Chemical Dynamics Simulations Research Articles

Role of OH Termination in Mitigating Friction of Diamond-like Carbon under High Load: A Joint Simulation and Experimental Study.

Diamond-like carbon (DLC) has recently attracted much attention as a promising solid-state lubricant because it exhibits low friction, low abrasion, and high wear resistance. Although we previously reported the reason why H-terminated DLC exhibits low friction based on a tight-binding quantum chemical molecular dynamics (TB-QCMD) simulation, experimentally, the low-friction state of H-terminated DLC is not stable, limiting its application. In the present work, our TB-QCMD simulations suggest that H/OH-terminated DLC could give low friction even under high loads, whereas H-terminated DLC could not. By using gas-phase friction experiments, we confirm that OH termination can indeed provide much more stable lubricity than H termination, validating the predictions from simulations. We conclude that H/OH-terminated DLC is a new low-friction material with high load capacity and high stable lubricity that may be suitable for practical use in industrial applications.

Adsorption of methylene blue cationic dye onto brookite and rutile phases of titanium dioxide: Quantum chemical and molecular dynamic simulation studies

This study reports the statistical physics modeling of the methylene blue cationic dye (MBCD) adsorption in aqueous solution on TiO2 surface. In order to comprehend the adsorption performance, theoretical investigations were done to collect extensive information about the chemical and physical properties of the molecules using quantum chemical parameters (QCP). Also, molecular dynamic and quantum descriptors were applied to better understand the dye adsorption on different phases of TiO2 (i.e., brookite and rutile). The molecular structures of MBCD acts as good electron donators to an empty d orbital of TiO2 due to the availability of electrons in both the lone pair on the N atoms and π electrons of the aromatic rings. The reactivity of optimized molecular structures was confirmed by the quantum chemical descriptors. Modeling results showed that the adsorption was performed with a horizontal position of MBCD molecules on both surfaces. Overall, the TiO2 showed the highest adsorption energies for protonated MBCD (N36N35) (-886.533 kcal/mol (MBCD/rutile-TiO2)) > −626.428 kcal/mol (MBCD/brookite-TiO2)), which implies that these sites prompt the adsorption on both surfaces. The analysis of the adsorption energy values showed an exothermic chemisorption process, which could be governed by steric parameters according to the results obtained with the molecular dynamics modeling.

Exploring the potential of novel phenolic compounds as potential therapeutic candidates against SARS-CoV-2, using quantum chemistry, molecular docking and dynamic studies

In the current study, the interaction of SARS-CoV-2 protein (A and B chains of nsp13) with different recently synthesized phenolic compounds (Sreenivasulu et al., Synthetic Communications, 2020, 112–122) has been studied. The interactions have been investigated by using molecular docking, quantum chemical and molecular dynamics simulations methods. The molecular structures of all the ligands are studied quantum chemically in terms of their optimized structures, 3-D orbital distributions, global chemical descriptors, molecular electrostatic potential plots and HOMO-LUMO orbital energies. All the ligands show reasonably good binding affinities with nsp-13 protein. The ligand L2 shows to have better binding affinities to Chain A and Chain B of nsp13 protein, which are −6.7 and −6.4 kcal/mol. The study of intermolecular interactions indicates that L2 shows different hydrophobic and hydrogen bond interactions with both chains. Furthermore, molecular dynamic simulations of the nsp13-L2 complex are obtained over a time scale of 60 ns, which indicates its stability and flexibility behavior as assessed in terms of its RMSD and RMSF graphs. The ADMET analysis also shows no violation of Lipinski rule (RO5) by studied phenolic compounds. We believe that the current findings will be further confirmed by in vitro and in vivo studies of these recent phenolic compounds for their potential as inhibitors for SARS-Co-V-2 virus.

The inhibition mechanism and adsorption behavior of three purine derivatives on the corrosion of copper in alkaline artificial seawater: Structure and performance

The inhibition mechanism and adsorption behavior of three purine derivatives (guanine (G), adenine (A), and hypoxanthine (I)) on the corrosion of copper in alkaline artificial seawater were studied by electrochemical tests, scanning electron microscopy (SEM), X-ray spectroscopy (XPS), quantum chemical calculation and molecular dynamics simulation. The results showed that the three inhibitors all delayed corrosion by indicating a protective film on the copper surface, and the order of their inhibition efficiency was I > G > A. The three inhibitors all obeyed the Langmuir adsorption model and belonged to a mixed physical and chemical adsorption. The G and I molecules were adsorbed on the copper surface in parallel, covering the copper surface to the greatest extent, thus playing a better inhibition effect. And the A was arranged obliquely at a certain angle with the copper surface, so its inhibition effect was relatively low. This research could help us explore the influence of functional groups on its inhibition performance and make improvements.

Efficiency of Gemini surfactant containing semi-rigid spacer as microbial corrosion inhibitor for carbon steel in simulated seawater

SRB is one of the main bacteria causing marine microbial corrosion. In order to reduce the loss of microbial corrosion, a Gemini surfactant (12-B-12) containing semi-rigid spacer was used to investigate the anti-bacterial and anti-corrosion performances of carbon steel in simulated seawater by weight-loss test, electrochemical method and surface morphology analysis. The results showed that the inhibition efficiency of 0.01 mM 12-B-12 was as high as 98.3% after 30 days of incubation in simulated seawater with SRB, and the planktonic and sessile SRB on the carbon steel surface can be reduced to undetectable level. Quantum chemical calculation and molecular dynamics simulation were used to study the structure–activity relationship.

Stereospecific collision-induced dissociation and vibrational spectroscopy of protonated cyclo (Tyr-Pro)

The protonated cyclo (LTyr-LPro) and cyclo (LTyr-DPro) dipeptides based on a diketopiperazine (DKP) ring are studied by tandem mass spectrometry in a Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometer. Collision-induced dissociation (CID) and infrared multiple-photon dissociation (IRMPD) spectroscopy results are interpreted with the aid of quantum chemical calculations and chemical dynamics simulations. All the conformers identified for each diastereomer, denoted c-LLH+ and c-LDH+, respectively, are protonated on the carbonyl group of the tyrosine. The most stable form has an extended structure with the aromatic ring oriented outside the DKP ring; it is stabilized by an OH+…π interaction. Distinct IR signatures are obtained for the extended conformers of c-LLH+ and c-LDH+, which differ by the strength of the OH+…π interaction, much stronger in c-LLH+. Less stable species with the aromatic ring folded over the DKP ring are kinetically trapped in our experimental conditions, but their IR spectrum is identical for c-LLH+ and c-LDH+. The main collision-induced dissociation products of the protonated dipeptides are analyzed using chemical dynamics simulations. More efficient CID is observed for c-LDH+, in particular for the formation of the iminium ion of tyrosine. In contrast to the monomers, the protonated dimers of c-LLH+ and c-LDH+ show identical IR spectra. This is explained in terms of a structure involving a single strong OH+…O interaction between subunits not sensitive to the absolute configuration of the residues, i.e., from a folded protonated monomer to an extended neutral monomer.

Theoretical study of the formation and nucleation mechanism of highly oxygenated multi-functional organic compounds produced by α-pinene.

In recent years, highly oxygenated organic molecules (HOMs) derived from photochemical reactions of α-pinene, the most abundant monoterpene, have been considered as important precursors of biogenic particles. However, the specific reactions of HOMs remain largely unknown, especially the corresponding formation and nucleation mechanism in the nanoscale. In this study, we implemented quantum chemical calculations and molecular dynamics (MD) simulations to explore the mechanism of the formation of HOM monomers/dimers by ozonolysis and autoxidation of α-pinene. Furthermore, we investigated the mechanisms of HOMs with different oxygen-to‑carbon (O/C) ratios and functional groups participating in neutral and ion-induced nucleation. The results show that the formation of HOMs is hardly affected by water, sulfuric acid and ions. In the ion-induced nucleation, HOM can dominate the initial nucleation steps; however, in the neutral nucleation, HOMs are more likely to participate in the growth stage. In addition, the nucleation ability of HOM has a bearing on the O/C ratio and the types of the functional groups. The current calculations provide valuable insight into the formation mechanism of the pure organic particles at low sulfuric acid concentrations.

Green synthesis of corrosion inhibitor with biomass platform molecule: Gravimetrical, electrochemical, morphological, and theoretical investigations

Considering the concept of green chemistry and the vision of human sustainability, a new corrosion inhibitor named N1-(2-aminoethyl)-N2-(2-(2-(furan-2-yl)-4,5-dihydro-1H-imidazol-1-yl) ethyl) ethane-1,2-diamine (NNED) is synthesized from biomass platform molecules. Both weight loss and electrochemical measurements demonstrated that the corrosion inhibitor had good anti-corrosion performance for carbon steel in 1 M HCl medium, with inhibition efficiency higher than 90% at lower level of inhibitor concentration (5 ppm). The adsorption of NNED on the steel surface was spontaneous and obeys the Langmuir adsorption isotherm. The corrosion morphology was studied by scanning electron microscopy (SEM) and atomic force microscopy (AFM). Force-distance curve directly quantified the adhesion force between the adsorption films and the metal surface. Quantum chemical calculation and molecular dynamics simulation were applied to study the corrosion inhibition mechanism.

Mechanism analysis of extractive distillation for separation of acetic acid and water based on quantum chemical calculation and molecular dynamics simulation

The selection of high efficiency and environmental protection entrainer is the inevitable requirement of extractive distillation sustainable development. According to the extraction mechanism, the σ-profile was drawn by COSMO-SAC model. Based on the quantum chemistry method, the interaction energy, deformation charge density and total charge density of different organic solvent, ionic liquids and acetic acid-water system were calculated. The binding energy between organic solvents, ionic liquids and acetic acid-water system was further analyzed by Gaussian software. The binding energies of organic solvent tetramethylene sulfone and 1-butyl-3-methylimidazolium dibutyl phosphate ([BMIM][BDP]) ionic liquid with acetic acid were - 934.9622 a.u., − 1610.6557 a.u., respectively. Through molecular dynamics simulation, the radial distribution functions of organic solvents and ionic liquids were calculated and compared at the molecular level, and the interaction between different molecules was analyzed. The cation plays a leading role. When Å = 4.5, ionic liquid and solvent interact strongly with acetic acid, respectively. The comprehensive results showed that tetramethylene sulfone and [BMIM][BDP] had better extraction effect. Finally, the self-diffusion coefficient of [BMIM][BDP] and HAc is 0.0105 cm2 / s. The combination of quantum chemical calculation and molecular dynamics simulation provides theoretical guidance for the effective separation of acetic acid-water system, which provides a certain reference for the selection of the best entrainer.

Wettability alteration by Smart Water multi-ion exchange in carbonates: A molecular dynamics simulation study

Smart Water ions (Ca2+, Mg2+, and SO42−) have been found to alter the wettability of oil-wet calcite surfaces, however, the widely proposed multi-ion exchange mechanism has never been understood on a molecular scale. In this work, a new model calcite surface with steps and locally charged sites was developed, and its properties were studied by quantum chemical calculations and molecular dynamics simulations to investigate the origin of the oil-wetness and its reversal by the Smart Water ions at temperatures ranging from 300 to 400 K. The simulation results using the proposed surface model are consistent with experimental results reported in the literature, including the Smart Water ions acting as the potential determining ions, and the oil carboxylate adsorption causing oil-wetness. The wettability alteration involves initial surface binding of Ca2+, which facilitates adsorption of SO42−. The latter enables the detachment of the Ca2+-carboxylate complexes at elevated temperatures (>350 K) where the ionic hydration shells are weakened as suggested by the increased interaction energy from less than −100 to over −400 kJ/mol between Ca2+ and SO42−, rationalizing the observed temperature dependence of the Smart Water effect. Overall, the presented simulations with the newly developed model calcite surface provide important new insights into wettability alteration effect of Smart Water ions, which has important implications for the optimization of the injection brines for enhanced oil recovery.

1-Phenyl-1H-tetrazol as Corrosion Inhibitor for Pipeline Steel in Sulfuric Acid Solution

1-Phenyl-1H-tetrazol (PHT) has been studied as an efficient corrosion inhibitor for X65 steel in sulfuric acid corrosion environment. Atomic force microscope test results show that PHT can effectively inhibit the corrosion of X65 steel in 0.5 M sulfuric acid solution. Quantum chemical calculations and molecular dynamics simulations show that PHT has a small energy gap value and a large dipole moment value, which is an excellent corrosion inhibitor. In addition, the adsorption of PHT on the Fe(110) surface adopts parallel adsorption and a large binding energy value, which shows that PHT can effectively inhibit the corrosion of X65 steel. Potentiodynamic polarization test results show that as the PHT concentration increases, the value of the corrosion current density decreases significantly. When the PHT concentration is 1 mM, the corrosion inhibition efficiency can reach 92.1%. In addition, the adsorption of PHT on the surface of X65 steel conforms to Langmuir adsorption, and the adsorption process is spontaneous.

Morphology Effects of Graphene Seeds on the Quality of Graphene Nucleation: Quantum Chemical Molecular Dynamics Simulations

The graphene growth on the Ni(111) surface in the presence of different graphene seeds C16 and C24 has been investigated at the atomic level by quantum chemical molecular dynamics simulations. The morphology effects of graphene seeds on the polygon growth behavior were explored by the random deposition of C2 species on the Ni(111) surface. The results demonstrated that in the presence of the graphene seeds, hexagons can be formed directly at the seed edges, different from the “pentagon-first” mechanism proposed before. At the edge of the seeds, different growth behaviors were observed depending on the specific edge structure. We found that the edge structures which are consisted of more carbon atoms prefer to form more hexagons, giving rise to the higher quality of graphene. Compared with the seed C16, C24 has more zigzag edge structures and is expected to produce more hexagons. This has been confirmed by our simulation, where the seed C24 produced higher quality graphene than C16. The results suggested that the morphology of the graphene seed could affect the quality of the graphene growth. Furthermore, the sequence growth along the edge structure of the seed is superior to the random growth on the metal surface.

Adsorption Mechanism of Potassium Oleate on Cobalt Surface Based on Cobalt Interconnection CMP: A Combined Experimental and DFT Investigation

Potassium oleate (PO) is a promising corrosion inhibitor to replace benzotriazole (BTA) for cobalt (Co) wiring in the integrated circuit (IC). The adsorption characteristics of different cobalt surfaces were characterized by the contact angle measurement. The formation of passive Co–PO film and the corrosion inhibitor efficiency of PO to cobalt was analyzed by electrochemistry and electrochemical impedance spectroscopy (EIS), and the change of chemical elements on the cobalt surface was analyzed by X-ray photoelectron spectroscopy (XPS). Furthermore, quantum chemical calculation and molecular dynamics simulation based on density functional theory (DFT) further revealed the adsorption mechanism of PO and cobalt at the molecular level. The results showed that Co–PO passivation film formed on the cobalt surface, besides, 2 mM PO has achieved the best inhibition efficiency on cobalt surface.

Capturing Water Networks during Ligand Binding with the Site-Identification by Ligand Competitive Saturation-Monte Carlo Approach

Water molecules impact interactions between proteins and their ligands, making a significant contribution to ligand binding orientation and affinity. Water molecules can significantly affect the energetics of ligand binding in a favorable or unfavorable manner associated, in part, with the energetic penalty for displacing waters that occupy a binding site. In computer-aided drug design, the challenge is to calculate water mediated interactions and their energetics between the ligand and the protein. In this work, an extension of the Site Identification by Ligand Competitive Saturation-Monte Carlo (SILCS-MC) docking approach is presented to determine the positioning of the water molecules in the binding site and estimate the energetic contribution of water to ligand binding. We employ this methodology on variety of protein targets where water mediated interactions between the protein and ligands plays an important role. The efficacy of this approach is reflected in rank-ordering ligand affinities, binding affinities predictions, and structure orientation of the ligands. The SILCS methodology is of utility for characterization of functional group affinities for the entire 3D region encompassed by a protein or other macromolecule. This approach is based on sampling the conformational space of multiple solutes representing various functional groups in the presence of explicit water of a protein target using a combination of oscillating chemical potential Grand Canonical Monte Carlo and Molecular Dynamics simulations. The presented approach offers new possibilities in revealing water networks and their contributions to the binding affinity of a ligand to a protein.

Eco-friendly rosin-based 6-dehydroabietic acylamino sodium as corrosion inhibitor for AA2024-T3 in alkaline solution by experimental and theoretical studies

To enhance the corrosion resistance of AA2024-T3 in aqueous NaOH (0.01 mol·L−1), the inhibition characteristics of the synthetic rosin-based anionic surfactant, 6-dehydroabietic acylamino sodium (6-DAS), were assessed using the static weight loss method, electrochemical impedance spectroscopy, potentiodynamic polarization curves, scanning electron microscopy, atomic force microscopy, X-ray photoelectron spectroscopy, UV–vis spectroscopy, and adsorption isotherm analysis. Simultaneously, quantum chemical calculations and molecular dynamics (MD) simulations were performed to predict and analyze the relationships between the molecular structure and inhibition efficiency. The results of the experiments revealed that 6-DAS achieved an inhibition efficiency of 92.95% as a valid corrosion inhibitor for AA2024-T3 in alkaline medium. Quantum chemical calculations showed that the anionic state of 6-DAS possessed a smaller band gap and a larger dipole moment than the neutral state, which indicated that anionic 6-DAS was easily adsorbed on the alloy surface in solution. This result was further proved by MD simulations, thereby strengthening the agreement between experimental results and theoretical calculations.

Structure and ion-ion interactions in trifluoroacetate-based ionic liquids: Quantum chemical and molecular dynamics simulation studies

Ionic liquids (ILs) raise quite interesting but complicated questions for computational study due to the fact that different interactions, e.g., electrostatic interactions, charge-transfer interactions, steric repulsion, dispersion and hydrogen bonding that determine structural organization of ILs, need to be described properly. In this work, we present a comprehensive understanding of structural properties and interactions between ions in trifluoroacetate-based ILs with ammonium cations containing ethyl groups with the general formula EtnNH4-n (n = 0–4). This study includes both gas-phase and implicit solvent calculations of single ionic pairs (DFT, QTAIM and NBO methods) and molecular dynamics (MD) simulations of the ILs themselves. Based on the gas-phase calculations we show that the ionic and molecular pairs with very strong hydrogen bonds are formed by diethylamine and triethylamine with trifluoroacetic acid, while only molecular pairs are generated from ammonia and ethylamine. Unlike this, the use of implicit solvent calculations for all compounds leads to the result that formation of ionic pairs becomes energetically more favorable which, in turn, improves the agreement with experiment. The trend in geometric parameters of hydrogen bonds obtained from MD simulations of the ILs is similar to that which is observed for the implicit solvent calculations of the ion pairs. The increase in the number of alkyl groups in the cation would decrease interaction between the ions as in the ionic pair, as well in the ionic liquid itself. Moreover, we suggest that the change in the ion-ion interaction is one of the most important factors that affects the melting points variation of the ILs for this series.

Initial competing chemical pathways during floating catalyst chemical vapor deposition carbon nanotube growth

Ferrocene (Fc) is an effective precursor for the direct synthesis of high quality single-walled carbon nanotubes (SWCNTs) via floating catalyst chemical vapor deposition (FCCVD). However, the formation mechanism of the Fe floating catalyst and the SWNCT growth precursors, such as carbon chains, during Fc decomposition are not well understood. Here, we report first principles nonequilibrium quantum chemical molecular dynamics simulations that investigate the decomposition of Fc during FCCVD. We examine the influence of additional growth precursors including ethylene, methane, CO, and CO2 on the Fc decomposition mechanism and show that the dissociation of these species into C2Hx radicals and C atoms provides the key growth agents for the nucleation of carbon chains from Fc-derived species such as cyclopentadienyl rings. Without an additional growth precursor, Fc decomposes via the spontaneous cleavage of Fe–C and C–H bonds, thereby enabling Fe atoms to cluster and form the floating catalyst. On the basis of these simulations, we detail the two competing chemical pathways present during the initial stages of FCCVD: Fe catalyst nanoparticle growth and carbon chain growth. The latter is accelerated in the presence of the additional growth precursors, with the identity of the precursor determining the nature of the balance between these competing pathways.

Theoretical studies on NH2 + NO2 reaction: Driven by reaction dynamics

Chemical dynamics simulations have been performed to study the NH2 + NO2 reaction on singlet potential energy surface at 298 K. To obtain more accurate potential energy surface, seven methods including MP2, B3LYP, OPBE, BhandH, HCTH407, M06 and M06–2X combined with aug-cc-pVDZ basis set were employed to calculate the properties of stationary points and the results are compared with the higher level CCSD(T) benchmark and the available theoretical and experimental values. The reaction reactivity, product branching ratio, and detailed microscopic reaction mechanisms are uncovered by direct dynamics simulations at the chosen B3LYP/aug-cc-pVDZ level of theory. The branching ratio between product P1 (N2O + H2O) : P2 (H2NO + NO) determined in current study is 0.22 : 0.78, which is in consistent with experimental observations. The study reveals a preference of P2 channel over P1 at 298 K, although the latter channel is more exothermic. This result indicates the dynamical factors govern the competition of two product channels. Three atomic mechanisms were determined and discussed in detail, in which the indirect reaction dominates. Interestingly, these indirect reactions follow the intrinsic reaction coordinate of the potential energy surface.

MD and DFT calculations on the structural variations of amino-cyclodextrin as a pH-sensitive carrier for smart carriage and release of Doxorubicin

Cyclodextrins have been widely employed as nanocarriers due to their unique structure and proper controlled drug delivery as well as nontoxicity, water solubility, and proper capacity to carry hydrophobic drugs. In addition, pH-sensitized compounds have found particular importance in the field of anticancer drug delivery. In this study, the structure of amino-β-cyclodextrin was theoretically explored as a pH-sensitive and smart carrier for Doxorubicin anticancer drug. To this end, quantum chemical calculation methods and molecular dynamics (MD) simulations were applied on amino-β-cyclodextrin to assess its ability to carry Doxorubicin anticancer drug. Quantum chemistry results indicated a deformation in the nanocarrier during protonation. Moreover, interaction energy and quantum molecular describers confirm the drug storage under non-protonated conditions and its release under protonation conditions. Hydrogen bonding, carrier-drug energy, and center of mass (COM) distances (obtained from MD simulation) also suggest drug carrying and releasing under non-protonated and protonated conditions, respectively.

Chemical dynamics simulations of energy transfer in CH4 and N2 collisions.

Chemical dynamics simulations have been performed to study the energy transfer from a hot N2 bath at 1000 K to CH4 fuel at 300 K at different bath densities ranging from 1000 kg m−3 to 30 kg m−3. At higher bath densities, the energy transfer from the bath to the fuel was rapid and as the density was decreased, the energy transfer rate constant decreased. The results show that in combustion systems with CH4 as a prototype fuel, the super pressure regimes control the fuel heating and combustion processes.