Computational Chemistry Lab Part2

Introduction

Modern chemists employ calculations side by side with wet chemistry. Calculations provide insight that is unobtainable experimentally. For example, direct stability comparisons, animations of vibrational modes (observable and non-observable), electronic structure and geometric parameters. Because calculations are complex and many approximations are made, experiments are crucial in providing reference points for comparison.

  • This lab is part of a synthetic/computational lab where you investigate four coordinate phosphine complexes of nickel(II).
    • for Ni(II) complexes there is a fine balance between forming cis-square planar, trans-square planar and tetrahedral geometries.
    • factors effecting the stability of each conformer are electronic structure, ligand type, ligand donating and accepting ability, ligand size and ligand chelating ability.
    • you will be synthesising and carrying out or interpreting calculations on NiCl2(PPh3)2 and NiCl2(dppe) (dppe=1,2-bis(diphenyl phosphino)ethane).
    • this lab links directly with your first year lectures on crystal field theory, molecular vibrations, UV-Vis spectroscopy and molecular orbital theory. It also links to material in year 2 particularly; MOs in inorganic chemistry and TM Coordination and Organometallic Chemistry. Material in year 3 which build from this lab include; the Computational Lab, Advanced TM Chemistry and Symmetry and Spectroscopy.
  • Before the lab
    • revise the first lab. It is assumed you are familiar with this material.
    • context is extremely important in computational chemistry. Some core references are provided below which it is assumed you have read.
  • This lab is set-up such that:
    • in the first section you are shown how to run the calculations and interpret the results on tetrahedral and square planar complexes of [NiCl4]2-.
    • important you must work through the first section carefully and in sequence, reading the explanations, otherwise you will get lost.
    • in the second section the instructions are minimal and apply the methods and knowledge from the first section to NiCl2(PPh3)2
      • and NiCl2(dppe).
    • the lab is assessed by a blackboard based quiz and by "samples" (unique codes called DOI's that link to your calculations). You need to submit your DOI's and and complete the quizz by 5pm Tues 3rd June
  • The compounds you will make, and calculate in these the two (synthetic and computational) labs are well established, however this area of chemistry is still active and of interest today! Consider for example the following recent publications:
    • Homogeneous Hydrogenation and Isomerization of 1-Octene Catalyzed by Nickel(II) Complexes with Bidentate Diarylphosphane Ligands, Inorg. Chem., 2013, Vol 52 (14), pp 8190-8201, DOI:10.1021/ic400973t
    • Hybrid Network Formation via Halogen Bonding of the Neutral Bromo-Substituted Organic Molecules with Anionic Metal-Bromide Complexes, Cryst. Growth Des., 2012, Vol 12 (8), pp 4149-4156 DOI:10.1021/cg300654e

Help and Feedback

Help is provided during the lab hours 2-5 on the 2 days the lab is running. Demonstrators are available to provide suggestions and to give immediate feedback on your questions.

In computational chemistry it is important to understand why a calculation has failed, if you don't know why your calculation has failed, ask! Don't change something randomly and keep repeating calculations, you will not be able to complete the lab in the allotted time.

As the software is on all of the chemistry department computers you can complete calculations outside of lab hours. However, support is provided ONLY during lab hours. Any questions outside of lab hours will be redirected to demonstrators working in the lab.

Lab Outline


Assessment must be completed by 5pm Tues 3rd June
  • Outline of the quiz questions in a word document "questions" that you can fill out as you progress through the lab.
  • You should go to blackboard to complete the quizz itself, which can be found under the synthesis lab section. Here is a direct link.
  • You can stop and save your quizz answers and there is no time limit on completing the quiz except for the date by which it must be completed. You will get an instant grade after completing the quizz.
  • Template word document "DOI's" to copy and pase your DOI links (to your completed calculations) into. The links will be passed through Turnitin to ensure each computation is unique.

Part1: [NiCl4]2- (2 hrs: half reading half calculations)

Part2: NiCl2(PPh3)2 Calculations (2 hrs: mostly calculations)

  • In this section you are only given brief instructions, you are expected to use the techniques and methods introduced above and apply them to a new molecule. Your are expected (without being specifically instructed to do so) to analyse your calculations in the ways described in the first section.
  • In order to make the calculations accessible in the time limits of the lab we replace the Ph groups in PPh3 with H-atoms, thus you are going to compute NiCl2(PH3)2
  • [NiCl2(PH3)2] can be square planar or tetrahedral, in addition the square planar isomer can also have cis or trans Cl ligands.
  • Carry out the following:
    • optimise the cis and trans square planar (SP) and tetrahedral (T) structures employing B3LYP. First employ a 3-21G and then 6-31G(d) basis set.
    • we use the lower level 6-31g(d) instead of the 6-311G(d,p) basis set in order to make the calculations accessible in the time limits of the lab
    • perform a frequency and population analysis for all your structures, and confirm that each structure is a minima on the potential energy surface.
    • include the DOIs for all of your 6-31G(d) level optimisation and frequency calculations in your word file.
  • Avoid problems:
    • don't forget to add the extra keywords required with the higher level basis sets: int=ultrafine scf=(conver=9).
    • in the presence of the ligands it is best to eliminate any symmetry within these molecules, ensure that you have C1 (ie no) symmetry for your calculations.
    • do not apply the extra "opt=z-matrix" to the square planar NiCl2(PH3)2 structure, this was applied to [NiCl4]2- as a special case.
    • trouble shooting

Part3: Analysis (2 hrs: mostly interpretation)

  • In this section you undertake to analyse your calculations and complete the online quizz (a link to blackboard was provided earlier)
  • Computational chemistry is not just about "running" a calculation, in-fact computational chemists only spend about 50% of their time doing this. The other 50% of time is spent analysing and interpreting results.
  • In the synthesis lab you will make NiCl2(dppe). However, there is not enough time in this lab for you to carry out these calculations and so the final frequency/pop files files are provided for you! To be consistent the Ph rings have been replaced with H-atoms, (as you have done with NiCl2(PPh3)2) I have denoted these structures as NiCl2(dHpe).
    • tetrahedral NiCl2(dHpe): DOI
    • square planar NiCl2(dHpe): DOI
  • A number of crystal structures exist for NiCl2(PPh3)2, the particular isomer present is sensitive to co-crystalates and the method of crystallisation. The following articles report crystal structures.
    • Two of the structures are in the database and can be accessed interactively. Go to http://webcsd.ccdc.cam.ac.uk/index.php and enter the WebCSD Identifier codes for (a) square planar:DUKHEW and (b) tetrahedral: CLTPNI02 structures. A Jmol rotatable structure will appear on which you can query bond distances and angles for comparison to your own computed data.
    • Trans-square planar:
      • B.Corain, B.Longato, R.Angeletti, G.Valle; Inorg.Chim.Acta (1985), 104, 15. DOI:10.1016/S0020-1693(00)83780-9
      • Batsanov, A. S. & Howard, J. A. K. (2001). Acta Cryst. E57, m308-m309. DOI:10.1107/S1600536801008741
      • Jorunn Sletten, Julia A. Kovacs, Journal of Crystallographic and Spectroscopic Research, 1993, Volume 23, Issue 3, pp 239-241. DOI:10.1007/BF01190053
    • Tetrahedral:
  • Questions to think about (in the quiz):
    • Which geometry is the most stable?
    • What is the energy difference between the different structures?
    • examine the geometry of the various structures
    • how do the Ni-Cl and Ni-P distances compare?
    • how do computed values compare to experimental ones?
    • examine the Ni-Cl vibrational modes
    • can you identify the Ni-Cl and Ni-P stretching modes?
    • examine the MOs for the tetrahedral and square planar complexes.
    • can you identify the d orbitals?
    • can you identify the ligand based orbitals?
    • how do these relate to crystal field theory?
    • determine the HOMO-LUMO excitation energies for the most stable complexes
    • how do these relate to the colour of the complexes?
    • how do these relate to crystal field theory?
    • what is the NBO charge on the Ni and Cl atoms for this series of complexes?

Provide some feedback! optional

  • Feedback is important because it allows us to tailor your learning experience. We ask for this now, while the course is still fresh. feedback form

Extra for Experts! optional

Part5: Using a better basis set

  • We can improve the reliability of the calculations by:
    • increasing the basis set to 6-311G(d,p)
    • including the full phenyl groups in the ligands
  • However these calculations are expensive!! the files are provided below:
    • tetrahedral NiCl2(dppe) file
    • cis square planar NiCl2(dppe) file
    • tetrahedral NiCl2(PPh3)2 file to be added
    • cis square planar NiCl2(PPh3)2 file
    • trans square planar NiCl2(PPh3)2 file
  • When we include the full ligand the tetrahedral NiCl2(PPh3)2 structure is no-longer stable, the ligand interactions force NiCl2(PPh3)2 to become square planar. However both the tetrahedral and cis-square planar NiCl2(dppe) complexes are stable.

References

  • core R.G. Hayter and F.S. Humiec, Square-Planar-Tetrahedral Isomerism of Nickel Halide Complexes of Diphenylalkylphosphines, Inorg. Chem., 1965, 4 (12), pp1701-1706, DOI: 10.1021/ic50034a006
  • Joao A.S. Bomfim, Fabio P. de Souza, Carlos A.L. Filgueiras, Alexsandro G. de Sousa, Maria Teresa P. Gambardella, "Diphosphine complexes of nickel: analogies in molecular structures and variety in crystalline arrangement", Polyhedron, Volume 22, Issue 12, 15 June 2003, Pages 1567-1573. DOI:10.1016/S0277-5387(03)00263-8
  • N.N. Greenwood & A. Earnshaw, Nickel, Palladium and Platinum in Chemistry of the Elements, Butterworth Heinemann, Oxford, UK, 1998 pp 1144-1172
Top