Chem3D Users Manual - CambridgeSoft

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Administrator • Second Positioned atom—Positioned in terms of the Origin atom and the First Positioned atom. There are two possible ways to position the Second Positioned atom, as described in the following example. In the left example, atom D is positioned in terms of a dihedral angle, thus the second angle is the dihedral angle described by A-B-C-D. This dihedral angle is the angle between the two planes defined by D-C-B and A-B-C. In the right example, if you view down the C-B bond, then the dihedral angle appears as the angle formed by D-C-A. A clockwise rotation from atom D to atom A when C is in front of B indicates a positive dihedral angle. In the left example, the Second Positioned atom is a specified distance from the First Positioned atom. In addition, the placement of the Second Positioned atom is specified by the angle between the Origin atom, the First Positioned atom, and the Second Positioned atom. In the right example, the Second Positioned atom is a specified distance from the Origin atom. In addition, the placement of the Second Positioned atom is specified by the angle between the First Positioned atom, the Origin atom, and the Second Positioned atom. Atoms Positioned by Three Other Atoms In the following set of illustrations, each atom D is positioned relative to three previously positioned atoms C, B, and A. Three measurements are needed to position D: a distance, and two angles. Atom C is the Distance-Defining atom; D is placed a specified distance from C. Atom B is the First Angle-Defining atom; D, C, and B describe an angle. Atom A is the Second Angle-Defining atom. It is used to position D in one of two ways: • By a dihedral angle A-B-C-D • By a second angle A-C-D. When D is positioned using two angles, there are two possible positions in space about C for D to occupy: a Pro-R position and a Pro-S position. NOTE: The terms Pro-R and Pro-S used in Chem3D to position atoms bear no relation to the Cahn-Ingold-Prelog R/S specification of the absolute stereochemical configuration of a chiral atom. Pro-R and Pro-S refer only to the positioning of D and do not imply any stereochemistry for C. C may be chiral, or achiral. The most convenient way to visualize how the Pro-R/Pro-S terms are used in Chem3D to position D is described in the following examples: 102•Manipulating Models CambridgeSoft Changing the Z-matrix
To position Atom D in Pro-S Orientation (left) and Pro-R Orientation (right): 1. Orient the Distance-Defining atom, C, the First Angle-Defining atom, B, and the Second Angle-Defining atom, A, such that the plane which they define is parallel to the X-Y plane. 2. Orient the First Angle-Defining atom, B, to be directly above the Distance-Defining atom, C, such that the bond joining B and C is parallel to the Y-axis, and the Second Angle-Defining atom, A, is somewhere to the left of C. Because H(14) is positioned by two bond angles, there are two possible positions in space about C(5) for H(14) to occupy; the Pro-R designation determines which of the two positions is used. If an atom is positioned by a dihedral angle, the three atoms listed in the information about an atom would all be connected by dashes, such as C(6)-C(3)-C(1), and there would be no Pro-R or Pro-S designation. In this orientation, D is somewhere in front of the plane defined by A, B and C if positioned Pro-R, and somewhere behind the plane defined by A, B and C if positioned Pro-S. When you point to or click an atom, the information box which appears can contain information about how the atom is positioned. Positioning Example If H(14) is positioned by C(5)-C(1), C(13) Pro-R, then the position of H(14) is a specified distance from C(5) as described by the H(14)-C(5) bond length. Two bond angles, H(14)-C(5)-C(1), and H(14)-C(5)-C(13), are also used to position the atom. The commands in the Set Z-Matrix submenu allow you to change the Z-matrix for your model using the concepts described previously. Because current measurements are retained when you choose any of the commands in the Set Z- Matrix submenu, no visible changes in the model window occur. Positioning by Bond Angles To position an atom relative to three previously positioned atoms using a bond distance and two bond angles: 1. With the Select tool, click the second angle-defining atom. 2. Shift-click the first angle-defining atom. 3. Shift-click the distance-defining atom. 4. Shift-click the atom to position. You should now have four atoms selected, with the atom to be positioned selected last. 5. From the Structure menu, point to Set Z-Matrix, and then choose Position by Bond Angles. ChemOffice 2005/Chem3D Manipulating Models • 103 Changing the Z-matrix
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License Information ChemOffice, Che
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A Guide to CambridgeSoft Manuals An
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Administrator Setting Molecular Sur
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Administrator Methods Available in
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Administrator Defining Atom Types.
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Administrator • Bond Angles—Dis
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Administrator The Building Toolbar
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Administrator The Calculation Toolb
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Administrator 1. Right-click in the
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Administrator modes and color setti
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Administrator 30 •Chem3D Basics C
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Administrator 2. Click the ChemDraw
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Administrator • Overall errors in
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Administrator Molecular Surfaces Mo
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Property Description Property Descr
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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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SOFTWARE The Merck Index • Encycl
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SOLUTIONS •Development and deploy
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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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DISCOVERY • Integrated with Regis
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DISCOVERY • Reagent lists can be
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DISCOVERY •Effectively manages da
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DISCOVERY • Catalog driven data m
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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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Chem3D Users Manual - CambridgeSoft

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