MIME

NMR-SHARC: Chemical MIME subtype for ab initio NMR

Chemical MIME subtype: ab initio NMR

This document contains a definition of a file format

for standardized exchange and storage

of ab initio calculated NMR data.

# + + + + + + + + + + + + + + + + + + + + #

# A general chemical markup language #

# will make this definition superfluous. #

# + + + + + + + + + + + + + + + + + + + + #

Suggested by: A. Dransfeld (dransfld@ccc.uni-erlangen.de)

first public Version = V. 0.9 proposed on: 21th May 1995

previous versions

this public Version is V. 2.0 suggested on: 25th Jan 1998

# This memo provides information for the Internet community. #

# This memo does not specify an Internet standard of any kind. #

# Distribution of this memo is unlimited. #

# -- SHARC is the acronym of "ab initio nmr SHared ARCive -- #

Extension: .sharc

(Extension under DOS: .sha)

Format:

# Essential lines in the SHARC file start with a record ID, left-justified. #

# Expressions in capital letters are record ID's specifying the record type. #

# Record types comprise the record ID and terms. #

# The terms (words in small letters) in the record type specification are #

# described in alphabetic order below. Some record types provide redundant #

# data. Nevertheless these records are required for consistency checking and #

# marking of parts (e.g. the N=...part is wrapped by the NUCS... (start tag) #

# and CHAR... (end tag) record. #

# Additional data, appended_data, is marked up by tags, which are #

# comments in HTML (see glossary for specification of these parts) #

Record types (order of appearance):

SHARC nmr_method mol_formula mol_char_mu opt_method point_group character

SHARCID sharc_contributor,sharc_time

TEXT comments [as many lines of this kind as required]

NUCS number_of_atoms

N=atom nuc_charge x_coord y_coord z_coord isotrop_shield xx_st xy_st xz_st yx_st yy_st yz_st zx_st zy_st zz_st

...... [as many lines of this kind as number_of_atoms]

CHAR molecular_charge

COUP atom_index_a atom_index_b coupling_constant in Hz

...... [as many lines of this kind as necessary to specify all non equal couplings ( a < - > b = b < - > a ) ]

NAME contributor_name

GROUP contributor_group

PERM contributor_defined_permission

appended_data (see glossary)

SHARCEND

Record types (description in alphabetic order):

# The terms (expressions in small letters) #

# are listed in alphabetic order. #

REMARK CHAR molecular_charge (required)

REMARK CHAR - Charge of the molecule

REMARK COUP coupling_constant (optional)

REMARK COUP - magnetic coupling constant

REMARK COUP UNITS: Hz

REMARK COUP

REMARK COUP atom_index_a and atom_index_b (optional)

REMARK COUP - Index of the atoms derived from their appearance

REMARK COUP in the geometry specification

REMARK COUP (no dummy atoms should appear nor be considered)

REMARK N= atom (required)

REMARK N= - element symbol

REMARK N=

REMARK N= nuc_charge (required, despite redundant)

REMARK N= - Charge of the nucleus

REMARK N=

REMARK N= x_coord y_coord z_coord

REMARK N= - Coordinates in standard orientation (required)

REMARK N= UNIT: Angstroem

REMARK N=

REMARK N= isotrop_shield

REMARK N= - isotropic magnetic shielding of the nucleus (required)

REMARK N= defined as 1/3 of the sum of the trace elements

REMARK N= of the magnetic shielding tensor

REMARK N= (NOT the so called "NMR chemical shift")

REMARK N= UNITS: ppm (with respect to the bare nucleus)

REMARK N=

REMARK N= xx_st xy_st xz_st yx_st yy_st yz_st zx_st zy_st zz_st

REMARK N= (optional)

REMARK N= - elements of the magnetic shielding tensor

REMARK N= in the axis system of the Standard Orientation

REMARK N= UNITS: ppm (with respect to the bare nucleus)

REMARK N= Keep in mind that the tensor can provide more information

REMARK N= about the shielding than the isotrop_shield)

REMARK NAME contributor_name (required)

REMARK NAME - Name of the person who contributed this entity.

REMARK NAME It may be either a real name, nick name or an

REMARK NAME e-mail address. The contributor_name which may

REMARK NAME be used and excluded characters are

REMARK NAME listed in the glossary.

REMARK NUCS number_of_atoms (required)

REMARK NUCS - Number of atoms in the molecule

REMARK PERM contributor_defined_permission (required)

REMARK PERM - The permission which may be set by the contributor

REMARK PERM (see glossary for specification

REMARK PERM of these possible permissions)

REMARK SHARC The "header line" is the part between the

REMARK SHARC record identifyer, "SHARC ", and the character

REMARK SHARC specification (e.g. @u).

REMARK SHARC The "header line" comprises information

REMARK SHARC which may be public, while the computational results

REMARK SHARC remain private knowledge.

REMARK SHARC The mol_char_mu term in the "header line" has special markup

REMARK SHARC to prevent occasional mixing with the mol_formula:

REMARK SHARC

REMARK SHARC character (required)

REMARK SHARC - Specification whether a structure is

REMARK SHARC @e derived from experiment,

REMARK SHARC @m a global minimum,

REMARK SHARC @n a local minimum,

REMARK SHARC @x a partially optimized geometry, or

REMARK SHARC @t a transition structure.

REMARK SHARC mol_char_mu (required)

REMARK SHARC - molecular charge

REMARK SHARC + multiplicity of the electron configuration if non-singulet

REMARK SHARC in _charge,multiplicity. format with "_" as start-tag,

REMARK SHARC "," as opional separator, and "." as end tag.

REMARK SHARC

REMARK SHARC mol_formula (required)

REMARK SHARC - Formula of the molecule with every element symbol (incl.BQ)

REMARK SHARC followed by its stoichiometric number (including "1").

REMARK SHARC

REMARK SHARC nmr_method (required)

REMARK SHARC - ab initio method/program:

REMARK SHARC CSGT = "continuous set of gauge transformations"

REMARK SHARC REFERENCE: T.A. Keith, R.F.W. Bader,

REMARK SHARC Chem.Phys.Lett. 1993, 223 (Vol.210).

REMARK SHARC IMPLEMENTATION: J.R. Cheeseman, G.W. Trucks,

REMARK SHARC T.A. Keith, M.J. Frisch,

REMARK SHARC J.Chem.Phys. 1996, in press.

REMARK SHARC GIAO = GIAO as implemented in TX90

REMARK SHARC REFERENCE: D. B. Chesnut, B. E. Rusiloski,

REMARK SHARC Chem. Phys. 1991, 157, 105.

REMARK SHARC GIAO-G94 = GIAO as implemente in GAUSSIAN94©

REMARK SHARC REFERENCE: J. R. Cheesman, G. W. Trucks,

REMARK SHARC A. T. Keith, M. J. Frisch

REMARK SHARC J.Chem.Phys. 1996, 104, 5497.

REMARK SHARC

REMARK SHARC IGLO = IGLO as implemented in IGLO Version '88

REMARK SHARC IGLO92 = IGLO as implemented in IGLO Version '92

REMARK SHARC REFERENCE: W. Kutzelnigg,

REMARK SHARC Israel J. Chem. 1980, 19, 193.

REMARK SHARC GIAO-MP2 = GIAO-MBPT2 ass implemented in ACES II Version 0.2

REMARK SHARC REFERENCE: J. Gauss, Chem. Phys. Letters 191, 614 (1992);

REMARK SHARC J. Gauss, J. Chem. Phys 99, 3629 (1993).

REMARK SHARC DMM = SOS-DFPT as implemented in MASTER(3.0)/DeMon92(1.0b)

REMARK SHARC REFERENCE: V.G. Malkin, O.L. Malkina, D.R. Salahub,

REMARK SHARC Chem.Phys.Lett., 204, 80 (1993);

REMARK SHARC V.G. Malkin, O.L. Malkina, D.R. Salahub,

REMARK SHARC Chem.Phys.Lett., 204, 87 (1993);

REMARK SHARC LORG = LORG as implemented in RPAC/GAUSSIAN90

REMARK SHARC REFERENCE: Bouman, T.D. , Hansen A.E. ,

REMARK SHARC Chem.Phys.Lett., 149, 510 (1988).

REMARK SHARC

REMARK SHARC - ab initio method/basis sets:

REMARK SHARC See basis set glossary

REMARK SHARC based on Standard basis Sets as used in GAUSSIAN92(c):

REMARK SHARC i.e. 6-31G(d), 6-31G(d,p), 6-311G(d)

REMARK SHARC and as supported by EMSL

REMARK SHARC http://www.emsl.pnl.gov:2080/forms/basisform.html

REMARK SHARC ( K. Schuchardt, D. Feller and the ECCH Team. The EMSL

REMARK SHARC Project, Pacific Northwest Laboratory, 1994. )

REMARK SHARC B2,B3 Huzinaga Basis sets augmanted according to Kutzelnigg...

REMARK SHARC dzp, tzp ... according to Ahlrichs...

REMARK SHARC

REMARK SHARC opt_method

REMARK SHARC - ab initio Method of geometry optimization:

REMARK SHARC Standard methods as used in GAUSSIAN92(TM): RHF, RMP2,

REMARK SHARC Standard basis Sets as used in GAUSSIAN92(TM):

REMARK SHARC 6-31GD, 6-31GDP, 6-311GD

REMARK SHARC and as supported by EMSL

REMARK SHARC http://www.emsl.pnl.gov:2080/forms/basisform.html

REMARK SHARC ( K. Schuchardt, D. Feller and the ECCH Team. The EMSL

REMARK SHARC Project, Pacific Northwest Laboratory, 1994. )

REMARK SHARCID The NMR-SHARC IDentifyer is a uniform identifier

REMARK SHARCID of ab initio NMR data archived in this NMR-SHARC format.

REMARK SHARCID

REMARK SHARCID The "sharc_contributor" is specified

REMARK SHARCID either by her/his contributor_name, e-mail address

REMARK SHARCID or by a combination of her/his login name and a

REMARK SHARCID specification of her/his research group.

REMARK SHARCID All sharc_contributor values should be registered

REMARK SHARCID in the NMR-SHARC glossary

REMARK SHARCID together with the real names of the contributor.

REMARK SHARCID

REMARK SHARCID The "sharc_time" is the date

REMARK SHARCID in ISO/R 2014-1971 format followed by the time zone and

REMARK SHARCID the time in hhmmss format

REMARK SHARCID

REMARK SHARCID Example: dransfld@ccc_erlangen,1997-03-29EST115502

REMARK SHARCID is a computation by dransfld in the research group

REMARK SHARCID ccc_erlangen which finished/archived less than five

REMARK SHARCID minutes before noon on the 29th of March 1997.

REMARK TEXT comments