Varian Cary 5000 User Manual

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User%guide%for%Cary%5000%absorption%spectrometer%

with%external%DRA%1800%attachment.%

(last&updated&03/17/2016)&

This"guide"is"for"use"of"the"Cary"5000"with"the"DRA"only.""For"use"without"the"DRA"as"a"
standard"transmission"spectrometer"see"the"User"guide"for"Cary"5000"in"absorption"
mode."

Important%warnings!%

• Do"not"unplug"or"plug"in"the"external"DRA"attachment"when"the"instrument"is"
on.""This"will"ruin"the"detectors"of"the"integrating"sphere"

• Do"not"put"white"light"into"the"DRA"with"the"DRA"electrically"connected"to"the"
Cary."

• Minimize"the"amount"of"time"that"the"integrating"sphere"is"open."Long-term"light"
exposure"hurt"the"detector"over"time."""

• Wear"clean"gloves"while"using"the"instrument"

• Do"not"use"liquid"or"powder"samples"in"the"integrating"sphere."

Quick%Start%for%using%DRA%

1. Turn"on"computer""

2. Check"lens"and"mirror"are"correct"for"your"measurement."

a. Install"Small"Sample"Kit"mirror"(M3"SSK)"or"regular"M3"mirror"if"needed"

b. If"using"SSK"install"correct"lens"L2."

3. Make"sure"cover"for"the"DRA"is"fully"closed"and"turn"Cary"on."

4. Click"on"the"Cary"icon"on"the"taskbar"

5. Wait"20"minutes"for"the"lamps"to"warm"up."

6. Select"Setup"

a. set"wavelength"range,"%T"or"%R"

b. Under"Options"tab:"set"slit"width"and"height,"SBW"to"2"nm,"Detector"and"

Grating"change"wavelengths"

c. Under"Baseline"tab:"chose"zero/baseline"

d. Under"Storage"tab:"Set"your"filename"

7. Make"sure"that"all"exits"of"the"integrating"sphere"are"blocked"with"full"reflectors."

8. Baseline%and"run"100%"T"scan,"then"block"the"sample"beam"at"the"entrance"to"the"
integrating"sphere"for"the"0%"T"scan.""If"using"an"aperture"holder"for"reflection"
measurements,"please"see"the"“Aperture"kit"for"small"samples”"section"on"page"4."""

9. Mount"your"sample"

10. Run"Spectra"

11. When"done"remove"sample"and"remount"reflectors."

12. Turn"off"Cary"

2"

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13. Shut"down"computer."

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Introduction%and%Help%

For"a"complete"guide"to"the"Cary"hardware"and"
open"the"Cary"“Scan”"program"and"click"on"the"

Help"tab."

For"the"basic"theory"of"diffuse"reflectance"
measurements,"useful"diagrams"of"the"diffuse"
reflectance"adaptor"(DRA),"alignment"tips"and"
procedures,"and"descriptions"of"all"the"DRA"
accessories"(VATH,"Small"Spot"Kit,"and"center"
mount"holders)"go"to"Help">"Help"topics">"
Accessories">"Cary"4000/5000/6000i">"Solid"
Sample">"external"DRA""

To"learn"more"about"the"software"and"taking"
measurements"in"the"Scan"menu,"go"to"Help">"
Help"topics">"Software"Applications">"Scan"

Turning%the%instrument%on:%

Open"the"Cary"Scan"program"on"the"taskbar"or"Desktop"

The"DRA"must"to"be"fully"closed"in"order"for"the"instrument"to"initialize."Turn"on"the"
instrument"(0/I"switch"on"the"lower"left"side"of"the"front"of"the"instrument).""In"the"Scan"
program,"watch"the"lower"left"corner"to"see"the"status"of"the"instrument."When"the"
traffic"light"is"green"(top"center"of"screen),"then"a"scan"can"be"run.""

Basics%configuration%and%alignment%

There"are"four"positions"in"which"the"sample"can"be"placed"for"use"with"the"integrating"
sphere"(see"Figure"1"andFigure"2)."

1. The"entrance"slot"to"the"integrating"
sphere"is"for"normal"incidence"diffuse"
transmission"

2. The"rear"slot"is"for"normal"incidence"
diffuse"reflection"

3. The"center"mount"holder"allows"for"
variable"angle"diffuse"reflectance"and"
transflectance"measurements"

4. In"addition,"the"VATH"(variable"angle"
transmission"holder)"accessory"can"be"
put"in"front"of"the"integrating"sphere"for"
variable"angle"specular"transmission"
measurements."If"you"would"like"to"use"

Figure&1&Integrating&sphere&entrance&slot.

!

Figure&2&Integrating&sphere&exit&slots.!

3"

"

the"VATH"accessory,"please"talk"to"one"of"the"GLAs"for"the"instrument"first."""

For"the"normal%or%large%sample%setup"there"are"three"positions"for"the"large"standard"
M3"mirror"(see"Figure"3"andFigure"4)that"correspond"to"the"three"sample"positions"
(Transmission,"Center,"and"Reflection).""Each"of"the"mirror"positions"will"focus"the"light"
onto"the"position"of"the"sample.""The"three"different"mirror"positions"are"marked"T"
(transmittance"slot),"C"(center"mount),"and"R"(rear"reflectance"slot)"in"Figure"3."Thus,"
the"mirror"needs"to"be"moved"to"the"right"position"depending"on"the"placement"of"your"
sample.""The"cable"for"the"DRA"can"get"in"the"way"of"moving"this"mirror.""Turn%off%the%
Cary%first,%if%you%need%to%unplug%the%DRA%to%move%the%mirror.""

For"the"small"sample"setup"(see"small"sample"discussion"below)"the"M3"mirror"is"
replaced"by"the"small"sample"kit"mirror"(M3"SSK)"in"the"T"position.""Lens"(L2)"mounts"in"
front"of"the"sample"(see"Figure"4).""There"are"three"lenses"that"can"be"used"again"for"the"
three"positons"marked"as"T,"C"or"R.""

Each"time"the"sample"configuration"is"changed,"the"optics"need"to"be"realigned,"such"
that"the"sample"and"reference"beams"are"not"clipped"at"the"entrance"to"the"integrating"
sphere"and"that"the"sample"beam"is"centered"on"the"sample.""

1. With"the"top"door"to"the"DRA"closed,"under"the"commands"menu"click"on"Go%to,"
and"then"type"in"550"nm."When"you"darken"the"room"lights,"you"should"see"a"
green"beam,"which"you"can"use"to"align"the"beam"onto"the"sample"(Alternatively,"
if"you"have"trouble"seeing"the"beam:"Block"the"sample"and"reference"beams"from"
entering"the"integrating"sphere."Under"the"commands"menu"go"to"align"to"
switch"the"gratings"to"zero"order"to"send"white"light"into"the"DRA.""The"white"
light"should"not"enter"the"integrating"sphere)"""

2. Most"of"the"mirrors"have"two"knobs,"which"you"can"rotate"to"adjust"the"vertical"
and"horizontal"positions"of"the"beam.""Start"with"mirror"M2"and"adjust"so"the"

Figure&3&Diffuse&Reflectance&Accessory&with &beam &p ath.&

4"

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beam"hits"the"center"of"mirror"M3"then"use"M3"so"the"beam"hits"the"center"of"the"
sample.""Some"of"the"mirrors"are"more"complicated"to"adjust"(although"these"can"
often"be"left"alone).""For"help"with"alignment,"talk"to"one"of"the"GLAs"and"read"
the"alignment"instructions,"which"can"be"found"under"Help."

Small%samples%

Most"typical"lab"samples"are"smaller"in"size"than"what"the"instrument"was"designed"to"
measure.""For"all"three"types"of"measurements"(T,"C,"and"R),"it"is"best"to"under"fill"the"
sample"area.""

Spot%size"-"There"are"two"ways"of"
reducing"the"beam"spot"size:"

1)"Slit%width:"The"simplest"way"is"

to"reduce"beam"size"is"by"the"slit"
width.""Click"on"the"Setup"the"

options"tab.""Under"slit"height,"

switch"to"Reduced.""It"takes"about"a"
minute"for"the"slit"to"change."

2)"Small%spot%kit:"There"are"also"a"

series"of"lenses"that"can"be"put"in"
the"optical"path"to"focus"the"beam"
into"a"smaller"spot"on"the"sample."
Again"there"are"three"lenses"with"
different"focal"lengths"and"marked"
T,"C,"and"R"for"the"three"positions"of"
the"integrating"sphere.""Also,"the"
large"mirror"(M3)"is"switched"out"
for"a"one"with"a"different"curvature;"
this"mirror"is"always"kept"in"the"T"
position,"regardless"of"the"type"of"
measurement"being"made."""

3)%Aperture%kit%for%reflection%
measurements%

For"normal"incidence"reflection"measurements,"the"open"circle"in"the"rear"of"the"
integrating"sphere"is"several"inches"in"diameter.""There"are"a"series"of"apertures,"
which"have"the"white"Spectralon"material"(same"roughened"Teflon"that"is"inside"the"
integrating"sphere),"that"can"slide"onto"the"slot"on"the"back"of"the"integrating"sphere.""
The"spring-loaded"mount"that"holds"the"sample"against"the"integrating"sphere"first"
needs"to"be"taken"off.""Slide"on"the"appropriate"aperture"and"then"either"tape"your"
sample"onto"the"back"of"the"aperture,"or"put"back"on"the"spring-loaded"sample"
mount."

If"the"beam"spot"overfills"the"aperture,"you"can"correct"for"this"“stray"light”"by"
performing"a"Zero/baseline"Correction.""Normally,"the"0%TBaseline"scan"is"run"by"
blocking"the"beam"before"it"enters"the"integrating"sphere,"which"accounts"for"

Figure&4&Photo&of&diffuse&reflectance&accessory&with&

beam&path.&

5"

"

electronic"noise.""In"this"case,"do"not"block"the"beam"so"that"the"0%TBaseline"
accounts"for"the"light"reflecting"on"the"edges"of"the"aperture.""

Performing!a!Zero/Baseline!Correction:"Select"this"option"to"apply"a"100%T"
baseline"correction"(100%TBaseline)"and"a"zero-line"correction"(0%TBaseline)"to"
the"sample"scan"(S)."This"correction"is"performed"with"the"raw"transmission"data"
and"is"thus:"

𝑆 − 0%𝑇𝐵𝑎𝑠𝑒𝑙𝑖𝑛𝑒

100%𝑇𝐵𝑎𝑠𝑒𝑙𝑖𝑛 − 0%𝑇𝐵𝑎𝑠𝑒𝑙𝑖𝑛𝑒

"

With"this"option,"the"Cary"will"prompt"you"to"perform"a"100%TBaseline"first,"
followed"by"a"0%TBaseline"when"you"perform"a"baseline"collection."

Basics%of%measurement%acquisition%

The"wavelength"range"is"1800"nm"to"250"nm."""Scans"normally"go"from"long"to"short"
wavelengths.""There"are"two"detectors,"a"PMT"and"an"InGaAs.""The"wavelength"at"which"
the"system"changes"from"one"to"the"other"(accompanied"by"a"grating"change)"can"be"
adjusted.""Usually"750"to"800"nm"is"a"good"value"for"this"change"over.""You"can"see"the"
change"in"the"spectrum"when"you"take"a"baseline"(%"Transmission"or"Reflection).""If"
you"see"a"step"in"the"spectrum,"it"may"mean"your"baseline"is"bad"or"that"your"sample"
has"a"polarization"dependency.""

Setup%–"The"setup"button"located"in"the"upper"left-hand"corner"defines"the"scan"

parameters.""The"following"useful"tabs"can"be"found"under"Setup.""

Cary!tab!!

Here"you"can"set"the"units"of"the"x-and"y"axes"(nm,"cm-1,"etc."and"A,"%T,"%R,"etc.),"
as"well"as"the"range"for"the"axes.""Under"scan"controls,"the"average"time"per"data"
point"and"the"data"interval"can"be"set"can"be"controlled.""Note"that"you"only"have"
independent"control"over"two"of"these"values."""

Options!tab!under!Setup!

Here"you"control"the"Beam"Mode,"Slit"Band"Width,"and"Slit"Height"(see&Appendix&
A&of&this&guide&for&more&info).""The"Double"beam"mode"needs"to"be"used"for"the"

integrating"sphere"measurements"and"the"SBW"is"typically"set"to"2nm.""

As"mentioned"earlier,"the"Slit"Height"can"be"used"to"decrease"the"beam"spot"size""

Typically,"the"UV-Vis"button"will"be"selected.""If"you"do"not"need"to"go"to"shorter"
wavelengths"than"400"nm,"you"can"select"the"Vis"button,"which"will"save"on"the"
lifetime"of"the"UV"lamp.""""

You"can"also"set"the"wavelength"at"which"the"Detector"and"grating"change.""Both"
of"these"are"typically"set"at"800"nm,"if"you"have"an"important"spectroscopic"
feature"at"800"nm,"you"can"move"the"change"over"+/-"50"nm"

Baseline!tab!!

This"tab"enables"you"to"choose"the"type"of"baseline(s)"that"you"want"to"use"in"the"
Scan"run."The"different"types"of"baseline"corrections"are"particularly"useful"with"

6"

"

some"of"the"Varian"accessories."You"can"collect"a"baseline"immediately"before"
scanning"a"sample"or"use"a"stored"baseline."

The"accuracy"of"your"baseline"determines"the"accuracy"of"your"measurement.""
You"should"perform"a"zero/baseline"correction"before"running"your"samples"
after"the"instrument"has"warmed"up"for"~20"minutes"using"the"same"scan"
parameters"that"you"will"use"for"your"sample.""

The"Cary"WinUV"system"collects"a"new"baseline"when"you"select"any"type"of"
baseline"correction"in"the"Baseline"tab"of"the"Setup"dialog"box"and"then"click"

Baseline"button"in"the"application"window."Depending"on"the"type"of"correction"

you"have"selected,"the"Cary"will"prompt"you"to"perform"either"one"or"two"
baseline"scans."The"first"is"a"100%Tbaseline"(for"the"DRA"with"the"100%"
reference"material"in"the"sample"positions)."The"second,"if"required,"is"a"
0%Tbaseline"(with"the"sample"beam"blocked)."

Once"the"baselines"have"been"collected,"they"will"be"automatically"applied"to"
each"collected"sample"data"point"as"it"is"displayed"(indicated"by"the"red"display)."
If"there"is"not"a"corresponding"data"point"in"the"current"baseline,"then"the"file"
will"be"interpolated"to"provide"the"correction."The"correction"applied"to"each"
point"is"dependent"on"the"selected"baseline"type"in"the"Baseline"tab.""

A"baseline"cannot"be"applied"to"a"sample"where"the"abscissa"range"of"the"sample"
exceeds"that"of"the"baseline."If"you"change"your"abscissa"range"to"one"outside"
that"of"the"baseline,"the"Cary"will"display"an"error"message."Also"the"red"text"in"
the"ordinate"display"which"indicates"that"baseline"correction"mode"is"activated"
will"disappear."

For"reflection"measurements"using"the"aperture"kit,"if"the"beam"spot"overfills"the"
aperture,"you"can"correct"for"this"“stray"light”"by"performing"a"Zero/baseline"
Correction.""Normally,"the"0%TBaseline"scan"is"run"by"blocking"the"beam"before"
it"enters"the"integrating"sphere,"which"accounts"for"electronic"noise."In"this"case,"
do"not"block"the"beam,"but"instead"remove"the"reflectance"port"cap"to"account"
for"the"light"reflecting"on"the"edges"of"the"aperture"(the"remainder"of"the"light"
should"pass"through"the"integrating"sphere"and"not"be"detected)."""

Performing&a&Zero/Baseline&Correction:"Select"this"option"to"apply"a"100%T"
baseline"correction"(100%TBaseline)"and"a"zero-line"correction"(0%TBaseline)"
to"the"sample"scan"(S)."This"correction"is"performed"with"the"raw"transmission"
data"and"is"thus:"

(𝑆 − (0%𝑇𝐵𝑎𝑠𝑒𝑙𝑖𝑛𝑒))

(100%𝑇𝐵𝑎𝑠𝑒𝑙𝑖𝑛𝑒 − 0%𝑇𝐵𝑎𝑠𝑒𝑙𝑖𝑛𝑒)

"

With"this"option,"the"Cary"will"prompt"you"to"perform"a"100%TBaseline"first,"
followed"by"a"0%TBaseline"when"you"perform"a"baseline"collection."

This"baseline"option"corrects"for"any"inherent"variations"in"the"electronic"zero"
line"of"the"instrument."You"should"use"this"baseline"option"if"your"samples"have"
areas"of"very"low"transmission"(high"absorbance)"as"any"variations"in"the"