Chem3D Users Manual - CambridgeSoft

More documents

Recommendations

Info

Administrator bond length between two atoms when one of the atoms is attached to a third atom which is electronegative. For example, the carbon-carbon single bond length in ethane is different than that in ethanol. The MM2 parameter set has only a single parameter for carbon-carbon single bond lengths (1.523Å). The use of electronegativity correction parameters allows the C-C bond in ethanol to be corrected. The electronegativity parameter used in the Electronegativity Corrections table is the 1-1-6 angle type, where atom type 1 is a C Alkane and atom type 6 is an O Alcohol. The value of this parameter is -0.009Å. Thus the C-C bond length in ethanol is 0.009Å shorter than the standard C-C bond length. MM2 Constants The MM2 Constants table (MM2 Constants.xml) contains parameters which Chem3D uses to compute the MM2 force field. Cubic and Quartic Stretch Constants Integrating the Hooke's Law equation provides the Hooke's Law potential function which describes the potential energy of the ball and spring model. The shape of this potential function is the classical potential well. dV –------ = F= – dx dx The Hooke's Law potential function is quadratic, thus the potential well created is symmetrical. The real shape of the potential well is asymmetric and is defined by a complicated function called the Morse Function, but the Hooke's Law potential function works well for most molecules. x x Vx ( ) = dV= k xdx= ∫° 0 ∫° 0 1 --kx 2 2 Certain molecules contain long bonds which are not described well by Hooke's Law. For this reason the MM2 force field contains a cubic stretch term. The cubic stretch term allows for an asymmetric shape of the potential well, thereby allowing these long bonds to be handled. However, the cubic stretch term is not sufficient to handle abnormally long bonds. Thus the MM2 force field contains a quartic stretch term to correct for problems caused by these abnormally long bonds. Type 2 (-CHR-) Bending Force Parameters for C-C-C Angles -CHR- Bending K for 1-1-1 angles -CHR- Bending K for 1-1-1 angles in 4-membered rings -CHR- Bending K for 22-22-22 angles in 3-membered rings These constants are distinct from the force constants specified in the Angle Bending table. The bending force constant (K) for the 1-1-1 angle (1 is the atom type number for the C Alkane atom type) listed in the MM2 Angle Bending parameters table is for an alkane carbon with two non-hydrogen groups attached. Angle bending parameters for carbons with one or two attached hydrogens differ from those for carbons with no attached hydrogens. Because carbons with one or two attached hydrogens frequently occur, separate force constants are used for these bond angles. The -CHR- Bending K for 1-1-1 angles allows more accurate force constants to be specified for the Type 1 (-CH2-) and Type 2 (-CHR-) interactions. In addition, the -CHR- Bending K for 1-1-1 angles in 282• Parameter Tables CambridgeSoft MM2 Constants
4-membered rings and the -CHR- Bending K for 22-22-22 angles (22 is the atom type number for the C Cyclopropane atom type) in 3-membered rings differ from the aforementioned -CHR- Bending K for 1-1-1 angles and thus require separate constants to be accurately specified. Stretch-Bend Parameters X-B,C,N,O-Y Stretch-Bend interaction force constant X-B,C,N,O-H Stretch-Bend interaction force constant X-Al,S-Y Stretch-Bend force constant X-Al,S-H Stretch-Bend force constant X- Si,P-Y Stretch-Bend force constant X-Si,P-H Stretch-Bend force constant X-Ga,Ge,As,Se-Y Stretch-Bend force constant The stretch-bend parameters are force constants for the stretch-bend interaction terms in the prior list of elements. X and Y represent any nonhydrogen atom. When an angle is compressed, the MM2 force field uses the stretch-bend force constants to lengthen the bonds from the central atom in the angle to the other two atoms in the angle. For example, the normal C-C-C bond angle in cyclobutane is 88.0°, as compared to a C-C-C bond angle of 110.8° in cyclohexane. The stretch-bend force constants are used to lengthen the C-C bonds in cyclobutane to 1.550Å, from a C-C bond length of 1.536Å in cyclohexane. Sextic Bending Constant Sextic bending constant ( * 10 ** 8) Chem3D uses the sextic bending constant to increase the energy of angles with large deformations from their ideal value. Dielectric Constants Dielectric constant for charges Dielectric constant for dipoles The dielectric constants perform as inverse proportionality constants in the electrostatic energy terms. The constants for the charge and dipole terms are supplied separately so that either can be partially or completely suppressed. The charge-dipole interaction uses the geometric mean of the charge and dipole dielectric constants. For example, when you increase the Dielectric constant for dipoles, a decrease in the Dipole/Dipole energy occurs. This has the effect of reducing the contribution of dipole-dipole interactions to the total steric energy of a molecule. Electrostatic and van der Waals Cutoff Parameters Cutoff distance for charge/charge interactions Cutoff distance for charge/dipole interactions Cutoff distance for dipole/dipole interactions Cutoff distance for van der Waals interactions These parameters define the minimum distance at which the fifth-order polynomial switching function is used for the computation of the listed interactions. MM2 Atom Types The MM2 Atom Types table (MM2 Atom Types.xml) contains the van der Waals parameters used to compute the force field for each atom in your model. Each MM2 Atom Type record contains eight fields: Atom type number, R*, Eps, Reduct, Atomic Weight, Lone Pairs, Quality, and Reference. Atom type number The Atom Type number field is the atom type to which the rest of the MM2 Atom Type Parameter record applies. The records in the MM2 Atom Type table window are sorted in ascending order of Atom Type Atom type number. Appendices ChemOffice 2005/Appendix Parameter Tables • 283 MM2 Atom Types
Page 1:
ChemOffice.Com ® ChemOffice ® Che
Page 4 and 5:
License Information ChemOffice, Che
Page 6 and 7:
· Licensed users of ChemOffice Ent
Page 8 and 9:
computer, except as provided below.
Page 10 and 11:
Q: IS IT OK TO COPY MY COLLEAGUE’
Page 12 and 13:
A Guide to CambridgeSoft Manuals An
Page 14 and 15:
Administrator Setting Molecular Sur
Page 16 and 17:
Administrator Methods Available in
Page 18 and 19:
Administrator Defining Atom Types.
Page 20 and 21:
Administrator • CambridgeSoft
Page 22 and 23:
Administrator provides a balance be
Page 24 and 25:
Administrator the activation each t
Page 26 and 27:
Administrator The following table d
Page 28 and 29:
Administrator • Stereo Pairs—A
Page 30 and 31:
Administrator • Bond Angles—Dis
Page 32 and 33:
Administrator The Building Toolbar
Page 34 and 35:
Administrator The Calculation Toolb
Page 36 and 37:
Administrator 1. Right-click in the
Page 38 and 39:
Administrator • In the Model Sett
Page 40 and 41:
Administrator modes and color setti
Page 42 and 43:
Administrator 30 •Chem3D Basics C
Page 44 and 45:
Administrator 2. Click the ChemDraw
Page 46 and 47:
3. Move the pointer over the C-C bo
Page 48 and 49:
Administrator Add serial numbers an
Page 50 and 51:
Administrator 5. Press the Enter ke
Page 52 and 53:
. Administrator b. From the Structu
Page 54 and 55:
Administrator In the Measurements t
Page 56 and 57:
A molecule of Epinephrine appears.
Page 58 and 59:
Administrator Tutorial 7: Docking M
Page 60 and 61:
Administrator To save the iteration
Page 62 and 63:
The allyl radical, CH 2 =CHCH 2·,
Page 64 and 65:
Administrator Determine the raw spi
Page 66 and 67:
Administrator atoms are relatively
Page 68 and 69:
To change the structural display ty
Page 70 and 71:
Administrator When sizing by partia
Page 72 and 73:
Administrator Depth Fading3D enhanc
Page 74 and 75:
• Select Parallel to rotate the r
Page 76 and 77:
Administrator • From the Computat
Page 78 and 79:
Administrator Surface Type Solid De
Page 80 and 81:
Administrator 2. Adjust the slider
Page 82 and 83:
Administrator Density surface is ca
Page 84 and 85:
Administrator 72 •Displaying Mode
Page 86 and 87:
Administrator The following table d
Page 88 and 89:
Administrator When Correct Atom Typ
Page 90 and 91:
Administrator To use the same text
Page 92 and 93:
Administrator Example 2. Building a
Page 94 and 95:
Administrator copied into blank tab
Page 96 and 97:
Administrator 3. Type the atom type
Page 98 and 99:
Administrator Clean Up Structure or
Page 100 and 101:
Setting Serial Numbers this step, y
Page 102 and 103:
Administrator Refining a Model Afte
Page 104 and 105:
Administrator Selecting Multiple At
Page 106 and 107:
Administrator New in Chem3D version
Page 108 and 109:
Administrator Dragging moves atoms
Page 110 and 111:
Administrator 3. Hold down the Shif
Page 112 and 113:
To position a plane in your model p
Page 114 and 115:
Administrator • Second Positioned
Page 116 and 117:
Administrator For example, consider
Page 118 and 119:
Administrator If you want to displa
Page 120 and 121:
Administrator Example: To examine t
Page 122 and 123:
Administrator Chem3D provides two o
Page 124 and 125:
Administrator change a property. By
Page 126 and 127:
Administrator To add to a group: 1.
Page 128 and 129:
To stop spinning: • On the Movie
Page 130 and 131:
Administrator If you want to … Th
Page 132 and 133:
Administrator EPS The PostScript fi
Page 134 and 135:
If you want the file to … Then cl
Page 136 and 137:
Molecular Design Limited MolFile (.
Page 138 and 139:
Administrator 7. Leave the last lin
Page 140 and 141:
Administrator 128•Printing and Ex
Page 142 and 143:
Administrator • Semiempirical Ext
Page 144 and 145:
Method Type Advantages Disadvantage
Page 146 and 147:
Administrator • A single point ca
Page 148 and 149:
Administrator • Molecular mechani
Page 150 and 151:
Administrator constant), while θ 0
Page 152 and 153:
Administrator The van der Waals int
Page 154 and 155:
Administrator 6. The modified value
Page 156 and 157:
the same wave function and a consta
Page 158 and 159:
Administrator A variety of other ba
Page 160 and 161:
Administrator Molecular wave functi
Page 162 and 163:
Administrator activation barriers.
Page 164 and 165:
3. From the Calculations menu, poin
Page 166 and 167:
minimizing a second model, the mini
Page 168 and 169:
Administrator move to lower the ene
Page 170 and 171:
. Administrator Molecular Dynamics
Page 172 and 173:
Administrator If you want to … Th
Page 174 and 175:
Administrator The Compute Propertie
Page 176 and 177:
Administrator To run a previously c
Page 178 and 179:
Administrator The procedures assume
Page 180 and 181:
Administrator improvements in each
Page 182 and 183:
Administrator • Overall errors in
Page 184 and 185:
Administrator The following table c
Page 186 and 187:
Administrator TRIPLET QUARTET QUINT
Page 188 and 189:
Administrator Chemical symbol ++ ba
Page 190 and 191:
Administrator 4. Click Run. A new m
Page 192 and 193:
Administrator Minimizing Energy Min
Page 194 and 195:
Administrator criteria, to optimize
Page 196 and 197:
Administrator 6. Hold down the S ke
Page 198 and 199:
Administrator Dipole Moment The dip
Page 200 and 201:
Administrator Molecular Surfaces Mo
Page 202 and 203:
The following table contains the ke
Page 204 and 205:
Administrator 3. Click in the model
Page 206 and 207:
Keyword Description 7. On the Prope
Page 208 and 209:
Administrator Hyperfine Coupling Co
Page 210 and 211:
Administrator 198•MOPAC Computati
Page 212 and 213:
Administrator If you want to … re
Page 214 and 215:
Administrator In the Results In tex
Page 216 and 217:
Administrator Repeating a Gaussian
Page 218 and 219:
Property Description Property Descr
Page 220 and 221:
Property Description Error Message
Page 222 and 223:
Administrator Property Electronic E
Page 224 and 225:
Administrator To specify the calcul
Page 226 and 227:
Administrator 3. Click Open. The ap
Page 228 and 229:
Administrator • Server—limits t
Page 230 and 231:
Administrator To perform property c
Page 232 and 233:
The Step 4 of 4 dialog box appears.
Page 234 and 235:
Administrator • From the ChemOffi
Page 236 and 237:
Administrator Accessing the Online
Page 238 and 239:
Administrator To find a structure t
Page 240 and 241:
Administrator 228• Accessing the
Page 242 and 243:
Administrator Performance Below are
Page 244 and 245: Administrator Defining Substructure
Page 246 and 247: Administrator If an atom can be ass
Page 248 and 249: Key Drag Shift+Drag Administrator Q
Page 250 and 251: Administrator 238• Keyboard Modif
Page 252 and 253: Administrator Example 3 In Example
Page 254 and 255: Administrator 14 13 H 2.197 -0.8229
Page 256 and 257: Administrator Connection tables by
Page 258 and 259: Administrator FORTRAN Formats The F
Page 260 and 261: 5 6 1.11606 3 109.41 5 109.41 -1 21
Page 262 and 263: Administrator 41 4 1 0 0 0 0 0 0 0
Page 264 and 265: Administrator 32 3 12 1 0 0 0 33 3
Page 266 and 267: Administrator 13 * 3D displacement
Page 268 and 269: Administrator The field value for C
Page 270 and 271: Administrator Line 4e: C 1.53597 1
Page 272 and 273: Administrator CONECT 4 2 9 10 11 CO
Page 274 and 275: Administrator COMPND ATOM HETATM CO
Page 276 and 277: Administrator Line 56 -2794 21139 6
Page 278 and 279: Administrator 7 2 10 1 8 3 6 1 9 3
Page 280 and 281: Administrator Line 16 6 C -0.559 1.
Page 282 and 283: Administrator 12. Line 30, “@BOND
Page 284 and 285: Parameter Table Use Parameter Table
Page 286 and 287: Administrator 3. Type the informati
Page 288 and 289: Administrator Geometry The geometry
Page 290 and 291: Administrator KS The KS, or bond st
Page 292 and 293: Administrator one attached hydrogen
Page 296 and 297: Administrator R* The R* field is th
Page 298 and 299: Administrator The V1 torsional cons
Page 300 and 301: Administrator VDW Interactions The
Page 302 and 303: Administrator Editing Parameters Yo
Page 304 and 305: Administrator 6. The pi molecular o
Page 306 and 307: Administrator Adding Parameters to
Page 308 and 309: Administrator fragments 84 paramete
Page 310 and 311: Administrator CC1 see Cartesian coo
Page 312 and 313: Administrator Copy As Bitmap comman
Page 314 and 315: Administrator Examining angles, tut
Page 316 and 317: Administrator density 67 editing 67
Page 318 and 319: Administrator editing 107 non-bonde
Page 320 and 321: Administrator repeating jobs 178 RH
Page 322 and 323: Administrator Rectification, when d
Page 324 and 325: Administrator all atoms 95 atoms or
Page 326 and 327: Administrator Translucent surface t
Page 328 and 329: Desktop Software Enterprise Solutio
Page 330 and 331: SOLUTIONS Enterprise Solutions APPL
Page 332 and 333: Desktop to Enterprise Solutions Che
Page 334 and 335: SOFTWARE E-Notebook Ultra Ultimate
Page 336 and 337: SOFTWARE ChemDraw Ultra Ultimate Dr
Page 338 and 339: SOFTWARE Chem3D Ultra Ultimate Mode
Page 340 and 341: SOFTWARE ChemFinder/Word • Search
Page 342 and 343: SOFTWARE The Merck Index • Encycl
Page 344 and 345:
SOLUTIONS •Development and deploy
Page 346 and 347:
SOLUTIONS •Adds chemical data typ
Page 348 and 349:
MANAGEMENT •Custom organization o
Page 350 and 351:
MANAGEMENT • Indexes chemical str
Page 352 and 353:
MANAGEMENT • E-Notebook Enterpris
Page 354 and 355:
DISCOVERY • Accessed through your
Page 356 and 357:
DISCOVERY • Integrated with Regis
Page 358 and 359:
DISCOVERY • Reagent lists can be
Page 360 and 361:
DISCOVERY •Effectively manages da
Page 362 and 363:
DISCOVERY • Catalog driven data m
Page 364 and 365:
DATABASES • Fully structure-searc
Page 366 and 367:
DATABASES • Encyclopedic referenc
Page 368 and 369:
DATABASES • Extensive collection
Page 370:
SERVICES · Business Case Developme
Page 375:
CS ChemOffice ® Desktop to Enterpr
show all

Chem3D Users Manual - CambridgeSoft

Create successful ePaper yourself

Delete template?

Save as template?