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Ma Y, Bao A, Guo X, Wang J. Carrier mobility and optical properties of a type-II GaSe/ZnS heterostructure as a photocatalyst: a first-principles study. Phys Chem Chem Phys 2024; 26:14980-14990. [PMID: 38739457 DOI: 10.1039/d4cp00972j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
In this paper, a new GaSe/ZnS van der Waals heterostructure (vdWH) was constructed and a systematic analysis of the electronic structure, interfacial properties, and transport and photocatalytic capacity of the GaSe/ZnS vdWH was performed by using first-principles calculations. It was found that the heterostructure exhibited excellent photocatalytic performance for water splitting. The direct band gap of the heterostructure calculated using the hybrid HSE06 functional was 2.19 eV, which had a good visible light absorption ability. The electronic structure of the type-II band arrangement effectively reduced the recombination of electron-hole pairs. The heterostructure also showed excellent transport ability, and the carrier mobility of electrons and holes along different directions was greatly improved. Additionally, as the electric field strength increased, the band gap width of the GaSe/ZnS vdWH narrowed and the heterostructure characteristics transitioned from semiconductor to metal properties, which were attributed to the appearance of near-free electronic (NFE) states induced by the strong electric field. Meanwhile, the optical absorption capacity of the heterostructure was greatly improved compared to the ZnS monolayer, reaching 1.44 × 105 cm-1 at an incident photon energy of 8.65 eV. Therefore, the GaSe/ZnS vdWH was proved to be an excellent photocatalytic material for water splitting in the present study.
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Affiliation(s)
- Yongqiang Ma
- National Key Laboratory for Electronic Measurement Technology, North University of China, Taiyuan, 030051, China.
| | - Aida Bao
- National Key Laboratory for Electronic Measurement Technology, North University of China, Taiyuan, 030051, China.
| | - Xin Guo
- National Key Laboratory for Electronic Measurement Technology, North University of China, Taiyuan, 030051, China.
| | - Jie Wang
- National Key Laboratory for Electronic Measurement Technology, North University of China, Taiyuan, 030051, China.
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Ruiz EPE, Thirumuruganandham SP, Lago JCL. Structural and Electromagnetic Signatures of Anatase and Rutile NTs and Sheets in Three Different Water Models under Different Temperature Conditions. Int J Mol Sci 2023; 24:14878. [PMID: 37834327 PMCID: PMC10573416 DOI: 10.3390/ijms241914878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 08/18/2023] [Accepted: 08/21/2023] [Indexed: 10/15/2023] Open
Abstract
Experimental studies of TiO2 nanotubes have been conducted for nearly three decades and have revealed the remarkable advantages of this material. Research based on computer simulations is much rarer, with research using density functional theory (DFT) being the most significant in this field. It should be noted, however, that this approach has significant limitations when studying the macroscopic properties of nanostructures such as nanosheets and nanotubes. An alternative with great potential has emerged: classical molecular dynamics simulations (MD). MD Simulations offer the possibility to study macroscopic properties such as the density of phonon states (PDOS), power spectra, infrared spectrum, water absorption and others. From this point of view, the present study focuses on the distinction between the phases of anatase and rutile TiO2. The LAMMPS package is used to study both the structural properties by applying the radial distribution function (RDF) and the electromagnetic properties of these phases. Our efforts are focused on exploring the effect of temperature on the vibrational properties of TiO2 anatase nanotubes and an in-depth analysis of how the phononic softening phenomenon affects TiO2 nanostructures to improve the fundamental understanding in different dimensions and morphological configurations. A careful evaluation of the stability of TiO2 nanolamines and nanotubes at different temperatures is performed, as well as the adsorption of water on the nanosurface of TiO2, using three different water models.
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Affiliation(s)
- Eduardo Patricio Estévez Ruiz
- Centro de Investigación de Ciencias Humanas y de la Educación (CICHE), Universidad Indoamérica, Ambato 180103, Ecuador;
- Grupo de Polímeros, Departamento de Física y Ciencias de la Tierra, Escuela Universitaria Politécnica, Universidade da Coruña, 15471 Ferrol, Spain;
| | | | - Joaquín Cayetano López Lago
- Grupo de Polímeros, Departamento de Física y Ciencias de la Tierra, Escuela Universitaria Politécnica, Universidade da Coruña, 15471 Ferrol, Spain;
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Romo TD, Grossfield A, Markelz AG. Persistent Protein Motions in a Rugged Energy Landscape Revealed by Normal Mode Ensemble Analysis. J Chem Inf Model 2020; 60:6419-6426. [PMID: 33103888 DOI: 10.1021/acs.jcim.0c00879] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Proteins are allosteric machines that couple motions at distinct, often distant, sites to control biological function. Low-frequency structural vibrations are a mechanism of this long-distance connection and are often used computationally to predict correlations, but experimentally identifying the vibrations associated with specific motions has proved challenging. Spectroscopy is an ideal tool to explore these excitations, but measurements have been largely unable to identify important frequency bands. The result is at odds with some previous calculations and raises the question what methods could successfully characterize protein structural vibrations. Here we show the lack of spectral structure arises in part from the variations in protein structure as the protein samples the energy landscape. However, by averaging over the energy landscape as sampled using an aggregate 18.5 μs of all-atom molecular dynamics simulation of hen egg white lysozyme and normal-mode analyses, we find vibrations with large overlap with functional displacements are surprisingly concentrated in narrow frequency bands. These bands are not apparent in either the ensemble averaged vibrational density of states or isotropic absorption. However, in the case of the ensemble averaged anisotropic absorption, there is persistent spectral structure and overlap between this structure and the functional displacement frequency bands. We systematically lay out heuristics for calculating the spectra robustly, including the need for statistical sampling of the protein and inclusion of adequate water in the spectral calculation. The results show the congested spectrum of these complex molecules obscures important frequency bands associated with function and reveal a method to overcome this congestion by combining structurally sensitive spectroscopy with robust normal mode ensemble analysis.
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Affiliation(s)
- Tod D Romo
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, New York 14642, United States
| | - Alan Grossfield
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, New York 14642, United States
| | - Andrea G Markelz
- Department of Physics, University at Buffalo, SUNY, Buffalo, New York 14260, United States
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Basith S, Lee Y, Choi S. Understanding G Protein-Coupled Receptor Allostery via Molecular Dynamics Simulations: Implications for Drug Discovery. Methods Mol Biol 2018; 1762:455-472. [PMID: 29594786 DOI: 10.1007/978-1-4939-7756-7_23] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Unraveling the mystery of protein allostery has been one of the greatest challenges in both structural and computational biology. However, recent advances in computational methods, particularly molecular dynamics (MD) simulations, have led to its utility as a powerful and popular tool for the study of protein allostery. By capturing the motions of a protein's constituent atoms, simulations can enable the discovery of allosteric hot spots and the determination of the mechanistic basis for allostery. These structural and dynamic studies can provide a foundation for a wide range of applications, including rational drug design and protein engineering. In our laboratory, the use of MD simulations and network analysis assisted in the elucidation of the allosteric hotspots and intracellular signal transduction of G protein-coupled receptors (GPCRs), primarily on one of the adenosine receptor subtypes, A2A adenosine receptor (A2AAR). In this chapter, we describe a method for calculating the map of allosteric signal flow in different GPCR conformational states and illustrate how these concepts have been utilized in understanding the mechanism of GPCR allostery. These structural studies will provide valuable insights into the allosteric and orthosteric modulations that would be of great help to design novel drugs targeting GPCRs in pathological states.
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Affiliation(s)
- Shaherin Basith
- National Leading Research Laboratory (NLRL) of Molecular Modeling & Drug Design, College of Pharmacy and Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul, Republic of Korea
| | - Yoonji Lee
- National Leading Research Laboratory (NLRL) of Molecular Modeling & Drug Design, College of Pharmacy and Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul, Republic of Korea
| | - Sun Choi
- National Leading Research Laboratory (NLRL) of Molecular Modeling & Drug Design, College of Pharmacy and Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul, Republic of Korea.
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Thirumuruganandham SP, Gómez EA, Lakshmanan S, Hamblin MR. Terahertz Frequency Spectroscopy to Determine Cold Shock Protein Stability upon Solvation and Evaporation - A Molecular Dynamics Study. IEEE TRANSACTIONS ON TERAHERTZ SCIENCE AND TECHNOLOGY 2017; 7:131-143. [PMID: 30881732 PMCID: PMC6419770 DOI: 10.1109/tthz.2016.2637380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Infrared (IR) and Terahertz (THz) spectroscopy simulations were carried out using CHARMM35b2 to determine protein stability. The stabilities of three bacterial cold shock proteins (Csps) originating from mesophiles, thermophiles and hyper- thermophiles respectively were investigated in this study. The three different Csps were investigated by Normal-Mode analysis and Molecular Dynamics simulation of THz spectra using the Hessian matrix for solvated systems, interpreted in the harmonic approximation at optimum near-melting temperatures of each homologue, by incorporating differences in the hydrous and anhydrous states of the Csps. The results show slight variations in the large scale protein motion. However, the IR spectra of Csps observed at the low frequency saddle surface region, clearly distinguishes the thermophilic and mesophilic proteins based on their stability. Further studies on protein stability employing low-frequency collective modes have the potential to reveal functionally important conformational changes that are biologically significant.
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Affiliation(s)
| | - Edgar A Gómez
- Programa de Física, Universidad del Quindío, Armenia, Colombia
| | - Shanmugamurthy Lakshmanan
- Department of Dermatology, Harvard Medical School, Boston, MA 02114, USA
- Wellman Center for Photomedicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Michael R Hamblin
- Department of Dermatology, Harvard Medical School, Boston, MA 02114, USA
- Wellman Center for Photomedicine, Massachusetts General Hospital, Boston, MA 02114, USA
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Kaczor AA, Selent J, Poso A. Structure-based molecular modeling approaches to GPCR oligomerization. Methods Cell Biol 2013; 117:91-104. [PMID: 24143973 DOI: 10.1016/b978-0-12-408143-7.00005-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Classical structure-based drug design techniques using G-protein-coupled receptors (GPCRs) as targets focus nearly exclusively on binding at the orthosteric site of a single receptor. Dimerization and oligomerization of GPCRs, proposed almost 30 years ago, have, however, crucial relevance for drug design. Targeting these complexes selectively or designing small molecules that affect receptor-receptor interactions might provide new opportunities for novel drug discovery. In order to study the mechanisms and dynamics that rule GPCRs oligomerization, it is essential to understand the dynamic process of receptor-receptor association and to identify regions that are suitable for selective drug binding, which may be determined with experimental methods such as Förster resonance energy transfer (FRET) or Bioluminescence resonance energy transfer (BRET) and computational sequence- and structure-based approaches. The aim of this chapter is to provide a comprehensive description of the structure-based molecular modeling methods for studying GPCR dimerization, that is, protein-protein docking, molecular dynamics, normal mode analysis, and electrostatics studies.
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Affiliation(s)
- Agnieszka A Kaczor
- Department of Pharmaceutical Chemistry, School of Pharmacy, University of Eastern Finland, Kuopio, Finland; Department of Chemical Technology of Pharmaceutical Substances with Computer Modeling Lab, Faculty of Pharmacy with Division of Medical Analytics, Medical University of Lublin, Lublin, Poland
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Computational Methods for the Assignment of Vibrational Modes in Crystalline Materials. TERAHERTZ SPECTROSCOPY AND IMAGING 2012. [DOI: 10.1007/978-3-642-29564-5_7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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Hu G, Michielssens S, Moors SLC, Ceulemans A. Normal Mode Analysis of Trp RNA Binding Attenuation Protein: Structure and Collective Motions. J Chem Inf Model 2011; 51:2361-71. [DOI: 10.1021/ci200268y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Guang Hu
- Department of Chemistry and INPAC Institute for Nanoscale Physics and Chemistry, Katholieke Universiteit Leuven, Celestijnenlaan 200F, B-3001 Leuven, Belgium
| | - Servaas Michielssens
- Department of Chemistry and INPAC Institute for Nanoscale Physics and Chemistry, Katholieke Universiteit Leuven, Celestijnenlaan 200F, B-3001 Leuven, Belgium
| | - Samuel L. C. Moors
- Department of Chemistry and INPAC Institute for Nanoscale Physics and Chemistry, Katholieke Universiteit Leuven, Celestijnenlaan 200F, B-3001 Leuven, Belgium
| | - Arnout Ceulemans
- Department of Chemistry and INPAC Institute for Nanoscale Physics and Chemistry, Katholieke Universiteit Leuven, Celestijnenlaan 200F, B-3001 Leuven, Belgium
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Bordallo HN, Boldyreva EV, Fischer J, Koza MM, Seydel T, Minkov VS, Drebushchak VA, Kyriakopoulos A. Observation of subtle dynamic transitions by a combination of neutron scattering, X-ray diffraction and DSC: A case study of the monoclinic l-cysteine. Biophys Chem 2010; 148:34-41. [DOI: 10.1016/j.bpc.2010.02.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2010] [Revised: 02/04/2010] [Accepted: 02/04/2010] [Indexed: 10/19/2022]
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