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<title>MCCCS Towhee (TraPPE United Atom)</title>
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<div align="center"><font size="5"><b><font face="Arial,Helvetica,sans-serif"><a name="top"></a>MCCCS Towhee (TraPPE United Atom)</font></b></font></div>
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<p> </p>
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<td width="700" valign="top"> <b>Overview</b>
<ul>
This section covers the TraPPE United Atom (TraPPE-UA) force field as it is implemented into the towhee_ff_TraPPE-UA file in the ForceFields directory.
All of the Towhee atom types for the TraPPE United Atom force field are listed, along with a short description of their meanings. For more information
about the TraPPE United Atom force field see the <a href="http://siepmann6.chem.umn.edu/">Siepmann group web site</a>.
Note that TraPPE United Atom is a Lennard-Jones (12-6) force field and can only be combined with other Lennard-Jones (12-6) force fields.
I would like to acknowledge Collin D. Wick, Jeff Potoff, and J. Ilja Siepmann for providing very useful guidance about implementing TraPPE-UA.
Any discrepencies (especially typos) from the published TraPPE-UA force field values had better not exist considering I helped create this
force field. The detail presented here for the TraPPE-UA force field is greater than the general level of detail for other forcefields due to the
close relation between the authors of Towhee and TraPPE-UA. If someone does find a discrepancy with the published values I would be extremely grateful
if they let me know about it. I welcome feedback on how this implementation compares with other programs.
</ul>
<b>References for TraPPE-UA</b>
<ul>
TraPPE-UA is still under development by the Siepmann group. Here is the current list of references.
<ul>
<li><a href="../references.html#martin_siepmann_1998_jpcb">Martin and Siepmann 1998 (JPCB)</a></li>
<li><a href="../references.html#martin_siepmann_1998_tca">Martin and Siepmann 1998 (TCA)</a></li>
<li><a href="../references.html#martin_siepmann_1999">Martin and Siepmann 1999</a></li>
<li><a href="../references.html#wick_et_al_2000">Wick <i>et al.</i> 2000</a></li>
<li><a href="../references.html#chen_et_al_2001">Chen <i>et al.</i> 2001</a></li>
<li><a href="../references.html#kamath_et_al_2004">Kamath <i>et al.</i> 2004</a></li>
<li><a href="../references.html#stubbs_et_al_2004">Stubbs <i>et al.</i> 2004</a></li>
</ul>
</ul>
<b>Typos and comments for TraPPE-UA</b>
<ul>
Here I list torsions that I believe are missing in the published TraPPE-UA papers. These torsions are therefore not implemented into Towhee.
<ul>
<dt><font color="red">alkanes</font></dt>
<li>CH<sub>x</sub> - CH - C - CH<sub>y</sub> torsion is missing. Example: 2,3,3-trimethylbutane.</li>
<li>CH<sub>x</sub> - C - C - CH<sub>y</sub> torsion is missing. Example: 2,2,3,3-quatramethylbutane.</li>
<dt><font color="red">alkenes</font></dt>
<li>CH<sub>x</sub> - CH2(sp3) - C(sp2 double bonded to C) - CH<sub>y</sub> torsion is missing. Example: 2-methyl-1-butene torsion involving
only single bonds.
</li>
<li>CH<sub>x</sub> - CH(sp3) - C(sp2 double bonded to C) - CH<sub>y</sub> torsion is missing. Example: 2,3-dimethyl-1-butene torsion involving
only single bonds.
</li>
<li>CH<sub>x</sub> - C(sp3) - C(sp2 double bonded to C) - CH<sub>y</sub> torsion is missing. Example: 2,3,3-trimethyl-1-butene torsion involving
only single bonds.
</li>
<dt><font color="red">alcohols</font></dt>
<li>CH<sub>x</sub> - CH2 - CH - OH torsion is missing. Example: 1-methylethanol.</li>
<li>CH<sub>x</sub> - CH2 - C - OH torsion is missing. Example: 1,1-dimethylethanol.</li>
<li>CH<sub>x</sub> - CH2 - C - OH torsion is missing. Example: 1,1,1-trimethylethanol.</li>
<dt><font color="red">ketones</font></dt>
<li>CH<sub>x</sub> - CH2(sp3) - C(sp2 double bonded to O) - CH<sub>y</sub> torsion is missing. Example: buta-2-one torsion involving only single
bonds.
</li>
<li>CH<sub>x</sub> - CH(sp3) - C(sp2 double bonded to O) - CH<sub>y</sub> torsion is missing. Example: 3-methylbuta-2-one
torsion involving only single bonds.
</li>
<li>CH<sub>x</sub> - C(sp3) - C(sp2 double bonded to O) - CH<sub>y</sub> torsion is missing. Example: 3,3-dimethylbuta-2-one
torsion involving only single bonds.
</li>
<dt><font color="red">ethers</font></dt>
<li>CH<sub>x</sub> - CH2(sp3) - CH(sp3) - O torsion is missing. Example: sec-butyl ethyl ether.</li>
<li>CH<sub>x</sub> - CH(sp3) - CH(sp3) - O torsion is missing. Example: 1,2-dimethylpropyl ethyl ether.</li>
<li>CH<sub>x</sub> - C(sp3) - CH(sp3) - O torsion is missing. Example: 1,2,2-trimethylpropyl ethyl ether.</li>
<li>CH<sub>x</sub> - CH2(sp3) - C(sp3) - O torsion is missing. Example: 1,1-dimethylpropyl ethyl ether.</li>
<li>CH<sub>x</sub> - CH(sp3) - C(sp3) - O torsion is missing. Example: 1,1,2-trimethylpropyl ethyl ether.</li>
<li>CH<sub>x</sub> - C(sp3) - C(sp3) - O torsion is missing. Example: 1,1,2,2-quatramethylpropyl ethyl ether.</li>
</ul>
<p></p>
A few angles for carboxylic acids were not listed in the <a href="../references.html#kamath_et_al_2004">Kamath <i>et al.</i> 2004</a> paper and
here I list the missing angle terms and then also list the terms Jeff Potoff suggested for use with these angles.
<ul>
<li>CH<sub>2</sub> - C(acid) - O in carboxylic acid is not listed. I used the similar CH<sub>3</sub> - C(acid) - O parameters.</li>
<li>CH<sub>2</sub> - C(acid) = O in carboxylic acid is not listed. I used the similar CH<sub>3</sub> - C(acid) = O parameters.</li>
</ul>
The functional form for one of the torsions was listed incorrectly in Equation 5 of the
<a href="../references.html#kamath_et_al_2004">Kamath <i>et al.</i> 2004</a> paper. That paper lists the torsion as
<ul>U<sub>torsion</sub> = c<sub>1</sub>[ 1 + cos( &phi + f<sub>1</sub> )] + c<sub>2</sub> [ 1 - cos(2 &phi)]</ul>
but the actual torsion potential used in that work (according to personal communication with Jeff Potoff) is
<ul>U<sub>torsion</sub> = c<sub>1</sub>[ 1 + cos( &phi + f<sub>1</sub> )] + c<sub>2</sub> [ 1 - cos<sup>2</sup>(&phi)]</ul>
and this correction was made in Towhee beginning with version 4.6.1.
<dt>A few torsions for carboxylic acids were not listed in the <a href="../references.html#kamath_et_al_2004">Kamath <i>et al.</i> 2004</a> paper
and here I list the missing torsion terms and then also list the terms Jeff Pottof suggested for use with these torsions.
<ul>
<li>CH<sub>x</sub> - CH<sub>2</sub> - C(acid) = O in carboxylic acid is not listed. This uses the OCOH carboxylic torsion.</li>
<li>CH<sub>x</sub> - CH<sub>2</sub> - C(acid) - O in carboxylic acid is not listed. This uses the linear alkane
CH<sub>x</sub> - CH<sub>2</sub> - CH<sub>2</sub> - CH<sub>x</sub> torsion.
</li>
</ul>
The functional form used for alkenes is listed incorrectly in Equation 5 of the
<a href="../references.html#wick_et_al_2000">Wick <i>et al.</i> 2000</a> paper. That equation should read
<ul>u<sub>tors</sub> = d<sub>0</sub> (&phi - &phi<sub>0</sub>)<sup>2</sup></ul>
</dt>
</ul>
<b>TraPPE-UA in Towhee</b>
<ul>
The official force field name for TraPPE United Atom in Towhee is 'TraPPE-UA'. Here I list all of the TraPPE-UA atom names for use in the
towhee_input file, along with a brief description. I created these atom names in order to work with the molecule assembler. TraPPE-UA is a
united-atom force field which lumps hydrogens onto their neighboring carbons. Note that hydrogens that are bonded to atoms other than carbon
are not lumped onto their neighboring atoms. The naming convention listed here began with version 4.4.1 as some changed were required in order to
implement TraPPE-6. The general pattern of the names is a list of the atoms that make up the group, followed by the types of atoms
that they are single bonded to, followed by the atoms they are double bonded to (prefixed with an '='), and ending in a code that represents the
bonding pattern of the atom. The <b>Bond Name</b> is also listed to facilitate comparision with the bond increment method listed down in the
coulombic section.
Please note that the capitalization and spacing pattern is important and must be followed exactly as listed here.
<ul>
<dt><font color="red">Argon</font></dt>
<li><b>'Ar'</b> : argon</li>
<dt><font color="red">Carbon (not bonded to any hydrogens)</font></dt>
<li><b>'Ccccc(sp3)'</b> : an sp<sup>3</sup> carbon.
This atom is single bonded to four carbon atoms.
Bond name <font color="green">Csp3</font>.
</li>
<li><b>'Cccco(sp3)'</b> : an sp<sup>3</sup> carbon.
This atom is single bonded to three carbon atoms and single bonded to one oxygen atom.
Bond name <font color="green">Csp3</font>.
</li>
<li><b>'Ccc=c(sp2)'</b> : an sp<sup>2</sup> carbon.
This atom is single bonded to two carbon atoms and double bonded to one carbon atom.
Bond name <font color="green">Csp2</font>.
</li>
<li><b>'Ccc=o(sp2)'</b> : an sp<sup>2</sup> carbon.
This atom is single bonded to two carbon atoms and double bonded to one oxygen atom.
Bond name <font color="green">Ccc=o(sp2)</font>.
</li>
<li><b>'Cco=o(sp2)'</b> : an sp<sup>2</sup> carbon.
This atom is single bonded to one carbon atom, single bonded to one oxygen atom, and double bonded to one oxygen atom.
Bond name <font color="green">Cco=o(sp2)</font>.
</li>
<li><b>'Caac(aro)'</b> : an aromatic carbon.
This atom is bonded to two aromatic carbon atoms and single bonded to one carbon atom.
Bond name <font color="green">Caro</font>.
</li>
<li><b>'Caaa(aro)'</b> : an aromatic carbon.
This atom is bonded to three aromatic carbon atoms.
Bond name <font color="green">Caro</font>.
</li>
<dt><font color="red">Carbon (united atom including 1 bonded hydrogen)</font></dt>
<li><b>'CHccc(sp3)'</b> : united-atom consisting of an sp<sup>3</sup> carbon and one bonded hydrogen.
This united-atom is single bonded to three carbon atoms.
Bond name <font color="green">Csp3</font>.
</li>
<li><b>'CHcco(sp3)'</b> : united-atom consisting of an sp<sup>3</sup> carbon and one bonded hydrogen.
This united-atom is single bonded to two carbon atoms and single bonded to one oxygen atom.
Bond name <font color="green">Csp3</font>.
</li>
<li><b>'CHc=c(sp2)'</b> : united-atom consisting of an sp<sup>2</sup> carbon and one bonded hydrogen.
This united-atom is single bonded to one carbon atom and double bonded to one carbon atom.
Bond name <font color="green">Csp2</font>.
</li>
<li><b>'CHc=o(sp2)'</b> : united-atom consisting of an sp<sup>2</sup> carbon and one bonded hydrogen.
This united-atom is single bonded to one carbon atom and double bonded to one oxygen atom.
Bond name <font color="green">CHc=o(sp2)</font>.
</li>
<li><b>'CHaa(aro)'</b> : united-atom consisting of an aromatic carbon and one bonded hydrogen.
This united-atom is bonded to two aromatic carbon atoms.
Bond name <font color="green">Caro</font>.
</li>
<dt><font color="red">Carbon (united atom including 2 bonded hydrogens)</font></dt>
<li><b>'CH2**(sp3)'</b> : united-atom consisting of an sp<sup>3</sup> carbon and two bonded hydrogens.
This united-atom is single bonded to any two non-hydrogen atoms.
Bond name <font color="green">Csp3</font>.
</li>
<li><b>'CH2=*(sp2)'</b> : united-atom consisting of an sp<sup>2</sup> carbon and two bonded hydrogens.
This united-atom is double bonded to any one non-hydrogen atom.
Bond name <font color="green">Csp2</font>.
</li>
<dt><font color="red">Carbon (united atom including 3 bonded hydrogens)</font></dt>
<li><b>'CH3*(sp3)'</b> : united-atom consisting of an sp<sup>3</sup> carbon and three bonded hydrogens.
This united-atom is single bonded to any non-hydrogen atom.
Bond name <font color="green">Csp3</font>.
</li>
<dt><font color="red">Carbon (united atom including 4 bonded hydrogens)</font></dt>
<li><b>'CH4'</b> : methane</li>
<dt><font color="red">Helium</font></dt>
<li><b>'He'</b> : helium</li>
<dt><font color="red">Hydrogen (not bonded to a carbon)</font></dt>
<li><b>'Ho'</b> : hydrogen bonded to one oxygen. Bond name <font color="green">Ho</font>.</li>
<li><b>'Hoacid'</b> : hydrogen bonded to one oxygen in a carboxylic acid.
Bond name <font color="green">Hoacid</font>.
</li>
<dt><font color="red">Oxygen</font></dt>
<li><b>'Och(sp3)'</b> : sp<sup>3</sup> oxygen atom that is single bonded to one carbon atom and single bonded to one hydrogen atom.
Bond name <font color="green">Och(sp3)</font>.
</li>
<li><b>'Occ(sp3)'</b> : sp<sup>3</sup> oxygen atom that is single bonded to two carbon atoms.
Bond name <font color="green">Occ(sp3)</font>.
</li>
<li><b>'O=c(sp2)'</b> : sp<sup>2</sup> oxygen atom that is double bonded to one carbon atom.
Bond name <font color="green">O=c(sp2)</font>.
</li>
</ul>
</ul>
<b>TraPPE-UA and the Molecule Assembler</b>
<ul>
The molecule builder is only partially functional for TraPPE-UA. The builder can assemble aliphatic hydrocarbons and alcohols, but it does not
work for aromatics. In the case of alkenes, TraPPE-UA has different torsional potentials for cis and trans and these can be distinguished using
the options in the 'advanced connectivity map'. TraPPE-UA also uses a rigid model for aromatics, which is currently problematic for Towhee.
</ul>
<b>Coulombic interactions</b>
<ul>
TraPPE-UA uses atom-centered point charges to represent the electrostatic interactions. Generally, there is no charge on any of the hydrocarbons,
but there are exceptions once other atoms are mixed into the molecules. Note that there is a 0.5 scaled 1-4 coulombic interaction built into the
most of the torsional potentials. This general rule is contradicted by some of the torsions for carboxylic acids. You can take a look at the
<a href="../references.html#force_fields_trappe">TraPPE-UA force field literature</a> to determine how to assign the charges, or you can try out
the 'bond increment' method for assigning charges on these molecules.
Here I list the bond increments using the bond names listed above. The value of the bond increment is added to the first atom listed and
subtracted from the second atom listed.
<ul>
<li><font color="green">Csp3</font> - <font color="green">Csp3</font>: 0.0</li>
<li><font color="green">Csp3</font> - <font color="green">Csp2</font>: 0.0</li>
<li><font color="green">Csp3</font> - <font color="green">Caro</font>: 0.0</li>
<li><font color="green">Csp2</font> - <font color="green">Csp2</font>: 0.0</li>
<li><font color="green">Caro</font> - <font color="green">Caro</font>: 0.0</li>
<li><font color="green">Ho</font> - <font color="green">Och(sp3)</font>: 0.435</li>
<li><font color="green">Csp3</font> - <font color="green">Och(sp3)</font>: 0.265</li>
<li><font color="green">Csp3</font> - <font color="green">Occ(sp3)</font>: 0.25</li>
<li><font color="green">CHc=o(sp2)</font> - <font color="green">Csp3</font>: 0.043</li>
<li><font color="green">CHc=o(sp2)</font> - <font color="green">O=c(sp2)</font>: 0.482</li>
<li><font color="green">Ccc=o(sp2)</font> - <font color="green">O=c(sp2)</font>: 0.424</li>
<li><font color="green">O=c(sp2)</font> - <font color="green">Cco=o(sp2)</font>: -0.45</li>
<li><font color="green">Csp3</font> - <font color="green">Cco=o(sp2)</font>: 0.12</li>
<li><font color="green">Och(sp3)</font> - <font color="green">Cco=o(sp2)</font>: -0.09</li>
<li><font color="green">Hoacid</font> - <font color="green">Och(sp3)</font>: 0.37</li>
</ul>
</ul>
<a href="../towhee_capabilities.html">Return to the Towhee Capabilities web page</a>
<p> </p>
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<i><font size="2">Send comments to:</font></i>
<font size="2"> <a href="mailto:marcus_martin@users.sourceforge.net">Marcus G. Martin</a>
<br></br>
<i>Last updated:</i> <!-- #BeginDate format:Am1 -->January 09, 2007<!-- #EndDate -->
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