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Administrator Connection Table . . . . . . . . . . . . . . . . . . . . . . . 118 Gaussian Input . . . . . . . . . . . . . . . . . . . . . . . . . 118 Gaussian Checkpoint . . . . . . . . . . . . . . . . . . . . 118 Gaussian Cube . . . . . . . . . . . . . . . . . . . . . . . . . . 118 Internal Coordinates . . . . . . . . . . . . . . . . . . . . 119 MacroModel Files . . . . . . . . . . . . . . . . . . . . . . . 119 Molecular Design Limited MolFile (.MOL) 120 MSI ChemNote . . . . . . . . . . . . . . . . . . . . . . . . 120 MOPAC Files . . . . . . . . . . . . . . . . . . . . . . . . . . 120 MOPAC Graph Files . . . . . . . . . . . . . . . . . . . . 122 Protein Data Bank Files . . . . . . . . . . . . . . . . . 122 ROSDAL Files (RDL) . . . . . . . . . . . . . . . . . . 122 Standard Molecular Data (SMD) . . . . . . . . 122 SYBYL Files . . . . . . . . . . . . . . . . . . . . . . . . . . . 122 Job Description File Formats . . . . . . . . . . . . . . . . 122 JDF Files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 122 JDT Files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 122 Exporting With the Clipboard . . . . . . . . . . . . . . . 123 Transferring to ChemDraw. . . . . . . . . . . . . . . . . 123 Transferring to Other Applications. . . . . . . . . . 123 Chapter 8: Computation Concepts Computational Methods Overview . . . . . . . . . . . 125 Uses of Computational Methods. . . . . . . . . . . . 126 Choosing the Best Method . . . . . . . . . . . . . . . . . 126 Molecular Mechanics Methods Applications Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 127 Quantum Mechanical Methods Applications Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 127 Potential Energy Surfaces . . . . . . . . . . . . . . . . 128 Potential Energy Surfaces (PES) . . . . . . . . . . 129 Single Point Energy Calculations . . . . . . . . . 129 Geometry Optimization . . . . . . . . . . . . . . . . . 130 Molecular Mechanics Theory in Brief . . . . . . . . . 131 The Force-Field. . . . . . . . . . . . . . . . . . . . . . . . . . . 132 MM2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 132 Bond Stretching Energy . . . . . . . . . . . . . . . . . 133 Angle Bending Energy . . . . . . . . . . . . . . . . . . . 133 Torsion Energy . . . . . . . . . . . . . . . . . . . . . . . . . 134 Non-Bonded Energy . . . . . . . . . . . . . . . . . . . . 135 van der Waals Energy . . . . . . . . . . . . . . . . . . . 135 Cutoff Parameters for van der Waals Interactions . . . . . . . . . . . . . . . . . . . . . . . . . . . . 135 Electrostatic Energy . . . . . . . . . . . . . . . . . . . . . 136 charge/charge contribution . . . . . . . . . . . . . . 136 dipole/dipole contribution . . . . . . . . . . . . . . 136 dipole/charge contribution . . . . . . . . . . . . . . 136 Cutoff Parameters for Electrostatic Interactions . . . . . . . . . . . . . . . . . . . . . . . . . . . 136 OOP Bending . . . . . . . . . . . . . . . . . . . . . . . . . . 137 Pi Bonds and Atoms with Pi Bonds . . . . . . 137 Stretch-Bend Cross Terms . . . . . . . . . . . . . . . 138 User-Imposed Constraints . . . . . . . . . . . . . . . 138 Molecular Dynamics Simulation . . . . . . . . . . . . 138 Molecular Dynamics Formulas . . . . . . . . . . . 139 Quantum Mechanics Theory in Brief . . . . . . . . . 139 Approximations to the Hamiltonian . . . . . . 140 Restrictions on the Wave Function . . . . . . . 141 Spin functions . . . . . . . . . . . . . . . . . . . . . . . . . . 141 LCAO and Basis Sets . . . . . . . . . . . . . . . . . . . 141 The Roothaan-Hall Matrix Equation . . . . . . 142 Ab Initio vs. Semiempirical . . . . . . . . . . . . . . 142 The Semi-empirical Methods. . . . . . . . . . . . . . . 142 Extended Hückel Method . . . . . . . . . . . . . . . 142 Methods Available in CS MOPAC . . . . . . . . . . 143 RHF . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 143 UHF . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 143 Configuration Interaction . . . . . . . . . . . . . . . 143 Approximate Hamiltonians in MOPAC . . . . . . . 144 Choosing a Hamiltonian. . . . . . . . . . . . . . . . . . . 144 MINDO/3 Applicability and Limitations . 144 MNDO Applicability and Limitations . . . . 145 AM1 Applicability and Limitations . . . . . . . 145 PM3 Applicability and Limitations . . . . . . . 146 MNDO-d Applicability and Limitations . . 146 Chapter 9: MM2 and MM3 Computations Minimize Energy . . . . . . . . . . . . . . . . . . . . . . . . . . . 147 Running a Minimization . . . . . . . . . . . . . . . . . . . 149 Queuing Minimizations . . . . . . . . . . . . . . . . . . . 150 Minimizing Ethane . . . . . . . . . . . . . . . . . . . . . . . 150 Comparing Two Stable Conformations of Cyclohexane. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 152 Locating the Global Minimum . . . . . . . . . . . 153 Molecular Dynamics . . . . . . . . . . . . . . . . . . . . . . . . 154 Performing a Molecular Dynamics Computation . . . . . . . . . . . . . . . . . . . . . . . . . . . . 154 CambridgeSoft
Dynamics Settings . . . . . . . . . . . . . . . . . . . . . . 155 Job Type Settings . . . . . . . . . . . . . . . . . . . . . . . 155 Computing the Molecular Dynamics Trajectory for a Short Segment of Polytetrafluoroethylene (PTFE) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 156 Compute Properties . . . . . . . . . . . . . . . . . . . . . . . . 158 Showing Used Parameters . . . . . . . . . . . . . . . . . . . 160 Repeating an MM2 Computation. . . . . . . . . . . . . 160 Using .jdf Files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 160 Chapter 10: MOPAC Computations MOPAC Semi-empirical Methods . . . . . . . . . . . . 162 Approximate Hamiltonians in MOPAC . . . . . 163 Choosing a Hamiltonian . . . . . . . . . . . . . . . . 163 MINDO/3 Applicability and Limitations . 164 MNDO Applicability and Limitations . . . . 164 AM1 Applicability and Limitations . . . . . . . 165 PM3 Applicability and Limitations . . . . . . . 165 MNDO-d Applicability and Limitations . . 166 Using Keywords . . . . . . . . . . . . . . . . . . . . . . . . . . . 166 Specifying the Electronic Configuration . . . . . . 168 Even-Electron Systems. . . . . . . . . . . . . . . . . . . . 170 Ground State, RHF. . . . . . . . . . . . . . . . . . . . . 170 Ground State, UHF . . . . . . . . . . . . . . . . . . . . 170 Excited State, RHF . . . . . . . . . . . . . . . . . . . . . 170 Excited State, UHF . . . . . . . . . . . . . . . . . . . . . 171 Odd-Electron Systems . . . . . . . . . . . . . . . . . . . . 171 Ground State, RHF. . . . . . . . . . . . . . . . . . . . . 171 Ground State, UHF . . . . . . . . . . . . . . . . . . . . 171 Excited State, RHF . . . . . . . . . . . . . . . . . . . . . . 171 Excited State, UHF . . . . . . . . . . . . . . . . . . . . . 171 Sparkles . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 171 Optimizing Geometry . . . . . . . . . . . . . . . . . . . . . . 172 MOPAC Files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 172 Running MOPAC Jobs . . . . . . . . . . . . . . . . . . . . 174 Minimizing Energy . . . . . . . . . . . . . . . . . . . . . . . . . 176 Notes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 177 Adding Keywords . . . . . . . . . . . . . . . . . . . . . . . . 177 Optimize to Transition State. . . . . . . . . . . . . . . . . 178 Example: . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 179 Computing Properties. . . . . . . . . . . . . . . . . . . . . . 180 MOPAC Properties . . . . . . . . . . . . . . . . . . . . . . 181 Heat of Formation, DHf . . . . . . . . . . . . . . . . 181 Gradient Norm . . . . . . . . . . . . . . . . . . . . . . . . . 181 Dipole Moment . . . . . . . . . . . . . . . . . . . . . . . . 182 Charges . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 182 Mulliken Charges . . . . . . . . . . . . . . . . . . . . . . . 182 Charges From an Electrostatic Potential. . . 182 Wang-Ford Charges . . . . . . . . . . . . . . . . . . . . . 183 Electrostatic Potential . . . . . . . . . . . . . . . . . . . 183 Molecular Surfaces . . . . . . . . . . . . . . . . . . . . . . 184 Polarizability . . . . . . . . . . . . . . . . . . . . . . . . . . . 184 COSMO Solvation in Water . . . . . . . . . . . . . 184 Hyperfine Coupling Constants . . . . . . . . . . . 184 Spin Density. . . . . . . . . . . . . . . . . . . . . . . . . . . . 185 Example 1. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 186 Example 2. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 187 Example 3. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 187 Example 4. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 189 Example 5. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 190 Example 6. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 191 Example 7. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 192 UHF Spin Density for the Ethyl Radical . . . . . 192 Example 8. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 193 Chapter 11: Gaussian Computations Gaussian 03 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 195 Minimize Energy . . . . . . . . . . . . . . . . . . . . . . . . . . . 195 The Job Type Tab . . . . . . . . . . . . . . . . . . . . . . . . . 195 The Theory Tab . . . . . . . . . . . . . . . . . . . . . . . . . . 196 The Properties Tab. . . . . . . . . . . . . . . . . . . . . . . . 197 The General Tab . . . . . . . . . . . . . . . . . . . . . . . . . . 197 Job Description File Formats . . . . . . . . . . . . . . . . 198 .jdt Format . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 198 .jdf Format . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 198 Computing Properties . . . . . . . . . . . . . . . . . . . . . . . 198 Creating a Gaussian Input File . . . . . . . . . . . . . . . 198 Running a Gaussian Input File . . . . . . . . . . . . . . . 199 Repeating a Gaussian Job . . . . . . . . . . . . . . . . . . . . 200 Running a Gaussian Job . . . . . . . . . . . . . . . . . . . . . 200 Chapter 12: GAMESS Computations Installing GAMESS . . . . . . . . . . . . . . . . . . . . . . . . . 201 Minimize Energy . . . . . . . . . . . . . . . . . . . . . . . . . . . 201 The Theory Tab . . . . . . . . . . . . . . . . . . . . . . . . . . 201 The Job Type Tab . . . . . . . . . . . . . . . . . . . . . . . . . 202 ChemOffice 2005
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compute the checksum for the upload
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Administrator Managing the Audit Se
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Administrator The field appears in
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Administrator contained box accordi
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Administrator In the form we are sh
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Administrator For example, if there
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Administrator 506• Managing Secti
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Administrator Several fields types
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Administrator • Default Font - yo
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The Section Type Configuration dial
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Administrator Example 1 In this exa
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Administrator See the following top
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Administrator Associating a list of
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Administrator • Username - An opt
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Administrator To add a property lis
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Administrator from the Property dro
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Administrator The Field Properties
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Administrator Another feature of ta
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Administrator 3. Right-click the Ta
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Administrator • SupplierID - the
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Administrator reactants and product
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Administrator • Certain types of
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Administrator To access the Add-In
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Administrator In the query table fi
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Administrator A menu appears with t
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Administrator Adding a Collection L
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Administrator A menu appears. 4. Se
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Administrator the Rename command in
Page 594 and 595:
Administrator contained collection
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Administrator Creating a Search Typ
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Administrator Chemical Structure Se
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Administrator To add states to a co
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Administrator • Unlocked Contents
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Administrator If the user wants to
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Administrator To view the export te
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Administrator To edit this data, 1.
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Administrator 584• User Administr
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Administrator 604 • CambridgeSoft
Page 638 and 639:
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Page 640 and 641:
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Administrator The CS ChemOffice SDK
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Administrator Defining Substructure
Page 648 and 649:
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Page 650 and 651:
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Page 652 and 653:
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Page 690 and 691:
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Page 700 and 701:
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Page 730 and 731:
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Page 744 and 745:
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Page 746 and 747:
Administrator Combi experiments 367
Page 748 and 749:
Administrator Creating (continued)
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Administrator Dihedral type field 6
Page 752 and 753:
Administrator Exporting (continued)
Page 754 and 755:
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Page 758 and 759:
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Page 760 and 761:
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Page 766 and 767:
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Page 768 and 769:
Administrator Search Details prefer
Page 770 and 771:
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Page 772 and 773:
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Page 774 and 775:
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Page 776 and 777:
Administrator xxxviii• CambridgeS
Page 778 and 779:
CAMBRIDGESOFT ChemOffice Desktop to
Page 780 and 781:
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Page 782 and 783:
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Page 784 and 785:
DESKTOP CS ChemDraw Chemical Struct
Page 786 and 787:
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Page 788 and 789:
DESKTOP CS ChemFinder Searching and
Page 790 and 791:
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Page 792 and 793:
ENTERPRISE ChemOffice WebServer Ent
Page 794 and 795:
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Page 796 and 797:
KNOWLEDGE E-Notebook Enterprise Des
Page 798 and 799:
KNOWLEDGE Document Manager Desktop
Page 800 and 801:
KNOWLEDGE 21CFR11 Compliance Electr
Page 802 and 803:
RESEARCH & Registration System Chem
Page 804 and 805:
RESEARCH & Inventory Manager Chemic
Page 806 and 807:
RESEARCH & CombiChem Enterprise Des
Page 808 and 809:
RESEARCH & BioAssay HTS Biological
Page 810 and 811:
RESEARCH & BioSAR Browser Biologica
Page 812 and 813:
CHEMICAL ChemACX Database Available
Page 814 and 815:
CHEMICAL The Merck Index Chemistry
Page 816 and 817:
CHEMICAL Chemical Databases Referen
Page 818 and 819:
CONSULTING & Consulting & Services
Page 821:
CS Software Problem Report For fast
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