Electrostatic Analysis Research Articles

Oxidative cyclopalladation triggers the hydroalkylation of alkynes

This report describes the oxidative cyclopalladation activation of a CC bond during the Pd-catalyzed hydroalkylation of alkynes and analyzes potential reaction pathways based on density functional theory calculations. The more favorable pathway in-volves an oxidative cyclopalladation to generate a palladacyclopropene intermediate, which is rarely examined in Pd-catalyzed alkyne transformations. The reaction pathway proposed herein is kinetically favorable relative to the commonly proposed alkyne insertion mode. Furthermore, the Laplacians of the electron density, interaction region indicators, Mayer bond orders, and localized orbital bonding are evaluated to determine the reaction processes and characterize the key intermediates. Theoretical calculations indicate covalent bonding between a Pd(II) center and the two C-atoms in three-membered palladacycle species. Finally, electrostatic potential analysis reveals that the regioselectivity is governed by the charge distribution on the palladacycle moiety during the protonation step.

Fast finite element electrostatic analysis with domain decomposition method

Accurate simulation of electrostatic field in electronic devices is very important to improve their performance. When the traditional finite element method is used to analyze the electrostatic field of large and complex structures, the calculation speed is slow and the computing resources are greatly consumed. Therefore, in this paper, we investigate electrostatic analysis with a non-overlapping domain decomposition method based on the scalar finite element method under a novel transmission condition. In order to improve the efficiency of matrix solving and reduce the memory consumption, the block Jacobi preconditioner is introduced. In addition, the multifrontal block incomplete Cholesky preconditioner is utilized to further improve the computational performance based on the block Jacobi preconditioner. Several numerical examples are simulated and compared with the analytical solutions and the commercial software Maxwell 3D. The results demonstrate the accuracy and efficiency of the proposed domain decomposition method.

Molecular electrostatics and pKa shifts calculations with the Generalized Born model. A tutorial through examples with Bluues2

Biomolecular electrostatics is of key importance for biological function and recognition. The continuum electrostatic model based on the Poisson-Boltzmann (PB) equation has been widely used to study biomolecular electrostatics. The solution of the PB equation gives the electrostatic potential over the space enclosing the molecule(s) of interest, typically obtained at points of a suitable grid.The Generalized Born (GB) model has been used to provide a useful approximation to the solution obtained by solving numerically the PB equation. The main advantage of the GB approach is to express the electrostatic energy of the system as the sum of pairwise interactions. The latter depend on geometric parameters (the GB radii) which depend on all atoms, and their radii, of the system. In this work we present a tutorial through examples for a more efficient and general version of the program Bluues which is able to compute:1) the generalized Born radius of each atom;2) the electrostatic potential at the surface of the molecule mapped to solvent accessible atoms;3) the solvent accessible surface in a PDB formatted file;4) the electrostatic potential in the volume surrounding the molecule;5) the electrostatic free energy and different contributions to it;6) the pH-dependent properties of proteins (total charge and pH-dependent free energy of folding) in the pH range −4 to 18;7) the pKa shifts due to molecular structure of all ionizable groups. Program summaryProgram Title: bluues2CPC Library link to program files:https://doi.org/10.17632/bx98gcrzbg.1Developer's repository link:https://github.com/federico-fogolari/bluues2Code Ocean capsule:https://codeocean.com/capsule/9338710Licensing provisions: GPLv3Programming language: CNature of problem: Biomolecular electrostatics is of key importance for biological function and recognition. Computation of electrostatic effects and their dissection in atomic contributions is a general problem in molecular modeling.Solution method: The GBR6 version of the Generalized Born (GB) model is implemented through surface integrals and all common molecular electrostatic analyses are performed by a single command line program.Additional comments including restrictions and unusual features: The program requires, as input, files in pqr format, which may be generated by independent software (e.g. babel, pdb2pqr). For the optional generation of the solvent excluded surface, the software msms must be installed and present in the path.

Bis(perfluoroaryl)chalcolanes ArF2Ch (Ch = S, Se, Te) as σ/π-Hole Donors for Supramolecular Applications Based on Noncovalent Bonding

Perfluorinated arenes (perfluoropyridine, perfluorotoluene, and perfluorobiphenyl) were converted to the bis(perfluoroaryl)chalcolanes ArF2Ch (Ch = S 59–88%, Se 54–84%, Te 10–41%) via the developed one-pot methodology. This method includes the generation of Na2Ch (formed in situ by the reduction of Ch with the system Na+[C10H8]·–) followed by its treatment with any one of the arenes. The crystal structures of (4-NC5F4)2S (2), (C12F9)2S (3) (p-CF3C6F4)2Se (4), (C12F9)2Se (6A,B; two polymorphs), (C12F9)2Te (9), and (4-NC5F4)2Te (8B; a novel polymorph) were determined by X-ray crystallography. In the solid state, compounds ArF2Ch are self-associated via σ-(Ch)-hole interactions with F (or N for 8B) and also π–π stacking between the arenes. The σ/π-hole donor properties of ArF2Ch were evaluated by molecular electrostatic potential surface analysis using the density functional theory approach. The maximum Vs(σ-hole) values (from +25 to +38 kcal/mol) increase in the order S < Se < Te along with an increase in the polarizability and decrease in the electronegativity of the Ch sites, while the π-hole depths (+14 to +20 kcal/mol) follow the opposite trend being the lowest for the TeII derivatives.

WR-3.4 Band Waveguide and Bandpass Filters Using Copper Additive Manufacturing

This article presents a waveguide with a pair of <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">${E}$ </tex-math></inline-formula> -plane bends and two waveguide bandpass filters (BPFs) which operate in WR-3.4 band (220–330 GHz). These devices are fabricated by a micro metal additive manufacturing (M-MAM) technology on copper in one piece. Both filters are fifth order and operate at a center frequency of 280 GHz with a bandwidth of 8 GHz. Cylindrical resonators are employed for filter design. The standard feed waveguides are designed in bend structures, facilitating the measurements. The M-MAM technology is a layer-by-layer additive manufacturing process constructing the waveguide devices in five layers. Since the layout of the devices has a strong impact on the electrostatic field distributions and hence the electroforming quality, both full-wave electromagnetic (EM) simulations and electrostatic analysis are simultaneously considered in the device design. It eases the subsequent electroforming and polishing processes, effectively improving the performance of the devices. The insertion losses and return losses of the measured filters are lower than 1.65 dB and better than 15 dB. The center frequency shifts are less than 0.3%. The excellent results attribute to the delicate co-design method between EM and electrostatic analyses encountered both in the filter design and in the additive manufacturing process.

Quantum chemical study of CO2 physisorption and chemisorption on EDA‐grafted graphene oxide

AbstractOrganic amine grafting on graphene oxide (GO) is a potentially good CO2 adsorbent. The mechanism of CO2 capture by ethylenediamine grafted GO (EDA‐GO) is studied in detail by quantum chemical method in this article. A reasonable adsorbent model is constructed, and through electrostatic potential analysis, it is found that the larger negative electrostatic potential (GOEP/GOCA: N(180)/N(30) site) is a better potential adsorption site. The physical adsorption energies are also larger (−44.37 kJ/mol, −49.90 kJ/mol) at the larger negative electrostatic potential sites. The quantum chemical calculation of CO2 adsorption is carried out at the optimal reaction site. Results show that EDA grafted on epoxy and carboxyl groups of GO have good adsorption performance for CO2. The catalytic effect of H2O in the atmosphere can significantly reduce the adsorption reaction energy, which only needs 20–45 kJ/mol. Compared with EDA‐GOEP, EDA‐GOCA has lower physical adsorption energy and chemical adsorption energy barrier. EDA‐GOCA has good adsorption performance. Moreover, the desorption energy barrier (29.0 kJ/mol) is slightly higher than the adsorption energy barrier (23.3 kJ/mol), which is conducive to adsorption and desorption repeatedly. It is helpful in the recycling and reuse of adsorbents. For the adsorption of CO2 by EDA‐GO, the conversion of hydroxyl and epoxy groups to carboxyl groups is very important. This study would contribute to the development and design of solid CO2 adsorbents based on GO. © 2023 Society of Chemical Industry and John Wiley &amp; Sons, Ltd.

Atomically dispersed nano Au clusters stabilized by Zr on the TS-1 surface: Significant enhancement of catalytic oxidation ability using H2 and O2

Au and Zr are uniformly loaded on the surface of TS-1 by coprecipitation method to obtain atomically dispersed Au-Zr binary clusters. The interaction between Au clusters, Zr and TS-1 is analyzed by Independent Gradient Model based on Hirshfeld partition (IGMH), adsorption energy of Au cluster, Mayer bond order. It is found that the existence of Zr is conducive to the stability of nano Au on TS-1 surface. The catalyst is applied to the gas phase epoxidation of C3H6 to obtain 14.06 % initial conversion, 93.93 % initial selectivity and 479.52 gPO·kgcat-1·h-1 initial productivity. It shows good stability in the continuous test for more than 50 h. Density functional theory (DFT) is used to calculate the possible catalytic reaction mechanism on the surface of atomically dispersed Au clusters. The whole process from C3H6 epoxidation reaction to catalyst regeneration is completely described. In the analysis of H2O desorption, the concept of “relay desorption” is proposed. Combined with charge and surface electrostatic potential analysis, the different attack directions of C3H6 on the catalyst surface are discussed in detail. This will provide guidance and help for the synthesis and catalytic application of nano Au catalysts.

Electric field analysis for hybrid high voltage DC circuit breaker

The structure and potential distribution of the 535kV HVDC circuit breaker are complex. In order to improve the reliability of insulation design in valve tower, this paper takes the forced commutation hybrid HVDC circuit breaker as the research object. Firstly, its topology and working principle are explained. Then, based on the insulation performance requirements of a flexible DC power grid demonstration project, and the electrostatic field analysis method, the electric field distribution and electrical shielding design of the HVDC circuit breaker are carried out. The results show that the reasonable electrical shielding design and application can effectively improve the electric field distribution of the DC circuit breaker. The maximum field intensity of the valve tower is 1.74kV/mm, located at the arc part of the U-shaped tubular shielding, and is lower than the corona inception gradient 3kV/mm. The field intensity of the valve unit in transfer branch generally shows a law of decreasing first and then increasing with the increase of the valve layer. Finally, the reliability of the insulation design is verified by experiments, which provides a reference for the insulation design of HVDC circuit breakers.

Effects of electric-field reshaping on voltage sensing in voltage-gated sodium channels.

Voltage-gated sodium channels (Navs) are responsible for the depolarizing phase of the action potential with essential roles in fast electrical signalling. Membrane depolarization triggers opening of Nav channels via activation of their voltage-sensing domains (VSD). The electric field across the membrane acts on a series of positively charged residues and induces their transmembrane relocation, which in turn triggers conformational changes that eventually lead to the opening of the sodium-conducting pore. Voltage dependence of the activation process can be described in terms of the gating charge that links energetics of VSD activation to the transmembrane voltage. Notably, the gating charge is defined by coupling of charged residues to the external electric field, whose shape is therefore crucial for Nav activation. Here, we employed molecular dynamics simulations of cardiac Nav1.5 and bacterial NavAb to gain atomic-level insights into the voltage-sensing mechanisms of Navs. Using our recently developed tool g_elpot to quantify VSD electrostatics with high spatial resolution, we found that, in contrast to earlier low-resolution studies, the electric field within VSDs of Nav channels has a complex isoform- and domain-specific shape, which prominently depends on the activation state of a VSD. Due to this field reshaping, not only translocated basic but also relatively static acidic residues contribute significantly to the gating charge. In the case of NavAb, we found that the transition between the resolved activated- and resting-state structures results in the gating charge of 8e, which is noticeably lower than experimental values of 12-16e. Our analysis of VSD electrostatics thus indicates that the resting-state structure represents an intermediate state of channel activation. In conclusion, our results provide an atomic-level description of the gating charge in Nav channels, and reveal the importance of electric-field reshaping for the energetics of voltage gating.

Comparative Surface Electrostatics and Normal Mode Analysis of High and Low Pathogenic H7N7 Avian Influenza Viruses.

Influenza A viruses are rarely symptomatic in wild birds, while representing a higher threat to poultry and mammals, where they can cause a variety of symptoms, including death. H5 and H7 subtypes of influenza viruses are of particular interest because of their pathogenic potential and reported capacity to spread from poultry to mammals, including humans. The identification of molecular fingerprints for pathogenicity can help surveillance and early warning systems, which are crucial to prevention and protection from such potentially pandemic agents. In the past decade, comparative analysis of the surface features of hemagglutinin, the main protein antigen in influenza viruses, identified electrostatic fingerprints in the evolution and spreading of H5 and H9 subtypes. Electrostatic variation among viruses from avian or mammalian hosts was also associated with host jump. Recent findings of fingerprints associated with low and highly pathogenic H5N1 viruses, obtained by means of comparative electrostatics and normal modes analysis, prompted us to check whether such fingerprints can also be found in the H7 subtype. Indeed, evidence presented in this work showed that also in H7N7, hemagglutinin proteins from low and highly pathogenic strains present differences in surface electrostatics, while no meaningful variation was found in normal modes.

Thyroid hormone transporters binding affinity of methoxypoly chlorinated biphenyls: Insights from molecular simulations and fluorescence competitive binding experiment

Triiodothyronine (T3) and thyroxine (T4) are essential for regulating cell metabolic rate and promoting the development and differentiation of brain tissue, especially in fetuses and newborns. In particular, it has been proved that MeO-PCBs have high binding to thyroid hormone transporters and can competitively bind to thyroid carrier proteins, thus destroying the transport of the thyroid hormone. Fluorescence competition binding experiments and docking results showed that the binding affinity decreased with the increase in number of chlorine atoms of MeO-PCBs. The interaction mechanism of MeO-PCBs with thyroid transporter (TTR) and thyroid binding globulin (TBG) was compared by computational simulation and the binding free energies were calculated by the molecular mechanics/Poisson-Boltzmann surface area (MM/PBSA) method. Electrostatic potential analysis, Hirshfeld surface analysis and electron density difference maps confirmed the existence of electrostatic interactions. Secondly, noncovalent interaction (NCI) analysis further indicated that the main driving force for the combination of MeO-PCBs to TTR and TBG were electrostatic interaction and van der Waals interaction. The conformational changes of the protein after binding were studied by a molecular dynamic simulation.

A DFT study on the transition metal doped BN and AlN nanocages as a drug delivery vehicle for the cladribine drug

Although considerable progress in chemotherapy drugs has been achieved, adverse side effects, the amount of drug release, and bioavailability are challenging problems that affect the treatment. In this work, the key role of transition metal doped-nanocages as a drug delivery vehicle was closely investigated by density functional theory (DFT) method. Bioavailable transition metal doped (M = Zn, Cu, Fe, Ni) BN and AlN nanocages were considered as a nano-vehicle for the cladribine drug. Electronic properties, topological analysis, electrostatic and vdW potential analysis were studied for complexes of drug-nanocages. The cladribine interacted with nanocages through NH2 and OH groups. Metal doping improved drug delivery features of nanocages through improving the polarity of the system. Among the metal-doped BN and AlN nanocages, ZnAl 11N12 showed the most favorable delivery vehicle for the cladribine with suitable adsorption energy −42.87 and −38.06 kcal/mol in gas and water phases, respectively. The analysis of density of states (DOS), H-L analysis, quantum theory of atoms in molecules (QTAIM), non-covalent interaction (NCI), and vdW potential showed that the nature of interactions between drug and nanocages is weak non-covalent which is beneficial for the release of the drug. The TD-DFT calculation showed that the maximum wavelength of complexes red shifted which is safer for tissues. The recovery time of cladribine under the body temperature is about 0.37 s which is beneficial for drug desorption. This detailed molecular level information could provide rational guidance for the design of novel drug vehicle for the cladribine.

A design strategy for performance improvement of capacitive sensors for in-flight oil-level monitoring aboard helicopters

Cylindrical capacitors are largely employed in avionic industry as contact submerged probes of level sensors for in-flight oil-level monitoring for many reasons: their high robustness, their long MTBF (Mean Time Between Failures), maintenance-free character, virtually infinite resolution readings and last, relatively low cost. However, the cylindrical capacitors suffer from low sensitivity mainly due to small oil permittivity. This is clearly a disadvantage which collides with the ever-increasing demand for higher static and dynamic performances. To improve that, the approach adopted here consists in tweaking the conventional design of this kind of sensors guided by the study of their limitations in terms of static errors and poor responsiveness caused by phenomena of capillarity, high viscosity, and vibrations. Indeed, sensitivity doubling is proved to be achieved without compromising the indispensable former qualities. This is shown by the results of electrostatic, fluid mechanics, and structural dynamics analyses presented with enough details. Numerical simulations have been carried out and are here presented to confirm results. To summarize, with respect to the conventional capacitive level sensors currently available on the market, the achievements of the proposed design are i) an improved sensitivity that, for engine oils, is greater than 700pF/m, ii) a lower cost even though extra-costs for surface perforation must be accounted for, iii) cancellation of systematic error due to capillary phenomena and iv) improved dynamic response. Also, accurate experimental verifications are being carried out and will be shared in a future paper.

Unusual Changes of C−H Bond Lengths in Chiral Zinc Complexes Induced by Noncovalent Interactions

AbstractIn order to better understand the effect of non‐covalent weak interactions on molecules, we have explored a variety of weak interactions, such as improper H‐bonding (HB), tetrel bonds (TBs) and halogen bonds, in fluorinated chiral zinc complexes. High resolution neutron diffraction studies revealed a methylene carbon‐hydrogen bond elongation and shortening due to TB and improper HB interactions, respectively. To show the accumulative effects of multiple weak interactions on the C−H bond, three types of tetrel bonds have been carefully examined. We have also shown how C−H bond elongation can be easily offset by forming an improper HB with the H atom from this C−H bond. Non‐covalent interaction and electrostatic potential analysis investigations have been used to affirm the nature of the interactions based on density functional theory (DFT) and other related calculations.

Unusual Changes of C−H Bond Lengths in Chiral Zinc Complexes Induced by Noncovalent Interactions

AbstractIn order to better understand the effect of non‐covalent weak interactions on molecules, we have explored a variety of weak interactions, such as improper H‐bonding (HB), tetrel bonds (TBs) and halogen bonds, in fluorinated chiral zinc complexes. High resolution neutron diffraction studies revealed a methylene carbon‐hydrogen bond elongation and shortening due to TB and improper HB interactions, respectively. To show the accumulative effects of multiple weak interactions on the C−H bond, three types of tetrel bonds have been carefully examined. We have also shown how C−H bond elongation can be easily offset by forming an improper HB with the H atom from this C−H bond. Non‐covalent interaction and electrostatic potential analysis investigations have been used to affirm the nature of the interactions based on density functional theory (DFT) and other related calculations.

Density functional theory study of the corrosion inhibition performance of 6-mercaptopurine and 6-thioguanine expired drugs toward the aluminium (111) surface.

The potentiality of the 6-mercaptopurine (MP) and 6-thioguanine (TG) expired drugs toward the corrosion inhibition of the aluminium (Al) (111) surface was widely investigated using a series of density functional theory (DFT) calculations. A competition between the anti-corrosive features of the studied drugs in the gas and aqueous phases was conducted on both neutral and protonated forms by means of quantum mechanical descriptors. The results of the electrostatic potential analysis demonstrated the prominent nucleophilic nature of the sulfur and nitrogen atoms over the structures of the examined drugs. The frontier molecular orbital theory findings outlined the higher preferability of TG over MP as a corrosion inhibitor. Upon determining the most beneficial configurations of the MP/TG⋯Al (111) complexes, first-principles molecular dynamics simulations were executed. Interestingly, the competence of the TG drug in the corrosion inhibition process of Al (111) was more extensive than that of the MP one, which was confirmed by the interaction energy values of -1.79 and -1.64 eV, respectively. Upon obtaining the relaxed complexes, the effect of the presence of water solvent on the adsorption process was studied. These findings provide a foundation for developing green anti-corrosive inhibitors for the aluminium surface.

Molecular Modeling Studies of β-Sitosterol Extract from Miconia burchellii Triana (Melastomataceae) from Brazilian Cerrado

The Brazilian Cerrado biome is considered one of the 25 hotspots worldwide that contain bioactive compounds due to its great biodiversity; however, the reduction of its native area over time due to the expansion of urbanization and agribusiness may have compromised knowledge of its biological variety. In this context, knowledge about Cerrado species can contribute to its biodiversity preservation. This study aims to describe the isolation, molecular architecture and theoretical calculations of the compound (3S,8S,9S,10R,13R,14S,17R)-17-[(2R,5R)-5-ethyl -6-methylheptan-2-yl]-10,13 dimethyl 2,3,4,7,8,9,11,12,14,15,16,17-dodecahydro1H-cyclopenta[a]phenanthren-3-ol, extracted from the Brazilian Cerrado Miconia burchellii plant. The supramolecular arrangement was described by Hirshfeld surface analysis, demonstrating the intermolecular interactions in the crystalline packing. The structure-property relationship shows the electrostatic potential map analysis, which reveals that the oxygen region is susceptible to electrophilic attack, and the frontier molecular orbital confirmed the kinetic stability of this compound. This study represents another step forward in the knowledge of compounds with pharmacological and medicinal properties extracted from the Cerrado.

Crystal structure, in silico molecular docking, DFT analysis and ADMET studies of N-(2-methoxy-benzyl)-acetamide

In this work, N-(2-methoxy-benzyl)-acetamide (2MBA) was synthesized from an amide derivative and it was characterized by FT-IR and NMR spectroscopy techniques. The crystal structure of 2MBA was also validated via single-crystal X-ray diffraction analysis. Crystal data for C10H13NO2 for 2MBA: Monoclinic, space group P21/n (no. 14), a = 9.1264(6) Å, b = 9.3375(7) Å, c = 11.9385(8) Å, β = 95.745(5)°, V = 1012.26(12) Å3, Z = 4, μ(MoKα) = 0.082 mm-1, Dcalc = 1.176 g/cm3, 5632 reflections measured (5.368° ≤ 2Θ ≤ 51.992°), 1990 unique (Rint = 0.0377, Rsigma = 0.0314) which were used in all calculations. The final R1 was 0.0583 (I &gt; 2σ(I)) and wR2 was 0.1444 (all data). The intermolecular interactions in 2MBA were theoretically examined by Hirshfeld surface analysis and 2D fingerprint plots. Moreover, the HOMO and LUMO energy gaps of 2MBA was calculated by DFT calculation with the B3LYP/6-311G++(d,p) method. The electron-withdrawing and donating sites of the 2MBA were confirmed via molecular electrostatic potential surface analysis. The present study discusses the title compound not only highlighted the crystallographic data but also revealed good molecular interactions together with an anticancer drug target, which is a targeting PARP protein, which was an important drug target in the treatment of breast cancer.

Identification and structural analysis of a carbohydrate-binding module specific to alginate, a representative of a new family, CBM96

Carbohydrate-binding modules (CBMs) are the noncatalytic modules that assist functions of the catalytic modules in carbohydrate-active enzymes, and they are usually discrete structural domains in larger multimodular enzymes. CBMs often occur in tandem in different alginate lyases belonging to the CBM families 13, 16, and 32. However, none of the currently known CBMs in alginate lyases specifically bind to an internal alginate chain. In our investigation of the multidomain alginate lyase Dp0100 carrying several ancillary domains, we identified an alginate-binding domain denoted TM6-N4 using protein truncation analysis. The structure of this CBM domain was determined at 1.35Å resolution. TM6-N4 exhibited an overall β-sandwich fold architecture with two antiparallel β-sheets. We identified an extended binding groove in the CBM using site-directed mutagenesis, docking, and surface electrostatic potential analysis. Affinity analysis revealed that residues of Lys10, Lys22, Lys25, Lys27, Lys31, Arg36, and Tyr159 located on the bottom or the wall of the shallow groove are responsible for alginate binding, and isothermal titration calorimetry analyses indicated that the binding cleft consists of six subsites for sugar recognition. This substrate binding pattern is typical for type B CBM, and it represents the first CBM domain that specifically binds internal alginate chain. Phylogenetic analysis supports that TM6-N4 constitutes the founding member of a new CBM family denoted as CBM96. Our reported structure not only facilitates the investigation of the CBM-alginate ligand recognition mechanism but also inspires the utilization of the CBM domain in biotechnical applications.

Mechanism for the adsorption of Per- and polyfluoroalkyl substances on kaolinite: Molecular dynamics modeling

Per- and polyfluoroalkyl substances (PFAS) have been detected in ecosystems globally and pose a serious threat to human health. Clay minerals are promising adsorbents for PFAS removal from contaminated water, thus it is crucial to understand the interactions between PFAS and clay minerals. This paper performed molecular dynamics simulations to reveal the complex behaviors and fundamental mechanisms of the adsorption of perfluoroalkyl sulfonic acids (PFSA) on the siloxane and hydroxyl external basal surfaces of kaolinite. The results demonstrate that adsorption is favorable on both the surfaces; however, their mechanisms are distinct. On the hydroxyl surface, PFSA anions exhibit a steady “point adsorption” mode, with the diffusion coefficients considerably lower than those in bulk aqueous solution. The terminal sulfonate groups form hydrogen bonds with the surface hydrogen atoms like a “three-pin plug”, with a matching molecular geometry. The molecular force and molecular electrostatic potential analyses suggest that the Coulomb electrostatic attraction force from kaolinite to the terminal sulfonate groups of PFAS anions is the predominant driving force of adsorption for the hydroxyl surface. The potential of mean force (PMF) calculations show that the PFSA anions have to go over an energy barrier, which is induced by hydration of the hydroxyl surface, to reach the stable adsorption position. On the siloxane surface, PFSA anions exhibit a mobile “surface adsorption” mode, with a relatively high freedom along the plane parallel to the surface. The diffusion coefficients of the PFSA anions adsorbed on the siloxane surface are slightly lower than those in bulk aqueous solution. The non-polar CF chains lie flat above the siloxane surface due to the hydrophobic interaction, while the terminal sulfonate groups stay relatively far away from the siloxane surface. A greater van der Waals repulsive force from the outer water molecules to the CF chains is the predominant driving force of adsorption, and pushes PFSA anions to the siloxane surface as PFSA anions approach kaolinite. The minimum values of the PMF of adsorbed PFSA anions on the siloxane surface are lower than those on the hydroxyl surface, indicating that adsorption stability is higher for the siloxane surface.