Ocean Optics CHEM2000-UV-VIS Guide

Operating Manual
and User’s Guide
CHEM2000 and CHEM2000-UV-VIS
Miniature Fiber Optic Spectrophotometers
Ocean Optics, Inc.
380 Main Street
Dunedin, FL 34698
[phone]
[phone] fax
For the latest information, consult our web site:
www.OceanOptics.com
Or, e-mail our Technical Service Department:
[email protected]
021400

Copyright © 2000 Ocean Optics, Inc.
All rights reserved. No part of this publication may be reproduced,
stored in a retrieval system, or transmitted, by any means, electronic,
mechanical, photocopying, recording, or otherwise, without written
permission from Ocean Optics, Inc.
This manual is sold as part of an order and subject to the condition that it
shall not, by way of trade or otherwise, be lent, re-sold, hired out or
otherwise circulated without the prior consent of Ocean Optics, Inc. in any
form of binding or cover other than that in which it is published.
Trademarks
Microsoft, Windows, Windows 95, Windows 98 and Windows NT are
either registered trademarks or trademarks of Microsoft Corporation.
Limit of Liability
Every effort has been made to make this manual as complete and as
accurate as possible, but no warranty or fitness is implied. The information
provided is on an “as is” basis. Ocean Optics, Inc. shall have neither
liability nor responsibility to any person or entity with respect to any loss or
damages arising from the information contained in this manual.

Table of Contents
Introduction................................................................................................................................1
Quick Start.................................................................................................................................. 4
Installing the PC2000 and OOIChem Software............................................................ 6
Using OOIChem Software.................................................................................................... 9
Display Functions.................................................................................................................. 10
Spectrometer Channel Selection............................................................................................. 10
Mode of Operation................................................................................................................... 10
Cursor Function Bar ................................................................................................................ 11
Text Box .................................................................................................................................. 12
Acquisition Parameters ........................................................................................................... 12
Reference Scan....................................................................................................................... 12
Dark Scan................................................................................................................................ 12
Subtract Dark........................................................................................................................... 13
Acquire Data Modes................................................................................................................ 13
Scaling the Graph.................................................................................................................... 13
File Menu Functions ............................................................................................................. 14
Save Spectral Values.............................................................................................................. 14
Save Kinetics Values............................................................................................................... 14
Open Spectrum Overlay.......................................................................................................... 14
Open Kinetics Values.............................................................................................................. 14
Printer Setup............................................................................................................................ 14
Print Spectra and Kinetics....................................................................................................... 14
Exit........................................................................................................................................... 14
Edit Menu Functions............................................................................................................. 15
Clear Spectrum Overlays ........................................................................................................15
Clear Kinetics Values .............................................................................................................. 15
Autoscale X ............................................................................................................................. 15
Autoscale Y ............................................................................................................................. 15
Show Kinetics Values.............................................................................................................. 15
Show Legends......................................................................................................................... 15
Spectrometer Menu Functions........................................................................................... 16
Scan......................................................................................................................................... 16
Select Concentration Wavelength........................................................................................... 16
Calculate Calibration Curve.....................................................................................................16
Enable Strobe.......................................................................................................................... 16
Spectrometer Configuration .................................................................................................... 16
Kinetics Configuration.............................................................................................................. 18
Hardware Configuration........................................................................................................... 18
CHEM2000 Sampling Components................................................................................ 19
ISS-2 Integrated Sampling System................................................................................... 19
400-µ
µµ
µm Diameter Optical Fiber.......................................................................................... 22
CHEM2000-UV-VIS Sampling Components................................................................ 23
ISS-UV-VIS Integrated Sampling System........................................................................ 23
300-µ
µµ
µm Solarization-resistant Optical Fiber................................................................... 26

Experiment Tutorial .............................................................................................................. 27
Absorbance Experiments.................................................................................................... 27
Transmission Experiments................................................................................................. 28
Reflection Experiments........................................................................................................ 29
Relative Irradiance Experiments ....................................................................................... 30
Concentration Experiments................................................................................................ 31
Kinetics Experiments ........................................................................................................... 33
Appendix A: Changing the Settings on the PC2000............................................... 34
Appendix B: PC2000 Pin-outs and Jumpers.............................................................. 36
Appendix C: Calibrating the Wavelength of Your Spectrometer....................... 37

Introduction
Ocean Optics miniature fiber optic spectrometers and accessories have revolutionized the analytical
instrumentation market by dramatically reducing the size and cost of optical sensing systems. More than
10,000 Ocean Optics spectrometers have been sold worldwide -- striking evidence of the far-reaching
impact of low-cost, miniature components for fiber optic spectroscopy. Diverse fields such as research and
development, industrial process control, medical diagnostics, environmental monitoring and of course,
education have benefited from access to Ocean Optics technology.
In fact, Ocean Optics has its roots in education. It formed in 1989 when Florida university researchers
developed a fiber optic pH sensor as part of an instrument designed to study the role of the oceans in global
warming. The researchers soon formed Ocean Optics, Inc. and their ingenious work earned a Small
Business Innovation Research grant from the U.S. Department of Energy. While designing the pH-
monitoring instrument, the researchers wanted to incorporate with their sensor a spectrometer small enough
to fit onto a buoy and were surprised to discover none existed. So, they built their own.
In 1992, the founders of Ocean Optics filled a substantial need in the research community and changed the
science of spectroscopy forever by introducing a breakthrough technology: the S1000 Miniature Fiber
Optic Spectrometer, nearly a thousand times smaller and ten times less expensive than previous systems.
Due to this dramatic reduction in size and cost of optical sensing systems, applications once deemed too
costly or impractical using conventional spectrometers were now feasible.
CHEM2000 and CHEM2000-UV-VIS Spectrophotometer Systems
The CHEM2000 and CHEM2000-UV-VIS Spectrophotometer Systems utilize the optical bench of our
second-generation miniature fiber optic spectrometer, the S2000, by mounting it onto an A/D converter and
turning the system into a PC plug-in spectrometer.
The CHEM2000 consists of four basic elements: a
PC2000 PC Plug-in Fiber Optic Spectrometer (350-
900 nm), a tungsten-halogen light source with
integrated cuvette holder, a 400-µm optical fiber, and
OOIChem operating software.
The CHEM2000UV-VIS also consists of four basic elements:
the PC2000-UV-VIS PC Plug-in Fiber Optic Spectrometer
(200-850 nm), a miniature deuterium tungsten light source
with integrated cuvette holder, a 300-µm solarization-
resistant optical fiber, and OOIChem operating software.
The light source supplies light to the sample. The light
transmitted through the sample is collected and sent to the spectrometer via the fiber. The spectrometer
measures the amount of light at each wavelength in the sampled spectrum. The A/D converter, on which
the spectrometer is mounted, transforms the analog data from the spectrometer into digital information that
is passed to a computer. Finally, the software performs basic acquisition and display functions on your data.
CHEM2000
CHEM2000-UV-VIS

2
PC2000 PC Plug-in Fiber Optic Spectrometer
The PC2000 is 2048-element linear CCD-array fiber optic spectrometer mounted on a 1 MHz A/D card that
fits easily into an ISA-bus slot in the PC. The spectrometer has a 25-µm slit and provides a resolution of 1.5
nm (FWHM). The 12-bit, 8-channel A/D card is single-ended and half-length. Though the standard
CHEM2000 and CHEM2000-UV-VIS are single-channel systems, additional slave spectrometer channels
can be purchased at any time to expand wavelength range or perform multiple tasks.
Light Source/Sample Holder
The ISS-2 Integrated Sampling System that comes with the CHEM2000 is a versatile light source/sample
holder with a tungsten-halogen bulb, a built-in filter slot for color-correcting and other uses and a sample
holder for 1-cm square cuvettes. The light source/sample holder is SMA-terminated for easy coupling to
optical fibers and has a 5-mm diameter f/2 collimating lens.
The ISS-UV-VIS Integrated Sampling System comes with the CHEM2000-UV-VIS. This light
source/sample holder has deuterium and tungsten bulbs, and a cuvette holder for 1-cm cuvettes. It occupies
7-1/2" x 4" and weighs <1 lb. The cuvette holder attaches directly to the light source and has a 5-mm
diameter f/2 collimating lens to collect the light and funnel it to the solarization-resistant optical fiber.
Optical Fiber
Included as part of the CHEM2000 is a 400-µm diameter, single-strand UV/VIS optical fiber that couples
easily via SMA terminations to the PC2000 and light source/sample holder. This silica-core, silica-clad
fiber is 2 meters in length. For the CHEM2000-UV-VIS, the included optical fiber is a 300-µm diamter
solarization-resistant patch cord that carries light from the sample to the spectrometer.
OOIChem Spectrometer Operating Software
OOIChem is our standard Windows operating software for the CHEM2000 and CHEM2000-UV-VIS
systems. It is a basic acquisition and display software that provides a real-time interface to a variety of
spectral-processing functions. OOIChem allows users to perform basic spectroscopic measurements such as
absorbance, transmission, relative irradiance, and concentration. OOIChem operates with Windows 95,
Windows 98 and Windows NT. Visit our web site at www.OceanOptics.com/Software_Updates.asp to
download free OOIChem upgrades.
OOIBase32 Spectrometer Operating Software
OOIBase32 is our standard spectrometer operating software that we provide free of charge to all customers.
While OOIChem is a basic acquisition and display program, OOIBase32 is user-customizable and a much
more advanced acquisition and display program. With OOIBase32 you have the ability to control all
system parameters; collect data from up to 8 spectrometer channels simultaneously and display the results
in a single spectral window; perform reference monitoring and time acquisition experiments; and use
numerous editing, viewing and spectral processing functions. At any time, users can receive free
OOIBase32 updates from our web site at www.OceanOptics.com/Software_Updates.asp.
These are the standard components for the CHEM2000 and CHEM2000-UV-VIS systems. However, we
offer a complete line of light sources, sampling holders, in-line filter holders, flow cells, and other sampling
devices; an extensive line of optical fibers and probes; and collimating lenses, attenuators, diffuse
reflectance standards and integrating spheres. All components have SMA terminations so that changing the
sampling system is as easy as unscrewing a connector and adding a new component or accessory.
This modular approach -- components are easily mixed and matched -- offers remarkable applications
flexibility. Users pick and choose from hundreds of products to create distinctive systems for an almost
endless variety of optical-sensing applications

3
Packing List
A packing list comes with each order. It is located inside a plastic bag attached to the outside of the
shipment box. The invoice is mailed separately. The items listed on your packing slip include all of the
components in your order. However, some items on your packing list are actually items installed into your
spectrometer, such as the grating and slit. The packing list also includes important information such as the
shipping address, billing address, and components on back order.
Wavelength Calibration Report
In your shipment box, you will find your spectrometer in a silver-gray anti-static bag. Your software
diskettes and Wavelength Calibration Report are packaged with this manual. A Wavelength Calibration
Report comes with every spectrometer channel, contains important information specific to your
spectrometer, and should be retained. Use the calibration coefficients and intercept numbers on your
Wavelength Calibration Report to calibrate the wavelength of your spectrometer.
Upgrades
Customers sometimes find that they need Ocean Optics to make a change or an upgrade to their system. In
order for Ocean Optics to make these changes, the customer must first contact us to obtain a Return
Merchandise Authorization (RMA) number and to receive specific instructions when returning a product.

4
Quick Start
The CHEM2000 and CHEM2000-UV-VIS systems are easy to set up, allowing the user to start collecting
data within minutes. This Quick Start provides brief instructions on installing your PC2000, installing and
configuring the software, and setting up your system. To find detailed directions on a specific component,
see the Table of Contents. (Detailed PC2000 installation instructions begin on page 6. Detailed OOIChem
software instructions begin on page 9.)
Step 1: Interface the PC2000 to your PC
The PC2000 is our fiber optic spectrometer mounted onto an A/D converter. The entire instrument is
installed into your PC. But first you must find available Base Address and IRQ values.
1. The default settings for our A/D products are a Base Address (or Input/Output Range) of 768 decimal
and an IRQ of 7. You will need to match Base Address and IRQ settings on the A/D card to available
settings in your computer. First determine which settings are not being used by other hardware devices.
•If you have Windows 95/98, go to Start | Settings | Control Panel. Double-click the System
icon. Choose the Device Manager tab and double-click on “Computer” at the top of the list of
devices. Under View Resources, note available settings -- numbers unassigned to hardware.
Remember that these I/O settings are expressed in hexadecimal and correspond to our Base
Address, which is given in decimal, followed by the hexadecimal equivalent in parenthesis.
•If you have Windows NT, go to Start | Programs | Administrative Tools (Common) | Windows
NT Diagnostics. Click on the Resources tab. Select the IRQ button. Find an available IRQ.
Select the I/O Port button. Find an available I/O Range (Base Address).
2. Note these available settings. When you first run OOIChem, you must enter these values in the
“Configure Hardware” dialog box.
3. Turn off the computer and take off the computer cover. Ground yourself to the computer chassis or
power supply and remove the PC2000 (spectrometer-A/D combination) from its static-shielded bag.
4. If necessary, change the position of the switches on the A/D converter. For the PC2000, there is only one
bank of switches on the A/D converter: the Base Address may be changed via the first 6 switches and the
IRQ may be changed via the last 3 switches. (See Appendix A on page 34 for switch positions.)
5. Insert the PC2000 into an ISA-bus slot. Make sure the connections are snug and restart your computer.
Step 2: Install OOIChem Software
Before installing OOIChem, make sure that no other applications are running.
1. Insert “Disk 1” into your floppy drive. (When prompted, insert Disks 2 and 3.) Execute Setup.exe.
2. At the “Welcome” dialog box, click Next>.
3. At the “Destination Location” dialog box, you can choose Browse to pick a destination directory.
Click Next>.
4. At the “Backup Replaced Files” dialog box, select either Yes or No. We recommend selecting Yes. If
you select Yes, you can choose Browse to pick a destination directory. Click Next>.
5. Select a Program Manager Group. Click Next>. At the “Start Installation” dialog box, click Next>.
6. At the “Installation Complete” dialog box, choose Finish>.
7. When prompted to do so, restart your computer when the installation is complete.
Step 3: Configure OOIChem Software
After you restart your computer, navigate to the OOIChem icon and select it. Now that the PC2000 and
software have been installed, you need to configure your software. The first time you run OOIChem after
installation, you must follow several prompts to configure your system before taking measurements.

5
Hardware Configuration
The Configure Hardware dialog box opens when you first run OOIChem. The parameters in this dialog
box are usually set only once -- when OOIChem is first installed and the software first opens.
1. Under Spectrometer Type, choose S2000/PC2000.
2. Under A/D Converter Type, choose ADC1000/PC2000.
3. Under Base Address, choose the same setting as the dip switches on the A/D converter (and the same
available setting you found in your computer). Remember that the Input/output Range (Base Address)
you selected was expressed in hexadecimal. In this dialog box, the base address is given in decimal,
followed by the hexadecimal equivalent in parenthesis. For example, “768 (0x0300)” gives the base
address as 768 decimal and 300 hexadecimal.
4. Under IRQ, choose the same setting as the dip switches on the A/D converter (and the same available
setting you found in your computer).
5. For your setup, only these parameters apply to your system. Click OK. You can always change these
settings once OOIChem is fully operational by selecting Spectrometer | Hardware Configuration.
Spectrometer Configuration
At this point, OOIChem should be acquiring data from your spectrometer. There should be a dynamic trace
responding to light near the bottom of the displayed graph. Now that OOIChem is running, you need to
configure your system. Select Spectrometer | Spectrometer Configuration from the menu.
•Coefficients. From the Wavelength Calibration Report that came with your system, enter the
coefficients for your CHEM2000 or CHEM2000-UV-VIS under Master.
•Trigger mode. Select No External Trigger, unless you have wired an external triggering device to the
spectrometer for synchronizing data with an external event.
•Graph and chart display mode. Choose Spectrum Only to only view live spectra from one
spectrometer channel. Choose Spectrum & Kinetics to view both real-time live spectra in the top half
of the graph and to view a chart displaying your kinetics experiment in the bottom half of the graph.
•Flash Delay. This function is for use with a strobe light source. The CHEM2000 and CHEM2000-UV-
VIS systems do not come with a strobe light source.
•Color Temperature. Enter the color temperature of your reference light source used in relative
irradiance measurements. For CHEM2000 users, your lamp has a color temperature of 3100 Kelvin.
For CHEM20000UV-VIS users, your light source does not have a known color temperature.
Acquisition Parameters
Set data acquisition parameters by choosing an integration period and selecting averaging and boxcar
smoothing values.
Text Box
Enter the operator name, or any other identifying text here. This text appears in your data files. You can
edit this text at any time.
Step 4: Connect Sampling Optics
If you have a CHEM2000, take your 400-µm fiber that came with your system, screw one end into the
SMA connector on the light source and screw the other end of the fiber into SMA connector on your
PC2000, which you have already installed in your computer. If you have a CHEM2000-UV-VIS, take your
300-µm solarization-resistant fiber that came with your system, screw one end into the SMA connector on
the light source and screw the other end of the fiber into SMA connector on your PC2000.
Step 5: Receive Data
Run OOIChem in Scope Mode and take a reference spectrum and a dark spectrum (see the Experiment
Tutorial section beginning on page 27 for details). Choose the absorbance, transmission, or relative
irradiance mode to take your sample measurements.

6
Installing the PC2000 and OOIChem Software
The PC2000 PC PLUG-IN SPECTROMETER has our 2048-element linear CCD-array fiber optic
spectrometer mounted onto an ADC1000 A/D card. The ADC1000 A/D CARD is a high-speed ISA-bus
analog-to-digital converter card that connects our miniature fiber optic spectrometers to desktop PCs. The
ADC1000 is a 12-bit, 8-channel, single-ended A/D card. This sturdy spectrometer-A/D card combination
fits easily into an ISA-bus slot in the PC. The following directions apply to both CHEM2000 and
CHEM2000-UV-VIS users.
Each device in or connected to your computer is assigned specific settings; it’s similar to giving each
device its own name so that your computer will know what to call and how to recognize the device. In
order for your PC2000 to work as a device in your computer, it has to be assigned a Base Address setting
and an IRQ setting. The default settings for each are:
Base Address (I/O Range) 768 decimal (300 hexadecimal)
IRQ (Interrupt Request) 07
These default values are set on the A/D converter. There are dip switches on the A/D converter and their
positions determine the values. These default values are set in the operating software as well. Most of the
time, these default settings will work with your computer. However, if you have many devices installed in
your computer, you may have a conflict; other devices may be using these settings. If there is a conflict
with another device in your computer, you must change the positions of the switches on the A/D converter.
For the PC2000, there is only one bank of switches on the A/D converter: the Base Address may be
changed via the first 6 switches and the IRQ may be changed via the last 3 switches. To first check your
computer to see which settings are available, follow the instructions for the Windows system that you use.
Windows 95 and Windows 98 Users:
Find Available Base Address and IRQ Settings
1. Go to Start | Settings | Control Panel and double-click on the System icon.
2. Choose the Device Manager tab and double-click on “Computer” at the top of the list of devices in
your computer.
3. Under View Resources, find available settings -- numbers unassigned to hardware. Note these
available settings for both the Interrupt request (IRQ) and the Input/output (Base Address). When you
first run OOIChem, you must enter these values in the “Configure Hardware” dialog box. (Remember
that Input/output settings are expressed in hexadecimal.)

7
For most computers, the default settings on our A/D converters work well. In the picture at left on
page 6, it appears that the Printer occupies IRQ Setting 07, but for most computers, our A/D
converters can share the IRQ 07 setting with a printer and conflicts will not arise. All computers have
multiple Base Address (Input/output) settings from which to choose.
Windows NT Users:
Find Available Base Address and IRQ Settings
1. Go to Start | Programs | Administrative Tools (Common) | Windows NT Diagnostics.
2. In the “Windows NT Diagnostics” dialog box, click on the Resources tab.
3. Select the IRQ button. Find an available IRQ -- a number unassigned to a device.
4. Select the I/O Port button. Find an available I/O Range (Base Address) -- a number or range of
numbers unassigned to a device. (The number is in hexadecimal.)
5. Note these available settings. When you first run OOIChem, you must enter these values in the
“Configure Hardware” dialog box.
With Windows NT, devices cannot share IRQs; each device must be assigned a unique IRQ.
Install the PC2000
1. Turn off the computer and remove the computer cover.
2. Ground yourself to the computer chassis or power supply.
3. Remove the PC2000 (spectrometer-A/D card combination) from its static-shielded bag.
4. If necessary, change the position of the switches on the A/D converter. Position the switches to match
the available settings you found in the previous section -- numbers not being used by other hardware
devices. See Appendix A on page 34 for switch setting positions.
5. Find an open ISA-bus slot and remove the slot protector.
6. Insert the PC2000 into an available expansion slot on the motherboard connector by gently rocking the
card into the slot. Make sure the card is fully seated in the motherboard before screwing the tab on the
PC2000 to the computer. Do not bend the card or move it from side to side once it is seated in the slot.
7. If you have a CHEM2000, take your 400-µm fiber that came with your system and screw one end into
the SMA connector on your PC2000. If you have a CHEM2000-UV-VIS, take your 300-µm
solarization-resistant fiber that came with your system and screw one end into the SMA connector on
your PC2000. Reinstall the cover.

8
Install OOIChem
The resolution of your computer's monitor must be 800 x 600 or better to use OOIChem software. Before
installing OOIChem, make sure that no other applications are running.
1. Insert “Disk 1” into your floppy drive. (When prompted, install Disks 2 and 3.) Execute Setup.exe.
2. At the “Welcome” dialog box, click Next>.
3. At the “Destination Location” dialog box, you can choose Browse to pick a destination directory.
Click Next>.
4. At the “Backup Replaced Files” dialog box, select either Yes or No. We recommend selecting Yes. If
you select Yes, you can choose Browse to pick a destination directory. Click Next>.
5. At the “Installation Complete” dialog box, choose Finish>.
6. When the installation is complete, you must restart your computer.
Run OOIChem
After you restart your computer, navigate to the OOIChem icon and select it. The first time you run
OOIChem after the installation, you must enter data into the Configure Hardware dialog box.
Configure Hardware
The Configure Hardware dialog box opens automatically the first time you run the software. The parameters
in this dialog box are usually set only once -- when OOIChem is first installed and the software first opens.
1. Under Spectrometer Type, choose
S2000/PC2000.
2. Under A/D Converter Type, choose
ADC1000/PC2000.
3. Under Base Address, choose the same setting as
the dip switches on the A/D converter (and the
same available setting you found in your
computer).
Remember that the Input/output Range (Base
Address) you selected was expressed in hexadecimal.
In this dialog box, the base address is given in
decimal, followed by the hexadecimal equivalent in
parenthesis. For example, “768 (0x0300)” gives the
base address as 768 decimal and 300 hexadecimal.
4. Under IRQ, choose the same setting as the dip
switches on the A/D converter (and the same
available setting you found in your computer).
5. Only these parameters apply to your system.
(Ignore the other settings; they apply to other
A/D converters.) Click OK. You can always change these settings once OOIChem is fully operational
by selecting Spectrometer | Hardware Configuration from the menu.
If you do not see the “Configure Hardware” screen, exit the software. Then select Start | Run, and
type c:\windows\ooidrv.ini for Windows 95/98 systems or c:\winnt\ooidrv.ini
for Windows NT systems. Notepad will open. Edit this file for our device driver by finding the
“Initialized” entry and making sure this line reads Initialized=0. Save the OOIDRV.INI file and
exit Notepad. Restart OOIChem. You should now see the “Configure Hardware” dialog box.

9
Using OOIChem Software
OOICHEM OPERATING SOFTWARE provides users with a real-time interface to a variety of acquisition,
signal processing, display, and measurement functions. The 32-bit software program operates with Windows
95/98 and Windows NT and performs basic absorbance, emission and kinetics functions, which are presented
in an easy-to-follow format that is ideal for undergraduate-level students and beginning spectroscopists.
OOIChem software provides users with five different modes of operation: Scope, Absorbance,
Transmission, Relative Irradiance, and Concentration. In addition, the software allows users to control data
acquisition features such as integration period, averaging, and boxcar smoothing -- directly from the
spectral graph display. Users can acquire data by taking manual single scans or by running continuous
scans, and add into the spectral window as many as 8 previously saved overlay spectra.
Users can also perform kinetics
experiments, which allows users
to monitor and report up to 4
single wavelengths or up to 2
calculated values from a
combination of wavelengths --
for example, an absorbance value
of 400 minus an absorbance value
of 700. A kinetics chart displays
the time series. When the
experiment is complete, the data
can be exported to an ASCII file
for additional processing.
Another exciting feature of OOIChem
is that users can control the
parameters for all system functions
such as acquiring data, designing the
graph display, and configuring the
cursor. Additional features of
OOIChem include the ability to save
data as ASCII files and to store and
retrieve sample spectra.
OOIChem software will be updated
and improved continuously. To
obtain free upgrades, visit out web
site at www.oceanoptics.com/Software_Updates.asp. In order to download free upgrades, you will need
the password found on the back of your Software and Resources Library CD.
If you find that you need more advanced spectrometer operating software, we have included, free of charge,
OOIBase32, a sophisticated, 32-bit, user-customizable advanced acquisition program. See the included
OOIBase32 manual for a list of functions and features.

10
Display Functions
Several functions are accessed not through the menu but through buttons and task bars directly on the display
screen, on the top and to the right of the graph area. (The resolution of your computer's monitor must be 800 x
600 or better to view OOIChem software.) From the display screen, you can choose a mode of operation,
configure the cursor, configure the graph, enter acquisition parameters, choose a mode to acquire data, take
reference, dark, and sample scans of your sample, and scale the graph.
Spectrometer Channel Selection
The Spectrometer Channel area allows you to animate the window for a
specific spectrometer channel. Though the standard CHEM2000 and
CHEM200-UV-VIS are single spectrometer channel systems, you can
purchase additional channels at any time. For now, select Master.
Mode of Operation
Scope
The signal graphed in Scope Mode is the raw voltage coming out of the A/D converter. Once you open
OOIChem and it begins to acquire data, you see the raw voltage from the detector expressed in A/D
counts. This spectral view mode is unique to Ocean Optics. It allows you to control signal processing
functions before taking absorbance, transmission, and relative irradiance measurements. Be careful
when using this mode, as it represents a combination of several factors:
the intensity of the light source, the reflectivity of the grating and the
mirrors in the spectrometer, the transmission of the fibers, the response
of the detector, and the spectral characteristics of the sample.
Scope Mode should primarily be used when selecting signal
acquisition parameters such as integration period, averaging and
boxcar smoothing; and when taking dark and reference scans.
Absorbance
Selecting this mode switches the spectral window into Absorbance Mode. Before this can occur, both a
dark and reference scan must be stored in Scope Mode. (See the Experiment Tutorial beginning on
page 27.) Absorbance is calculated by the following equation. When this equation is evaluated for each
pixel of the detector, the absorbance spectrum is produced.
Sλ- Dλ
Aλ= - log10 (Rλ- Dλ)
where Sis the sample intensity at wavelength λ,Dis the dark intensity at wavelength λ,Ris the
reference intensity at wavelength λ.
Transmission
Selecting this mode switches the spectral window into Transmission Mode. This is also the spectral
processing mode used for Reflection spectroscopy, as the math necessary to compute reflection is
identical to transmission. Before this can occur, both a dark and reference scan must be stored in Scope
Mode. (See the Experiment Tutorial beginning on page 27.) The transmission of a solution is
calculated by the following equation:
Sλ- Dλ
%Tλ= Rλ- Dλx 100%
where Sis the sample intensity at wavelength λ, Dis the dark intensity at wavelength λ, Ris the
reference intensity at wavelength λ.

11
Relative Irradiance
Selecting this mode switches the spectral window into Relative Irradiance Mode. The reference
spectrum must be made in Scope Mode with a blackbody of known color temperature. (CHEM2000-
UV-VIS users cannot make relative irradiance measurements because the light source that comes with
the system is not a blackbody source with a known color temperature.) A dark spectrum is usually
obtained by preventing light from entering the fiber that connects to the spectrometer. (See the
Experiment Tutorial beginning on page 27.) Relative irradiance spectra are a measure of the intensity
of a light source relative to a reference emission source. Relative irradiance is calculated by the
following equation:
Sλ- Dλ
Iλ= Bλ(Rλ- Dλ)
where Bis relative energy of the reference calculated from the color temperature in Kelvin, Sis the
sample intensity at wavelength λ, Dis the dark intensity at wavelength λ, Ris the reference intensity
at wavelength λ.
Concentration
Concentration is the amount of a specified substance in a solution. Graphs of absorbance vs.
concentration are known as Beer’s Law plots. These are calculated by first measuring the light that is
absorbed from a series of solutions with different known concentrations. The length of the sample --
such as the path length of our cuvette holder -- and the wavelength chosen for monitoring the amount
of light absorbed, are constants. Then a linear plot derived from the scans of these standard solutions
with known concentrations is obtained. The plot is then used to determine the unknown concentrations
of solutions. (See the Experiment Tutorial beginning on page 27.)
The absorbance of a solution is related to the concentration of the species within it. The relationship,
known as Beer’s Law, is:
Aλ= ελcl
where Ais the absorbance at wavelength λ, εis the extinction coefficient of the absorbing species
at wavelength λ, c is the concentration and lis the optical pathlength.
Cursor Function Bar
+Sign
When the +is selected, the pointer becomes a crosshair symbol, enabling you to drag the cursor around
the graph.
Magnify Symbols
When the magnify symbol is selected, you can choose from among 6
magnify functions. The function chosen will remain in use until another
magnify icon or the crosshair symbol is selected. Clockwise, beginning with
the top left symbol, the magnify icons perform the following functions:
1. magnifies a specific area by clicking and dragging a box around an area
2. zooms in on the horizontal scale, but the vertical scale remains the same
3. zooms in on the vertical scale, but the horizontal scale remains the same
4. zooms in approximately one point vertical and horizontal, click once or press continuously
5. zooms out approximately one point vertical and horizontal, click once or press continuously
6. reverts to the last zoom function
Cursor Diamond
To move the cursor left or right in small increments in the graph area, click on the left and right
sections of the move cursor diamond. The top and bottom sections of the diamond will send the
cursor to the next or previous channel in your system. (The CHEM2000 and CHEM2000-UV-
VIS are single channel systems. However, additional channels can be purchased at any time.)

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Cursor Properties
In this bar, you can label the cursor and monitor the
cursor’s X value and Y value. To the right of the X and Y values
of the cursor is a cursor selection button that allows you to choose
a cursor style and a point style. You can also choose a color for
the cursor and whether or not to display the name of the channel
the cursor is currently reporting. Finally, you can bring the cursor
to the center of the spectrum or center the spectrum around the
cursor’s current position.
Text Box
This box allows you to enter an operator name and any other text to identify your experiment. This text
appears in your data files. You can edit this text at any time.
Acquisition Parameters
Integration Period
Enter a value to set the integration period in milliseconds for an active spectrometer channel. The
integration period of the spectrometer is analogous to the shutter speed of a camera. The higher the
value specified for the integration period, the longer the detector “looks” at the incoming photons. If
your scope mode intensity is too low, increase this value. If the intensity is too high, decrease the value.
While watching the graph trace in Scope Mode, adjust the integration period and other acquisition
parameters until the signal intensity level is approximately 3500 counts.
Average
Enter a value to implement a sample averaging function that averages the
specified number of spectra. The higher the value entered the better the signal-to-
noise ratio. The S:N improves by the square root of the number of scans averaged.
Boxcar Smooth
Enter a value to implement a boxcar smoothing technique that averages across
spectral data. This method averages a group of adjacent detector elements. A
value of 5, for example, averages each data point with 5 points (or bins) to its left and 5 points to its
right. The greater this value, the smoother the data and the higher the signal-to-noise ratio. However, if
the value entered is too high, a loss in spectral resolution results. The S:N improves by the square root
of the number of pixels averaged.
Reference Scan
Selecting the Reference button activates a prompt to make sure your light is on. You then must choose to
either Store or Cancel your reference scan. A reference spectrum is taken with the light source on and a
blank in the sampling region. Storing a reference spectrum is requisite before the software can calculate
absorbance, transmission, and relative irradiance spectra. This command merely stores a reference spectrum.
To permanently save the reference spectrum to disk, select File | Save Spectral Values from the menu.
Dark Scan
Selecting the Dark button activates a prompt to make sure the light path is blocked.
You then must choose to either Store or Cancel your dark scan. A dark spectrum is
taken with the light path to the spectrometer blocked. Storing a dark spectrum is
requisite before the software can calculate absorbance, transmission, and relative
irradiance spectra. This command merely stores a dark spectrum. To permanently save
the reference spectrum to disk, select File | Save Spectral Values from the menu.

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Subtract Dark
Selecting this box subtracts the current dark spectrum from the spectra being displayed. This command is
useful if you are trying to look at a change in an emission spectrum or are trying to eliminate from the
spectra fixed pattern noise caused by a very long integration period. The subtract dark spectrum function
only acts on spectra displayed in Scope Mode.
Acquire Data Modes
Chart Active
When Spectrum & Kinetics is chosen as the Graph and chart display mode in the Spectrometer
Configuration dialog box, the Chart Active function becomes visible in the display area above the
Scan button. This function is responsible only for the Kinetics chart. By
deselecting this function, users can use the scan button and collect data in just
the spectrum section of the graph. If the function is enabled, choosing the scan
button results in the collection of data in both the spectrum section of the graph
and the kinetics section of the graph.
Scan/Stop Button
When in Single mode, the Scan button acts as a snapshot. After selecting the
Single mode, click on the Scan button to take a scan. The button depresses and
Stop replaces Scan. The button will stay depressed until the scan has been completed (the time set in
the Integration Period box).
When in Continuous mode, the Scan button continuously takes scans. After each integration cycle,
another scan will immediately begin. The button depresses and Stop replaces Scan. Click on Stop to
halt the scanning process and discontinue acquiring data.
Scaling the Graph
You can change the vertical and/or horizontal scales of the graph by simply clicking on an X and Y
endpoint and manually typing in a value. The graph will then resize itself.

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File Menu Functions
Save Spectral Values
Select File | Save Spectral Values from the menu to save the current spectrum. Text box entries and
acquisition parameters are included in the headers of these files. You can then use these files as overlays or
import them into other software programs, such as Microsoft Excel.
Save Kinetics Values
Select File | Save Kinetics Values from the menu to save kinetics data. Text box entries and acquisition
parameters are included in the headers of these files. You can then import them into other software
programs, such as Microsoft Excel.
Open Spectrum Overlay
Select File | Open Spectrum Overlay from the menu to open a dialog box that allows you to open a
previously saved spectrum and to open it as an overlay (a static spectrum) while still acquiring live data.
You can open up to 8 overlays in the graph.
Open Kinetics Values
Select File | Open Kinetics Values from the menu to open a dialog box that allows you to open a
previously saved kinetics chart.
Printer Setup
Select File | Printer Setup from the menu to select and configure a printer for printing graphical spectra or
kinetics data.
Print Spectra and Kinetics
Select File | Print Spectra from the menu to print a spectrum, or select File | Print Kinetics from the
menu to print kinetics data.
Exit
Select File | Exit from the menu to quit OOIChem. A message box appears asking you if you are sure you
want to exit the software.

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Edit Menu Functions
Clear Spectrum Overlays
Select Edit | Clear Spectrum Overlays from the menu to remove static spectra from the graph.
Clear Kinetics Values
Select Edit | Clear Kinetics Values from the menu to clear both the kinetics values from the chart and
to clear the kinetics traces. A message box then appears, asking if you are sure you want to clear the
kinetics chart.
Autoscale X
The Autoscale X function automatically adjusts the horizontal scale of a current graph so the entire
horizontal spectrum fills the display area.
Autoscale Y
The Autoscale Y function automatically adjusts the vertical scale of a current graph so the entire vertical
spectrum fills the display area.
Show Kinetics Values
When setting up your kinetics experiment, you
must first select Spectrometer | Spectrometer
Configuration from the menu and make sure that Spectrum & Kinetics is selected next to Graph and
chart display mode. Then configure your experiment by selecting Spectrometer | Kinetics
Configuration from the menu. When you select your wavelengths, the values from these wavelengths
will be displayed above the kinetics chart if this function is enabled.
Show Legends
Select Edit | Show Legends to enable or disable the legends for the spectral trace,
overlays, and kinetics traces. When the legends are displayed, you can opt to configure
the traces by simply clicking on the legend trace you want to configure. You have the
opportunity to choose from several aesthetic functions such as: the plot design of the
spectrum, the point style used in the spectrum, the line style and width desired, color of
the plot, and a bar plot design. You can also choose to fill the baseline in the spectrum.
Utilize this function to differentiate one spectral trace from another.

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Spectrometer Menu Functions
Scan
When the Single mode is selected in the display screen, the Scan menu function acts as a snapshot. After
selecting the Single mode, select Spectrometer | Scan from the menu to take one scan of the sample.
When the Continuous mode is selected in the display screen, select Spectrometer | Scan from the menu to
continuously take scans.
Select Concentration Wavelength
This function is used when calculating the unknown concentration of a substance in a solution. You select
this function after you take an absorbance measurement of a standard solution with a known concentration.
Choose the wavelength of the highest peak in your absorbance spectrum. Then select Spectrometer |
Calculate Calibration Curve from the menu and complete the rest of your concentration experiment. See
pages 31-32 for step-by-step instructions on calculating concentrations.
Calculate Calibration Curve
Concentration is the amount of a specified substance in a solution. In order to calculate concentration, you
must take absorbance measurements of a series of solutions with different known concentrations. The
length of the sample and the wavelength chosen for monitoring the amount of light absorbed are constants.
Then a linear plot from taking these scans is obtained. This Calibration Curve is used to determine the
unknown concentrations. See pages 31-32 for step-by-step instructions on calculating concentrations and on
using this dialog box.
Enable Strobe
This function allows you to enable or disable the triggering of external strobes through the spectrometer.
You would only select Spectrometer | Strobe Enable from the menu if you were operating an external
strobe source. The CHEM2000 and CHEM2000-UV-VIS systems do not include a strobe light source.
However, the ISS-UV-VIS that comes with the CHEM2000-UV-VIS can be turned off and on through the
software and this function.
Spectrometer Configuration
Intercept
From the Wavelength Calibration Report that
came with your system, enter the Intercept
under the Master column. Though the
CHEM2000 and CHEM2000-UV-VIS come
with only a Master spectrometer channel,
additional spectrometer channels can be added
at any time. Contact an Applications Scientist
for more information.
First, Second and Third Coefficients
From the Wavelength Calibration Report that
came with your system, enter the First
Coefficient, Second Coefficient and Third
Coefficient under the Master column. Though
the CHEM2000 and CHEM2000-UV-VIS come
with only a Master spectrometer channel,
additional spectrometer channels can be added
at any time.