Routines for synthesis planning

• Material balance - calculates amount and volume of compounds, including compounds obtained in a synthesis. Yields and excess are taken into consideration.
• Composition - Calculates molecular formula from element composition
• Charge estimation - Calculates atomic charges in molecule.
• Concentrations - Units of concentrations re-calculation
• Dilution of solvents - Concentrations calculations for two solutions mixing.

This command of Common Chemistry submenu is used to call routine to calculate material balance of chemical reaction. Structure or Molecular weight should be entered to calculate material balance. Material balance dialog (fig.15-1) will be arisen then.

• To build a reaction:

a) Click Build reaction button
b) Draw reaction components in Structure Editor window arisen
c) Enter Stoichiometry coefficient

• To add component of reaction click New component button, then define structure by clicking twice on structure area, then select stoichiometry coefficient. For undefined structure click button and type bruto-formula in line notation. Typing is case sensitive, parenthesis are forbidden.
• To remove component click its area then click Delete component button. Deleted component’s area will be colored by red and confirmation message will be arisen.
• To calculate yield from weight click the button and enter the weight.
• To calculate weight from yield select (type) the yield value.
• To calculate volume enter density.

 
Charge calculation procedure

The partial atomic net charges calculations are based on quantum chemical representation of bonds in the sense of the valence bond (VB) theory. The basis of the method is as follows.

Three terms constituting the partial atomic charges are considered:

(i) The first term is determined by sigma orbital interactions. In diatomic molecule A-B the charges are assumed to be proportional to the difference in electronegativities, q(A)=constant*(c(B)-c(A)), where q(A) is the charge on atom A and the c(i) are the Pauling electronegativities. The same expression for the chain of atoms A-B-...-Z in the most general form is q(A)=constant*(c(B)-c(A))*f(r), where f(r) is a monotonically decreasing function of the distance r between the atomic nuclei. In order to model molecules in a graph-theoretical manner, the distance in the molecular graph was used as an estimation of r. The Yukawa’s potential expression for f(r) was used to simulate inductive electronic effects in a quantum mechanical manner. The final expression for s charges is

where N is the number of atoms in the molecule.

(ii) The p inductive term is determined using the expression

q(i)= - Sum(j=1,N){cos(pr)*[c(i)-c(j)]*[2^(-r(i,j)/2ln2)]/r(i,j)}

(iii) In order to account for the back donation of electron density from lone pairs which interact with p system, cos(pr/2) instead of cos(pr) in Eq(ii) was used to reproduce donation to the atoms placed at even steps (second position in fluorobenzene for example) from the atom containing the lone pair.

Reference: D.B.Kireev, V.I.Fetisov, N.S.Zefirov, Approximate molecular electrostatic potential computations: applications to quantitative structure-activity relationships, J. of Molecular Structure (Theochem), 304 (1994) 143-150