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Routines for Synthesis Planning


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.

Material balance

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.

Material balance
  • 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 pic 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 pic button and enter the weight.
    • To calculate weight from yield select (type) the yield value.
    • To calculate volume enter density.

    Composition

    Composition

    This command of Common Chemistry submenu is used to call routine to calculate brutto-formula from atomic composition and molecular weight. To execute calculations type the atomic compositions and enter molecular weight in appropriate edit-controls of dialog (fig.15-2). Tick Valence check box to take into consideration valence rules. The obtained candidates may be sorted by Molecular weight or Deviation value.






    Charge estimation

    Charge estimation

    This command of Common Chemistry submenu is used to call routine to calculate atomic charge distribution. To calculate charges enter the structure to be investigated. To observe charge click desired atom or select row in a table. Two partial charge constituents - pi and sigma may be observed separately.






    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 q(i)=Sum(j=1,N){[c(i)-c(j)]/(10ln2)*r*2^r}

    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

    Concentrations

    Concentrations

    This command of Common Chemistry submenu is used to call routine to convert concentrations into another units. To do it enter the Structure or type Molecular weight first, then type density in Concentrations dialog (fig.15-4). Type the concentration value which should be recalculated into corresponding edit-control. The values of concentration in other units are observed in appropriate edit-controls.





    Dilution

    Dilution

    The Dilution command of Common Chemistry submenu is used to calculate weights of substances, volumes, and solution concentrations, which is obtained by mixing of two other solutions. Except for density, other parameters can be calculated, if relative parameters are entered in corresponding edit-controls. The calculations results can be written into text file by pressing Save button.