User 870ab5b546
07-02-2017 15:23:45
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:
- Can the MarvinJS user control the minimization method? If so, how?
- What is the default minimization method, and why does it put the iBu group in the axial position?