Chem3D Users Manual - CambridgeSoft

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Administrator • Semiempirical Extended Hückel, MINDO/3, MNDO, MNDO-d, AM1 and PM3 methods through Chem3D and CS MOPAC. • Ab initio methods through the Chem3D Gaussian or GAMESS interface. Uses of Computational Methods Computational methods calculate the potential energy surfaces (PES) of molecules. The potential energy surface is the embodiment of the forces of interaction among atoms in a molecule. From the PES, structural and chemical information about a molecule can be derived. The methods differ in the way the surface is calculated and in the molecular properties derived from the energy surface. The methods perform the following basic types of calculations: • Single point energy calculation—The energy of a given spacial arrangement of the atoms in a model or the value of the PES for a given set of atomic coordinates. • Geometry optimization—A systematic modification of the atomic coordinates of a model resulting in a geometry where the net forces on the structure sum to zero. A 3-dimensional arrangement of atoms in the model representing a local energy minimum (a stable molecular geometry to be found without crossing a conformational energy barrier). • Property calculation—Predicts certain physical and chemical properties, such as charge, dipole moment, and heat of formation. Computational methods can perform more specialized functions, such as conformational searches and molecular dynamics simulations. Choosing the Best Method Not all types of calculations are possible for all methods and no one method is best for all purposes. For any given application, each method poses advantages and disadvantages. The choice of method depend on a number of factors, including: • The nature of the molecule • The type of information sought • The availability of applicable experimentally determined parameters (as required by some methods) • Computer resources The three most important of the these criteria are: • Model size—The size of a model can be a limiting factor for a particular method. The limiting number of atoms in a molecule increases by approximately one order of magnitude between method classes from ab initio to molecular mechanics. Ab initio is limited to tens of atoms, semiempirical to hundreds, and molecular mechanics to thousands. • Parameter Availability—Some methods depend on experimentally determined parameters to perform computations. If the model contains atoms for which the parameters of a particular method have not been derived, that method may produce invalid predictions. Molecular mechanics, for example, relies on parameters to define a force-field. Any particular force-field is only applicable to the limited class of molecules for which it is parametrized. • Computer resources—Requirements increase relative to the size of the model for each of the methods. Ab initio: The time required for performing computations increases on the order of N 4 , where N is the number of atoms in the model. 130•Computation Concepts CambridgeSoft Computational Methods Overview
Semiempirical: The time required for computation increases as N 3 or N 2 , where N is the number of atoms in the model. MM2: The time required for performing computations increases as N 2 , where N is the number of atoms. In general, molecular mechanical methods are computationally less expensive than quantum mechanical methods. The suitability of each general method for particular applications can be summarized as follows. Molecular Mechanics Methods Applications Summary Molecular mechanics in Chem3D apply to: • Systems containing thousands of atoms. • Organic, oligonucleotides, peptides, and saccharides. • Gas phase only (for MM2). Useful techniques available using MM2 methods include: • Energy Minimization for locating stable conformations. • Single point energy calculations for comparing conformations of the same molecule. • Searching conformational space by varying a single dihedral angle. • Studying molecular motion using Molecular Dynamics. Quantum Mechanical Methods Applications Summary Useful information determined by quantum mechanical methods includes: • Molecular orbital energies and coefficients. • Heat of Formation for evaluating conformational energies. • Partial atomic charges calculated from the molecular orbital coefficients. • Electrostatic potential. • Dipole moment. • Transition-state geometries and energies. • Bond dissociation energies. The semiempirical methods available in Chem3D and CS MOPAC apply to: • Systems containing up to 120 heavy atoms and 300 total atoms. • Organic, organometallics, and small oligomers (peptide, nucleotide, saccharide). • Gas phase or implicit solvent environment. • Ground, transition, and excited states. Ab initio methods, available through the Gaussian interface, apply to: • Systems containing up to 150 atoms. • Organic, organometallics, and molecular fragments (catalytic components of an enzyme). • Gas or implicit solvent environment. • Study ground, transition, and excited states (certain methods). The following table summarizes the method types: ChemOffice 2005/Chem3D Computation Concepts • 131 Computational Methods Overview
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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 Chem3D Ultra Ultimate Mode
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DISCOVERY • Accessed through your
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DATABASES • Fully structure-searc
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DATABASES • Encyclopedic referenc
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DATABASES • Extensive collection
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SERVICES · Business Case Developme
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CS ChemOffice ® Desktop to Enterpr
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