Chem3D Users Manual - CambridgeSoft

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Administrator Molecular Surfaces Molecular surfaces calculate the data necessary to render the Total Charge Density, Molecular Electrostatic Potential, Spin Density, and Molecular Orbitals surfaces. Polarizability The polarizability (and hyperpolarizability) property provides information about the distribution of electrons based on presence of an applied electric field. In general, molecules with more delocalized electrons have higher values for this property. Polarizability data is often used in other equations for evaluation of optical properties of molecules. For more information see the MOPAC online manual, page 214. The polarizability and hyperpolarizability values reported are the first order (alpha) tensors (xx, yy, zz, xz, yz, xy), second order (beta) tensors and third order (gamma) tensors. NOTE: Polarizabilities cannot be calculated using the MINDO/3 potential function. COSMO Solvation in Water The COSMO method is useful for determining the stability of various species in a solvent. The default solvent is water. For more information, see the MOPAC online manual. To run the COSMO method, make the following selections in the MOPAC Interface: • On the Job & Theory tab, select COSMO in the Solvent field. • On the Properties tab, check the COSMO Area and/or COSMO Volume properties. You must check each property you want to see in the results. NOTE: You can also use the Miertus-Scirocco-Tomasi solvation model, which is available using the H2O keyword. This method is recommended only for water as the solvent. A discussion of this method can be found in the MOPAC online documentation. Hyperfine Coupling Constants Hyperfine Coupling Constants are useful for simulating Electron Spin Resonance (ESR) spectra. Hyperfine interaction of the unpaired electron with the central proton and other equivalent protons cause complex splitting patterns in ESR spectra. ESR spectroscopy measures the absorption of microwave radiation by an unpaired electron when it is placed under a strong magnetic field. Hyperfine Coupling Constants (HFCs) are related to the line spacing within the hyperfine pattern of an ESR spectra and the distance between peaks. Species that contain unpaired electrons are as follows: • Free radicals • Odd electron molecules • Transition metal complexes • Rare-earth ions • Triplet-state molecules For more information see the MOPAC online manual, page 34. 188•MOPAC Computations <strong>CambridgeSoft</strong> Computing Properties
The following table contains the keywords automatically sent to MOPAC and those you can use to affect this property. Keyword UHF Description Automatically sent to MOPAC if you choose “Open Shell (Unrestricted)” wave functions to specify the use of the Unrestricted Hartree-Fock methods. UHF Spin Density The UHF Spin Density removes the closed shell restriction. In doing so, separate wave functions for alpha and beta spin electrons are computed. For more information see the MOPAC online manual, page 152. The following table contains the keywords automatically sent to MOPAC and those you can use to affect this property. Keyword Description Hyperfine GEO-OK Automatically sent to MOPAC to specify the hyperfine computation. Automatically sent to MOPAC to override checking of the Z-matrix. UHF Automatically sent to MOPAC if you choose “Open Shell (Unrestricted)” wave functions to specify the use of the Unrestricted Hartree-Fock methods. MMOK Automatically sent to MOPAC to specify Molecular Mechanics correction for amide bonds. Use the additional keyword NOMM to turn this keyword off. Spin Density Spin density arises in molecules where there is an unpaired electron. Spin density data provides relative amounts of alpha spin electrons for a particular state. Spin density is a useful property for accessing sites of reactivity and for simulating ESR spectra. Two methods of calculating spin density of molecules with unpaired electrons are available: RHF Spin Density and UHF Spin Density. GEO-OK MMOK SPIN Automatically sent to MOPAC to override checking of the Z-matrix. Automatically sent to MOPAC to specify Molecular Mechanics correction for amide bonds. Use the additional keyword NOMM to turn this keyword off. You can add this keyword to print the spin density matrix in the *.out file. RHF Spin Density RHF Spin Density uses the 1/2 electron correction and a single configuration interaction calculation to isolate the alpha spin density in a molecule. This method is particularly useful when the UHF Spin Density computation becomes too resource intensive for large molecules. For more information see the MOPAC online manual, page 28. ChemOffice 2005/<strong>Chem3D</strong> MOPAC Computations • 189 Computing Properties
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SOLUTIONS Enterprise Solutions APPL
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DISCOVERY • Accessed through your
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DATABASES • Extensive collection
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SERVICES · Business Case Developme
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