IR and Raman:

Capturing the Artistry of Spectral Interpretation

Michael BorutaOptical Spectroscopy Product Manager, ACD/Labs

Contents

Background 2

Where We Have Been for the Past 10 Years 3

What is Possible Today? 4

When No Structure is Available 5

Databasing—How Much Effort? 6

Store, Share, and Re-use 6

References 7

In the scientific world, sharing information is one of the

key factors in the advancement of science. Fortunately for

IR spectroscopists and, to a slightly lesser extent, Raman

spectroscopists, there exist a number of excellent text books1-3

in which the authors have shared with us their compiled

information about spectrum-to-structure correlations. These

correlations help us understand and interpret the spectra we

work with every day.

In a corporate environment it is common for individuals to,

over time, gain detailed knowledge about the correlation

between some spectral features and the materials they work

with on a daily basis. This knowledge often exceeds the more

general information available in text books. However, until

recently, there has not been a method available to capture

that specialized knowledge. It either resides in the mind of

the individual or is sometimes handwritten on a chart and

filed away—hardly useful to propagate knowledge sharing

throughout the corporate environment or to share with future

spectroscopists.

This paper will briefly touch on analytical data management

while focusing primarily on a means of capturing spectrum-to-

structure correlations for IR and Raman spectra. We will discuss

methods that can be used to obtain, archive, and retrieve this

knowledge so that, once derived, it will remain a resource

within the laboratory beyond the confines of individual analyst

expertise. The aim of such a system is to not only capture

your own knowledge but also to combine it with that of your

colleagues to help you make better decisions.

Background

Infrared and Raman spectroscopy are valuable tools for many

different kinds of materials and are used to acquire chemical

and structural information such as verifying a proposed

chemical structure, or confirming the presence of functional

groups. Unfortunately the interpretation of the resulting spectra

can often be a difficult and time-consuming task, therefore

spectral interpretation has traditionally fallen under the realm of

the experienced spectroscopist.

In the past there used to be much more time available for

training—for older more experienced spectroscopists to transfer

their knowledge to younger/less experienced users. While

mentoring still exists, the time available for such training has

decreased in an age where researchers are continually expected

to do more with less. The situation is most pronounced in areas

such as spectral interpretation—often referred to as an art,

because so much of it is based on the experience of the user.

Several factors make spectral interpretation difficult for the

inexperienced. Two of the most common are the overlap of

regions where certain functional groups can exhibit bands,

and the movement of bands due to the physical or chemical

environment. Traditional methods of interpreting these spectra

rely heavily on the expert’s experience, the use of multiple

reference books or spectra, and some preconceived ideas about

the chemistry of the material in question. Spectral searching can

assist with interpretation; however, it has mostly been used as

an aid to chemical identification.

Historically, the primary resource for information on spectrum-

to-structure correlations has been personal experience, the

expertise of their colleagues or one of the many reference books

on the subject of group frequencies. More recently several

software programs have become available to assist in the

interpretation of spectra.

Collections of correlation tables and charts (often from several

different sources or books) containing information about the

band frequencies of various functional groups can contain

hundreds or thousands of known characteristic frequencies.

Manually searching these tables requires considerable time and

effort, even for experienced spectroscopists.

2

The most predominant method for capturing spectrum-to-

structure correlations in the past has been hand written notes

on printed spectra. The charts were often indexed and saved

in filing cabinets for future reference. A major drawback of

this system is the difficulty in finding the right chart with the

right information when needed. It is often easier to re-run and

re-analyze a compound than it is to track down the original

information. This can be a significant waste of time and

resources to reproduce or relearn what was already known.

Yet, the information contained on these charts is an important

resource to a corporation’s current and future needs as it is a

product of the organization’s costly investment in research. IR

and Raman information in particular might serve to categorize

particular compounds or classes of compounds that are of

interest to the corporation, often for legal purposes. A second

purpose is to provide a resource for colleagues to share

information and knowledge that has been created over many

years.

Figure 1. Example of a spectrum on a paper chart with hand

written notations.

Many scientists still rely on paper copy to “archive” the

interpretations they make. Some may use annotation abilities

within the instrument’s software while others have moved

to tools like MS Power Point where they can draw a structure

fragment or write a note near a peak. These methods are

primarily used for reporting purposes. This methodology is

adequate for a one time assessment of some spectral feature.

However, if there is a desire to retain and share the knowledge

gained, these methods leave much to be desired.

Where We Have Been for the Past 10 Years

We have progressed in many areas for storage of analytical

spectroscopic data for IR and Raman instruments over the

past couple of decades. Today software is available from most

instrument manufacturers to manage and database spectral

data. Several software packages can also manage textual

data and peak tables. These software programs allow an easy

means to search for and retrieve this data. There also exist a few

independent software providers that can provide the means to

include structures with the data and, in some cases, multiple

data types such as IR and Raman in the same database.

With some of these software packages it is now possible to

take the spectral data, combine it with a structure, and add

annotations on the spectrum to indicate the spectrum-to-

structure correlations for reporting purposes (see figure 2).

Figure 2. Digital spectrum with annotations—same sample as

figure 1.

Although digitally annotating a spectrum in Microsoft

PowerPoint or another software package is better than writing

notes on a chart (the ink will not fade and the handwriting

is easier to read) we are still essentially writing notes on a

spectrum. This method is adequate for producing reports, both

paper and electronic, but leaves much to be desired in terms of

sharing information with colleagues.

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What is Possible Today?

A new software tool, ACD/Optical Workbook, is now available

that allows spectroscopists to store the spectrum-to-structure

correlations for their own experimental data on in-house

compounds. This software is part of the ACD/Labs Spectrus

family of chemical and analytical knowledge management

software.

ACD/Optical Workbook is an advanced tool for processing and

interpretation of a variety of optical spectroscopy techniques

including IR and Raman. Optical Workbook addresses the

challenge of making spectrum-to-structure correlations and

facilitates knowledge sharing through flexible reporting and

powerful library searching capabilities. Optical Workbook

can import IR or Raman spectra from most instruments

and public formats such as JCAMP-DX and ACSII text files.

Optical Workbook also includes advanced data processing

and structure confirmation tools for optical techniques as

well as basic processing and interpretation for NMR, MS, and

chromatography. It can also be used to draw structures, or

structures can be copied and pasted from other drawing

packages.

Once a spectrum and structure exist in the software, highlight

a structural fragment by clicking and dragging around the

fragment. A built-in knowledgebase can be used to assist in

finding the general regions where the structure fragment’s

bands may be found. Once the structure fragment is

highlighted, clicking on a peak creates the correlation.

Figure 3 shows an example of assigning the CH2 symmetric

stretch. In this figure several of the CH2 groups in the molecule

have been highlighted. The software shows the suggested

bands that could belong to the CH2 group. The user has the

option of using some or all of the suggested bands.

Figure 3. Assigning the CH2 symmetric stretch band.

ACD/Optical Workbook includes separate knowledgebases for

IR and Raman to assist with interpreting spectra and making

assignments.

Once an assignment is made, the user may edit the suggested

vibration mode. Figure 4 shows the vibration assignments being

changed from C=O to an Amide I C=O for a nylon spectrum. The

user can assign all or part of the spectrum and structure.

Correlations made can be one-to-many or many-to-one. A

single structure fragment can be “linked” to several peaks, or a

single peak “linked” to several parts of the structure. Once saved,

the spectrum, structure, and any correlations made are stored

together as a single file.

Figure 4. The C=O vibration is

changed to the Amide I band

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Figure 5: Assigning one peak to several structure fragments, or

one fragment to several peaks.

Once the assignments have been made it becomes easy to

see just what parts of the spectrum relate to what fragments

in the structure, or how a fragment in the structure relates to

peaks in the spectrum. All of the information is now linked—

so hovering the mouse over a peak highlights the structure

fragment and the row in the assignment table

\\

Figure 6: Mousing over the peak at 1736 cm-1 highlights the

peak, the C=O in the structure, and the corresponding row in

the assignment table.

When No Structure is Available

Creating spectrum-to-structure correlations requires an existing

structure. However it may often be the case that a full structure

is not known. To allow for this, Optical Workbook has been

designed to work with structural fragments. Multiple fragments

can be added to any spectrum and each fragment can be

partially or fully assigned.

Assignments can also be made directly from a row in the

knowledgebase to a peak(s) in the spectrum. Multiple rows can

be assigned and each time a row is used a structure fragment

will be added to the data.

Figure 7: Partial structures and partial assignments may be

used for cases where a complete structure/assignment is not

available or not required.

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Databasing—How Much Effort?

What effort is required on the part of the user to create and

save this accumulated knowledge? For the spectrum-to-

structure correlations there is very little extra effort. Effort has

already been expended to acquire a spectrum and provide

some interpretation. This interpretation can be done in the

Optical Workbook software and it is automatically available

for reports or databasing. If the interpretation has been

done outside of the software, it is a matter of importing the

spectrum and structure, then simply clicking and dragging to

link the assignments which have already been made; no re-

interpretation of the data is needed.

Store, Share, and Re-use

Once the assignments are made, putting the spectrum, structure, and its assignments, along with any additional textual data, into

an analytical database can be accomplished with just a single mouse click.

These libraries of spectra along with their structures or

fragments, assignments, other interpretations, and associated

information can be accessed by colleagues around the globe,

now or in the future. Data can be searched by spectrum,

structure, or meta data to view and even manipulate existing

information.

Results from a search can be overlaid with a query spectrum

to see the assigned bands matching your query spectrum and

helping to identify the part of the structure which matched your

query. This is especially useful in cases where exact matches

may not exist and you are looking to help classify or interpret

the unknown spectrum. Optical Workbook includes a small IR

database of assigned polymers and a small Raman database of

assigned amino acids as a basis for spectral searching.

6

pKa•LogP•LogD•Aqueous Solubility•Boiling Point•Sigma•Batch•P-gp

Specificity•Oral Bioavailability•Absolv•Passive Absorption•Blood Brain Barrier

Penetration•Distribution•P450 Inhibitors•P450 Substrates•P450 Regioselectivity•PK

Explorer•hERG Inhibition•P450 Inhibition•Genotoxicity•Acute Toxicity (Rodent

LD50)•Aquatic Toxicity•Irritation•Endocrine System Disruption•Health Effects

Figure 8: Spectral search results with the assignment feature

being used to help identify the spectra-structure correlations

of matching peaks.

The ability to assign spectra-structure correlations is not

limited to just IR spectral correlations. The software has been

designed for optical spectroscopy and may be used with

Raman or even UV-vis spectra. Once a spectrum has been

assigned, the information can be stored in a database. The

database can then be searched by spectrum, structure, sub-

structure, or peaks. Now when an unusual band appears it

is easy to check the in-house knowledgebase to see if this

information has been previously defined. A simple search

will retrieve all records of interest along with any band

assignments that have previously been made.

ACD/Labs databases created with advanced tools such as

ACD/Optical Workbook, save the human interpretation of

the data with the spectrum, thereby cataloging spectrum-to-

structure correlations. This expertise can be made available

as a local database on a desktop computer, or part of a global

enterprise-wide database using ACD/Labs’ scalable Analytical

and Chemical Knowledge Management solutions.

Research organizations make large investments in developing

knowledge to solve current research problems and are now

beginning to realize the value of capturing that knowledge to

be reapplied to future research. Not only the tangible results

of analytical experiments and assays, but the tacit knowledge

and interpretations that have until now been relegated to

the mind of a single in-house expert. This knowledge would

eventually be lost upon retirement or as people leave the

company. With ACD/Optical Workbook, this knowledge can be

easily stored and retrieved when it is needed, by new users or

by users throughout a corporation.

References

1. George Socrates, Infrared and Raman Characteristic Group

Frequencies: Tables and Charts, Wiley, 2004

2. J.R. Ferraro and K. Nakamoto, Introductory Raman

Spectroscopy, Academic Press, San Diego, 1994.

3. D. Lin-Vien, N.B. Colthrup, W.G. Fately, and J.G. Graselli, The

handbook of Infrared and Raman Characteristic frequencies

of Organic molecules

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