PMIFST

Principal Moments of Inertia From STructure

        This program takes in either Cartesians or connectivity definitions of molecular structure, calculates moments of inertia etc., and allows viewing, 3-D rotation and structural checks.

        The original purpose has been to check the validity of structural declarations and prediction of rotational constants, but it is now also used as a rapid viewer for inspection of structural results from various programs, including STRFIT and various ab initio packages. Principal features:

  • use of Cartesians (in Angstroms or bohr) or internal structural coordinates to declare the molecule (note that the latter are also used in the structure fitting program STRFIT)
  • dummy atoms can be used to show, among others, the orientation of the dipole moment, orientation of the diagonal quadrupole tensor etc.
  • rotational constants of isotopic species can be rapidly evaluated since nuclear masses are easily modified on-line by using common isotope notation i.e. 37Cl, 13C, etc.
  • bonds, angles, dihedral angles can be checked, including angles between bonds and principal axes
  • PostScript printout of molecule in the displayed orientation is possible for those familiar with the gle graphics package.
  • current limit on the number of atoms is 200
 
  Current version
PMIFST.FOR The listing - this is intended for CVF6.5+ compilation
PMIFST.EXE CVF6.6A executable for Win95/Pentium I upwards. Key properties of the graphics, i.e. window size and the display font are now read from the file PMIFST.CFG (below). The colour depth of the display should be at least 8 bits (256 colours).

Running conditions and installation are identical to those discussed in connection with SVIEW

PMIFST.CFG Configuration file for PMIFST, which has to reside in the directory C:\ROT.
  Examples
PMIFST.GIF Snapshot of a typical display screen
CUBE.COR Simple Cartesian data
C70.COR Cartesian data in atomic units from the ab initio world - note that bond location fails if you read this in as Angstrom data
PRMW.PMI CART type input for pyrimidine...water complex - use of mnemonics in a data file and use of dummy atoms
SABKET.PMI CART type input - data for the molecule which prompted creation of this program. If you want to know whether it was studied by rotational spectroscopy, the answer is yes! See JACS 100, 8166, 1978.
SABKET.PS PostScript file produced from the gle dump of a previewed orientation of the structure in the file above
  Legacy versions
PMIFST_5.FOR The final version for MSF5/VGA graphics
PMIFST_5.EXE Executable for the above - it should run on all versions of DOS/WIN which allow full screen MS-DOS mode
 

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STRFIT

STRucture FITting to rotational data

        This program was originally written for determination of effective structures of hydrogen bonded complexes. It is based on the principles outlined by R.H.Schwendeman in "Structural parameters from rotational spectra", a chapter in "Critical evaluation of chemical and physical structural information", D.R.Lide and M.A.Paul, Eds., National Academy of Science, Washington, D.C. (1974). For a similar approach see also: P.Nosberger,A.Bauder, and Hs.H.Gunthard, "A versatile method for molecular structure determinations from ground state rotational constants", Chem. Phys. 1, 418-425 (1973).

        Although the program has been very useful in determination of partial geometries, it can also be used for complete geometry determination. When I wrote this program it was natural for me to call it STRFIT, and I only found out much later that this is the same name that Schwendeman chose for one of his programs (the chapter in Lide+Paul, p.107) - apologies for any confusion. In any case the current program has been written completely independently of its namesake.

        This program can currently fit the following types of geometry:

  • r0 - from a direct fit to the supplied ground state constants
  • rz (r* or rav) - from fit to supplied ground state constants and harmonic vibration-rotation contributions to moments of inertia calculated with a program like VIBCA
  • r0av or similar corrected geometry from fit to supplied ground state constants and vibration-rotation corrections from an external model
  • NEW: rm(1), rm(2) , rm(1L), rm(2L), etc. - see J.K.G. Watson, A. Roytburg., W. Ulrich, J. Mol. Spectrosc. 196, 102-119 (1999).

        Principal features:

  • internal coordinates (bond lengths and angles) are fitted directly to moments of inertia (not rotational constants) in a nonlinear least-squares procedure
  • rotational constants from many isotopically substituted species can be used simultaneously, it is also possible to fit to linear combinations B+C and A+B of rotational constants, as well as to planar moments of inertia
  • the geometry is declared in the CART connectivity scheme used by PMIFST and can be checked by using that program
  • the fitted structure is echoed to file STRFIT.PMI for direct inspection with PMIFST
  • degenerate internal parameters (i.e. those which have many repetitions owing to symmetry) are easily specified
  • isotopic changes in structural parameters can be specified when sensible
  • any parameter that can be fitted can also be fixed at an assumed value if desired

       Following the extension of the program to fit the various rm( ) geometries of Watson the current reference for citing the use of STRFIT is: Z. Kisiel, J. Mol. Spectrosc. 218, 58-67 (2003).

 
STRFIT.FOR The listing, to be compiled with any 32-bit FORTRAN compiler. It is recommended that the extension .STF be reserved for the data
STRFIT.EXE The executable for Windows 95+.
  Examples
OCSe.STF and OCSe.RES The data and results files reproducing the rm(2) fit for OCSe from Table 6 of the Watson, Roytburg, Ulrich paper.
HCN.STF and HCN.RES Reproduction of the rm(1L) fit for HCN from Table 7 of the Watson, Roytburg, Ulrich paper.

Note the use of commenting in the data file: any number of comment lines beginning with a ! character are allowed before any line declaring a repeat count (such as NO OF PARAMETERS). These comments are echoed to the output.

Annotations are also allowed past the 52nd column of all data lines past the CART block - those are simply ignored on input and will not be echoed to output.

H2O.STF and H2O.RES Reproduction of the 'with cab' rm(2L) fit for H2O from Table 5 of the Watson, Roytburg, Ulrich paper
O3.STF and O3.RES Reproduction of the rm(2) fit for ozone from Table 8 of the Watson, Roytburg, Ulrich paper. The solution is very well defined and there is no need to preset the values of any of the c or d parameters.
HNCO.STF, HNCO.RES Reproduction of the rm(2) fit for HNCO from Table 9 of the Watson, Roytburg, Ulrich paper
H2CCC.STF, H2CCC.RES Reproduction of the rm(2) fit for H2CCC from Table 10 of the Watson, Roytburg, Ulrich paper
H2OHCL.STF, H2OHCL.RES The data and results files for the rm(L) fit for H2O...HCl from column V, Table 6 of Z.Kisiel, J.Mol.Spectrosc. 218, 58-67 (2003).
  Older examples
CHLPROP.STF The data set for chloropropane (8 isotopomers), set up on the basis of Tobiason+Schwendeman J.Chem.Phys. 40,1014(1964)
CHLPROP.RES Abbreviated results file for the above, which can be compared with the results in Table 2 of the Schwendeman chapter in the Lide, Paul book
CHEX.STF The data set for cyclohexane as set up in J.Mol.Struct. 350, 247 (1995) - note the use of dummy atoms and repeated coordinates
W2HCL.STF Data set for the hydrogen bonded trimer (H2O)2HCl - to fit the r* geometry as published in J. Chem. Phys. 112, 5767-5776 (2000). The necessary corrections are obtained with: GAMESS -> FCONV -> VIBCA.
 

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KRA

KRAitchman's substitution coordinates

EVAL

EVALuation of internals from Cartesians

        KRA embodies a standard implementation of Kraitchman's equations for single isotopic substitution. The equations are directly out of Gordy & Cook, and the programmed possibilities are:

  1. on axis substitution in a linear/symmetric top
  2. off-axis substitution in a symmetric top
  3. substitution in an inertial plane of an asymmetric top with several options of using the planarity condition
  4. general substitution in an asymmetric rotor

        Errors in the determined coordinates are calculated from propagation of uncertainties in the measured rotational constants, and then the usually much larger Costain's error is added (ie. dz=0.0015/|z| Angstr., see C.C.Costain, Trans.Am.Crystallogr.Assoc. 2, 157-164(1966)).


        EVAL is a simple tool to convert Cartesians and their cited errors into internals and their errors. The available internals are bond lengths, bond angles, and dihedral angles, but since the errors on dihedrals have not yet been required, they are not programmed in.

 
  KRA
KRA.FOR The listing, the data is best kept in a file with extension .KRA, and the output is made to KRA.OUT
KRA.EXE Windows executable
   
PRM.KRA The data set for pyrimidine (4 isotopomers), as in J.Mol.Spectrosc. 195, 332-339(1999)
KRA.OUT Output for the above
   
  EVAL
EVAL.FOR The listing, the data is best assigned extension .EVA, output is to screen and to EVAL.OUT
EVAL.EXE Windows executable
   
PRM.EVA The data set for pyrimidine, which has been derived from a prior run of KRA
EVAL.OUT Output for the above
 

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CORSCL

Scaling of trial molecular geometry declared in Cartesian coordinates

        The main purpose of this program is to enhance the accuracy of prediction of rotational spectra for isotopic species of a molecule before its precise geometry has been determined.

        The program allows scaling of ab initio, ar any other, trial geometry for the molecule to best reproduce experimental rotational constants. The resulting scaled geometry can then be used to evaluate rotational constants for the isotopic species with the help of the PMIFST program.

 
CORSCL.FOR The listing.
CORSCL.EXE TheWindows executable. Input is from two files:

1/ user specified file containint the trial geometry in the .COR standard of PMIFST.

2/ a single line ASCII file named CORSCL.INP, which contains the values of rotational constants A,B,C (in MHz) for the declared isotopic species

The scaling factor is determined online by trial and eror. Once done the rescaled geometry is written to file CORSCL.OUT for further use in PMIFST.

   
CAMPH.COR The sample input file with trial geometry of the camphor molecule from an ab initio calculation.
CORSCL.INP Experimental rotational constants for the isotopic species declared in the file above.
CORSCL.OUT The output output file after a session with CORSCL, which established that best overall reproduction of experimental moments of inertia is with scaling factor of 1.0025. Note that this may not be the most useful way of scaling as, for example, for a prolate molecule you might want to aim for best reproduction of B and C, and might not care that much about A.

You can check the results for camphor against the actual experimental isotopic values in PCCP 5,820(2003)

 

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RGDFIT

FITting of coordinates of a RareGas atom in a Dimer with a molecule

        This program embodies the simple idea that formation of a dimer between a molecule and a rare-gas atom is equivalent to adding a point mass to the molecule, so that coordinates of the added atom can be calculated from the moments of inertia of the molecule and of the dimer. The geometry of the molecule is not explicitly required in this step. The downside is of course sensitivity of the derived coordinates to unavoidable vibration-rotation contributions to moments of inertia, but if these can be subtracted, the reliability will increase.

        Exposition of the method has been given in Suenram, Fraser, Lovas, J.Chem.Phys. 89,6141(1988) and this particular program has been used to obtain the results reported in Kisiel, Fowler, Legon, J.Chem.Phys. 95,2283(1991).

 
RGDFIT.FOR The listing, input is from a file specified by the user (it is recommended to use the molecule name as file name, and Rg name for extension). Output is to screen, and a printable copy is also written to file RGDFIT.OUT
RGDFIT.EXE Windows executable
   
VINF.AR Specimen data for the Vinyl Fluoride-Argon dimer - in this case there is a particularly high sensitivity of results to the input data, Ar complexes to more heavily fluorinated ethylene gave more reliable results. See the discussion in the KFL paper.
RGDFIT.OUT The output for the data above. Note that for a general molecule there are eight solutions to the position of the Rg atom - the printout assumes that the molecule is planar and lists only the four distinguishable solutions for such case - the other four solutions can be obtained by changing the sign of the Z-coordinate.
 

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