond-order approach revealed that species and their corresponding lifetimes were strongly dependent on the chosen approach, indicating significant implications for the development of chemical mechanisms and chemical kinetics models using the results of reactive MD simulations.

The pathways of the [formula omitted] hydrogenation by NiCu/ZnO from DFT molecular dynamics simulations

Metal nanoparticles supported on semiconductor surfaces have been proposed as promising nanocatalyst candidates of CO2 conversion to energy carrier molecules such as formic acid or carbon monoxide, which can be used as a feedstock for fuels synthesis. This study is focused on the bimetallic Cu/Ni nanoparticles supported on the ZnO. The respective reaction mechanisms have been studied by means of the Molecular Dynamics with the DFT methodology. The results suggest that on CuNi/ZnO CO2 hydrogenation to formate pathway is more favorable than carboxyl route. These pathways are competitive with the CO2 reduction to CO.

Molecular insights into the loading and dynamics of anticancer drugs on silicene and folic acid-conjugated silicene nanosheets: DFT calculation and MD simulation

The adsorption behavior of Anastrozole (ANA) and Melphalan (MEL) anticancer drugs on the surface of silicene nanosheet (SNS) and functionalized SNS with folic acid (FA-SNS) is investigated and compared using the density functional theory (DFT) and molecular dynamics (MD) simulation. The DFT calculation is performed at the M06-2X/6–31G** level to characterize the optimized geometry properties of the designed complexes. The calculated adsorption energies are in the range from −65.59 to −144.23 kJ/mol, indicating the drug absorption on the surface of SNS and FA-SNS is exergonic. The π-π interaction between the drugs and SNS surface is the main driving force in the formation of drug-carriers complexes. The quantum theory of atoms in molecule (QTAIM) results reveal that the interaction of SNS and FA-SNS with both drugs has a non-covalent nature. The natural bond orbital (NBO) analysis shows that the charge is transferred from the drug molecules to carrier in all of the investigated complexes. Furthermore, MD simulations reveal that the contribution of van der Waals energy in drug-carrier interactions is more than electrostatic energy. Also, the obtained results demonstrate that the movement of drug molecules toward the carriers is spontaneous. Our study provides insights into the drug delivery capability of SNS and FA-SNS for the delivery of two drugs (ANA and MEL). Communicated by Ramaswamy H. Sarma