Unix, Remote Computing, and NMR Calculations on a Linux Cluster n1 at UNCW

1

• Unix, Remote Computing, and NMR Calculations on
  a Linux Cluster n1 at UNCW

2
Objectives

• Certain carbocations may exist as structures in
  which the positive charge is localized mainly on
  one carbon (classical) or spread over several
  carbons (non-classical) due to bridging or other
  delocalization.
• In this lab we will do calculations to predict
  the lowest energy structure for a given
  carbocation. We will also calculate the NMR
  shielding values of the carbon atoms in the
  cations.

3

• The difference in the sum of the carbon atom
  isotropic shielding values between the parent
  hydrocarbon and the cation (which is equal to the
  difference in the sum of their chemical shifts)
  have been correlated to the nature of the
  carbocation (classical or non-classical).
• If the absolute difference (hydrocarbon
  parent-cation) is gt350 ppm, the cation is
  considered to be classical if the difference is
  lt250 ppm, it is considered to be non-clasical.

4
NMR Isotropic Shielding Values
(Gaussian mistakenly reports these as Isotropic
Shielding Tensors)
Differences in shielding values differences in
chemical shifts
5
Ethane/ethyl/bridged ethenium ion
Isotropic Shielding Values (in ppm )
194 194 388
148 (-118) 30
61 61 122
Difference from 388
358 262

(classical)
(non-classical)
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Objectives

• Because NMR calculations require large basis sets
  for accuracy, you will use a computer faster than
  a pc these calculations will be performed
  remotely on an 8 processor Linux cluster at UNCW.
• This machine is a Linux-based platform, so you
  will need to learn how to do remote computing and
  a few Unix commands.
• You will also learn how to use Gaussian 03, a
  widely used quantum chemistry computational
  software package.

7
Logging on to a remote computer

• Well use puTTy (icon in Applications folder) for
  secure connections to logon to
• n1.dobo.uncw.edu
• (this is Linux cluster, called n1)
• Login (on n1)
• martin
• password (Ill enter this)

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Unix Commands

• Useful Unix commands
• pwd (tells you what directory you are in)
• mkdir NMR (makes a new directory named NMR)
• ls la (gives a complete listing of files in
  directory)
• cd .. (changes directories to the next higher
  directory)
• cd (changes directories to your home, or login
  dir.)
• cp filename1.dat filename2.dat (makes a copy of a
  file, giving it a different filename)

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Other useful Unix commands

• cp filename1.dat dirname1/filename2.dat (makes a
  copy of a file, saves it in a different directory
  and gives it a different filename)
• mv filename1.dat dirname2/filename1.dat (moves a
  file to a different directory, keeping the same
  name)
• mv filename1.dat dirname2/filename2.dat (moves a
  file to a different directory, and changes the
  filename)
• rm filename1.dat (removes (deletes) a file)
• rmdir dirname1 (removes (deletes) a directory it
  must be empty first could use rm dirname1 r,
  but this is dangerous
• exit (or logout) (logs you off the computer)

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vi text editor commands

• vi filename.dat (opens filename.dat in text
  editor must be in same directory as file, or
  else must use pathname/filename)
• i (enters insert mode Esc gets you out of
  any mode)
• a (enters append mode Esc gets you out of
  any mode)
• x (enters delete mode Esc gets you out of
  any mode)
• r (single character overstrike mode upper
  case R is for multiple character overstrike
  mode)
• dd (deletes entire line)
• ZZ (exits vi editor, saving changes)
• q! (exits vi editor without saving changes)

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Editing an input file for Gaussian

• Gaussian 03 requires input files with a .dat
  (or .com) extension
• The file must be in a certain format, shown on
  the following slide
• Spacing is critical (blank spaces or no spaces
  and blank lines must be exactly as called for)
• The molecule description (Cartesian coordinates
  or Z-matrix) is free-form any number of spaces
  between adjacent columns is OK

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Format of Gaussian input file

• chk/tmp/yourdirname/filename.chk
• HF/6-31G nosymm opt freq
• (blank line)
• (title or any comments you wish to add go here)
• (blank line)
• 1 1 (charge multiplicity )
• molecular specificationXYZ coordinates or
  Z-matrix goes here
• (blank line)
• --Link1--
• chk/tmp/yourdirname/filename.chk
• HF/6-31G geomallcheckpoint nosymm popnpa
  nmr
• (blank line)

(the red section is a link to an nmr job)
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Submitting a Gaussian job

• An executable script called xg03 has been written
  to automate the submission process for Gaussian
  03 calculations.
• xg03 filename.dat

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Checking on a Gaussian job

• After a job has been submitted, note the .job and
  .out files in your directory an .error file
  indicates a finished job.
• A copy of the .out file may be viewed at any time
  without interrupting the calculation type cat
  filename.out to scroll through the file very
  quickly to the end use the elevator bar to go
  back into the file.
• Alternatively, use more filename.out and the
  spacebar to view the file one screen at a time

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Objectives for Tuesdays lab

• Logon to the account
• Create a directory for your scratch files
• mkdir /tmp/425_nhm
• Make a copy of the H.dat file to a file having
  your initials in the filename
• cp H.dat Hnhm.dat
• Use the vi editor to edit the file H.dat

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Objectives for Tuesdays lab

• vi Hnhm.dat (use vi editing commands to change
  the directory and filename in the first line)
• submit H.dat for Gaussian 03 calculation.
• xg03 Hnhm
• When the job is finished, examine the output
  file
• more Hnhm.out

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Objectives for Tuesdays lab

• Build a model of each of your isomeric
  carbocations in Titan
• Optimize each of them using semi-empirical MO
  theory (AM1 or PM3). If this changes the
  structure from what you want, re-build the
  structure using constraints if needed and skip
  the semi-empirical MO optimization step.
• Save the structures as .pdb files
• Open them in GaussView save them as Cartesian
  Coordinate files (with a .dat extension).
• Note the atom numbering. A sketch or a copy of
  the structure with atom numbers will be helpful.

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Objectives for Tuesdays lab

• Edit the .dat files using Notepad on a pc or vi
  on n1 to conform to the Gaussian 03 format used
  by n1. (see handout)
• Use WINSCP3 to copy the files to an account on n1
  (our Linux cluster).
• Alternatively, use puTTY to access n1, then open
  a new file in vi, then copy and paste your .dat
  file.
• Submit them by typing the command
• xg03 filename.dat
  

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Visualizing Gaussian results

• Transmit a copy of the .out file from n1 to the
  local pc this is done using WINSCP3.
• We use a program GaussView that opens Gaussian
  .out files and renders models of structures in
  various types of representations.
• Observe each structure and make measurements on
  each structure as needed to determine if it is
  a classical or non-classical carbocation.

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Objectives for the Next lab

• Repeat the entire process, this time modeling the
  parent hydrocarbon (alkane).
• Perform the data analysis, including calculating
  the difference in the sums of the chemical
  shielding values between the parent hydrocarbon
  and each carbocation structure.
• Visualize the carbocations, copy the structure to
  put in your report, and make measurements as
  needed to determine whether each is classical or
  non-classical.

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Objectives for the Next lab

• Also obtain the NMR Isotropic Shielding values
  and the npa charges on the carbon atoms in each
  structure. These can be done using the vi editor
  and some commands (e.g., grep) as indicated in
  the lab handout.
• Analyze the data (NMR shielding values, npa
  charges, energies, bond lengths and bond angles)
  to determine whether the carbocation you modeled
  exists as a classical or non-classical structure,
  according to the HF/6-31G calculations.