Chem3D Users Manual - CambridgeSoft

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Administrator The procedures assume you have a basic understanding of the computational concepts and terminology of semi-empirical methods, and the concepts involved in geometry optimization (minimization) and single-point computations. For more information see “Computation Concepts” on page 129. For help with MOPAC, see the online MOPAC manual at: http://www.cachesoftware.com/mopac/Mopac2002 manual/ MOPAC Semiempirical Methods The method descriptions that follow represent a very simplified view of the semi-empirical methods available in Chem3D and CS MOPAC. For more information see the online MOPAC manual. Extended Hückel Method Developed from the qualitative Hückel MO method, the Extended Hückel Method (EH) represents the earliest one-electron semi-empirical method to incorporate both σ and p valence systems. It is still widely used, owing to its versatility and success in analyzing and interpreting groundstate properties of organic, organometallic, and inorganic compounds of biological interest. Built into Chem3D, EH is the default semi-empirical method used to calculate data required for displaying molecular surfaces. The EH method uses a one-electron Hamiltonian with matrix elements defined as follows: H µµ = – I µ H µν = 0.5K( H µµ + H νν )S µν µ ≠ ν where I µ is the valence state ionization energy (VSIE) of orbital µ as deduced from spectroscopic data, and K is the Wolfsberg-Helmholtz constant (usually taken as 1.75). The Hamiltonian neglects electron repulsion matrix elements but retains the overlap integrals calculated using Slater-type basis orbitals. Because the approximated Hamiltonian (H) does not depend on the MO expansion coefficient C νi , the matrix form of the EH equations: can be solved without the iterative SCF procedure. RHF The default Hartree-Fock method assumes that the molecule is a closed shell and imposes spin restrictions. The spin restrictions allow the Fock matrix to be simplified. Since alpha (spin up) and beta (spin down) electrons are always paired, the basic RHF method is restricted to even electron closed shell systems. Further approximations are made to the RHF method when an open shell system is presented. This approximation has been termed the 1/2 electron approximation by Dewar. In this method, unpaired electrons are treated as two 1/2 electrons of equal charge and opposite spin. This allows the computation to be performed as a closed shell. A CI calculation is automatically invoked to correct errors in energy values inherent to the 1/2 electron approximation. For more information see “Configuration Interaction” on page 167. With the addition of the 1/2 electron approximation, RHF methods can be run on any starting configuration. UHF HC=SCE The UHF method treats alpha (spin up) and beta (spin down) electrons separately, allowing them to occupy different molecular orbitals and thus have different orbital energies. For many open and closed shell systems, this treatment of electrons 166•MOPAC Computations CambridgeSoft MOPAC Semi-empirical Methods
esults in better estimates of the energy in systems where energy levels are closely spaced, and where bond breaking is occurring. UHF can be run on both open and closed shell systems. The major caveat to this method is the time involved. Since alpha and beta electrons are treated separately, twice as many integrals need to be solved. As your models get large, the time for the computation may make it a less satisfactory method. Configuration Interaction The effects of electron-electron repulsion are underestimated by SCF-RHF methods, which results in the overestimation of energies. SCF-RHF calculations use a single determinant that includes only the electron configuration that describes the occupied orbitals for most molecules in their ground state. Further, each electron is assumed to exist in the average field created by all other electrons in the system, which tends to overestimate the repulsion between electrons. Repulsive interactions can be minimized by allowing the electrons to exist in more places (i.e. more orbitals, specifically termed virtual orbitals). The multi-electron configuration interaction (MECI) method in MOPAC addresses this problem by allowing multiple sets of electron assignments (i.e., configurations) to be used in constructing the molecular wave functions. Molecular wave functions representing different configurations are combined in a manner analogous to the LCAO approach. For a particular molecule, configuration interaction uses these occupied orbitals as a reference electron configuration and then promotes the electrons to unoccupied (virtual) orbitals. These new states, Slater determinants or microstates in MOPAC, are then linearly combined with the ground state configuration. The linear combination of microstates yields an improved electronic configuration and hence a better representation of the molecule. Approximate Hamiltonians in MOPAC There are five approximation methods available in MOPAC: • AM1 • MNDO • MNDO-d • MINDO/3 • PM3 The potential energy functions modify the HF equations by approximating and parameterizing aspects of the Fock matrix. The approximations in semi-empirical MOPAC methods play a role in the following areas of the Fock operator: • The basis set used in constructing the 1- electron atom orbitals is a minimum basis set of only the s and p Slater Type Orbitals (STOs) for valence electrons. • The core electrons are not explicitly treated. Instead they are added to the nucleus. The nuclear charge is termed N effective . For example, Carbon as a nuclear charge of +6-2 core electrons for a effective nuclear charge of +4. • Many of the 2-electron Coulomb and Exchange integrals are parameterized based on element. Choosing a Hamiltonian Overall, these potential energy functions may be viewed as a chronological progression of improvements from the oldest method, MINDO/3 to the newest method, PM5. However, although the ChemOffice 2005/Chem3D MOPAC Computations • 167 MOPAC Semi-empirical Methods
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A Guide to CambridgeSoft Manuals An
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Administrator Setting Molecular Sur
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Desktop Software Enterprise Solutio
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SOLUTIONS Enterprise Solutions APPL
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Desktop to Enterprise Solutions Che
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SOFTWARE E-Notebook Ultra Ultimate
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SOFTWARE ChemDraw Ultra Ultimate Dr
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SOFTWARE Chem3D Ultra Ultimate Mode
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SOFTWARE ChemFinder/Word • Search
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SOLUTIONS •Adds chemical data typ
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MANAGEMENT •Custom organization o
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MANAGEMENT • Indexes chemical str
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MANAGEMENT • E-Notebook Enterpris
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DISCOVERY • Accessed through your
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