students guide to shelxtl

7/25/2019 Students Guide to SHELXTL

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Students guide to SHELXTL:

We will first give an overview of the programs structure and then deal step by step withhow it is used to solve and refine a structure.Overview of program structure

The program only requires three files of which one (name.p4p) is only used at the verybeginning. An overview of the program and its structure is given below

!"#$%T$&%'#'

name.hl* name.p4p

name.ins

name.prp* name.pcf

!"#$%T$&%!

name.res

!"#$%T$&%'

name.ins

!"#$%T$&%$

name.res

name.lst

name.lst

+verview of !"#$%T$

edit

Thus the initial input files are the name.hl file and the name.p4p.The hl file is the measured data as obtained from the %,ray diffractometer and contains(usually) the results of several thousand measurements. #ach individual measurementwould have the format 2 4 3 12041.0 163.468


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The first three numbers are those of the set of -iller planes from which the reflectioncame. The fourth number is the measured intensity and the fifth number is the error in themeasured intensity.The p4p file contains the cell constants (three lengths* a* b* c* and three angles* , , )and other information about how the data was collected.

y using these two files several things can be done at the beginning using the program%'#'/. #0amine the e0perimentally measured data1. 2etermine the space group3. Write the initial instruction file (name.ins) for solving the structure.

+nce we have the initial name.ins file we can use it to solve the structure using 2irect-ethods via the program %!. These methods are based on probabilities about thedistribution of electron density within the unit cell. Two factors on which it is based arethe fact that in a real unit cell the electron density has to be always a positive number. A

second fact is that the electron density is not evenly spread out but concentrated in certainlocations* i.e. atom positions. The net result is that in favorable circumstances (and wewill only loo at favorable circumstances) we can obtain a solution which gives us atomicpositions5.

The output from %! is a file called name.res (results file). All calculations give such a fileas well as a name.lst file which details what the program actually did5. This file isvisuali6ed with the aid of the program %'#' (which is the graphical viewer that we canuse to loo at the molecules&solution)."ere we can loo at the results of the calculation (either structure solution or structurerefinement) determine what atoms are present and name them. After this is done the

result is then written to the name.ins file.This new name.ins file is then used as input to the program %$ (structure refinementprogram) to improve the model. The %$ program produces a new name.res file. This fileis then visuali6ed in the %' structure viewer and the model improved by including moreatoms. The improved model is then again written to the name.ins file which is then usedfor further refinement using %$.

These steps are repeated until all the atoms have been found* identified* and labeled.

Detailed instructions of how to use SHELXTL

A XPEP/. 7irst we have to start the program. When we open we see that there is a menu baracross the top with several options. The only ones that we will be using are 'ro8ect*%#'* %!* %$* %'* %9:7* and #dit. We always begin with 'ro8ect which either starts anew pro8ect or opens an already e0isting 'ro8ect.

1. !o we use the left most pull down menu called 'ro8ect.


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3. We see that we have several options so we have to mae a choice(a) ;ew < if we are beginning a new pro8ect(b) +pen < if we are coming bac to a pro8ect we have already started woring onWe will assume that this is a new pro8ect and go through those steps.

4. We chose +pen. ;ow we have to browse through the directories to find the files forour pro8ect. #ach pro8ect will have its own folder. :n our case the folders will be in afolder on the 2estop.

=. We open the folder of the structure we want to wor on.

>. ;ow in the window we see two files listed? name.hl and name.p4p. We can clic oneither to highlight it.

@. ;ow at the top we have to give the pro8ect a name. :n principle we could call itanything but usually we give it the same name as the file name. This pro8ect name is what

we would loo for if we were coming bac to re,visit the structure so giving it a namewould help us to find it better (after all if you are lie me you might have been dealingwith several hundred pro8ects).

. After we have named the pro8ect and chosen the file the window closes and we see thepro8ect name and pro8ect path. The pro8ect path is where all programs will go to find thefiles for input into programs and where all output files will be written.

B. ;ow we are ready to begin. +ur first tas is to e0amine the data* determine the spacegroup and proposed molecular formula* and write the files which will be used to solve thestructure.

/C. All mentioned in B is achieved through the use of the program %'#' so we openthis program from our graphic user interface.

//. When we loo at this pull down menu we see we have two options. %'#' or"DE%'#'. We could actually use either in most cases. "owever* we would usuallychose %'#' unless the data file was too large to be read by %'#'* in which case wewould use "DE%'#' (huge %'#').

/1. After choosing %'#' we see several things(i) The program has automatically read in the data from the data files* name.hl andname.p4p.(ii) The program has looed at lattice type and made a suggested choice which is insquare bracets. Whenever the program maes a choice about some parameter it isalways enclosed in square bracets. This choice is based on systematically absentreflections in the hl class of reflections. "ere the types of lattice are listed as' A 9 : 7 +bv ev AllDnless we have good reasons not to* we always accept the choice made by the program.!ince the choice made by the program is indicated in the square bracets (e.g.* '5) if we


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want accept this choice all we have to do is use the F#nterG ey. This is also true for theother options mentioned below. :f we agree with the choice made by the program all wehave to do is press the Fenter ey.

/3. After choosing the lattice type the program ne0t wants to search for higher metric

symmetry (option "5 in the menu). This is because to find such higher metric symmetrywe need a whole data set which is usually not available until after all the data has beencollected so we can only do it at this stage.

/4. This is a very important step so we should discuss it a little. 2epending on crystalsystem (triclinic* monoclinic* orthorhombic* etc) there are various classes of reflectionswhich should have the same value (minor variations are allowed* lie crystal shape*absorption problems* etc). 7or instance in the monoclinic system the following reflectionsshould be equivalenthkl = h-kl = -hk-l = -h-k-l7or orthorhombic

hkl = hk-l = h-kl = -hkl= h-k-l = -hk-l = -h-kl = -h-k-l!o the program averages the reflections which should be equivalent for a given systemand reports a merging factor (int)5. This value should be as low as possible (ideally6ero but since these are real measurements this is never the case). :n our case we willaccept any value less than C./C. :f there are several options we chose the one with the onewith the highest symmetry which has a reasonable value for (int). Dsually the programhas made this choice for us.

/=. ;ow we are given the option of either determining the space group or inputting it !5.We will accept this.

/>. :f we wanted we would choose :5 at this stage but we usually want to let the programdetermine the space group so we choose !5.

/@. ;ow the program gives us the option of changing the crystal system but usually wego with the choice of the program.

/. ;ow the program gives us the option of changing the crystal lattice but usually we gowith the choice of the program.

/B. The program now groups reflections into classes and loos for systematically absentreflections. ased on these absences it suggests a possible space group. !ometimes thereis more than one choice as the systematically absent reflections only give informationabout translational elements of symmetry such as glide planes and screw a0es.

1C. ased on the systematically absent reflections and taing into account some otherfactors* such as the frequency with which the space group has been found in other nownstructures* the program maes a suggestion as to what is the correct space group. Dsuallythis is correct and we can accept its choice.


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1/. After we have accepted the space group the program has highlighted option 9 (defineunit cell contents). This is where we are going to enter the e0pected formula for thecompound we are woring on so we accept this.

11. :n some instances the e0pected formula has already been entered during data

collection and this will appear at the top of the page. :f this is present we will accept it."owever* in other cases the formula was not entered and we have to enter ourselves.There are some conventions as to how we enter the formula (although the order in whichwe enter the elements does not affect the correct operation of the programs). We alwaysstart with carbon* then hydrogen* and then the other elements in order of increasingatomic number. !ingle letter elements are entered as upper case (9apital letters) andelements with symbols containing two letters have the first letter upper case and thesecond letter lower case. After each element symbol we give the number of that type ofelement in the e0pected formula. As an e0ample91= "1 ;4 +4 9l1 9u:n our case for this compound we will use the formula

9/1 " ;4 +113. After we enter the formula the program does some calculations based on the formula.(i) !ince it nows what the cell constants are and hence the volume of the unit cell* basedon the formula that was entered it will calculate the number of formula units in the unitcell (to the nearest whole number).(ii) :t calculates the density. :n the old days it was e0pected that there would be availablethe measured density but these days very few people measure the density of their crystals.(iii) :t calculates the average atomic volume for non,hydrogen atoms. :n most crystalsthis number is usually very close to / so if we see that number it is a good sign.(iv) :t calculates the per cent (H) composition. :f you have previously had you compoundanaly6ed these values should agree.

14. After entering the formula and checing that the number maes sense we acceptoption #5 to get bac to the main menu.

1=. ;ow we see that the program is highlighting option 75 which sets up the files weneed to solve the structure. We accept this.

1>. The program now creates the I.ins file needed to solve the structure and displays theresult.

1@. ;ow we have to name the files.(i) Dsually we have the name already suggested in square bracets* e.g. 9-15. :f this isthe case we accept this.(ii) +ccasionally there is no suggestion as to name. This happens when the order of thea0es in the unit cell has to be changed to get the space group in the conventional setting.This is quite common if the crystal system is orthorhombic.(iii) !o we either accept the name suggested by the program or enter a new name.


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(iv) The program now ass if we want to overwrite the hl file and has option ;5. Wehave to say FJG so that the program writes the necessary files

1@. After writing the files the program has option K5 highlighted as it thins we arefinished. We accept this.

1. ;ow we need to loo at the I.ins file and edit it (if necessary). To do this we use theedit option from the menu bar and pull down to show F#dit insG

1B. This opens the I.ins file for editing. We see it loos lieT:T$ cmCB,1 in '1(/)&c9#$$ C.@/C@3 /1./>@4 >.B=B /1.@1B> BC.CCC /[email protected]/ BC.CCCL# 4.CC C.CCC3 C.CCC/ C.CCC3 C.CCC C.CC3 C.CCC$ATT /!J-- ,%* C.=MJ* C.=,L!7A9 9 " ;

D;:T 4= 4= BT#7"N$7 4#;2

There are several things to note here.(i) This is a file used to solve the structure using 2irect -ethods.(ii) :t consists of a series of lines* each of which begins with a four letter code(iii) The first it T:T$. This 8ust gives a title and can be anything. %'#' has given a titlewhich includes the structure code (file name) and space group.(iv) The ne0t line starts with 9#$$ and reports first the wavelength used. :f the files hasbeen written by %'#' it will always have the value C.@/C@3 which is the wavelength of%,ray generated from a -o anode in the %,ray tube. This is the default wavelength."owever* sometimes the data has been obtained using a 9u anode which has a differentwavelength (/.=4/@ O). This is the case for this structure so the line9#$$ C.@/C@3 /1./>@4 >.B=B /1.@1B> BC.CCC /[email protected]/ BC.CCC!hould be changed to9#$$ /.=4/@ /1./>@4 >.B=B /1.@1B> BC.CCC /[email protected]/ BC.CCCThe rest of the line reports the cell constants.(v) The ne0t line starts with L#. This is a composite of L (the number of formula unitsin the unit cell) and #* the errors in the cell constants.(vi) The ne0t line reports the lattice type (' A 9 : 7 etc) as a code (e.g.* / for '* @ for 9*etc). The value can be M or ,. "ere we see / (which is positive). This means that the unitcell (but not necessarily the molecule) contains a center of symmetry (center of inversion)as part of its symmetry elements.(vii) The ne0t line lists the unique set of symmetry elements which defines the spacegroup. :n the case of the space group '1/&c these are four such elements1. x, y, z

2. -x, -y, -z

3. -x, 0.5+y, 0.5-z


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4. x, 0.5-y, 0.5+z

#lement / is always present in every space group. #lements / and 1 indicate a center ofinversion. 3 is the result of the screw a0is and glide plane. 4 is the same as 3 with the signof 0* y* and 6 changed. !ince $ATT / has already indicated the space group iscentrosymmetric and all space groups contain element /* both of these are not necessary.

#lement 3 is unique and thus is specified on the !J-- card (!J-- ,%* C.=MJ* C.=,L).#lement 4 is 8ust 3 with the signs changed due to the fact that for every F0*y*6G elementthere is a F,0* ,y* ,6G element. !o the program only has to list the unique element and allothers can be derived from this.(i0) The ne0t line indicates what elements are present (or e0pected as at this point wehavent solved the structure and dont now for sure what is there). Dsually in this line 9is first then " followed by the rest of the atom types in order of increasing atoms number.(0) This list the unit cell contents for each type of atom listed in the !7A9 line. Thenumbers come from the formula we entered in %'#' multiplied by the L value on line1.(0i) The first seven line will be in every I.ins file from now on (although we might have

to edit the !7A9 and D;:T lines if when we solve the structure it turns out to be differentfrom what we e0pected).(0ii) The ne0t line 8ust contains FT#7G. This is the instruction to solving program (%!)to attempt to solve using 2irect -ethods. :f you wanted to use an alternative method* liethe "eavy Atoms method then this would change to F'ATTG. This could be used if themolecule contained an atom (or atoms) which were much heavier than the rest. :n mostcases you will be using T#7.(0iii) The ne0t line"N$7 4Pust tells the program what format to e0pect in the I.hl file containing the measureddata.

3C. There is one line we should enter after the first @ lines. This is to report at whattemperature the data was collected. :n this case it was ,/>3 Q9 so we add the lineT#-' ,/>3after the D;:T line.

3/. ;ow we are finished editing the I.ins file. :f we made any changes we should saveand e0it

31. ;ow we attempt to solve it using the program F%!G on the main menu bar. This hasno pull down menu so as soon as we use it the program commences.

33. The important points to notice from the output on the screen are(i) The 97+- number which the 'rogram has used which is indicated by having FIGafter the value (e.g. C.C4I) .(ii) The F#G values reportedoth these are near the bottom of the output. oth the 97+- values should be as smallas possible. Ralues for e less than C.1 usually indicate that the structure has been solved.


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34. When a program (lie %! or %$) does any calculations it uses an I.ins file(instruction file) and writes a I.res file (results file). :n addition it also writes a I.lst file.This file contains details about what the program actually did. :t is useful to trac downproblems or to understand what the program did.3=. ;ow we have to loo at what the solution loos lie. To do this we use the program

F%'G on the top menu bar. This reads the I.res by default.3>. When we open the program the program there are a lot of words followed by%'SSThis is where we enter four letter commands which tell the program what to do. :f we areunsure of what commands are possible we can type"#$'This will lit all possible commands. :f we want information about a particular commandwe type"#$' AA2This would list details about how to use this command.

3@. :n our case usually the first command whenever we open %' is7-+$ (or 7-+$&;)This reads in the contents of the I.res file. :n this case it will read in the contents of theI.res which contains the structure solution (if %! was successful).

What has happened when %! was used in step 31 above is the program has phased someof the data (obtained the correct phase) using probability methods and then calculated amap of the electron density of the unit cell. 7rom this map of electron density it hassearched for possible locations of atoms (areas where the electron density is larger thanthe surrounding areas* called peas). :t has then obtained both the pea height (electrondensity) and location for each pea and written it to the I.res file as an unassigned atom(the program does not now what ind of atom corresponds to each pea). Dnassignedpeas are given the symbol K followed by a number corresponding to where it is in thelist of peas. Thus the largest pea would be K/* the ne0t largest K1* etc.

3. When we type 7-+$ it reads in the I.res file and lists the contents (in this case areseries of K values).

3B. We could loo at this by using the following commands-'$;'+P (or 2:AE)(i) The -'$; instruction calculates the best mean plane through all the atoms and thenmaes this plane perpendicular to the screen (usually the best view for displaying themolecules).(ii) '+P displays the molecule in a way that we can manipulate it using the tools on theright side of the screen (mouse or eyboard driven). Dsing this we can move the moleculeto get better views. 2:AE also displays the molecule but in a fi0ed view but does alsoallow us to view the molecule while also displaying%'SS


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which enables us to type in commands.

4C. This first view has the loo of an organic molecule (we see rings) but there appear tobe K peas in areas where there should be no atoms. This is because the %! program has8ust listed a certain number of peas (usually more than there are atoms) and some 8ust

correspond to noise. :t would help us if we could remove those peas which are 8ustnoise. To do this we have to have the command line (%'SS). !o if you have used 2:AEto display you can enter the necessary commands but if you used '+P (which has theadvantage of being able to rotate the molecule) we need to e0it this. This can be easilyaccomplished by pressing the F#scG ey once of twice.

4/. With the %'SS displayed we type in :;7+ (short for information) which listsinformation about the K peas (or atoms if there were any). There are /1 columns of data.What we are interested at this stage is contained in the last column under FpeaG. This isthe pea height. +n looing at the values we see that they gradually decline for the first/ Ks (K/ to K/) and then there is a sudden change from /==.B/ to =4.>/. This is an

indication of where the real atoms end and noise begins (this drop off is usually present inan organic compound but often not when the compound contains a heavy atom).emoving peas after K/ will improve our view.

41. We can remove these peas using the commandN:$$ K/B to K13

43. ;ow we can loo at the result using 2:AE (pressing enter twice). This displays themolecule while allowing us to use commands (%'SS).

44. We see that it loos lie an organic molecule. We now it contains 9* "* ;* and +. :fwe now what the structure is supposed to loo lie then we can mae atom assignments.We can also use pea height to help us. +bviously + contains more electrons than ;* and; more than 9. !o we would e0pect to that the + and ; atoms should be the larger peasand thus near the top of the list.

4=. We can use the ':9N instruction by typing this in after %'SS and pressing enter.

4>. ;ow we see the K pea with the largest number (K/) is flashing. This means we canlabel it. We type in an appropriate label (9/) and press enter. ;ow K/@ is flashing. :f wewant to number the 9s systematically then this would probably be 9= so we type this in.;ow K/> is flashing so we type 9>.

4@. :f we mae a mistae and want to go bac and change labels on any atom then thiscan be done by pressing the acspace () ey. :f we are not sure about a label for aparticular K and want to go on to the ne0t K pea then we can press the space bar. :f wewant to delete a particular K without labeling it we press the FenterG ey.

4. We eep going in this way until all atoms are labeled.


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4B. +nce we label the last K pea and press enter again we get bac to the main menu.Jou can also get bac to main menu at any time during the labeling process by pressingthe F&G (forward slash) ey.

=C. :f we are not happy with labeling we have chosen and want to rename some atoms

this can be done in two ways(i) ':9N followed by a list of atoms to be renamed. Then as each is highlighted type in anew label.(ii) ;A-# Fold nameG Fnew nameG7or each atom to be renamed.(iii) We can always chec on any atom and see what bond lengths and bond angles itmaes with other attached atoms using the commandA;E (!ond distances and angles) and then the name of an atom* e.g.*A;E 913 to see bond distances and angles for atoms attached to 913.

=/. :f we are satisfied with the result of the atom labeling then we should save this result

by using the command!AR# FfilenameG this filename can be any name but you should be able to remember it.: usually use the file name that corresponds to the structure being solved. This writes afile Fname.savG that only %' can read. This can be re,called at any time while in %' byusing the command;#%T FfilenameGJou should mae a habit to write a FsavG file every time you use %' and before you writeout the results to the ins file.

=1. ;ow you are ready to write the named atom list to the I.ins file for refinement(improvement of the structure). This is done using the command7:$# FfilenameG The filename in this case will be FcmCB,1G but in general will be thename of the structure you are woring on.After carrying out this command the program ass where to get the instructions from andhas its suggestion in square bracets cmCB,1.res5. Dsually this is correct so you 8ustpress the enter ey. After that you can quit the program by entering eitherKD:T+r#%:T

=3. ;ow we want to loo at the I.ins file again to see how it has changed. !o we use theF#dit insG option and loo at the file.

=4. We see several things have changed(i) The first seven lines are unchanged ( lines if we have a T#-' ,/>3)(ii) There are some new lines. The first has$.!. 4$.!. means carry out least squares refinement and 4 means 4 cycles of least squaresrefinement. The 4 is there for historical reasons to do with computer speed. :n ancienttimes it would tae several hours to do 3 or 4 cycles and the result would be BCH


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converged after this number. ;ow with modern computers 4 cycles might tae less than asecond. !o we want to increase this number to at least .(iii) The ne0t three instructions+;27-A' 1

'$A; 1C!hould be replaced withA9TA /3=9+;7+;2 "

==. What do these all meanU(i) A9TA /3= A9TA comes from the crystallographic 8ournal A9TA9J!TA$$+EA'":9A. This instruction is made up of two parts. A9TA meansprepare all the files needed at the end for publication (say in A9TA9J!TA$$+EA'":9A). :t also does what the 7-A' 1 and +;2 instructions

would do so these become unnecessary. The F/3=G calculates data coverage out to a 1,theta value of /3=Q. This is needed later.(ii) 9+;7 9+;7 is short for conformation. This is an instruction to prepare a torsionangle table for all atoms in the structure.(iii) +;2 " This is an instruction to prepare a bond distance and bond angles tableand include values involving the "s

=> The ne0t line is7RA /.CCCCC(i) 7RA means Ffree variableG. These are values the program will refine to get bettervalues during the refinement process. There can be @ free variables on a line and if moreare needed then there can be a second (or more) line starting with 7RA.(ii) There is a value on this line F/.CCCCCG. This is the first free variable and is alwaysreserved for the overall scale factor (+!7). This is used to put the observed andcalculated data (7s or structure factors) on the same scale during refinement. This isnecessary because while the calculated structure factor* 7c* is defined by what atoms arein the molecule and thus is a fi0ed number* the observed structure factor* 7o* (which is8ust the square root of the intensity as measured on the diffractometer i.e. 7oV :) is not afi0ed number and values can vary depending on what si6e crystal was used.

=@. The ne0t lines contain the atom list. There are several important things to note(i) atom label the first four fields (spaces) are reserved for atom label. Thus an atom labelcannot be longer than this (9/13a would not be an allowable label).(ii) The ne0t column contains a number which corresponds to that atom type in the !7A9line. :t is this number and not the la"elwhich determines the atom type.(iii) The ne0t three lines list the coordinates of each atom. These coordinates aree0pressed as fractions of the corresponding cell lengths (0 as a fraction of a* y as afraction of b* 6 as a fraction of c).(iv) The ne0t number (//.CCCCC) is the occupancy factor for each atom. This number ismade up of two parts / and /.CCCCC. The first / tells the program that the ne0t number


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(whatever it is) cannot be changed. The number /.CCCCC is the actual value and meansthat the atom is a full weight atom (i.e. not on a symmetry element of the space group).(v) The last column contains the thermal parameters. This is a measure of the e0tent towhich each atom is vibrating as all atoms are in motion e0cept at absolute 6erotemperature. This value starts out at C.C=CCC but will be refined (improved) during the

least squares refinement.=. ;ow that we have looed at the I.ins file we can carry out the refinement. 7irst closethe ins file and save if any changes have been made.

=B. ;ow use the command on the menu line F%$G. When you pull down there are twovalues F%$ and F%"G. The first is for normal si6e structures while the latter is for thoseproblems which are too big for %$. We choose %$.

>C. The program carries out the number of cycles we requested in the $.!. instruction in ethe I.ins files used. The details of what it did are in the I.lst file produced (along with the

new I.res). :n the printout you see on the screen* however* there are several interestingfeatures.(i) :t reports a / values (about > lines from bottom). The value is the criterion onwhich the quality of a crystal structure is based. We are trying to construct a model of themolecule so that the calculated structure factors (7c) agree with the observed structurefactors (7c). !o / reflects that difference. 7or perfect agreement / V C since/ V X(7o< 7c)5& X 7o

"owever in practice any value less than C.C= is considered a good (publishable) result.At this stage we are not finished as we havent found all the atoms (no "s yet) and arenot totally sure that our atom assignment type is correct for all atoms. Therefore the value is not yet near C.C= but is certainly better that what you would e0pect if the atomswere randomly scattered in the unit cell ( S C.=)(ii) Three lines from bottom it reports the highest remaining pea in the (difference)7ourier. A difference 7ourier is where the contribution of the nown structure issubtracted to find any missing atoms (or miss,assigned atoms). -issing atoms lie 9* ;*or + would result in peas of height S 4 (even higher for heavier atoms). The largestpea is only around 1 so this tells us that we have probably found all non,hydrogenatoms.

>/. :f the previous step was successful* now we want to improve this result. 7irst we looat the menu under #dit and select Fcopy res to insG. Then we loo in the I.ins file tochec what has been done.(i) We see that the thermal parameters (which started out all being C.C=CCC) all now havetheir own values.(ii) elow the #;2 instruction we see the list of K (unassigned) peas (none of which arelarger than 4)

>1. ;ow we have to improve the model. +ne way to do this is to allow the atoms tovibrate anisotropically. Dp to now we have only been allowing the atoms to vibrate


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isotropically (equally in all directions). 9onsider the following diagram showing twoatoms bonded together

X Y

X Y

+bviously* due to the constraints of the bond the atoms should more easily vibrate in adirection perpendicular to the bond that in a direction parallel to the bond. Thus ourisotropic vibration is not realistic. We can improve this is we allow non,equal amplitudesof vibration in different directions* .i.e.* instead of having the vibration of the atomsdescribe a sphere* have these vibrations describe an ellipse. An ellipse is characteri6ed by> parameters* 3 for the amplitudes in the 0* y* and 6 directions* and 3 to describe the

orientation of this ellipse in space.To do this we add to the I.ins file the four letter commandA;:!This can be placed anywhere between the D;:T and 7RA lines.

>3. ;ow we close and save the I.ins file and do more refinement using %$.

>4. We see that the value drops significantly and the si6e of the highest pea in the7ourier also drops significantly.

>=. ;ow we loo at the structure again using %'

%'SS 7-+$%'SS -'$;%'SS '+P (or 2:AE);ow we see that most of the unassigned K peas loo lie they are " atoms attach to 9atoms."owever* one disconcerting aspect is that these K peas have bonds drawn to more than/ 9. This is due to the covalent radius built into the 9 (and other) atoms and the K peas.These radii are used by the program to construct bonds. When ever two atoms are closerthan the sum of their covalent radii a bond is drawn between them in the %' display.The default covalent radius for a K pea is the same as that for 9. !ince these Ks aremainly "s and since the covalent radius of a " atom is much less than that of a 9 theseKs come within bonding distance of more than one 9* hence the additional bonds.

>>. "ow are we going to assign the "s to the atoms. The easiest way is to let theprogram do this for us(i) Nill at K peas by typingN:$$ K The FG is used to indicate all of the following types of atoms so K is allKs * " is all "s* 9 is all 9s etc.(ii) ;ow we can add "s to all 9 atoms by typing


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"A22 9 This adds " atoms to all 9s. ;ot only that but the program can distinguishbetween sp1* sp3or aromatic 9 atoms and add the appropriate number of " atoms in thecorrect location.(iii) After using this command we should loo and see if everything has been donecorrectly. !o we use '+P so we can rotate the molecule to loo at it from all sides. :f it

loos correct we can press the escape ey.(iv) ;ow we should save as before by using the command!AR# filename(v) ;ow we write the result to the I.ins file by using the command7:$# filename

>@. ;ow we use the #dit function to loo at the I.ins file.(i) we see that "s have been added after each 9 which has "s attached(ii) efore and after each " (or set of "s if there is more than one " on consecutivelines) there are A7:% followed by a number. The first A7:% tells the program what indof " is present. The second A7:% C finishes.

(iii) A7:% commands have the formA7:% mnm stands for the type of "* n for how it is treated during refinement.m V / This is for a single " attached to an sp39m V 1 This is for a two "s attached to an sp39m V 3 This is for a three "s attached to an sp39m V 4 This is for a single "s attached to an sp1or aromatic 9m V This is for a single " attached to and + (e.g.* alcohol)m V B This is for a terminal VV9"1 or VV;"1Mgroup.m V /3 This is for a three "s attached to an sp3 the 9"3group is allowed to rotate to findthe best fit to the electron densityn V 3 This means the " is FridingG on the 9 to which it is attached* i.e.* when the 9moves during refinement the " also moves to preserve its geometry.n V @ This is used along with m V /3 to give A7:% /3@. This allows the 9"3group torotate to find the best fit to the electron density.

We usually do not have to mae any changes as the program has set this up for us.

>. ;ow we close the I.ins file (and save if we made any changes) and do furtherrefinement to improve the model.

>B. ;ow we again use the #dit function on the menu bar to copy the I.ins file to the I.resfile. ;ow we are getting near the end of the refinement process and have to tae intoaccount some new factors. The first is the weighting scheme. :f we open the I.ins file wesee 8ust above the 7RA lineWE"T C./CCCThis is the weighting scheme used during the least squares refinement. The weightingscheme assigns weights to each observation (data point from hl file) based on its errorvalue. !o far we havent had to worry about this but now we are getting to the end of therefinement we have to use the best available weighting scheme. :f we have 8ust copied the


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Ires file to the Iins file this is found in the I.ins file after the #;2 card. We copy thiswhole line (usually consisting of two numbers) and past it in the Iins file replacing theprevious WE"T line. ;ow we close and save the I.ins file and do further refinement.!tep >B is repeated until the suggested weighting scheme is the same as the previous one.

@C. ;ow we have to chec that the formula is correct. This is done by looing at the listfile (I.lst) in the pull,down menu in !"#$%T$. The formula is incorrect is the list ofatoms in the ins file does not match the number of atoms as speificied on the D;:T card.:f the formula is incorrect (and only if it is incorrect < if it correct this is not included inthe I.lst file) and the items do not match then in the list you will see something lie

Dnit,cell contents from D;:T instruction and atom list resp.

9 >C.CC =.CC" =C.CC 1=.CC; 4.CC 4.CC

+ /C.CC >.CC!# =.CC 4.CC 4.CC 4.CC

The numbers for each atoms should match. :f you have found all atoms (including "s)then you have to edit the I.ins file to update the D;:T line with the correct formula. Atthe same time you should mae sure that the L# line is correct for the correct numberof molecules (or formula units) in the unit cell.

@/. The last thing we have to do now is have a sorted atom list contained in the I.ins file.This is best accomplished in %' so open this program from the menu bar and type inSS7-+$;ow we want to sort the atom list. 7irst see what the list of atoms loos lie by typingSS:;7+

@1. Dsually the best order for the atoms is to have them in the order of decreasing atomtype (as listed in the !7A9 card). Thus the heaviest would be listed first and the lightestlast (" atoms will automatically be sorted when you list the atom names so we do nothave to sort them). The command to sort isSS!+TThis command is followed by the list of atom names to be sorted (on the same line as the!+T).Jou do not have to list all atoms in / line as you can use this command multiple times.

@3. +nce you have sorted the list you have to save it so enterSS!AR# filenameSS7:$# filenameSSKD:T

E#$%E&E%T $S #$%$SHED'


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;ow what happensU We have to get the structure ready for publication. This is a threestep process/. 'reparing tables

1. !tructure validation using checcif3. 'reparing diagrams

students guide to shelxtl

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