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Gill WA, Alhokbany N, Janjua MRSA. Adsorption of molecular hydrogen on Be 3Al 2(SiO 3) 6-beryl: theoretical insights for catalysis, hydrogen storage, gas separation, sensing, and environmental applications. RSC Adv 2024; 14:3782-3789. [PMID: 38274172 PMCID: PMC10809057 DOI: 10.1039/d3ra07480c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 01/12/2024] [Indexed: 01/27/2024] Open
Abstract
Employing a combination of Density Functional Theory (DFT) calculations and Molecular Dynamics (MD) simulations, the adsorption of molecular hydrogen (H2) on Be3Al2(SiO3)6-beryl, a prominent silicate mineral, has been studied. The crystal structure of beryl, which consists of interconnected tetrahedral and octahedral sites, provides a fascinating framework for comprehending H2 adsorption behavior. Initial investigation of the interaction between H2 molecules and the beryl surface employed DFT calculations. We identified favorable adsorption sites and gained insight into the binding mechanism through extensive structural optimizations and energy calculations. H2 molecules preferentially adsorb on the exposed oxygen atoms surrounding the octahedral sites, producing weak van der Waals interactions with the beryl surface, according to our findings. To further investigate the dynamic aspects of H2 adsorption, MD simulations employing a suitable force field were conducted. To precisely represent interatomic interactions within the Be3Al2(SiO3)6-beryl-H2 system, the force field parameters were meticulously parameterized. By subjecting the system to a variety of temperatures, we were able to obtain valuable information about the stability, diffusion, and desorption kinetics of H2 molecules within the beryl structure. The comprehensive understanding of the H2 adsorption phenomenon on Be3Al2(SiO3)6-beryl is provided by the combined DFT and MD investigations. The results elucidate the mechanisms underlying H2 binding, highlighting the role of surface oxygen atoms and the effect of temperature on H2 dynamics. This research contributes to a fundamental understanding of hydrogen storage and release in beryllium-based silicates and provides valuable guidance for the design and optimization of materials for hydrogen storage, catalysis, gas separation, sensing and environmental applications.
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Affiliation(s)
- Waqas Amber Gill
- Departamento de Química Física, Universidad de Valencia Avda Dr Moliner, 50, E-46100 Burjassot Valencia Spain
| | - Norah Alhokbany
- Department of Chemistry, King Saud University Riyadh 11451 Saudi Arabia
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2
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Gill WA, Aziz MT, Darwish HW, Janjua MRSA. Exploring HCl-HCl interactions: QZVPP calculations, improved Lennard-Jones potential, and second virial coefficient analysis for thermodynamics and industrial applications. RSC Adv 2024; 14:1890-1901. [PMID: 38192328 PMCID: PMC10772863 DOI: 10.1039/d3ra04387h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 12/13/2023] [Indexed: 01/10/2024] Open
Abstract
In this paper, we present a comprehensive analysis of HCl-HCl interactions, including QZVPP calculations, energy fitting, conformation validation, and the determination of the second virial coefficient B using improved Lennard-Jones (ILJ) potential parameters. To acquire accurate interaction energies, initial QZVPP calculations are performed on approximately 1851 randomly generated HCl-HCl conformations. Then, these energies are used to fit an improved Lennard-Jones potential energy surface, allowing for a robust description of HCl-HCl interactions. The ILJ potential parameters are then used to validate particular HCl dimer conformations, ensuring their stability and consistency with experimental observations. The correlation between calculated and experimental conformations strengthens the validity of the ILJ potential parameters. In addition, the second viral coefficient B is calculated at various temperatures using the ILJ potential. The obtained B values are compared to experimental data, demonstrating close agreement, and validating the ILJ potential's ability to accurately capture the intermolecular interactions and gas-phase behavior of the HCl-HCl system. The results of this study demonstrate the effective implementation of QZVPP calculations, energy fitting, and ILJ potential parameters in validating HCl-HCl conformations and accurately determining the second virial coefficient B. The high degree of concordance between calculated B values and experimental data demonstrates the validity of the ILJ potential and its suitability for modeling HCl-HCl interactions. This research contributes to a greater comprehension of HCl-HCl interactions and their implications for numerous chemical and atmospheric processes. The validated conformations, energy fitting method, and calculated second virial coefficients provide valuable instruments for future research and pave the way for more accurate modeling and simulations of HCl-HCl systems.
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Affiliation(s)
- Waqas Amber Gill
- Departamento de Química Física, Universidad de Valencia Avda Dr Moliner, 50, Burjassot E-46100 Valencia Spain
| | - Muhammad Tariq Aziz
- Department of Chemistry, Government College University Faisalabad Faisalabad 38000 Pakistan
| | - Hany W Darwish
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University P.O. Box 2457 Riyadh 11451 Saudi Arabia
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3
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Zhou J, Jia S, Xue X, Hao X, Zeng Q, Wang X, Ren X. Structural and dynamical studies of CH- πbonded CH 4-C 6H 6dimer by ultrafast intermolecular Coulombic decay. NANOTECHNOLOGY 2023; 34:165102. [PMID: 36645904 DOI: 10.1088/1361-6528/acb358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 01/16/2023] [Indexed: 06/17/2023]
Abstract
The inner-valence ionization and fragmentation dynamics of CH4-C6H6dimer induced by 200 eV electron impact is studied utilizing a multi-particle coincidence momentum spectroscopy. The three-dimensional momentum vectors and kinetic energy release (KER) of the CH4++C6H6+ion pairs are obtained by coincident momentum measurement. Our analysis on the absolute cross sections indicates that the intermediate dication CH4+-C6H6+is preferentially produced by the removal of an inner-valence electron from CH4or C6H6and subsequent relaxation of ultrafast intermolecular Coulombic decay followed by two-body Coulomb explosion. Combining withab initiomolecular dynamics (AIMD) simulations, the real-time fragmentation dynamics including translational, vibrational and rotational motions are presented as a function of propagation time. The revealed fragmentation dynamics are expected to have a potential implication for crystal structure imaging with various radiation sources.
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Affiliation(s)
- Jiaqi Zhou
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an 710049, People's Republic of China
| | - Shaokui Jia
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an 710049, People's Republic of China
| | - Xiaorui Xue
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an 710049, People's Republic of China
| | - Xintai Hao
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an 710049, People's Republic of China
| | - Qingrui Zeng
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an 710049, People's Republic of China
| | - Xing Wang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an 710049, People's Republic of China
| | - Xueguang Ren
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an 710049, People's Republic of China
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Miao L, Chen S, Yang H, Hong Y, Sun L, Yang J, Sun G, Liu Y, Li C, Zang H, Cheng Y. Enhanced bioremediation of triclocarban-contaminated soil by Rhodococcus rhodochrous BX2 and Pseudomonas sp. LY-1 immobilized on biochar and microbial community response. Front Microbiol 2023; 14:1168902. [PMID: 37065135 PMCID: PMC10098447 DOI: 10.3389/fmicb.2023.1168902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Accepted: 03/02/2023] [Indexed: 04/18/2023] Open
Abstract
Triclocarban (TCC), an emerging organic contaminant (EOC), has become a severe threat to soil microbial communities and ecological security. Here, the TCC-degrading strain Rhodococcus rhodochrous BX2 and DCA-degrading strain Pseudomonas sp. LY-1 (together referred to as TC1) were immobilized on biochar to remove TCC and its intermediates in TCC-contaminated soil. High-throughput sequencing was used to investigate the microbial community structure in TCC-contaminated soil. Analysis of co-occurrence networks was used to explore the mutual relationships among soil microbiome members. The results showed that the immobilized TC1 significantly increased the removal efficiency of TCC from 84.7 to 92.7% compared to CK (no TC1 cells on biochar) in 10 mg/L TCC liquid medium. The utilization of immobilized TC1 also significantly accelerated the removal of TCC from contaminated soil. Microbial community analysis revealed the crucial microorganisms and their functional enzymes participating in TCC degradation in soil. Moreover, the internal labor division patterns and connections of TCC-degrading microbes, with a focus on strains BX2 and LY-1, were unraveled by co-occurrence networks analysis. This work provides a promising strategy to facilitate the bioremediation of TCC in soil, which has potential application value for sustainable biobased economies.
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Affiliation(s)
- Lei Miao
- College of Resources and Environment, Northeast Agricultural University, Harbin, China
- Key Laboratory of Swine Facilities Engineering, Ministry of Agriculture and Rural Affairs, Harbin, China
| | - Siyuan Chen
- College of Resources and Environment, Northeast Agricultural University, Harbin, China
- Key Laboratory of Swine Facilities Engineering, Ministry of Agriculture and Rural Affairs, Harbin, China
| | - Hua Yang
- College of Resources and Environment, Northeast Agricultural University, Harbin, China
- Key Laboratory of Swine Facilities Engineering, Ministry of Agriculture and Rural Affairs, Harbin, China
| | - Yaqi Hong
- College of Resources and Environment, Northeast Agricultural University, Harbin, China
- Key Laboratory of Swine Facilities Engineering, Ministry of Agriculture and Rural Affairs, Harbin, China
| | - Liwen Sun
- College of Resources and Environment, Northeast Agricultural University, Harbin, China
- Key Laboratory of Swine Facilities Engineering, Ministry of Agriculture and Rural Affairs, Harbin, China
| | - Jie Yang
- College of Resources and Environment, Northeast Agricultural University, Harbin, China
- Key Laboratory of Swine Facilities Engineering, Ministry of Agriculture and Rural Affairs, Harbin, China
| | - Guanjun Sun
- College of Resources and Environment, Northeast Agricultural University, Harbin, China
- Key Laboratory of Swine Facilities Engineering, Ministry of Agriculture and Rural Affairs, Harbin, China
| | - Yi Liu
- College of Resources and Environment, Northeast Agricultural University, Harbin, China
- Key Laboratory of Swine Facilities Engineering, Ministry of Agriculture and Rural Affairs, Harbin, China
| | - Chunyan Li
- College of Resources and Environment, Northeast Agricultural University, Harbin, China
- Key Laboratory of Swine Facilities Engineering, Ministry of Agriculture and Rural Affairs, Harbin, China
| | - Hailian Zang
- College of Resources and Environment, Northeast Agricultural University, Harbin, China
- Key Laboratory of Swine Facilities Engineering, Ministry of Agriculture and Rural Affairs, Harbin, China
| | - Yi Cheng
- Key Laboratory of Swine Facilities Engineering, Ministry of Agriculture and Rural Affairs, Harbin, China
- College of Plant Protection, Northeast Agricultural University, Harbin, China
- *Correspondence: Yi Cheng,
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Ojeda-López R, Ramos-Sánchez G, García-Mendoza C, C. S. Azevedo D, Guzmán-Vargas A, Felipe C. Effect of Calcination Temperature and Chemical Composition of PAN-Derived Carbon Microfibers on N 2, CO 2, and CH 4 Adsorption. MATERIALS 2021; 14:ma14143914. [PMID: 34300825 PMCID: PMC8305112 DOI: 10.3390/ma14143914] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 07/02/2021] [Accepted: 07/08/2021] [Indexed: 02/05/2023]
Abstract
This work investigates the interplay of carbonization temperature and the chemical composition of carbon microfibers (CMFs), and their impact on the equilibration time and adsorption of three molecules (N2, CO2, and CH4). PAN derived CMFs were synthesized by electrospinning and calcined at three distinct temperatures (600, 700 and 800 °C), which led to samples with different textural and chemical properties assessed by FTIR, TGA/DTA, XRD, Raman, TEM, XPS, and N2 adsorption. We examine why samples calcined at low/moderate temperatures (600 and 700 °C) show an open hysteresis loop in nitrogen adsorption/desorption isotherms at -196.15 °C. The equilibrium time in adsorption measurements is nearly the same for these samples, despite their distinct chemical compositions. Increasing the equilibrium time did not allow for the closure of the hysteresis loop, but by rising the analysis temperature this was achieved. By means of the isosteric enthalpy of adsorption measurements and ab initio calculations, adsorbent/adsorbate interactions for CO2, CH4 and N2 were found to be inversely proportional to the temperature of carbonization of the samples (CMF-600 > CMF-700 > CMF-800). The enhancement of adsorbent/adsorbate interaction at lower carbonization temperatures is directly related to the presence of nitrogen and oxygen functional groups on the surface of CMFs. Nonetheless, a higher concentration of heteroatoms also causes: (i) a reduction in the adsorption capacity of CO2 and CH4 and (ii) open hysteresis loops in N2 adsorption at cryogenic temperatures. Therefore, the calcination of PAN derived microfibers at temperatures above 800 °C is recommended, which results in materials with suitable micropore volume and a low content of surface heteroatoms, leading to high CO2 uptake while keeping acceptable selectivity with regards to CH4 and moderate adsorption enthalpies.
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Affiliation(s)
- Reyna Ojeda-López
- Laboratório de Pesquisa em Adsorção e Captura de CO2 (LPACO2), Departamento de Engenharia Química, Universidade Federal do Ceará (UFC), Fortaleza 60455-760, CE, Brazil;
- Departamento de Química, Universidad Autónoma Metropolitana-Iztapalapa (UAM-I), 09340 Mexico City, Mexico;
- Correspondence: (R.O.-L.); (C.F.)
| | - Guadalupe Ramos-Sánchez
- Departamento de Química, Universidad Autónoma Metropolitana-Iztapalapa (UAM-I), 09340 Mexico City, Mexico;
- CONACYT, Universidad Autónoma Metropolitana-Iztapalapa (UAM-I), 09340 Mexico City, Mexico
| | - Cinthia García-Mendoza
- Laboratorio de Nanotecnología, Centro de Investigación de Ciencia y Tecnología Avanzada de Tabasco (CICTAT), División Académica de Ingeniería y Arquitectura, Universidad Juárez Autónoma de Tabasco (UJAT), 86690 Tabasco, Mexico;
| | - Diana C. S. Azevedo
- Laboratório de Pesquisa em Adsorção e Captura de CO2 (LPACO2), Departamento de Engenharia Química, Universidade Federal do Ceará (UFC), Fortaleza 60455-760, CE, Brazil;
| | - Ariel Guzmán-Vargas
- Laboratorio de Investigación en Materiales Porosos, Catálisis Ambiental y Química Fina, ESIQIE, Instituto Politécnico Nacional (IPN), 07738 Mexico City, Mexico;
| | - Carlos Felipe
- Departamento de Biociencias e Ingeniería, Centro Interdisciplinario de Investigaciones y Estudios sobre Medio Ambiente y Desarrollo (CIIEMAD), Instituto Politécnico Nacional (IPN), 07340 Mexico City, Mexico
- Correspondence: (R.O.-L.); (C.F.)
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6
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Vekeman J, Faginas-Lago N, Lombardi A, Sánchez de Merás A, García Cuesta I, Rosi M. Molecular Dynamics of CH 4/N 2 Mixtures on a Flexible Graphene Layer: Adsorption and Selectivity Case Study. Front Chem 2019; 7:386. [PMID: 31214569 PMCID: PMC6557170 DOI: 10.3389/fchem.2019.00386] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Accepted: 05/14/2019] [Indexed: 11/25/2022] Open
Abstract
We theoretically investigate graphene layers, proposing them as membranes of subnanometer size suitable for CH4/N2 separation and gas uptake. The observed potential energy surfaces, representing the intermolecular interactions within the CH4/N2 gaseous mixtures and between these and the graphene layers, have been formulated by adopting the so-called Improved Lennard-Jones (ILJ) potential, which is far more accurate than the traditional Lennard-Jones potential. Previously derived ILJ force fields are used to perform extensive molecular dynamics simulations on graphene's ability to separate and adsorb the CH4/N2 mixture. Furthermore, the intramolecular interactions within graphene were explicitly considered since they are responsible for its flexibility and the consequent out-of-plane movements of the constituting carbon atoms. The effects on the adsorption capacity of graphene caused by introducing its flexibility in the simulations are assessed via comparison of different intramolecular force fields giving account of flexibility against a simplified less realistic model that considers graphene to be rigid. The accuracy of the potentials guarantees a quantitative description of the interactions and trustable results for the dynamics, as long as the appropriate set of intramolecular and intermolecular force fields is chosen. In particular it is shown that only if the flexibility of graphene is explicitly taken into account, a simple united-atom interaction potential can provide correct predictions. Conversely, when using an atomistic model, neglecting in the simulations the intrinsic flexibility of the graphene sheet has a minor effect. From a practical point of view, the global analysis of the whole set of results proves that these nanostructures are versatile materials competitive with other carbon-based adsorbing membranes suitable to cope with CH4 and N2 adsorption.
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Affiliation(s)
- Jelle Vekeman
- Dipartimento di Chimica, Biologia e Biotecnologie, Università degli Studi di Perugia, Perugia, Italy.,Instituto de Ciencia Molecular, Universidad de Valencia, Valencia, Spain
| | - Noelia Faginas-Lago
- Dipartimento di Chimica, Biologia e Biotecnologie, Università degli Studi di Perugia, Perugia, Italy.,Consortium for Computational Molecular and Materials Sciences (CMS2), Perugia, Italy
| | - Andrea Lombardi
- Dipartimento di Chimica, Biologia e Biotecnologie, Università degli Studi di Perugia, Perugia, Italy.,Consortium for Computational Molecular and Materials Sciences (CMS2), Perugia, Italy
| | | | | | - Marzio Rosi
- Dipartimento di Ingegneria Civile e Ambientale, Università degli Studi di Perugia, Perugia, Italy
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7
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Vekeman J, G Cuesta I, Faginas-Lago N, Wilson J, Sánchez-Marín J, Sánchez de Merás A. Potential models for the simulation of methane adsorption on graphene: development and CCSD(T) benchmarks. Phys Chem Chem Phys 2018; 20:25518-25530. [PMID: 30277488 DOI: 10.1039/c8cp03652g] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Different force fields for the graphene-CH4 system are proposed including pseudo-atom and full atomistic models. Furthermore, different charge schemes are tested to evaluate the electrostatic interaction for the CH4 dimer. The interaction parameters are optimized by fitting to interaction energies at the DFT level, which were themselves benchmarked against CCSD(T) calculations. The potentials obtained with both the pseudo-atom and full atomistic approaches describe accurately enough the average interaction in the methane dimer as well as in the graphene-methane system. Moreover, the atom-atom potentials also correctly provide the energies associated with different orientations of the molecules. In the atomistic models, charge schemes including small charges allow for the adequate representation of the stability sequence of significant conformations of the methane dimer. Additionally, an intermediate charge of -0.63e on the carbon atom in methane leads to bond energies with errors of ca. 0.07 kcal mol-1 with respect to the CCSD(T) values for the methane dimer. For the graphene-methane interaction, the atom-atom potential model predicts an average interaction energy of 2.89 kcal mol-1, comparable to the experimental interaction energy of 3.00 kcal mol-1. Finally, the presented force fields were used to obtain self-diffusion coefficients that were checked against the experimental value found in the literature. The no-charge and Hirshfeld charge atom-atom models perform extremely well in this respect, while the cheapest potential considered, a pseudo-atom model without charges, still performs reasonably well.
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Affiliation(s)
- J Vekeman
- Instituto de Ciencia Molecular, Parc cientifico de la Universidad de Valencia, C/Catedrático José Beltrán 2, E-46980 Paterna, Spain.
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8
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Marchione D, McCoustra MRS. Non-covalent interaction of benzene with methanol and diethyl ether solid surfaces. Phys Chem Chem Phys 2016; 18:20790-801. [DOI: 10.1039/c6cp01787h] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
We have investigated the interactions involved at the interface of binary, layered ices (benzene on methanol and on diethyl ether) by means of laboratory experiments and ab initio calculations on model clusters.
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9
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Albertí M, Amat A, Farrera L, Pirani F. From the (NH3)2–5 clusters to liquid ammonia: Molecular dynamics simulations using the NVE and NpT ensembles. J Mol Liq 2015. [DOI: 10.1016/j.molliq.2015.09.016] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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10
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Aβ1-25-Derived Sphingolipid-Domain Tracer Peptide SBD Interacts with Membrane Ganglioside Clusters via a Coil-Helix-Coil Motif. Int J Mol Sci 2015; 16:26318-32. [PMID: 26540054 PMCID: PMC4661814 DOI: 10.3390/ijms161125955] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Revised: 10/19/2015] [Accepted: 10/22/2015] [Indexed: 12/30/2022] Open
Abstract
The Amyloid-β (Aβ)-derived, sphingolipid binding domain (SBD) peptide is a fluorescently tagged probe used to trace the diffusion behavior of sphingolipid-containing microdomains in cell membranes through binding to a constellation of glycosphingolipids, sphingomyelin, and cholesterol. However, the molecular details of the binding mechanism between SBD and plasma membrane domains remain unclear. Here, to investigate how the peptide recognizes the lipid surface at an atomically detailed level, SBD peptides in the environment of raft-like bilayers were examined in micro-seconds-long molecular dynamics simulations. We found that SBD adopted a coil-helix-coil structural motif, which binds to multiple GT1b gangliosides via salt bridges and CH–π interactions. Our simulation results demonstrate that the CH–π and electrostatic forces between SBD monomers and GT1b gangliosides clusters are the main driving forces in the binding process. The presence of the fluorescent dye and linker molecules do not change the binding mechanism of SBD probes with gangliosides, which involves the helix-turn-helix structural motif that was suggested to constitute a glycolipid binding domain common to some sphingolipid interacting proteins, including HIV gp120, prion, and Aβ.
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11
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Albertí M, Amat A, Aguilar A, Huarte-Larrañaga F, Lucas JM, Pirani F. A molecular dynamics study of the evolution from the formation of the $${\text {C}}_{6}{\text {F}}_{6}$$ C 6 F 6 –( $${\text {H}}_{2}{\text {O}})_{n}$$ H 2 O ) n small aggregates to the $${\text {C}}_{6}{\text {F}}_{6}$$ C 6 F 6 solvation. Theor Chem Acc 2015. [DOI: 10.1007/s00214-015-1662-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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12
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Accurate analytic intermolecular potential for the simulation of Na+ and K+ ion hydration in liquid water. J Mol Liq 2015. [DOI: 10.1016/j.molliq.2015.01.029] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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13
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Sugibayashi Y, Hayashi S, Nakanishi W. Dynamic and static behavior of hydrogen bonds of the X–H⋯π type (X = F, Cl, Br, I, RO and RR′N; R, R′ = H or Me) in the benzene π-system, elucidated by QTAIM dual functional analysis. Phys Chem Chem Phys 2015; 17:28879-91. [DOI: 10.1039/c5cp04885k] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The nature of the X–H-*-π interactions in X–H-*-π(C6H6) (X = F, Cl, Br, I, HO, MeO, H2N, MeHN and Me2N) was elucidated by applying QTAIM dual functional analysis. The interactions were all classified by pure closed-shell interactions and characterized to have the vdW nature.
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Affiliation(s)
- Yuji Sugibayashi
- Department of Material Science and Chemistry
- Faculty of Systems Engineering
- Wakayama University
- Wakayama 640-8510
- Japan
| | - Satoko Hayashi
- Department of Material Science and Chemistry
- Faculty of Systems Engineering
- Wakayama University
- Wakayama 640-8510
- Japan
| | - Waro Nakanishi
- Department of Material Science and Chemistry
- Faculty of Systems Engineering
- Wakayama University
- Wakayama 640-8510
- Japan
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14
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Cunha WF, Gargano R, Garcia E, Politi JRS, Albernaz AF, Martins JBL. Rovibrational energy and spectroscopic constant calculations of CH 4 ⋯ CH 4, CH 4 ⋯ H 2 O, CH 4 ⋯ CHF 3, and H 2 O ⋯ CHF 3 dimers. J Mol Model 2014; 20:2298. [DOI: 10.1007/s00894-014-2298-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Accepted: 05/05/2014] [Indexed: 11/28/2022]
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15
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Albertí M, Aguilar A, Huarte-Larrañaga F, Lucas JM, Pirani F. Benzene–Hydrogen Bond (C6H6–HX) Interactions: The Influence of the X Nature on their Strength and Anisotropy. J Phys Chem A 2014; 118:1651-62. [DOI: 10.1021/jp410917x] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- M. Albertí
- IQTCUB,
Departament de Química Física, Universitat de Barcelona, Barcelona, Spain
| | - A. Aguilar
- IQTCUB,
Departament de Química Física, Universitat de Barcelona, Barcelona, Spain
| | - F. Huarte-Larrañaga
- IQTCUB,
Departament de Química Física, Universitat de Barcelona, Barcelona, Spain
| | - J. M. Lucas
- IQTCUB,
Departament de Química Física, Universitat de Barcelona, Barcelona, Spain
| | - F. Pirani
- Dipartimento
di Chimica, Università di Perugia, Perugia, Italy
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16
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Du L, Gao J, Bi F, Wang L, Liu C. A polarizable ellipsoidal force field for halogen bonds. J Comput Chem 2013; 34:2032-40. [PMID: 23804187 DOI: 10.1002/jcc.23362] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2013] [Revised: 05/14/2013] [Accepted: 05/29/2013] [Indexed: 01/22/2023]
Abstract
The anisotropic effects and short-range quantum effects are essential characters in the formation of halogen bonds. Since there are an array of applications of halogen bonds and much difficulty in modeling them in classical force fields, the current research reports solely the polarizable ellipsoidal force field (PEff) for halogen bonds. The anisotropic charge distribution was represented with the combination of a negative charged sphere and a positively charged ellipsoid. The polarization energy was incorporated by the induced dipole model. The resulting force field is "physically motivated," which includes separate, explicit terms to account for the electrostatic, repulsion/dispersion, and polarization interaction. Furthermore, it is largely compatible with existing, standard simulation packages. The fitted parameters are transferable and compatible with the general AMBER force field. This PEff model could correctly reproduces the potential energy surface of halogen bonds at MP2 level. Finally, the prediction of the halogen bond properties of human Cathepsin L (hcatL) has been found to be in excellent qualitative agreement with the cocrystal structures.
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Affiliation(s)
- Likai Du
- Key Lab of Colloid and Interface Chemistry, Ministry of Education, Institute of Theoretical Chemistry, School of Chemistry and Chemical Engineering, Shandong University, Jinan, 250100, People's Republic China
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17
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Albertí M, Amat A, De Angelis F, Pirani F. A Model Potential for Acetonitrile: from Small Clusters to Liquid. J Phys Chem B 2013; 117:7065-76. [DOI: 10.1021/jp402827y] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- M. Albertí
- IQTCUB, Departament de Química
Física, Universitat de Barcelona, Barcelona, Spain
| | - A. Amat
- Computational
Laboratory for
Hybrid/Organic Photovoltaics (CLHYO), Istituto CNR di Scienze e Tecnologie Molecolari, Perugia, Italy
| | - F. De Angelis
- Computational
Laboratory for
Hybrid/Organic Photovoltaics (CLHYO), Istituto CNR di Scienze e Tecnologie Molecolari, Perugia, Italy
| | - F. Pirani
- Dipartimento di Chimica, Università di Perugia, Perugia, Italy
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18
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Albertí M, Pirani F, Laganà A. Carbon Dioxide Clathrate Hydrates: Selective Role of Intermolecular Interactions and Action of the SDS Catalyst. J Phys Chem A 2013; 117:6991-7000. [DOI: 10.1021/jp3126158] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- M. Albertí
- IQTCUB, Departament
de Química
Física, Universitat de Barcelona, Barcelona, Spain
| | - F. Pirani
- Dipartimento
di Chimica, Università di Perugia, Perugia, Italy
| | - A. Laganà
- Dipartimento
di Chimica, Università di Perugia, Perugia, Italy
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