Intermediate Peak Explanation

The below is a summary of the literature search I performed in order to explain the shoulder in [C4mim][TF] around .8 to 1.1 inverse angstroms and why it might possibly vanish for the doped [C­4mim][TF] samples. After the individual summaries from each reference, I will make my own concluding remarks.

Some of the resource materials are too large to upload but I have them saved to a folder on my flashdrive.


J. Phys. Chem. B  114, 16838 (2010)

The compounds explored in this reference are as follows: [C6mim][Cl], [C8mim][PF6], [C10mim][PF6].

The authors make a claim that for the above compounds that the structure factors for the liquid below 2 inverse angstroms are often similar of the structure factor in a powdered crystal simulation of the same sample. They continue by saying this is from a similar structuring of the liquid as was in the solid crystal, although the length scale is on a longer range in the liquid. The specific contributions of the peak at .9 inverse angstroms in liquid arise from the positive cation-cation and anion-anion terms summed with the negative cross terms. They make the definite claim the peak/shoulder arises from “short interionic distance between polar groups of the same charge.” The authors make an equivalent interpretation later on that the feature can be, “Also interpreted as a periodicity in the absence of ions of opposite charge at that particular distance”.



J. Chem. Eng. Data.  59, 3120 (2014)

See Table 1 of reference for specific cation to anion pairings (there are 14 different pairings).

The authors in this work call the feature which is generally around 8.8 inverse nanometers an intermediate peak which shows “the periodicity of the polar network for each IL (alternation between ions of opposite and similar charge.” This statement is in agreement with the reference from the last section.

The authors explore structure factors of [C6mim][C4SO3] and [C6mim][Ntf2], noting the intermediate peak at 8.8 inverse nanometers in [C6mim][Ntf2] shifts to 9.3 inverse nanometers when [Ntf2] is replaced with [C4SO3]. The authors state that a smaller anion polar head allows for a more compact polar network. The intermediate peak becomes a shoulder in this case because “the combination of lower intensities with shifts to higher q-values (and the corresponding approach to the contact peak [strong peak at 14 inverse nanometers]) justifies the transformation of the intermediate peak into a shoulder at 9.3 inverse nanometers.”

The authors make the intermediate peak in [C4NH3][Ntf2] (at 9.1 inverse nanometers) vanish by replacing the anion with Carboxylates [CnCOO].  The authors state that, “the polar network is composed by small ionic heads (the –NH3 and –COO groups).” The authors then go on to describe the resulting structure which forms in [C4NH3][C1COO]:

We have a necklace-like polar network that is extremely thin and flexible in the midst of nonpolar regions that even with only C4 chains occupy a relatively large proportion of the available volume. Such a fact will hinder the emergence of any intermediate-range ordering/periodicity.

In other words, the bonding of the cation and anion heads eliminates the intermediate peak which means the polar network no longer has intermediate ordering.

A comparison of four anions is made, keeping the cation as [C4mim]+. The anions are [Ntf2], [PF6], [S1SO3], [C1COO]. The authors go on and list the anions which have the strongest intermediate peak (around 8.5 inverse nanometers) to anions having more subdued peaks (around 9.5 inverse nanometers). The order is [Ntf2], [PF6], [C1SO3], and [C1COO]. Acetate ([C1COO]) is the smallest anion and it also has the most subdued intermediate peak. A summarizing claim is made by the authors which states that the diminishing or vanishing of the intermediate peak occurs when, “the protic Ils revert to the corresponding neutral species.” Protic simply means that the species is able to donate a Hydrogen atom, resulting in Hydrogen bonding.


J. Chem. Phys.  134, 104509 (2011)

In this article the structure of [Cnmim][Br] with n = 2,4,6 is explored. The authors note a shoulder at 1.1 inverse angstroms which is most evident for n=2. They contribute the shoulder to the positive peaks in the ring center to ring center and anion to anion correlations with the strong negative peak in the cross terms and state that this is exhibited in molten salts through charge ordering.  A reference (J. Phys. Chem. B 114, 12623 (2010)), which only looked at the n=2 case, reached these conclusions and initially explained the phenomenon. The cation ring and the anion have 34 and 36 electrons respectively which is how the authors explain the shoulder/peak’s small amplitude.


Concluding remarks

After reading the above articles, along with many others, we now have a better understanding of the intermediate shoulder/peak feature present in some ionic liquids. The feature’s cause becomes apparent in the molecular dynamic simulations. The partial structure factors of the cation to cation and anion to anion terms contribute positively to the total structure factor around the q values for this feature whereas the cross terms contribute negatively. These structure factors give insight to the intermediate peak resulting from an intermediate ordering of the polar species, giving rise to what the above authors refer to as a polar network. Experiments have explored different combinations of cations to anions and have provided fruitful results. In general, the larger cation and anion polar heads have a more distinct intermediate peak. Smaller polar heads lead to an intermediate peak which is hidden by the main “contact peak” around 1.5 inverse angstroms. The intermediate peak will also go away if the cation and anion form a neutral species in the ionic liquid, as is the case for protic ionic liquids, which effectively disrupts the intermediate ordering of the polar network.

The above conclusion leads me to two possibilities happening in the doped [C­4mim][TF] samples. The first involves the doping element forming a neutral species (ion pair) which would mean the intermediate ordering of the polar network would no longer be present (or would be dampened) in our experiment as was the case for the protic ionic liquids. The other possibility is that the smaller doping element makes the ordering in our liquid more compact and therefore shifts the intermediate feature into the larger scattering peak around 1.5 inverse angstroms, effectively hiding it in the much larger peak.

Castner vs Cummings Report (Updated)

In this post I explain a couple of key differences and similarities between a communication written by the Castner group and a letter written by the Cummings group. I have attached both sources with their supplemental information as I reference figures from them in my report below.

Castner group source with supporting information:

Communication; X-ray scattering from ionic liquids with pyrrolidinium cations

Supporting Information for Communication; xray scattering from ionic liquids with pyrrolidinium cations

Cummings group source with supporting information:

Alkyl Chain Length and Temperature Effects on Structural Properties of pyrrolidinium based ionic liquids; a combined atomistic simulation and small angle x ray scattering study

Supporting Information for Alkyl Chain Length and Temperature Effects on Structural Properties of Pyrrolidinium-based Ionic Liquids; a Combined Atomistic Simulation and Small Angle X-ray Scattering Study




In both works, groups explore the 1-alkyl-1-methylpyrrolidinium cation and we expect the same anion although the Castner group calls it bis(trifluoromethylsulfonyl)amide whereas the Cummings group labels the anion as bis(trifluoromethanesulfonyl)imide.They mention the electrochemical window (5.3 V and 5.9 V claims by Castner and Cummings respectively) being higher than other ionic liquids which is why it is the chosen ionic liquid under study. Both groups look at chain lengths of n=4, 6, 8, and 10 on the cation but the Cummings group looks at the additional tail length of n=3. The Castner group collected WAXS from Advanced Photon Source beam line 11 ID-C (105.1Kev) and SAXS at National Synchrotron Light Source beam line X9 (capable of 6-20 KeV) using a 2 mm quartz capillary. The Cummings group used a 1 mm quartz capillary and only collected SAXS using a Anton Paar SAXSess mc2 instrument which uses a Cu K-alpha wavelength (~8 KeV). Both groups used the PDFgetX2 program to generate structure functions but only the Castner group mentions using FIT2D.

Castner makes the claim that in the q range of 0.003 and 2 inverse angstroms in the structure function is due to intermolecular correlations whereas q > 2 inverse angstroms are intramolecular correlations. Cummings implies much the same when he mentions that his group’s SAXS q range of 0.01-2.8 inverse angstroms will cover intermolecular as well as longer range intramolecular real space lengths.


The groups agree on the temperature evolution between roughly 0.6 to 1.5 inverse angstroms where increasing temperature results in peak position shifting to lower q values and attribute the changing density as the reason for this shift. This is shown in Castner’s figure 2 and Cummings’s figure 4. Cummings obtains interesting results for low q s(q) which I will discuss later.

The sources are in agreement for how changing the chain lengths from n=8 to 10 at roughly an ambient temperature (Castner at 295 K and Cummings at 298 K) effects the position of the second and third peaks (around .84 and 1.35 inverse angstroms). The groups both do a Bragg type analysis on the position of these peaks from a chain length evolution from n=6, 8 and 10. The Castner group obtains a slope of 1.8 angstroms per methyl group whereas Cummings gets a slope of 2, exhibited in Castner’s figure 3 and Cummings’s supporting information figure S4. Castner also points out that the “inverse of the peak maxima scales linearly with density,” and mentions this trend is present in other ionic liquids.


Castner Conclusion

Castner cites information from a couple of sources and makes a summarizing claim “FSDP cannot always be interpreted as an aggregation of the cation alkyl chains.” He interprets the FSDP as evidence of “intermediate range charge ordering that arises between the first and second shell neighbors in a liquid composed of asymmetrical ions.” He concludes that molecular dynamic simulations are needed to break down the peaks to their various constituents to better understand the low q behavior of s(q).

Cummings MD simulations

Cummings performs the suggested Molecular Dynamic simulation exploration for the IL under study. Results in figure 1 clearly show that the cation tails do in fact bunch together in patterned regions which grow in size as chain length increases. In the supporting information figure S1, Radial Distribution Functions of the cation/anion terms and cross terms as well as a pyrrolidinium to anion term are shown. We notice that as the alkyl variations in the cation are made, the anion to anion RDF is relatively unaltered. Further, the cation to anion RDF decreases with increasing chain length whereas the pyrrolidinium to anion correlation shows the opposite trend (the correlation increases with growing chain length).

Cummings SAXS results

Castner only collected SAXS data for an ambient temperature whereas Cummings has a full range of SAXS data collected at differing temperatures and chain lengths. Cummings observed for a fixed chain length (especially 8 and 10) that as temperature increases, the FSDP position shifts to HIGHER Q VALUES (shown in Cummings’s figure 4). This contradicts the density decrease expectation of the position shifting to lower q values with increased temperature which is expected for experiments in general. Castner mentions this trend specifically for the sample, which confirms the contradiction. To explain this anomaly, Cummings labels two peaks in low q valued S(q) and follows them at differing chain lengths and temperatures. The first peak is due to “nearest neighbor polar group separation” and the second peak is from the “alkyl chain-separated polar group distance.” He includes a figure in the supplemental information, labeled figure S4, which follows the two separate peaks’ positions and heights for the chain length alterations. In figure S5 Cummings mentions a total shift of his two labeled peak positions due to temperature evolution from 298 K to 363 K for all the different chain lengths. Cummings points out that the most important inference to be made from figure S4 is that as n decreases, the two different peaks begin to overlap and merge into a larger, single peak. Cummings concludes that longer chain length tails tend to coil [what others have called ‘interdigitization’]. Recall that Castner warned us that a FSDP may not be due to alkyl chain aggregation and suggested MD simulations to straighten out the true cause. Cummings has constituent contributions to S(q) which confirm the tail bunching behavior and offers a possible explanation.

Cummings Interpretation of SAXS with MD

Cummings states that within this ionic liquid system there are two main types of forces, “strong charge ordering of the ions and the weaker van der Waals influence of the alkyl chains.”  Results from the temperature exploration indicate that van der Waals forces of the alkyl chain dominate at ambient temperature. At higher temperatures the van der Waals interactions fall off and the other force dominates. In other words, as the temperature of the system increases the cation tail has a higher probability of diffusing from its nonpolar aggregate which results in the observed shift toward high q of the associated peak in s(q). Since the first neighbor ionic distances depend on density rather than temperature, diffusion is necessary.


General Conclusion

To sum up, Castner and Cummings groups explored what we suspect to be the same compound, what we call C4mPyrrTFSI. Caster had a general start to understanding the structure through WAXS data, concluding that MD simulations are necessary for more detailed information. Cummings picks up the study performing SAXS measurements and actually performing MD simulations. Together these allow Cummings to make claims about alkyl tail interdigitization. Temperature has a counter intuitive effect of the alkyl tail behavior which is explained as a balance of two forces: van der Waals and charge ordering of ions. At lower temperatures the van der Waals forces dominate, but at higher temperature the charge ordering of the ions dominates resulting in a counter intuitive shift to shorter scale structure exhibited by a higher q position of the FSDP.


Faber Ziman Weighting Factors

After many attempts I am proud to announce that I have finally found the Faber Ziman Weighting Factors for the following compounds:

  • C4mimTF
  • C6mimTF
  • C8mimTF
  • C10mimTF
  • C4mimTF:LiTF (10:1 doped)
  • C4mimTF:NaTF (10:1 doped)
  • C4mimTF:KTF (10:1 doped)
  • C2mPyrrTFSI
  • C3mPyrrTFSI
  • C4mPyrrTFSI

FZWF CORRECT AT LAST (spreadsheet)

FZWF explanation (relevant notes with last day explaining the implications of weighting factors for the doped species)

I have a spreadsheet which shows my calculations for each of these. It also contains a summary tab which displays the weighting factors of the above 10 compounds all in one place. There are two doped sections: the first explores the weighting factors as if the doping species remained its own entity, the second assumes the positively charged doping species bonds to a negatively charged triflate. We make this assumption from past experience with doped benzene.






Batch script, Fit2D, PDFgetX2 Process Summary

In this post I will explain the general process for analyzing x-ray diffraction data using a strawberry perl batch script, Fit2D, and PFDgetX2.

After data collection, the process below is utilized to process the data and eventually produce a structure function.

General process:

Strawberry Perl Script

Update the batch script file found: batch_sample55to59sampledark0to4    (This needs to be saved as a .pl file. I had to upload as a .txt due to WordPress uploading restrictions) and modify it for the specific sample changing the data path, sample file, empty capillary file, and the output path. To run and execute this script the command ‘perl filename’ must be entered in the strawberry perl command line. The directory in the command line must match the directory in which the file is saved. Changing the directory in this command line is done by entering ‘cd nameofdirectory’ to enter the designated directory from the current one. The command ‘cd ..’ goes up in the directory hierarchy . Lastly, the command ‘dir’ lists the sub-directories and files in the current working directory. I have a copy of the gain map and the executable used in the batch script saved to my flashdrive.

Cation: The batch script seems to have some issues at times reaching the 16 bit unsigned integer limit as shown in one of my previous posts .

Before you move on you should have a processed silicon image with the empty capillary subtraction, a processed sample image with the sample dark subtraction, and a processed empty image with the empty dark subtraction all done using the batch script in strawberry perl.


Import the processed empty file into Fit2D, and create a mask to make dead, overactive, and pixels blocked by the beam stop not count in the integration to come. I recommend using the significant pixel mask, a less than threshold mask, a greater than threshold mask, and a polygon mask around the beam stop. Save the resulting mask for the future.

We then use the processed silicon file and load the mask file to generate the detector specifications by a silicon calibration. Be sure to enter an approximate detector distance, x ray wavelength, pixel size and, fix the x-ray wavelength. Once we have the detector specifications, we may now generate  .chi intensity plots for the processed sample and processed empty file. It is important to integrate over q-space.

Before moving on you should now have a .chi plot of intensity for the processed sample and one for the processed empty.


In PDGgetX2, load the following history file: PDFgetX2_history (I had to change the file type and am unsure of how this will change its availability in the program)  and then use the processed sample .chi plot along with the processed empty .chi plot as input files in the sample and background input locations. Change the working directory to where these .chi files are stored. Update the sample composition, mut, x ray wavelength, data range, and any other parameters and generate the s(q). Save a history file for use later.

This concludes the processing I am familiar with.

C4mimTF analysis

This post focuses on just the C4mimTF compound although it will become this structure factor will be very similar to the 10:1 doped C4mimTF_NaTF and C4mimTF_KTF explored in a previous post.

Below are a copy of my notes and an excel sheet with tabs that have files used, detector specifications and sample composition information.

Notes for C4mimTF

C4mimTF file spreadsheet


There are two images below. The first is the s(q) produced for C4mimTF with the same PDFgetX2 parameters as the energy dependence study. The second image is the 67KeV part of the energy dependence study because that is the same energy used to analyze the C4mimTF sample. Observe that the C4mimTF sample s(q) closly resembles the s(q) plots generated for C4mimTF_NaTF and C4mimTF_KTF analyzed earlier.


Energy Dependence of C4mimTF_NaTF and C4mimTF_KTF

In the attached files I explore the energy dependence for X-ray diffraction of C4mimTF_NaTF and C4mimTF_KTF doped at a ratio of 10:1.

My notes dictating the exploration and excel sheet with the following: redbook notes, files used in study, detector specifications, and sample composition. The two files are listed below.

Energy Dependence Study

Energy Study Excel Workbook

I did have some trouble getting the correct sample composition at first which should be kept in mind when looking at the initial analysis. I make note of this retrospectively in my notes. The image below was created using the correct composition.

The 4 images compiled into a single image below summarizes the energy study for both samples. The upper images are for the sample having the NaTF anion and the lower images are for the sample with the KTF anion. The left images are for data taken at 67KeV and the images on the right are for the 100KeV data.




C4mPyrrTFSI temperature dependence analysis

In these files, I explore the temperature dependence for C4mPyrrTFSI with data taken in two sessions: session one explores 300K to 400K every 10K whereas session two explores 400K to 430K every 10K. My analysis actually started out looking at data taken at 340.065K and then evolved into looking at the other temperatures.

C4mPyrrTFSI_340.065 analysis

C4mPyrrTFSI other temperature analysis


340.065K Analysis as described in C4mPyrrTFSI_340.065 analysis

The following gallery shows what happens when the batch sum goes past its 16 bit unsigned limit of 65535 as mentioned in the analysis. The following images included are:

  • Empty First Frame
  • Summed Empty frames 0 to 19 (past limit)
  • Summed Empty frames 55 to 59
  • Sample first frame
  • Summed Sample frames 0 to 19 (past limit)
  • Summed Sample 55 to 59







 Other Temperature Analysis C4mPyrrTFSI other temperature analysis

First sharp diffraction peak observed for 300K (as mentioned in the analysis) explained by way of images below which show the s(q) in question and the batch summed diffraction data for the sample and empty side by side. This FSDP turns out to be caused by fluorescence from the beam stop due to a beam size that was too large.


Analysis of all other temperatures were conducted which I have saved histories for.


Cu47Zr45Al8 exploration of PDFgetX2 parameters

Here is a copy of my notes for June 17-19:

6_17,18,19_2015 enotes

The notes mention generic file names for specific parameter explorations. Below are galleries that correspond to those specified explorations.

The attached files primarily explore the PDFgetX2 parameters listed below for Cu47Zr45Al8:

  • Container multiplicative coefficient (mul con)
  • High Q slider bar
  • Multiplicative constant with fluorescence=0
  • Fluorescence with mul con 1.0
  • “good looking” s(q) with varying fluorescence and mul con
  • Attenuation Coefficient (mut)
  • High Q s(q) straightening by mut, mul con, and fluorescence



Container multiplicative coefficient (mul con) exploration



High Q slider bar exploration



Multiplicative Constant exploration with fluorescence =0.0


Fluorescence exploration with mul con 1.0


“good looking” s(q) with varying fluorescence and mul con


Attenuation coefficient (mut) exploration


High Q s(q) straightening