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3D minimization in MarvinJS
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Bob

Joined: 15 Jun 2004
Posts: 2629

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Link to postPosted: Tue Feb 07, 2017 4:23 pmPost subject: 3D minimization in MarvinJS Reply with quote

Hi,

I did a 3D minimization of this structure in MarvinJS 17.1.23 using JChem Web Services 16.1.18:

<cml><MDocument><MChemicalStruct><molecule molID="m1"><atomArray><atom id="a1" elementType="C" x3="-0.616792276034779" y3="-1.2175843712843797" z3="1.1849956053639206" mrvMap="1"/><atom id="a2" elementType="C" x3="-1.9146287916170923" y3="-0.8743923392274213" z3="0.48804248789203797" mrvMap="2"/><atom id="a3" elementType="C" x3="-1.9104072332267048" y3="-1.3174189240642333" z3="-0.9582168676775588" mrvMap="3"/><atom id="a4" elementType="C" x3="-0.7109351514236871" y3="-0.7801944763904444" z3="-1.707088297094335" mrvMap="4"/><atom id="a5" elementType="C" x3="0.5869181850092071" y3="-1.1232895165645205" z3="-1.010152776032342" mrvMap="5"/><atom id="a6" elementType="C" x3="0.5826055182811165" y3="-0.6803591844400956" z3="0.4360572369982132" mrvMap="6"/><atom id="a7" elementType="O" x3="-0.5329852590287332" y3="-2.3039952318284365" z3="1.156927367220609" lonePair="2"/><atom id="a8" elementType="R" x3="-2.690960891219792" y3="-1.4571881290031126" z3="0.9837818736041195" sgroupRef="sg1"/><atom id="a9" elementType="H" x3="-0.6060767257930455" y3="-1.066724623354683" z3="2.264452187833826"/><atom id="a10" elementType="H" x3="-2.2996728276128318" y3="0.12827988580769023" z3="0.6737559755208331"/><atom id="a11" elementType="H" x3="-1.8018369349493133" y3="-2.401920124218674" z3="-0.9451923832141964"/><atom id="a12" elementType="H" x3="-2.7872249876790627" y3="-0.8629742245244116" z3="-1.4194875480131801"/><atom id="a13" elementType="H" x3="-0.6903484337552972" y3="-1.3006934124246572" z3="-2.6645626020461166"/><atom id="a14" elementType="H" x3="-0.7947659673748456" y3="0.30621523623575986" z3="-1.67904670997072"/><atom id="a15" elementType="H" x3="0.6477416325315788" y3="-2.2115011193421052" z3="-0.9961522113389513"/><atom id="a16" elementType="H" x3="1.363204975897892" y3="-0.5403820648741869" z3="-1.5058318264829613"/><atom id="a17" elementType="H" x3="0.47400350018037596" y3="0.40413893204658413" z3="0.42304044010766295"/><atom id="a18" elementType="H" x3="1.4594481673833473" y3="-1.1347806001213856" z3="0.8973035331194894"/></atomArray><bondArray><bond atomRefs2="a1 a2" order="1" id="b1"/><bond atomRefs2="a1 a6" order="1" id="b2"/><bond atomRefs2="a2 a3" order="1" id="b3"/><bond atomRefs2="a3 a4" order="1" id="b4"/><bond atomRefs2="a4 a5" order="1" id="b5"/><bond atomRefs2="a5 a6" order="1" id="b6"/><bond atomRefs2="a1 a7" order="1" id="b7"/><bond atomRefs2="a2 a8" order="1" id="b8"/><bond atomRefs2="a1 a9" order="1" id="b9"/><bond atomRefs2="a2 a10" order="1" id="b10"/><bond atomRefs2="a3 a11" order="1" id="b11"/><bond atomRefs2="a3 a12" order="1" id="b12"/><bond atomRefs2="a4 a13" order="1" id="b13"/><bond atomRefs2="a4 a14" order="1" id="b14"/><bond atomRefs2="a5 a15" order="1" id="b15"/><bond atomRefs2="a5 a16" order="1" id="b16"/><bond atomRefs2="a6 a17" order="1" id="b17"/><bond atomRefs2="a6 a18" order="1" id="b18"/></bondArray><molecule id="sg1" molID="m2" role="SuperatomSgroup" title="iBu"><atomArray><atom id="a19" elementType="C" x3="-2.690960891219792" y3="-1.4571881290031126" z3="0.9837818736041195" sgroupAttachmentPoint="1"/><atom id="a20" elementType="C" x3="-3.460960885059793" y3="-2.7909214516665806" z3="0.9837818736041195"/><atom id="a21" elementType="C" x3="-2.690960891219792" y3="-4.124654774330043" z3="0.9837818736041195"/><atom id="a22" elementType="C" x3="-5.000960872739789" y3="-2.7909214516665806" z3="0.9837818736041195"/><atom id="a23" elementType="H" x3="-2.8747852712627684" y3="-0.885302442890342" z3="1.893317666919117"/><atom id="a24" elementType="H" x3="-1.6732571368482416" y3="-1.5789768381961387" z3="0.6129091479270403"/><atom id="a25" elementType="H" x3="-3.460960885059793" y3="-2.7909214516665806" z3="-0.10621812639588035"/><atom id="a26" elementType="H" x3="-2.5092997627143148" y3="-4.439313868432258" z3="2.01144372892857"/><atom id="a27" elementType="H" x3="-3.280053986191139" y3="-4.884290939368844" z3="0.4699509459418958"/><atom id="a28" elementType="H" x3="-1.7385455392374887" y3="-3.9943367974956736" z3="0.4699509459418958"/><atom id="a29" elementType="H" x3="-5.364294206073115" y3="-2.7909214516665806" z3="2.01144372892857"/><atom id="a30" elementType="H" x3="-5.364294206073115" y3="-1.9009401784553581" z3="0.4699509459418958"/><atom id="a31" elementType="H" x3="-5.364294206073115" y3="-3.6809027248777992" z3="0.4699509459418958"/></atomArray><bondArray><bond atomRefs2="a19 a20" order="1" id="b19"/><bond atomRefs2="a20 a21" order="1" id="b20"/><bond atomRefs2="a20 a22" order="1" id="b21"/><bond atomRefs2="a19 a23" order="1" id="b22"/><bond atomRefs2="a19 a24" order="1" id="b23"/><bond atomRefs2="a20 a25" order="1" id="b24"/><bond atomRefs2="a21 a26" order="1" id="b25"/><bond atomRefs2="a21 a27" order="1" id="b26"/><bond atomRefs2="a21 a28" order="1" id="b27"/><bond atomRefs2="a22 a29" order="1" id="b28"/><bond atomRefs2="a22 a30" order="1" id="b29"/><bond atomRefs2="a22 a31" order="1" id="b30"/></bondArray></molecule></molecule></MChemicalStruct><MElectronContainer occupation="0 0" radical="0" id="o1"><MElectron atomRefs="m1.a7" difLoc="0.0 0.0 0.0"/><MElectron atomRefs="m1.a7" difLoc="0.0 0.0 0.0"/></MElectronContainer><MElectronContainer occupation="0 0" radical="0" id="o2"><MElectron atomRefs="m1.a7" difLoc="0.0 0.0 0.0"/><MElectron atomRefs="m1.a7" difLoc="0.0 0.0 0.0"/></MElectronContainer></MDocument></cml>

and it minimized to this:

<cml><MDocument><MChemicalStruct><molecule molID="m1"><atomArray><atom id="a1" elementType="C" x3="-3.0814067959079927" y3="-1.791755683059714" z3="0.4061188972798042" mrvMap="1"/><atom id="a2" elementType="C" x3="-3.434585333385665" y3="-0.7214685242206983" z3="-0.6838631415882953" mrvMap="2"/><atom id="a3" elementType="C" x3="-4.97064825105595" y3="-0.44045070495712557" z3="-0.6063261798412974" mrvMap="3"/><atom id="a4" elementType="C" x3="-5.4098526407700485" y3="0.05843519575864641" z3="0.7961765320601285" mrvMap="4"/><atom id="a5" elementType="C" x3="-5.009596839215463" y3="-0.9458257934571513" z3="1.910344234504025" mrvMap="5"/><atom id="a6" elementType="C" x3="-3.515407486247499" y3="-1.3661189698843972" z3="1.838927263678142" mrvMap="6"/><atom id="a7" elementType="O" x3="-1.6919117910246213" y3="-2.109521533099041" z3="0.389152316784543" lonePair="2"/><atom id="a8" elementType="R" x3="-2.5253153957590975" y3="0.5582374712748549" z3="-0.6031636774395794" sgroupRef="sg1"/><atom id="a9" elementType="H" x3="-3.6024671262383237" y3="-2.720637925080506" z3="0.15725722542273604"/><atom id="a10" elementType="H" x3="-3.2388382612637643" y3="-1.1909482317959252" z3="-1.6525780084407755"/><atom id="a11" elementType="H" x3="-5.51331923342355" y3="-1.3640053067968916" z3="-0.8315485605526654"/><atom id="a12" elementType="H" x3="-5.275948798245638" y3="0.2789896766202566" z3="-1.3662514474709568"/><atom id="a13" elementType="H" x3="-6.494443419361342" y3="0.19362711164907623" z3="0.8069158604852192"/><atom id="a14" elementType="H" x3="-4.960175370997084" y3="1.0331180218463425" z3="1.0008190685807998"/><atom id="a15" elementType="H" x3="-5.207633350700622" y3="-0.494476989054208" z3="2.8862718805739536"/><atom id="a16" elementType="H" x3="-5.636922425642992" y3="-1.8385876701963955" z3="1.8271980072250158"/><atom id="a17" elementType="H" x3="-3.35126591872531" y3="-2.2016921203004007" z3="2.524150099545812"/><atom id="a18" elementType="H" x3="-2.8900040117198" y3="-0.5402279677001013" z3="2.1854967117049133"/></atomArray><bondArray><bond atomRefs2="a1 a2" order="1" id="b1"/><bond atomRefs2="a1 a6" order="1" id="b2"/><bond atomRefs2="a2 a3" order="1" id="b3"/><bond atomRefs2="a3 a4" order="1" id="b4"/><bond atomRefs2="a4 a5" order="1" id="b5"/><bond atomRefs2="a5 a6" order="1" id="b6"/><bond atomRefs2="a1 a7" order="1" id="b7"/><bond atomRefs2="a2 a8" order="1" id="b8"/><bond atomRefs2="a1 a9" order="1" id="b9"/><bond atomRefs2="a2 a10" order="1" id="b10"/><bond atomRefs2="a3 a11" order="1" id="b11"/><bond atomRefs2="a3 a12" order="1" id="b12"/><bond atomRefs2="a4 a13" order="1" id="b13"/><bond atomRefs2="a4 a14" order="1" id="b14"/><bond atomRefs2="a5 a15" order="1" id="b15"/><bond atomRefs2="a5 a16" order="1" id="b16"/><bond atomRefs2="a6 a17" order="1" id="b17"/><bond atomRefs2="a6 a18" order="1" id="b18"/></bondArray><molecule id="sg1" molID="m2" role="SuperatomSgroup" title="iBu"><atomArray><atom id="a19" elementType="C" x3="-2.5253153957590975" y3="0.5582374712748549" z3="-0.6031636774395794" sgroupAttachmentPoint="1"/><atom id="a20" elementType="C" x3="-2.7851623301572306" y3="1.6989203136834055" z3="-1.6461732167012837"/><atom id="a21" elementType="C" x3="-1.950738101647606" y3="2.9645307624015156" z3="-1.2976146068774355"/><atom id="a22" elementType="C" x3="-2.510728721935011" y3="1.2525509313467946" z3="-3.1093275405102427"/><atom id="a23" elementType="H" x3="-2.6177138974483802" y3="0.9875938811219889" z3="0.3969384394181471"/><atom id="a24" elementType="H" x3="-1.4813144133030236" y3="0.24749421926321924" z3="-0.7109247560539488"/><atom id="a25" elementType="H" x3="-3.8308851274405664" y3="2.006845061891662" z3="-1.577610045585789"/><atom id="a26" elementType="H" x3="-2.2078803938672977" y3="3.3265610677526194" z3="-0.2996247995432154"/><atom id="a27" elementType="H" x3="-2.1592884629094513" y3="3.767221966583346" z3="-2.007958375810712"/><atom id="a28" elementType="H" x3="-0.8823038219451126" y3="2.743732528934397" z3="-1.3249062649311356"/><atom id="a29" elementType="H" x3="-3.196823498008843" y3="0.4585524938683217" z3="-3.405556980603111"/><atom id="a30" elementType="H" x3="-1.484705757576737" y3="0.8923853340801879" z3="-3.216466432854889"/><atom id="a31" elementType="H" x3="-2.6621156840716766" y3="2.086222971184417" z3="-3.7973517514019806"/></atomArray><bondArray><bond atomRefs2="a19 a20" order="1" id="b19"/><bond atomRefs2="a20 a21" order="1" id="b20"/><bond atomRefs2="a20 a22" order="1" id="b21"/><bond atomRefs2="a19 a23" order="1" id="b22"/><bond atomRefs2="a19 a24" order="1" id="b23"/><bond atomRefs2="a20 a25" order="1" id="b24"/><bond atomRefs2="a21 a26" order="1" id="b25"/><bond atomRefs2="a21 a27" order="1" id="b26"/><bond atomRefs2="a21 a28" order="1" id="b27"/><bond atomRefs2="a22 a29" order="1" id="b28"/><bond atomRefs2="a22 a30" order="1" id="b29"/><bond atomRefs2="a22 a31" order="1" id="b30"/></bondArray></molecule></molecule></MChemicalStruct><MElectronContainer occupation="0 0" radical="0" id="o1"><MElectron atomRefs="m1.a7" difLoc="0.0 0.0 0.0"/><MElectron atomRefs="m1.a7" difLoc="0.0 0.0 0.0"/></MElectronContainer><MElectronContainer occupation="0 0" radical="0" id="o2"><MElectron atomRefs="m1.a7" difLoc="0.0 0.0 0.0"/><MElectron atomRefs="m1.a7" difLoc="0.0 0.0 0.0"/></MElectronContainer></MDocument></cml>

Note that the iBu group went from equatorial to axial, and the OH group went from axial to equatorial. This is wrong, regardless of whether we are doing a global minimization or a gradient minimization. So, two questions:

  1. Can the MarvinJS user control the minimization method? If so, how?
  2. What is the default minimization method, and why does it put the iBu group in the axial position?
Bob

Joined: 15 Jun 2004
Posts: 2629

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Link to postPosted: Thu Feb 16, 2017 6:36 pmPost subject: Reply with quote

No response?

Daniel
ChemAxon personnel
Joined: 22 Jan 2012
Posts: 315

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Link to postPosted: Mon Feb 20, 2017 2:35 pmPost subject: Reply with quote

Dear Bob, 

We are investigating this issue. We will answer as soon as possible for your question.

Thank you for your patience.

Daniel

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