Detailed Molecular Simulations Research Articles

Depressurization-induced production of shale gas in organic-inorganic shale nanopores: A kinetic Monte Carlo simulation

Methane gas production from unconventional reservoirs, such as shale formations, is in high demand due to the global energy needs. However, maximizing production remains challenging due to the ultra-tight porosity, heterogeneity, and complex nature of shale rocks under high pressure. To address this issue, we employ a novel kinetic Monte Carlo (kMC) simulation to investigate the molecular-level behavior of shale gas in both homogeneous and heterogeneous organic-inorganic shale nanopores. This approach not only provides accurate computations of shale gas under high pressure but also aims to uncover the mechanisms of shale gas storage at reservoir pressure and production during pressure drawdown. Our findings indicate that organic shale ultramicropores (pore width < 0.7 nm) contribute significantly to the highest storage capacity of shale gas but pose challenges for production capacity solely through depressurization. In contrast, the free gas zone is the primary source of shale gas production from mesoporous shales, which has a high recovery efficiency but a low production capacity due to less pronounced interaction effects from the shale surface. The heterogeneous nature of shale surfaces leads to asymmetric distributions of density and potential energy across pore widths, with methane molecules favoring locations near organic pore walls due to stronger attractive interactions, while inorganic pore walls facilitate shale gas migration. Interestingly, the optimal ultramicropore size yields the highest recovery efficiency of shale gas via depressurization, characterized by a transition from near-commensurate to incommensurate molecular packing between reservoir and post-drawdown pressures. Based on these detailed molecular simulations, further research is necessary to develop innovative techniques for enhancing shale gas recovery, especially in micropores.

An adenine-based metal-organic framework with tailored pore environment for adsorption separation of C2H2 from C2H4 and CO2

The separation of acetylene (C2H2) from mixtures with ethylene (C2H4) and carbon dioxide (CO2) is crucial yet challenging in the chemical industry. Based on the adsorption separation technology, it is desirable to design and develop efficient adsorbents for C2H2 separation. In this work, we present an adenine-based metal-organic framework (Cu-AD-HEA), which features tailored pore environment with Lewis basic sites within the specific intersecting channels for the separation of C2H2 from mixtures with C2H4 and CO2. The obtained Cu-AD-HEA exhibits exceptional adsorption capacity for C2H2 and demonstrates competitive adsorption selectivity for C2H2/C2H4 and C2H2/CO2. Furthermore, dynamic breakthrough results further illustrate the superior dynamic separation of C2H2 over C2H4 and CO2. Moreover, detailed molecular simulations and density functional theory (DFT) calculations elucidate that C2H2 is preferentially captured in a tailored pore environment of Cu-AD-HEA with stronger binding affinity through CH⋯N/O hydrogen bonds and C–H⋯π or π⋯π interactions. This work offers an effective MOF-based adsorbent for the separation of C2H2 from mixtures with C2H4 and CO2.

Tailoring a MOF‐based adsorbent with partitioned aliphatic pore spaces for efficient CH4 purification from natural gas

AbstractSeparation of CH4 from natural gas is an essential but extremely challenging process in the petrochemical industry. Here, we tailored a MOF‐based adsorbent with partitioned aliphatic pore spaces through the simultaneous incorporation of the aliphatic sites and the symmetrically matched partition agent. The resulting adsorbent demonstrates exceptional adsorption capacity for C3H8 and C2H6 compared to CH4, along with remarkably competitive adsorption selectivities for C3H8/CH4 and C2H6/CH4. Breakthrough experiments further support the excellent dynamic separation efficiency of the adsorbent for the purification of CH4 from natural gas. Moreover, detailed density functional theory calculations and molecular simulations elucidate the synergistic interactions between the aliphatic sites and the partitioned pore spaces within the adsorbent, which promote the stronger binding affinities for C3H8 and C2H6 over CH4.

Probing Structural Defects in MOFs Using Water Stability.

Defects in the crystal structures of metal-organic frameworks (MOFs), whether present intrinsically or introduced via so-called defect engineering, can play strong roles in the properties of MOFs for various applications. Unfortunately, direct experimental detection and characterization of defects in MOFs are very challenging. We show that in many cases, the differences between experimentally observed and computationally predicted water stabilities of MOFs can be used to deduce information on the presence of point defects in real materials. Most computational studies of MOFs consider these materials to be defect-free, and in many cases, the resulting structures are predicted to be hydrophobic. Systematic experimental studies, however, have shown that many MOFs are hydrophilic. We show that the existence of chemically plausible point defects can often account for this discrepancy and use this observation in combination with detailed molecular simulations to assess the impact of local defects and flexibility in a variety of MOFs for which defects had not been considered previously.

Chiral separation and molecular modeling study of decursinol and its derivatives using polysaccharide-based chiral stationary phases

Plant-based bioactive substances have long been used to treat inflammatory ailments, owing to their low toxicity and cost-effectiveness. To enhance plant treatment by eliminating undesirable isomers, optimizing the chiral separation techniques in pharmaceutical and clinical studies is important. This study reported a simple and effective method for chiral separation of decursinol and its derivatives, which are pyranocoumarin compounds with anti-cancer and anti-inflammatory properties. Baseline separation (Rs >1.5) was achieved using five different polysaccharide-based chiral stationary phases (CSPs) that differed in chiral origin, chiral selector chemistry, and preparation technique. To separate all six enantiomers simultaneously, n-hexane and three alcohol modifiers (ethanol, isopropanol, and n-butanol) were used as mobile phases in the normal-phase mode. The chiral separation ability of each column with various mobile phase compositions was compared and discussed. As a result, amylose-based CSPs with linear alcohol modifiers demonstrated superior resolution. Three cases of elution order reversal caused by modifications of CSPs and alcohol modifiers were observed and thoroughly analyzed. To elucidate the chiral recognition mechanism and enantiomeric elution order (EEO) reversal phenomenon, detailed molecular docking simulations were conducted. The R- and S-enantiomers of decursinol, epoxide, and CGK012 exhibited binding energies of –6.6, –6.3, –6.2, –6.3, –7.3, and –7.5 kcal/mol, respectively. The magnitude of the difference in binding energies was consistent with the elution order and enantioselectivity (α) of the analytes. The molecular simulation results demonstrated that hydrogen bonds, π–π interactions, and hydrophobic interactions have a significant impact on chiral recognition mechanisms. Overall, this study presented a novel and logical approach of optimizing chiral separation techniques in the pharmaceutical and clinical industries. Our findings could be further applied for screening and optimizing enantiomeric separation.

Identifying High-Performance Metal–Organic Frameworks for Low-Temperature Oxygen Recovery from Helium by Computational Screening

Metal–organic frameworks (MOFs) are an important class of porous crystalline materials for applications ranging from gas adsorption and separation to catalysis. There are thousands of potential MOFs available for separation applications. We developed a computational approach to screen MOFs for the separation of oxygen–helium mixtures at low temperatures (100–200 K), conditions that were motivated by issues associated with propulsion in space-based settings. We used detailed molecular simulations for a small number of MOFs to develop screening methods that were then used to estimate the optimum temperatures for separations using pressure swing adsorption for 2932 MOFs from the CoRE MOF database and the swing capacity and oxygen–helium selectivity at these temperatures. We used the stability of the best-performing structures in the presence of moisture as a means to provide a short list of high-performance materials. In addition to identifying specific materials for oxygen–helium separations, this approach could prove useful for selecting adsorbents for other gas separations.

Sensitive turn-off detection of nitroaromatics using fluorescent tetraphenylethylene phosphonate derivative

The derivatisation of tetraphenylethylene is broadly utilized to synthesize molecular sensor for detecting explosives among other analytes, the effects of such alteration have been little investigated. Herein, we report the sensing of various nitro phenols using fluorescence signals produced by (4-(1, 2, 2-tris (4-phosphonophenyl) vinyl) phenyl) phosphonic acid octasodium salt (TPPE). It is observed that the fluorescence of TPPE at 411 nm and 432 nm are quenched in the presence 2,4,6-trinitrophenol (TNP) via electron transfer between weak TPE donor and acceptor mechanism. Moreover, TPPE – TNP association is based on non-covalent interaction including hydrogen-bonding and electrostatic interactions. TPPE shows strong binding affinity and selectivity towards TNP over various other nitroaromatic analytes. The sensing detection limit (LOD) towards TNP is 4.58 × 10−9 M. In detailed molecular simulation experiments are performed to investigate the non-covalent interaction, oscillation frequency, possible transitions and energy levels of molecular complexation between TPPE and TNP. This study supports the sensing mechanism of TPPE towards TNP, suggesting suitable interaction mode between the receptor and PA.

Quantitative Structure-Property Relationship Analysis for the Prediction of Propylene Adsorption Capacity in Pure Silicon Zeolites at Various Pressure Levels.

This work is devoted to the development of quantitative structure–property relationship (QSPR) models using various regression analyses to predict propylene (C3H6) adsorption capacity at various pressures in zeolites from a topologically diverse International Zeolite Association database. Based on univariate and multilinear regression analysis, the accessible volume and largest cavity diameter are the most crucial factors determining C3H6 uptake at high and low pressures, respectively. An artificial neural network (ANN) model with five structural descriptors is sufficient to predict C3H6 uptake at high pressures. For combined pressures, the prediction of an ANN model with pore size distribution is pleasing. The isosteric heat of adsorption (Qst) has a significant impact on the improvement of the prediction of low-pressure gas adsorption, which finely classifies zeolites into high or low C3H6 adsorbers. The conjunction of high-throughput screening and QSPR models contributes to being able to prescreen the database rapidly and accurately for top performers and perform further detailed and time-consuming computational-intensive molecular simulations on these candidates for other gas adsorption applications.

Molecular level investigation on the impact of geometric isomers as fluorinated ligands in SIFSIX MOF for natural gas sweetening

ABSTRACT In natural gas (NG), significant amounts of hydrogen sulfide (H2S) and carbon dioxide (CO2) are the most menacing contaminants that cause degradation of the purity of fuel. We considered fluorine-functionalized MOFs and employed cheaper and faster computational simulation techniques to understand the adsorption process. Hence, this includes structural optimization of newly designed fluorine-functionalized MOF with Density Functional Theory (DFT) and further Grand Canonical Monte Carlo (GCMC) simulation at room temperature on those MOFs for understanding in detail the adsorptive separation process on sour gases. However, the main emphasis has been made on the adsorptive separation of H2S gas from sour gas. Eventually, the fluorination of organic ligand in [(SiF6)Ni(1,2-di(pyridin-4-yl)ethyne)2] MOF has resulted in an excellent H2S/CO2 separation performance from NG because of the different geometrical isomers. The cis isomer of 1,2-di(pyridin-4-yl)ethyne as ligand in MOF, i.e., SIFSIX-Ni-dpe-3-cis, shows a high CO2 affinity than H2S; on the contrary, the trans isomer of 1,2-di(pyridin-4-yl)ethyne as ligand in MOF, i.e., SIFSIX-Ni-dpe-3-trans, has H2S selective over CO2 and CH4. So, the resulting affinity variation indicates that structural variation by the stereochemistry of ligands in MOF plays a significant role in NG purification, which is further validated through detailed molecular simulation analysis.

Preparation and Chemical/Physical Characterization of Individual Nanoscaled Fibrils

Abstract:Polymer-based nanofibril finds its application in various fields including tissue engineering, environmental monitoring, food packaging, and micro/nanoelectromechanical systems. These nanofibrils are subjected to chemical treatment and constant stress, which may cause permanent deformation to the fibrils when it is used. Therefore, the synthesis of well-defined nanofibrils and characterization techniques are key elements in identifying desired chemical and physical properties for suitable applications. Many methods have been developed to prepare individual nanofibrils, including electrospinning, phase separation, template synthesis, and self-assembly. Among all, self-assembly offers simple, efficient, and lowcost strategies that produce high-ordered nanofibrils using noncovalent interactions including hydrogen bonding, electrostatic interactions, π-π interactions, and hydrophobic interactions. The first part of the review provides detailed molecular interactions and simulations that can be controlled to achieve the formation of well-defined individual nanofibrils. The second part of the review describes the various existing tools to characterize the chemical and physical properties of single nanofibrils including atomic force microscopy. In the final part of the review, recently developed novel nanotools that measure the mechanical properties of nanofibrils are described. By bridging the gap between molecular interactions and resulting nanoscale fibirls, physical and chemical properties may lead to the construction of novel nanomaterials in the area of nanoscience and nanotechnology.

Synthesis, structural, vibrational, molecular docking and nonlinear optical studies of (E)-N′-(2,3-dimethoxybenzylidene)-4-fluorobenzohydrazide

Organic nonlinear optical single crystals of (E)-N′-(2,3-dimethoxybenzylidene)-4-fluorobenzohydrazide (DMB-FBH) were synthesized and grown using slow evaporation crystallization from ethanol solution. The single crystal X-ray diffraction scattering revealed that the DMB-FBH crystallised in the tetragonal crystal system with a centro symmetric space group of I 41/a. The crystallographic bond lengths and bond angles were compared with the values generated from optimized molecular geometry based on quantum chemical calculations. The functional group vibrations were identified theoretically by density functional theory with B3LYP 6–311 G (d,p) basis set using Gaussian 09 software package and their vibrations were compared with the experimental FT-IR spectra. The UV-visible and the fluorescence emission spectra of the DMB-FBH in aqueous solutions were recorded. The HOMO-LUMO energy level pictogram addressed the intramolecular charge transfer (ICT) interaction between donor and acceptor moieties and their impact on the energy gap was determined. Different interactions such as O···H, N···H, C···C and C···H in DMB-FBH were quantified via fingerprint plots and these results were compared with that of similar structure. The detailed molecular docking simulation was carried out with M. tuberculosis protein [PDB ID:2 × 22]. The third order nonlinear optical susceptibility (χ3) of DMB-FBH was confirmed experimentally by Z-scan method and their conversion efficiency was higher than the other hydrazones derivatives. In short, this work discusses the crystal structure, identification and quantification of the molecular interactions, thermal, antimycobacterial and optical properties of new hydrazone derivative.

Computational methods to study enveloped viral entry.

The protein-membrane interactions that mediate viral infection occur via loosely ordered, transient assemblies, creating challenges for high-resolution structure determination. Computational methods and in particular molecular dynamics simulation have thus become important adjuncts for integrating experimental data, developing mechanistic models, and suggesting testable hypotheses regarding viral function. However, the large molecular scales of virus-host interaction also create challenges for detailed molecular simulation. For this reason, continuum membrane models have played a large historical role, although they have become less favored for high-resolution models of protein assemblies and lipid organization. Here, we review recent progress in the field, with an emphasis on the insight that has been gained using a mixture of coarse-grained and atomic-resolution molecular dynamics simulations. Based on successes and challenges to date, we suggest a multiresolution strategy that should yield the best mixture of computational efficiency and physical fidelity. This strategy may facilitate further simulations of viral entry by a broader range of viruses, helping illuminate the diversity of viral entry strategies and the essential common elements that can be targeted for antiviral therapies.

Near-physiological-temperature serial crystallography reveals conformations of SARS-CoV-2 main protease active site for improved drug repurposing

The COVID-19 pandemic has resulted in 198 million reported infections and more than 4 million deaths as of July 2021 (covid19.who.int). Research to identify effective therapies for COVID-19 includes: (1) designing a vaccine as future protection; (2) de novo drug discovery; and (3) identifying existing drugs to repurpose them as effective and immediate treatments. To assist in drug repurposing and design, we determine two apo structures of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) main protease at ambient temperature by serial femtosecond X-ray crystallography. We employ detailed molecular simulations of selected known main protease inhibitors with the structures and compare binding modes and energies. The combined structural and molecular modeling studies not only reveal the dynamics of small molecules targeting the main protease but also provide invaluable opportunities for drug repurposing and structure-based drug design strategies against SARS-CoV-2.

Does the SARS-CoV-2 Spike Protein Receptor Binding Domain Interact Effectively with the DPP4 (CD26) Receptor? A Molecular Docking Study.

ACE2 has been established as the main receptor for SARS-CoV-2. Since other human coronaviruses are known to use co-receptors for viral cell entry, it has been suggested that DPP4 (CD26) could be a potential additional binding target or co-receptor, supported by early molecular docking simulation studies. However, recent biophysical studies have shown this interaction to be very weak. We have conducted detailed molecular docking simulations to predict the potential binding interactions between the receptor binding domain (RBD) of the spike protein of SARS-CoV-2 and DPP4 and compare them with the interactions observed in the experimentally determined structure of the complex of MERS-CoV with DPP4. Whilst the overall binding mode of the RBD of SARS-CoV-2 to DPP4 is predicted to be similar to that observed in the MERS-CoV-DPP4 complex, including a number of equivalent interactions, important differences in the amino acid sequences of SARS-CoV-2 and MERS-CoV result in substantially weakened interactions with DPP4. This is shown to arise from differences in the predicted proximity, nature and secondary structure at the binding interface on the RBD of SARS-CoV-2. These findings do not support DPP4 being a significant receptor for SARS-CoV-2.

Delayed Linker Addition (DLA) Synthesis for Hybrid SOD ZIFs with Unsubstituted Imidazolate Linkers for Propylene/Propane and n-Butane/i-Butane Separations.

We present a novel synthesis strategy termed delayed linker addition (DLA) to synthesize hybrid zeolitic-imidazolate frameworks containing unsubstituted imidazolate linkers (Im) with SOD topology (hereafter termed Im/ZIF-8). Im linker incorporation can create larger voids and apertures, which are important properties for gas storage and separation. To date, there have been only a handful of reports of Im linkers incorporated into ZIF-8 frameworks, typically requiring arduous and complicated post synthesis approaches. DLA, as reported here, is a simple one-step synthesis strategy allowing high incorporation of Im linker into the ZIF-8 framework while still retaining its SOD topology. We fabricated mixed-matrix membranes (MMMs) with 6FDA-DAM polymer and Im/ZIF-8 obtained via DLA as a filler. The Im/ZIF-8-containing MMMs showed excellent performance for both propylene/propane and n-butane/i-butane separation, displaying permeability and ideal selectivity well above the polymer upper bound. Moreover, highly detailed molecular simulations shed light to the aperture size and flexibility response of Im/ZIF-8 and its improved diffusivity as compared to ZIF-8.

Delayed Linker Addition (DLA) Synthesis for Hybrid SOD ZIFs with Unsubstituted Imidazolate Linkers for Propylene/Propane and n‐Butane/i‐Butane Separations

AbstractWe present a novel synthesis strategy termed delayed linker addition (DLA) to synthesize hybrid zeolitic‐imidazolate frameworks containing unsubstituted imidazolate linkers (Im) with SOD topology (hereafter termed Im/ZIF‐8). Im linker incorporation can create larger voids and apertures, which are important properties for gas storage and separation. To date, there have been only a handful of reports of Im linkers incorporated into ZIF‐8 frameworks, typically requiring arduous and complicated post synthesis approaches. DLA, as reported here, is a simple one‐step synthesis strategy allowing high incorporation of Im linker into the ZIF‐8 framework while still retaining its SOD topology. We fabricated mixed‐matrix membranes (MMMs) with 6FDA‐DAM polymer and Im/ZIF‐8 obtained via DLA as a filler. The Im/ZIF‐8‐containing MMMs showed excellent performance for both propylene/propane and n‐butane/i‐butane separation, displaying permeability and ideal selectivity well above the polymer upper bound. Moreover, highly detailed molecular simulations shed light to the aperture size and flexibility response of Im/ZIF‐8 and its improved diffusivity as compared to ZIF‐8.

Correction to: The effect of atomic point charges on adsorption isotherms of CO2 and water in metal organic frameworks

Recently, we presented a detailed and systematic molecular simulation study of the effect of point charges on adsorption of carbon dioxide and water in a series of typical MOF materials [1]. Unfortunately, we have since detected a mistake in one of the input files pertaining to water adsorption isotherm simulations—concretely, the structure of the water molecule was modelled as linear instead of obeying the correct H-O-H angle of 109.47o for the SPC/E model [2]. As we later found out, this led to a significant underestimation of the amount adsorbed in all water isotherms reported in our original paper, although the relative differences between isotherms obtained using different charge sets are qualitatively the same. We have repeated all the water adsorption simulations, and report the new results here in graphical format. With the exception of a few minor statements, which we also correct below, the conclusions of the original work remain unchanged.

High-barrier polyimide containing fluorenol moiety: Gas barrier properties and molecular simulations

An intrinsic high-barrier polyimide (9-OH-FPPI) was prepared through the polycondensation reaction of pyromellitic dianhydride (PMDA) with a novel diamine (9-OH-FPDA) containing fluorenol moiety. The synthesized polyimide displays superior barrier performances, possessing water vapor transmission rate (WVTR) and oxygen transmission rate (OTR) low to 1.64 g·m−2·day−1 and 0.66 cm3·m−2·day−1, respectively. Meanwhile, 9-OH-FPPI also demonstrates high thermal stability with a glass transition temperature (Tg) of 410 °C, 5% weight-loss temperature (Td5%) of 577 °C under N2 and coefficient of thermal expansion (CTE) of 5.65 ppm/K. A detailed molecular simulation study as well as positron annihilation lifetime spectroscopy (PALS) and wide angle X-ray diffraction (WAXD) analysis have been carried out to reveal the barrier mechanism. The results reveal that the introduction of fluorenol moiety not only enhances the rigidity and regularity of polymer backbone, but also improves the interchain cohesion of PI matrix, which in turn lead to high crystallinity, low free volume and poor chains mobility of 9-OH-FPPI. The high crystallinity and low free volume decrease the diffusion and solubility of gases in polyimide matrix. In addition, the poor chains mobility further suppresses the gases diffusion. Simultaneous reductions of gases diffusion and solubility promote the barrier properties of 9-OH-FPPI. The as-synthesized polyimide exhibits wide application prospects in the flexible electronic packaging industry.

Current investigations in theoretical studies of nanostructure–liquid interfaces

Wettability of surfaces is a significant factor affecting properties like water dispersion, spreading, evaporation, dissociation and etc. Surface wettability and wetting behavior of a surface are a subject of broad interest, there is then a great interest to understand better liquid–solid interfaces and water contact angle, in addition to the potential applications in micro- and nano fluidics. This subject is interesting as the growing attractions on the wetting and dynamical properties of water on 2D materials. Also, two clearly defined rigid water layers on solid surfaces are a well-known phenomenon and have been described on several surfaces. Detailed molecular dynamic simulation studies on the origin of this phenomenon are also of general interest. In this current review, recent attempts concerning to the wettability of graphene, graphene oxide and also some metal surfaces obtained by theoretical are presented. Their result contents, therefore, is of interest in order to understand the behavior of water nano-droplets when physisorbed on different substrates. The information is relevant for experimental teams working in this subject, with application in areas as catalysis, friction, surface chemistry, adsorption, etc.

Fabrication of pebax-1657-based mixed-matrix membranes incorporating N-doped few-layer graphene for carbon dioxide capture enhancement

In this study, an environmentally friendly method was developed to fabricate N-doped few-layer graphene (N-FLG)/Pebax mixed-matrix membranes (MMMs) for CO2 capture. A supermixer was introduced to ensure homogeneity of the N-FLG in the Pebax solution, and a highly efficient method of N-FLG/Pebax MMM preparation was achieved. The membrane structures were analyzed by SEM, while the N-FLG morphology was examined by SEM, AFM, XPS and EDX. A detailed molecular simulation was applied to mimic and predict the behavior of and interaction between membranes and gas molecules. Through the simulation, an independent analysis of transport-related characteristics, such as diffusivity, solubility and permeability, was achieved. In addition, the simulation indicated that the affinity of N-FLG for CO2 molecules improves the CO2 capture performance, that the membranes are solubility-dependent when prepared with low contents of N-FLG and that the effect of diffusivity increases as the addition of N-GO increases above 5 wt%. The simulation results were highly correlated with the experimental results, while the experimental gas permeability results showed that the optimal performance of N-FLG/Pebax MMM was obtained with the addition of 4 wt% N-FLG, providing CO2 permeability and CO2/N2 selectivity of 239.8 Barrer and 95.5, respectively. Pebax-1657-based MMMs incorporating N-FLG nanosheets fabricated by an environmentally friendly method can therefore be considered a promising material for CO2 capture applications.