Computational Chemistry Tutorial: 4. Conformational Analysis with TINKER
Introduction to Conformational Analysis
The structure that you built and optimized may or may not correspond to the lowest energy structure. In case of large molecules, the initial structure is likely to be different from the lowest energy conformer. For not too large flexible molecules, the lowest energy structure can be found by generating a large number of different conformations and minimizing each. Different conformers are generated by systematically or randomly altering the torsional angles in the molecule. Such analysis is commonly called the conformational analysis. Conformational analysis requires a large number of energy evaluations and is practical only using molecular mechanics force fields. In order to perform conformational analysis, the program should be able to recognize your molecule and assign suitable force field parameters. Because parameters for some molecular connectivities are missing, not all molecules can be analyzed with many common force fields.
Using TINKER for Conformational Analysis
We will be using a general-purpose molecular modeling software TINKER to perform conformational analysis of isopropanol. One of the reasons for using TINKER is that it is free and you can install TINKER on your personal Linux, Windows XP or MacOS computer. TINKER provides a suite of molecular-mechanics based modeling tools that can be executed from the Unix shell, linked to a third party program, such as molden, or launched from TINKER's own Java-based graphical user interface ffe. For example, the geometry optimization that you performed in MOLDEN in the earlier part invoked TINKER's minimize program to find a local minimum. In this part, you will learn how to run TINKER programs interactively using the Unix shell.
- Type scan on the Unix shell on the workstation. This will start one of the conformational analysis programs that comes with TINKER. The scan program searches for minima by following user-defined number of vibrational modes that correspond to torsional motions of groups.
- Give the name of the file that contains the structure of isopropanol (isopropanol.xyz).
- If a file isopropanol.key was generated during successful MOLDEN minimization, the program will ask you to confirm few run parameters. The default values are fine.
- If a file isopropanol.key is not present, the program asks for the force field file. The suitable file is at /usr/local/tinker-4.2/params/mm3.prm, then requests to confirm run settings.
- Each conformer found will be written to its own file (e.g. isopropanol.001, isopropanol.002, ....). Use the TINKER's program analyze to calculate Total Potential Energy and energy components of each conformer (this is also listed during the scan in the last column). Note that you can give the answers to questions TINKER asks on the command line. For example, to calculate the Total Potential Energy of conformer 1, type analyze isopropanol.001 E. Write down the total energy for each structure and identify the lowest energy structure. Calculate the relative energy of the higher energy structure by subtracting its energy from the energy of the lowest energy conformer.
- Examine each of the conformers found with the program MOLDEN. Type molden isopropanol.001 to analyze structure of the first conformer. Measure the HO-CH dihedral angle in each conformer. From MOLDEN, write each structure out to its own PDB file (e.g. isopropanol_cf1.pdb, isopropanol_cf2.pdb, ...) because PDB is more universal file format than TINKER's xyz.
- Close MOLDEN.
Superimposing Molecules
It is often useful to compare the three-dimensional structure of a drug candidate with the known bioactive conformer of a known ligand. One may also want to compare different conformers a molecule to see the differences between low-energy and higher energy conformers. This is often best accomplished by superimposing molecules. Molecules can be superimposed either graphically or automatically by the computer. Most commercial molecular modeling programs allow superimposing molecules. Several free programs, such as gOpenMol, PyMOL, UCFS Chimera, and MOLDEN allows users to superimpose molecules graphically. TINKER allows both automatic (via superpose program) and graphical (via the Force Field Explorer GUI) superposition of molecules. The automatic superposition in TINKER is performed using the superpose program by minimizing the RMS difference between atomic positions.
- Start MOLDEN by typing molden at the directory where the structure files (isopropanol.001, isopropanol.002,... ) are.
- Click on the Read button. A window titled Molden File Select opens.
- Select the first file (e.g. isopropanol.001). Another window titled Structures opens with the name of the open structure shown.
- Select the second file (e.g. isopropanol.002). Notice that this structure was added in the Structures window.
- Close the Molden File Select window.
- In the Structures window, click on the molecule name on the top field. The molecule that is selected in the top panel is the active structure that is also shown on graphically. Notice that you can sequentially display each of the conformers that you selected earlier.
- In the Structures window, select the first conformer in the top field, and the second conformer in the bottom Field, and click on Align. Read the instructions, then hit OK to close the instructions panel. Notice that both structures are displayed simultaneously. A copy of the active conformer (isopropanol.002) is shown in pale blue color, the inactive reference conformer (isopropanol.001) is in red.
- Use mouse to rotate (left mouse button) and translate (SHIFT-left mouse button) the active conformer such that the carbon skeletons overlap approximately. Recall that when you hit Esc once, you can move both structures; if you hit Esc again, you can only move the active structure.
- Hit Tab key on the keyboard. The cursor changes into a square. Select three pairs of atoms for automatic superposition. To select the first pair, click on the secondary carbon in the first structure and then on the equivalent carbon in the second structure. Select two more pairs of identical atoms. After selecting the last pair, MOLDEN will superimpose the structures. Rotate the superimposed structures and examine the differences.
- After alignment, the first structure contains the reference structure (isopropanol.001) and also a copy of the superimposed active structure (isopropanol.002). You can measure distances within each structure, and also between atoms in different structures. For example, you can estimate the length of displacement that a hydrogen atom undergoes upon 120 degree rotation by measuring the distance of the hydroxyl hydrogen in isopropanol.001 to the same hydrogen in isopropanol.002.
- You can delete individual structures but you cannot close the Structures window.
Locating Saddle Points
The highest point along the lowest-energy path between two stable conformers corresponds to the rotational saddle point. Knowing the energy of such saddle points is important because the height of the rotational barrier determines how rapidly the interconversion between isomers occurs. The rotation around most single bonds is rapid because the rotational barrier is fairly low. However, in some systems the rotational barrier around single bonds is high due to steric hindrance. For example, the barrier around the rotation of the carbon-carbon single bond in 1,1-binaphthyls is so high that one can separate two optical antipodes (atropomers); such molecules serve as useful chiral catalysts or materials for chiral liquid crystals.
Conformational analysis algorithms can be modified such that saddle points can be optimized. The simplest approach would be to start with a structure close to the saddle point and use the Newton-Rhapson optimization method without checking for the curvature. In TINKER, the keyword SADDLEPOINT in the key file during minimization with the newton program will signal that a saddle point is being sought. Add a keyword saddlepoint to the end of the key file (e.g. isopropanol_ecl.key) with a text editor, save the file, and then run the program newton from the Unix shell using the initial guess structure for the saddle point (e.g. isopropanol.xyz) as an input. Keep in mind that the Newton-Rhapson search is likely to converge to the nearest stationary point; there may be other saddle points that it will not find without your guidance. Alternatively, TINKER's program saddle can be used to locate a saddle point between the two minima.