<SPAN style="COLOR: blue">Build</SPAN> <SPAN style="COLOR: blue">Set Atom Type</SPAN> <SPAN style="COLOR: purple"> </SPAN><SPAN style="mso-bidi-font-size: 10.0pt">(</SPAN> <SPAN style="COLOR: blue"> </SPAN>), <SPAN style="COLOR: blue">Set Charge</SPAN> <SPAN style="COLOR: purple"> </SPAN><SPAN style="mso-bidi-font-size: 10.0pt">(</SPAN> <SPAN style="COLOR: blue"></SPAN>), <SPAN style="COLOR: blue">Constrain Geometry</SPAN> <SPAN style="COLOR: purple"> </SPAN>(<SPAN style="COLOR: blue"> </SPAN>), , .
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<SPAN style="COLOR: blue">Build</SPAN> <SPAN style="COLOR: blue">Constrain bond length</SPAN>, , , .
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<SPAN style="mso-ansi-language: EN-US"> <SPAN lang=EN-US style="COLOR: blue">Constrain Bond Torsion</SPAN> <SPAN lang=EN-US> </SPAN></SPAN><SPAN style="mso-ansi-language: EN-US"> </SPAN><SPAN style="mso-ansi-language: EN-US"> </SPAN> <SPAN style="COLOR: blue">Build</SPAN> <SPAN style="COLOR: blue"> </SPAN> , .
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, , <SPAN style="COLOR: blue">Select</SPAN> <SPAN style="COLOR: blue"> </SPAN> <SPAN style="FONT-FAMILY: Symbol"></SPAN> <SPAN style="COLOR: blue">Multiple Selections</SPAN><SPAN style="COLOR: purple; mso-bidi-font-style: italic"> </SPAN>(<SPAN style="COLOR: blue"> </SPAN>). . <SPAN style="COLOR: teal">L-</SPAN> <SPAN style="FONT-FAMILY: Wingdings">;</SPAN> , .
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<![if!supportLists]><SPAN style="FONT-SIZE: 10pt; mso-bidi-font-size: 12.0pt">1.<SPAN style="FONT: 7pt 'Times New Roman'"> </SPAN></SPAN><![endif]> <SPAN style="COLOR: blue">Display</SPAN> <SPAN style="FONT-FAMILY: Symbol"></SPAN> <SPAN style="COLOR: blue">Show Hydrogen Bonds</SPAN><SPAN style="COLOR: purple"> </SPAN> (<SPAN style="COLOR: blue"> </SPAN>)
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<![if!supportLists]><SPAN style="FONT-SIZE: 10pt; mso-bidi-font-size: 12.0pt">2.<SPAN style="FONT: 7pt 'Times New Roman'"> </SPAN></SPAN><![endif]> <SPAN style="COLOR: blue">Recompute H Bonds</SPAN><SPAN style="COLOR: purple"> </SPAN> (<SPAN style="COLOR: blue"> </SPAN>)
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<SPAN style="FONT-SIZE: 16pt; mso-bidi-font-size: 18.0pt">5.<o:p></o:p></SPAN><SPAN style="FONT-SIZE: 16pt; COLOR: #993300; mso-bidi-font-size: 18.0pt"> 2D 3D (</SPAN><SPAN style="FONT-SIZE: 16pt; COLOR: #993300; mso-bidi-font-size: 13.5pt">)<o:p></o:p></SPAN>
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, 1--3--2 .
<![if!supportLists]><SPAN style="FONT-SIZE: 10pt; mso-bidi-font-size: 12.0pt">1.<SPAN style="FONT: 7pt 'Times New Roman'"> </SPAN></SPAN><![endif]> <SPAN style="COLOR: blue">Build</SPAN> <SPAN style="COLOR: blue">Default elements</SPAN>
<![if!supportLists]><SPAN style="FONT-SIZE: 10pt; mso-bidi-font-size: 12.0pt">2.<SPAN style="FONT: 7pt 'Times New Roman'"> </SPAN></SPAN><![endif]> (<SPAN style="FONT-FAMILY: Symbol"></SPAN>) <SPAN style="COLOR: blue">Allow ions</SPAN> (<SPAN style="COLOR: blue"> </SPAN>) <SPAN style="COLOR: blue">Explicit hydrogens</SPAN> (<SPAN style="COLOR: blue"> </SPAN>). <SPAN style="COLOR: blue">Explicit hydrogens</SPAN> , .
<![if!supportLists]><SPAN style="FONT-SIZE: 10pt; mso-bidi-font-size: 12.0pt">3.<SPAN style="FONT: 7pt 'Times New Roman'"> </SPAN></SPAN><![endif]> () .
<![if!supportLists]><SPAN style="FONT-SIZE: 10pt; mso-bidi-font-size: 12.0pt">4.<SPAN style="FONT: 7pt 'Times New Roman'"> </SPAN></SPAN><![endif]> :
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<SPAN style="FONT-SIZE: 14pt; COLOR: #993300; mso-bidi-font-size: 12.0pt"> :<o:p></o:p></SPAN>
<SPAN style="COLOR: maroon"><![if!supportEmptyParas]><![endif]> <o:p></o:p></SPAN>
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<![if!supportLists]><SPAN style="FONT-SIZE: 10pt; mso-bidi-font-size: 12.0pt">1.<SPAN style="FONT: 7pt 'Times New Roman'"> </SPAN></SPAN><![endif]> <SPAN style="COLOR: blue">Sa</SPAN><SPAN lang=EN-US style="COLOR: blue; mso-ansi-language: EN-US">v</SPAN><SPAN style="COLOR: blue">e </SPAN> (<SPAN style="COLOR: blue"></SPAN>).
<![if!supportLists]><SPAN style="FONT-SIZE: 10pt; mso-bidi-font-size: 12.0pt">2.<SPAN style="FONT: 7pt 'Times New Roman'"> </SPAN></SPAN><![endif]> . , . <SPAN style="COLOR: blue">File name</SPAN> (, )
<![if!supportLists]><SPAN style="FONT-SIZE: 10pt; mso-bidi-font-size: 12.0pt">3.<SPAN style="FONT: 7pt 'Times New Roman'"> </SPAN></SPAN><![endif]>, <SPAN style="COLOR: blue">Save as type </SPAN> (<SPAN style="COLOR: blue"> </SPAN>) <SPAN style="COLOR: green">HIN</SPAN>.
<![if!supportLists]><SPAN style="FONT-SIZE: 10pt; mso-bidi-font-size: 12.0pt">4.<SPAN style="FONT: 7pt 'Times New Roman'"> </SPAN></SPAN><![endif]><SPAN style="COLOR: teal">L-</SPAN> <SPAN style="COLOR: blue">OK</SPAN>.
<![if!supportLists]><SPAN style="FONT-SIZE: 10pt; mso-bidi-font-size: 12.0pt">5.<SPAN style="FONT: 7pt 'Times New Roman'"> </SPAN></SPAN><![endif]>
, ( <SPAN lang=EN-US style="COLOR: blue; mso-ansi-language: EN-US">Save</SPAN> <SPAN style="COLOR: blue">File</SPAN> ). .
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<SPAN style="FONT-SIZE: 14pt; COLOR: #993300; mso-bidi-font-size: 12.0pt"> <o:p></o:p></SPAN>
<![if!supportLists]><SPAN style="FONT-SIZE: 10pt; mso-bidi-font-size: 12.0pt">1.<SPAN style="FONT: 7pt 'Times New Roman'"> </SPAN></SPAN><![endif]> <SPAN style="COLOR: blue">Display</SPAN> <SPAN style="COLOR: blue"> </SPAN> <SPAN style="COLOR: blue">Labels</SPAN> <SPAN style="COLOR: blue"> </SPAN>(<SPAN style="COLOR: blue"></SPAN>).
<![if!supportEmptyParas]><![endif]><o:p></o:p><![if!supportLists]><SPAN style="FONT-SIZE: 10pt; mso-bidi-font-size: 12.0pt">2.<SPAN style="FONT: 7pt 'Times New Roman'"> </SPAN></SPAN><![endif]> <SPAN style="COLOR: purple"></SPAN> <SPAN style="COLOR: purple"> </SPAN> <SPAN style="COLOR: blue">None</SPAN>. <SPAN style="COLOR: blue">Symbol</SPAN>, <SPAN style="COLOR: blue">Name</SPAN>, <SPAN style="COLOR: blue">Number</SPAN> <SPAN style="COLOR: blue"> </SPAN> ., <SPAN style="COLOR: teal">L-,</SPAN> <SPAN style="COLOR: blue">OK</SPAN>.
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<![if!supportLists]><SPAN style="FONT-SIZE: 10pt; mso-bidi-font-size: 12.0pt">3.<SPAN style="FONT: 7pt 'Times New Roman'"> </SPAN></SPAN><![endif]> .
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<![if!supportLists]><SPAN style="FONT-SIZE: 10pt; mso-bidi-font-size: 12.0pt">2.<SPAN style="FONT: 7pt 'Times New Roman'"> </SPAN></SPAN><![endif]> . <SPAN style="COLOR: aqua">C </SPAN>( ) <SPAN style="COLOR: red">O</SPAN> ( ). .
<![if!supportLists]><SPAN style="FONT-SIZE: 10pt; mso-bidi-font-size: 12.0pt">3.<SPAN style="FONT: 7pt 'Times New Roman'"> </SPAN></SPAN><![endif]> , <SPAN style="COLOR: blue">Build</SPAN> <SPAN style="COLOR: blue">Model Build </SPAN> (<SPAN style="COLOR: blue"> </SPAN>). 2D () 3D.
<![if!supportEmptyParas]><![endif]> <o:p></o:p><![if!supportLists]><SPAN style="FONT-SIZE: 10pt; mso-bidi-font-size: 12.0pt">4.<SPAN style="FONT: 7pt 'Times New Roman'"> </SPAN></SPAN><![endif]> , , <!--[if gte vml 1]><v:shape id=_x0000_i1031
style="WIDTH: 15pt; HEIGHT: 14.25pt" type="#_x0000_t75"><v:imagedata
o:title="26"
src="./chapter_05.files/image010.png"></v:imagedata></v:shape><![endif]--><![if!vml]><![endif]> <SPAN style="mso-spacerun: yes"> </SPAN>(<SPAN style="COLOR: red">Rotate out-of plane</SPAN>, <!--[if gte vml 1]><v:shape id=_x0000_i1032
style="WIDTH: 14.25pt; HEIGHT: 15pt" type="#_x0000_t75"><v:imagedata
o:title="27"
src="./chapter_05.files/image012.png"></v:imagedata></v:shape><![endif]--><![if!vml]><![endif]> <SPAN style="COLOR: red">Translate</SPAN>).
<![if!supportLists]><SPAN style="FONT-SIZE: 10pt; mso-bidi-font-size: 12.0pt">5.<SPAN style="FONT: 7pt 'Times New Roman'"> </SPAN></SPAN><![endif]> <SPAN style="COLOR: blue">Build</SPAN> <SPAN style="COLOR: blue">Add Hydrogens </SPAN> (<SPAN style="COLOR: blue"> </SPAN>)
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<![if!supportLists]><SPAN style="FONT-SIZE: 10pt; mso-bidi-font-size: 12.0pt">6.<SPAN style="FONT: 7pt 'Times New Roman'"> </SPAN></SPAN><![endif]> , <SPAN style="COLOR: blue">Display</SPAN> <SPAN style="COLOR: blue">Show Hydrogens</SPAN> (<SPAN style="COLOR: blue"> </SPAN>) <SPAN style="COLOR: blue">Add Hydrogens</SPAN>.
<![if!supportLists]><SPAN style="FONT-SIZE: 10pt; mso-bidi-font-size: 12.0pt">7.<SPAN style="FONT: 7pt 'Times New Roman'"> </SPAN></SPAN><![endif]> .
<SPAN style="FONT-SIZE: 16pt; mso-bidi-font-size: 24.0pt">6. <o:p></o:p></SPAN><SPAN style="FONT-SIZE: 16pt; mso-bidi-font-size: 24.0pt"><![if!supportEmptyParas]><![endif]> <o:p></o:p></SPAN><SPAN style="FONT-SIZE: 16pt; COLOR: #993300; mso-bidi-font-size: 24.0pt"> HyperChem<o:p></o:p></SPAN>
<SPAN style="COLOR: blue">Setup ( )<o:p></o:p></SPAN>
<SPAN style="COLOR: blue">Setup</SPAN> . : , - (10 , 3) - (ab initio) .
<SPAN style="COLOR: blue">Setup</SPAN> - - , . , <SPAN style="COLOR: blue">Setup</SPAN>, <SPAN style="COLOR: blue">Compute</SPAN>, .
HyperChem (MM+, AMBER, BIO+ OPLS), - ( , CNDO, INDO, MINDO3, MNDO, AM1, PM3, ZINDO/1 ZINDO/S), (ab initio) .
<SPAN style="COLOR: blue">Setup </SPAN> :<![if!supportEmptyParas]><![endif]> <o:p></o:p>
<TBODY><SPAN lang=EN-US style="mso-bidi-font-size: 10.0pt; mso-ansi-language: EN-US">Molecular mechanics<o:p></o:p></SPAN> <SPAN lang=EN-US style="mso-bidi-font-size: 10.0pt; mso-ansi-language: EN-US">(</SPAN><SPAN style="mso-bidi-font-size: 10.0pt"></SPAN><SPAN style="mso-bidi-font-size: 10.0pt; mso-ansi-language: EN-US"> </SPAN><SPAN style="mso-bidi-font-size: 10.0pt"></SPAN><SPAN lang=EN-US style="mso-bidi-font-size: 10.0pt; mso-ansi-language: EN-US">)</SPAN><SPAN lang=EN-US style="mso-ansi-language: EN-US"><o:p></o:p></SPAN> | <SPAN style="mso-bidi-font-size: 10.0pt"> Molecular mechanics ( ), ( -) <o:p></o:p></SPAN> |
<SPAN style="mso-bidi-font-size: 10.0pt">Semi-empirical<o:p></o:p></SPAN> <SPAN style="mso-bidi-font-size: 10.0pt">()</SPAN><o:p></o:p> | <SPAN style="mso-bidi-font-size: 10.0pt"> (Semi-empirical) - ab initio<o:p></o:p></SPAN> |
Ab Initio<o:p></o:p> | <SPAN style="mso-bidi-font-size: 10.0pt"> Ab Initio ( -) . <o:p></o:p></SPAN> |
Periodic box<o:p></o:p> ( )<o:p></o:p> | <SPAN style="mso-bidi-font-size: 10.0pt"> (Periodic Box) , <o:p></o:p></SPAN> |
<SPAN style="mso-bidi-font-size: 10.0pt">Restraints ()<o:p></o:p></SPAN> | <SPAN style="mso-bidi-font-size: 10.0pt"> (Restraints) ( ) 1, 2, 3 4 . , .<o:p></o:p></SPAN> |
Set velocity<o:p></o:p> ( )<o:p></o:p> | <SPAN style="mso-bidi-font-size: 10.0pt"> (Set Velocity). , . - .<o:p></o:p></SPAN> |
<SPAN style="mso-bidi-font-size: 10.0pt"> (Network)<o:p></o:p></SPAN> | <SPAN style="mso-bidi-font-size: 10.0pt"> (Network) -, </SPAN><o:p></o:p> |
<SPAN style="mso-bidi-font-size: 10.0pt">Select paprameter set<o:p></o:p></SPAN><SPAN style="mso-bidi-font-size: 10.0pt">( )<o:p></o:p></SPAN> | <SPAN style="mso-bidi-font-size: 10.0pt"> </SPAN><o:p></o:p> |
<SPAN lang=EN-US style="mso-bidi-font-size: 10.0pt; mso-ansi-language: EN-US">Compile parameter file <o:p></o:p></SPAN><SPAN lang=EN-US style="mso-bidi-font-size: 10.0pt; mso-ansi-language: EN-US">(</SPAN><SPAN style="mso-bidi-font-size: 10.0pt"></SPAN><SPAN style="mso-bidi-font-size: 10.0pt; mso-ansi-language: EN-US"> </SPAN><SPAN style="mso-bidi-font-size: 10.0pt"></SPAN><SPAN style="mso-bidi-font-size: 10.0pt; mso-ansi-language: EN-US"> </SPAN><SPAN style="mso-bidi-font-size: 10.0pt"></SPAN><SPAN lang=EN-US style="mso-bidi-font-size: 10.0pt; mso-ansi-language: EN-US">)<o:p></o:p></SPAN> | <SPAN style="mso-bidi-font-size: 10.0pt"> , HyperChem<o:p></o:p></SPAN> |
<SPAN style="mso-bidi-font-size: 10.0pt">Reaction map<o:p></o:p></SPAN> <SPAN style="mso-bidi-font-size: 10.0pt">( )</SPAN><o:p></o:p> | <SPAN style="mso-bidi-font-size: 10.0pt"> , .. . , </SPAN><o:p></o:p> </TBODY> |
<SPAN style="FONT-SIZE: 16pt; mso-bidi-font-size: 13.5pt">
6.1.<o:p></o:p></SPAN><SPAN style="FONT-SIZE: 16pt; COLOR: #993300; mso-bidi-font-size: 13.5pt"> ()<o:p></o:p></SPAN>
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<SPAN style="COLOR: blue">Setup</SPAN> , , , - ( - (ab initio)).
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