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It may be run by . it should be very useful for private study as a revision aid. Arguslab is available directly on Campus cluster PCs. with active teaching by demonstrators. .  This exercise is intended primarily to be used in a three-hour drylab session. After that.

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This covers all elements of the Periodic Table because it is not restricted to known atom types in its parameterisation. with a moderate library of useful molecules. though the range of elements covered is much less. AM1 or PM3 semiempirical levels. as well as single point calculations using these.1 of Arguslab has good facilities for calculating electron density or orbital surfaces at the semiempirical levels. Arguslab offers geometry optimisation using the MNDO. It can also map another property. Arguslab offers quite good on-screen molecule-building facilities. and displaying them. though it does use some common ones. There are also single point semiempirical calculations using Extended Huckel (for a bigger element coverage) or ZINDO (for excited states for UV/visible absorption prediction). e.g. Version 3. similarly to the display facilities of Chime (see Notes: An electronic model of methyl thiirane). and wherever possible one needs to reoptimise at a higher level. This will be the subject of a further document: Drylab: Calculating Surfaces using Arguslab  . Arguslab can do geometry optimisations using the UFF force field. The viewer is mouse-controlled quite similarly to Rasmol/Chime. The resulting energies are distinctly different from those obtained using some of the more conventional force fields. electrostatic potential. For this. onto a surface.

for the files created and read by Arguslab. One of these could be Argus.xml. using Windows Explorer. on its first read or write. molden.g. which need to be managed. and then beneath that folders for your various types of work. it will remember where to look at least for the duration of that signon. you will be able more easily to delete. By keeping its files separate from your other computer acitivities.xyz files for input to other programs. but it can also write . superfluous ones it leaves behind. It creates (and leaves behind) a lot of temporary files. e. Once you have pointed Arguslab to h:\work\argus (or whatever you set up). . I recommend that you never work directly in the home directory of this (i. áp Arguslab has been set up to write to and read from your own H: drive file space. . directly in My Documents). Arguslab writes its own format of molecule file. but rather create a folder called Work beneath this.e.

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you need to save your molecule with whatever name you want  doing a geometry optimisation     . áp In Arguslab. This is so that all the ancillary files will .  áp To start work. you should   press the 'New' button (top left) to get a new molecule screen.  you should press the 'Open' button to read in a molecule which you have saved previously in the your Argus directory.

You will find that if you have molecule windows open. áp It is best not to maximise the molecule window.  . files will be saved automatically with the name you used previously. Just drag its bottom right corner so that it fills most of the Arguslab worktop. If you forget to change the file name before modifying a molecule. possibly destroying data which you wanted to keep. this will just close one of these. click File Exit. áp To stop using Arguslab. have the right names. because then its title bar will display the name by which you are currently saving the files. You need to do it repeatedly to close all the windows (if you have several open) and then stop the program.

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     áp Press 'New' button (top left) to get a new molecule screen áp Read chair .

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. cc6 is the petroleum industry shorthand for . . so they will be compatible with any programs.. then when you have found the right file.. right click in the window áp Click the select button (diagonal yellow arrow) then click anywhere on the black background to get rid of the manipulator frame áp Save in your Argus directory as cc6cuff ?p BWT advice: keep names to 8 characters or less. Fragment Library.  from the fragment library by pressing the 'Add fragment' button (pencil pointing to benzene ring).

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OK Bunsen ?p You will see this goes more slowly than the force field method. The middle c stands for chair conformation. but nothing about it afterwards. to do PM3. are useful. then do the calculation by pressing the calculate button (Bunsen burner?) áp Save (this will overwrite your previous . you might have a Notepad window open (available from the PC desktop) and copy and paste the numbers with suitable annotations. It appears that you are intended to .] Close the output viewing window áp Save as cc6cpm3 ready to do a PM3 optimisation áp Set up Calculation. This is the UFF energy of chair cyclohexane. but is still very fast for this size of molecule áp Save áp List the output as before: you can see that Arguslab tells you a lot about the molecule  optimisation.xml file with the optimised version) áp Read the output using the list output button (looks like a sheet with writing on it) and note down the energy onto paper (a small positive number of Hartree units to high precision: you need all the digits!) from the end of the output file. set up to do a UFF geometry optimisation. [If you were doing this in real research. áp On the Calculation menu. which are only too easy with these tedious long numbers. OK the dialogue box. ?p Include the method which will produce the files in the file name: here the uff ending says that you are about to do a UFF geometry optimisation. so as to avoid the possibility of copying errors. which help you to make up file names self-evident to you. Optimise geometry. : any ideas. You could then save from Notepad to a text file afterwards.

áp Set this up by Calculation. including the final energy. Bunsen áp Now you can list the new (single point) output. run a single point calculation after the geometry optimisation to obtain the properties. and note down the energy in Hartrees (negative: this is electronic energy) from the last page of the output O. Energy: notice that you have to click PM3 again: it does not remember from last time.

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you will not accidently join atoms together by clicking on them ?p You can intentionally make a bond between two atoms by holding down the Shift key while clicking the two atoms in succession áp With the left mouse button. so that you can see it as a chair.) áp Change to Add atoms mode (button to right of select mode button) áp Click on the 4-coordinate C button áp Make sure the Automatic bond button (red bond joining blue atoms) is  lit ?p If Automatic bond mode is not on. Otherwise you may find the optimisation routine stops before it finds the minimum (in which case you can press Bunsen to continue with another bout) áp Save áp View the result by rotating the molecule . with the head atom on the left and the foot atom on the right. It should highlight yellow. rather than breaking just one ring bond and trying to rotate singly attached carbon to the right position for boat. hold down the shift key. click on the atom at the foot of the chair. and click on the other terminal carbon atom. (In this program. and so that you can see all the atoms separately ?p The button with an arrow with a red ring around its shaft switches left drag to rotate the molecule around the z axis ?p The intersecting elipses button switches back to x or y rotate áp In select mode. so that you can change the maximum number of steps from 100 to 200 before you start. and right click to put a carbon there áp Hold down shift. to remove that carbon. select one of the currently terminal carbon atoms áp Place the mouse cursor as carefully as possible where you judge the missing carbon of the boat conformation should be. so as to close the ring áp Change to Select mode áp Press the add hydrogens button (H) áp Save áp To do a UFF geometry optimisation you could press the pincers button (for pulling things roughly into shape?) but you might as well use Calculation Optimize geometry to set it up. Cylinder Normal) áp Turn the molecule so that you are looking at the ring approximately edge-ways on. for this molecule. Display settings. áp Open your model cc6cuff áp Save as cc6tbuff áp Remove hydrogens with the Delete Hydrogens button (H with an eraser) áp View as sticks (View. it is easiest to remove it altogether. Then press the delete button on the keyboard.

and find the PM3 energy of the result. áp Find the UFF energy as for the chair conformer. it does not matter for present purposes which one you have found. c. As they are of equal energy by symmetry. If you have. then do a PM3 geometry optimisation (file name cc6tbpm3). as before. and you need to do this experiment again ?p You will not have found a boat conformer (C2v symmetry) because this is not stable for this molecule: it is a saddle point between two twist-boat enantiomers ?p You should have found one of these twist-boat conformers. ?p You should not have landed back in the chair form. you did not get your built geometry close enough to that of the required conformer.

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converting the energies to kJ mol-1. would convert to  = [more stable]/[less stable] = 12198 ?p What is your assessment of the UFF and PM3 methods for finding energies for this molecule?  . this is a useful number to store for present purposes áp Convert each of the two energy differences to an equilibrium constant. Which is the more stable? áp By careful use of hand calculator. 8. the experimental energy difference is 23 kJ mol-1. you should have found that the UFF and PM3 methods have given the same order of stabilities for the two conformers. ° is the gas constant. find the energy of the less stable conformer relative to the energy of the more stable. To convert from Hartrees to J mol-1.  áp Remembering that one gives positive energies and the other negative. which on the present basis (ignoring entropy). multiply by 2625515. not kJ mol-1. for each method.3145 J K-1 mol-1 (another good constant to store!) áp According to Goodman. using the Boltzman distribution:  = exp (-_c/ ° ) Remember that _chas to be in J mol-1. Use = 294 K. If you have spare storage in your calculator.

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 áp To know where you are in modelling methyl.

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you need to find the symmetry elements in twist-boat . hexane conformers.

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which means that it has (only) three mutually perpendicular 2 axes: one threading the centre of the ring. the molecule is chiral. The molecule has 2 symmetry. and rotate the model so that you look down each of these axes in turn. i. . one through two opposite carbons. and one through the middles of two opposite bonds áp Display sticks. this is one enantiomer . and convince yourself that they are indeed 2 axes. Leave the model so that you are looking down the axis which passes through the bonds áp Because there are no improper axes (including planes or centres of inversion) in 2.e.

?p The top two carbons on your screen should now come towards you from back left to front right. ?p Turn the model carefully about the x axis (i.e. downward left drag) until you are looking down the axis which threads the ring. or — .

you use the models of the two conformers of . The other enantiomer has the bond going the other way O       In this part of the exercise. you always get back to the same sense.—. If you turn the ring through 180° in either direction.

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 . Write these down. do a preliminary UFF optimisation. áp Be very careful to use Save as. to create models of the five conformers of methylcyclohexane. to save each model with a different name. then a PM3 single point calculation to get relative energies. which you have saved. and calculate energies relative to that of the most stable of the five conformers.. For each.  you start to construct it from the . then a PM3 geometry optimisation.

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  model. otherwise you are very likely to overwrite the .

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  model by accident. which will be a nuisance because you will need to use it again for constructing the next conformer of methylcyclohexane áp Start with twist boat .

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in select mode. These will give two different conformers of methylcyclohexane ?p Possible filenames: mecc6tbparuff and mecc6tbperpuff áp To substitute the methyl group. áp When you have done the three twist boat conformers. go on to the chair conformer of . . then do UFF optimisation. Select C sp3 áp Add hydrogens to the new carbon. rather than reaching the number of cycles limit. so replacing either by CH3 will give the same conformer ?p The two H atoms on the distant carbon are related to the first two by the C2 axis which passes through bonds. etc. using the Add H button áp Save. left click on Change atom. so replacing any of these  H's will give the same conformer ?p Possible filename: mecc6tbonuff (difficult to keep this short! the 'on' means attached to C  a C2 axis) áp Look down the axis which passes through the bonds ?p On each C nearest to the axis. On the drop-down menu which results. right click on the H to be replaced. Save and go on to the PM3 optimisation. Make sure the job has converged. while its symmetry is fresh in your mind áp Look down the axis which passes through carbon atoms ?p The two H atoms on the near carbon are related by the symmetry axis. there are two kinds of H: one approximately parallel to the axis. and one approximately perpendicular to it.

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not directly towards you ?p These H's are called 'equatorial' and are related by the S6 axis.  áp This has D3d symmetry. i.e.e. so they are all equivalent . so that you see the ring as a regular hexagon ?p On every carbon there is a hydrogen pointing outwards. so it has a S6 axis threading the ring áp Look down this S6 axis. i.

the MM2 relative energies are: 0. When you have the book to hand. there are three H atoms pointing directly towards you. in kJ mol-1 ?p According to Goodman. see which has the lowest energy ?p Calculate the PM3 energy of each of the others relative to it. 24. try comparing it with your notes from these exercises    .61. parallel to the S6 axis ?p There are another three.44. and 30.68. which is which. ?p Possible filename for the methyl derivative: mecc6cequuff ?p In the same view. so you should not be able to see them ?p These six H's are called 'axial' ?p Possible filename for the methyl derivative: mecc6caxuff áp When you have all five conformers.02 kJ mol-1 ?p How do the differences between these compare with yours? It is not completely clear from his pictures. related to these by the S6 axis. 26. 7. pointing directly away from you.

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Students are expected to have already learnt basic modelling operations using Arguslab. As with the first exercise. Drylab: Modelling using Arguslab. with active teaching by demonstrators. It may be run by . and instructions given there will not be repeated here. Arguslab is available directly on Campus cluster PCs.  This exercise is intended primarily to be used in a three-hour drylab session. the present one should be very useful for private study as a revision aid. . and will particularly help students to understand the parts of the modelling lecture course dealing with surfaces. in the first drylab session.

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You will map its electrostatic potential onto one of these. In this exercise. " . you will create a model of methyl vinyl ketone ! and display some of its molecular orbitals as surfaces. and come to some conclusions about the reactivity of the molecule..

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  áp Start Arguslab áp Press the New button (top left) to get a new molecule screen ?p The window is automatically set to Add Atoms mode (button with pencil pointing to a blue ball) and Automatic bond on (button with red bond joining two blue atoms) .

at a suitable distance from the methyl carbon. left click the carbonyl carbon to select it. then shift right click to add the oxygen You should have an appropriately shaped skeleton. right click to add this towards the left of the window áp Click the 3-coordinate C button. do it again until it does converge áp Save again þ  . then. If it stops after 100 iterations without converging. shift right click to add and join the carbonyl carbon áp Shift right click to add the alpha vinyl carbon. áp Click the Select button to exit from Add atoms mode áp Add hydrogens with the H button. áp Set Automatic bond off. so that you will only make bonds when you shift click a selection áp Starting with 4-coordinate C for the methyl group. You should get the right number áp Save the molecule as mevnket áp Use the pincers button to do a UFF geometry optimisation. and again to complete the vinyl group áp Change to 1-coordinate O.

so that you can follow them when you improve the geometry. you have hit a bug: simply left click the first atom again to start again áp The bond angle symbol nearly to the right of the top tool bar should now be ungreyed. you do multiple selections by left clicking the first atom.. or at least set the display back to View Display settings.. in the order end. If everything turns yellow. in order to read the numbers for the angles áp Write down the three bond angles. (b) the sum of the angles? (The sum should be exactly 360º for planarity) ° . switch the display to ball and stick. end.  Here you will measure the three bond angles at the carbonyl carbon. In this case the middle atom is always the carbonyl carbon áp In Arguslab. using View Display settings. Cylinder Normal. The correct skeletal atom balls only should turn yellow. Click it to put a green angle monitor on the screen áp Repeat for the other two angles áp You may need to rotate the molecule a little. noting which is which ?p What do you learn about (a) the equality of the angles. and set monitors on these. then holding down the Control key while left clicking the other (two) atoms in turn ?p Do this for the first of the three angles.. áp So that you can aim with the mouse more easily. Ball cylinder Normal áp To measure angles (here as in other modelling programs) you need to select the three atoms forming the angle. middle..

 þ    áp Save as mevnketpm3 .

áp Calculation Optimise Geometry PM3 OK áp Click the Bunsen button ?p As the optimisation proceeds. but consider also steric effects)    . Save again áp Write down the new values of the bond angles ?p Why do you think they have changed in this way? (Remember VSEPR. you will see the angle monitor values change áp When the optimisation has succeeded.

and 16 ?p Do not change the grid spacing suggested by Arguslab áp OK OK out of the dialog áp Click the Bunsen button ?p You will see (in the text window) Arguslab calculating two-dimensional slices of the cubic grid for each MO and for the ESP. which will be named automatically áp Switch off the angle monitors using Monitor Remove All Monitors áp Set up a single point Calculation Energy ?p Select PM3 and click the Surface Properties button ?p Click Electrostatic Potential ?p In the Click Orbitals to Plot box. 15 (LUMO). click MOs 13. Arguslab will store the resulting three-dimensional array of values as a separate file. at each of a cubic grid of points covering the space occupied by the molecule. and of the electrostatic potential. For each function you select. but nothing yet appears in the picture           A . 14 (HOMO).     In this step you will calculate the values of some wavefunctions.

e. We need to view the whole molecule. Generally.g. of a wavefunction. e.g. to select a plane which contains all the features of interest of a delocalised MO. in three-dimensional space. The three-dimensional counterpart of a contour is a .  is a line in  -dimensional space which connects points having a particular value. Contour plots of wavefunctions in a plane through a molecule are used in elementary teaching of MO theory of symmetric molecules. however. it is not possible. it contains one or two bonds. They may be useful for bigger molecules if a plane can be found which passes through a region of interest. and hardly ever easy.

which have a particular value of some property. Arguslab now just needs to select all the entries in its stored array which have your selected value of a contour level. In the previous section. which passes through all points in -dimensional space. so the surface will also rotate. so it can draw a view of a surface connecting these selected coordinates. you calculated some MOs and the ESP of the molecule at all points of a three- dimensional grid. For an orbital which you want to display. click Properties Surfaces . áp On the main menu bar. Just as it can draw on the screen a perspective view of a plastic ball to represent an atom. so that you can see different features of it. As you rotate the model on the screen to see different atoms.

then type m. so that your viewpoint is in the O nodal plane . In three dimensions. then click the word mesh which appears ?p Do not try to alter the word in the box by typing directly. áp Left drag the cube for MO 16 into the empty Grid box of the central work area of the dialog box.e. you have a tree of Grid Files (which you stored in the last section) áp Click the + against RHF MOs áp You should see four cube symbols representing the cubic grids you have calculated. áp The larger the contour value. selecting the contour value usually needs to be done by trial and error.07 áp So that you can see the model of the molecular geometry through the surface. select the icon for it (an object with a torch shining on it) and click the Toggle Display button ?p The icon in the Currently Defined Surfaces tree will light up. since any number of non-intersecting lines in the chosen plane can be seen at the same time. wavefunction values of +0. Cylinder Normal áp Positive and negative surfaces (i. it is usually practicable to see only one surface at a time. áp On the left of the resulting dialog box.07 and -0.. or in the case of orbitals with nodes. so that you cannot see one inside the other. In a two-dimensional contour plot. to show which one(s) you want switched on áp OK out of the dialog box áp If you are still in ball and stick view. otherwise you may hit a bug áp Press Create áp A new Simple Surface icon will appear in the tree of Currently Defined Surfaces on the right side of the dialog box áp To switch the display of the surface on. áp A higher value tends to emphasise the difference in size between different lobes ?p If you choose too high a value. useful detail will be lost áp Set the Contour Value to 0. It is initially set to 'Simple Surface'. set Render Mode to mesh ?p Do this by clicking the Render Mode dropdown arrow. several different contour values are often plotted at once. to explore what information different values will yield. you will not see the smaller lobes at all ?p If you choose too low a value. since higher values of the wavefunction are occur nearer to the nuclei. one positive and one negative surface joining points with plus or minus a particular numerical value respectively. change to sticks with View Display settings.. You can change this to 'MO above LUMO' to remind you of what you will be looking at In real research. where you will be able to set up the contour value and kind of display you want áp The next typein box below the name of the grid file contains a name for the surface. the smaller the spatial extent of the surface. This is because surfaces for orbitals (or ESP) are closed surfaces.07) are coloured blue and red respectively áp Turn the molecule to look in the plane of the conjugated system.

g. in the same way. e.g.07 ?p On viewing each.  Õ O or OÕ) ?p Why are the lobes on oxygen smaller than those on carbon? Now you can look at the other three MOs you have calculated. . for MOs 15 (LUMO). as follows áp Go back to Properties Surfaces ?p The dialog box will reopen in the state in which you last saw it áp Select the lit up surface icon. ?p In each case. ?p How many antibonding nodes are visible? ?p Can you name this orbital type (e. when we consider reactivity áp MO 14 (HOMO): ?p As this MO contains electrons in the ground state of the molecule. answer the following questions: áp MO 15 (LUMO): ?p Why is this orbital more stable than MO 16? ?p How many antibonding nodes are visible? ?p Observe that this MO is both bonding and antibonding at the same time p Which atomic contacts is it bonding across. where should they be? p Can you reinterpret this MO as being mainly a lone pair orbital? p What does this tell you about the reality of lone pairs. and nearly empty antibonding orbitals. set the Contour Value to 0. 'lone pairs')? If so. but MOs as they are usually calculated are delocalised and are either exactly full (singly or usually doubly occupied) or exactly empty in a particular state áp MO 13 (MO below HOMO): ?p What combination of localised orbitals best corresponds to this MO? c   . and click the Toggle Display button to turn it off (before in due course you turn another one on) áp Repeat the above procedure for creating surfaces. in ordinary MO theory like this? p NBO analysis is able to reassign the calculated electron density to nearly full lone pair or bonding orbitals. and which is it antibonding across. 14 (HOMO) and 13 (MO below HOMO). and the types of these bonds or antibonding effects ( or O ?p Remember the rule from elementary MO teaching that stable molecules usually have MOs filled with electrons up to and including the non-bonding valence orbitals p Would you expect this molecule to have any non-bonding valence electrons (i. in that order. O or ? ?p Which carbon atom carries the biggest lobes? p This will be important later. it will have a real bonding or antibonding effect ?p Make a list of which atomic contacts this MO is bonding across and which it is antibonding across. and what are the types of these bonds.e.

generate a simple surface for the Electrostatic Potential gridfile. we could instead map the ESP onto a surface of total electron density. using the same settings as for the MOs which you studied áp This surface is not very helpful: it shows that the space around the oxygen feels a negative potential. and toggle off the display of the ESP surface áp Click the Mapped tab on the top of the central work area of the dialog box ?p This is similar to the simple surface work area. which you could have guessed from elementary ideas of electronegativity ?p Changing the contour level. for a very large molecule). which we shall use here. but has two boxes to fill in instead of one áp Into the Main (Grid 1) box. altering the level. It is of interest when considering the attack of charged or dipolar nucleophiles or electrophiles on the molecule.17 ?p Min Map Value to -0. but colour it according to the value of the ESP at each point. and hence did not want to know about the LUMO. does not allow more interesting variations in the ESP to be identified áp To attract a negatively charged or strongly dipolar nucleophile. áp From Properties Surfaces. In the absence of electronic method data. In an earlier section you have already calculated the ESP at every point of the cubic grid covering the molecule. and that around the rest of the molecule feels a positive potential. which you can do within the Properties Surfaces dialog box by dragging the surface icon back onto the work area in the middle. of Colors to 200 áp Set Render Mode to transparent.g. but on the distribution of the whole electron density and of the nuclei. drag the ESP Grid File cube áp Call the surface 'ESP onto LUMO' áp Set the Contour Value to 0.07 as before áp For most useful colouring (found by trial and error so as to maximise differences between sites of attack) set ?p Max Map Value to 0. is to show the LUMO as a translucent surface. or. It does not depend on a knowledge of individual orbitals. there needs to be a high positive potential where there is also a dense lobe of the LUMO ?p A method has to be used which can show the values of the LUMO wavefunction and the ESP at the same time at the same point ?p A popular method. so that you have a more continuous surface than a mesh to display the colour on áp Click Create . drag the LUMO (MO 15) Grid File cube icon áp Into the Mapped (Grid 2) box.02 ?p Num. if electronic data were not available at all (e. onto a Van der Waals radii surface áp Raise the Properties Surfaces dialog box. then pressing Update. using a range of colours rather than just two for positive and negative p If we were not interested in a covalently bonded transition state.Electrostatic potential is the repulsive or attractive energy felt by a unit positive charge as a result of the combined effect of nuclei and electrons in the molecule. it can be calculated approximately from electronegativities.

and OK out áp Look into the plane of the O node as before ?p You should see that only the lobes on the carbonyl carbon are violet. áp A surface icon should appear in the Currently Defined Surfaces tree. which has the biggest lobes.07 ?p Only a very small portion of the LUMO. feels a negative potential áp Write down a conclusion about the likely sites of attack of ?p a soft nucleophile. at this contour level. in which the need for overlap is balanced against good electrostatic attraction p . dipolar nucleophile. the highest ESP on the scale (>+0.15). is tinged with cyan. on the outside where they could be attacked ?p The terminal vinyl carbon. representing about +0. under Mapped Surface áp Toggle Display of it on. depending on good overlap in a covalent transition state ?p a hard.