Computer Modeling of Organic Compounds

Transcription

1 Computer Modeling of Organic Compounds Molecular Modeling of Organic Compounds Structure, Energy, and Conformation 1

2 Models and Modeling Chemists must use models to conceptualize the structures and properties of chemicals since we cannot visualize molecules and chemical systems directly. Models used by chemists range from simple physical models (e.g. ball and stick structural models) to complex mathematical equations (rate equations, wave functions, statistical calculations). Visualization With Computers Recent advances in computers and computer graphics make it possible to represent the results of the mathematical calculations on chemical systems as visual computer-generated representations. Today, you are going to use laptop computers to calculate dipole moments of simple molecules, and conformational energies of some alkanes and cycloalkanes. 2

3 Conformational Calculations The computer will use a mathematical model called molecular mechanics to calculate strain energies for a given molecular structure. In molecular mechanics, strain energy equals the sum of bond-stretching strain, bond-angle strain, torsional strain, and steric strain. The parameters for these strain calculations have been derived from comparisons with known molecules. E strain = E stretch + E angle +E torsion + E steric Conformational Variation After calculating the total strain for a particular structure, the computer can then vary the structure slightly (bond angles or lengths, dihedral angles) and recalculate the energy. If the energy is lower than that for the first structure, the modified structure is accepted and another structural variation is made. 3

4 Energy Minima Multiple repeats of this structural variation and calculation of strain energy will lead to a structure in which any structural variation leads to a higher energy this structure is an energy minimum on the multidimensional structural surface. It is important to note that the computer cannot distinguish between a local minimum and the global minimum. Therefore, it may take multiple calculations starting from different starting points to ensure finding a global minimum. Energy Minima A E n e r g y * Local minimum * B Global minimum Structure variation (bond angles, length, etc.) 4

5 Energy Minima We can also put constraints on a calculation such as a restricting a particular dihedral angle to a single value and use the computer to vary all other structural parameters to calculate a lowest energy structure given the constraint. We will use this method to determine structures and energies for a large number of specific dihedral angles for the C 2 -C 3 bond of butane. Visualization of Results The results of molecular modeling can be presented as graphs of energy vs. some structural parameter, or as computergenerated representations. We can use the computer to report values for bond angles, bond lengths, and dihedral angles of the computed structures. This analysis allows us to acquire a feel for which bond distortions cost the most energy (dihedral angle, bond angles, bond lengths, etc.). 5

6 Visualization of Results Visualization of Results The result of these computer calculations is not reality, but it is a model that usually gives us more information than a ball-and stick model. It is also important to remember that a real molecule is not a single specific structure. It is continually undergoing structural changes as a result of bond vibrations, bond rotation, etc. 6

7 Experimental Procedure Our objective is for you to obtain results from numerous computer calculations to allow you to make some comparisons and structure analyses. Therefore, we are not expecting you to become experts with the Spartan molecular modeling program. We are going to give you step-by-step instructions to follow at the beginning. With later examples, we expect you to be able to repeat these same steps. Experimental Procedure, Cont. You will work in groups of two (with one group of three if there is an odd number of students in the lab). One student should operate the computer, and one should read the instructions. Change places during the lab period. Be very careful with the computers, they are much more expensive than a beaker or filter flask. 7

8 Computer Use Make sure your computer is connected to the network. You should see an icon at the lower right of your screen that shows two monitors with a blue globe at the lower right. On the worksheet carbon numbers (C-1, C- 3, etc.) refer to the carbon numbers in the IUPAC name. The computer will number carbons arbitrarily. DO NOT use the computer numbers. Experimental Procedure, Cont. There are FIVE parts to this experiment. Results from ALL five parts need to be completed BEFORE you leave the lab today. There will be 6 pages of worksheet information to fill out in lab. You will be able finish on time if you work diligently through the instructions. Your TA must initial your worksheet and each of your printouts before you leave lab. 8

9 Post-lab The post-lab Results and Discussion and post-lab Questions are combined in your lab Manual (incorrectly labeled In-lab Observations) Complete these components and turn in both your Worksheet and Post-lab as your lab report Experimental Procedure - M.P. Most of you need to take a melting point of your recrystallized product from last week. Both partners should take a break from the computer to take melting points when a Mel-Temp is available. Not everyone can wait until the end of lab to attempt to get a melting point. 9

10 Experimental Procedure - M.P. IMPORTANT. DO NOT WORK WITH CHEMICALS AROUND THE COMPUTERS! Mel-Temps are available at the back of the room. Prepare your m.p. capillaries at the front or back of the room, NOT at a workstation. Clean-up Dispose of your used melting point tubes in the glassware box at the front of the lab. Dispose of your recrystallization product in the appropriately labeled bottle in the hood. 10

11 Clean-up Recrystallization products IMPORTANT!!!!!!!! Do NOT dispose of ANY chemicals or filter papers that have been in contact with chemicals into the trash bins!!!! Any TA observing this should deduct points for a safety violation. You endanger the health of custodial workers when you do this. No Chemicals into trash!!! 11