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calculation of one or all of the properties mentioned above. ACD/ChemSketch User's Guide 90 Calculating Macroscopic Properties Once chosen, the calculated property is displayed in a Calculation Result dialog box. The text content of this can be immediately pasted on the ChemSketch screen if desired by clicking on the Copy to Editor button. For example, choosing Tools>Calculate& >All properties for benzoic acid will show the following dialog: 11.2.2 Automatic Display on Status Bar It is also possible to view the macroscopic property directly on the status bar as shown: Just click on the box to the far right on the status bar and choose the property desired. By default, this is set to molecular weight. In the example shown, the dielectric constant, µ20, has been specified. ACD/ChemSketch User s Guide 91 Calculating Macroscopic Properties 11.3 Algorithms for Calculating Macroscopic Properties At the heart of the additive-constitutive calculation algorithm of all physico-chemical properties in ChemSketch lies the presumption that these properties can be estimated using additive atomic or group increments. Apart from molecular weight (MW), which is trivial to calculate, the algorithms may be divided into three general groups: " basic macroscopic properties: Molar Volume (MV), Molar Refractivity (MR) and Parachor (Pr); " derived macroscopic properties: density (d) , refractive index (n) and surface tension ( ); and " the dielectric constant (Permittivity). Basic macroscopic properties such as Molar Volume (MV), Molar Refractivity (MR) and the Parachor (Pr) are calculated first for the input structure. The atomic additive increments in such an algorithm depend on the bonds (single, double, aromatic, etc.) of this atom and on neighboring atoms. ChemSketch rapidly analyzes the input structure to determine the class of each atom, i.e., whether it is cyclic, aromatic, aliphatic, etc. The prediction algorithms for density (d) , refractive index (n) and surface tension ( ) are founded on well known physico-chemical formula which can be found in most physical chemistry textbooks. These express d, n and as functions of MV, MR or Pr. Once the MV, MR or Pr, have been predicted by additive means, it is straightforward to predict d, n and using these formula. The determination of the additive-constitutive atomic increments for MV, MR and Pr were obtained internally by ACD using large experimental databases relating structure to density, refractive index and surface tension. The MV, MR and Pr were recalculated from d, n and . These parameters are proprietary information of Advanced Chemistry Development. The prediction of the dielectric constant (permittivity) resembles very closely the prediction of Boiling Point, which is a separate ACD product from ChemSketch. Senior scientists at ACD discovered an additive function, which relates the dielectric constant to other macroscopic properties which can be additively treated, such as MV. Once this relationship was discovered, the additive-constitutive atomic increments for this function were obtained using large databases consisting of molecular structures and their observed dielectric constants. Using the function and estimated MV for the input structure, its dielectric constant can be quickly predicted. 11.3.1 Molar Volume, MV By definition, MW MV = . d ChemSketch calculates molar volume from additive increments. The additive atomic increments were obtained using a database of density and calculated MW. ACD/ChemSketch User s Guide 92 Calculating Macroscopic Properties 11.3.2 Molar Refractivity, MR The Lorentz-Lorenz equation relates refractive index, density, and refractive index: n2 - 1 MW MR = Å" 2 n + 2 d ChemSketch calculates molar refractivity from additive increments. The additive atomic increments were obtained using a database of density, refractive index and calculated MW. 11.3.3 Parachor, Pr By definition, MW ëø öø 14 Pr = ìø ÷ø íø øø d ChemSketch calculates the parachor from additive increments. The additive atomic increments were obtained using a database of density, surface tension, and calculated MW. 11.3.4 Density, d By definition, MW d = MV ChemSketch calculates the density from MW and the calculated molar volume (see above). 11.3.5 Refractive Index, n By the Lorentz-Lorenz equation, 2 Å" MR + MV n = MV - MR ChemSketch calculates the refractive index from the molar volume and molar refractivity, both of which are calculated as above. 11.3.6 Surface Tension, By definition, Pr 4 ëø öø = ìø ÷ø íø øø MV ChemSketch calculates the surface tension from calculated MV (see above) and calculated Pr (see above). ACD/ChemSketch User s Guide 93 Calculating Macroscopic Properties 11.3.7 Dielectric Constant, (Permittivity) ( ) f = f ( MV , AdditiveFunction) ChemSketch calculates the dielectric constant from calculated MV (see above) and a proprietary empirical additive function. 11.3.8 Polarizability This property is calculated from the Molar Refractivity (MR) (see Section 11.3.2) as follows: Polarizability = 0.3964308 Å" MR 11.3.9 Monoisotopic, Nominal and Average Mass Monoisotopic mass (Mmi) is the exact mass of the most abundant stable isotope that can occur naturally. Nominal Mass (Mn) is the sum of the approximated monoisotopic masses of the elements forming the molecule. Average Mass (Mav) is the calculated mass of a particle based on the atomic weights of the elements from which it is composed. 11.4 Correlation Statistics with Experimental Data 11.4.1 Distribution of Molar Refractivity Prediction Error 120 100 80 60 40 20 -1.3 -0.9 -0.5 -0.1 0.3 0.7 Vertical scale: Number of Tested Structures Horizontal scale: ACD Molar Refractivity Estimation Error Number of tested structures: 592 MRexp = 0.99901(±0.00067) MRcalc + 0.026(±0.025) R=0.999867, StD=0.23 ACD/ChemSketch User s Guide 94 Calculating Macroscopic Properties 11.4.2 Distribution of Molar Volume Prediction Error 140 120 100 80 60 40 20 -12 -8 -4 0 4 8 12 Vertical scale: Number of Tested Structures Horizontal scale: ACD/Molar Volume Estimation Error Number of tested structures: 671 MVexp = 0.9989(±0.0020) MVcalc + 0.18(±0.29) R=0.998626, StD=2.74 11.4.3 Distribution of the Parachor Prediction Error 90 80 70 60 50 40 30 20 10 -12 -8 -4 0 4 8 12 Vertical scale: Number of Tested Structures Horizontal scale: ACD/Parachor Estimation Error Number of tested structures: 377 Prexp = 0.9978(±0.0015) Prcalc + 0.68(±0.46) R=0.99958, StD=3.11 ACD/ChemSketch User s Guide 95 Calculating Macroscopic Properties 11.4.4 Distribution of the Refractive Index Prediction Error 180 160 140 120 100 80 60 40 20 -0.07 -0.05 -0.03 -0.01 0.01 0.03 0.05 Vertical scale: Number of Tested Structures Horizontal scale: ACD/Refractive Index Estimation Error Number of tested structures: 665 n20exp = 0.98035(±0.0073) n20calc + 0.028(±0.011) R=0.982, StD=0.012 11.4.5 Distribution of the Density Prediction Error 180 160 140 120 100 80 60 40 20 -0.16 -0.08 0.00 0.08 0.16 Vertical scale: Number of Tested Structures Horizontal scale: ACD/Density Estimation Error Number of tested structures: 671 d20exp = 0.9947(±0.0036) d20calc + 0.0052(±0.0036) R=0.995683, StD=0.028 ACD/ChemSketch User s Guide 96 Calculating Macroscopic Properties 11.4.6 Distribution of the Surface Tension Prediction Error 100 90 80 70 60 50 40 30 20 10 -12 -8 -4 0 4 8 12 Vertical scale: Number of Tested Structures Horizontal scale: ACD/Surface Tension Estimation Error Number of tested structures: 432 st20exp = 0.998(±0.018) st20calc + 0.08(±0.53) R=0.934720, StD=2.84 11.4.7 Distribution of the Dielectric Constant (Permittivity) Estimation Error 30 25 20 15 10 5 -0.25 -0.125 0 0.125 0.25 Vertical scale: Number of Tested Structures Horizontal scale: Dielectric constant (Permittivity) Estimation Error Number of tested structures: 85 Note: Derived only for hydrocarbons µexp = 1.005(0.033)µexp 0.013(0.072) R=0.9588, StD=0.079 ACD/ChemSketch User s Guide 97 12. Special Function Keys 12.1 Objectives The ChemSketch Window is an extremely versatile molecular structure input editor. For this [ Pobierz caÅ‚ość w formacie PDF ] |