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Administrator one attached hydrogen atom. In this case the – XR2– and –XRH– values for the 1-8-1 angle type are identical. As in the N,N,N-triethylamine example above, the only attached non-hydrogen atom is a lone pair. –XH2– –XH2– is the optimal value of a bond angle where the central atom of that bond angle is also bonded to two hydrogen atoms. For example, the optimal value of the 1-1-3 angle type for propionic acid is the –XH2– bond angle of 110.0°, since the central carbon (C-2) has two attached hydrogen atoms. Record Order Pi Atoms The Pi Atoms table (Conjugated Pisystem Atoms.xml) contains the parameters which are used to correct bond lengths and angles for pi atoms in your model. In Chem3D, additional information is used to compute the pi system portions of the MM2 force field for the pi atoms in your model. The records in the Pi Atoms table are comprised of six fields: Atom Type, Electron, Ionization, Repulsion, Quality, and Reference. Atom Type The Atom type number field contains the atom type number to which the rest of the Conjugated Pisystem Atoms record applies. When sorted by angle type, the order of the records in the Angle Bending table, the 4-Membered Ring Angles table and the 3-Membered Ring Angles table is as follows: 1. Records are sorted by the second atom type number in the Angle Type field. For example, the record for bond angle type 1-2-1 is before the record for bond angle type 1-3-1. 2. For multiple records where the second atom type number is the same, the records are sorted by the first atom type number in the Angle Type field. For example, the record for bond angle type 1-3-2 is listed before the record for bond angle type 2-3-2. 3. For multiple records where the first two atom type numbers are the same, the records are sorted by the third atom type number in the Angle Type field. For example, the record for bond angle type 1-1-1 is listed before the record for bond angle type 1-1-2. Electron The Electron field contains the number of electrons that a particular pi atom contributes to the pi system. For example, an alkene carbon, atom type number 2, contributes 1 electron to the pi system whereas a pyrrole nitrogen, atom type number 40, contributes 2 electrons to the pi system. Ionization The Ionization field contains the amount of energy required to remove a pi electron from an isolated pi atom. The units of the ionization energy by electron volts (eV). The magnitude of the ionization energy is larger the more electronegative the atom. For example, an alkene carbon has an ionization energy of -11.160 eV, and the more electronegative pyrrole nitrogen has an ionization energy of -13.145 eV. Repulsion The Repulsion field contains a measure of: 658• Parameter Tables <strong>CambridgeSoft</strong> Pi Atoms
• The energy required to keep two electrons, each on separate pi atoms, from moving apart and • The energy required to keep two electrons, occupying the same orbital on the same pi atom, from moving apart. The units of the repulsion energy are electron volts (eV). The repulsion energy is more positive the more electronegative the atom. For example, an alkene carbon has an repulsion energy of 11.134 eV, and the more electronegative pyrrole nitrogen has an repulsion energy of 17.210 eV. Pi Bonds The Pi Bonds table (Conjugated PI System Bonds.xml) contains parameters used to correct bond lengths and bond angles for bonds that are part of a pi system. In Chem3D, additional information is used to compute the pi system portions of the MM2 force field for the pi bonds in a model. There are five fields in records in the Pi Bonds table: Bond Type, dForce, dLength, Quality, and Reference. Bond Type The Bond Type field is described by the atom type numbers of the two bonded atoms. For example, bond type 2-2 is a bond between two alkene carbons. dForce The dForce field contains a constant used to decrease the bond stretching force constant of a particular conjugated double bond. The force constant Kx for a bond with a calculated pi bond order x is: K x = K 2 - (1 - x) * dForce where K 2 is the force constant for a nonconjugated double bond, taken from the Bond Stretching table. The higher the value of K x for the bond between two pi atoms, the more difficult it is to compress or stretch that bond. dLength The dLength field contains a constant used to increase the bond length of any conjugated double bond. The bond length lx for a bond with a calculated pi bond order x is: l x = l 2 + (1 - x) * dLength where l 2 is the bond length of a non-conjugated double bond, taken from the Bond Stretching table. The higher the value of l x for the bond between two pi atoms, the longer that bond is. Record Order When sorted for Bond Type, the order of the records in the Conjugated Pisystem Bonds table is as follows: 1. Records are sorted by the first atom type number in the Bond Type field. For example, the record for bond type 2-2 is listed before the record for bond type 3-4. 2. For records where the first atom type number is the same, the records are sorted by the second atom type number in the Bond Type field. For example, the record for bond type 2- 2 is listed before the record for bond type 2-3. Electronegativity Adjustments The parameters contained in the Electronegativity Adjustments table (Electronegativity Adjustments.xml) are used to adjust the optimal Appendices <strong>ChemOffice</strong> 2005/Appendix Parameter Tables • 659 Pi Bonds
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