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Advances in Molecular Modeling in Chemistry

A special issue of Molecules (ISSN 1420-3049). This special issue belongs to the section "Computational and Theoretical Chemistry".

Deadline for manuscript submissions: closed (31 December 2023) | Viewed by 11149

Special Issue Editors

School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, China
Interests: physical chemistry of surfactant; computer simulation about surface science; molecular simulation on self-assemble system
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Shiling Yuan
E-Mail Website
Guest Editor
Key Lab of Colloid and Interface Chemistry, Shandong University, Jinan 250100, China
Interests: molecular simulation on polymer; surfactant; self-assembly
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Molecular modeling is playing a crucial role in chemistry investigations. With the development of computing powers, large-scale simulations can be achieved. Molecular modeling has been applied successfully in many areas of chemistry. For example, the behavior of liquid solutions, proteins, DNA, polysaccharides, lipid membranes, crystals, amorphous solids or any combination of them, the process of adsorption or desorption at interfaces, protein folding, self-assembly, etc.

Aside from the widely spread application of molecular modeling, the techniques of simulation also developed rapidly. Many simulation techniques emerged, including ab initio molecular dynamics, polarizable force field, reactive molecular dynamics, machine learning accelerated simulation, metadynamics, etc.

This Special Issue invites original papers and reviews reporting molecular simulation works including quantum chemistry calculation, molecular dynamic simulation, Monte Carlo simulation, etc., or combined experiment and simulation work. This issue also welcomes focused review articles that examine the state of the art, identify emerging trends, and suggest future directions for the application of molecular modeling methods.

Dr. Heng Zhang
Prof. Dr. Shiling Yuan
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Molecules is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • molecular modeling
  • applications
  • quantum chemistry calculation
  • molecular dynamic simulation
  • Monte Carlo simulation etc.
  • combined experiment and simulation works

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Published Papers (13 papers)

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Research

16 pages, 11161 KiB  
Article
In Silico Investigations on the Synergistic Binding Mechanism of Functional Compounds with Beta-Lactoglobulin
Molecules 2024, 29(5), 956; https://doi.org/10.3390/molecules29050956 - 22 Feb 2024
Viewed by 241
Abstract
Piceatannol (PIC) and epigallocatechin gallate (EGCG) are polyphenolic compounds with applications in the treatment of various diseases such as cancer, but their stability is poor. β-lactoglobulin (β-LG) is a natural carrier that provides a protective effect to small molecule compounds and thus improves [...] Read more.
Piceatannol (PIC) and epigallocatechin gallate (EGCG) are polyphenolic compounds with applications in the treatment of various diseases such as cancer, but their stability is poor. β-lactoglobulin (β-LG) is a natural carrier that provides a protective effect to small molecule compounds and thus improves their stability. To elucidate the mechanism of action of EGCG, PIC, and palmitate (PLM) in binding to β-LG individually and jointly, this study applied molecular docking and molecular dynamics simulations combined with in-depth analyses including noncovalent interaction (NCI) and binding free energy to investigate the binding characteristics between β-LG and compounds of PIC, EGCG, and PLM. Simulations on the binary complexes of β-LG + PIC, β-LG + EGCG, and β-LG + PLM and ternary complexes of (β-LG + PLM) + PIC, (β-LG + PLM) + EGCG, β-LG + PIC) + EGCG, and (β-LG + EGCG) + PIC were performed for comparison and characterizing the interactions between binding compounds. The results demonstrated that the co-bound PIC and EGCG showed non-beneficial effects on each other. However, the centrally located PLM was revealed to be able to adjust the binding conformation of PIC, which led to the increase in binding affinity with β-LG, thus showing a synergistic effect on the co-bound PIC. The current study of β-LG co-encapsulated PLM and PIC provides a theoretical basis and research suggestions for improving the stability of polyphenols. Full article
(This article belongs to the Special Issue Advances in Molecular Modeling in Chemistry)
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17 pages, 8769 KiB  
Article
Size- and Voltage-Dependent Electron Transport of C2N-Rings-Based Molecular Chains
Molecules 2023, 28(24), 7994; https://doi.org/10.3390/molecules28247994 - 07 Dec 2023
Viewed by 589
Abstract
C2N-ring-based molecular chains were designed at the molecular level and theoretically demonstrated to show distinctive and valuable electron transport properties that were superior to the parent carbonaceous system and other similar nanoribbon-based molecular chains. This new -type molecular chain presented an [...] Read more.
C2N-ring-based molecular chains were designed at the molecular level and theoretically demonstrated to show distinctive and valuable electron transport properties that were superior to the parent carbonaceous system and other similar nanoribbon-based molecular chains. This new -type molecular chain presented an exponential attenuation of the conductance and electron transmission with the length. Essentially, the molecular chain retained the electron-resonant tunneling within 7 nm and the dominant transport orbital was the LUMO. Shorter molecular chains with stronger conductance anomalously possessed a larger tunnel barrier energy, attributing to the compensation of a much smaller HOMO–LUMO gap, and these two internal factors codetermined the transport capacity. Some influencing factors were also studied. In contrast to the common O impurity with a tiny effect on electron transmission of the C2N rings chain, the common H impurity clearly improved it. When the temperature was less than 400 K, the electron transmission varied with temperature within a narrow range, and the structural disorder deriving from proper heating did not greatly modify the transmission possibility and the exponentially decreasing tendency with the length. In a non-equilibrium condition, the current increased overall with the bias but the growth rate varied with size. A valuable negative differential resistance (NDR) effect appeared in longer molecular chains with an even number of big carbon–nitrogen rings and strengthened with size. The emergence of such an effect originated from the reduction in transmission peaks. The conductance of longer molecular chains was enhanced with the voltage but the two shortest ones presented completely different trends. Applying the bias was demonstrated to be an effective way for C2N-ring-based molecular chains to slow down the conductance decay constant and affect the transport regime. C2N-ring-based molecular chains show a perfect application in tunneling diodes and controllable molecular devices. Full article
(This article belongs to the Special Issue Advances in Molecular Modeling in Chemistry)
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12 pages, 2635 KiB  
Article
Mechanistic Studies on Aluminum-Catalyzed Ring-Opening Alternating Copolymerization of Maleic Anhydride with Epoxides: Ligand Effects and Quantitative Structure-Activity Relationship Model
Molecules 2023, 28(21), 7279; https://doi.org/10.3390/molecules28217279 - 26 Oct 2023
Viewed by 611
Abstract
Previous work has indicated that aluminum (Al) complexes supported by a bipyridine bisphenolate (BpyBph) ligand exhibit higher activity in the ring-opening copolymerization (ROCOP) of maleic anhydride (MAH) and propylene oxide (PO) than their salen counterparts. Such a ligand effect in Al-catalyzed MAH-PO copolymerization [...] Read more.
Previous work has indicated that aluminum (Al) complexes supported by a bipyridine bisphenolate (BpyBph) ligand exhibit higher activity in the ring-opening copolymerization (ROCOP) of maleic anhydride (MAH) and propylene oxide (PO) than their salen counterparts. Such a ligand effect in Al-catalyzed MAH-PO copolymerization reactions has yet to be clarified. Herein, the origin and applicability of the ligand effect have been explored by density functional theory, based on the mechanistic analysis for chain initiation and propagation. We found that the lower LUMO energy of the (BpyBph)AlCl complex accounts for its higher activity than the (salen)AlCl counterpart in MAH/epoxide copolymerizations. Inspired by the ligand effect, a structure-energy model was further established for catalytic activity (TOF value) predictions. It is found that the LUMO energies of aluminum chloride complexes and their average NBO charges of coordinating oxygen atoms correlate with the catalytic activity (TOF value) of Al complexes (R2 value of 0.98 and ‘3-fold’ cross-validation Q2 value of 0.88). This verified that such a ligand effect is generally applicable in anhydride/epoxide ROCOP catalyzed by aluminum complex and provides hints for future catalyst design. Full article
(This article belongs to the Special Issue Advances in Molecular Modeling in Chemistry)
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14 pages, 4524 KiB  
Article
Tunable Electronic Transport of New-Type 2D Iodine Materials Affected by the Doping of Metal Elements
Molecules 2023, 28(20), 7159; https://doi.org/10.3390/molecules28207159 - 19 Oct 2023
Cited by 1 | Viewed by 656
Abstract
2D iodine structures under high pressures are more attractive and valuable due to their special structures and excellent properties. Here, electronic transport properties of such 2D iodine structures are theoretically studied by considering the influence of the metal-element doping. In equilibrium, metal elements [...] Read more.
2D iodine structures under high pressures are more attractive and valuable due to their special structures and excellent properties. Here, electronic transport properties of such 2D iodine structures are theoretically studied by considering the influence of the metal-element doping. In equilibrium, metal elements in Group 1 can enhance the conductance dramatically and show a better enhancement effect. Around the Fermi level, the transmission probability exceeds 1 and can be improved by the metal-element doping for all devices. In particular, the device density of states explains well the distinctions between transmission coefficients originating from different doping methods. Contrary to the “big” site doping, the “small” site doping changes transmission eigenstates greatly, with pronounced electronic states around doped atoms. In non-equilibrium, the conductance of all devices is almost weaker than the equilibrium conductance, decreasing at low voltages and fluctuating at high voltages with various amplitudes. Under biases, K-big doping shows the optimal enhancement effect, and Mg-small doping exhibits the most effective attenuation effect on conductance. Contrastingly, the currents of all devices increase with bias linearly. The metal-element doping can boost current at low biases and weaken current at high voltages. These findings contribute much to understanding the effects of defects on electronic properties and provide solid support for the application of new-type 2D iodine materials in controllable electronics and sensors. Full article
(This article belongs to the Special Issue Advances in Molecular Modeling in Chemistry)
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12 pages, 3165 KiB  
Article
Electron Transport Properties of Graphene/WS2 Van Der Waals Heterojunctions
Molecules 2023, 28(19), 6866; https://doi.org/10.3390/molecules28196866 - 29 Sep 2023
Cited by 1 | Viewed by 834
Abstract
Van der Waals heterojunctions of two-dimensional atomic crystals are widely used to build functional devices due to their excellent optoelectronic properties, which are attracting more and more attention, and various methods have been developed to study their structure and properties. Here, density functional [...] Read more.
Van der Waals heterojunctions of two-dimensional atomic crystals are widely used to build functional devices due to their excellent optoelectronic properties, which are attracting more and more attention, and various methods have been developed to study their structure and properties. Here, density functional theory combined with the nonequilibrium Green’s function technique has been used to calculate the transport properties of graphene/WS2 heterojunctions. It is observed that the formation of heterojunctions does not lead to the opening of the Dirac point of graphene. Instead, the respective band structures of both graphene and WS2 are preserved. Therefore, the heterojunction follows a unique Ohm’s law at low bias voltages, despite the presence of a certain rotation angle between the two surfaces within the heterojunction. The transmission spectra, the density of states, and the transmission eigenstate are used to investigate the origin and mechanism of unique linear I–V characteristics. This study provides a theoretical framework for designing mixed-dimensional heterojunction nanoelectronic devices. Full article
(This article belongs to the Special Issue Advances in Molecular Modeling in Chemistry)
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14 pages, 31826 KiB  
Article
Comparison of H2O Adsorption and Dissociation Behaviors on Rutile (110) and Anatase (101) Surfaces Based on ReaxFF Molecular Dynamics Simulation
Molecules 2023, 28(19), 6823; https://doi.org/10.3390/molecules28196823 - 27 Sep 2023
Viewed by 567
Abstract
The relationship between structure and reactivity plays a dominant role in water dissociation on the various TiO2 crystallines. To observe the adsorption and dissociation behavior of H2O, the reaction force field (ReaxFF) is used to investigate the dynamic behavior of [...] Read more.
The relationship between structure and reactivity plays a dominant role in water dissociation on the various TiO2 crystallines. To observe the adsorption and dissociation behavior of H2O, the reaction force field (ReaxFF) is used to investigate the dynamic behavior of H2O on rutile (110) and anatase (101) surfaces in an aqueous environment. Simulation results show that there is a direct proton transfer between the adsorbed H2O (H2Oad) and the bridging oxygen (Obr) on the rutile (110) surface. Compared with that on the rutile (110) surface, an indirect proton transfer occurs on the anatase (101) surface along the H-bond network from the second layer of water. This different mechanism of water dissociation is determined by the distance between the 5-fold coordinated Ti (Ti5c) and Obr of the rutile and anatase TiO2 surfaces, resulting in the direct or indirect proton transfer. Additionally, the hydrogen bond (H-bond) network plays a crucial role in the adsorption and dissociation of H2O on the TiO2 surface. To describe interfacial water structures between TiO2 and bulk water, the double-layer model is proposed. The first layer is the dissociated H2O on the rutile (110) and anatase (101) surfaces. The second layer forms an ordered water structure adsorbed to the surface Obr or terminal OH group through strong hydrogen bonding (H-bonding). Affected by the H-bond network, the H2O dissociation on the rutile (110) surface is inhibited but that on the anatase (101) surface is promoted. Full article
(This article belongs to the Special Issue Advances in Molecular Modeling in Chemistry)
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18 pages, 3610 KiB  
Article
Evaluation of the Toxicity Potential of the Metabolites of Di-Isononyl Phthalate and of Their Interactions with Members of Family 1 of Sulfotransferases—A Computational Study
Molecules 2023, 28(18), 6748; https://doi.org/10.3390/molecules28186748 - 21 Sep 2023
Viewed by 1077
Abstract
Di-isononyl phthalates are chemicals that are widely used as plasticizers. Humans are extensively exposed to these compounds by dietary intake, through inhalation and skin absorption. Sulfotransferases (SULTs) are enzymes responsible for the detoxification and elimination of numerous endogenous and exogenous molecules from the [...] Read more.
Di-isononyl phthalates are chemicals that are widely used as plasticizers. Humans are extensively exposed to these compounds by dietary intake, through inhalation and skin absorption. Sulfotransferases (SULTs) are enzymes responsible for the detoxification and elimination of numerous endogenous and exogenous molecules from the body. Consequently, SULTs are involved in regulating the biological activity of various hormones and neurotransmitters. The present study considers a computational approach to predict the toxicological potential of the metabolites of di-isononyl phthalate. Furthermore, molecular docking was considered to evaluate the inhibitory potential of these metabolites against the members of family 1 of SULTs. The metabolites of di-isononyl phthalate reveal a potency to cause liver damage and to inhibit receptors activated by peroxisome proliferators. These metabolites are also usually able to inhibit the activity of the members of family 1 of SULTs, except for SULT1A3 and SULT1B1. The outcomes of this study are important for an enhanced understanding of the risk of human exposure to di-isononyl phthalates. Full article
(This article belongs to the Special Issue Advances in Molecular Modeling in Chemistry)
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12 pages, 10650 KiB  
Article
Molecular Dynamics Simulations on the Adsorbed Monolayers of N-Dodecyl Betaine at the Air–Water Interface
Molecules 2023, 28(14), 5580; https://doi.org/10.3390/molecules28145580 - 22 Jul 2023
Viewed by 689
Abstract
Betaine is a kind of zwitterionic surfactant with both positive and negative charge groups on the polar head, showing good surface activity and aggregation behaviors. The interfacial adsorption, structures and properties of n-dodecyl betaine (NDB) at different surface coverages at the air–water [...] Read more.
Betaine is a kind of zwitterionic surfactant with both positive and negative charge groups on the polar head, showing good surface activity and aggregation behaviors. The interfacial adsorption, structures and properties of n-dodecyl betaine (NDB) at different surface coverages at the air–water interface are studied through molecular dynamics (MD) simulations. Interactions between the polar heads and water molecules, the distribution of water molecules around polar heads, the tilt angle of the NDB molecule, polar head and tail chain with respect to the surface normal, the conformations and lengths of the tail chain, and the interfacial thickness of the NDB monolayer are analyzed. The change of surface coverage hardly affects the locations and spatial distributions of the water molecules around the polar heads. As more NDB molecules are adsorbed at the air–water interface, the number of hydrogen bonds between polar heads and water molecules slightly decreases, while the lifetimes of hydrogen bonds become larger. With the increase in surface coverage, less gauche defects along the alkyl chain and longer NDB chain are obtained. The thickness of the NDB monolayer also increases. At large surface coverages, tilted angles of the polar head, tail chain and whole NDB molecule show little change with the increase in surface area. Surface coverages can change the tendency of polar heads and the tail chain for the surface normal. Full article
(This article belongs to the Special Issue Advances in Molecular Modeling in Chemistry)
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14 pages, 7403 KiB  
Article
Detachment of Dodecane from Silica Surfaces with Variable Surface Chemistry Studied Using Molecular Dynamics Simulation
Molecules 2023, 28(12), 4765; https://doi.org/10.3390/molecules28124765 - 14 Jun 2023
Cited by 1 | Viewed by 685
Abstract
The adsorption and detachment processes of n-dodecane (C12H26) molecules were studied on silica surfaces with variable surface chemistry (Q2, Q3, Q4 environments), using molecular dynamics simulations. The area density of the silanol groups varied [...] Read more.
The adsorption and detachment processes of n-dodecane (C12H26) molecules were studied on silica surfaces with variable surface chemistry (Q2, Q3, Q4 environments), using molecular dynamics simulations. The area density of the silanol groups varied from 9.4 to 0 per nm2. The shrinking of the oil–water–solid contact line was a key step for the oil detachment, due to water diffusion on the three-phase contact line. The simulation results showed that oil detachment was easier and faster on a perfect Q3 silica surface which had (≡Si(OH))-type silanol groups, due to the H-bond formation between the water and silanol groups. When the surfaces contained more Q2 crystalline type which had (≡Si(OH)2)-type silanol groups, less oil detached, due to the formations of H-bonds among the silanol groups. There were no silanol groups on the Si-OH 0 surface. Water cannot diffuse on the water–oil–silica contact line, and oil cannot detach from the Q4 surface. The detachment efficiency of oil from the silica surface not only depended on the area density, but also on the types of silanol groups. The density and type of silanol groups depend on the crystal cleavage plane, particle size, roughness, and humidity. Full article
(This article belongs to the Special Issue Advances in Molecular Modeling in Chemistry)
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18 pages, 3278 KiB  
Article
Harmonic Vibrational Frequency Simulation of Pharmaceutical Molecules via a Novel Multi-Molecular Fragment Interception Method
Molecules 2023, 28(12), 4638; https://doi.org/10.3390/molecules28124638 - 08 Jun 2023
Viewed by 876
Abstract
By means of a computational method based on Density Functional Theory (DFT), using commercially available software, a novel method for simulating equilibrium geometry harmonic vibrational frequencies is proposed. Finasteride, Lamivudine, and Repaglinide were selected as model molecules to study the adaptability of the [...] Read more.
By means of a computational method based on Density Functional Theory (DFT), using commercially available software, a novel method for simulating equilibrium geometry harmonic vibrational frequencies is proposed. Finasteride, Lamivudine, and Repaglinide were selected as model molecules to study the adaptability of the new method. Three molecular models, namely the single-molecular, central-molecular, and multi-molecular fragment models, were constructed and calculated by Generalized Gradient Approximations (GGAs) with the PBE functional via the Material Studio 8.0 program. Theoretical vibrational frequencies were assigned and compared to the corresponding experimental data. The results indicated that the traditional single-molecular calculation and scaled spectra with scale factor exhibited the worst similarity for all three pharmaceutical molecules among the three models. Furthermore, the central-molecular model with a configuration closer to the empirical structure resulted in a reduction of mean absolute error (MAE) and root mean squared error (RMSE) in all three pharmaceutics, including the hydrogen-bonded functional groups. However, the improvement in computational accuracy for different drug molecules using the central-molecular model for vibrational frequency calculation was unstable. Whereas, the new multi-molecular fragment interception method showed the best agreement with experimental results, exhibiting MAE and RMSE values of 8.21 cm−1 and 18.35 cm−1 for Finasteride, 15.95 cm−1 and 26.46 cm−1 for Lamivudine, and 12.10 cm−1 and 25.82 cm−1 for Repaglinide. Additionally, this work provides comprehensive vibrational frequency calculations and assignments for Finasteride, Lamivudine, and Repaglinide, which have never been thoroughly investigated in previous research. Full article
(This article belongs to the Special Issue Advances in Molecular Modeling in Chemistry)
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14 pages, 3618 KiB  
Article
Prediction of Ethanol-Mediated Growth Morphology of Ammonium Dinitramide/Pyrazine-1,4-Dioxide Cocrystal at Different Temperatures
Molecules 2023, 28(11), 4534; https://doi.org/10.3390/molecules28114534 - 03 Jun 2023
Cited by 2 | Viewed by 902
Abstract
The crystal morphology of high energetic materials plays a crucial role in aspects of their safety performance such as impact sensitivity. In order to reveal the crystal morphology of ammonium dinitramide/pyrazine-1,4-dioxide (ADN/PDO) cocrystal at different temperatures, the modified attachment energy model (MAE) was [...] Read more.
The crystal morphology of high energetic materials plays a crucial role in aspects of their safety performance such as impact sensitivity. In order to reveal the crystal morphology of ammonium dinitramide/pyrazine-1,4-dioxide (ADN/PDO) cocrystal at different temperatures, the modified attachment energy model (MAE) was used at 298, 303, 308, and 313 K to predict the morphology of the ADN/PDO cocrystal under vacuum and ethanol. The results showed that under vacuum conditions, five growth planes of the ADN/PDO cocrystal were given, which were (1 0 0), (0 1 1), (1 1 0), (1 1 −1), and (2 0 −2). Among them, the ratios of the (1 0 0) and (0 1 1) planes were 40.744% and 26.208%, respectively. In the (0 1 1) crystal plane, the value of S was 1.513. The (0 1 1) crystal plane was more conducive to the adsorption of ethanol molecules. The order of binding energy between the ADN/PDO cocrystal and ethanol solvent was (0 1 1) > (1 1 −1) > (2 0 −2) > (1 1 0) > (1 0 0). The radial distribution function analysis revealed that there were hydrogen bonds between the ethanol and the ADN cations, van der Waals interactions with the ADN anions. As the temperature increased, the aspect ratio of the ADN/PDO cocrystal was reduced, making the crystal more spherical, which helped to further reduce the sensitivity of this explosive. Full article
(This article belongs to the Special Issue Advances in Molecular Modeling in Chemistry)
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14 pages, 2645 KiB  
Article
A MD Simulation Prediction for Regulation of N-Terminal Modification on Binding of CD47 to CD172a in a Force-Dependent Manner
Molecules 2023, 28(10), 4224; https://doi.org/10.3390/molecules28104224 - 22 May 2023
Viewed by 1367
Abstract
Cancer cells can evade immune surveillance through binding of its transmembrane receptor CD47 to CD172a on myeloid cells. CD47 is recognized as a promising immune checkpoint for cancer immunotherapy inhibiting macrophage phagocytosis. N-terminal post-translated modification (PTM) via glutaminyl cyclase is a landmark [...] Read more.
Cancer cells can evade immune surveillance through binding of its transmembrane receptor CD47 to CD172a on myeloid cells. CD47 is recognized as a promising immune checkpoint for cancer immunotherapy inhibiting macrophage phagocytosis. N-terminal post-translated modification (PTM) via glutaminyl cyclase is a landmark event in CD47 function maturation, but the molecular mechanism underlying the mechano-chemical regulation of the modification on CD47/CD172a remains unclear. Here, we performed so-called “ramp-clamp” steered molecular dynamics (SMD) simulations, and found that the N-terminal PTM enhanced interaction of CD172a with CD47 by inducing a dynamics-driven contraction of the binding pocket of the bound CD172a, an additional constraint on CYS15 on CD47 significantly improved the tensile strength of the complex with or without PTM, and a catch bond phenomenon would occur in complex dissociation under tensile force of 25 pN in a PTM-independent manner too. The residues GLN52 and SER66 on CD172a reinforced the H-bonding with their partners on CD47 in responding to PTM, while ARG69 on CD172 with its partner on CD47 might be crucial in the structural stability of the complex. This work might serve as molecular basis for the PTM-induced function improvement of CD47, should be helpful for deeply understanding CD47-relevant immune response and cancer development, and provides a novel insight in developing of new strategies of immunotherapy targeting this molecule interaction. Full article
(This article belongs to the Special Issue Advances in Molecular Modeling in Chemistry)
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11 pages, 4253 KiB  
Article
Molecular Dynamics Study on the Aggregation Behavior of Triton X Micelles with Different PEO Chain Lengths in Aqueous Solution
Molecules 2023, 28(8), 3557; https://doi.org/10.3390/molecules28083557 - 18 Apr 2023
Cited by 1 | Viewed by 1286
Abstract
The aggregation structure of Triton X (TX) amphiphilic molecules in aqueous solution plays an important role in determining the various properties and applications of surfactant solutions. In this paper, the properties of micelles formed by TX-5, TX-114, and TX-100 molecules with different poly(ethylene [...] Read more.
The aggregation structure of Triton X (TX) amphiphilic molecules in aqueous solution plays an important role in determining the various properties and applications of surfactant solutions. In this paper, the properties of micelles formed by TX-5, TX-114, and TX-100 molecules with different poly(ethylene oxide) (PEO) chain lengths in TX series of nonionic surfactants were studied via molecular dynamics (MD) simulation. The structural characteristics of three micelles were analyzed at the molecular level, including the shape and size of micelles, the solvent accessible surface area, the radial distribution function, the micelle configuration, and the hydration numbers. With the increase of PEO chain length, the micelle size and solvent accessible surface area also increase. The distribution probability of the polar head oxygen atoms on the surface of the TX-100 micelle is higher than that in the TX-5 or TX-114 micelle. In particular, the tail quaternary carbon atoms in the hydrophobic region are mainly located at the micelle exterior. For TX-5, TX-114, and TX-100 micelles, the interactions between micelles and water molecules are also quite different. These structures and comparisons at the molecular level contribute to the further understanding of the aggregation and applications of TX series surfactants. Full article
(This article belongs to the Special Issue Advances in Molecular Modeling in Chemistry)
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