BS1002 carbon monoxide molecules were built and
BS1002 Biophysical ChemistrySPARTAN 1:Introduction to computational chemistry calculations of electronic structure and bondingChong Jia YunU1840984DIntroductionUsing a computer software called Spartan, users can build molecules and derive useful data such as the structure and bonding energy of the interested molecule within a short span of time.AimThe practical aims to depict bonding concepts and orbitals of molecules through the computation of organic compounds using Spartan. This is achieved by building molecules, performing calculations and analysing results.
OutlineDuring this lab session, acrylonitrile, cyclohexanone, oxygen and carbon monoxide molecules were built and analysed. Measurements of acrylonitrile and cyclohexanone were made with Equilibrium Geometry calculation using basis set 3-21G*. Measurements of oxygen and carbon monoxide molecules were made with Density Functional calculation using basis set 6-31G* except for finding energy using Energy calculation with basis set 6-31G*.Calculation records to be accounted for in report:All bond distances, total energy, dipole moment and two selected bond angles of acrylonitrile.Total energy, dipole moment and a figure of the LUMO orbital of cyclohexanone.Total energies of all states of oxygen molecule.
Total energies and bonding energy calculation of carbon monoxide and oxygen molecules.Exercise 1: Computation for acrylonitrileFigure SEQ Figure * ARABIC 1: Acrylonitrile (ball-and-spoke model)Bond distances in the moleculeBond Bond distanceC3 – C2 1.427 ÅC2 = C1 1.
319 ÅN1 ? C3 1.140 ÅC1 – H2, C1 – H3, C2 – H4 1.072 ÅBond distanceBond distance is the internuclear distance between two atoms that are covalently bonded. It is dependent on the size of atoms that are bonded and the bond order. From the above results, C3 – C2 has a greater bond distance than the bond distance between a carbon atom and a hydrogen atom even though they all have single bonds. This is because the smaller the size of the atoms, the shorter the bond distance. Since a H atom is smaller than a C atom, a H atom can be more closely bonded to a C atom as compared to two carbon atoms, thus shorter bond distance between hydrogen and carbon.
The above results also reflect the effect of bond order on bond distance. The bond distance increases as such: N1 ? C3 < C2 = C1 < C3 – C2. This is because the higher the bond order between any 2 atoms, the greater the degree of orbital overlap, the stronger the bond, the shorter the bond distance. Bond Bond orderC3 – C2 1C2 = C1 2N1 ? C3 3In this case, N1 ? C3 has the highest bond order, thus it has the shortest bond distance.Total energy and dipole momentTotal energy: -168.820401 hartreesDipole moment: 4.
03 debyeDipole momentWhen atoms of 2 different elements form a covalent bond, the bonding electrons are not equally shared between the atoms due to each atom having a different electronegativity. The more electronegative atom will attract the bonding electrons more strongly. This will result in the more electronegative atom acquiring a partial negative charge and the other atom acquiring a partial positive charge. This separation of charge results in a dipole and the formation of a polar covalent bond.
Value of two selected bond angles (between three connected atoms)Bond Bond angleC3 – C2 – H4 115.69°N1 – C3 – C2 179.89°Bond angleExercise 2: Computation for cyclohexanoneFigure SEQ Figure * ARABIC 2: Cyclohexanone (ball-and-spoke model)Total energy and dipole moment Total energy: – hartreesDipole moment: debyeLUMO orbitalFigure SEQ Figure * ARABIC 3: LUMO orbitalFigure SEQ Figure * ARABIC 4: LUMO orbitalFigure SEQ Figure * ARABIC 5: LUMO mapComment on the result with respect to reactivityExercise 3: Determine the ground state of O2 moleculeFigure SEQ Figure * ARABIC 6: O2 molecule (ball-and-spoke model)Total energy of all statesTotal energy of oxygen molecule (unpaired): -150.267048 hartreesTotal energy of oxygen molecule (paired): -150.204729 hartreesGround state of oxygenCompare the HOMO and LUMO orbitalsFigure SEQ Figure * ARABIC 7: aLUMOFigure SEQ Figure * ARABIC 8: bLUMOFigure SEQ Figure * ARABIC 9: aHOMOFigure SEQ Figure * ARABIC 10: bHOMODiscussionExercise 4: Which molecule CO or O2 is more stableFigure SEQ Figure * ARABIC 11: Carbon monoxide (ball-and-spoke model)Energy of CO: -113.270306 hartreesEnergy of O2: -150.267048 hartreesEnergy of C: -37.830235 hartreesEnergy of O: -75.036232 hartreesBonding energy of CO= -113.270306 – -37.830235 + (-75.036232)= -0.403839 hartreesBonding energy of O2= -150.267048 – -75.036232 + (-75.036232)= -0.194584 hartreesDiscussionConclusionReferences