Name: probe type ii band alignment in one-dimensional van der waals heterostructures using first-principles calculations
Uploaded: 2019-10-12T13:00:00
Description: Watch this Scientific Journal Video about Probe Type II Band Alignment in One-Dimensional Van Der Waals Heterostructures Using First-Principles Calculations at JoVE.com

This work was supported from China Postdoctoral Science Foundation (Grant No. 2017M612348), Qingdao Postdoctoral Foundation (Grant No. 3002000-861805033070) and from the Young Talent Project at Ocean University of China (Grant No. 3002000-861701013151). The authors thank Miss Ya Chong Li for preparing the narration.

1. Optimize the atomic structure.
<ol>
	<li>Prepare four input files for structure relaxation calculation by VASP: INCAR, POSCAR, POTCAR, and KPOINTS. 
	NOTE: There are specified parameters in the INCAR file that define the calculation. The line &#34;EDIFFG = 0.02&#34; in the INCAR file indicates that all atoms are relaxed until the force on each atom is &#60;0.02 eV/&#197;. The POSCAR file contains the atomic geometry information. The initial lattice parameters in the POSCAR file can be chosen from theoretical<su...

<ol>
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The calculations for electronic properties in sections 2, 3, and 4 would be similar among various nanoscale materials. The initial atomic model in step 1 should be carefully designed to extract meaningful information. For example, the factor for selecting the model could be the size or chirality of the materials. Also, the initial atomic model in step 1.1 should be reasonably prepared for low-cost structure relaxation. Taking the nanocomposite in the protocol as an example, the NR should be encapsulated inside the NT in ...

The worldwide demand for clean and sustainable energy has spurred research for promising materials to reduce dependence on finite petroleum resources. Simulations are more efficient and economical than experiments in accelerating the search for new functional materials1. Material design from a theoretical perspective2,3,4 is now more and more popular due to rapid advances in computational resources and theory developments, making computational simulations more reliable5. The density functional theory (DFT) calculations implemented in many codes are becoming more robust and yield reproducible results6.
The Vienna Ab initio Simulation Package&#160;(VASP)7 presents one of the most promising DFT codes for predicting molecular and crystalline properties and more than 40,000 studies making use of this code have been published. Most work is performed at the Perdew-Burke-Ernzerhof (PBE) functional level8, which underestimates the band gap sizes, but captures the essential trends in band alignment and band offsets3. This protocol aims to outline the details of investigating the band edge profiles and bandgaps of nanoscale materials for clean and renewable energy using this computational tool. More examples using VASP are available at https://www.vasp.at.
This report presents the computational screening of one-dimensional (1D) vdW heterostructures with type II band alignments9 for a promising application in photocatalytic water splitting4. Specifically, nanoribbons (NRs) encapsulated inside nanotubes (NTs) are examined as an example10. To address noncovalent interactions, vdW corrections using the DFT-D3 method are included11. The DFT calculations in steps 1.2, 2.2, 3.2, 3.5.2, and section 4 by VASP are performed using a Portable Batch System (PBS) script by the high-performance research computers in the CenTOS system. An example of a PBS script is shown in the Supplementary Materials. The data postprocessing by the P4VASP software in step 3.3 and the figure plot by the xmgrace software in step 3.4 are carried on a local computer (laptop or desktop) in the Ubuntu system.

<table>
	<tbody>
		<tr>
			<td>Nanotube Modeler</td>
			<td>Developed by Dr. Steffen Weber</td>
			<td>NanotubeModeler1.8</td>
			<td>http://www.jcrystal.com/products/wincnt/NanotubeModeler.exe</td>
		</tr>
		<tr>
			<td>P4VASP</td>
			<td>Orest Dubay</td>
			<td>p4vasp 0.3.30</td>
			<td>Open source, available at www.p4vasp.at</td>
		</tr>
		<tr>
			<td>v2xsf</td>
			<td>Developed by Dr. Jens Kunstmann</td>
			<td>v2xsf</td>
			<td>http://theory.chm.tu-dresden.de/~jk/software.html</td>
		</tr>
		<tr>
			<td>VASP software</td>
			<td>Computational Materials Physics, Dept. of Physics, University of Vienna</td>
			<td>vasp.5.4.1</td>
			<td>https://www.vasp.at</td>
		</tr>
		<tr>
			<td>VMD software</td>
			<td>Theoretical and Computational Biophysics Group, University of Illinois at Urbana-Champaign</td>
			<td>vmd1.9.3</td>
			<td>https://www.ks.uiuc.edu/Research/vmd</td>
		</tr>
		<tr>
			<td>xcrysden</td>
			<td>Dept. of Physical and Organic Chemistry, Jozef Stefan Institute</td>
			<td>XCrySDen1.5.60</td>
			<td>http://www.xcrysden.org/</td>
		</tr>
		<tr>
			<td>Xmakemol</td>
			<td>Developed by M. P. Hodges</td>
			<td>xmakemol5.16</td>
			<td>https://www.nongnu.org/xmakemol/XmakemolDownloads.html</td>
		</tr>
		<tr>
			<td>Xmgrace software</td>
			<td>Grace Development Team under the coordination of Evgeny Stambulchik</td>
			<td>xmgrace5.1.25</td>
			<td>http://plasma-gate.weizmann.ac.il/Grace/</td>
		</tr>
	</tbody>
</table>

probe type ii band alignment in one-dimensional van der waals heterostructures using first-principles calculations

Computational tools based on density-functional theory (DFT) enable the exploration of the qualitatively new, experimentally attainable nanoscale compounds for a targeted application. Theoretical simulations provide a profound understanding of the intrinsic electronic properties of functional materials. The goal of this protocol is to search for photocatalyst candidates by computational dissection. Photocatalytic applications require suitable band gaps, appropriate band edge positions relative to the redox potentials. Hybrid functionals can provide accurate values of these properties but are computationally expensive, whereas the results at the Perdew-Burke-Ernzerhof (PBE) functional level could be effective for suggesting strategies for band structure engineering via electric field and tensile strain aiming to enhance the photocatalytic performance. To illustrate this, in the present manuscript, the DFT based simulation tool VASP is used to investigate the band alignment of nanocomposites in combinations of nanotubes and nanoribbons in the ground state. To address the lifetime of photogenerated holes and electrons in the excited state, nonadiabatic dynamics calculations are needed.

Zigzag BN-NRs encapsulated inside armchair BN-NTs (11,11) were chosen as representative examples for a 1D vdW heterostructure. The lattice parameters were taken from Sahin et al.20. For convenience, zigzag NRs are abbreviated Zn, where n represents the III&#8211;V dimers along the width14. The encapsulation energy EL from step 2.3 was used as a rough estimate for the energetic stability of the nanocomposite. The EL values of Z2, Z...

Watch this Scientific Journal Video about Probe Type II Band Alignment in One-Dimensional Van Der Waals Heterostructures Using First-Principles Calculations at JoVE.com

Probe Type II Band Alignment in One-Dimensional Van Der Waals Heterostructures Using First-Principles Calculations

Calculations performed by the Vienna Ab initio Simulation Package can be used to identify the intrinsic electronic properties of nanoscale materials and predict the potential water-splitting photocatalysts.

Computational tools based on density-functional theory (DFT) enable the exploration of the qualitatively new, experimentally attainable nanoscale ...

This protocol reports a computational screening of photo catalyst with type two bond alignment by first principles Softwire vast expressive Calais, boron nitrite nanoribbons encapsulated inside nanotubes. And taking other examples. Step one, optimize the atomic structure.Prepare for input files for structure relaxation calculation by vast, INCAR, POSCAR, POTCAR, and KPOINTS. There are specified parameters in the file INCAR that define the calculation. The line in the file INCAR enclosed by blue box, in case that all atoms are relaxed until the force on each atom is less than 0.028 per atom.The file POSCAR contains the atomic geometry information. The initial lattice parameters in the file, POSCAR can be chosen from the radical or experimental references. As indicated by orange box.KPOINTS defines a KPOINT mesh and POSCAR is still the potential file generates the initial structure of boron nitrites nanoribbon for POSCAR. First download POSCAR for boron nitrites box unit from the website of The Materials Project. They used V2SXF to convert POSCAR to a file with SXF format.The SXF file can be right expression. Type V2SXF POSCAR onto no in band two system. And output POSCAR SXFGZ tab gunzi POSCAR, delta SXF-GZ.And output POSCAR SXF. We'll use xcrysden to build supercell of boron nitrite. Type xcrysden-sxf POSCAR.Xsf.Select the menu, modifying number of illness drawn and extend the style in X and Y direction. Select the menu, file. Save XSF structure to export the super cell structure.Use xmakemol to open the super cell by typing xmakemol-f supercell. Select the menu, and add it visible. Click toggle to delay the atoms inside the ranging and cast nanoribbon with desired width and chirality.Boron nitrites nanotube can be constructed by nanotube modeler, open nanotube modeler EXC in Window system. Select the menu, select type B-N. And specify the chirality.Select the menu, file, save XYZ table to export this structure. Use VMD Southwire to check the atomic structure before start making the calculation job. Type VMD onto internal VMD system.In the opened VMD main window. Select the menu, file, molecule, and find the POSCAR through the browse window. Load POSCAR by the type MAGE and the score POSCAR.Display the structure by different styles in the graphical representations drawing methods window. For example, choose CPK. Each atom is represented by a sphere and each bond is represented by a stake.Type qsub job. pbs to submit the job to the computer. Class to a portable batch systems script.This is a example of the script which named job.pbs. After the job finished, if ratio requires accuracy stopping structure energy minimization appears at the end of output lock. The converging result is a pend.The resulting POSCAR will be used as an input file POSCAR for the following calculations. For analyzing electronic properties of materials. Step two.Calculate the encapsulation energy. Type mkdir nanocomposite isolated-nanoribbon isolated-nanotube to create qsub folders for nanocomposite, nanoribbon and nanotube internal in Linux system. Prepare one PBS script, job.pbs and four input files INCAR, POSCAR, POTCAR and KPOINTS. For energy, calculation in each folder. The input file POSCAR in the same way that relaxes structure and count CAR forms that one.Go to each folder and type qsub job. pbs onto internal Linux system. The series of mated jobs will perform the static self consistent energy calculations of nanocomposites, isolates nanoribbon, isolates nanotube respectively.Next track the total energy from the file OUTCAR for each system back up command. After finishing the static self-consistent calculations then compute the encapsulation energy as shown in this formula. The periodic interaction of the nanocomposite is allow Z axis and L is the lattice constant of the unit cell, along Z.The encapsulation energy can be used as an estimate for the energetic stability of nanocomposite.Step three, extract the electronic properties from the band structure. Prepare one PBS, script job. pbs and the six input files.INCAR, POSCAR, POTCAR, KPOINTS, CHGCAR, and CHG. For band-calculations, said ICHARG equals 11 in INCAR. The pre-conversion CHGCAR and CHG files are from static self-consistent calculations.The KPOINT sampling in KPOINTS is in line-mode. Type qsub job. pbs onto internal Linux system to submit the job.Use p4vasprun to generate the projected band. Load vasprun. xml by typing p4v vasprun.xml on terminal. Select the menu, electronic local DOS bands. Control and then select bands.Specify the atomic numbers of nanotube in the label atoms selection. Get the atomic number by pointing to the corresponding atoms using VMD. Specify the color, type, and size of symbol for the projected band structure.Those menus symbol and the symbol size. Press the menu, add new line. The graph will show the band structure with the contributions from nanotube.Then repeat the same procedure to gather projected band with contributions from nanoribbon. Select the menu graph export. Export the graph into the file with agr format.For example, saved as 11-4.agr. Use XM grades to ID the projected bands. Type xmgrace11-4.agr on terminal to start xmgrace in menu system. Select the menu, plot access properties to ID the label and the range of the axes. Select the manual plot set appearance to read the energy value as specified band number and key point.Release band maximum and the conduction band minimum of nanotube or nanoribbon can be right from the projected band with the contributions of nanotube or nanoribbons respectively. Then calculate the valence band offset, conduction band offset and the band gap. Select the menu, file, point to export the graph with APS formats.Calculate the band decompose to charge density for VBM and CBM. Prepare one pbs, script job. pbs and seven input files, INCAR, POSCAR, POTCAR, KPOINTS, WAVECAR, CHGCAR, and CHG.Specify the band numbers for CBM and VBM. Then type IBAND in INCAR. Use the single corresponding KPOINT for each band edge.The point converges CHGCAR, CHG. And the WAVECAR files, are from static self-consistent calculations. Type qsub job.pbs onto internal Linux system to submit the job. Use VMD to plot VBM and CBM in real space after the job finished. Start a VMD session and load POSCAR.Select the menu, file, new molecule in the VMD main window. Find the PARCHG through the browse window. Load the PARCHG by the type, press and score PARCHG.Select the menu, draw solid surface and show a solid surface in the graphical representations window. Change the ISO value to an appropriate value, for example 0.02. Change the color of the ISO surface though the menu coloring method.Step four, modulate the electronic properties of the nanocomposite by external fields. Add a transverse electric field to the nanocomposite. Prepare one PBS, script job.pbs and the four input files, INCAR, POSCAR, POTCAR, and KPOINTS. Define the strength of the electric field by the tag e-field in units of eV Astrum. Set LDIPOL equals T, set IDIPOL equals 2.And the electric field will be applied allow Y axis. Perform static self-consistent calculations and band structure calculations, following steps two and three without structure optimization. Add a longitudinal test of strength to the nanocomposite, chain the lattice parameter along the periodical direction to consider the string effect.For example, to optimize the lattice parameter of nanocomposite along the axis is 2.5045 Astrum If applied 1%and the axial tensile strength along the Z through action. Change the lattice parameter in POSCAR to 2.529545 Astrum. Relax the modify structure following step one, perform static self-consistent calculations and band structure calculations, following steps two and three.Representative results. The encapsulation energy can be used as a rough estimate for the energetic stability of the nanocomposite. The encapsulation energy of boron nitrite nanoribbons, a 2, a 3, and a 4 encapsulated inside the boron nitrite nanotube 11, 11 are 0.033 eV Astrum, 0.068 eV Astrum and 0131 eV Astrum respectively.Although the encapsulation energy varies by an order of magnitude with the nanoribbon size, all three nanocomposites present type two band alignment. This is a band structure of boron nitrite and nanoribbons, a four encapsulated inside the boron nitrite nanotube, 11, 11. Valence band maximum and the conduction band minimum located at nanotube and nanoribbon respectively.The staggered band alignment is beneficial for light currents to the main mechanism of charge transport is as follows. The photo generates electric ad hull in nanoribbons at the X point. Then the whole dissociates from nanoribbons to nanotube.The calculated valence band offset is 317 micro eV. It is larger than the thermal energy at 300 Kelvins which is about 13 micro eV. This effectively decreases the recombination rate of photo-generated carriers.To enhance light harvest through a wide spectrum, this transfers electric field and longitudinal tensile strength are applied to boron nitrite nanoribbons, a four encapsulated inside the boron nitrite nanotube, 11, 11. This is the evolution of band edges relative to the vacuum level, and reacts to no field. A substantial gap reduction up to near 0.95 eV is observed in this nanocomposite by both external fields.More importantly, the staggered band alignment is preserved against the diffuse. The redox potentials of water are marked by the blue dashed lines. The band edges are relative to the redox potentials indicate that such a nanocomposite may be promising for water splitting.Conclusion.It is rapid and efficient to use a computational screening approach to discover low dimensional materials that possess properties suitable for solo water splitting. Such a one dimensional system can propose to integrate a photo-catalated hydrogen generation and safe capsule style reach. The photo-generated electrons could be collected by nanoribbon, protons penetrate through the nanotube to generate hydrogen molecule joined by electrostatic attraction.The produced hydrogen is completely isolated within the nanotube to avoid unwanted reverse reaction or explosion. The first principles calculations will underestimate the gap status using the PPE functional. But they can capture the essential trends in band alignment and band offsets.More accurate values of valence band offset, conduction band offset and the band gap are needed if compared with experimental work, operate functional would be rather employed, which will be time consuming than PPE function. Besides to address the lifetime of photo generated hulls and electric in static states nano diabetics deny me some calculations that are needed. This is important to design photo-catalysts with long lifetime careers.

Research

JoVE Journal

Chemistry

Preparation and Use of Samarium Diiodide (SmI2) in Organic Synthesis: The Mechanistic Role of HMPA and Ni(II) Salts in the Samarium Barbier Reaction

Preparation and Use of Samarium Diiodide SmI2 in Organic Synthesis: The Mechanistic Role of HMPA and NiII Salts in the Samarium Barbier Reaction

Although initially considered an esoteric reagent, SmI2 has become a common tool for synthetic organic chemists. SmI2 is generated through the addition of ...

Analyzing Protein Dynamics Using Hydrogen Exchange Mass Spectrometry

All cellular processes depend on the functionality of proteins. Although the functionality of a given protein is the direct consequence of its unique ...

Quantitative and Qualitative Examination of Particle-particle Interactions Using Colloidal Probe Nanoscopy

Colloidal Probe Nanoscopy (CPN), the study of the nano-scale interactive forces between a specifically prepared colloidal probe and any chosen substrate ...

Iridium(III) Luminescent Probe for Detection of the Malarial Protein Biomarker Histidine Rich Protein-II

IridiumIII Luminescent Probe for Detection of the Malarial Protein Biomarker Histidine Rich Protein-II

This work outlines the synthesis of a non-emissive, cyclometalated Ir(III) complex, Ir(ppy)2(H2O)2+ (Ir1), which elicits a rapid, long-lived ...

Post Column Derivatization Using Reaction Flow High Performance Liquid Chromatography Columns

A protocol for the use of reaction flow high performance liquid chromatography columns for methods employing post column derivatization (PCD) is ...

On-line Analysis of Nitrogen Containing Compounds in Complex Hydrocarbon Matrixes

The shift to heavy crude oils and the use of alternative fossil resources such as shale oil are a challenge for the petrochemical industry. The ...

Non-equilibrium Microwave Plasma for Efficient High Temperature Chemistry

A flowing microwave plasma based methodology for converting electric energy into internal and/or translational modes of stable molecules with the purpose ...

Low Pressure Vapor-assisted Solution Process for Tunable Band Gap Pinhole-free Methylammonium Lead Halide Perovskite Films

Organo-lead halide perovskites have recently attracted great interest for potential applications in thin-film photovoltaics and optoelectronics. Herein, ...