Shakib, Farnaz

English

Digital Commons @ New Jersey Institute of Technology (NJIT)

New Jersey Institute of Technology Digital Commons @ NJIT Chemistry, Environmental and Forensic Science Syllabi NJIT Syllabi Spring 2023 Chem 437-102: Appl Computatnl Chem & Mol Mod and Chem 737-102 Farnaz Shakib Follow this and additional works at: https://digitalcommons.njit.edu/chem-syllabi Recommended Citation Shakib, Farnaz, "Chem 437-102: Appl Computatnl Chem & Mol Mod and Chem 737-102" (2023). Chemistry, Environmental and Forensic Science Syllabi. 475. https://digitalcommons.njit.edu/chem-syllabi/475 This Syllabus is brought to you for free and open access by the NJIT Syllabi at Digital Commons @ NJIT. It has been accepted for inclusion in Chemistry, Environmental and Forensic Science Syllabi by an authorized administrator of Digital Commons @ NJIT. For more information, please contact digitalcommons@njit.edu.     Chemistry:   Spring 2023 Course Syllabus   NJIT Academic Integrity Code: All Students should be aware that the Department of Chemistry & Environmental Science (CES) takes the University Code on Academic Integrity at NJIT very seriously and enforces it strictly. This means that there must not be any forms of plagiarism, i.e., copying of homework, class projects, or lab assignments, or any form of cheating in quizzes and exams. Under the University Code on Academic Integrity, students are obligated to report any such activities to the Instructor.   COURSE INFORMATION  Course Description: Principles and applications of quantum chemistry; Static electronic structure calculations, Solving Schrodinger equation via Hartree-Fock method, Density Functional Theory; Molecular dynamics simulations, building force-fields, concept of ensembles; Ab-initio molecular dynamics. Introduction to software Gaussian, CP2K and DL_POLY Quantum as well as visualizing packages Avogadro, Gaussview and VMD.  Number of Credits: 3   Course-Section and Instructors  Course-Section Instructor  CHEM 437-102, R 6pm – 8:50 pm Farnaz A. Shakib (Website)  CHEM 737-102, R 6pm – 8:50 pm  Farnaz A. Shakib    Course Presentation:                                   In person: Guttenberg Info Tech Center 2400  Course Partitions:                              Lectures on theoretical concepts/Hands-on lab sessions January 19 – March 23                              Exam on theoretical concepts March 30                             Working on Projects and Final Presentations: April 6 – April 27   Office Hours: Every week on Mondays at 4-6pm.                                 In-person: Tiernan hall Rm 368                               WebEx: https://njit.webex.com/meet/shakibnjit.edu       There is no textbook for this course.    University-wide Withdrawal Date: The last day to withdraw with a W is Monday, April 3, 2023. It will be strictly enforced.         Learning Outcomes: At the end of the course, the student will be able to  • Construct the Schrödinger equation for simple systems  • Create input configuration of molecules for static electronic structure calculations • Create input files for molecular dynamics simulations • Be familiar with bash scripting • Be able to turn numerical data to visual plots and results • Be able to run calculations on high performance computing clusters • Describe the differences between classical and quantum mechanics  • Build force fields for molecular dynamics • Describe the differences between classical and quantum-mechanical dynamics simulations • Analyze the molecular dynamics trajectories • Be able to carry out a computational project all the way from making the input files to analyzing the results  Canvas: There is a course Canvas site that will include significant resources and updates of importance to this course, both for the lecture and laboratory portions. Please check it frequently, and also make sure to check or forward your NJIT email in order to receive important announcements. Furthermore, all the office hours and discussions will be conducted through Canvas.   POLICIES All CES students must familiarize themselves with, and adhere to, all official university-wide student policies. CES takes these policies very seriously and enforces them strictly.  Grading Policy: The final grade in this course will be determined as follows:  Lab Homework 20 Class Participation Solving problems in class, active role in asking and answering questions  25 Exam on Theoretical Concepts 25 Final Presentation 30  Your final letter grade in this course will be based on the following tentative curve:  Pay attention D grade is only applicable for undergraduate students.   A 88-100 C 60-64.5 B+ 78-87.9 D 55-59.9 (undergrad) B 70-77.9 F < 55 (undergrad) C+ 65-69.9  F   < 60 (grad)             Attendance Policy: Attendance at all classes is not mandatory but extremely encouraged due to the nature of the topic which cannot be simply learnt through “getting the notes.”   Homework Policy: Homework is an expectation of the lab section of the course. They are meant to help you honing your basic scripting and computational skills. Homework is due for grading one day before the class (i.e. till 6pm on the Wednesday before the class). Graded homework will be returned the next day after the lecture and they will be discussed during the lecture.   Exams: There will be one exam covering the theoretical concepts discussed in the class. Note that the exam will be held online. The exam is closed book/notebooks but students are allowed to prepare a double sided A4 page of any material related to class and keep it with themselves during the exam. A picture of this information sheet should be uploaded to Canvas along with the answers to the exam problems.  Makeup Exam Policy: There will normally be NO MAKE-UP EXAMS during the semester. In the event that a student has a legitimate reason for missing an exam, the student should contact the Dean of Students office and present written verifiable proof of the reason for missing the exam, e.g., a doctor’s note, police report, court notice, etc. clearly stating the date AND time of the mitigating problem. The student must also notify the CES Department Office/Instructor that the exam will be missed so that appropriate steps can be taken to make up the grade.  Cellular Phones: All cellular phones and other electronic devices must be switched off during all class times. Such devices must be stowed in bags during exams or quizzes.   ADDITIONAL RESOURCES  Accommodation of Disabilities: Office of Accessibility Resources and Services (formerly known as Disability Support Services) offers long term and temporary accommodations for undergraduate, graduate and visiting students at NJIT.  If you are in need of accommodations due to a disability please contact Chantonette Lyles, Associate Director at the Office of Accessibility Resources and Services at 973-596-5417 or via email at lyles@njit.edu. The office is located in Fenster Hall Room 260. A Letter of Accommodation Eligibility from the Office of Accessibility Resources Services office authorizing your accommodations will be required.  For further information regarding self-identification, the submission of medical documentation and additional support services provided please visit the Accessibility Resources and Services (OARS) website at:  http://www5.njit.edu/studentsuccess/disability-support -services/                Course Outline   Lecture Date Theoretical Concepts Hands-on Lab 1 01/19/2023 Tour of HPC/Introduction to Computational Chemistry Introduction to Linux/Bash scripting/vi editor/homework 2 01/26/2023 Quantum mechanics (QM), Time-dependent and time-independent Schrödinger equations, Matrix representation of QM representation Gnuplot/plotting functions/homework 3 02/02/2023 Electronic structure calculations, Hartree-Fock (HF) method, density functional theory (DFT) Creating input files with Avogadro software/simple minimization 4 02/09/2023 Basis sets 1, Thermochemistry  Electronic structure calculations of benzene in the gas phase/MOs/vibrational analysis/Comparing HF and DFT 5 02/16/2023 Basis sets 2, Solvent effect Electronic structure calculations of organic compounds in solution/Implicit solvent 6 02/23/2023 Introduction to Ab Initio Molecular Dynamics (AIMD) vs classical MD, concept of force fields and periodic boundary conditions Analysis of prepared MD trajectories with VMD package, Convergence of E, T, P/ concept of RDF   7 03/02/2023 Classical molecular dynamics (MD), Equations of motions Compiling Packmol, Preparing input files with Packmol for MD, organic compounds in aqueous solution 8 03/09/2023 Concept of ensembles for MD simulations, DL_POLY Quantum Compiling DL_POLY Quantum, Introduction to FIELD, CONFIG and CONTROL files, running simulations 9 03/16/2023 Spring recess, no class   10 03/23/2023 Analysis of the MD simulations ran before recess, Questions and answers before the exam Assigning groups for the final project to look into interested topics 11 03/30/2023 Exam on theoretical concepts       12 04/06/2023 Going over the exam, Discussing the topics for the final project Assigning projects to groups for final projects 13 04/13/2023 Working on projects  14 04/20/2023 Working on projects  15 04/27/2023 Final presentations   

Chem 437-102: Appl Computatnl Chem & Mol Mod and Chem 737-102

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Chem 437-102: Appl Computatnl Chem & Mol Mod and Chem 737-102

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