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 theoretical3 or experimental references12,13. The KPOINTS file defines the k point mesh and POTCAR is the pseudopotential file. The order of atom types in POSCAR should be the same as that in POTCAR. Examples of input files for structure relaxation are shown in the Supplementary Materials (except the pseudopotential file, which needs a license from VASP).
	<ol>
		<li>Generate the initial structure of boron nitride (BN) nanoribbons (NR) for &#34;POSCAR&#34;.
		<ol>
			<li>Download the POSCAR file for the BN bulk unit from https://materialsproject.org.</li>
			<li>Use v2xsf to convert the POSCAR file to a file in xsf format that can be read by xcrysden. Type v2xsf POSCAR on the terminal in the Ubuntu system to get &#34;POSCAR.xsf.gz&#34;. Type gunzip POSCAR.xsf.gz and output the POSCAR.xsf file.</li>
			<li>Use xcrysden to build the BN supercell.
			<ol>
				<li>Type xcrysden --xsf POSCAR.xsf on the terminal in the Ubuntu system. Select the menu Modify/Number of Units Drawn and extend the cell in the X and Y directions.</li>
				<li>Select the menu File/Save XSF Structure to export the supercell structure, named &#34;supercell&#34;. 
				NOTE: The name of the structure is an arbitrary definition.</li>
			</ol>
			</li>
			<li>Use xmakemol to open the supercell. Type xmakemol -f supercell on the terminal in the Ubuntu system. Select the menu Edit/Visible. Click Toggle to delete the atoms inside the region and cut the NR to the desired width and chirality.</li>
		</ol>
		</li>
		<li>Generate the initial structure of the BN nanotube (NT) for POSCAR. Download &#34;NanotubeModeler&#34; from http://www.jcrystal.com/products. Open NanotubeModeler.exe in the Windows system. Select the menu Select type/B-N and specify the chirality. Select the menu File/Save XYZ table to export the structure.</li>
		<li>Generate the initial structure of the nanocomposite by encapsulating the NR (from step 1.1.1) inside the NT (from step 1.1.2). 
		NOTE: The encapsulation can be finished by adjusting the Cartesian coordinates of the NR and the NT10,14,15.</li>
		<li>Use the vmd software to check the atomic structure before submitting the calculation job.
		<ol>
			<li>Type vmd on the terminal in the Ubuntu system. In the opened vmd main window, select the menu File/New Molecule and find the POSCAR file through the Browse window. Load POSCAR by typing VASP_POSCAR.</li>
			<li>Display the structure in different styles in the Graphical Representations/Drawing Method window. 
			NOTE: For example, once the CPK is chosen, each atom (bond) is represented by a sphere (stick). The installation guide and full tutorial of vmd are available at http://www.ks.uiuc.edu/Research/vmd.</li>
		</ol>
		</li>
	</ol>
	</li>
	<li>Type qsub job.pbs on the terminal in the Linux system to submit the job to the computer cluster. 
	NOTE: &#34;job.pbs&#34; represents the name of the PBS script. The name of the PBS script is an arbitrary definition. The four input files together with the PBS script should be at the working directory. The command qsub job.pbs will be used in steps 2.2, 3.2, 3.5.2, and section 4. An example of a PBS script can be found in the supplementary coding file. After the submitted job is finished, if &#34;reached required accuracy - stopping structural energy minimization&#34; appears at the end of the output log, the converged result is obtained. The resulting CONTCAR file will be used as the input file POSCAR in steps 2.1, 3.1, 3.5.1, 3.5.3.1, 4.1.1, 4.1.4, and section 4.2.</li>
</ol>
2. Calculate the encapsulation energy.
<ol>
	<li>Type mkdir nanocomposite isolated-nanoribbon isolated-nanotube to create three folders for the nanocomposite, the NR, and the NT on a terminal in a Linux system. Prepare one PBS script &#34;job.pbs&#34; and four input files INCAR, POSCAR, POTCAR, and KPOINTS for the energy calculation in each folder. 
	NOTE: The input file POSCAR is the file named CONTCAR with the relaxed structure from step 1. Examples of input files are given in Supplementary Materials (except POTCAR).</li>
	<li>Go to each folder and type qsub job.pbs on the terminal in the Linux system. 
	NOTE: The three submitted jobs will perform the static self-consistent energy calculations for the nanocomposite, isolated NR, and isolated NT, respectively.</li>
	<li>Extract the total energy from the file OUTCAR for each system after finishing the static self-consistent calculations. Type grep &#8220;free energy TOTEN&#8221; ./nanocomposite/OUTCAR | tail -n 1, grep &#8220;free energy TOTEN&#8221; ./isolated-nanoribbon/OUTCAR | tail -n 1, and grep &#8220;free energy TOTEN&#8221; ./isolated-nanotube/OUTCAR | tail -n 1. Define the three displayed values as ENT+NR, ENR, and ENT, respectively. Calculate the encapsulation energy per angstrom: EL = (ENT+NR - ENT -ENR)/L14,15. 
	NOTE: The periodical direction in each system is along the Z axis and L is the lattice constant of the unit cell along the Z axis. Test calculations of the energy dependence on the plane wave cutoff energy and the k point mesh are needed. The encapsulation energy can be used as an estimate for the energetic stability of the nanocomposite.</li>
</ol>
3. Extract the electronic properties from the band structure.
<ol>
	<li>Prepare one PBS script &#34;job.pbs&#34; and six input files: INCAR, POSCAR, POTCAR, KPOINTS, CHGCAR, and CHG for band calculation. Set ICHARG = 11 in INCAR. 
	NOTE: The preconverged CHGCAR and CHG files are from the static self-consistent calculations in step 2.2. The band analysis is at the PBE level. The k point sampling in the KPOINTS file is in line-mode. Examples of input files for this step can be found in the Supplementary Materials (except POTCAR).</li>
	<li>Type qsub job.pbs on the terminal in the Linux system to submit the job.</li>
	<li>Use P4VASP to generate the projected band.
	<ol>
		<li>Load &#34;vasprun.xml&#34; by typing p4v vasprun.xml on terminal in the Ubuntu system. 
		NOTE: &#34;p4v&#34; is used to start P4VASP. The file &#34;vasprun.xml&#34; should be at the working directory.</li>
		<li>Select the menu Electronic/Local DOS+bands control and then Select/Bands.
		<ol>
			<li>Specify the atomic numbers of NT in the section Atom selection. Get the atomic number by pointing to the corresponding atoms using vmd as mentioned in step 1.1.4. Specify the color, type, and size of the symbol for the projected band structure through the menu Symbol and Symbol size. Press the menu Add new line. 
			NOTE: The graph will show the band structure with contributions from the NT.</li>
			<li>Repeat the same procedure following step 3.3.2.1 to get the projected band with contributions from the NR.</li>
		</ol>
		</li>
		<li>Select the menu Graph/Export. Export the graph into a file with an agr format (for example, as &#34;11-4.agr&#34;). 
		NOTE: The output data of the projected bands by P4VASP are in three columns where the third one represents the weighting.</li>
	</ol>
	</li>
	<li>Use xmgrace to edit the projected band.
	<ol>
		<li>Type xmgrace 11-4.agr on the terminal to start xmgrace in the Ubuntu system. Select the menu Plot/Axis properties to edit the label and range of the axis.</li>
		<li>Select the menu Plot/Set appearance to read the energy value at the specified band number and k point. 
		NOTE: The valence band maximum (VBM) and conduction band minimum (CBM) of NR/NT can be read from the projected band with contributions on NR/NT, respectively. According to the band alignments, heterostructures can be classified into three types: type I (VBMNT &#60;VBMNR &#60;CBMNR &#60;CBMNT or VBMNR &#60;VBMNT &#60;CBMNT &#60;CBMNR), type II (VBMNT &#60;VBMNR &#60;CBMNT &#60;CBMNR or VBMNR &#60;VBMNT &#60;CBMNR &#60;CBMNT), or type III (VBMNT &#60;VBMNT &#60;CBMNR &#60;CBMNR or VBMNR &#60;VBMNR &#60;CBMNT &#60;CBMNT)9.</li>
		<li>Calculate the valence band offset (VBO), conduction band offset (CBO), and the band gap following Kang et al.16.</li>
		<li>Select the menu File/Print to export the graph with eps format.</li>
	</ol>
	</li>
	<li>Calculate the band decomposed charge density for the VBM and CBM.
	<ol>
		<li>Prepare one PBS script &#34;job.pbs&#34; and seven input files: INCAR, POSCAR, POTCAR, KPOINTS, WAVECAR, CHGCAR, and CHG. Specify the band numbers for the CBM and VBM by the tag IBAND in INCAR. Use the single corresponding k point for each band edge. 
		NOTE: The preconverged CHGCAR, CHG, and WAVECAR files are from the static self-consistent calculations in step 2.2. Examples of input files for this step are given in the Supplementary Materials (except POTCAR).</li>
		<li>Type qsub job.pbs on the terminal in the Linux system to submit the job.</li>
		<li>Use vmd to plot the VBM and CBM in real space after the job is finished.
		<ol>
			<li>Start a vmd session and load the POSCAR file as in step 1.1.4.</li>
			<li>Select the menu File/New Molecule in the vmd main window. Find the PARCHG file through the Browse window. Load PARCHG by typing VASP_PARCHG.</li>
			<li>Select the menus Draw/Solid Surface and Show/Isosurface in the Graphical Representations window. Change the isovalue to an appropriate value (for example, 0.02). Change the color of the isosurface through the menu Coloring Method. 
			NOTE: This is an intuitive analysis for band types with respect to that in step 3.4. Generally, the atomic structure is arranged away from the boundary, otherwise the visualized charge density is not shown in a continuous manner. Please see Supplemental Figure 1 for details.</li>
		</ol>
		</li>
	</ol>
	</li>
</ol>
4. Modulate the electronic properties of the nanocomposite (NT encapsulated inside NR) by external fields.
<ol>
	<li>Add a transverse electric field to the nanocomposite17.
	<ol>
		<li>Prepare one PBS script &#34;job.pbs&#34; and four input files: INCAR, POSCAR, POTCAR, and KPOINTS.</li>
		<li>Define the strength of the electric field by the tag &#34;EFIELD&#34; in units of eV/&#197;.</li>
		<li>Set LDIPOL = T. Specify IDIPOL with an exact value (1, 2, or 3). 
		NOTE: These two tags are added to include dipole corrections. The electric field will be applied along the X, Y, or Z axis by setting the value of IDIPOL to 1, 2, or 3.</li>
		<li>Perform the static self-consistent calculations and band structure calculations following sections 2 and 3 without structural optimization. 
		NOTE: Previous studies indicate that electric fields over 5 V/&#197; can be used to modify the band gap of BN-NT and BN-NR without deforming the structure18,19.</li>
	</ol>
	</li>
	<li>Add a longitudinal tensile strain to the nanocomposite.
	<ol>
		<li>Change the lattice parameters along the periodical direction to reflect the strain effect. 
		NOTE: For example, the optimized lattice parameter of the nanocomposite along the Z axis is 2.5045 &#197;. If 1% uniaxial tensile strain is applied along the Z direction, change the lattice parameter in POSCAR to 2.5045 x 1.01 = 2.529545 &#197;.</li>
		<li>Relax the modified structure following section 1.</li>
		<li>Perform static self-consistent calculations and band structure calculations following sections 2 and 3.</li>
	</ol>
	</li>
</ol>

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The authors have nothing to disclose.

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 a symmetrical manner. Otherwise, it will be time consuming to search the optimized structure by VASP.
To consider the effect of an electric field, an artificial dipole sheet is added in the middle of the vacuum part in the periodic unit cell in VASP22. The vacuum region should not be too broad and the electric field should be weak enough to avoid artificial field emission23.
Whereas the effect of the strain can be simply realized by changing the lattice parameter in POSCAR, in the nanocomposite the situation would be more complex. The elastic responses of the NR and NT may be different from each other, undergoing the same strength. This will lead to a disproportionate structure. For example, when the uniaxial tensile strain is applied along the periodical direction, the optimized lattice parameter of the NT and NR along this direction changes from an initial 1.8 &#197; to 2.0 &#197;, and 2.2 &#197;, respectively. Large supercells are required for modeling: at least 11 unit cells of NT and 10 unit cells of NR in this case (11 x 2.0 &#197; = 10 x 2.2 &#197; = 22 &#197;).
While ground state electronic properties of materials can be determined by VASP quite well, to address the lifetime of photogenerated holes and electrons existing in an excited state, it is better to perform nonadiabatic dynamics calculation24. This is important to design photocatalysts with long lifetime carriers4.
The role of the computational approach performed by VASP plays into the discovery of novel materials and the screening for potential photocatalysts to assist experimental efforts. The band alignment at the PBE level in water splitting is not as convincing as quantitative experimental work. More accurate values of the band edges relative to the redox potentials, CBO, and VBO are needed. It would be best to use the Heyd-Scuseria-Ernzerhof (HSE) hybrid functional25, but it is more time consuming than PBE. Nevertheless, the results at the PBE level could be efficient for suggesting strategies for the enhancement of photocatalytic activity.
It should be mentioned that the computational design by VASP will also enable the prediction of solar cell materials, thermoelectric materials, lithium battery materials, gas capture materials, etc.2. High-throughput calculations have been combined with the machine learning procedures for better materials prediction and lower computational cost26,27.

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, Z3, and Z4 encapsulated inside BN-NT (11,11) were -0.033 eV/&#197;, -0.068 eV/&#197;, and -0.131 eV/&#197;, respectively10, as shown in Figure 1. Although EL varied by an order of magnitude with BN-NR size, all three nanocomposites presented type II band structures (from step 3.4) superior to the all-carbon cases14, where type II only emerged for NR with only one appropriate size inserted in NT14.
The band structure of the nanocomposite from step 3.2, BN-NT (11,11) + Z4, is shown in Figure 2. VBM/CBM locates at NT/NR (from step 3.5), respectively. The staggered band alignment was beneficial for light harvesting. The main mechanism of charge transfer is as follows: the photo generates electrons and a hole in Z4 at the X point, shown in Figure 3, and then the hole dissociates from Z4 (kX) to NT (11,11) (kVBM, the k point of VBM for this nanocomposite), shown in Figure 4. The calculated VBO (from step 3.4.3) is 317 meV, larger than the thermal energy at 300 K (KT ~30 meV), and effectively decreases the recombination rate of the photogenerated carriers10.
To enhance light harvesting through a wide spectrum, both transverse electric fields and longitudinal tensile strains are applied to BN-NT (11,11) + Z4. The evolution of band edges relative to the vacuum level from step 4 is shown in Figure 5. A substantial gap reduction up to near 0.95 eV is observed in this nanocomposite by external fields. More importantly, the staggered band alignment is preserved10. Based on these results, such a 1D system is expected to integrate photocatalytic hydrogen generation and safe capsule storage21. The photogenerated electrons could be collected by NR. Driven by electrostatic attraction, protons penetrate through the NT to generate a hydrogen molecule. The produced hydrogen is completely isolated within the nanotube to avoid an unwanted reverse reaction or explosion.
<img alt="Figure 1" class="xfigimg" src="/files/ftp_upload/60180/60180fig01.jpg" /> 
Figure 1: Zigzag BN nanoribbons Z2, Z3, and Z4 encapsulated inside a BN nanotube (11,11). The encapsulation energy (EL) is listed under each structure. <a href="https://www-jove-com.remotexs.ntu.edu.sg/files/ftp_upload/60180/60180fig01large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<img alt="Figure 2" class="xfigimg" src="/files/ftp_upload/60180/60180fig02.jpg" /> 
Figure 2: Band structure of BN nanotube (11,11) + BN nanoribbon Z4. The contributions from the nanotube and nanoribbon to the energy bands are represented in red and blue spheres, respectively. The left insets show the charge density distributions of the CBM and the VBM states (isovalue 0.02 e/&#197;3). This figure was adapted from Gong et al.10 with permission from The Royal Society of Chemistry. <a href="https://www-jove-com.remotexs.ntu.edu.sg/files/ftp_upload/60180/60180fig02large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<img alt="Figure 3" class="xfigimg" src="/files/ftp_upload/60180/60180fig03.jpg" /> 
Figure 3: The photo generates electrons and a hole in the BN nanoribbon Z4 at the X point. <a href="https://www-jove-com.remotexs.ntu.edu.sg/files/ftp_upload/60180/60180fig03large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<img alt="Figure 4" class="xfigimg" src="/files/ftp_upload/60180/60180fig04.jpg" /> 
Figure 4: The hole dissociates from the BN nanoribbon Z4 (kX) to the BN nanotube (11,11) (kVBM, the k point of VBM for this nanocomposite). <a href="https://www-jove-com.remotexs.ntu.edu.sg/files/ftp_upload/60180/60180fig04large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<img alt="Figure 5" class="xfigimg" src="/files/ftp_upload/60180/60180fig5a.jpg" /> 
Figure 5: Band edge modulation of the BN nanotube (11,11) and the BN nanoribbon Z4 by external fields. Evolution of band edges relative to the vacuum level under (A) an electric field and (B) uniaxial tensile strain. The negative direction of electric field is denoted from the lower edge atom B to the upper edge atom N of Z4. The reduction potential of H+/H2 and the oxidation potential of O2/H2O are -4.44 eV and -5.67 eV at pH = 0, respectively. The pH = 7 shifts the water&#8217;s redox potentials (by pH x 0.059 eV) to -4.027 eV and -5.257 eV, respectively, shown as blue dashed lines. This figure was reproduced from Gong et al.10 with permission from The Royal Society of Chemistry. <a href="https://www-jove-com.remotexs.ntu.edu.sg/files/ftp_upload/60180/60180fig05large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<img alt="Supplemental Figure 1" src="/files/ftp_upload/60180/60180supfig1.jpg" /> 
Supplemental Figure 1: (A) Atomic structure of a BN nanotube (11,11) + BN nanoribbon Z4 arranged away from the boundary and its corresponding conduction band minimum (B). (C) Atomic structure of a BN nanotube (11,11) and BN nanoribbon Z4 aligned with one boundary and its corresponding conduction band minimum (D). <a href="https://www-jove-com.remotexs.ntu.edu.sg/files/ftp_upload/60180/60180supfig01.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
Supplementary Coding File: <a href="https://www-jove-com.remotexs.ntu.edu.sg/files/ftp_upload/60180/supplementary_file1.docx" target="_blank">Please click here to view this file (Right click to download).</a>

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 ...

probe-type-ii-band-alignment-one-dimensional-van-der-waals

Nanyang Technological University

Research

JoVE Journal

Chemistry

7.5K Views.  Ocean University of China. Dit protocol rapporteert een computationele screening van foto katalysator met type twee band uitlijning door de eerste principes Softwire enorme expressieve Calais, boor nitriet nanoribbons ingekapseld in nanobuisjes. En het nemen van andere voorbeelden. Stap één, optimaliseer de atoomstructuur.Bereid je voor op invoerbestanden voor de berekening van de structuurontspanning door grote, INCAR, POSCAR, POTCAR en KPOINTS. Er zijn opgegeven parameters in het bestand INCAR die de bereken...

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

Preparation and Use of Samarium Diiodide (SmI2) in Organic Synthesis: The Mechanistic Role of HMPA and Ni(II) 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 molecular iodine to samarium metal in THF.1,2-3 It is a mild and selective single electron reductant and its versatility is a result of its ability to initiate a wide range of reductions including C-C bond-forming and cascade or sequential reactions. SmI2 can reduce a variety of functional groups including sulfoxides and sulfones, phosphine oxides, epoxides, alkyl and aryl halides, carbonyls, and conjugated double bonds.2-12 One of the fascinating features of SmI-2-mediated reactions is the ability to manipulate the outcome of reactions through the selective use of cosolvents or additives. In most instances, additives are essential in controlling the rate of reduction and the chemo- or stereoselectivity of reactions.13-14 Additives commonly utilized to fine tune the reactivity of SmI2 can be classified into three major groups: (1) Lewis bases (HMPA, other electron-donor ligands, chelating ethers, etc.), (2) proton sources (alcohols, water etc.), and (3) inorganic additives (Ni(acac)2, FeCl3, etc).3
Understanding the mechanism of SmI2 reactions and the role of the additives enables utilization of the full potential of the reagent in organic synthesis. The Sm-Barbier reaction is chosen to illustrate the synthetic importance and mechanistic role of two common additives: HMPA and Ni(II) in this reaction. The Sm-Barbier reaction is similar to the traditional Grignard reaction with the only difference being that the alkyl halide, carbonyl, and Sm reductant are mixed simultaneously in one pot.1,15 Examples of Sm-mediated Barbier reactions with a range of coupling partners have been reported,1,3,7,10,12 and have been utilized in key steps of the synthesis of large natural products.16,17 Previous studies on the effect of additives on SmI2 reactions have shown that HMPA enhances the reduction potential of SmI2 by coordinating to the samarium metal center, producing a more powerful,13-14,18 sterically encumbered reductant19-21 and in some cases playing an integral role in post electron-transfer steps facilitating subsequent bond-forming events.22 In the Sm-Barbier reaction, HMPA has been shown to additionally activate the alkyl halide by forming a complex in a pre-equilibrium step.23
Ni(II) salts are a catalytic additive used frequently in Sm-mediated transformations.24-27 Though critical for success, the mechanistic role of Ni(II) was not known in these reactions. Recently it has been shown that SmI2 reduces Ni(II) to Ni(0), and the reaction is then carried out through organometallic Ni(0) chemistry.28
These mechanistic studies highlight that although the same Barbier product is obtained, the use of different additives in the SmI2 reaction drastically alters the mechanistic pathway of the reaction. The protocol for running these SmI2-initiated reactions is described.

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

A straightforward procedure for the preparation of samarium diiodide (SmI2) in THF is described. The role of two main additives namely hexamethylphosphoramide (HMPA) and Ni(acac)2 in Sm mediated reactions is demonstrated in the Sm-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 amino acid sequence, it is only realized by the folding of the polypeptide chain into a single defined three-dimensional arrangement or more commonly into an ensemble of interconverting conformations. Investigating the connection between protein conformation and its function is therefore essential for a complete understanding of how proteins are able to fulfill their great variety of tasks. One possibility to study conformational changes a protein undergoes while progressing through its functional cycle is hydrogen-1H/2H-exchange in combination with high-resolution mass spectrometry (HX-MS). HX-MS is a versatile and robust method that adds a new dimension to structural information obtained by e.g. crystallography. It is used to study protein folding and unfolding, binding of small molecule ligands, protein-protein interactions, conformational changes linked to enzyme catalysis, and allostery. In addition, HX-MS is often used when the amount of protein is very limited or crystallization of the protein is not feasible. Here we provide a general protocol for studying protein dynamics with HX-MS and describe as an example how to reveal the interaction interface of two proteins in a complex. &#160;&#160;

Protein conformation and dynamics are key to understanding the relationship between protein structure and function. Hydrogen exchange coupled with high-resolution mass spectrometry is a versatile method to study the conformational dynamics of proteins as well as characterizing protein-ligand and protein-protein interactions, including contact interfaces and allosteric effects.

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 using the Atomic Force Microscope (AFM), can provide key insights into physical interactions present within colloidal systems. Colloidal systems are widely existent in several applications including, pharmaceuticals, foods, paints, paper, soil and minerals, detergents, printing and much more.1-3 Furthermore, colloids can exist in many states such as emulsions, foams and suspensions. Using colloidal probe nanoscopy one can obtain key information on the adhesive properties, binding energies and even gain insight into the physical stability and coagulation kinetics of the colloids present within. Additionally, colloidal probe nanoscopy can be used with biological cells to aid in drug discovery and formulation development. In this paper we describe a method for conducting colloidal probe nanoscopy, discuss key factors that are important to consider during the measurement, and show that both quantitative and qualitative data that can be obtained from such measurements.

Colloidal probe nanoscopy can be used within a variety of fields to gain insight into the physical stability and coagulation kinetics of colloidal systems and aid in drug discovery and formulation sciences using biological systems. The method described within provides a quantitative and qualitative means to study such systems.

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

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 phosphorescent signal when coordinated to a histidine-containing protein immobilized on the surface of a magnetic particle. Synthesis of Ir1, in high yields,is complete O/N&#160;and involves splitting of the parent cyclometalated Ir(III) chloro-bridged dimer into two equivalents of the solvated complex. To confirm specificity, several amino acids were probed for coordination activity when added to the synthesized probe, and only histidine elicited a signal response. Using BNT-II, a branched peptide mimic of the malarial biomarker Histidine Rich Protein II (pfHRP-II), the iridium probe was validated as a tool for HRP-II detection. Quenching effects were noted in the BNT-II/Ir1 titration when compared to L-Histidine/Ir1, but these were attributed to steric hindrance and triplet state quenching. Biolayer interferometry was used to determine real-time kinetics of interaction of Ir1 with BNT-II. Once the system was optimized, the limit of detection of rcHRP-II using the probe was found to be 12.8 nM in solution. When this protein was immobilized on the surface of a 50 &#181;m magnetic agarose particle, the limit of detection was 14.5 nM. The robust signal response of this inorganic probe, as well as its flexibility of use in solution or immobilized on a surface, can lend itself toward a variety of applications, from diagnostic use to imaging.

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

Robust detection reagents are of increasing necessity for developing new malaria diagnostic tools. An iridium(III) probe was designed that emits long-lasting luminescent signal in the presence of a histidine-rich malarial protein biomarker. Detection of the protein either in solution or immobilized on a magnetic particle affords flexibility in application.

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 presented. A major difficulty in adapting PCD to modern HPLC systems and columns is the need for large volume reaction coils that enable reagent mixing and then the derivatization reaction to take place. This large post column dead volume leads to band broadening, which results in a loss of observed separation efficiency and indeed detection in sensitivity. In reaction flow post column derivatization (RF-PCD) the derivatization reagent(s) are pumped against the flow of mobile phase into either one or two of the outer ports of the reaction flow column where it is mixed with column effluent inside a frit housed within the column end fitting. This technique allows for more efficient mixing of the column effluent and derivatization reagent(s) meaning that the volume of the reaction loops can be minimized or even eliminated altogether. It has been found that RF-PCD methods perform better than conventional PCD methods in terms of observed separation efficiency and signal to noise ratio. A further advantage of RF-PCD techniques is the ability to monitor effluent coming from the central port in its underivatized state. RF-PCD has currently been trialed on a relatively small range of post column reactions, however, there is currently no reason to suggest that RF-PCD could not be adapted to any existing one or two component (as long as both reagents are added at the same time) post column derivatization reaction.

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

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

Sequencing of Plant Wall Heteroxylans Using Enzymic, Chemical (Methylation) and Physical (Mass Spectrometry, Nuclear Magnetic Resonance) Techniques

This protocol describes the specific techniques used for the characterization of reducing end (RE) and internal region glycosyl sequence(s) of heteroxylans. De-starched wheat endosperm cell walls were isolated as an alcohol-insoluble residue (AIR)1 and sequentially extracted with water (W-sol Fr) and 1 M KOH containing 1% NaBH4 (KOH-sol Fr) as described by Ratnayake et al. (2014)2. Two different approaches (see summary in Figure 1) are adopted. In the first, intact W-sol AXs are treated with 2AB to tag the original RE backbone chain sugar residue and then treated with an endoxylanase to generate a mixture of 2AB-labelled RE and internal region reducing oligosaccharides, respectively. In a second approach, the KOH-sol Fr is hydrolyzed with endoxylanase to first generate a mixture of oligosaccharides which are subsequently labelled with 2AB. The enzymically released ((un)tagged) oligosaccharides from both W- and KOH-sol Frs are then methylated and the detailed structural analysis of both the native and methylated oligosaccharides is performed using a combination of MALDI-TOF-MS, RP-HPLC-ESI-QTOF-MS and ESI-MSn. Endoxylanase digested KOH-sol AXs are also characterized by nuclear magnetic resonance (NMR) that also provides information on the anomeric configuration. These techniques can be applied to other classes of polysaccharides using the appropriate endo-hydrolases.

Sequencing of Plant Wall Heteroxylans Using Enzymic, Chemical Methylation and Physical Mass Spectrometry, Nuclear Magnetic Resonance Techniques

This protocol describes the specific techniques used for the structural characterization of reducing end (RE) and internal region glycosyl sequence(s) of heteroxylans by tagging the RE with 2 aminobenzamide prior to enzymatic (endoxylanase) hydrolysis and then analysis of the resultant oligosaccharides using mass spectrometry (MS) and nuclear magnetic resonance (NMR).

This protocol describes the specific techniques used for the characterization of reducing end (RE) and internal region glycosyl sequence(s) of ...

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 composition of heavy crude oils and shale oils varies substantially depending on the origin of the mixture. In particular they contain an increased amount of nitrogen containing compounds compared to the conventionally used sweet crude oils. As nitrogen compounds have an influence on the operation of thermal processes occurring in coker units and steam crackers, and as some species are considered as environmentally hazardous, a detailed analysis of the reactions involving nitrogen containing compounds under pyrolysis conditions provides valuable information. Therefore a novel method has been developed and validated with a feedstock containing a high nitrogen content, i.e., a shale oil. First, the feed was characterized offline by comprehensive two-dimensional gas chromatography (GC &#215; GC) coupled with a nitrogen chemiluminescence detector (NCD). In a second step the on-line analysis method was developed and tested on a steam cracking pilot plant by feeding pyridine dissolved in heptane. The former being a representative compound for one of the most abundant classes of compounds present in shale oil. The composition of the reactor effluent was determined via an in-house developed automated sampling system followed by immediate injection of the sample on a GC &#215; GC coupled with a time-of-flight mass spectrometer (TOF-MS), flame ionization detector (FID) and NCD. A novel method for quantitative analysis of nitrogen containing compounds using NCD and 2-chloropyridine as an internal standard has been developed and demonstrated.

A method combining comprehensive two-dimensional gas chromatography with nitrogen chemiluminescence detection has been developed and applied to on-line analysis of nitrogen containing compounds in a complex hydrocarbon matrix.

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 of efficiently driving non-equilibrium chemistry is discussed. The advantage of a flowing plasma reactor is that continuous chemical processes can be driven with the flexibility of startup times in the seconds timescale. The plasma approach is generically suitable for conversion/activation of stable molecules such as CO2, N2 and CH4. Here the reduction of CO2 to CO is used as a model system: the complementary diagnostics illustrate how a baseline thermodynamic equilibrium conversion can be exceeded by the intrinsic non-equilibrium from high vibrational excitation. Laser (Rayleigh) scattering is used to measure the reactor temperature and Fourier Transform Infrared Spectroscopy (FTIR) to characterize in situ internal (vibrational) excitation as well as the effluent composition to monitor conversion and selectivity.

This article describes a flowing microwave reactor that is used to drive efficient non-equilibrium chemistry for the application of conversion/activation of stable molecules such as CO2, N2 and CH4. The goal of the procedure described here is to measure the in situ gas temperature and gas conversion.

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, we present a protocol for the fabrication of this material via the low-pressure vapor assisted solution process (LP-VASP) method, which yields ~19% power conversion efficiency in planar heterojunction perovskite solar cells. First, we report the synthesis of methylammonium iodide (CH3NH3I) and methylammonium bromide (CH3NH3Br) from methylamine and the corresponding halide acid (HI or HBr). Then, we describe the fabrication of pinhole-free, continuous methylammonium-lead halide perovskite (CH3NH3PbX3 with X = I, Br, Cl and their mixture) films with the LP-VASP. This process is based on two steps: i) spin-coating of a homogenous layer of lead halide precursor onto a substrate, and ii) conversion of this layer to CH3NH3PbI3-xBrx by exposing the substrate to vapors of a mixture of CH3NH3I and CH3NH3Br at reduced pressure and 120 &#176;C. Through slow diffusion of the methylammonium halide vapor into the lead halide precursor, we achieve slow and controlled growth of a continuous, pinhole-free perovskite film. The LP-VASP allows synthetic access to the full halide composition space in CH3NH3PbI3-xBrx with 0&#160;&#8804; x&#160;&#8804; 3. Depending on the composition of the vapor phase, the bandgap can be tuned between 1.6 eV&#160;&#8804; Eg&#160;&#8804; 2.3 eV. In addition, by varying the composition of the halide precursor and of the vapor phase, we can also obtain CH3NH3PbI3-xClx. Films obtained from the LP-VASP are reproducible, phase pure as confirmed by X-ray diffraction measurements, and show high photoluminescence quantum yield. The process does not require the use of a glovebox.

Here, we present a protocol for the synthesis of CH3NH3I and CH3NH3Br precursors and the subsequent formation of pinhole-free, continuous CH3NH3PbI3-xBrx thin films for the application in high efficiency solar cells and other optoelectronic devices.

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

A Closed-Type Wireless Nanopore Electrode for Analyzing Single Nanoparticles

Measuring the intrinsic features of single nanoparticles by nanoelectrochemistry holds deep fundamental importance and has potential impacts in nanoscience. However, electrochemically analyzing single nanoparticles is challenging, as the sensing nanointerface is uncontrollable. To address this challenge, we describe here the fabrication and characterization of a closed-type wireless nanopore electrode (WNE) that exhibits a highly controllable morphology and outstanding reproducibility. The facile fabrication of WNE enables the preparation of well-defined nanoelectrodes in a general chemistry laboratory without the use of a clean room and expensive equipment. One application of a 30 nm closed-type WNE in analysis of single gold nanoparticles in the mixture is also highlighted, which shows a high current resolution of 0.6 pA and high temporal resolution of 0.01 ms. Accompanied by their excellent morphology and small diameters, more potential applications of closed-type WNEs can be expanded from nanoparticle characterization to single molecule/ion detection and single-cell probing.

Here, we present a protocol for fabrication of a closed-type wireless nanopore electrode and subsequent electrochemical measurement of single nanoparticle collisions.

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

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