cyclohexanone

If I draw cyclohexane with all 12 H atoms, do a 3D minimization, replace one of the CH2 groups with a C=O, and then 3D minimize again, the program returns a twist-boat conformation of cyclohexanone as the lowest energy structure. This result is wrong; cyclohexanone's lowest energy conformation is a chair. Seeing as how the compound starts out as a chair, I doubt the problem is that it's finding a local minimum.

I have tried to reproduce this problem using the 5.0.2.1 (http://www.chemaxon.com/marvin/examples/webstart/index.html) using the following steps:


-place a cyclohexane template


-CTRL+3 to generate a chair 3D conformer


-Place a double bond on one of the carbons


-Replace the carbon on the end of the placed double bond to oxygen


-Structure - add explicit hydrogenes


-Structure - Clean 3D - Cleaning method - Gradient optimize


-Invoke optimization with CTRL - 3


It remains in the chair conformation for me. Could you attach the starting structure which optimized from chair to the twisted boat?

The error apparently depends on exactly how the structure is drawn, but this structure minimized incorrectly in both Marvin 4.1.14 and MarvinBeans 5.0.6.1.

Code:

<?xml version="1.0" ?> <MDocument>   <propertyList>     <property dictRef="viewEulerAngles" title="viewEulerAngles">       <array size="3" dataType="xsd:double">-1.016808942010331 0.03848152177171671 -0.006997177445924827</array>     </property>   </propertyList>   <MChemicalStruct>     <molecule molID="m1">       <atomArray           atomID="a1 a2 a3 a4 a5 a6 a7 a8 a9 a10 a11 a12 a13 a14 a15 a16 a17"           elementType="C C C C C C H H H H H H H H H H O"           x3="-0.5506813707742395 -0.010765682857237764 1.5407656828484777 2.080681370789372 1.5407656993113912 -0.010765699312840736 -1.6427149415038318 -0.24454364675443524 -0.3601729086429888 -0.40439103648264446 1.8901729086358354 1.9343910364779784 1.7745436467717683 3.172714941501947 1.9343910217146454 1.8901729113062427 -0.8390442800193386"           y3="1.43953400722548 -0.015225471842978249 -0.03934245151101335 0.7242127190466937 2.17897225539441 2.2030892097037484 1.4240436095421127 1.965272241493339 -0.5093613662089862 -0.5718952449309339 -1.0740854414463044 0.4245327685785734 0.19847452109192115 0.7397031488785148 2.7356419839736508 2.673108126493381 2.8289477455489496"           z3="0.005133469968804838 -0.036638319630794454 0.005133514382716706 1.24410628491611 1.2858780783124397 1.244106288166554 0.031963662936043594 -0.9054718212989277 -0.9461671156161768 0.8203920900558246 0.031963674974112045 -0.9054718554388252 2.1547115971267266 1.2172761104726295 0.42884766830157584 2.1954068628322783 2.2275470265196744"           />       <bondArray>         <bond atomRefs2="a1 a2" order="1" />         <bond atomRefs2="a1 a6" order="1" />         <bond atomRefs2="a2 a3" order="1" />         <bond atomRefs2="a3 a4" order="1" />         <bond atomRefs2="a4 a5" order="1" />         <bond atomRefs2="a5 a6" order="1" />         <bond atomRefs2="a1 a7" order="1" />         <bond atomRefs2="a1 a8" order="1" />         <bond atomRefs2="a2 a9" order="1" />         <bond atomRefs2="a2 a10" order="1" />         <bond atomRefs2="a3 a11" order="1" />         <bond atomRefs2="a3 a12" order="1" />         <bond atomRefs2="a4 a13" order="1" />         <bond atomRefs2="a4 a14" order="1" />         <bond atomRefs2="a5 a15" order="1" />         <bond atomRefs2="a5 a16" order="1" />         <bond atomRefs2="a6 a17" order="2" />       </bondArray>     </molecule>   </MChemicalStruct> </MDocument>

This structure also minimized to a twist-boat in Marvin 5.0.6.1 on your demo page:

Code:

<?xml version="1.0" ?> <cml> <MDocument>   <MChemicalStruct>     <molecule molID="m1">       <atomArray           atomID="a1 a2 a3 a4 a5 a6 a7 a8 a9 a10 a11 a12 a13 a14 a15 a16 a17"           elementType="C C C C C C O H H H H H H H H H H"           x2="-0.2750000059604645 -1.608669347008723 -1.608669347008723 -0.2750000059604645 1.058669335087794 1.058669335087794 2.3923484569158298 -0.9979902426973442 0.447990230776415 -2.4247552437620157 -3.1477314822942972 -3.1477314822942972 -2.424755243762016 -0.9979902426973442 0.447990230776415 1.8747552318410867 2.5977314703733683"           y2="1.0450338763497093 0.2750169357906689 -1.265016945327412 -2.0350338858864525 -1.265016945327412 0.2750169357906689 1.045016935790669 2.4047710265310047 2.404771026531005 1.581004611506016 0.3287546667644338 -1.3187546763011764 -2.571004621042759 -3.394771036067748 -3.3947710360677483 -2.571004621042759 -1.318754676301177"           />       <bondArray>         <bond atomRefs2="a1 a2" order="1" />         <bond atomRefs2="a1 a6" order="1" />         <bond atomRefs2="a2 a3" order="1" />         <bond atomRefs2="a3 a4" order="1" />         <bond atomRefs2="a4 a5" order="1" />         <bond atomRefs2="a5 a6" order="1" />         <bond atomRefs2="a6 a7" order="2" />         <bond atomRefs2="a1 a8" order="1" />         <bond atomRefs2="a1 a9" order="1" />         <bond atomRefs2="a2 a10" order="1" />         <bond atomRefs2="a2 a11" order="1" />         <bond atomRefs2="a3 a12" order="1" />         <bond atomRefs2="a3 a13" order="1" />         <bond atomRefs2="a4 a14" order="1" />         <bond atomRefs2="a4 a15" order="1" />         <bond atomRefs2="a5 a16" order="1" />         <bond atomRefs2="a5 a17" order="1" />       </bondArray>     </molecule>   </MChemicalStruct> </MDocument> </cml>

Thank you for the structures, i was able to reproduce the problem using them. I will look after what went wrong and will notify You in this topic.