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WIREs Comput Mol Sci
Impact Factor: 25.113

WebMO: Web‐based computational chemistry calculations in education and research

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Abstract WebMO is a web‐based interface for all major quantum chemistry programs. WebMO uses a server–client architecture that installs on a single server or cluster computer and provides access to state‐of‐the‐art computational chemistry programs from a standard web browser. The web interface provides a 3‐D molecular editor, pre‐defined calculations types, job submission and monitoring, visualization of results, and user management tools. Barriers to using state‐of‐the‐art computational chemistry in teaching and research are minimized through WebMO's universal accessibility, its intuitive and uniform interface to all programs, no software to install on client computers, and support for multiple users with a single instance. Applications of WebMO throughout the undergraduate curriculum are provided. The extensible open‐architecture design allows for collaboration among educators, researchers, quantum chemistry program developers, and the WebMO interface developers. This article is categorized under: Computer and Information Science > Visualization Electronic Structure Theory > Ab Initio Electronic Structure Methods Software > Quantum Chemistry
Using Jupyter notebooks to access and process computational results. Python code in a Jupyter notebook retrieves results from a WebMO vibrational frequency calculation, calculates the partition function, and plots the internal energy and heat capacity as a function of temperature
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Modeling solids and materials. The WebMO Cartesian coordinate editor supports definition of unit cells, creation of supercells, and creation of slabs along Miller planes. The crystal structure of NaCl is illustrated here
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Electrostatic potential surface of guanine. Electrostatic potential surface is computed from occupied molecular orbitals and displayed with a color‐code map on an electron density isosurface. Sites for hydrogen bonding are readily visible
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Backbonding. Overlap of a metal d‐orbital and CO π*‐bond is easily computed and visualized using WebMO
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Symmetry elements. WebMO can calculate the point group of molecular structures and display their symmetry elements. WebMO can also symmetrize nearly symmetric structures
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Potential energy curve of HCl. Coordinate scan of bond length at CCSD/6‐31G(d) model chemistry. Additional points at the bottom of the potential can be exported to Excel and fit to a parabola, from which the spring constant (k = 2•0.5937 Ha/Å2 = 517.7 Nm−1) and vibrational frequency (= 2995 cm−1) can be calculated
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Molecular orbital of ozone. Geometry optimization, molecular orbitals, and NBO bonding calculation illustrate in‐plane π‐bonding results in a partial bond between the outer oxygen atoms and reduces the bond angle to less than 120°
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Computed NMR spectrum of 4‐aminophenol. TMS offset and first‐order splitting are implemented by WebMO. NMR spectra are interactive, as clicking on a peak highlights the corresponding nuclei
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Conformational energy scan. Coordinate scan about the C1–C2–C3–C4 dihedral angle of butane at PM3 model chemistry, illustrating anti, gauche, and eclipsed energetics. Coordinate scan plots are interactive, so that clicking on an energy point displays the corresponding molecular geometry
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Dipole moments. Dipole moment of H2O
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VSEPR structures. “Seesaw” VSEPR molecular shape of SF4
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WebMO technology. WebMO uses a web‐based client–server model. Perl scripts are installed on a server. Web pages are delivered to the user and provide interactivity with JavaScript and 3‐D visualization with WebGL. Jobs are submitted to engines via an internal or external queue, their progress is monitored, and output is stored for future viewing. WebMO can interact with external services for user authentication and chemical information lookup
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Job manager. The WebMO job manager allows users to create, monitor, and view jobs. One can also organize jobs into folders, import legacy calculations, and export results
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Visualizing molecular orbitals. WebMO can display molecular orbitals as phase‐indicated isosurfaces, or as color‐coded values on a scrollable cross‐section plane
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Interactive spectra. Clicking on a peak in an infrared (or NMR) spectrum will display the corresponding molecular vibration (or nuclei)
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Calculation job options. Basic job options are specified similarly for all calculations. Advanced job options are optional and depend on calculation type and engine
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WebMO 3‐D editor. The WebMO editor allows users to easily create or import molecular structures. Atoms and bonds are added by clicking and dragging. Structures are cleaned‐up using Lewis valences, VSEPR structures, and idealized or mechanics‐based geometries. Bond lengths, bond angles, and dihedral angles may all be individually specified. Mechanics energy, symmetry, and extended Huckel molecular orbital calculations are available within the editor
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Computational chemistry usage in science. The number of publications each year that include the topic of density functional theory was searched with web of science, illustrating continued growth of computation in chemical modeling in science literature
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Browse by Topic

Software > Quantum Chemistry
Electronic Structure Theory > Ab Initio Electronic Structure Methods
Computer and Information Science > Visualization

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