Final Project Assignment

Transcription

1 Chemistry Fall 2015 Dr. Jean M. Standard September 30, 2015 Final Project Assignment The final project for the Computational Chemistry course consists of a journal-style research paper describing computations carried out on a molecular system or systems of your choice. The final project is an individual project and is worth 150 points. For the final project, you must use at least one of the major computational techniques covered in class as part of your study. In addition, you must have some literature or experimental results with which to compare your computational study. The topic of your project must be approved by Dr. Standard to make sure that it is computationally tractable in the time allotted. IMPORTANT DATES: Deadline for Project Approval: 6:00 PM, WEDNESDAY, NOVEMBER 4, Final Project Due Date: 5:30 PM, MONDAY, DECEMBER 7, FINAL PROJECT SPECIFICS Selection of Topic and Computational Methods The molecular system chosen for the project may be any system that interests you. You may be interested in a particular molecular system or chemical reaction from an undergraduate or graduate research project, or even from another class. You may select one molecule to study, or you may look at trends in a family of molecules, or you might choose a specific chemical reaction. In any case, you should consider what you want to learn about the system or reaction in order to help plan your computational approach. Some sample topics from previous semesters are listed on page 4 for your information. The major computational techniques that have been or will be covered in class include molecular mechanics, conformation searching, molecular orbital methods, and molecular dynamics. The computational methods that you select to perform your project will depend on the type of system you are studying and what you want to learn about it. For large molecules, only molecular mechanics or dynamics may be appropriate. For small to moderately-sized systems, you might want to compare molecular orbital results to molecular mechanics. A study involving a molecule with a number of flexible torsions may require conformation searching to be carried out. If you are interested in a specific chemical reaction, molecular orbital techniques might be the most appropriate methods to employ. In some cases, we have covered only the basics of a particular technique in class. For example, semiempirical molecular orbital methods will only be briefly discussed in class; however, these methods allow the application of quantum techniques to somewhat larger molecular systems. If the system of interest falls in this range, individual assistance will be provided so that you can perform the required calculations. Results for Comparison To go along with selection of your molecular system of interest, you also must ensure that there are available results from previous experimental or computational studies for comparison. This may be in the form of literature articles on the same or similar molecular systems, or it may be in the form of unpublished experimental spectra and/or other data from work carried out in your research group.

2 2 Approval of Topic Once you have selected a molecular system, a computational approach, and have verified that results are available with which to compare your study, fill out the approval form on the last page of this handout and submit it to be approved. Dr. Standard will get back to you within a few days with an approval or further suggestions. The main concern is that there is enough computing for you to do but that the amount of computing is not too large for you to handle. If the amount of computing is deemed to be too much, a smaller related system may be suggested. If the amount of computing needs to be increased, further studies may be advised. The Journal-Style Research Paper The grade you receive on the final project will be based upon the research paper you submit. The paper should be written in journal format, and should be a minimum of 10 double-spaced pages in length (maximum 1" margins) using a 12-point Times Roman font. A maximum of one page total of tables may be included in the page count (more tables may be included; however, they will not be included in the page count). In addition, figures will not be included in the page count, though you may include as many as you like. For examples of journal-style papers, see current issues of J. Phys. Chem. A brief description of the required content, along with the grading scale, follows. Paper Format The final project paper should consist of the following sections: 1. TITLE Include a descriptive title of your project. 2. ABSTRACT Include a brief description of the project, the methods used, and the results obtained. A sentence or two summarizing the main comparisons or conclusions should be given. The abstract generally should be brief, no more than one paragraph (a few sentences). 3. INTRODUCTION The introduction should outline the problem you studied and why you were studying it. A literature survey should be presented which describes previous computational or experimental work related to your project. Note that the literature survey does not have to be exhaustive. Use recent references rather than older ones if available, especially if they are previous computational studies. A range of 4-8 references related to your project is acceptable for the literature survey, but at least one of them must be computational in nature. 4. COMPUTATIONAL PROCEDURES/METHODS The computational methods that you employed in your study should be presented. Include a discussion of why you chose the particular methods you did. Describe parameters used, optimization procedures, etc. For molecular mechanics methods, this would include the force field used, the method employed for energy minimization, and the gradient tolerances. For conformation searching, this would include the number of flexible torsions, search methodology, and fold rotation. For molecular orbital methods, this would include the basis set and level of theory used. For molecular dynamics, this would include the force field, time step, total simulation time, temperature, and heating and cooling times. (This section takes the place of an "Experimental" section.) 5. RESULTS The Results section should include a presentation of your major results. Include figures and tables where appropriate. Remember that in a journal, there is space for only the most significant results, so tabulating every single number that you obtained in the calculations is not appropriate. Select those results that answer the research question you posed. Also, please keep in mind that only one page of tables and none of the figures will be counted in the 10-page minimum; this is not meant to downplay the role of graphical or tabular representations of scientific data and results, but rather to ensure that there is a substantive amount of written material to go along with the figures and tables.

3 3 6. DISCUSSION/CONCLUSIONS Include a comparison with previous literature results (either experimental or computational or both) and/or work being done currently in your research group. Discuss the validity of your results, taking into account any approximations in the methods chosen. Try to answer and explain the research questions that you posed in the introduction. 7. REFERENCES References should be keyed to the text. Follow the format given in journals such as J. Phys. Chem. or J. Org. Chem. for reference citations. Grading Scale The final project paper will be graded on the following scale: Abstract: 10 Introduction: 40 Procedures Section: 20 Results and Presentation of Results: 40 Discussion/Conclusions: 30 References: 10 Total: 150

4 4 Some Previous Final Project Topics Computational studies of chrysoporphyrin and corannuleneporphyrin (MO) Conformational analysis of muironolide A (MM, Conf) DFT studies of gas phase oxyacids (HClO 4, H 2 SO 4, and H 3 PO 4 ) and oxyacid-water complexes (MO) Geometries, binding energies, and charges of BX 3 -NR 3 Lewis Acid Base Adducts (MO) Capsaicin computational study: To compare MMFF to DFT low energy conformers and DFT reliability to predict experimental NMR spectrum (MM, Conf, MO) Conformational analysis of a reactive carbonyl intermediate in the N-heterocyclic carbene (NHC) catalyzed [5+2] cycloaddition of 2,4,6-triphenylpyrlium-4-olate and α-chlorohydrocinnamaldehyde (MM, Conf, MO) Vibrational analysis of common gasoline additives: methanol, ethanol, and methyl-t-butyl-ether (MO) Isotopic effects on the hydrogenation of benzene and ethylene (MO) Conformational analysis of dihydropyran oligolides (MM, Conf) Comparison of macrocyclic pyrroles (MO) Structures and vibrational frequencies of large conjugated hydrocarbons (MO) Conformational analysis of acetylthiocarbohydrazone and acetylcarbohydrazone (MM, Conf) Structures and properties of substituted cyclohexane conformations (MO, Conf) Studies of the molecular dynamics of CH 2 NO 2 H in various solvents (MM, MD) Vibrational analysis of cyclooctatetraene and its anion radical (MO) Determination of ionophores selectivity for ion binding (MM, MD) Understanding Copper (I)-Olefin Bond Strength Trends from Density Functional Calculations (MO) The transition state in the transformation of D-ribofuranose to D-ribose (MO) Molecular dynamics of betaine-like molecules (MM, MD) Determination of heats of formation and heat capacities for hypersonic aircraft fuel candidates (MO) Structure of p-benzoquinone and its anion radical (MO) Analysis of crown ethers with various ion pairs for the halogenation of nonpolar solvents (MM, MD) Investigation of halogen-substituted ylides (MO) Computational studies of porphyrins and porphyrinogens (MM, MD, MO) Study of the interactions between R and S enantiomers of 1-1-naphthylethylamine and sec-butylamine (MO) A study on the effect of N-pyridylmethyl-Ephedra systems as catalysts in the asymmetric addition of diethylzinc to aldehydes (MO) Predicting the structure of a novel carbinolamide by examination of the NMR spectra of a known compound (MO) A theoretical study of the reaction of atomic oxygen O( 3 P) with propargyl alcohol (MO) Determination of relative proton affinities for OTC pharmaceuticals using a combination of semi-empirical (AM1) and density functional theory (B3LYP) computational methods (MO) Study of the pk a of the hydroxyl group of N-(hydroxymethyl)benzamide derivatives (MO) Semi-empirical study of 5,6-dihydro-4H-1,3,4-oxadiazines (Conf, MO) Computational analysis of the formation of simple symmetrical carbodiimides: dimethylcarbodiimide, diethylcarbodiimide, and diarylcarbodiimide (MO) Density functional theory NMR and EPR calculations on three isocyanurate compounds and COT isocyanate (MO) Computational study of ruthenium(iii) complexes (MO) IR and NMR determination of N-(hydroxy-4-cyanobenzyl)acetamide (MM, MO) Computational study of a series of poly(p-phenylene) derivatives (MO) A DFT study of the formation of 2-methyl-2-pentene via an E2 reaction (MO) Computational comparison of ring strain in cycloketo-enol tautomers (MO) Ab initio study of phenyl-substituted cyclopropanes (MO) Geometry Optimization and Characterization of Three Nitroxide Spin Labels (MO) The Trans Effect in Palladium Complexes (MO) Rotational Energy Barrier Effects on Spin Density of Alkoxy-substituted Cyclooctatetraene Radical Anions (MO) Perturbation of Spin Density Distribution Due to Deuterium Substitution of 16-annulene Anion Radicals (MO) Semiempirical Study of the Effect of Local Environment on Cysteine Reactivity (MO) Molecular Dynamics Study of the Conformations of Enterobactin-Fe(III) Complexes (MM, Conf, MD) Semiempirical Determination of the Properties of Phthalocyanine Derivatives (MO) Ab Initio Study of the Reaction of Hexamethyldisilazane with Trimethylsilanol (MO) Theoretical Study of Molybdenum Bidentate Tetracarbonyl Complexes (MO) Semiempirical Calculations of Tetracorannulenoporphyrin (MO) Ab Initio Study of Binding Properties of Alkali and Alkakline Earth Metal Cations to Sulfonic Acid (MO)

5 5 Chemistry Fall 2015 Name Date Final Project Approval Form What is the molecular system(s) or chemical reaction that you propose to study? What specific things do you want to learn about the molecular system? What computational method or methods do you propose to employ? Discuss how these methods will be used to answer the questions posed about the system. Please attach an example literature reference or sample experimental data that you will use for comparison with your computational study. Explain briefly the types of comparisons you plan to make. Approved by Dr. Standard / Date: