Chemistry in Computers: From Educational Tools to Computational Chemistry

1. Chemistry in Computers:From Educational Tools to Computational Chemistry Rituraj Kalita Sr. Lecturer in Chemistry, Cotton College, Guwahati (web-site: www.geocities.com/riturajkalita) Essay & Presentation Finalized in: June, 2006 (web-page: www.geocities.com/riturajkalita/ccworkshop.htm)

2. Chemistry in Computers – Why? • Chemistry is a science of mobile three-dimensional entities (species) such as molecules, radicals, ions & macromolecules etc., and of their mutual interactions. Two-dimensional and static figures on paper or on the blackboard can’t properly explain or represent these! • So, chemistry-education is greatly facilitated with in-computer visual models and visual software-packages, say in stereochemistry & organic-reaction mechanisms. • The branch of computational chemistry (also called theoretical chemistry) utilizes quantum mechanics etc. to theoretically calculate thermodynamic, spectroscopic & kinetic properties of chemical species, existing or even hypothetical. This job requires immense computations!

3. Visual Models & Packages: Those Pre-built for You • There remains several multimedia software packages for aiding in one’s chemistry learning, either available in the market or even freely obtainable on the internet. • These packages include visual models of molecules that can be rotated / translated by the user, and moving visual models of reactions such as of SN1 & SN2 reaction-types. • The internationally reputed chemistry textbooks for the degree & postgraduate levels also, nowadays, provide a CD containing such visual models relevant to the book, • Such a multimedia package has also been developed at the Chemistry Department of Pandu College, Guwahati!

4. Pre-built Visual Models: A Rotating Model of Iodo-Methane(may now observe the slight rotation)

5. Visual Models & Packages: Models to be Built by You • Packages discussed above do not offer a facility for creating your own visual models, or for modifying the existing ones. • In contrast, drawing packages such as ISIS/Draw and modelling packages such as ArgusLab allows you to create your own molecular-structure drawings/ models. • Any such drawing or modelling package is based on the idea that a molecule or radical can be represented by specifying the nuclear-framework only, i.e., only by the specification of the identities and positions of each of the constituent nuclei. The electrons constantly keep moving to form the electron-cloud, and so are un-specifiable. So, there, you need to draw out only the nuclear-framework.

6. The Drawing Package ISIS/Draw: Drawing Structures for Word-Processors • Ever needed to draw chemical structures using Microsoft Word or PageMaker? Or using Paint? It’s too difficult. • ISIS/Draw is meant for that purpose: to draw chemical structures for putting them into a word-processor document such as an news-essay, or into a presentation (e.g., power-point) file to present in front of a gathering. • ISIS/Draw is developed by MDL Information Systems Inc. (USA), and is available to anybody as a freeware. • To get ISIS/Draw from the internet, search for ISIS/Draw in a search engine (e.g., www.google.com), locate the home-page (it is now www.mdli.com) of MDL, and download ISIS/Draw (and its help-system)

7. The Modelling Package ArgusLab: 3-D Visual Models of Molecular Systems • ISIS/Draw does not give you a full-fledged 3-D model of the structure you’ve drawn. The picture formed can’t be rotated to understand its 3-dimensional intricacies! • So we may use ArgusLab, a leading Chemical Modelling Software, to draw in it proper visual models. • ArgusLab is developed by Planaria Software, (www.planaria-software.com), and is available for free. • ArgusLab allows us to draw structures as if on paper, substitute, move, and delete atoms, and fix distances in space. We can here grow structures with complete control of stereochemistry. Even drug-macromolecule docking could be performed in ArgusLab now .

10. The Basis Behind the Visual View: Hidden Nuclear-Framework Mathematics • In case of any visual molecular model worth this term, the view isn’t preserved in the form a image (picture) file as it would have made 3-D rotations rather impossible! • The visual model is actually preserved as a text file (with extensions .xyz, .c3d or .mop etc.) that contains list of the identities (H, C, N, O etc.) & position-coordinates of all the constituent nuclei, and also the molecular net charge. • The model-viewer software-package such as ArgusLab, ORTEP or Protein Explorer can read such data from such molecular-model text file, and then generates the visual view instantaneously to be viewed by the user.

11. The Basis Behind the Visual View: An Actual Nuclear-Framework Expression • In the following molecular model file of the .xyz type, the identities of the nuclei and their Cartesian (x,y,z) position-coordinates are kept listed (1 line for 1 nucleus) • The unit of distance for the position-coordinates is Angstrom (10–10 m) as a universally accepted convention

12. The Basis Behind the Visual View: Two Types of Framework Specifications • The above specification isn’t, however, the only possible way of specification for the molecular nuclear-framework. • Such Cartesian specifications are used in case of .xyz (XYZ type) and .c3d (Chem-3D type) files. However in the .mop (Mopac type) files etc., specification is in another way, called the z-matrix relative-coordinates specification. • In this way, a nuclear position is specified relative to a bond-distance, a bond-angle and a dihedral-angle with respect to some other (pre-specified) nuclei. This way is, obviously, closer to any chemist’s heart. • The angles are kept, by universal convention, in degrees.

13. The Basis Behind the Visual View: Z-Matrix Type Coordinates-Specification

14. The Mathematical Basis of the Visual: Computational Chemistry Flies Herefrom • For any computational chemistry computation-package to theoretically calculate the properties of any molecule or any other chemical species, the molecule or chemical species must be specified to it in a definitive manner. • The afore-mentioned mathematical aspect of the (molecular) model serves exactly this purpose. Thus the computational software knows what species to calculate. • A computational software-package (such as PC-GAMESS, a freeware) is a very powerful tool at the hand of chemists. Using it along with a PC for several hours, they can calculate properties of (not-so-big) chemical species even without doing any experiment! Even the pre-assumed molecular structure may be made better via optimization.

15. Does Computational Chemistry Work? A Study of a Silly Chemical Reaction • As we can see here, computational chemistry can really predict whether two molecules will react or not! • Prediction is faster and better for small ones. • To do that, we need to make a model of the molecule-combination (supermolecule) with the molecules far apart, then ask the package for a structure-optimization. • For larger molecules, meaningful computation requires more accurate level of computations: this means much more computer-time (hours for ~50 atom supermolecule) • To find that NH3 & BF3 will react with DE~65 kJ mol–1, forming N-B coordinate bond ~2 Ao long etc., takes only less than a minute using PC-Gamess in a Pentium-II PC

16. Computational Chemistry Working: Some Works that PC-GAMESS Does Are • Calculation of molecular energies at diff. levels of accuracy • Calculation of molecular electronic wavefunctions • Calculation of dipole and multi-pole moments • Optimization of the pre-assumed molecular structure • Calculation of vibrational normal modes, vibrational frequencies and IR-spectra intensities • Prediction of reactivity and reaction-path (with mechanism) • Calculation of electron density as a function of space

17. Demonstration of ArgusLab v4.0(Demonstration to be Performed by the Instructor) Learning: about Builder Toolkit, Add Atoms Mode & Auto Bonds in ArgusLab about drawing (non-H) main-chain with proper bond distance & bond angle Building (i.e., drawing) a molecular-structure model of butanol Showing (adding) & hiding hydrogen atoms in the above model Substituting an H-atom to change model to that of 2-methyl butanol Rotating, z-Rotating, Translating & Zooming the model Saving the molecular-structure model as an .xyz file in disk Auto-correcting the built (i.e., drawn) structural geometry of model Closing, then opening the pre-saved molecular-structure model file Viewing the above structural model with & without atom-labels Deleting an hydrogen atom to build model of a radical species Building model of 2-nitro toluene from Benzene in Builder Toolkit

18. Demonstration of PC-GAMESS v6.4 (Demonstration to be Performed by the Instructor) • Installing PC-GAMESS helper package developed by this author • Copying nuclear coordinates from a .xyz file created by ArgusLab • Replacing nuclear coordinates part in the Work2Do.inp input file • Introducing suitable 2nd column in that nuclear coordinates part • Checking this PC-GAMESS input file for format, multiplicity etc. • Running PC-GAMESS with this modified & checked input file • Searching the output file for the final energy (find Total Energy=) • Searching output to observe optimization (find Coordinates of all) • Copying the nuclear coordinates from the last-optimized geometry • Replacing nuclear coordinates to modify .xyz file by pasting these • Removing the odd 2nd column and saving the corrected .xyz file • Opening this .xyz file with ArgusLab to view optimized structure

19. Thank You for Patient Viewing!