ZnGlyThr Metal Organic Framework

Jmol.jmolCheckbox(jmolApplet0, "isosurface i1 color [x00FF00] center {7.048658894743519 16.587454890730665 9.23759116618376} sphere 1.7 translucent 0.3", "isosurface i1 off;", "Show pore size") Jmol.jmolCheckbox(jmolApplet0, "draw cylinder width 2.1 {-1.1748410825125886 17.073488490730664 9.23759116618376} {15.27215891748741 17.073488490730664 9.23759116618376}; color draw [xFF6600]", "draw off", "Show channel") Jmol.jmolBr() Jmol.jmolCheckbox(jmolApplet0, "polyhedra 6 bonds {zinc} collapsed [xFF9900]","polyhedra off;", "Show zinc octahedra") Jmol.jmolCheckbox(jmolApplet0, "load ../model/naomimodel/ZnGlyThrdeletedsome.cif {2 2 2}; showunitcell=false; showaxes=false; moveto 0.0 { -5 1000 5 90.23}; zoom 150; delay 0.01; isosurface henry '../jvxl/ZnGlyThr.jvxl' ","isosurface henry off", "Show cavity fill") Jmol.jmolBr() Jmol.jmolCheckbox(jmolApplet0, "slab 50; slab on;","slab off;", "Show cut away") Jmol.jmolCheckbox(jmolApplet0, "load ../model/naomimodel/ZnGlyThrdeletedsome.cif {2 2 2}; showunitcell=false; showaxes=false; moveto 0.0 { -5 1000 5 90.23}; zoom 150; navigate 5 center {7.048658894743519 16.587454890730665 9.23759116618376} / 5 rotate 180; set zslab 40; set zshade on; set echo top center; font echo 16 sansserif; color echo [xFF9900]; echo |click and drag to have a look around the pore", "load ../model/naomimodel/ZnGlyThrdeletedsome.cif {2 2 2}; showunitcell=false; showaxes=false; moveto 0.0 { -5 1000 5 90.23}; zoom 150; set navigationmode false; set perspectivedepth off", "Fly to the centre of the pore") Jmol.jmolBr() Jmol.jmolCheckbox(jmolApplet0, "showunitcell=true; zoom 120", "showunitcell=false", "Show unit cell") Jmol.jmolButton(jmolApplet0, "load ../model/naomimodel/ZnGlyThrdeletedsome.cif {2 2 2}; showunitcell=false; showaxes=false; moveto 0.0 { -5 1000 5 90.23}; zoom 150", "Reset") Jmol.jmolBr(); Jmol.jmolButton(jmolApplet0, "load ../model/naomimodel/ZnGlyThrdeletedsome.cif {2 2 2}; showunitcell=false; showaxes=false; moveto 0.0 { 585 683 438 166.19}; center {0.75 11.1 9.6}; zoom 300; set echo top center; font echo 16 sansserif; color echo [xFF9900]; echo |glycylthreonine linker|threonine residue; display atomno=148; delay 1; display displayed or atomno=163 or atomno=149; delay 1; display displayed or atomno=159 or atomno=160; delay 1; display displayed or atomno=161 or atomno=162; delay 1; display displayed or atomno=146 or atomno=147; delay 1; display displayed or atomno=164 or atomno=167 or atomno=166 or atomno=165; delay 1; display displayed or atomno=153 or atomno=154; delay 1; display displayed or atomno=155 or atomno=145; echo|glycylthreonine linker|glycine residue; delay 1; display displayed or atomno=156 or atomno=158 or atomno=157; delay 1; display displayed or atomno=150 or atomno=151 or atomno=152", "Build up glycylthreonine") Jmol.jmolBr() Jmol.jmolButton(jmolApplet0, "load ../model/naomimodel/ZnGlyThrdeletedsome.cif {2 2 2}; showunitcell=false; showaxes=false; moveto 0.0 { 528 -824 -206 14.36}; center atomno=288; zoom 150; display atomno=288; set echo top center; font echo 16 sansserif; color echo [xFF9900]; echo |zinc; delay 1; display displayed or atomno=172; echo |oxygens; delay 1; display displayed or atomno=289; delay 1; display displayed or atomno=691; delay 1; display displayed or atomno=528; delay 1; display displayed or atomno=696; echo |nitrogens; delay 1; display displayed or atomno=294; delay 1; echo |glycylthreonine linkers; display displayed or atomno=187 or atomno=173 or atomno=183 or atomno=184 or atomno=185 or atomno=186 or atomno=170 or atomno=171 or atomno=188 or atomno=189 or atomno=190 or atomno=177 or atomno=178 or atomno=179 or atomno=169 or atomno=180 or atomno=181 or atomno=182 or atomno=174 or atomno=176 or atomno=175 or atomno=191; delay 1; display displayed or atomno=543 or atomno=529 or atomno=539 or atomno=540 or atomno=541 or atomno=542 or atomno=526 or atomno=527 or atomno=544 or atomno=546 or atomno=547 or atomno=545 or atomno=533 or atomno=534 or atomno=535 or atomno=525 or atomno=536 or atomno=538 or atomno=537 or atomno=530 or atomno=532 or atomno=531; delay 1; display displayed or atomno=696 or atomno=697 or atomno=698 or atomno=702 or atomno=703 or atomno=704 or atomno=701 or atomno=691 or atomno=699 or atomno=700 or atomno=705 or atomno=706 or atomno=707 or atomno=708 or atomno=692 or atomno=693 or atomno=710 or atomno=713 or atomno=712 or atomno=711 or atomno=709 or atomno=695 or atomno=694; delay 1; display displayed or atomno=294 or atomno=295 or atomno=296 or atomno=300 or atomno=301 or atomno=302 or atomno=299 or atomno=289 or atomno=297 or atomno=298 or atomno=303 or atomno=304 or atomno=305 or atomno=290 or atomno=291 or atomno=306 or atomno=308 or atomno=311 or atomno=309 or atomno=310 or atomno=307 or atomno=293 or atomno=292; delay 0.1; echo", "Build up core structure")

Jmol.jmolMenu(jmolApplet0,[
[“”, “Select symmetry options”],
[“save orientation name; load ”{1 1 1}; restore orientation name; center; showunitcell=false; showaxes=false”, “1 by 1 by 1”],
[“save orientation name; load ”{2 2 2}; restore orientation name; center; showunitcell=false; showaxes=false”, “2 by 2 by 2”],
[“save orientation name; load ”{3 3 3}; restore orientation name; center; showunitcell=false; showaxes=false”, “3 by 3 by 3”],
[“save orientation name; load ”{4 4 4}; restore orientation name; center; showunitcell=false; showaxes=false”, “4 by 4 by 4”],
]);

ZnGlyThr

ZnGlyThr is a peptide-based MOF (metal organic framework) with the chemical formula [Zn(GlyThr)2], made from Zn2+ Jmol.jmolLink(jmolApplet0, “load ../model/naomimodel/ZnGlyThrdeletedsome.cif {2 2 2}; showunitcell=false; showaxes=false; moveto 0.0 { -5 1000 5 90.23}; polyhedra 6 bonds {zinc} collapsed [xFF9900]; zoom 150; delay 1; moveto 2 { -5 1000 5 90.23} 400.0 0.0 0.0 {2.93690849964129 8.144178890730673 9.23759116618376}; delay 0.5; wireframe on; spacefill off; select zinc and connected(6) or oxygen and connected(zinc and connected(6)) or nitrogen and connected(zinc and connected(6)); wireframe 0.2; percentVdwAtom=23; set zSlab 40; set zShade on”, “nodes”, “jmolLink1”) and glycylthreonine Jmol.jmolLink(jmolApplet0, “load ../model/naomimodel/ZnGlyThrdeletedsome.cif {2 2 2}; showunitcell=false; showaxes=false; moveto 0.0 { -5 1000 5 90.23}; zoom 150; delay 1; moveto 2 { -5 1000 5 90.23} 487.41 0.0 0.0 {0.75 11 9.6}; delay 0.5; select zinc or oxygen and connected(zinc) or nitrogen and connected(zinc); wireframe on; select zinc; spacefill off; set zSlab 48; set zShade on”, “linkers”, “jmolLink2”). Each Zn2+ is bonded to four dipeptide molecules with a distorted octahedral geometry. Two of the dipeptide molecules form a Jmol.jmolLink(jmolApplet0, “load ../model/naomimodel/ZnGlyThrdeletedsome.cif {2 2 2}; showunitcell=false; showaxes=false; moveto 0.0 { -5 1000 5 90.23}; zoom 150; delay 1; moveto 3 { -5 1000 5 90.23} 400.0 0.0 0.0 {2.93690849964129 8.144178890730673 9.23759116618376} 24.226115093834608 {0 0 0} 0 0 0 3.0 0.0 0.0; delay 0.5; select all; color translucent 0.65; select zinc or oxygen and connected(carbon and connected(carbon and connected(nitrogen and connected(zinc)))) or carbon and connected(carbon and connected(nitrogen and connected(zinc))) or carbon and connected(nitrogen and connected(zinc)) or nitrogen and connected(zinc); wireframe 0.2; color cpk; set zSlab 53; set zShade on; moveto 2 { -155 977 -148 83.62}”, “5-membered ring chelate”, “jmolLink3”).
This is a 2D layered framework with Jmol.jmolLink(jmolApplet0, “load ../model/naomimodel/ZnGlyThrdeletedsome.cif {2 2 2}; showunitcell=false; showaxes=false; moveto 0.0 { -5 1000 5 90.23}; zoom 150; delay 1; moveto 3 { -739 475 -478 107.3}; calculate hbonds (hydrogen and connected(nitrogen and connected(0, zinc))) (oxygen); color hbonds [x00FF00]; hbonds 0.1”, “interlayer hydrogen bonds”, “jmolLink4”) (green dashed lines). It is a rigid framework with very small structural changes when solvent is removed, unlike ZnGlySer.

C.Marti-Gastaldo, J.E.Warren, K.C.Stylianou, N.L.O.Flack, M.J.Rosseinsky (2012) Angew.Chem.,Int.Ed. ,51,11044

()

How useful was this page?

Click on a star to rate it!

Average rating / 5. Vote count:

No votes so far! Be the first to rate this page.

As you found this page useful...

Follow us on social media!

We are sorry that this page was not useful for you!

Let us improve this page!

Tell us how we can improve this page (in your own language if you prefer)? If you would like a response, please include your email address e.g. [email protected]

Provided by the