DFT-MD Simulations Research Articles

Self-Assembly, Adaptive Response, and in,out-Stereoisomerism of Large Orthoformate Cryptands.

We report on triethylene glycol-based orthoformate cryptands, which adapt their bridgehead configurations in response to metal templates and intramolecular hydrogen bonding in a complex manner. In contrast to smaller 1.1.1-orthoformate cryptands, the inversion from out,out-2.2.2 to in,in-2.2.2 occurs spontaneously by thermal homeomorphic isomerization, i. e., without bond breakage. The global thermodynamic minimum of the entire network, which includes an unprecedented third isomer (in,out-2.2.2), could only be reached under conditions that facilitate dynamic covalent exchange. Both inversion processes were studied in detail, including DFT calculations and MD simulations, which were particularly helpful for explaining differences between equilibrium compositions in solvents chloroform and acetonitrile. Unexpectedly, the system could be driven to the in,out-2.2.2 state by using a metal template with a size mismatch with respect to the out,out-2.2.2 cage.

Ions Tune Interfacial Water Structure and Modulate Hydrophobic Interactions at Silica Surfaces.

The structure and ultrafast dynamics of the electric double layer (EDL) are central to chemical reactivity and physical properties at solid/aqueous interfaces. While the Gouy-Chapman-Stern model is widely used to describe EDLs, it is solely based on the macroscopic electrostatic attraction of electrolytes for the charged surfaces. Structure and dynamics in the Stern layer are, however, more complex because of competing effects due to the localized surface charge distribution, surface-solvent-ion correlations, and the interfacial hydrogen bonding environment. Here, we report combined time-resolved vibrational sum frequency generation (TR-vSFG) spectroscopy with ab initio DFT-based molecular dynamics simulations (AIMD/DFT-MD) to get direct access to the molecular-level understanding of how ions change the structure and dynamics of the EDL. We show that innersphere adsorbed ions tune the hydrophobicity of the silica-aqueous interface by shifting the structural makeup in the Stern layer from dominant water-surface interactions to water-water interactions. This drives an initially inhomogeneous interfacial water coordination landscape observed at the neat interface toward a homogeneous, highly interconnected in-plane 2D hydrogen bonding (2D-HB) network at the ionic interface, reminiscent of the canonical, hydrophobic air-water interface. This ion-induced transformation results in a characteristic decrease of the vibrational lifetime (T1) of excited interfacial O-H stretching modes from T1 ∼ 600 fs to T1 ∼ 250 fs. Hence, we propose that the T1 determined by TR-vSFG in combination with DFT-MD simulations can be widely used for a quantitative spectroscopic probe of the ion kosmotropic/chaotropic effect at aqueous interfaces as well as of the ion-induced surface hydrophobicity.

Molecular dynamics simulation of graphene sinking during chemical vapor deposition growth on semi-molten Cu substrate

Copper foil is the most promising catalyst for the synthesis of large-area, high-quality monolayer graphene. Experimentally, it has been found that the Cu substrate is semi-molten at graphene growth temperatures. In this study, based on a self-developed C–Cu empirical potential and density functional theory (DFT) methods, we performed systematic molecular dynamics simulations to explore the stability of graphene nanostructures, i.e., carbon nanoclusters and graphene nanoribbons, on semi-molten Cu substrates. Many atomic details observed in the classical MD simulations agree well with those seen in DFT-MD simulations, confirming the high accuracy of the C–Cu potential. Depending on the size of the graphene island, two different sunken-modes are observed: (i) graphene island sinks into the first layer of the metal substrate and (ii) many metal atoms surround the graphene island. Further study reveals that the sinking graphene leads to the unidirectional alignment and seamless stitching of the graphene islands, which explains the growth of large single-crystal graphene on Cu foil. This study deepens our physical insights into the CVD growth of graphene on semi-molten Cu substrate with multiple experimental mysteries well explained and provides theoretic references for the controlled synthesis of large-area single-crystalline monolayer graphene.

Atomistic Simulations of COSAN: Amphiphiles without a Head-and-Tail Design Display "Head and Tail" Surfactant Behavior.

Cobaltabisdicarbollide (COSAN) anions have an unexpectedly rich self-assembly behavior, which can lead to vesicles and micelles without having a classical surfactant molecular architecture. This was rationalized by the introduction of new terminology and novel driving forces. A key aspect in the interpretation of COSAN behavior is the assumption that the most stable form of these ions is the transoid rotamer, which lacks a "hydrophilic head" and a "hydrophobic tail". Using implicit solvent DFT calculations and MD simulations we show that in water, 1) the cisoid rotamer is the most stable form of COSAN and 2) this cisoid rotamer has a well-defined hydrophilic polar region ("head") and a hydrophobic apolar region ("tail"). In addition, our simulations show that the properties of this rotamer in water (interfacial affinity, micellization) match those expected for a classical surfactant. Therefore, we conclude that the experimental results for the COSAN ions can now be understood in terms of its amphiphilic molecular architecture.

Atomistic Simulations of COSAN: Amphiphiles without a Head‐and‐Tail Design Display “Head and Tail” Surfactant Behavior

AbstractCobaltabisdicarbollide (COSAN) anions have an unexpectedly rich self‐assembly behavior, which can lead to vesicles and micelles without having a classical surfactant molecular architecture. This was rationalized by the introduction of new terminology and novel driving forces. A key aspect in the interpretation of COSAN behavior is the assumption that the most stable form of these ions is the transoid rotamer, which lacks a “hydrophilic head” and a “hydrophobic tail”. Using implicit solvent DFT calculations and MD simulations we show that in water, 1) the cisoid rotamer is the most stable form of COSAN and 2) this cisoid rotamer has a well‐defined hydrophilic polar region (“head”) and a hydrophobic apolar region (“tail”). In addition, our simulations show that the properties of this rotamer in water (interfacial affinity, micellization) match those expected for a classical surfactant. Therefore, we conclude that the experimental results for the COSAN ions can now be understood in terms of its amphiphilic molecular architecture.

Functionalized graphene oxide as a new generation corrosion inhibitor for industrial pickling process: DFT and experimental approach

The present work deals with the synthesis of p-aminophenol functionalized graphene oxide (PAP-GO) and its inhibition behavior on mild steel corrosion in 1 M HCl using experimental and computational techniques. The morphology and chemical structure of the synthesized PAP-GO were analyzed by FT-IR, XRD, TEM, Raman, and XPS spectra. Electrochemical impedance spectroscopy (EIS) and potentiodynamic polarization experimental methods were employed to study the corrosion inhibition efficiency of PAP-GO. EIS study suggests that the inhibition efficiencies of PAP-GO and p-aminophenol (PA) increase with increasing their concentrations. It was observed that PAP-GO acts as better inhibitor for mild steel corrosion and it showed maximum inhibition efficiency of 92.86% at as low as 25 mgL−1 concentration. Potentiodynamic polarization study revealed that PAP-GO acts as mixed type inhibitor and predominantly shows cathodic behavior. PAP-GO adsorption onto the mild steel surface was examined using X-ray photoelectron spectroscopy (XPS), scanning electron microscopy (SEM), and energy dispersive X-ray spectroscopy (EDX) techniques. The electrochemical and surface studies were supported by DFT calculations and MD simulations methods. A good correlation between the finding of computational and experimental results were derived.

Ultrasound induced green synthesis of pyrazolo-pyridines as novel corrosion inhibitors useful for industrial pickling process: Experimental and theoretical approach

Abstract Three pyrazolo-pyridine derivatives namely, (PPs) (4-(4-methoyphenyl)3,5-dimethyl-1,4,7,8-tetrahydrodipyrazolopyridine) (PP-1), 3,5dimethyl-4-phenyl-1,4,7,8-tetrahydrodipyrazolopyridine (PP-2) and (3,5-dimethyl-4-(3-nitrophenyl)-1,4,7,8-tetrahyddrodipyrazolopyridine) (PP-3) having different substituents was synthesized using ultrasound mediated one step multicomponent reactions and evaluated as corrosion inhibitors for mild steel in acidic medium of 1 M HCl. Protection ability of the synthesized PPs was determined using several experimental and computational modeling methods. Results showed that PP-3 having electron withdrawing nitro (–NO2) substituent showed lowest inhibition ability and PP-1 having electron releasing methoxy (–OCH3) substituent showed the highest inhibition efficiency. Inhibition efficiencies of the tested PP molecules followed the order: PP-1 (96.4%; –OCH3) > PP-2 (94.2%; –H) > PP-1 (91.1%; –NO2). Electrochemical studies suggested that PPs acted as interface and mixed type of corrosion inhibitors and their adsorption at the metal-electrolyte interfaces obeyed the Langmuir adsorption isotherm model. SEM and AFM analyses were adopted to measure the surface morphology of inhibited and uninhibited metallic surfaces. Experimental results were corroborated by results derived from DFT modeling and MD simulations.

Investigation of the temperature in dense carbon near the solid-liquid phase transition between 100 GPa and 200 GPa with spectrally resolved X-ray scattering

We present experiments investigating dense carbon at pressures between 100 GPa and 200 GPa and temperatures between 5,000 K and 15,000 K. High-pressure samples with different temperatures were created by laser-driven shock compression of graphite and varying the initial density from 1.53 g/cm3 to 2.21 g/cm3 and the drive laser intensity from 7.1 TW/cm2 to 14.2 TW/cm2. In order to deduce temperatures, spectrally resolved X-ray scattering was applied to determine ion-ion structure factors at a scattering vector of k = 4.12·1010m−1, which shows high sensitivity to temperature for the investigated sample conditions. After comparison to corresponding DFT-MD simulations, we were able to assign each structure factor a temperature. This information is indicative of the expected temperature range for the melting line of carbon at high pressures and can be compared to theoretical predictions.

Removing phenol contaminants from wastewater using graphene nanobuds: DFT and reactive MD simulation investigations

Phenol and phenolic compounds are extensively found in effluents and are toxic even at low concentrations hence their elimination from aqueous solutions is necessary. In the present work, the interaction of phenol and water molecules with graphene and graphene nanobud (GNB) was investigated using DFT-D3 calculations with revPBE/def2-TZVP model of theory. Various binding sites and ways of approach for phenol/water molecule approaching the selected adsorbents were evaluated. We found that water molecule tends to interact weakly with both graphene and GNB compared with the phenol molecule. The strength of adsorption for GNB at the top of the fullerene cage as well as near the neck site and onto the graphene surface was found to be stronger for phenol rather than water molecule. This can be attributed to the existence of simultaneous π-π stacking and electrostatic attractions for phenol/adsorbent system. Our first-principles calculations showed that binding nature of interacting molecules depends strongly on the long-range non-local dispersion forces but slightly to the solvent entity. The obtained binding energies compared with the experimental and highly accurate quantum-mechanical values available in literature for water/benzene adsorbed onto the graphene surface. Moreover, the adsorption ability and capacity of GNB was verified by reactive MD simulation carrying out at ambient condition. The desirable binding strength obtained accompanied with high specific surface area of GNB (due to fastened buckyballs) compared with the graphene lead to practically arrest these novel hybrid nano-materials as superior adsorbents for phenol adsorption and remediation from water-contaminated environment.

Machine Learning Forces Trained by Gaussian Process in Liquid States: Transferability to Temperature and Pressure

We study a generalization performance of the machine learning (ML) model to predict the atomic forces within the density functional theory (DFT). The targets are the Si and Ge single component systems in the liquid state. To train the machine learning model, Gaussian process regression is performed with the atomic fingerprints which express the local structure around the target atom. The training and test data are generated by the molecular dynamics (MD) based on DFT. We first report the accuracy of ML forces when both test and training data are generated from the DFT-MD simulations at a same temperature. By comparing the accuracy of ML forces at various temperatures, it is found that the accuracy becomes the lowest around the phase boundary between the solid and the liquid states. Furthermore, we investigate the transferability of ML models trained in the liquid state to temperature and pressure. We demonstrate that, if the training is performed at a high temperature and if the volume change is not so large, the transferability of ML forces in the liquid state is high enough, while its transferability to the solid state is very low.

Thermal conductivity of dissociating water—an ab initio study

The thermal conductivity of partially dissociated and ionised water is calculated in a large-scale study using density functional theory (DFT)-based molecular dynamics (MD) simulations. In doing so, the required heat current of the nuclei is calculated by mapping the effective particle interactions from the DFT-MD simulations onto classical pair potentials. It is demonstrated that experimental and theoretical thermal conductivity data for liquid heavy water and for ice VII are well reproduced with this efficient procedure. Moreover, the approach also allows for an illustrative interpretation of the characteristics of the thermal conductivity in the dense chemically reacting fluid. The thermodynamic conditions investigated here range from densities between 0.2 and 6 g cm−3 and temperatures between 600 and 50 000 K, which includes states highly relevant for understanding the interiors of water-rich planets like Uranus and Neptune and exoplanets of similar composition.

Diffraction Signal from Sodium Cluster in Hard Carbon: A Combined Experimental and Computational Study

Na-ion batteries have attracted increasing attention as large-scale energy storage devices. Hard carbon is a standard anode material owing to its large capacity and good cycling stability1, 2. However, sodium storage mechanism of hard carbon has not been fully understood due to its low crystallinity and diversity of microstructure. This study aimed to systematic understanding of the relationship between microstructure and sodium storage behavior with special attention to the diffraction signal from sodium cluster confined in nanopores. Hard carbons were synthesized by hydrothermal treatment of sucrose and subsequent high-temperature carbonizations at T = 1000-1900 °C (denoted as HC-T). The charge-discharge tests were carried out using half-cells. As the heat-treatment temperature increased, the capacity of the high potential region (> 0.2 V) decreased while the plateau region (< 0.2 V) become dominant. HC-1400 showed the highest overall capacity (347 mAh g-1) and initial coulombic efficiency (95.2%). Reaction mechanism analyses were performed on three representative samples, HC-1000, HC-1400, and HC-1900. Ex-situ small angle X-ray scattering (SAXS) measurements revealed (i) the nanopores become larger with decreasing their number for higher annealing temperatures, (ii) insertion of sodium into the nanopores proceeded under ca. 0.07 V. When electrodes were overcharged exceeding the sodium deposition voltage (ca. –0.01 V), the sodium density in the nanopores became comparable to that of bulk bcc sodium. Besides, apparent smaller capacity of HC-1900 was analyzed to be a kinetic observation with larger cathodic polarization. Careful ex-situ X-ray diffraction measurements have detected smaller mean interlayer distances in order of HC-1900 < HC-1400 < HC-1000. Expansion of interlayer distance upon sodium insertion was observed for HC-1000 and HC-1400, but not at all for HC-1900, suggesting the existence of a threshold interlayer distance to allow sodium insertion. Importantly, for the first time, we have succeeded to detect a broad peak appeared around 29° as a signature of sodium insertion into the nanopores, and its origin was analyzed to be diffraction from sodium clusters in the nanopores using DFT-MD simulations. Based on these analyses, criteria for better hard carbon will be discussed in the poster. Figure 1

Mean-force scattering potential for calculating optical properties of dense plasmas

We assess the relative importance of ionic structure on the opacity of dense plasmas by using the potential of mean force as a scattering potential within the Kubo-Greenwood formalism. We compare results from the potential of mean force, which includes realistic ionic structure, to results using an average atom potential, which includes only a crude treatment of ionic structure. Comparisons with less approximate but more expensive DFT-MD simulations for aluminum plasma reveal that the mean force generally improves agreement for DC conductivity. We also see improvement when applying the mean force to free-free transitions, whereas for bound-bound and bound-free transitions the mean force leads to poorer agreement on transition energies. Further, we assess the impact of accounting for correlations within the plasma at the temperature and density conditions relevant to iron opacity measurements at Sandia’s Z machine facility [Bailey et al., Nature 517:56-59, 2015] and find that these correlations do not account for the discrepancy between the measurements and leading opacity calculations.

Computational Protocol to Understand P450 Mechanisms and Design of Efficient and Selective Biocatalysts.

Cytochrome P450 enzymes have gained significant interest as selective oxidants in late-stage chemical synthesis. Their broad substrate scope enables them to be good candidates for their use in non-natural reactivity. Directed evolution evolves new enzyme biocatalysts that promote alternative reactivity for chemical synthesis. While directed evolution has proven useful in developing biocatalysts for specific purposes, this process is very time and labor intensive, and therefore not easily repurposed. Computational analysis of these P450 enzymes provides great insights into the broad substrate scope, the variety of reactions catalyzed, the binding specificity and the study of novel biosynthetic reaction mechanisms. By discovering new P450s and studying their reactivities, we uncover new insights into how this reactivity can be harnessed. We discuss a standard protocol using both DFT calculations and MD simulations to study a variety of cytochrome P450 enzymes. The approach entails theozyme models to study the mechanism and transition states via DFT calculations and subsequent MD simulations to understand the conformational poses and binding mechanisms within the enzyme. We discuss a few examples done in collaboration with the Tang and Sherman/Montgomery groups toward elucidating enzyme mechanisms and rationally designing new enzyme mutants as tools for selective C–H functionalization methods.

Insights into the adsorption mechanism and dynamic behavior of tetracycline antibiotics on reduced graphene oxide (RGO) and graphene oxide (GO) materials

Adsorption mechanism and dynamic behavior studies of TCs by the DFT method and MD simulations.

Spectroscopic BIL-SFG Invariance Hides the Chaotropic Effect of Protons at the Air-Water Interface

The knowledge of the water structure at the interface with the air in acidic pH conditions is of utmost importance for chemistry in the atmosphere. We shed light on the acidic air-water (AW) interfacial structure by DFT-MD simulations of the interface containing one hydronium ion coupled with theoretical SFG (Sum Frequency Generation) spectroscopy. The interpretation of SFG spectra at charged interfaces requires a deconvolution of the signal into BIL (Binding Interfacial Layer) and DL (Diffuse Layer) SFG contributions, which is achieved here, and hence reveals that even though H 3 O + has a chaotropic effect on the BIL water structure (by weakening the 2D-HBond-Network observed at the neat air-water interface) it has no direct probing in SFG spectroscopy. The changes observed experimentally in the SFG of the acidic AW interface from the SFG at the neat AW are shown here to be solely due to the DL-SFG contribution to the spectroscopy. Such BIL-SFG and DL-SFG deconvolution rationalizes the experimental SFG data in the literature, while the hydronium chaotropic effect on the water 2D-HBond-Network in the BIL can be put in perspective of the decrease in surface tension at acidic AW interfaces.

Analysis of Diffusion in Solid-State Electrolytes through MD Simulations, Improvement of the Li-Ion Conductivity in β-Li3PS4 as an Example.

Molecular dynamics simulations are a powerful tool to study diffusion processes in battery electrolyte and electrode materials. From molecular dynamics simulations, many properties relevant to diffusion can be obtained, including the diffusion path, amplitude of vibrations, jump rates, radial distribution functions, and collective diffusion processes. Here it is shown how the activation energies of different jumps and the attempt frequency can be obtained from a single molecular dynamics simulation. These detailed diffusion properties provide a thorough understanding of diffusion in solid electrolytes, and provide direction for the design of improved solid electrolyte materials. The presently developed analysis methodology is applied to DFT MD simulations of Li-ion diffusion in β-Li3PS4. The methodology presented is generally applicable to diffusion in crystalline materials and facilitates the analysis of molecular dynamics simulations. The code used for the analysis is freely available at: https://bitbucket.org/niekdeklerk/md-analysis-with-matlab. The results on β–Li3PS4 demonstrate that jumps between bc planes limit the conductivity of this important class of solid electrolyte materials. The simulations indicate that the rate-limiting jump process can be accelerated significantly by adding Li interstitials or Li vacancies, promoting three-dimensional diffusion, which results in increased macroscopic Li-ion diffusivity. Li vacancies can be introduced through Br doping, which is predicted to result in an order of magnitude larger Li-ion conductivity in β–Li3PS4. Furthermore, the present simulations rationalize the improved Li-ion diffusivity upon O doping through the change in Li distribution in the crystal. Thus, it is demonstrated how a thorough understanding of diffusion, based on thorough analysis of MD simulations, helps to gain insight and develop strategies to improve the ionic conductivity of solid electrolytes.

Insights into Magneto-Optics of Helical Conjugated Polymers.

Materials with magneto-optic (MO) properties have enabled critical fiber-optic applications and highly sensitive magnetic field sensors. While traditional MO materials are inorganic in nature, new generations of MO materials based on organic semiconducting polymers could allow increased versatility for device architectures, manufacturing options, and flexible mechanics. However, the origin of MO activity in semiconducting polymers is far from understood. In this paper, we report high MO activity observed in a chiral helical poly-3-(alkylsulfone)thiophene (P3AST), which confirms a new design for the creation of a giant Faraday effect with Verdet constants up to (7.63 ± 0.78) × 104 deg T-1 m-1 at 532 nm. We have determined that the sign of the Verdet constant and its magnitude are related to the helicity of the polymer at the measured wavelength. The Faraday rotation and the helical conformation of P3AST are modulated by thermal annealing, which is further supported by DFT calculations and MD simulations. Our results demonstrate that helical polymers exhibit enhanced Verdet constants and expand the previous design space for polythiophene MO materials that was thought to be limited to highly regular lamellar structures. The structure-property studies herein provide insights for the design of next-generation MO materials based upon semiconducting organic polymers.

Spectroscopic characterization of 8-hydroxy-5-nitroquinoline and 5-chloro-8-hydroxy quinoline and investigation of its reactive properties by DFT calculations and molecular dynamics simulations

Combined spectroscopic and computational study of two 8-hydroxyquinoline derivatives, 8-hydroxy-5-nitroquinoline (8H5NQ) and 5-chloro-8-hydroxyquinoline (5CL8HQ) has been performed in order to perform detailed characterization and evaluation of their reactive properties. Spectroscopic characterization of 8-hydroxyquinoline derivatives has been performed by means of IR and FT-Raman techniques, while computational study has been performed by set of DFT calculations and MD simulations in order to address global and local reactive properties. Spectroscopic properties have also been obtained with DFT calculations as well, and the obtained results have been mutually compared. The calculated values of dipole moment, polarizability, first and second order hyperpolarizability values indicate that the title compounds exhibit NLO behaviour and hence may be considered for further development of NLO materials. NBO analysis is made to study the stability of the molecular systems arising from hyper conjugative interactions and charge delocalization. The docked ligands form stable complexes with dehydrogenase inhibitor which gives binding affinity value of −6.2 kcal/mol for 5CL8HQ and-5.8 kcal/mol for 8H5NQ and the docking results suggest that the compounds might exhibit inhibitory activity against ACP reductase.

WITHDRAWN: Ultrasound induced green synthesis of pyrazolo-pyridines as novel corrosion inhibitors useful for industrial pickling process: Experimental and theoretical approach

Abstract Three pyrazolo-pyridine derivatives namely, (PPs) (4-(4-methoyphenyl)3,5-dimethyl-1,4,7,8-tetrahydrodipyrazolopyridine) (PP-1), 3,5dimethyl-4-phenyl-1,4,7,8-tetrahydrodipyrazolopyridine (PP-2) and (3,5-dimethyl-4-(3-nitrophenyl)-1,4,7,8-tetrahyddrodipyrazolopyridine) (PP-3) having different substituents was synthesized using ultrasound mediated one step multicomponent reactions and evaluated as corrosion inhibitors for mild steel in acidic medium of 1 M HCl. Protection ability of the synthesized PPs was determined using several experimental and computational modeling methods. Results showed that PP-3 having electron withdrawing nitro (–NO2) substituent showed lowest inhibition ability and PP-1 having electron releasing methoxy (–OCH3) substituent showed the highest inhibition efficiency. Inhibition efficiencies of the tested PP molecules followed the order: PP-1 (96.4%; –OCH3) > PP-2 (94.2%; –H) > PP-1 (91.1%; –NO2). Electrochemical studies suggested that PPs acted as interface and mixed type of corrosion inhibitors and their adsorption at the metal-electrolyte interfaces obeyed the Langmuir adsorption isotherm model. SEM and AFM analyses were adopted to measure the surface morphology of inhibited and uninhibited metallic surfaces. Experimental results were corroborated by results derived from DFT modeling and MD simulations.