Ocean Optics CHEM2000-UV-VIS, CHEM2000 Operating Manual And User Manual

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Operating Manual

and

User’s Guide

CHEM2000 and CHEM2000-UV-VIS Miniature Fiber Optic Spectrophotometers

Ocean Optics, Inc. 380 Main Street Dunedin, FL 34698 (727) 733-2447 (727) 733-3962 fax

For the latest information, consult our web site: www.OceanOptics.com

Or, e-mail our Technical Service Department: TechSupport@OceanOptics.com

021400

All rights reserved. No part of this publication may be reproduced, stored in a retr ieval system, or tr ansmitted, by any means, elect r onic, 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 with out 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 trademark s of Microsoft Corp or ation.

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

Quick Start

Installing the PC2000 and OOIChem Software Using OOIChem Software

Display Functions

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

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

Clear Spectrum Overlays ........................................................................................................ 15

Clear Kinetics Values .............................................................................................................. 15

Autoscale X ............................................................................................................................. 15

Autoscale Y .............................................................................................................................15

Show Kinetics Values..............................................................................................................15

Show Legends......................................................................................................................... 15

Spectrometer Menu Functions

Scan.........................................................................................................................................16

Select Concentration Wavelength...........................................................................................16

Calculate Calibration Curve.....................................................................................................16

Enable Strobe.......................................................................................................................... 16

Spectrometer Configuration .................................................................................................... 16

Kinetics Configuration..............................................................................................................18

Hardware Configuration........................................................................................................... 18

................................................................................................................................1

..................................................................................................................................4

............................................................ 6

.................................................................................................... 9

.................................................................................................................. 10

............................................................................................................. 14

............................................................................................................. 15

........................................................................................... 16

CHEM2000 Sampling Components

ISS-2 Integrated Sampling System 400-

m Diameter Optical Fiber

µµµµ

CHEM2000-UV-VIS Sampling Components

ISS-UV-VIS Integrated Sampling System 300-

m Solarization-resistant Optical Fiber

µµµµ

................................................................................ 19

................................................................................... 19

.......................................................................................... 22

................................................................ 23

........................................................................ 23

................................................................... 26

Experiment Tutorial

Absorbance Experiments

.............................................................................................................. 27

.................................................................................................... 27

Transmission Experiments Reflection Experiments

........................................................................................................ 29

Relative Irradiance Experiments Concentration Experiments Kinetics Experiments

........................................................................................................... 33

................................................................................................. 28

....................................................................................... 30

................................................................................................ 31

Appendix A: Changing the Settings on the PC2000 Appendix B: PC2000 Pin-outs and Jumpers

.............................................................. 36

............................................... 34

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 o f 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 Resea rch grant from the U.S. Department of Energy. While d esigning the pHmonitoring 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.

CHEM2000

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-µ 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.

m solarization-

The CHEM2000 consists of four basic elements: a PC2000 PC Plug-in Fiber Optic Spectrometer (350900 nm), a tungsten-halogen light source with

integrated cuvette holder, a 400OOIChem operating software.

m optical fiber, and

CHEM2000-UV-VIS

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-µ 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.

m slit and provides a resolution of 1.5

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 300solarization-resistant patch cord that carries light from the sample to the spectrometer.

m diamter

OOIChem Spectrometer Operatin g 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

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 i n your order. However, some items on your packing list are actually i t ems 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.

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 soft ware, and setting up your system. To find detailed directions on a specific component,

Table of Contents

see the 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

icon. Choose the devices. Under 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

NT Diagnostics

Select the

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

5. Insert the PC2000 into an ISA-bus slot. Make sure the connections are snug and restart your computer.

. (Detailed PC2000 installation instructions begin on page 6. Detailed OOIChem

Device Manager

View Resources

. Click on the

I/O Port

button. Find an available I/O Range (Base Address).

Start | Settings | Control Panel

tab and double-click on “Computer” at the top of the list of

, note available settings -- numbers unassigned to hardware.

Start | Programs | Administrative Tools (Common) | Windows

Resources

tab. Select the

Appendix A

IRQ

on page 34 for switch positions.)

. Double-click the

button. Find an available IRQ.

System

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

2. At the “Welcome” dialog box, click

3. At the “Destination Location” dialog box, you can choose

Next>

Click

4. At the “Backup Replaced Files” dialog box, select either

you select Yes, you can choose

5. Select a Program Manager Group. Click

6. At the “Installation Complete” dialog box, choose

7. When prompted to do so,

Step 3: Configure OOIChem Software

After you restart your computer, navigate to the OOIChem icon and select it. Now that the PC2000 and software ha ve been installed, you ne ed to configure your software. The first time you run OOIChem after installation, you must follow several prompts to configure your system before taking measurements.

Next>

Browse

restart your computer

to pick a destination directory. Click

Next>

. At the “Start Installation” dialog box, click

Browse

Yes

Finish>

when the installation is complete.

to pick a destination directory.

or No. We recommend selecting Yes. If

Next>

Setup.exe

Next>

Hardware Configuration

Configure Hardware

The box are usually set only once -- when OOIChem is first installed and the software first opens.

1. Under

2. Under

3. Under

4. Under

5. For your setup, only these parameters apply to your system. Click OK. You can always change these

Spectrometer Type A/D Converter Type Base Address

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 b y the hexadecimal equivalent in parent hesis. For example, “ address as 768 decimal and 300 hexadecimal.

IRQ

, choose the same setting as the dip switches on the A/D converter (and the same available

setting you fou nd in yo ur computer).

settings once OOIChem is fully operational by selecting

dialog box opens when you first run OOIChem. The parameters in this dialog

, choose S2000/PC2000.

, choose ADC1000/PC2000.

, choose the same setting as the dip switches on the A/D converter (and the same

768 (0x0300)

Spectrometer | Hardware Configuration

” gives the base

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

Coefficients.

•

coefficients for your CHEM2000 or CHEM2000-UV-VIS under

Trigger mode.

•

spectrometer for synchronizing data with an external event.

Graph and chart display mode.

•

spectrometer channel. Choose of the graph and to view a chart displaying your kinetics experiment in the bo ttom half of the graph.

Flash Delay.

•

VIS systems do not come with a strobe light source.

Color Temperature.

•

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.

From the Wavelength Calibration Report that came with your system, enter the

Select No E xternal Trigger, unless yo u have wired an external triggering device to the

This function is for use with a strobe light source. The CHEM2000 and CHEM2000-UV-

Spectrometer | Spectrometer Configuration

Choose

Spectrum & Kinetics

Enter the color temperature of your reference light source used in relative

Spectrum Only

to view both real-time live spectra in the top half

to only view live spectra from one

Master

from the menu.

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

m solarization-resistant fiber that came with your system, screw one end into the SMA connector on

300the 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

Tutorial

irradiance mode to take your sample measurements.

section beginning on page 27 for details). Choose the absorbance, transmission, or relative

Experiment

Installing the PC2000 and OOIChem Software

PC2000 PC P

The spectrometer mounted onto an ADC1000 A/D card. The 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.

LUG-IN SPECTROMETER

has our 2048-element linear CCD-array fiber optic

ADC1000 A/D C

ARD

is a high-speed ISA-bus

Windows 95 and Windows 98 Users:

Find Available Base Address and IRQ Settings

1. Go to

2. Choose the

3. Under

Start | Settings | Control Panel

Device Manager

your computer.

View Resources

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.)

tab and double-click on “Computer” at the top of the list of devices in

, find available settings -- numbers unassigned to hardware. Note these

and double-click on the

System

icon.

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

2. In the “Windows NT Diagnostics” dialog box, click on the

3. Select the

4. Select the

5. Note these available settings. When you first run OOIChem, you must enter these values in the

Start | Programs | Administrative Tools (Common) | Windows NT Diagnostics

Resources

IRQ

button. Find an available IRQ -- a number unassigned to a device.

I/O Port

numbers unassigned to a device. (T he number is in hexadecimal.)

“Configure Hardware” dialog box.

With Windows NT, devices cannot share IRQs; each device must be assigned a unique IRQ.

button. Find an available I/O Range (Base Address) -- a number or range of

tab.

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 availab le settings you found in the previous section -- numbers not bei ng used by other hardware devices. See

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-

the SMA connector on your PC2000. If you have a CHEM2000-UV-VIS, take your 300-µ solarization-resistant fiber that came with your system and screw one end into the SMA connector on your PC2000. Reinstall the cover.

Appendix A

Install the PC2000

on page 34 for switch setting positions.

m fiber that came with your system and screw one end into

Install OOIChem

The resolution of your computer's monitor must be 800 x 600 or better to use OOIChem software. Before installing OO IChem, make sure that no other applic ations are running.

Setup.exe

1. Insert “Disk 1” into your floppy drive. (When prompted, install Disks 2 and 3.) Execute

2. At the “Welcome” dialog box, click

3. At the “Destination Location” dialog box, you can choose

Next>

Click

4. At the “Backup Replaced Files” dialog box, select either

you select Yes, you can choose

5. At the “Installation Complete” dialog box, choose

6. When the installation is complete,

Next>

Browse

Yes

or No. We recommend selecting Yes. If

Browse

to pick a destination directory. Click

Finish>

you must restart your computer

to pick a destination directory.

Next>

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 in this dialog box are usually set only once -- when OOIChem is first installed and the software first opens.

1. Under

2. Under

3. Under

Spectrometer Type

S2000/PC2000.

A/D Converter Type

ADC1000/PC2000.

Base Address

the dip switches on the A/D converter (and the same availab le setting you found in your computer).

dialog box opens automatically the first time you run the software. The parameters

, choose

, choose the same setting as

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, “ base address as 768 decimal and 300 hexadecimal.

4. Under

5. Only these parameters apply to your system.

IRQ

, choose the same setting as the dip switches on the A/D converter (and the same available setting you found in your computer).

(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

If you do not see the “Configure Hardware” screen, exit the software. Then select 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.

Spectrometer | Hardware Configuration

768 (0x0300)

” gives the

from the menu.

Start

Run

, and

Using OOIChem Software

HEM OPERATING SOFTWARE

OOIC

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.

provides users with a real-time interface to a variety of acquisition,

Users can also perform kinetics experiments, whic h all o ws user s 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

www.oceanoptics.com/Software_Updates.asp

site at 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.

. In order to download free upgrades, you will need

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

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.

Master

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 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.

- D

Aλ = - log

where S is the sample intensity at wavelength λ, D is the dark intensity at wavelength λ, R is the reference intensity at wavelength λ.

(

Rλ - D

)

Experiment Tutorial

beginning on

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 calculated by the following equation:

%Tλ =

where S is the sample intensity at wavelength λ, D is the dark intensity at wavelength λ, R is the reference intensity at wavelength λ.

Experiment Tutorial

Sλ - D

x 100%

- D

beginning on page 27.) The transmission of a solution is

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. (CHEM2000UV-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

of a light source relative to a reference emission source. Relative irradiance is calculated by the following equation:

Iλ = B

(

where B is relative energy of the reference calculated from the color temperature in Kelvin, S is the sample intensity at wavelength λ, D is the dark intensity at wavelength λ, R is the reference intensity at wavelength λ.

beginning on page 27.) Relative irradiance spectra are a measure of the intensity

- D

Rλ - D

)

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

The absorbance of a solution is related to the concentration of the species within it. The relationship, known as Beer’s Law, is:

where A is the absorbance at wavelength λ, ε is the extinction coefficient of the absorbing species at wavelength λ, c is the concentration and l is the optical pathlength.

Experiment Tutorial

beginning on page 27.)

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 dia mond 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.)

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 re porting. Fina l ly, 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-tonoise 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 impro ves 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

Store

either 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

Cancel

your reference scan. A reference spectrum is taken with the light source on and a

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 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

Store

Cancel

File | Save Spectral Values

your dark sca n

A dark spectrum is

from the menu.

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

Spectrum & Kinetics

When

Configuration

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.

dialog box, the

is chosen as the

Chart Active

Scan/Stop Button

When in 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 ha s b een completed (the time set in the Integration Period box).

Single

mode, the Scan button acts as a snapshot. After selecting the

Graph and chart display mode

function becomes visible in the display area above the

in the

Spectrometer

When in another scan will immediately begin. The button depresses and Stop rep laces Scan. Click on Stop to halt the scanning process and discontinue acquiring data.

Continuous

mode, the Scan button continuously takes scans. After each integration cycle,

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.

File Menu Functions

Save Spectral Values

File | Save Spectral Values

Select 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

File | Save Kinetics Values

Select 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

File | Open Spectrum Overlay

Select previously saved spectrum and to open it as an overlay (a static spectrum) while still acquiring live data. You can open up to 8 overl ays in the graph.

Open Kinetics Values

File | Open Kinetics Values

Select previously saved kinetics chart.

from the menu to save the current spectrum. Text box entries and

from the menu to save kinetics data. T e xt bo x entries and acquisitio n

from the menu to open a dialog box that allows you to open a

Printer Setup

File | Printer Setup

Select kinetics data.

from the menu to select and configure a printer for printing graphical spectra or

Print Spectra and Kinetics

File | Print Spectra

Select menu to print kinetics data.

from the menu to print a spectrum, or select

Exit

File | Exit

Select want to exit the software.

from the menu to quit OOIChem. A message box appears asking you if you are sure you

File | Print Kinetics

from the

Edit Menu Functions

Clear Spectrum Ov erlays

Edit | Clear Spectrum Overlays

Select

Clear Kinetics Values

Edit | Clear Kinetics Values

Select 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 horizontal spectrum fills the display area.

function automatically adjusts the horizontal scale of a current graph so the entire

Autoscale Y

The spectrum fills the display area.

function automatically adjusts the vertical scale of a current graph so the entire vertical

Show Kinetics Values

When setting up your kineti cs experiment, you must first select

Configuration chart display mode Configuration

will be displayed above the kinetics chart if this function is enabled.

Spectrometer | Spectrometer

from the menu and make sure that

. Then configure your experiment by selecting

from the menu. When you select your wavelengths, the values from these wavelengths

from the menu to remove static spectra from the graph.

from the menu to clear both the kinetics values from the chart and

Spectrum & Kinetics

Spectrometer | Kinetics

is selected next to

Graph and

Show Legends

Edit | Show Legends

Select 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.

to enable or disable the legends for the spectral trace,

Spectrometer Menu Functions

Scan

When the selecting the Single mode, select When the 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

Calculate Calibration Curve

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.

Single

mode is selected in the display screen, the Scan menu function acts as a snapshot. After

Continuous

Spectrometer | Scan

mode is selected in the display screen, select

from the menu and complete the rest of your concentration experiment. See

from the menu to take one scan of the sample.

Spectrometer | Scan

from the menu to

Spectrometer |

Enable Strobe

This function allows you to enable or disable the triggering of external strobes through the spectrometer. You would only select 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 | Strobe Enable

from the menu if you were operating an external

Spectrometer Configuration

Intercept

From the Wavelength Calibration Report that came with your system, enter the under 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.

Master

column. T hough the

First, Second and Third Coefficients

From the Wavelength Calibration Report that came with your system, enter the

Coefficient, Second Coefficient Coefficient

the CHEM2000 and CHEM2000-UV-VIS come with only a Master spectrometer channel, additional spectrometer channels can be added at any time.

under the

Master

Intercept

First

Third

and

column. Though

Trigger Mode

With the CHEM2000 or CHEM2000-UV-VIS and OOIChem Operating Software, you have two methods of acquiring data. In the “free running.” That is, the spectrometer is continuously scanning, acquiring, and transferring data to your computer, according to parameters set in the software. In this mode, however, there is no way to synchronize the scanning, acquiring and transferring of data with an external event.

No External Trigger Mode

(or Normal Mode), the spectrometer is

To synchronize data acquisition with an external event, the available. It involves connecting an external triggering device

External Software Trigger Mode

!!!!

to the spectrometer and then applying

an external trigger to the spectrometer before the software receives the data. In this mode, the spectrometer is “free running,” just as it is in the Normal Mode. The spectrometer is continually scanning and collecting data. With each trigger, the data collected during the integration period is transferred to the software. All acquisition parameters, such as the integration period, are still set in the software. You should use this mode if you are using a continuous light source and its inte nsity is constant before, during and after the trigger.

!!!!

In order for you to use the External Software Triggering option, it is imperative that you know the specifications and limitations of your triggering device. The design of your triggering device may prevent you from using the external software triggering mode as it is described here.

To use the External Software Trigger Mode:

1. Supply a line from your triggering device to Pin 3 of the J2 Accessory Connector on the PC20000 to

provide the positive voltage +5VDC to the spectrometer. (See figure for pin location.) We do not advise using an outside source to supply the voltage, as it is based on a referenc ed ground and your reference may be different from ours. Using Pin 3 to supply voltage ensures that the spectrometer will receive the appropriate voltage for the trigger event.

2. Supply a line from Pin 8 of the J2 Accessory Connector

to your triggering device. (See figure for pin location.)

3. Set your acquisition parameters in the software.

4. Select

5. Once you select

Spectrometer | Spectrometer Configuration

from the menu and choose

External Software Trigger

, it will appear on your computer that your spectrometer is unresponsive. Instead, i t is waiting for the trigger. Activate your triggering device.

J2 (D-SUB-15) Accessory Connector (female)

Graph and chart display mode

If you choose can be displayed in the graph area. If you choose spectrometer channel and up to 8 overlays can be displayed in the in the top half of the graph area. A kinetics chart monitoring values from up to 4 wavelengths and 2 of their arithmetic calculatio ns ca n be displayed in the in the bottom half of the graph area, if the

Spectrum Only

, spectra from one real-time spectrometer channel and up to 8 overlays

Spectrum & Kinetics

Chart Active

, spectra from one real-time

function is enabled.

Flash Delay

The value entered here sets the delay, in milliseconds, between strobe signals sent out of the spectrometer. This function allows you to enable or disable the triggering of external strobes through the spectrometer. You would only enter a value in this box if you were operating an external strobe source. The CHEM2000 and CHEM2000-UV-VIS systems do not include a strobe light source.

Color Temperature

This box allows you to enter the color temperature (in Kelvin) of your light source. In order to calculate relative irradiance, the reference spectrum must be made in Scope Mode with a blackbody light source of known color temperature. This data is necessary for the software to complete calculations for relative irradiance measurements. For CHEM2000 users, your lamp has a color temperature of 3100 Kelvin. (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.)

Kinetics Configuration

Spectrometer | Kinetics Configuration

Select a kinetics experiment. In the of time, from up to 4 single wavelengths and up to two mathematical combinations of these wavelengths.

Kinetics Configuration

from the menu to configure and establish the parameters for

dialog box, you can collect spectral data as a function

Data from a kinetics experiment will not be displayed in the graph unless you c hoo se

Spectrometer Configuration display mode

area, you will also still see real-time spectra in the top half of the graph area.

. This way, not only will your kinetics experiment be d isp layed in the bottom half of the graph

from the menu and select

Spectrum & Kinetics

Spectrometer |

next to

Graph and chart

Preset Duration

Enter a value to set the length of time for the entire kinetics process. Be sure to select hours, minutes and se conds. Your kinetics experiment can not exceed a duration of 24 hours.

Preset Sampling Interval

Enter a value to set the frequency of the data collected in a kinetics process. Be sure to select hours, minutes and seconds.

Wavelength

Enter the single wavelengths from which you wish to collect data. You can collect data from up to 4

a, b, c

single wavelengths, characterized as

, and d.

Display

If you want the data graphed from these single wavelengths, or from the mathematical calculations of these wavelengths (described below), select the display box to the right of your values.

Mathematical Calculations

In the boxes next to from the single wavelengths you specified as which represents the calculation used in the box next to

x =

and

y =

, you have the opportunity to perform calculations on the data collected

Hardware Configuration

This command opens the Configure Hardware dialog box. It allows you to configure the specific type of hardware connecting the spectrometer to the computer. For the CHEM2000 and CHEM2000-UV-VIS systems, you only need to select from

Base Address (I/O Range) Request)

for other Ocean Optics systems. The parameters in this dialog box are usually set only once -- when OOIChem is first installed and the software first starts. There is no reason to change these parameters unless you need to alter the IRQ or Base Address values. (See pages 6-8 for details about changing the IRQ and Base Address values and about this dialog box.)

Spectrometer, A/D Converter Type

IRQ (Interrupt

and

. The remaining hardware parameters are

a, b, c

, and d. Also in the box next to

x =

y =

, you can use x,

CHEM2000 Sampling Components

ISS-2 Integrated Sampling System

The CHEM2000 comes with a light source/sample holder combination called the ISS-2 Integrated Sampling System. It is a fully integrated tungsten halogen light source and 1-cm square cuvette holder that couples to the PC2000 with optical fiber to create a small-footprint system from ~350 to 900 nm. The ISS-2 has a 900hour bulb with a color temperature of 3100 Kelvin and has a 5-mm diameter f/2 collimating lens. In the ISS2, the fan is not enclosed in the base; it is exposed and should be handled with care.

Parts Included

• ISS-2 light source and cuvette holder assembly

• 12VDC wall transformer for providing power

• 1-cm square, plastic cuvette for holding samples

• Screwdriver for adjusting the fit of the cuvette

• Allen wrench for adjusting the collimating lens

Caution!

The light source becomes

DO NOT insert plastic or flammable materials in the filter slot. The materials could melt or ignite.

The unit could ignite flammable materials that come in contact with the metal housing.

There is an exposed fan on the bottom of the light source/sample holder. Handle with care.

HOT

during operation. Handle with care.

Operation

Adjusting the Fit of the Cuvette for the ISS-2

The ISS-2 is designed to hold 1-cm square cuvettes. When properly adjusted, the cuvette should fit snugly into the holder.

1. Locate the two ball plunger screws.

2. Use the screwdriver to loosen the two ball plunger screws until the ball end of each screw is just

visible in the holder.

3. Insert your cuvette into the holder.

4. Gently tighten the screws until the ball contacts the cuvette and starts to compress.

over-tighten.

Turning On the ISS-2

1. Attach the 400-µm optical fiber that came with you CHEM2000 to the SMA connector on the front of

the sample holder and attach the other end of this fiber to the SMA connector on the PC2000 installed in your computer .

2. Plug the wall transformer into a standard 110 V outlet. Plug the 12 V output into the back of your ISS-2.

For users of European-version wall transformers, plug the transformer into a standard 220 V outlet.

3. Find the on/off switch on the back of the ISS-2. Turn the lamp on.

4. Allow ~30 minutes to stabilize before using.

Do not

Using the Filter Slots in the ISS-2

The filter slots (one at the light source, a second in the sample holder) can be used to hold filters or light blocks. The most useful filters include an FG-3 blue filter for increasing the relative energy near 400 nm and 800 nm compared to 600 nm, an IR cutoff filter to reduce stray light below 750 nm, and a 550 nm high-pass filter to eliminate second-order effects on Shortwave NIR measurements.

1. To install a filter at the light source, simply insert the filter into the filter slot. The slot accommodates

filters up to 3 mm thick and accepts color-correcting and longpass filters (round or square). There is no clamp to hold the filter in place.

2. To install a filter in the sample holder filter slot, loosen the filter clamping screw with an Allen wrench

and insert the filter into the filter slot. The filter slot can accommodate filters up to 6 mm thick. Clamp the filter in place by gently tightening with an Allen wrench.

Replacing the Bulb on the ISS-2

1. Order a replacement bulb.

2. Turn off the lamp and detach the power supply. Allow the lamp to cool.

3. Remove the fan from the bottom of the lamp by loosening the four screws securing it to the base. Two

of the four screws also hold the two front legs in place. Once the screws are loosened, gently pull the fan, along with the legs, away from the lamp.

4. Now that the fan is removed, use an Allen wrench to loosen the set screw that is underneath the fan.

This screw holds the bulb in place. You do not need to remove the set screw -- loosening it is sufficient.

5. Locate the two set screws at the back of the lamp, one above each back leg. These two screws keep the

two halves of the lamp together. Remove the two screws.

6. Gently separate the two halves of the lamp and pull the bulb out of its housing.

7. Detach the wire and socket from the lamp leads. Remove bulb unit and discard.

8. Plug the new bulb into the socket and slide it forward into the front of the lamp as far as it will go.

9. Tighten the set screw on the bottom of the lamp to hold the bulb in place.

10. Close the two halves of the lamp, being ca reful not to pinch the wire s.

11. Replace the two screws at the back of the lamp and secure the fan to the bottom of the lamp.

Spectral Output of the ISS-2

This graph represents a blackbody curve for the 3100 K color-temperature, tungsten-halogen light source. The actual spectral output of the lamp will vary due to the spectrometer configuration, grating efficiency, the sampling optics used, and the detector’s efficiency.

1.2

0.8

0.6

0.4

Normalized Intensity

0.2

300 500 700 900 1100 1300 1500 1700 1900

Wa vel ength (nm)

900-hour bulb / 3100K

ISS-2 Specifications

Path length: 1 cm Collimating lens: BK 7 glass (~360 nm - 2 µm*), 5 mm diameter, f/2 Collimating lens termination: SMA 905 Filter slot: accepts filters up to ¼" (6 mm) in thickness Base material: aluminum Spectral range: 360 nm - 2 µm*

Dimensions: Power input: 12 VDC/800 mA, 7-20 VDC/0.5-2 amps

Power output: 6.5 watts Bulb life: 900 hours Bulb color temperature: 3100K Output to bulb: 5 volts/1.3 amps Output regulation: 0.2% voltage Time to stabilized output:

* The useable range of the ISS-2 is limited to the wavelength range of the spectrometer to which it is

coupled -- i.e., though the spectral range of the ISS-2 goes to 2 µm, it can only "see" to 900 nm when used with the PC2000 that came with your CHEM2000.

** The amount of time it takes for the lamp to achieve a stabilized output will vary. A fan cools the lamp;

therefore the lamp may take much less than 30 minutes to stabilize.

9.0 cm x 5.0 cm x 3.2 cm (LWH)

3.5" x 2.0" x 1.25" (LWH)

~30 minutes

µµµµ

400-

The 400-µm diameter optical fiber that comes with your CHEM2000 is a single-strand optical fiber. The active part of the fiber consists of a silica core, surrounded by a silica cladding material. The fiber is very fragile, and if not protected by a suitable buffer material, would be nearly useless for most applications. The buffer materials are polymer coatings that provide mechanical strength. Cabling further protects the buffer-coated fiber. Our standard laboratory cabling is blue PVC. The ends of the fibers are cleaved, epoxied into the SMA connectors, and polished. Follow the guidelines below when handling your fiber.

m Diameter Optical Fiber

Care and Use Guidelines

When fibers break, they stop transmitting light. Inspect fibers by eye to determine if light is being

!!!!

transmitted. Bending the fiber will cause attenuation. To minimize this effect, add extra strain relief to both ends

!!!!

of the fiber. Do not exceed the temperature specifications for the materials involved: 2000C for the fiber, 1000C

!!!!

for PVC cabling, 100 Do not allow the fiber to be bent at a sharp angle. A bending radius of less than 1" is dangerous.

!!!!

Keep connectors and probe tips covered when the fibers are not being used.

!!!!

Clean the ends of the fibers with lens paper and distilled water, alcohol or acetone. Avoid scratching

!!!!

the surface. Do not immerse fiber ends in caustic materials or other solutions that can damage glass.

!!!!

C for standard epoxy.

Specifications

Jacket: Sheathing/cabling: PVC (standard) Connector/termination: SMA 905 Fiber core: pure fused silica Cladding: doped fused silica Fiber profile: step-index multi-mode Numerical aperture: 0.22 Recommended minimum bend radiu s: momentary = 10 cm, long term = 16 cm

Nylon (temperature range -40 to 100° C)

CHEM2000-UV-VIS Sampling Components

ISS-UV-VIS Integrated Sampling System

The ISS-UV-VIS Integrated Sampling System that comes with the CHEM2000-UV-VIS is a combination of a RF deuterium source with a tungsten halogen bulb connected to a cuvette holder for 1-cm cuvettes. 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 that also comes with the CHEM2000-UV-VIS. The ISS-UV-VIS can be operated manually or through the software.

Parts Included

• ISS-UV-VIS Deuterium Tungsten Light Source/Cuvette Holder

• Power cord for connecting the ISS-UV-VIS to outlet

• 15-pin accessory cable for software control of the ISS-UV-VIS

Caution!

The beam emerging from the ISS-UV-VIS produces low levels of ultraviolet radiation. Direct eye contact

could cause eye injury. Safety eyewear is recommended.

Never look directly into the light source, sight down the beam into the source or stare at the diffuse

reflected beam.

Dangerous voltages present. NO serviceable parts inside unit. To replace bulbs, contact Ocean Optics.

This instrument should not be used for any clinical or diagnostic purposes.

!!!!

Handle with care. Dropping the instrument may cause permanent damage.

!!!!

Operation

Adjusting the Fit of the Cuvette for the ISS-UV-VIS

The ISS-UV-VIS is designed to hold 1-cm square cuvettes. When properly adjusted, the cuvette should fit snugly into the holder.

1. Locate the two ball plunger screws.

2. Use the screwdriver to loosen the two ball plunger screws until the ball end of each screw is just

visible in the holder.

3. Insert your cuvette into the holder.

4. Gently tighten the screws until the ball contacts the cuvette and starts to compress.

over-tighten.

Setting Up the ISS-UV-VIS

1. Attach the 300-µm solarization-resistant optical fiber that came with you CHEM2000-UV-VIS to the

SMA connector on the front of the sample holder and attach the other end of this fiber to the SMA connector on the PC2000 installed in your computer.

Do not

2. Plug the wall transformer into a standard 110 V outlet. Plug the 12 V output into the back of your

12V

ISS-UV-VIS above the transformer into a standard 220 V outlet. At this time, the green LED indicator light on the front of the lamp will be lit. This indicator light only means that the lamp is receiving power, not that the deuterium and tungsten bulbs are on.

label. For users of European-version wall transformers, plug the

Operating the ISS-UV-VIS Manually

1. Find the switch on the back of the ISS-UV-VIS.

2. There are three positions:

position. There can be up to a 1.5 second delay between switching the lamp to on and the bulbs igniting. If the lamp has not been used recently, the deuterium bulb may take up to 60 seconds to ignite.

3. For 0.3% peak-to-peak stability, allow 30 minutes warm-up time before taking your measurements.

On, Off

, and

Remote

. For Manual operation, move the switch to the

Operating the ISS-UV-VIS through Software

1. Take the 15-pin accessory cable and plug one end into the PC2000 installed into your computer.

Connect the other end of the accessory cable into the back of the ISS-UV-VIS.

2. Find the switch on the back of the ISS-UV-VIS. There are three positions:

For Software operation, move the switch to the position enables you to control the lamp through the software, whether you are using OOIChem or OOIBase32.

3. When using OOIChem, sele ct

in the ISS-UV-VIS on and off.

4. When you want to control the ISS-UV-VIS through our more advanced OOIBase32 Spectrometer

Operating software, select or deselect the bar above the graph area to turn the light source in the ISS-UV-VIS on and off. Refer to the

OOIBase32 Spectrometer Operating Software Manual

4. There can be up to a 1.5 second delay between turning the bulbs on via the software and the bulbs

igniting. If the lamp has not been used recently, the deuterium bulb may take up to 60 seconds to ignite.

5. For 0.3% peak-to-peak stability, allow 30 minutes warm-up time before taking your measurements.

Spectrometer | Enable Strobe

Remote

Strobe Enable

position. Moving the switch to the

from the menu to turn t he light sourc e

box in the Acquisition Parameter dialog

for more details.

On, Off

, and

Remote

Disabling the Tungsten or Deuterium Bulb

It is possible to disable the deuterium or the tungsten bulb in the ISS-UV-VIS. Both bulbs are enabled at the time of manufacture. In order to disable the deuterium or tungsten bulb, you must remove the casing of the ISS-UV-VIS.

Disabling the Deuterium Bulb

Jumper block JA of the ISS-UV-VIS's circuit board controls the deuterium bulb. Short pins 2-3 (that is, place a jumper over pins 2-3 of JA) to enable the deuterium bulb. Short the pins 1-2 (that is, place a jumper over pins 1-2 of JA) to disable the deuterium bulb.

Disabling the Tungsten Bulb

Jumper block JB of the ISS-UV-VIS's circuit board controls the tungsten bulb. Short pins 2-3 (that is, place a jumper over pins 2-3 of JB) to enable the tungsten bulb. Short pins 1-2 (that is, place a jumper over pins 1-2 of JB) to disable the tungsten bulb.

Bulb Replacement

The deuterium and tungsten bulbs cannot be replaced by unauthorized personal. To replace a bulb in the ISS-UV-VIS, contact Ocean Optics.

Specifications

Deuterium wavelength range: 200-400 nm Tungsten wavelength range: 360-850 nm Deuterium bulb life: 800 hours Tungsten bulb life: 2,000 hours Ignition delay: ~1.5 seconds to 60 seconds

Peak-to-peak stability: Connector: SMA 905

Power input: 12 V Power requirement: 12 VDC/420 mA Power consumption: 5 watts (deuterium 3.8 watts, tungsten 1.2 watts)

0.3% in 30 minutes

1.0% in 10 minutes

µµµµ

300-

The 300-µm Diameter Solarization-resistant Optical Fiber that comes with your CHEM2000-UV-VIS is a single-strand optical fiber. The active part of our solarization-resistant fibers consists of a silica core, surrounded by a silica cladding material. The fiber is then coated in aluminum. Our standard laboratory cabling is blue PVC. Our solarization-resistant fibers are best used for applications where exposure to longterm UV light occurs.

Solarization is the loss of transparency in glass due to exposure to ultraviolet radiation. If you are using a UV light source, the UV radiation degrades the silica in a standard patch cord fiber over time, resulting in increased overall absorption values and invalid data. This degradation is called so larization, which is the formation of “color centers” or silica molecules with an unbound pair of electrons. These color centers have an absorption band that is centered at 215 nm. In regular HOH fibers (our standard fibers), the concentration of these color centers grows until nearly all UV light in the 215 nm region is blocked.

Other solarization-resistant fibers are hydrogen-loaded but their solarization-resistant properties do not last as the hydrogen eventually leaks out of the silica -- meaning that these hydrogen-doped solarizationresistant fibers have a “shelf life.” With Ocean Optics solarization-resistant op tical fibers, there is no shelf life.

m Diameter Solarization-resistant Optical Fiber

Care and Use Guidelines

When fibers break, they stop transmitting light. Inspect fibers by eye to determine if light is being

!!!!

transmitted. Bending the fiber will cause attenuation. To minimize this effect, add extra strain relief to both ends

!!!!

of the fiber. Do not exceed the temperature specifications for the materials involved: 2000C for the fiber, 1000C

!!!!

for PVC cabling, 100 Do not allow the fiber to be bent at a sharp angle. A bending radius of less than 1" is dangerous.

!!!!

Keep connectors and probe tips covered when the fibers are not being used.

!!!!

Clean the ends of the fibers with lens paper and distilled water, alcohol or acetone. Avoid scratching

!!!!

the surface. Do not immerse fiber ends in caustic materials or other solutions that can damage glass.

!!!!

C for standard epoxy.

Specifications

Nylon (temperature range -40 to 100° C)

Experiment Tutorial

When you are ready to begin your experiment, you should have already installed the PC2000, installed OOIChem, set up your light source/sample holder, and connected your fiber from the PC2000 to your light source/sample holder.

Now you are ready to take your measurements. Because of the components making up your CHEM2000 and CHEM2000-UV-VIS, your system is ideal for absorbance and transmission. The CHEM2000 can also make relative irradiance measurements. If, however, you wish to utilize your system for other measuring funct ions, additional products might be required. Contact an Ocean Optics Application s Scientist for options.

Absorbance Experiments

Absorbance spectra are a measure of how much light is absorbed by a sample. The software calculates absorbance (

) using the following equation:

- D

Aλ = - log

where S is the sample intensity at wavelength λ, D is the dark intensity at wavelength λ, R is the reference intensity at wavelength λ.

(

Rλ - D

)

Common applications include the quantification of chemical concentrations in aqueous or gaseous samples. To take an absorbance measurement:

1. Select

2. While still in

3. Begin an absorbance measurement by first making sure the sample is in place and nothing is blocking

Scope

Adjust acquisition parameters so that the peak intensity of the reference signal is about 3500 counts. Take a reference spectrum by first makin g sure nothing is blocking the light path going to your spectr ometer. The analyte you want to measure must be absent while taking a reference spectrum. Take the reference reading b y clicking the reference spectrum. To save a spectrum, you must select Storing a reference spectrum is requisite before the software can calculate absorbance spectra.

your spectrometer. (If possible, do not turn off the light source . If you must turn off your l ight source to store a dark spectrum, make sure to allow enough time for the lamp to warm up before continuing your experiment.) Ta ke the dark rea ding by clicking the (This command merely stores a dark spectrum. To save a spectrum, you must select

Spectral Values

absorbance spectra. the light going to your sample. Then select

display area. Click on the scan will be taken. If click on the

!!!!

If at any time any sampling variable changes -- including integration period, averaging, boxcar smoothing, distance from light source to sample, etc. -- you must store a new reference and dark spectrum.

Stop

Mode of Operation

under

Reference

Scope Mode

from the menu.) Storing a dark spectrum is requisite before the software can calculate

button. To save the spectrum, select

, take a dark spectrum by first completely blocking the light path going to

Scan

button in the display area to take a scan. If

Continuous

in the software display area. Make sure the signal is on scale.

button in the software display area. (This command merely stores a

File | Save Spectral Values

Dark

button in the software display area.

Absorbance

is selected, the spectrometer will continuously take scans until you

File | Save Spectral Values

Mode of Operation

under

Single

from the menu.)

File | Save

in the software

is selected, only one

from the menu.

Transmission Experiments

Transmission is the percentage of energy passing through a system relative to the amount that passes through the reference. Transmission Mode is also used to show the portion of light reflected from a sample. Transmission and reflection measurements require the same mathematical calculation. The transmission is

- D

) relative to a standard substance (such as air). The software calculates

x 100%

expressed as a percentage (

(or

) by the following equation:

%Tλ =

where S is the sample intensity at wavelength λ, D is the dark intensity at wavelength λ, R is the reference intensity at wavelength λ.

Common applications include measurement of transmission of light through solutions, optical filters, optical coatings, and other optical elements such as lenses and fibers.

!!!!

For transmission of light through solutions, we offer a transmission dip probe with screw-on, removable tips in 2-mm, 5-mm or 10-mm path lengths. Contact Ocean Optics for more information.

To take a transmission measurement:

1. Select

Scope

Mode of Operation

under

in the software display area. Make sure the signal is on scale. Adjust acquisition parameters so that the peak intensity of the reference signal is about 3500 counts. Take a reference spectrum by first making sure no thing is blocking the light path going to your spectrometer. The analyte you want to measure must be absent while taking a reference spectrum. Take the reference reading by clicking the merely stores a reference spectrum. To save a spectrum, you must select

Reference

button in the software display area. (This command

File | Save Spectral Values

from the menu.) Storing a reference spectrum is requisite before the software can calculate transmission spectra.

2. While still in

Scope Mode

, take a dark spectrum by first completely blocking the light path going to your spectromete r. (If possib l e, do not turn off the light source. If you must turn off your light source to store a dark spectrum, make sure to allow enough time for the lamp to warm up before continuing your experiment.) Take the dark reading by clicking the command merely stores a dark spectrum. To save a spectrum, you must select

Values

from the menu.) Storing a dark spectrum is requisite before the software can calculate

Dark

button in the software display area. (This

File | Save Spectral

transmission spectra.

3. Begin a transmission measurement by first making sure the sample is in place and nothing is blocking

the light going to your sample. Then select display area. Click on the scan will be taken. If click on the

Stop

button. To save the spectrum, select

Scan

button in the display area to take a scan. If

Continuous

is selected, the spectrometer will continuously take scans until you

Transmission

File | Save Spectral Values

Mode of Operation

under

in the software

Single

is selected, only one

from the menu.

!!!!

Reflection Experiments

Reflection is the return of radiation by a surface, without a change in wavelength. The reflection may be:

• Specular, in which the angle of incidence is equal to the angle of reflection.

• Diffuse, in which the angle of incidence is not equal to the angle of reflection.

Every surface returns both specular and diffuse reflections. Some surfaces may return mostly specular reflection, others more diffuse reflection. The glossier the surface, the more specular the reflection. Reflection is expressed as a percentage ( our WS-1 white reference for a diffuse reflection measurement):

- D

%Rλ =

where S is the sample intensity at wavelength λ, D is the dark intensity at wavelength λ, R is the reference intensity at wavelength

- D

x 100%

Common applications include measuring the reflection properties of mirrors, anti-reflection coatings, and measuring the visual properties of the color in paints, graphic arts, plastics, and food products.

!!!!

The components that came with the CHEM2000 and CHEM2000-UV-VIS will not allow the user to make reflection measurements. A reflection probe is necessary. We offer several components for reflection measurements such as a variety of reflection probes, a reflection probe holder, diffuse reflectance standards and an integrating sphere. Contact Ocean Optics for more information.

) relative to the reflection from a standard substance (such as

λ.

To take a reflection measurement:

1. Select

Scope

Mode of Operation

under

in the software display area. Make sure the signal is on scale. Adjust acquisition parameters so that the peak intensity of the reference signal is about 3500 counts. Take a reference spectrum by first makin g sure nothing is blocking the light path going to your spectr ometer. The analyte you want to measure must be absent while taking a reference spectrum. Take the reference reading b y clicking the reference spectrum. To save a spectrum, you must select

Reference

button in the software display area. (This command merely stores a

File | Save Spectral Values

from the menu.)

Storing a reference spectrum is requisite before the software can calculate reflection spectra.

2. While still in

Scope Mode

, take a dark spectrum by first completely blocking the light path going to your spectrometer. (If possible, do not turn off the light source . If you must turn off your l ight source to store a dark spectrum, make sure to allow enough time for the lamp to warm up before continuing your experiment.) Ta ke the dark rea ding by clicking the (This command merely stores a dark spectrum. To save a spectrum, you must select

Spectral Values

from the menu.) Storing a dark spectrum is requisite before the software can calculate

Dark

button in the software display area.

File | Save

reflection spectra.

3. Begin a reflection measurement by first making sure the sample is in place and nothing is blocking the

light going to your sample. Then select

Transmission

Mode of Operation

under

in the software display area. The mathematics required to calculate reflection measurements are identical to those necessary to compute a transmission spectrum. Click on the scan. If continuously take scans until you click on the

Spectral Values

!!!!

Single

is selected, only one scan will be taken. If

Stop

button. To save the spectrum, select

from the menu.

Scan

button in the display area to take a

Continuous

is selected, the spectrometer will

File | Save

Relative Irradiance Experiments

Irradiance is the amount of energy at each wavelength from a radiant sample. In relative terms, it is the fraction of energy from the sample compared to the energy collected from a lamp with a blackbody energy distribution, normalized to 1 at the energy maximum. Relative irradiance is calculated by the following equation:

- D

Iλ = B

(

where Bλ is relative energy of the reference calculated from the color temperature in Kelvin, S is the sample intensity at wavelength λ, D is the dark intensity at wavelength λ, R is the reference intensity at wavelength λ.

Common applications include characterizing the light output of LEDs, incandescent lamps and other radiant energy sources such as sunlight. Also included in irradiance measurements is fluorescence, in which case the spectrometer measures the energy given off by materials that have been excited by light at a shorter wavelength.

!!!!

The components that came with the CHEM2000-UV-VIS will not allow the user to make relative irradiance measurements. Only CHEM2000 users can perform relative irradiance measurements. In order to make relative irradiance measurement, the reference spectrum must be made in Scope Mode with a blackbody light source of known color temperature. This color temperature is needed in order to calculate relative irradiance. The light source that comes with the CHEM2000-UV-VIS is not a blackbody light source with a known color. To purchase a blackbody light source, contact Ocean Optics.

Rλ - D

)

To take a relative irradiance measurement:

1. Select

2. Select

3. While still in

4. Begin a relative irradiance measurement by first positioning the fiber at the light or emission source

Spectrometer | Spectrometer Configuration

the color temperature in Kelvin of the reference lamp you are going to use is entered here. The color temperature of the tungsten halogen light source that came with your CHEM2000 has a color temperature of 3100 Kelvin. Click OK.

Scope

by adjusting acquisition parameters. Take a reference spectrum of your reference lamp. Take the reference reading by clicking the merely stores a reference spectrum. To save a spectrum, you must select from the menu.) Storing a reference spectrum is requisite before the software can calculate relative irradiance spectra.

spectrometer. Take the dark reading by clicking the command merely stores a dark spectrum. To save a spectrum, you must select

Values

from the menu.) Storing a dark spectrum is requisite before the software can calculate relative

irradiance spectra.

you wish to measure. Then select display area. Click on the scan will be taken. If click on the

!!!!

Stop

Mode of Operation

under

Scope Mode

button. To save the spectrum, select

, take a dark spectrum by first completely blocking light from going to your

Scan

button in the display area to take a scan. If

Continuous

in the software display area. Make sure the signal is on scale

Reference

Relative Irradiance

is selected, the spectrometer will continuously take scans until you

button in the software display area. (This command

from the menu. Next to

Dark

button in the software display area. (This

Mode of Operation

under

File | Save Spectral Values

Color Temp

File | Save Spectral Values

File | Save Spectral

in the software

Single

is selected, only one

from the menu.

, make sure

Concentration Experiments

The absorbance of a solution is related to the concentration of the species within it. The relationship, known as Beer’s Law, is:

Aλ =

where A is the absorbance at wavelength λ, ε is the extinction coefficient of the absorbing species at wavelength λ, c is the concentration and l is the optical pathlength.

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 prepared by measuring the light absorbed by 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. A linear plot from taking scans of these standard solutions with known concentrations is then obtained. The plot is then used to determine the unknown concentrations of substances in solutions.

In order to discover the unknown concentration of a substance in a solution, you must first take spectral scans of a series of solutions with different known concentrations of the same substance. You begin this process by taking an absorbance spectrum of the solution with the highest known concentration.

1. Select

2. While still in

3. Take the solution with the highest known concentration and put it in the cuvette holder. Make sure

4. Now select the wavelength for monitoring the concentration of your solutions by choosing

Scope

Adjust acquisition parameters so that the peak intensity of the reference signal is about 3500 counts. Take a reference spectrum by first making sure no thing is blocking the light path going to your spectrometer. The solution with the highest known concentration you want to measure must be absent while taking a reference spectrum. Take the reference reading by clicking the software display area. To save the spectrum, select

nothing is blocking the light going to your sample. Then select

Operation

To save the spectrum, select

| Select Concentration Wavelength

the spectrum of the solution with the highest known concentration and choose

Mode of Operation

under

Scope Mode

. Click on the

in the software display area. Make sure the signal is on scale.

Reference

File | Save Spectral Values

, take a dark spectrum by first completely blocking the light path going to

Dark

button in the software display area. To

File | Save Spectral Values

Scan

button in the display area to take a scan. Make sure

File | Save Spectral Values

from the menu. Move the cursor to the highest absorbance peak of

from the menu.

Absorbance

from the menu.

under

Select

button in the

Mode of

Single

is selected.

Spectrometer

5. Remove the solution with the highest known concentration. Select

Calibration Curve

begin taking scans of the r est of your series of standard solutions with known concentrations, from the lowest known concentration to highest, all while working in this dialog box.

6. If you wish, you can take a new reference and a new dark scan for each solution by choosing

Dark

necessary. If no reference or dark scan is taken at this point, the software will use the reference and dark scans taken in Steps 1 and 2 to calculate absorbance.

7. Take the solution with the lowest known concentration and put it in the cuvette holder. Enter the known

concentration of the standard solution in the chart in the

Scan | Reference

and

from the menu. The Calculate Calibration Curve dialog box opens. Now you will

Spectrometer | Calculate a

from the menu of this dialog box. However, in this case, it is not

Concentration

column, next to

Solution #1

Scan |

8. Click the

Scan

button or select

Scan | Solution

from the menu. The absorbance value will appear next to the concentration for Solution #1. At any point, you can select the dialog box of all data.

Edit | Clear

from the menu to clear

9. Take Solution #1 out of the cuvette holder and put in another standard solution with the next highest

known concentration. Enter the known concentration of the standard solution in the chart in the

Concentration

10. Click the

column, next to

Scan

button or select

Solution #2

Scan | Solution

from the menu. The absorbance value will appear next to the concentration for Solution #2.

11. You may continue to scan solutions with known concentrations. You must scan at least 2 in or d e r to

achieve a calibration curve.

12. When you have completed taking scans of your solutions with known concentrations, click the

Calibration Curve

necessary to compute Beer’s Law and to find the unknown concentration of a solution.

button. You will then ha ve the

13. At this time, you may also select a label for your concentration values, such at

Concentration Units

14. Select

Edit | Show Legend

box. This is only a label and does not affect the data in any way.

from the menu to display the legend for the calibration curve. The legend

Intercept

and

Slope

of your curve. The Slope is the

Moles per Liter

allows you to choose a plot design, point style, line style, line width and plot color. Select

Palette

from the menu to display a variety of options for configuring the curve. The palette provides

View

, in the

Edit | Show

features such as autoscaling, graph formatting, value precision, mode mapping, and graph positioning.

15. You can select

current calibration curve data, select

16. Select

File | Close

File | Print

from the menu for the dialog box to print the dialog box. To save the

File | Save

from the menu for the dialog box.

from the menu for the dialog box to close this dialog box and return to the

main windo w.

17. When a message box asks if you would like to use this calibration curve when calculating

concentration values, select

Yes

18. Now that you are back in the main display window, place the solution with the unknown concentration

of a substance in the cuvette holder.

19. Under

Mode of Operation

, select

Concentration

. Click the

Scan

button to receive your

concentration values.

Kinetics Experiments

Spectrometer | Kinetics Configuration

Select a kinetics experiment. In the of time, from up to 4 single wavelengths and up to two mathematical combinations of these wavelengths.

A kinetics experiment will not be displayed in the graph unle ss you

Spectrometer |

choose

Spectrometer Configuration

from the menu and choose

Spectrum & Kinetics Graph and chart display mode

This way, not only will your kinetics exp eriment be displayed in the bottom half of the graph area, you will also still see a spectrometer channel’s real-time spectra in the top half of the graph area.

To run a kinet i cs experiment:

1. In the graph area, select acquisition parameters, such as integration period, averaging, and boxcar

smoothing values. Do not change these parameters for the duration of the kinetics experiment.

2. Select

3. Enter a

4. Enter a

5. Under

6. If you want the data graphed from these single wavelengths, or from the mathematical calculations

7. In the boxes next to

8. Click OK to confirm the parameters and close the dialog box.

9. Click the

10. Click the

11. Select

Spectrometer | Kinetics Configuration

dialog box.

Preset Duration

hours, minutes and seconds. The duration of your kinetics experiment cannot exceed 24 hours.

Preset Sampling Interval

Be sure to select hours, minutes and seconds. Data from a timed acquisitio n is stamped with a time that is accurate to 1 millisecond.

Wavelength

data from up to 4 single wavelengths, characterized as a, b, c, and d.

(described in the next step), select the from the single wavelengths you specified as

represents the calculation used in

Scan

button to begin the kinetics experiment. Make sure that top half of the graph displays a real-time full wavelength spectrum. The bottom half of the graph displays the data for the selected wavelengths and their derived arithmetic calculations. Each data set is stored with a time stamp.

Stop

button to stop the experiment. However, if a

experiment will automatically stop after the designated time has passed.

File | Save Kinetics Values

spectrometer’s serial number, active channel and acquisition parameters in a header. This file can be opened with any text or spreadsheet editor.

Kinetics Configuration

next to

value to set the length of time for the entire kinetics process. Be sure to select

value to set the frequency of the data collected in a kinetics process.

, enter the single wavelengths from which you wish to collect data. You can collect

x =

and

y =

, you have the opportunity to perform calculations on the data collected

x =

from the menu to save a tab-delimited ASCII file with the

from the menu to configure and establish the parameters for

dialog box, you can collect spectral data as a function

from the menu to open the Kinetics Configuration

Display

box to the right of your values.

a, b, c

, and d. In the

y =

box, you can also use x, which

Continuous

Preset Duration

is selected. The

time was selected, the

Appendix A: Changing the Settings on the PC2000

Base Address Settings

To change the Base Address settings on the PC2000, find the bank of switches on the A/D converter. The Base Address may be change d via the first 6 switches (the IRQ may be changed via the last 3 switches). Switches in the OFF position have the decimal values shown. Switches in the ON position have a value of zero. The Base Address is the sum of the values of the switches. In the default setting, switches 5 and 6 are added to give a value of 768. A few of the many combinations for Base Address settings are below. After you have changed the switches, reinstall the card and change the software settings to match the hardware settings. (See pages 6-8 for instructions.) The gray block indicates the position of the switch.

= Switch is in the on, upward position

Example: 768 decimal = Hex300 = 0x300 (Default Setting)

Switch # 123456 ON OFF

Decimal equivalent 16 32 64 128 256 512 Value as shown 256 512

Example: 784 decimal = Hex310 = 0x310

Switch # 123456 ON OFF

Value as shown 16 256 512

Example: 800 decimal = Hex320 = 0x320

Switch # 123456 ON OFF

Value as shown 32 256 512

Example: 816 decimal = Hex330 = 0x330

Switch # 123456 ON OFF

Value as shown 16 32 256 512

Interrupt Request Settings

To change the IRQ settings on the PC2000, see the bank of switches on the A/D converter. The IRQ may be changed via the last 3 switches. The following matrix defines the different IRQ settings by sw itch positions 7, 8, and 9. In the default setting, the IRQ is set to 7. Other combinations for IRQ settings are belo w. After you have changed the switches, reinstall the card and change the software settings to match the hardware settings. (See pages 6-8 for instructions.) The gray block indicates the position of the switch.

= Switch is in the on, upward position

IRQ 7 (Default Setting)

Switch # 789 ON OFF

IRQ 3

Switch # 789 ON OFF

IRQ 4

Switch # 789 ON OFF

IRQ 5

Switch # 789 ON OFF

IRQ 9

Switch # 789 ON OFF

IRQ 10

Switch # 789 ON OFF

IRQ 11

Switch # 789 ON OFF

Appendix B: PC2000 Pin-outs and Jumpers

It is not necessary for the average user to worry about the interconnect scheme, as the cables supplied with all of the units need only be plugged into the matching connectors on the hardware. However, if the need arises to design and fabricate your own cabling system, the following tables supply the necessary information.

H1 Header Pins (Slave Header)

Pin Function

1 Channel 1 (slave 1) 2 Channel 2 3 Channel 3 4 Channel 4 5 Channel 5 6 Channel 6 7 Channel 7 8GND

9GND 10 S0 11 Reserved 12 Multiple Strobe 13 Single Strobe 14 Reserved 15 F read (ROG) 16 F clock

J2 (D-SUB-15) Connectors

Pin Function

1 Strobe Single Fire

2 Strobe Multiple Fire

3+5 VDC

4 External Hardware Trigger

5 External Synchronization

6 Analog Channel 7 Input

7 Analog Channel 6 Input

8 External Software Trigger

9 Analog Channel 1 10 Ground 11 Analog Channel 4 12 Analog Channel 5 13 Digital Out 0 (Strobe Enable or Lamp On/Off) 14 Analog Channel 3 15 Analog Channel 2

Appendix C: Calibrating the Wav elength of Your Spectrometer

The following describes how to calibrate the wavelength of your spectrometer. Though each spectrometer is calibrated before it leaves Ocean Optics, the wavelength for all spectrometers will drift slightly as a function of time and environmental conditions.

You are going to be solving the following equation, which shows that the relationship between pixel number and wavelength is a third-order polynomial . . .

= I + C

. . . where λ is the wavelength of pixel p, I is the wavelength of pixel 0, C1 is the first coefficient (nm/pixel), C calculating the values for I and the three Cs.

is the second coefficient (nm/pixel2), and C3 is the third coefficient (nm/pixel3). You will be

p + C

p2 + C

Setting Up

To re-calibrate the wavelength of your spectrometer, you will need the following:

• A light source that produces spectral lines. Ocean Optics HG-1 Mercury-Argon lamp is ideal for this

purpose. If you do not have an HG-1, you will need a spectral line source that produces several (at least 4-6) spectral lines in the wavelength region of your spectrometer.

• Your spectrometer.

• An optical fiber (the fibers that came with your CHEM2000 and CHEM2000-UV-VIS will work fine).

• Either a spreadsheet program (Excel or Quattro Pro, for example) or a calculator that performs third-

order linear regressions. If you are using Microsoft Excel, choose

AnalysisToolPak

check

AnalysisTookPak-VBA

and

Tools | Add-Ins

from the menu and

Calibrating the Wavelength

of Your Spectrometer

1. After placing OOIChem into Scope Mode, take a spectrum of your light source that produces spectral

lines. Adjust the integration period until there are several peaks on the screen that are not off-scale.

2. Move the cursor to one of the peaks and carefully position it so that it is at the point of maximum

intensity. Record the pixel number that is displayed in the cursor function bar (located above right of the graph). Repeat this step for all of the peaks in your spectrum.

3. Using your spreadsheet, create a table like the one shown on the next page. In the first column, place

the exact or true wavelength of the spectral lines that you used. Most calibration line sources come with a wavelength calib ration sheet . If you do not have a wavelength calibration sheet for your light source, you can probably find the wavelengths for your spectral lines (if they are being produced by pure elements) in the first column of the worksheet. In the second column of this worksheet, place the observed pixel number. In the third column, calculate the pixel number squared, and in the fourth column, calculate the pixel number cubed.

Independent Dependent Values computed from

Variable Variables the regression output

True

Wavelength

(nm)

253.65

296.73

302.15

313.16

334.15

365.02

404.66

407.78

435.84

546.07

576.96

579.07

696.54

706.72

727.29

738.40

751.47

Pixel #

175 296 312 342 402 490 604 613

694 1022 1116 1122 1491 1523 1590 1627 1669

Pixel #

30625 87616

97344 116964 161604 240100 364816 375769 481636

1044484 1245456 1258884 2223081 2319529 2528100 2647129 2785561

Pixel #

5359375 25934336 30371328 40001688 64964808

117649000 220348864 230346397

334255384 1067462648 1389928896 1412467848 3314613771 3532642667 4019679000 4306878883 4649101309

Predicted

Wavelength

253.56

296.72

302.40

313.02

334.19

365.05

404.67

407.78

435.65

546.13

577.05

579.01

696.70

706.62

727.24

738.53

751.27

Difference

0.09

0.01

-0.25

0.13

-0.05

-0.04

-0.01

0.00

0.19

-0.06

-0.09

0.06

-0.15

0.10

0.06

-0.13

0.19

4. Now you are ready to calculate the wavelength calibration coefficients. In your spreadsheet program,

find the functions to perform linear regressions.

if using Quattro Pro, look under if using Excel, look under

Tools | Advanced Math

Analysis ToolPak

5. Select the true wavelength as the dependent variable (Y). Select the pixel number, pixel number

squared and the pixel number cubed as the independent variables (X). After you execute the regression, an output similar to the one shown below is obtained.

Regression Statistics

Multiple R 0.999999831 R Square 0.999999663 Adjusted R Square 0.999999607 Standard Error 0.125540214 Observations 22

intercept

Coefficients Standard Error

Intercept 190.473993 0.369047536

first coefficient

X Variable 1 0.36263983 0.001684745 X Variable 2 -1.174416E-05 8.35279E-07 X Variable 3 -2.523787E-09 2.656608E-10

third coefficient

second coefficient

6. The numbers of importance are indicated in the above figure. You will need to record the Intercept as

well as the First, Second, and Third Coefficients. Also, look at the value for R squared. It should be very close to 1. If it is not, you have probably assigned one of your wavelengths incorrectly.

7. Select

Spectrometer | Spectrometer Configuration

from the menu. Update the wavelength coefficients.

Ocean Optics CHEM2000-UV-VIS, CHEM2000 Operating Manual And User Manual

Specifications and Main Features

Frequently Asked Questions

User Manual