T-shaped Stacking Research Articles

Effect of microwave electric field on asphaltene aggregation in a heavy oil system: MD and DFT investigation

An in-depth understanding of asphaltene aggregation is vital for the viscosity reduction of heavy oils, and essential for fully utilizing heavy oil resources. Therefore, the influence of microwave electric field on the aggregation of asphaltene in the heavy oil system was investigated via Molecular Dynamic simulation and Density Functional Theory calculation. The aggregation forms, interaction types and rheological behavior of asphaltene and other components were calculated by processing the trajectories. The results reveal that microwave electric fields play a significant role in the packing morphology of asphaltenes and other components at the micro-molecular level, leading to changes in the apparent viscosity of heavy oil system. It can be clearly manifested that under 5 V/nm of microwave electric field, asphaltenes primarily stack in π - π, connecting intimately with resin, constructing a stable colloidal structure of the system with high viscosity. Whereas, by enhancing the electric field, π-π stacking will gradually be destroyed, resulting in viscosity reduction. The T-shaped stacking of asphaltenes is favorable to form at 20 V/nm, inducing a stable network among the components, which is detrimental to the viscosity reduction. The achievements further confirm that an appropriate microwave electric field is the key to reducing the viscosity. In addition, considering the thermal and non-thermal effects of microwave, it is explored that microwave is more effective at low temperature. Therefore, the efficient combination of microwave power and treatment temperature is the critical factor to achieve better viscosity reduction effect.

ARDG Analysis of Asphaltene Molecular Viscosity and Molecular Interaction Based on Non-Equilibrium Molecular Dynamics Simulation.

Understanding the noncovalent (weak) interactions between asphaltene molecules is crucial to further comprehending the viscosity and aggregation behavior of asphaltenes. In the past, intermolecular interactions were characterized indirectly by calculating the radial distribution function and the numerical distribution of distances/angles between atoms, which are far less intuitive than the average reduced density gradient (aRDG) method. This study selected three representative asphaltene molecules (AsphalteneO, AsphalteneT, and AsphalteneY) to investigate the relationship between viscosity and weak intermolecular interactions. Firstly, a non-equilibrium molecular dynamics (NEMD) simulation was employed to calculate the shear viscosities of these molecules and analyze their aggregation behaviors. In addition, the types of weak intermolecular interactions of asphaltene were visualized by the aRDG method. Finally, the stability of the weak intermolecular interactions was analyzed by the thermal fluctuation index (TFI). The results indicate that AsphalteneY has the highest viscosity. The aggregation behavior of AsphalteneO is mainly face-face stacking, while AsphalteneT and AsphalteneY associate mainly via offset stacking and T-shaped stacking. According to the aRDG analysis, the weak interactions between AshalteneT molecules are similar to those between AshalteneO molecules, mainly due to van der Waals interactions and steric hindrance effects. At the same time, there is a strong attraction between AsphalteneY molecules. Additionally, the results of the TFI analysis show that the weak intermolecular interactions of the three types of asphaltene molecules are relatively stable and not significantly affected by thermal motion. Our results provide a new method for better understanding asphaltene molecules' viscosity and aggregation behavior.

Effects of microwave electric field on the structure and association behaviour of asphaltenes: MD and DFT study

Asphaltenes are prone to aggregation through complex macromolecular interactions, resulting in high-viscosity crude oil. The aggregation behaviour of asphaltene in different solvents under microwave fields was simulated and studied by molecular dynamics in this research. Furthermore, the nature of asphaltene monomers and the interactions of dimers were investigated by density functional theory to explore the contribution of the microwave electric field on asphaltene aggregation. The results show that the microwave electric field is beneficial for breaking T-shaped stacking and forming π-π stacking, which greatly reduces hydrogen bonds and weakens the molecular interactions, thus effectively inhibiting the proceeding of aggregation. Applying an electric field with a strength of 8 V/nm has been found to have the best asphaltene dispersion efficiency. This work innovatively reveals the microscopic behaviour of asphaltenes in various solvents by microwave irradiation, contributing to the disassociation of heavy oil micelles with microwave introduction.

Effect of Polar Molecule Aggregation on the Stability of Crude Oil/Water Interface: A Molecular Simulation Study

Abstract To ensure the efficient operation of crude oil dehydration and sewage treatment technology in oilfield surface production system, the effect mechanism of polar components represented by asphaltene and resin on the formation and stability of oil-water emulsion needs to be revealed at nanoscale. In this paper, the molecular dynamics simulation method was used to construct the crude oil/polar component/water system models with different molar ratios of asphaltene to resin by adjusting the number of asphaltene and resin molecules, so as to reveal the molecular arrangement and aggregation process and film forming characteristics of asphaltene, resin, and their mixture at the oil-water interface. The simulated results showed that the aggregation process of asphaltene molecules under the influence of hydrogen bonds can be divided into three stages. The addition of resin molecules enhanced the connection between molecules of all polar components at the interface. The π−π stacking and T-shaped stacking structures were found in all aggregations, and the higher the molar ratio of asphaltene molecules, the higher the proportion of π−π stacking structure. With the increase of the molar ratio of asphaltene to resin increases from 0 : 1 to 1 : 0, the interfacial film thickness and interface formation energy increase from 2.366 nm and -143.89 kJ/mol to 3.796 nm and -304.09 kJ/mol, respectively, which indicated that asphaltene molecules play a more significant role in promoting the formation of interfacial film and maintaining its structural stability than resin molecules. The investigations in this study provide theoretical support for demulsification of the crude oil emulsion.

Towards an understanding of diffusion mechanism of bio-rejuvenators in aged asphalt binder through molecular dynamics simulation

The use of reclaimed asphalt pavement (RAP) is a hot research topic in the field of road engineering, as there are still many issues to overcome so as to become standard engineering applications. The diffusion of virgin/aged asphalt binder is a key process to improve RAP performance. In this study, the asphalt binder diffusion models were developed by molecular dynamics (MD) simulation. Two kinds of bio-rejuvenators (BR-1 and BR-5) were chosen to represent the straight-chain and aromatic structures, respectively. The method of relative concentration, radial distribution function (RDF), and microstructure morphology were used to evaluate the effect of bio-rejuvenators on the diffusion process of virgin/aged asphalt binder. The results showed that bio-rejuvenators had a positive effect on the fusion process between virgin and aged asphalt binder. The volume diffusion coefficient based on asphalt binder diffusion models indicated that the bio-rejuvenators accelerated the fusion process between the virgin and asphalt binder. After adding bio-rejuvenators to the aged asphalt binder, the agglomeration intensity in the SARA fractions was reduced to different degrees. Due to the aging of asphalt binder, asphaltenes formed different types of micro-stacking phenomena such as “T-shaped stacking,” “Face to Face stacking,” and “Offset Face to Face stacking.” The bio-rejuvenators of BR-1 and BR-5 exerted different regenerative effects during the diffusion process of aged asphalt binder. For BR-1, the “Pull-Out” and “Intercalation” effect can be observed in the process of asphaltene deagglomeration. “Pull-Out” is the main regenerative effect of BR-5 in aged asphalt binder. A strong electrostatic interaction occurs between BR-5 and PAHs in asphaltenes. Thus, BR-5 achieves the goal of aged asphalt binder regeneration by attracting PAHs.

Warfarin and vitamin K epoxide reductase: a molecular accounting for observed inhibition

AbstractVitamin K epoxide reductase (VKOR), an endoplasmic reticulum membrane protein, is the key enzyme for vitamin K–dependent carboxylation, a posttranslational modification that is essential for the biological functions of coagulation factors. VKOR is the target of the most widely prescribed oral anticoagulant, warfarin. However, the topological structure of VKOR and the mechanism of warfarin's inhibition of VKOR remain elusive. Additionally, it is not clear why warfarin-resistant VKOR mutations identified in patients significantly decrease warfarin's binding affinity, but have only a minor effect on vitamin K binding. Here, we used immunofluorescence confocal imaging of VKOR in live mammalian cells and PEGylation of VKOR's endogenous cytoplasmic-accessible cysteines in intact microsomes to probe the membrane topology of human VKOR. Our results show that the disputed loop sequence between the first and second transmembrane (TM) domain of VKOR is located in the cytoplasm, supporting a 3-TM topological structure of human VKOR. Using molecular dynamics (MD) simulations, a T-shaped stacking interaction between warfarin and tyrosine residue 139, within the proposed TY139A warfarin-binding motif, was observed. Furthermore, a reversible dynamic warfarin-binding pocket opening and conformational changes were observed when warfarin binds to VKOR. Several residues (Y25, A26, and Y139) were found essential for warfarin binding to VKOR by MD simulations, and these were confirmed by the functional study of VKOR and its mutants in their native milieu using a cell-based assay. Our findings provide new insights into the dynamics of the binding of warfarin to VKOR, as well as into warfarin's mechanism of anticoagulation.

Computational study of peptide plane stacking with polar and ionizable amino acid side chains.

Parallel and T-shaped stacking interactions of the peptide plane with polar and ionizable amino acid side chains (including aspartic/glutamic acid, asparagine/glutamine, and arginine) are investigated using the quantum mechanical MP2 and CCSD computational methods. It is found that the electrostatic interaction plays an essential role in determining the optimal stacking configurations for all investigated stacking models. For certain complexes, the dispersion interaction also contributes considerably to stacking. In the gas phase, the stacking interaction of the charged system is stronger than that of the neutral system, and T-shaped stacking is generally more preferred than parallel stacking, with the stacking energy in the range of -4 to -18 kcal/mol. The solvation effect overall weakens stacking, especially for the charged system and the T-shaped stacking configurations. In water, the interaction energies of different stacking models are comparable.

Aromatic stacking interactions govern catalysis in aryl-alcohol oxidase.

Aryl-alcohol oxidase (AAO, EC 1.1.3.7) generates H2 O2 for lignin degradation at the expense of benzylic and other π system-containing primary alcohols, which are oxidized to the corresponding aldehydes. Ligand diffusion studies on Pleurotus eryngii AAO showed a T-shaped stacking interaction between the Tyr92 side chain and the alcohol substrate at the catalytically competent position for concerted hydride and proton transfers. Bi-substrate kinetics analysis revealed that reactions with 3-chloro- or 3-fluorobenzyl alcohols (halogen substituents) proceed via a ping-pong mechanism. However, mono- and dimethoxylated substituents (in 4-methoxybenzyl and 3,4-dimethoxybenzyl alcohols) altered the mechanism and a ternary complex was formed. Electron-withdrawing substituents resulted in lower quantum mechanics stacking energies between aldehyde and the tyrosine side chain, contributing to product release, in agreement with the ping-pong mechanism observed in 3-chloro- and 3-fluorobenzyl alcohol kinetics analysis. In contrast, the higher stacking energies when electron donor substituents are present result in reaction of O2 with the flavin through a ternary complex, in agreement with the kinetics of methoxylated alcohols. The contribution of Tyr92 to the AAO reaction mechanism was investigated by calculation of stacking interaction energies and site-directed mutagenesis. Replacement of Tyr92 by phenylalanine does not alter the AAO kinetic constants (on 4-methoxybenzyl alcohol), most probably because the stacking interaction is still possible. However, introduction of a tryptophan residue at this position strongly reduced the affinity for the substrate (i.e. the pre-steady state Kd and steady-state Km increase by 150-fold and 75-fold, respectively), and therefore the steady-state catalytic efficiency, suggesting that proper stacking is impossible with this bulky residue. The above results confirm the role of Tyr92 in substrate binding, thus governing the kinetic mechanism in AAO.

Carboxyl-peptide plane stacking is important for stabilization of buried E305 of Trichoderma reesei Cel5A.

Hydrogen bonds or salt bridges are usually formed to stabilize the buried ionizable residues. However, such interactions do not exist for two buried residues D271 and E305 of Trichoderma reesei Cel5A, an endoglucanase. Mutating D271 to alanine or leucine improves the enzyme thermostability quantified by the temperature T50 due to the elimination of the desolvation penalty of the aspartic acid. However, the same mutations for E305 decrease the enzyme thermostability. Free energy calculations based on the molecular dynamics simulation predict the thermostability of D271A, D271L, and E305A (compared to WT) in line with the experimental observation but overestimate the thermostability of E305L. Quantum mechanical calculations suggest that the carboxyl-peptide plane stacking interactions occurring to E305 but not D271 are important for the carboxyl group stabilization. For the protonated carboxyl group, the interaction energy can be as much as about -4 kcal/mol for parallel stacking and about -7 kcal/mol for T-shaped stacking. For the deprotonated carboxyl group, the largest interaction energies for parallel stacking and T-shaped stacking are comparable, about -7 kcal/mol. The solvation effect generally weakens the interaction, especially for the charged system. A search of the carboxyl-peptide plane stacking in the PDB databank indicates that parallel stacking but not T-shaped stacking is quite common, and the most probable distance between the two stacking fragments is close to the value predicted by the QM calculations. This work highlights the potential role of carboxyl amide π-π stacking in the stabilization of aspartic acid and glutamic acid in proteins.

Structural Basis of Substrate Specificity and Selectivity of Murine Cytosolic 5′-Nucleotidase III

Cytosolic 5'-nucleotidase III (cN-III) is responsible for selective degradation of pyrimidine 5'-monoribonucleotides during maturation of reticulocytes to erythrocytes. The lack of this enzymatic activity due to genetic aberrations or lead poisoning results in a mild to moderate nonspherocytic hemolytic anemia. In affected individuals, pyrimidine nucleotides as well as their precursor polymers and their off-path metabolites accumulate in erythrocytes, interfering with their proper function in ways that are not yet fully understood. This report describes the first X-ray structure of a catalytically inactivated variant of murine cN-III with a natural substrate, uridine 5'-monophosphate, in the active site at 1.74Å resolution. The structure captures in an atomic detail the closed conformation that cN-III adopts upon substrate binding. Structure and sequence analysis coupled with enzymatic characterization of several mutants confirmed that the aromatic ring of a nitrogenous base of substrate nucleotide is stabilized by parallel π-stacking interactions with conserved aromatic rings of Trp113 and His68. The nitrogenous base is further stabilized by T-shaped stacking with the conserved aromatic ring of Tyr114, as well as by polar contacts with side chains of Thr66 and Ser117. Two water molecules help to stabilize the nucleotide binding by bridging it to protein residues Asp72 and His68 via hydrogen bonds. Finally, fully conserved Glu96 is responsible for recognition of ribose ring via two hydrogen bonds. The presented substrate complex structure elucidates how cN-III achieves specificity for pyrimidine 5'-nucleotides and how it selects against purine 5'-nucleotides.

Supramolecular structures via hydrogen bonds and π-stacking interactions in novel anthraquinonedisulfonates of zinc, nickel, cobalt, copper and manganese

By using 1,10-phenanthroline as a blocking ligand, six new disulfonate complexes were hydrothermaly obtained and their self-assembling interactions studied, namely: [Co2(2,6-AQDS)2(Phen)4] (1) (2,6-AQDS=anthraquinone-2,6-disulfonate, Phen=1,10-phenanthroline), a dimeric molecular complex that exhibits 2D structure via π–π aromatic slipped and T-shaped stacking interactions; a series of isostructural compounds with formula [M(1,5-AQDS)(Phen)2(H2O)] (M=Co,Ni,Cu, and Zn, compounds 2, 3, 5, 6, respectively), (1,5-AQDS = anthraquinone-1,5-disulfonate, and [Mn(2,6-AQDS)(Phen)2(H2O)]·H2O (4). The metals cations are in octahedral coordination in all of them. These molecular complexes are arranged into 3D supramolecular structure by combination of π–π aromatic slipped and T-shaped stacking interactions, as well as O–H···O hydrogen bonds and C–H···O interactions. Studies on the catalytic activity of the obtained compounds for the oxidation of the methyl phenyl sulphide showed that [Ni(1,5-AQDS)(Phen)2(H2O)], 3, and [Co(1,5-AQDS)(Phen)2(H2O)], 2, act as heterogenous catalysts, being the nickel compound the most active and selective for this reaction.

Conglomerate formation and crystal structure of 4-phenyl-1,3-thiazolidin-2-one

Racemic 4-phenyl-1,3-thiazolidin-2-one (4-PTO) crystallizes in the form of conglomerate. The conglomerate formation has been confirmed by analyzing Weissenberg X-ray photographs and IR, Raman spectra of the racemate and the enantiopure 4-PTO crystals. The crystal structure of 4-PTO has been determined by X-ray diffraction, and the structural features are compared with those of other 4-phenyl-1,3-oxazolidin-2-one derivatives in order to understand the structural factors leading to the conglomerate formation. In 4-PTO crystals, the N-H⋯O intermolecular hydrogen bonds are formed between the amide groups of neighboring molecules in a homochiral zigzag chain. In addition, the intermolecular S⋯O close contacts are observed between the thioether and the carbonyl groups in the same chain unit. Moreover, the phenyl groups of homochiral 4-PTO molecules of different chain units take the T-shaped stacking orientation to each other due to the aromatic CH/π interaction. These structural factors altogether reinforce the homochiral supramolecular assembly of chain structural units in the 4-PTO crystal.

Morphology of Aggregated Asphaltene Structural Models

Aggregated asphaltene structural models have been generated through a molecular simulation geometry optimization process, using periodic boundary conditions. This methodology has been validated by first applying it to a pure aromatic system. Initially, a random distribution of 35 molecules was chosen and a geometry optimization process was performed, allowing the cell dimensions to vary without restrictions. The structure factor (S(k)) of an optimized final cell was obtained and compared with experimental results, and the agreement between theoretical and experimental S(k) profiles was satisfactory. This methodology was next used in the analysis of the morphology of 32 asphaltene model molecules and their aromatic cores; asphaltene model molecules were taken from literature. It is remarkable that face-to-face stacking of asphaltene aggregates was observed, as well as π-offset and T-shaped stacking geometries. Finally, the effect of aliphatic chains on the aggregates was also analyzed.

Ethylene physisorption on C 60 fullerene

Monte Carlo computer simulation results on the adsorption of ethylene on C 60 fullerene are employed to locate the adsorption sites observed for the adsorption of other simple gases. The distributions of molecules according to the gas–solid interaction energy obtained from the simulations are in agreement with experimental results reported in the literature. We focused our attention on the isotherm obtained at 150 K. At this temperature, the molecules with a certain gas–solid energy have been identified and their location employed to find out the adsorption sites. This sort of distribution has been averaged over all the equilibrated configurations generated during the simulation. The results obtained confirm the assignment of adsorption sites previously reported for the adsorption of N 2, Ar, and CO 2. The distribution of molecules over the gas–gas interaction energy is also analyzed and the obtained results suggest that the adsorbed molecules prefer a T-shaped stacking. This conclusion is obtained through the analysis of the distributions with the aid of the gas–gas interaction potential. This observation agrees with recently published results by other authors. The information obtained from the microdensity profiles has also been employed to locate the adsorption sites.