Vibrational Spectroscopy

and the
Molecular Vibrations

Rui Fausto & Gülce Ögrüc-Ildiz

Department of Chemistry - University of Coimbra

Portugal

&

Department of Physics - Istanbul Kültür University

Turkey
 Day 1 – Lecture 1

Summary:
1. Introduction.

2. The vibrations of a molecule (part I).

Classical treatment for di and polyatomic molecules. The harmonic
oscillator. The Wilson Decius and the Gwin methods.
Around 60 B. C., T. Lucretius Carus wrote:

Forsitun et rosea sol alte lampade lucens

possideat multum caecisfervorihus ignem
circum se, nullo qui sit fulgore notatus,
aestiferum ut tantum radiorum exaugeut ictum.
Lucretius
(Perhaps the sun, shining with a high rosy Carus
torch, is surrounded by more fire with invisible
heat, which is not recognized by its glare, thus
amplifying the heat-transferring power of the
rays.

Citation from Nonnenmacher , 1961)

Spectroscopy (Fundamentals)

ν= c/λ

E= hν (Planck)

E= mc 2 = hc/λ
λ = h/p (Louis de Broglie)

Propagation of wave

E´´
hν Energy states of the
molecular system
ΔE= hν
E´
Spectroscopy (Fundamentals)
The spectrum of the electromagnetic radiation

IR
Transitions between molecular energy levels
Time scales
A brief History of Vibrational Spectroscopy

Edme Mariotte 1686 Noticed that heat emerging from a fireplace can be focused by a
(F) mirror but does not pass through a glass plate.
Carl Wilhelm Scheele 1781 Confirmed the observations of Mariotte.
(D)
William Hershel 1800 Showed that there is invisible but heat-transporting radiation
(D, UK) beyond the red (infrared) end of the solar spectrum.
Macedonio Melloni 1835 Constructed the first mid-infrared spectrometer with a NaCl
(I) optics.
Anders Jonas Ångström 1868 Determined the exact wavelengths of the Fraunhofer lines in
(SW) the solar spectrum by using diffraction gratings - which had
already been made and used by Fraunhofer himself in 1821 -
with up to 10000 lines per inch (about 4000 lines per cm)!
Eugene von Lommel 1878 Described anomalies of fluorescence, the color of which is
(D) dependent on the nature of the sample and the frequency of the
exciting radiation. (First effective observation of the still unknown
Raman effect).
William de Wiveleslie 1881 Obtained the first spectra of molecular vibrations: they
Abney and Edward prepared photographic emulsions, which were sensitive in the
Robert Festing near infrared region up to 1200 nm, and photographed the
(UK) absorption spectra of 48 organic liquids.
A brief History of Vibrational Spectroscopy

Albert A. Michelson 1890 Introduced the two-beam interferometer.

(USA)
Anders Jonas Ångström 1890 Recorded the absorptions of carbon monoxide, carbon dioxide,
(SW) carbon disulphide, methane, benzene and others.

Julius Scheiner 1892 Obtained the infrared spectra of 20 compounds and concluded
(D) that: “all compounds containing the methyl, CH 3 group had an
absorption band at 3.45 μm.” (Group frequency concept!...)
William Coblentz 1905 Published an Atlas containing absorption spectra of 120
(USA) organic compounds (a two years work during his post-doctoral
research program using instruments he built in the course of his
graduate research program).

He observed that different isomers give rise to different spectra,

and that there are also characteristic vibrations of the CH 2 or
CH 3, NH 2, C6H6, NO 2, OH, and NCS groups.

Unfortunately, the importance of this work, published by a physicist,

and its consequences was not acknowledged by chemists. It was not
until the Second World War that this new method began to find broad
acceptance .
A brief History of Vibrational Spectroscopy

Various 1923- Smekal (1923), Kramers and Heisenberg (1925), Schrodinger

1927 (1926), and Dirac (1927) predicted the Raman effect from
Quantum Mechanics.
Chandrasekhara V. 1928 Publication of the paper “A New Type of Secondary Radiation’ in
Raman and K. S. Nature, on February 16th, 1928. (Experimental observation of the
Krishnan (IND) then designated Raman effect). Nobel Prize in 1930
1950 Until ~1950, Raman spectroscopy was applied more often than IR
and only rarely the two types of spectra were jointly evaluated.
The reverse became true after 1950, when automatically
recording infrared spectrometers were introduced to the market.

“The most important, the most fundamental and the deepest investigations are
those that affect human life and activities most profoundly. Only those scientists
who have laboured, not with the aim of producing this or that, but with the sole
desire to advance knowledge ultimately prove to be the greatest benefactors of
humanity.“

Raman, C. V.; Chandralekha (2010). Why the Sky is Blue: Dr. C.V. Raman Talks
about Science. Tulika Books. p. 17.
A brief History of Vibrational Spectroscopy

Perkin Elmer, Inc. 1957 Some 100 Model 21 Infrared spectrometers were sold along with
about 300 of the low-cost Model 137 Infracord.
Theodore Maiman 1960 Invention of the LASER.
(USA)
60’ies Grating spectrometers replaced the prism instruments; Fourier
Transform based IR instruments made their debut in the
market.
70’ies Introduction of double and triple monochromators and of
diode arrays and charge-coupled devices (CCDs).
Martin Fleischmann, 1973 Discover of the Surface Enhanced Raman Spectroscopy (SERS)
Patrick Hendra and technique.
James McQuillan
(UK)
90’ies Debute of NIR-FT Raman spectrometers.

Vibrational imaging techniques. Time-resolved techniques.

The progress of the modern Vibrational Spectroscopy is also strongly

related with the developments in the field of Computational Chemistry.
 Energy/ν of oscillation

❖ Frequencies
❖ Intensities
❖ Bands format
❖ Polarization
Classical model for molecular vibrations

Degrees of freedom (total) : 3N

Translactions(X,Y,Z): 3
Rotations(Rx,Ry,Rz) : 3
Vibrations: 3N-6

Iz = 0
E x(Rot) = ½ Ix ω2 = 0

Vibrations: 3N-5
Decoupling of external and internal modes

Coriolis Forces

Centrifugal Forces
Other fundamental approximations

Electron mass = 9.10938188 × 10 -31 kg

- Born Oppenheimer Approximation
Proton mass = 1.67262158 × 10-27 kg

5 orders of magnitude difference

- Mechanical Harmonic Approximation
Diatomic Molecules

2V = f r2
m1m2
μ
2T = μ (dr/dt)2 m 1 + m2
=

r = A cos(2πνt + φ)

ro -
Polyatomic Molecules

d ∂T ∂V
. + = 0
dt ∂r i ∂r i

Newton’s equations

Vibration internal coordinates

Polyatomic Molecules
Harmonic force constants: f ij

V ≈ Vo + Σ (∂V/∂r )
i o ri + 1/2 Σ(∂ V/∂r ∂r )
2
i j o r irj

= = Harmonic potential
0 0

F, G -1 (3N-6 x 3N-6)
R (3N-6 x 1)
FG Method of Wilson and Decius

Secular equation

For a diatomic molecule:

λ1 = F 11G11 = f / μ

i.e.,
3N-6 eigenvalues λ
F11 = f

G11 = 1/μ
Setting up the G matrix

with
(3N-6 x 3N-6) (3N-6 x 3N) (3N x 3N) (3N x 3N-6) (3N-6 x 1) (3N-6 x 3N) (3N x 1)

Setting up the F matrix

Nowadays, the F matrix is obtained from ab initio or DFT

electronic calculations: F x, which is then converted to Fr
The L matrix and the NORMAL COORDINATES

λ1
λ2
λ3 ...
λ3N-6

Eigenvalues

Eigenvectors

(Need normalization)
LtFL = Λ

L = [L1:L2:L3: ... :L3N-6] Q = L-1r

Normal coordinates
Potential and Kinetic Energy in terms of the
NORMAL COORDINATES

Note:

ri are only geometric coordinates

Qi are linear combinations of r i , but

they must be mass weighted,
otherwise the masses had to
appear in the kenetic energy
equation

Hence, L -1, which transforms the r i coordinates

into the Qi coordinates must contain mass
contributions!...
Each λ i corresponds to a
harmonic force constant in In fact,
the Normal Coordinates’
system.
[Lt] -1L-1 = G -1
L tL = G
The normalization of the FG eigenvectors
and the Potential Energy Distribution (PED)

V = ½ λi Q i 2 Etotal = V + T
For the maximum amplitude of vibration,

V = 0, so that T=0
Hence,

LitFLi = λi
Etotal = V oo λ
Σ α,β Li(α)Li(β)Fαβ = λi

PEDi(Fαβ) = 100 Li(α)Li(β)Fαβ/λi

The complete normal coordinate analysis according
To the FG Wilson and Decius Method

Data:

-Cartesian coordinates of the atoms X

-Definition of internal coordinates r = BX
-Atomic masses M-1
-Harmonic force constants F

Calculation of G (and F)

Diagonalization of FG |FG-λE| =
0
The complete normal coordinate analysis according
To the FG Wilson and Decius Method

Results:

-Vibrational frequencies νi (from λ i )

νi
1
√ λ
=
2
π i

-Normal coordinates Qi (from Li )

-PEDs PEDi (Fα,β) (from Li and λi )

Normal coordinate analysis for WATER MOLECULE

Vibrational modes (degrees of freedom) = 3 x 3 – 6 = 3

1- Setting X

Å
Normal coordinate analysis for WATER MOLECULE

2- Defining the internal coordinates and calculation of matrix B

B
Normal coordinate analysis for WATER MOLECULE

3- Atomic masses and construction of matrix M-1

mO = 15.99491 1/mo
mH = 1.00783 1/mo
1/mo
1/mH
1/mH
1/mH
1/mH
1/mH
1/mH
Normal coordinate analysis for WATER MOLECULE

4 - Setting G

5 - Setting F

mdyn Å–1 , mdyn Å rad–2 ou mdyn rad –1

Normal coordinate analysis for WATER MOLECULE

6 - Setting FG and diagonilizing it

RESULTS
Normal coordinate analysis for WATER MOLECULE

RESULTS
 Day 1 – Lecture 2
Day 2 – Lecture 3

Summary:
1. Group Theory and molecular symmetry (part 1).
Symmetry operations and point groups. Matricial representations of
point groups. Irreducible representations. Great Theorem of
Orthogonality.

2. Group Theory and molecular symmetry (part 2).

Character tables. The symmetry species of the molecular vibrations.
Symmetry is easily recognizable
in objects.

Reflexion

Reflexion
Rotation
Inversion

Reflexion
Rotation
Inversion
The symmetry operations are:

-Rotations about axes

-Reflexions in planes

-Combinations of the above

For a given object, the whole set of symmetry operations

constitute a mathematical GROUP.
Symmetry POINT GROUPS

In Group Theory, a Group is a mathematical set in which it is

defined na operation exhibiting the following properties:

1. It is an internal operation (if A and B belong to the group,

then C = AB also belongs to the group)

2. It has a neutral elemento (or unity), E (so that AE = EA = A)

3. Each elemento has an inverse (then, AB = E, B being A-1)

4. Displays the associative property ((A(BC) = (AB)C)

If it also displays the comutative property (AB = BA) the

group is designated by cumutative or abelian.
Symmetry POINT GROUPS

In the contexto of symmetry, the set of symmetry operations define

the group and the internal operation corresponds to the
successive aplication of two symmetry operations of the set

Other important definitions:

- The order of the group, g, is the number of elements of the

group.

- A group may contain subgroups or smaller order, the order of

these groups being submultiple of the order of the group

(by definition the group itself and the neutral element are
subgroups of a group, by definition).
Symmetry POINT GROUPS

- In a group one can define classes of elements, from the

equality:

A = Y-1 A´ Y (similarity transformation)

A and A´ are designated by mutually conjugated elements. A

set of mutually conjugated elements define a class of
symmetry.

The number of symmetry classes of a group is the índex of the

group.

The number of elements in each class of the group is a

submultiple of the order of the group. (The índex, in general, is
not!...)
Symmetry POINT GROUPS

The first task to undertake the symmetry analysis of a

molecule is to identify the symmetry point group to which it
belongs.

Starting to identify if the molecule belongs to one of the

special groups, such as those to which belong the following
types of molecules:

Linear molecules (either

centrosymmetric or
non-centrosymmetric
Ih

Molecules with the

same symmetry of the
regular polygones
C60
Symmetry POINT GROUPS

Cs - Molecules with only a plane of reflexion (σ):

Ci - Molecules with only na inversion center (i):

Symmetry POINT GROUPS

C1 - Molecules with no symmetry element:

Symmetry POINT GROUPS

For the general case, one can use the

following dicotomic diagram (bottom part),
by means of which the symmetry point Y
groups can be easily determined.

Special Groups?

E – Identity
σ – Reflexion σh - horizontal N N
σv - vertical
σd - diagonal
Cn – Rotation 2π/n
N
An n axis generates n symmetry operations {Cn ,
Cn 2, …, Cn n-1 , Cn n =E}
Y
I – Inversion Y
Sn – Improper Rotation 2p/n followed N

by reflexion
Y
It generates n symmetry operations if n is even
[S n, Sn2, ... S nn–1 , Snn =E] and 2n symmetry operations
if n is odd [S n, Sn2, ... S nn–1 , Snn =E, Snn+1, ... S n2n =E].
C type groups:

D type groups:
S type groups:

Queries:
C2 D3h C5V C2h

H 2 O2
Multiplication Tables for SYMMETRY POINT GROUPS

Multiplication tables allow the simple identification

of the inverse elements and of subgroups.
Similarity Transformation Tables

A = Y-1 A´
Y
Similarity Transformation Tables
Matricial Representations of Symmetry Point Groups

Matrix operator representing the rotation about the

C2 axis in the point group C2v .

Full representation of the C2v point group.

PROBLEM !...

The matrices representing the

group depend of the vectorial
space and also of the orientation
of the axes!...
Representation of Point Groups by the Traces of the
Matrices Representing the Symmetry Operations

In a given vectorial space, the traces of the matrices representing the same symmetry
operation are invariant. This allows to represent the Point Groups in a unique way using
the traces of the matrices representing the symmetry operations in theat vectorial space
instead of using the matrices themselves.

C2v

Remember the matrices….

Irreducible and Reducible Representations of a Group
C2v
3x3 matrices

2x2 matrices
Each set of matrices respecting the Multiplication Table
of the group and put in conrrespondence one-to-one
with the symmetry operations of the group, constitute a
representation of the group.

In passing from a set of matrices of higher dimension to

matrices of lower dimension one says that the
representation of the group has been reduced.
1x1 matrices
When no more reductions are possible, the set of
matrices obtained are designated as na IRREDUCIBLE
REPRESENTATION OF THE GROUP
Irreducible and Reducible Representations of a Group

Whatever is the representation of a symmetry point group, it can be reduced to the irreducible
representations of the group, through the Great Theorem of Orthogonality, which states that the
irreducible representations of the group (in terms of the traces of the representing matrices) are
orthogonal and normalized to the order of the group.

Or:

Representations of order 1 are always irreducible. However, irreducible representations of orders 2

and 3 may also exist. Since objects exist in a tridimensional space, irreducible representativos of
order greater than 3 are not possible.
Decomposition of Reducible Representations into
Irreducible ones

Reducible representations can be expanded in terms of the irreducible representations of

the group:

The coefficients (a1, a2, etc…) represent the number of times that each one of the
irreducible representations of the group is contained in the reducible representation and
can be obtained using the formula below that is a result of the Great Theorem of
Orthogonality:

The sum of the orders of the irreducible representations times the associated coefficient
of expansion must equal the order of the reducible representation.
Characters Tables
Characters Tables sumarize the relevant information for a given symmetry point group, in
particular its set of irreducible representations:

A, B – Irreducible representations of order 1: A – Symmetric for rotation about the principal axis
B – Anti-symmetric
E – Irreducible representations of order 2.
F – Irreducible representations of order 3.

• For groups with inversion center, subscripts g (gerade; even) or u (ungerade; odd) apply if
symmetric or anti-symmetric, respectively, regarding the inversion opperation.
• Subscripts 1,2 refer to representations that are symmetric or anti-symmetric, respectively in
relation to the reflexion in vertical planes;
• Superscripts ´ or ´´ refer to representations that are symmetric or anti-symmetric,
respectively, in relation to reflexions in the horizontal plane.
Characters Tables

Symmetry opperations belonging to the same class have always equal characters in a given
representation (irreducible or reducible).
The Symmetry Species of the Molecular Vibrations

The case of Water!...

?
 4000 2000 400
Wavenumber (cm -1 )

WATER – Raman Spectrum

Raman Intensity
4000 2000 400
-1
Raman Shit (cm )

All vibrations active in both Infrared and

Raman!...

2 bands polarized; 1 band depolarized,

in the Raman spectra:

0 ≤ ρ⊥ /ρ// ≤ 0.75
The Symmetry Species of the Molecular Vibrations

The case of trichloromethane!...

C3v
All vibrations are active in both Infrared
and Raman!...

6 bands in the spectra, corresponding to

9 vibrational modes, from which 3 are
degenerated (belong to the irreducible
representation E )

3 bands polarized; 3 band depolarized,

in the Raman spectra:

0 ≤ ρ⊥ /ρ// ≤ 0.75
 Day 2 – Lecture 4

Summary:
1. The vibrations of a molecule (part 2).
Introduction to quantum chemistry treatment of molecular vibrations.
Anharmonicities. Hot transitions. Calculation of vibrational frequencies using
Quantum Chemistry Programs.
Quantum Mechanics and Molecular Vibrations
(QM treatment of the harmonic oscillator)

or, if x o = 0

T(x) = p2/2m

Since x now ranges over the entire real line , the boundary conditions on are conditions at
.
At , the potential energy becomes infinite. Therefore, it must follow that as , . Hence,
we can state the boundary conditions as .
Quantum Mechanics and Molecular Vibrations
(QM treatment of the harmonic oscillator)

Solutions
:
Quantum Mechanics and Molecular Vibrations
(anharmonicities)

Note:
a) Relative intensity of fundamental and 1st overtone
b) Anharmonicity: 2 ν CO > ν 2CO
c) Spectrum of 13CO
Calculation of Vibrational Data Using QM Packages

The example of Gaussian

For B3LYP/6-311++G(d,p) we use 0.978
or 0.95 and
0.98
1189 cm-1

1810 cm-1
 Day 3 – Lecture 5

Summary:
1. The vibrations of a molecule (part 3).
Using symmetry adapted coordinates within the FG method
 Symmetry-Adapted Coordinates

Matrices are (3N-6)x(3N-6) Wilson & Decius FG Method

or (3N(x(3N) Gwin Method

Can we work with smaller matrices?

Yes!... If we use symmetry-addapted coordinates we can replace the global matrices by

sets of smaller matrices with sizes of the symmetry species related matrices. For
exemple, for water, one can replace 3x3 matrices for a set of 2x1 (A 1 ) and 1x1 (B 1 )
matrices.
Symmetry-Addapted Coordinates

For water:

Natural internal coordinates: Δr1 = Δr(O-H1)

Δr2 = Δr(O-H2)
Δα = Δδ(H1-O-H2)

How to define symmetry-addapted coordinates?

Symmetry-Adapted Coordinates

A1 A2

B1 B2
Symmetry-Adapted Coordinates
NOTE that the symmetry coordinates ARE NOT the normal coordinates.
These later are linear combinations of the first:

whereas

and

Then, also:
Examples to solve in the class:
 Day 3 – Lecture 6

Summary:
1. The concept of group frequency and correlation charts.
2. Band fitting, smoothing and deconvolution
The Infrared spectrum

Each stretching and bending vibration occurs with a characteristic frequency

as the atoms and charges involved are different for different bonds

The y-axis on an IR In regions where

spectrum is in units of % no oscillating
transmittance coordinate is
interacting with
IR light,
In regions where the transmittance
electromagnetic field of nears 100%
an oscillating coordinate
interacts with IR light of
the same ν –
transmittance is low
(light is absorbed)
The Infrared spectrum

~
The x-axis of the IR spectrum is in units of wavenumbers, ν , which is the
number of waves per centimeter in units of cm-1.

(Remember E = hν~ or E = hc/λ)

The concept of group frequency

1. The basic use of the IR spectra is to detect functional groups.

2. Because the IR looks at the interaction of IR light with actual

internal coordinates, it provides a unique qualitative probe into the
functionality of a molecule.

3. Since most “types” of internal coordinates in molecules require

roughly the same energy to be deformed, e.g., C=C and C=O
bonds, C-H and N-H bonds they show up in similar regions of the
IR spectrum.

4. Remember all functional groups are made of multiple atoms and

therefore show up as multiple IR bands.

5. There are vibrations that are delocalized over all the molecule.
These do not fit the concept of “group frequency”.
The concept of group frequency

The four primary regions of the IR spectrum (referred to stretching modes)

Bonds to H Triple bonds Double bonds Single Bonds

O-H single bond C≡C C=O C-C

N-H single bond C≡N C=N C-N
C-H single bond C=C C-O

Fingerprint
Region

4000 cm-1 2700 cm-1 2000 cm-1 1600 cm-1 400 cm-1

❖ In-plane bendings.
❖ Out-of-plane bendings.
❖ Torsions
Group frequencies
Alkanes – combination of C-C and C-H bonds

• Methylene (CH2) and methyl (CH3) bends 1360-1470 cm-1

• Methylene waggings 1280-1330 cm-1
• Methylene twistings 1200-1280 cm-1
• Rocking modes (methylene and methyl); C-C stretch 800-1200 cm-1
• sp 3 C-H stretchings 2800-3000 cm-1 (s)

Octane
Group frequencies
Alkenes – C=C and vinyl C-H bonds

• C=C stretch 1620-1680 cm-1 (weaker as substitution increases)

• vinyl C-H stretch 3000-3100 cm-1

• Note that the bonds of alkane are still present!

1-Octene
Group frequencies
Alkynes – C≡C and C-H bonds
• C≡C stretch 2100-2260 cm-1
• C-H for terminal alkynes 3200-3300 cm-1 (s)
• Remember internal alkynes ( R-C≡C-R ) would not have this band!

1-Octyne
Group frequencies
Aromatics

• Due to the delocalization of electrons in the ring, where the bond order
between carbons is 1 ½, the stretching frequency for these bonds is
slightly lower in energy than normal C=C. These bonds show up as a
pair of sharp bands, 1500 (s) & 1600 cm-1 (m), where the lower
frequency band is stronger
• C-H bonds off the ring show up similar to vinyl C-H (3000-3100 cm-1)

Ethyl benzene
Group frequencies
Ethers – C-O-C group

• Show a strong band for the antisymmetric C-O-C stretch at 1050-1150 cm-1

• Otherwise, dominated by the hydrocarbon component of the rest of the

molecule

Diisopropyl ether
Group frequencies
Alcohols – OH group

• Show a strong, broad band for the O-H stretch from 3200-3400 cm-1
• Like ethers, show a band for C-O stretch between 1050-1260 cm-1

• The characteristic shape of the OH stretching band is due to the presence

of hydrogen bonding. For isolated alcohol monomers, the band appears at
ca. 3600-3650 cm -1

1-butanol
Group frequencies
Amines – NH2 group

• NH2 stretchings 3200-3500 cm-1 ; sym. and asym. modes

• NH2 deformation 1590-1650 cm-1
• NH2 wagg 780-820 cm-1

2-aminopentane
Group frequencies
Aldehydes – CHO group

• C=O stretch 1720-1740 cm-1 (s)

• sp 2 C-H in-plane bending 1400-1450 cm-1 (s)
• sp 2 C-H stretch as a doublet at 2720 & 2820 cm-1 (w) (Fermi doublet)

Cyclohexyl
carboxaldehyde
Group frequencies
Carboxylic Acids – COOH group

• C=O stretching 1700-1725 cm-1

• Mixed C-O stretching / COH bend 1250-1420 cm-1
• The highly dissociated O-H stretch broad band 2400-3500 cm-1

4-phenylbutyric acid
 Liquid
Formic Acid IR spectra

Solid

Liquid and crystalline phases

Argon matrix
(10 K)

3618

Isolated in argon matrix

Group frequencies
Nitriles - the –C≡N group
• C≡N stretching 2100-2280 cm -1

• This peak is usually much more intense than that of the

alkyne due to the electronegativity difference between carbon
and nitrogen (more polarized bond)

propionitrile
Table of group frequencies (Common Organic Molecules)
Table of group frequencies (Common Organic Molecules)
Table of group frequencies (Inorganic Materials)

Handbook of Infrared and Raman

Spectra of Inorganic Compounds and
Organic Salts, Four-Volume Se

by

Richard A. Nyquist, Ronald O. Kagel, Curtis L.

Putzig , M. Anne Leugers

Libraries of Spectra (on line):

http://www.ftir.cz/INLIBINTRO.html
http://matematicas.udea.edu.co/~carlopez/ac60068a007.pdf
Table of group frequencies
(Biomolecules)
Group frequencies (Proteins - chains)

The peptide group, the structural repeat unit of proteins, gives up to 9 characteristic bands named Amide
A, B, I, II ... VII.
The Amide A band (about 3500 cm -1) and Amide B (about 3100 cm -1) originate from a Fermi resonance
between the first overtone of Amide II and the N-H stretching vibration.
The Amide I band (between 1600 and 1700 cm -1) is mainly associated with the C=O stretching vibration and
is directly related to the backbone conformation. Amide II results from the N-H bending vibration and from
the C-N stretching vibration. This band is conformationally sensitive.
Amide III and IV are very complex bands resulting from a mixture of several coordinate displacements. The
out-of-plane motions are found in Amide V, VI andVII.
Determination of Secondary Structures of Proteins

Amide I
Lysozyme
is an antimicrobial enzyme produced by Native
animals that forms part of the innate
immune system.
unordered

turn
β−sheet
α−helix s

Denaturated

In native form, Lysozyme has five alfa-helical

regions. There are also five regions of beta-sheet
and a large amount of random coil and beta-
turns.
Determination of Secondary Structures of Proteins
Lipids

Vibrations of lipids are essentially those of the methyl and methylene groups :

Some caracteristics of the bands of these groups are related with the
conformations assumed by the lipids
Lipids

wCH
gauche-terminal 2

ben ben
t t

all-trans progress. 1400-1300 (low int)

gauche-terminal
bent g +tg-; bent g+tg+
bent tg+g +t
bent g -ttg +; bent g-ttg +
Lipids

ν CH2 as. and ν CH2 s.

ν CH2 s
(Phosphatidylcoline vs.Temperature). (n-C 21H44).
The transition gel-sol occurs at 42 ºC. TI→II and Tf correspond to a solid-solid
transition and fusión of chains.
Lipids

triclini orthorrombic hexagonal

c

Raman (ν CH region).

Lipids in different crystallization

systems:
n-C 24H 50, triclinic;
n-C 72H 146 , orthorrombic and hexagonal.
Sugars

Spectra of sugars are dominated by CH, OH, an CO bands:

−α-D-glucose (C 6 H12O 6 ),

Possible forms of D-glucose: (a) Fisher projection of the

-β-D-fructofuranosyl-α-D-
open-chain form, (b) α-D-glucopyranose, (c) β-D-gluco- glucospiranose (sacarose; C12H22O 11)
pyranose, (d) α-D-glucofuranose, (e) β-D-glucofuranose. In
-4-o-α-D-glucopyranosil-α-D-glucose
water solution, the open-chain and the glucopyranoses are
in equilibrium at pH 7, the α-D-glucopyranose being (maltose; C 12H22O 11)
dominant. The glucofuranoses of D-Glucose were never
Processing of Spectra - Base line subtraction (correction)
- Smoothing
- Derivatives spectra
- Self-deconvolution

Base line subtraction (correction)

Processing of Spectra
Smoothing
The simplest smoothing algorithm is the
rectangular boxcar or unweighted sliding-
average smooth; it simply replaces each point
in the signal with the average of m adjacent
points, where m is a positive integer called the
smooth width. For example, for a 3-point
smooth (m = 3):

The triangular smooth is like the rectangular

smooth, above, except that it implements a
weighted smoothing function. For a 5-point
smooth (m = 5):

for j = 3 to n-2

In both of these cases, the integer in the

denominator is the sum of the coefficients in The left half of this signal is a noisy peak. The right half is
the numerator, which results in a “unit-gain” the same peak after undergoing triangular smoothing.
which preserves the area under peaks.
Processing of Spectra
Derivatives

1st Derivative 2nd Derivative

Derivatives of a function increase sensibility…

Use of derivatives spectra is a good way to identify component-bands in

overlapped signals!...
Processing of Spectra
Derivatives Note that the number of bands
observed is equal to the derivative
order plus one.
Processing of Spectra
Derivatives

A B
Inverte secon derivativ β α β

a
Absorban

a b
b c
c
d
ce

d
d

f e
f
d

1720 1700 1680 1660 1640 1620 1600 1700 1680 1660 1640 1620 1600
Wavenumber Wavenumber

S-layer proteins of Lactobacillus kefir

Processing of Spectra
Self-Deconvolution

The recorded spectrum:

can be expressed as the convolution of the instrumental function (related with the non-infinitesimal shape
of the slit of the spectrometer and that defines the intrinsec format of the bands, in general a Gaussian
function (exp(-Δ|x|2); where Δ is the width at half height, a Lorentzian function (exp(-Δ|x|)), or yet by a
mixture of both types of functions (exp(-Δ|x| ρ), 1< ρ <2):

With a spectrum of higher resolution:

The aim of the deconvolution procedure is to extract the function:

This is possible using the Convolution Theorem that states that:

Where is the inverse Fourier transform and D(x,L) an apodization function whose parameter L
defines the interval where D(x,L)≠ 0. I0(x) is the Fourier transform (interferogram) of the function .
Processing of Spectra
Self-Deconvolution

Wavenumber
Processing of Spectra
Curve fitting

- Base line correction

- Smooting

- 1st, 2nd, … derivatives; deconvolution

(identification of number and maxima of
bands)

- Choice of function to fit

- Curve fitting

Voigt function:
Processing of Spectra
Curve fitting

- The Gaussian pro le works well for

solid samples, powders, gels or resins.

- The Lorentzian pro le works best

for gases, but can also t liquids in many
cases.

- The best functions for liquids are the

combined G-L function or the Voigt
pro le.
 Processing of Spectra
Curve fitting

Curve fitting can always produce SOME RESULTS…

It is essential to use the available knowledge on the system in order to get

PHYSICALLY MEANING RESULTS !...
 Day 4 – Lecture 7

Summary:
1. Exploring the experimental techniques (part 1).

Infrared Spectroscopy.
Fundamentals (to remind…)
 Equipment
Monochromator

Detector

IR source

• Dispersive instruments:
with a monochromator to be used in the mid-IR
region for spectral scanning and quantitative
analysis.

• Fourier transform IR (FTIR) systems:

widely applied and quite popular in the far-IR and
mid-IR spectrometry.

• Nondispersive instruments:
use filters for wavelength selection or an infrared-
absorbing gas in the detection system for the
analysis of gas at specific wavelength.
Equipment

IR source

Nernst Glower heated rare earth oxide rod (~1500 K) 1-50 µm

(mid- to far-IR)

Globar heated SiC rod (~1500 K) 1-50 µm

(mid- to far-IR)

W filament lamp 1100 K 0.78-2.5 µm

(Near-IR)

Hg arc lamp plasma 50 - 300 µm

(far-IR)

CO2 laser stimulated emission lines 9-11 µm

Equipment

Detector / transducer

Thermocouple Thermoelectric effect -dissimilar metal cheap, slow,

junction insensitive
Bolometer Ni, Pt resistance thermometer (thermistor) Highly sensitive
<400 cm-1

Pyroelectric Tri glycine sulfate piezoelectric material fast and sensitive

(mid IR)

Photoconducting PbS, CdS, Pb Se light sensitive cells fast and sensitive

(near IR)
Equipment Sample
Plotter

Source

Optical system Reference

Detector
Monochromator

DETECTOR

Sampling SOURCE
Area

MONOCHROMATOR
(Grating)
Double-beam IR dispersive spectrometer
Equipment

Optical system

• Reflection gratings
(made from various plastics): the groove spacing is greater (e.g. 120 grooves mm-1). To
reduce the effect of overlapping orders and stray radiation, filters or a preceding prism
are usually employed. Two or more gratings are often used with several filters to scan a
wide region.
• Mirrors
but not lenses are used to focus and collimate the IR radiation. Generally made from
Pyrex or another material with low coefficient of thermal expansion. Front surfaces
coated with a vacuum-deposited thin metal film of Al, Ag or Au.
• Windows
are used for sample cells and to permit various compartment to be isolated from the
environment.
❖ transparent to IR over the wavelength region
❖ inert to the various chemicals analyzed
❖ capable of being shaped, ground, and polished to the desired optical quality
Equipment - FTIR

1. The Fourier transform method provides an alternative to the use of

monochromators based on dispersion.
2. In conversional dispersive spectroscopy, frequencies are separated and
only a small portion is detected at any particular instant, while the
remainder is discarded. The immediate result is a frequency-domain
spectrum.
3. Fourier transform infrared spectroscopy generates time-domain spectra or
space-domain data as the immediately available data, in which the intensity
is obtained as a function of time or space.
4. Direct observation of a time-domain (or space-domain) spectrum is not
immediately useful because it is not possible to deduce, by inspection,
frequency-domain spectra from the corresponding time-domain (or space-
domain) waveform (Fourier transform is thus introduced).
Equipment - FTIR

Single-beam FTIR
Spectrometer

In one arm of the interferometer, the IR source radiation travels through the beamsplitter to
the fixed mirror back to the beamsplitter through the sample and to the detector. In the
other arm, the IR source radiation travels to the beamsplitter to the movable mirror, back
through the beamsplitter to the sample and to the detector. The difference in pathlengths of
the two beams is the retardation δ.
An He-Ne laser is used as a monochromatic reference source. The laser beam is sent
through the interferometer in the opposite direction to that of the IR beam.
Equipment – FTIR: The interferogram and the FT
Equipment – FTIR: Measuring process
Equipment – FTIR: Advantages

–1
• very high resolution (< 0.1 cm )

• very high sensitivity (nanogram quantity)

• High S/N ratios - high throughput

Few optics, no slits mean high intensity of light

• Rapid (<10 s)

• Reproducible

• Inexpensive
Basic sample preparation techniques

The preparation of samples for infrared spectrometry is often the most

challenging task in obtaining an IR spectrum. Since almost all substances
absorb IR radiation at some wave length, and solvents must be carefully chosen
for the wavelength region and the sample of interest.

Gases

• A gas sample cell consists of a cylinder of glass or sometimes a metal. The cell is closed at both ends
with an appropriate window materials (NaCl/KBr) and equipped with valves or stopcocks for introduction
of the sample.
• Long pathlength (>10 cm) cells – used to study dilute (few molecules) or weakly absorbing samples.
• Multipass cells – more compact and efficient instead of long-pathlength cells. Mirrors are used so that
the beam makes several passes through the sample before exiting the cell. (Effective pathlength > 10 m).
 Basic sample preparation techniques

Liquids

• Pure or soluted in transparent solvent – not water (attacks windows)

• The sample is most often in the form of liquid films (“sandwiched” between two NaCl plates)
• Adjustable pathlength (0.015 to 1 mm) – by Teflon spacer
Basic sample preparation techniques

Solid
s

Alkali halide discs:

1. A milligram or less of the fine ground sample mixed with about 100 mg of
dry KBr powder in a mortar or ball mill.
2. The mixture compressed in a die to form transparent disc.
Mulls (mixture of saturated hydrocarbons)
1. Grinding a few milligrams of the powdered sample with a mortar or with
pulverizing equipment. A few drops of the mineral oil added (grinding
continued to form a smooth paste).
2. The IR of the paste can be obtained as the liquid sample.
Transmitance IR Technique
Reflectance IR Techniques

In the reflection spectroscopy techniques, the absorption properties of

a sample can be extracted from the reflected light.

• Internal reflection.
• External reflection.

✔ In internal reflection method, interaction of the electromagnetic radiation on the

interface between the sample and a medium with a higher refraction index is studied

✔ External reflectance techniques arise from the radiation directly reflected from the
sample surface.
Reflectance IR Techniques

Internal reflectance spectroscopy (IRS)

n = refraction index

Total nternal reflection.

Internal reflectance Spectroscopy (IRS) date back to the initial work of Jacques Fahrenfort
and N.J.Harrrick that independently devised the theories of IRS spectroscopy and suggested
a wide range of applications. Internal reflection Spectroscopy is often termed as attenuated
total reflection (ATR) spectroscopy.
Reflectance IR Techniques
In ATR spectroscopy a crystal with a high refractive index and excellent IR
transmitting properties is used as internal reflection element and is placed in
close contact with the sample. the reflection spectroscopy techniques, the
absorption properties of a sample can be extracted from the reflected light.

The resultant attenuated radiation as a function of wavelength produces an ATR spectrum

which is similar to the conventional absorption spectrum except for the band intensities at
longer wavelengths.

This difference is due to the dependency of the penetration depth on wavelength: at

longer wavelength, the evanescent wave penetrates deeper into the sample, thus, the
absorption bands at longer wavelengths are relatively more intense than those shorter
wavelengths.
Reflectance IR Techniques
✔ Diamond: High transparency, resistant //
expensive.

✔ Germanium: Samples with high

refractive index // limited range

✔ Zinc Selenide: Extended range // easily

damageable

✔ ATR IS EXCELLENT FOR MOST OF

TYPES OF SAMPLES… But requires
intimate contact between the crystal and
the material to study!
Materials used in ATR crystals
 Reflectance IR Techniques

External reflectance spectroscopy (ERS)

1. Specular reflectance
The reflectance spectra differ from
those recorded in transmission.

They appear as "derivative-like"

bands.

These spectra can be converted

into absorption one by using of
Kramers-Kronig transformation (K-
Specular techniques provide a reflectance measurement for K) that is available in most
reflective materials, and a reflection–absorption (transflectance) spectrometer software packages.
measurement for the surface films deposited on, or pressed
against reflective
surfaces.

The most common applications of this techniques are evaluation of surfaces

such as: coating, thin films, contaminated metal surface.
 Reflectance IR Techniques (Specular reflectance)

Kramers-Kronig transformation (K-K)

Specular reflectance spectra

Transmission spectrum
Reflectance IR Techniques

External reflectance spectroscopy (ERS)

1. Difuse reflectance (DRS; DRIFTS)

Diffuse reflectance spectroscopy is

associated with the reflected lights
which are produced by diffuse
scattering.

Since regular reflection distorts the

DRS spectra, the regular reflection
component should be eliminated in
diffuse reflectance measurements.

In diffuse reflectance spectroscopy, there is no linear relation between the

reflected light intensity (band intensity) and concentration.

The empirical Kubelka-Munk equation relates the intensity of the reflected radiation to
the concentration that can be used for quantitative evaluation. the corrected spectrum
demonstrates a linear relationship between band intensit
y and the sample concentration.
Reflectance IR Techniques

Difuse reflectance (DRS; DRIFTS)

In this method, the sample can be

analyzed either directly in bulk
form or as dispersions in IR
transparent matrices such as KBr
and KCl.

Particles size, homogeneity, and packing density of powdered samples

play important role on the quality of spectrum. A sample with smaller
particle size having narrow size distribution is preferred.

Diffuse reflectance measurement in near-IR is more common than in

mid-IR, Because non-absorbing scattering substrates are rare in mid-IR,
and also more efficient scattering occurs at shorter wavelengths (near-
IR).
Reflectance IR Techniques (Summary)
Reflectance IR Techniques (Comparison)
IR Spectroscopy as a tool to investigate H-bonding
Propionic acid
H-bonded OH

H-bonded C=O

H-bonding introduces
Ar matrix remarkable changes in
the IR spectra

δ δ+
-
δ
“Free” C=O δ δ+ -
- +
“Free” OH
IR Spectroscopy as a tool to investigate H-bonding

Empirical correlations

Acetic acid

Donnor group:
Stretching frequency increases
Bending frequencies decrease
IR Spectroscopy and electronic effects

2-butanone
propylamide
Absorbance

Wavenumber

Effect of electron delocalization

Weakening of the C=O bond /decrease of the

νC=O stretching frequency
IR Spectroscopy (temperature effects)

Increase of temperature
Cytosine (film)
-Broadening of bands
due to the increase of
the dispersion of the
vibrational levels
wNH2
-Weakening of the
H-bond strength
γ NH2
(decrease and
pronounced broadening
of the wNH2 and γNH2
bands

-Skeletal bands much

-1
Wavenumber/ cm less affected
 Day 4 – Lecture 8

Summary:
1. Exploring the experimental techniques (part 1).

Raman Spectroscopy.
Fundamentals (to remind…)

Complimentary nature or Raman and IR

spectroscopies
 Raman Spectroscopy

❖ Studying scattering of light by transparent media.

❖ Serendipitous discovery in 1921.
❖ Phenomenon named for Raman in 1928.
❖ His illuminating source was sunlight!!
❖ Nowadays: LASERS
Raman Spectroscopy
Laser

Detector

Monochromator

Photomultiplier

Monochromator
Sample

Computer

LASER

Plotter
Raman Spectroscopy – Advantages
(water is a weak scatterer)
Raman Spectroscopy – Advantages
(Provides easy access to low wavenumber bands)
Raman Spectroscopy

Advantages Disadvantages
(Others)

-Non-destructive -Fluorescence can be a problem,

sometimes it can be “burned” out
-Flexible sampling of the sample (excitation with
any phase or size red laser can typically avoid it)
no preparation
-Particulate scatter (~ν4) can be a
-Glass cells significant problem, filtering
good medium for cell design, low cost (both chemical and optical) helps.

-Fiber optics: -Sensitivity of the samples

up to 100 m, routine (biologically in particular)

-Enhanced by resonance, surface -Cost of equipment and

interactions maintenance
 Raman Spectroscopy

Rayleigh band

Raman spectrum of an exhausting tube from a car

Raman shift /cm -1

Note:
a) Relative intensities of Raman and Rayleigh bands
b) Format and frequency of the H2 O bands
c) Observation of bands due to molecules of type X2
155
Raman Spectroscopy
Resonance Raman Spectroscopy
Resonance Raman Spectroscopy
Resonance Raman Spectroscopy
Resonance Raman Spectroscopy
 Resonance Raman Spectroscopy

Electronic
Excited State

(a) Raman
Ground State
(b) Pre-resonance Raman
(c) Fluorescence Raman
(d) Resonance Raman
Resonance Raman Spectroscopy
(Enzyme – Substrate Studies)

Papain
Cysteinic protease
212 Amino Acid residues
 Resonance Raman Spectroscopy
(Enzyme – Substrate Studies)

Carbonyl group
νC=O involved in H-
Ph = 3 bonding (form II)

1800 1725 1650 O

Carbonyl group
involved in C
hydrophobic R S-enzyme
environment (form I)

2 conformers for the intermediate.

Only one was found to be reactive (v (reaction) is porportional to population of II)
Resonance Raman Spectroscopy
(Probing Geometries of Excited States)
Resonance Raman Spectroscopy
(Probing Geometries of Excited States)
Resonance Raman Spectroscopy
(Probing Geometries of Excited States)
 Raman Mapping

Mitochondria

Optical image Fluorescence

Image

Raman maps
Raman Mapping
Elemental X-ray maps
Material coating (Cerium based coating)
Optical image

Raman mapping images

Encontrar video com Raman mapping!
 Day 5 – Lectures 9 and 10

Summary:
Exploring the experimental techniques:

Matrix Isolation spectroscopy.

What is a cryogenic inert matrix?

- Low-temperature solid (metastable) diluted

solution, with an inert solvent (rare gas).
The Matrix Isolation method

LARS VEGARD, “The Light Emitted from Solidi ied Gases and its Relation to Cosmic
Phenomena” , Nature, 114 (1924) 357.

September 6, 1924

“When an inert gas which contains traces of nitrogen is condensed on the cold surface, the layer will contain
small nitrogen particles surrounded by an inert substance. In this state, we should expect nitrogen to behave
in a similar way as if the particles exist in free space.”
The Matrix Isolation method

WHITTLE, DOWS and PIMENTEL, “Matrix Isolation Method for the

Experimental Study of Unstable Species” , Journal of Chemical Physics, 22
(1954) 1943.

BERKELEY - USA

NORMAN and PORTER, “Trapped Atoms and Radicals in a Glass

«Cage»”, Nature, 174 (1954) 508.

CAMBRIDGE - UK
The Matrix Isolation method

June 22 / September 11

NORMAN and PORTER, “Trapped Atoms and

Radicals in a Glass «Cage»” , Nature, 174 (1954) 508.

George Porter (1920-2002)

Nobel Prize Winner 1967 (fast
reactions)

“Here we describe a general method for the preparation of highly reactive free radicals and atoms under
conditions which permit their observation at high concentrations for an inde initely long period of time.”
The Matrix Isolation method

September 7 / November

WHITTLE, DOWS and PIMENTEL , “Matrix Isolation

Method for the Experimental Study of Unstable Species”, Journal of
Chemical Physics, 22 (1954) 1943.

George Pimentel
(1922-1989)
“The MATRIX ISOLATION method proposed here involves accumulation of a reactive substance under
environmental conditions which prevent reaction. The intent of the method is to trap active molecules in a
solid matrix of inert material [...]. If the temperature is su iciently low, the matrix will inhibit diffusion of the
trapped molecules, thus holding the active molecules effectively immobile in a nonreactive environment.”
The Matrix Isolation method
Organic Chemists Join In

CHAPMAN, McINTOSH and PACANSKY, “Photochemistry of July 7 / 1972

a-pyrone in Argon at 8 K” , Journal of the American Chemical Society,
95 (1973) 244.

AMES - USA

LIN and KRANTZ, “Matrix Preparation of Cyclobutadiene”, Journal July 12 / 1972

of Chemical Society Chemical Communications, 1316 (1972) 1111.

NEW YORK - USA

PONG and SHIRK , “Photochemistry of a-pyrone in Solid Argon” , July 31 / 1972

Journal of the American Chemical Society, 95 (1973) 248.

CHICAGO - USA
The Matrix Isolation method
Organic Chemists Join In

Dewar isomer Cyclobutadiene

O
O
O hν hν
+ CO 2
O

hν

Z O O
O
O
O

O
!
O
O O This was not the whole story..
E O .
O
O
Some years ago, we presented the
Aldehyde-ketene 2nd Chapter of this fantastic journey...
Matrix isolation FTIR and theoretical study of
α-pyrone photochemistry
S. Breda, I. Reva, L. Lapinski and R. Fausto
PCCP, 2004, 6, 929.
The Matrix Isolation method

■ Main advantages are due to:

✔ Very low work temperature (usually 4-25 K)

Suppression of rotational structure, “hot” vibrational transitions and subtractive
combination modes

✔ Chemical inertia of the host matrix

Minimization of the guest / host intermolecular interactions

✔ Appreciable rigidity of the matrix

Inhibition of diffusion (except in a very few cases - very small molecules;
bimolecular processes are virtually suppressed; cage-con ined photo-chemistry)

✔ Very low concentration of the guest (in general, S/M < 10 -3)
Virtual absence of guest / guest intermolecular interactions
Matrix Isolation: main applications

✔ Studies on REACTIVE SPECIES (stabilization)

✔ Identi ication and characterization of CONFORMERS and TAUTOMERS

(high resolution; conformational cooling)

• Study of WEAKLY BOUND SPECIES and SMALL ASSOCIATES, including

H-bonded species (small concentration)

✔ COMPLEX PHOTOCHEMISTRY (cage effect)

✔ Investigation of INTRAMOLECULAR ENERGY RELAXATION processes

(high resolution / selective excitation)

• Novel NOBLE GAS CHEMISTRY ( irst covalent argon compound was

produced and studied by this method)
Matrix Isolation: main applications

✔ Studies on REACTIVE SPECIES (stabilization)

✔ Identi ication and characterization of CONFORMERS and TAUTOMERS

(high resolution; conformational cooling)

• Study of WEAKLY BOUND SPECIES and SMALL ASSOCIATES, including

H-bonded species (small concentration)

✔ COMPLEX PHOTOCHEMISTRY (cage effect)

✔ Investigation of INTRAMOLECULAR ENERGY RELAXATION processes

(high resolution / selective excitation)

• Novel NOBLE GAS CHEMISTRY ( irst covalent argon compound was

produced and studied by this method)
Matrix Isolation: main applications

✔ Studies on REACTIVE SPECIES (stabilization)

✔ Identi ication and characterization of CONFORMERS and TAUTOMERS

(high resolution; conformational cooling)

• Study of WEAKLY BOUND SPECIES and SMALL ASSOCIATES, including

H-bonded species (small concentration)

✔ COMPLEX PHOTOCHEMISTRY (cage effect)

✔ Investigation of INTRAMOLECULAR ENERGY RELAXATION processes

(high resolution / selective excitation)

• Novel NOBLE GAS CHEMISTRY ( irst covalent argon compound was

produced and studied by this method)
Matrix Isolation: main applications

✔ Studies on REACTIVE SPECIES (stabilization)

✔ Identi ication and characterization of CONFORMERS and TAUTOMERS

(high resolution; conformational cooling)

• Study of WEAKLY BOUND SPECIES and SMALL ASSOCIATES, including

H-bonded species (small concentration)

✔ COMPLEX PHOTOCHEMISTRY (cage effect)

✔ Investigation of INTRAMOLECULAR ENERGY RELAXATION processes

(high resolution / selective excitation)

• Novel NOBLE GAS CHEMISTRY ( irst covalent argon compound was

produced and studied by this method)
Matrix Isolation: main applications

✔ Studies on REACTIVE SPECIES (stabilization)

✔ Identi ication and characterization of CONFORMERS and TAUTOMERS

(high resolution; conformational cooling)

• Study of WEAKLY BOUND SPECIES and SMALL ASSOCIATES, including

H-bonded species (small concentration)

✔ COMPLEX PHOTOCHEMISTRY (cage effect)

✔ Investigation of INTRAMOLECULAR ENERGY RELAXATION processes

(high resolution / selective excitation)

• Novel NOBLE GAS CHEMISTRY ( irst covalent argon compound was

produced and studied by this method)
Matrix Isolation: main applications

✔ Studies on REACTIVE SPECIES (stabilization)

✔ Identi ication and characterization of CONFORMERS and TAUTOMERS

(high resolution; conformational cooling)

• Study of WEAKLY BOUND SPECIES and SMALL ASSOCIATES, including

H-bonded species (small concentration)

✔ COMPLEX PHOTOCHEMISTRY (cage effect)

✔ Investigation of INTRAMOLECULAR ENERGY RELAXATION processes

(high resolution / selective excitation)

• Novel NOBLE GAS CHEMISTRY ( irst covalent argon compound was

produced and studied by this method)
Matrix Isolation: limitations

• The substance to be studied or its precursor must have a RELATIVELY

HIGH VAPOUR PRESSURE and SUBLIMATE WITHOUT DECOMPOSITION

• BIMOLECULAR CHEMISTRY IS NOT generally AVAILABLE

• CAGE-EFFECT, favoring recombination MIGHT PREVENT UNIMOLECULAR

PROCESSES that work in other experimental conditions (e.g., solution)

• Thick matrices are not optically adequate; STUDIES BASED ON VERY WEAK
ABSORPTIONS IN DILLUTED MATRICES ARE A CHALLENGE

• QUANTITATIVE STUDIES ARE NOT EASY to be run due to dif iculties in

determining absolute concentrations
Matrix Isolation: limitations

• The substance to be studied or its precursor must have a RELATIVELY

HIGH VAPOUR PRESSURE and SUBLIMATE WITHOUT DECOMPOSITION

• BIMOLECULAR CHEMISTRY IS NOT generally AVAILABLE

• CAGE-EFFECT, favoring recombination MIGHT PREVENT UNIMOLECULAR

PROCESSES that work in other experimental conditions (e.g., solution)

• Thick matrices are not optically adequate; STUDIES BASED ON VERY WEAK
ABSORPTIONS IN DILLUTED MATRICES ARE A CHALLENGE

• QUANTITATIVE STUDIES ARE NOT EASY to be run due to dif iculties in

determining absolute concentrations
Matrix Isolation: limitations

• The substance to be studied or its precursor must have a RELATIVELY

HIGH VAPOUR PRESSURE and SUBLIMATE WITHOUT DECOMPOSITION

• BIMOLECULAR CHEMISTRY IS NOT generally AVAILABLE

• CAGE-EFFECT, favoring recombination MIGHT PREVENT UNIMOLECULAR

PROCESSES that work in other experimental conditions (e.g., solution)

• Thick matrices are not optically adequate; STUDIES BASED ON VERY WEAK
ABSORPTIONS IN DILLUTED MATRICES ARE A CHALLENGE

• QUANTITATIVE STUDIES ARE NOT EASY to be run due to dif iculties in

determining absolute concentrations
Matrix Isolation: limitations

• The substance to be studied or its precursor must have a RELATIVELY

HIGH VAPOUR PRESSURE and SUBLIMATE WITHOUT DECOMPOSITION

• BIMOLECULAR CHEMISTRY IS NOT generally AVAILABLE

• CAGE-EFFECT, favoring recombination MIGHT PREVENT UNIMOLECULAR

PROCESSES that work in other experimental conditions (e.g., solution)

• Thick matrices are not optically adequate; STUDIES BASED ON VERY WEAK
ABSORPTIONS IN DILLUTED MATRICES ARE A CHALLENGE

• QUANTITATIVE STUDIES ARE NOT EASY to be run due to dif iculties in

determining absolute concentrations
Matrix Isolation: limitations

• The substance to be studied or its precursor must have a RELATIVELY

HIGH VAPOUR PRESSURE and SUBLIMATE WITHOUT DECOMPOSITION

• BIMOLECULAR CHEMISTRY IS NOT generally AVAILABLE

• CAGE-EFFECT, favoring recombination MIGHT PREVENT UNIMOLECULAR

PROCESSES that work in other experimental conditions (e.g., solution)

• Thick matrices are not optically adequate; STUDIES BASED ON VERY WEAK
ABSORPTIONS IN DILLUTED MATRICES ARE A CHALLENGE

• QUANTITATIVE STUDIES ARE NOT EASY to be run due to dif iculties in

determining absolute concentrations
Standard Matrix Isolation set up

Pressure: ca. 10 -7-10-8 mbar

Concentration: < 10-3 S/M

Work temperature: 4 < T< 100 K Inlet for gaseous

Refrigeran sample
t
Matrix gases: Ne, Ar, Kr, Xe, N2
Vacuum
Chamber Valv
e
Valv Inlet
e matrix
for
gas
Gas Mixing
inlet bulb
Valv
Valv
e
e
Cold
substrate

Valv
e
High- pumping
vacuum system
Standard Matrix Isolation set up

Pressure: ca. 10 -7-10-8 mbar

Concentration: < 10-3 S/M

Work temperature: 4 < T< 100 K Inlet for gaseous

Refrigeran sample
t
Matrix gases: Ne, Ar, Kr, Xe, N2
Vacuum
Chamber Valv
e
Valv Inlet
e matrix
for
gas
Gas Mixing
inlet bulb
Valv
Valv
e
e
Cold
substrate

Valv
e
High- pumping
vacuum system
Standard Matrix Isolation set up

Pressure: ca. 10 -7-10-8 mbar

Concentration: < 10-3 S/M

Work temperature: 4 < T< 100 K Inlet for gaseous

Refrigeran sample
t
Matrix gases: Ne, Ar, Kr, Xe, N2
Vacuum
Chamber Valv
e
Valv Inlet
e matrix
for
gas
Gas Mixing
inlet bulb
Valv
Valv
e
e
Cold
substrate

Valv
e
High- pumping
vacuum system
Standard Matrix Isolation set up

Pressure: ca. 10 -7-10-8 mbar

Concentration: < 10-3 S/M

Work temperature: 4 < T< 100 K Inlet for gaseous

Refrigeran sample
t
Matrix gases: Ne, Ar, Kr, Xe, N2
Vacuum
Chamber Valv
e
Valv Inlet
e matrix
for
gas
Gas Mixing
inlet bulb
Valv
Valv
e
e
Cold
substrate

Valv
e
High- pumping
vacuum system
Standard Matrix Isolation set up

Pressure: ca. 10 -7-10-8 mbar

Concentration: < 10-3 S/M

Work temperature: 4 < T< 100 K Inlet for gaseous

Refrigeran sample
t
Matrix gases: Ne, Ar, Kr, Xe, N2
Vacuum
Chamber Valv
e
Valv Inlet
e matrix
for
gas
Gas Mixing
inlet bulb
Valv
Valv
e
e
Tunable Laser (IR) or Cold
Broadband IR source substrate

Valv
e
High- pumping
vacuum system
Standard Matrix Isolation set up

Pressure: ca. 10 -7-10-8 mbar

Concentration: < 10-3 S/M

Work temperature: 4 < T< 100 K Inlet for gaseous

Refrigeran sample
t
Matrix gases: Ne, Ar, Kr, Xe, N2
Vacuum
Chamber Valv
e
Valv Inlet
e matrix
for
gas
Gas Mixing
inlet bulb
Valv
Valv
e
e
Tunable Laser (IR) or Cold
Broadband IR source substrate

Valv
Tunable Laser (UV) or e
Broadband UV source
High- pumping
vacuum system
IR spectroscopy for matrix-isolated species

• Gas phase:
Gas phase – Broad bands (ca. 50 cm-1)
T= 295 K ✔ Rotational Structure
P= 2 mbar ✔ “Hot” transitions
✔ Overlapping vibrations

▪ Crystal:
– Even broader bands
Crystal - solid film
T= 50 K ✔ Intermolecular interactions
✔ Correlation field interactions
– Band maxima shifted when
compared to gas phase data

▪ Matrix-isolated:
Ar matrix – Sharp line-like character (0.1-2 cm -1)
T= 11 K
S/M molar ratio= 5x10 -2 – Very small frequency shifts when
compared to gas phase data

– Selectivity and sensitivity increase

cm -1 by a factor of 10-100
350 330 140 120 100 80 60
0 0 0 0 0 0 0
IR spectra of HClO4
Standard Matrix Isolation set up

Vacuum system: Primary dry rotatory pump + Turbomolecular pump

or
High performance diffusion pump
(10-6-10-8 mbar)

-Thermal isolation of the cryostat and purity of the matrix

-Matrix gas and sample in-let systems

Cryostat: Closed-cycle He refrigeration system

or
Continuous lux He refrigeration system
(4 K < Tmin < 10 K)

-Cold inger temperature controller and meter

-Optically transparent substrate (CsI)
-Transparent external windows [KBr + irradiation windows (Quartz, KBr)]
Standard Matrix Isolation set up

Matrix gas and sample in-let systems:

1. Vacuum line with pre-mixing reservoir

Sample
holder

Ar
Pre-
mixing
reservoi
r

FTIR

Temp.
contrl.
Cryostat head
Standard Matrix Isolation set up

Matrix gas and sample in-let systems:

2. Co-deposition
a) Simple manometric method
b) Double thermostatable Knudsen cell with controlling valve
d) Mini-oven assembled inside the cryostat

Helium

Heliu
m
Cold finger Cold finger
at ca. at ca. 7.5 K
Sampl 7.5K Argon
e
Valv P = 10 mbar
-7

e P = 10 -7 mbar

CsI CsI

Knudsen
cell Argo Temperature Sample
n controller
General strategy

Low temperature matrix isolation

✔ Narrowband IR-induced transformations

✔ Narrowband UV/Vis-induced
transformations

✔ Thermally-induced processes

Infrared spectroscopy probing

First observed IR-induced isomerization
R. T. Hall and G. C. Pimentel
Isomerization of Nitrous Acid: An Infrared Photochemical Reaction,
J. Chem. Phys., 38 (1963) 1889.

Broadband (Hg lamp) ❖ Excitation of the νOH

3650-3200 cm -1 stretching fundamental
(38-43 kJ mol-1)
❖ Broadband irradiation
(Hg lamp)

❖ Different optical ilters

ΔE = 2.1 ± 1.0 kJ mol-1

ΔE # = 40 ± 3 kJ mol-1

“The IR-induced isomerization of nitrous acid can be “Perhaps the most important conclusion in this work is the
considered to be a new type of photochemical reaction. implied high ef iciency of intramolecular energy transfer
Study of this reaction is possible only because of the among the vibrational degrees of freedom of a vibrationally
unique potentialities of the matrix isolation technique.” excited molecule.”
Narrowband (N)IR isomerization of Formic Acid
M. Pettersson, J. Lundell, L. Khriachtchev and M. Räsänen, J. Amer. Chem. Soc. , 119 (1997) 11715.
E. M. S. Maçôas, L. Khriachtchev, M. Pettersson, R. Fausto and M. Räsänen, J. Amer. Chem. Soc., 125 (2003) 16188.

Mika Jan Markku Leonid Ermelinda Rui Fausto

Pettersson Lundell Räsänen Khriachtchev Maçôas

0.12

ci
s 0.09

0.06

0.03 ci
s
7080 7060 6960 6940 6920
-1
Wavenumber (cm )
Narrowband (N)IR isomerization of Formic Acid
M. Pettersson, J. Lundell, L. Khriachtchev and M. Räsänen, J. Amer. Chem. Soc. , 119 (1997) 11715.
E. M. S. Maçôas, L. Khriachtchev, M. Pettersson, R. Fausto and M. Räsänen, J. Amer. Chem. Soc., 125 (2003) 16188.

Mika Jan Markku Leonid Ermelinda Rui Fausto

Pettersson Lundell Räsänen Khriachtchev Maçôas

NIR

0.12

ci
s 0.09

0.06

0.03 ci
s
7080 7060 6960 6940 6920
-1
Wavenumber (cm )
Narrowband (N)IR isomerization of Formic Acid
M. Pettersson, J. Lundell, L. Khriachtchev and M. Räsänen, J. Amer. Chem. Soc. , 119 (1997) 11715.
E. M. S. Maçôas, L. Khriachtchev, M. Pettersson, R. Fausto and M. Räsänen, J. Amer. Chem. Soc., 125 (2003) 16188.

Mika Jan Markku Leonid Ermelinda Rui Fausto

Pettersson Lundell Räsänen Khriachtchev Maçôas

NIR

0.12

ci trans
s 0.09
trans site 1

0.06

0.03 ci
s
7080 7060 6960 6940 6920
-1
Wavenumber (cm )
Narrowband (N)IR isomerization of Formic Acid
M. Pettersson, J. Lundell, L. Khriachtchev and M. Räsänen, J. Amer. Chem. Soc. , 119 (1997) 11715.
E. M. S. Maçôas, L. Khriachtchev, M. Pettersson, R. Fausto and M. Räsänen, J. Amer. Chem. Soc., 125 (2003) 16188.

Mika Jan Markku Leonid Ermelinda Rui Fausto

Pettersson Lundell Räsänen Khriachtchev Maçôas

NIR

0.12

ci trans
s 0.09
trans site 1

0.06

0.03 ci
s
7080 7060 6960 6940 6920
-1
Wavenumber (cm )
Narrowband (N)IR isomerization of Formic Acid
M. Pettersson, J. Lundell, L. Khriachtchev and M. Räsänen, J. Amer. Chem. Soc. , 119 (1997) 11715.
E. M. S. Maçôas, L. Khriachtchev, M. Pettersson, R. Fausto and M. Räsänen, J. Amer. Chem. Soc., 125 (2003) 16188.

Mika Jan Markku Leonid Ermelinda Rui Fausto

Pettersson Lundell Räsänen Khriachtchev Maçôas

NIR

0.12
site 2
ci trans
s 0.09
trans site 1

0.06

0.03 ci
s
7080 7060 6960 6940 6920
Conformer, mode and matrix-site selectivity -1
Wavenumber (cm )
General mechanism for IR-induced isomerization

Conforme
Conformer
rI I

V= 2
2

V= 1
… …
1

V= 0
I I
0 I
Torsional reactive coordinate
Coordinate to excite
General mechanism for IR-induced isomerization

Conforme
Conformer
rI I

V= 2
2

V= 1
… …
1

V= 0
I I
0 I
Torsional reactive coordinate
Excited coordinate
General mechanism for IR-induced isomerization

Conforme
Conformer
rI I

Phonon assisted intramolecular

vibrationalenergy relaxation
V= 2
2

V= 1
… …
1

V= 0
I I
0 I
Torsional reactive coordinate
Excited coordinate
General mechanism for IR-induced isomerization

Conforme
Conformer Conformer
rI I IIII

Phonon assisted intramolecular

vibrationalenergy relaxation
V= 2
2 Internal rotation

V= 1
… …
1

V= 0
I I
0 I
Torsional reactive coordinate
Excited coordinate
General mechanism for IR-induced isomerization
(N)IR-induced cis → trans Isomerization in FORMIC ACID may occur at:
- higher than the energy barrier:
is relatively insensitive to the nature of the excited mode (low mode speci icity)
- lower than the energy barrier:
(tunneling assisted by solid-state relaxation)

4651 355
νOH + CO/COH def 2 The calculated torsional potential of formic acid,
1 νOH the vibrational energy levels, and wavefunctions
from the variational calculations
0.2 3516
0. 2νC=O
1 0.05 16 % 84
4184 500 %
0
Quantum yield

0.0 νOH + γ OH
1 400
0

1E-3 4174 300 99

1%

)
νCH + CO/COH def. 0

1
-
1x10 -4 %
E(c
m
200
1E-4 2955 0

νCH 100 trans

0 ci
1E-5 0 s
500 450 400 350 300 -9 0 9 18 27
0 0 0 0 - 0 0 0 0
Dihedral angle (degrees) 0
Wavenumber (cm1
)
“Highlanders” may “behave”…. differently…
Conformation Selective Photochemistry – FORMIC ACID

U CO2 + H2
V
trans Photolysis of FORMIC ACID strongly depends
upon the conformation of the reactant.

I τC-
O
U CO CO 2 Photolysis: of trans

R V +
C
O

Absorbanc
H 2O
Photolysis of cis and

ci trans
Photolysis of cis
e
s
Wavenumbers
(cm -1)
“Highlanders” may be… “Strange”…
Isomerizations by
Tunneling
After pumping of the trans form by selective photoexcitation, this form returns back to cis by tunnelling (using the Arrhenius
formula k=A*exp(-E a/kT) and the torsional frequency as pre-exponential factor A, a rate constant by over-the-barrier
reaction of 10 -16 s -1 is calculated even at 60 K).

1 . The tunneling rate depends crucially on the solid

host and in most cases also on the local matrix
photoexcitation
morphology (matrix-site effect).
over the barrier
X
2. At least three factors contribute to the observed
differences in the tunneling rates:
(a) Change in the barrier height due to
“solvation”.

tunnelling (b) In different rare gases tunneling may occur

between different levels. The coupling between
vibrational levels can vary strongly and therefore the
ci tran effect on the tunneling rate can be large.
s s (c) Change of the magnitude of the energy gap
between the tunneling levels changes the order of the
phonon process providing the energy dissipation.
Narrowband IR-induced
Transformations

ACT I
Scene -1
The case of 2-Fluorobenzoic Acid (FBA)
4 4

2 ~
1
~1 4
3
3

1 2 4
2.8 kJ mol -1
2
1 3 ~2
0
~4
0

3 4
7.7 kJ mol -1 29.4 kJ
mol -1
Conformers 1 and 2 shall be present in • The 2 → 1 barrier allows trapping of both forms
the gas phase prior to deposition
• The 4 → 2 barrier is nearly half of the 3→ 1 barrier
The case of 2-Fluorobenzoic Acid (FBA)

Ar matrix (as-
deposited)

6947
6954
6973
1

6965
2

1
2

As-deposited
Irradiated (6947 cm -1 )
Irradiated (6954
• Conformers 1 and 2 present in the matrix cm-1 )

• Irradiation at 6965 and 6973 cm -1 doesn’t allow 3 2 1

4
to observe any spectral changes
• Irradiation at 6947 and 6954 cm -1 induces
conversion of 1 into 3.
The case of 2-Fluorobenzoic Acid (FBA)
The relevance of intramolecular interactions!...
.

1 2

3
The case of 2-Fluorobenzoic Acid (FBA)
The relevance of intramolecular interactions!...
.
1 3
~4
0

1 2

6947 cm -1
6954

Stabilized by OH...F intramolecular H-

bond
The case of 2-Fluorobenzoic Acid (FBA)
The relevance of intramolecular interactions!...
.
1 3
~4
0

1 2

4
6947 cm -1 6965 cm -1
6954 6973 2
~2
0

Small barrier

3 4

Stabilized by OH...F intramolecular H-

bond
The case of 2-Fluorobenzoic Acid (FBA)
The relevance of intramolecular interactions!...
.
1 3
~4
0

1 2

4
6947 cm -1 6965 cm -1 Fast
6954 6973 2
tunnelin ~2
g 0

Small barrier

3 4

Stabilized by OH...F intramolecular H-

bond
The case of 2-Fluorobenzoic Acid (FBA)
The relevance of intramolecular interactions!...
.
1 3
~4
0

1 2

4
6947 cm -1 6965 cm -1 Fast
6954 6973 2
tunnelin ~2
g 0

Small barrier

3 4

Stabilized by OH...F intramolecular H-

bond
The case of 2-Fluorobenzoic Acid (FBA)
The relevance of the matrix medium.... N2 matrix !..
.
Conf. 3-1
2

6934 cm-1
6942 6912 cm-1
6914
6920

6934 cm-1
6942 6934 cm-1
6942

As-deposited As-deposited
The case of 2-Fluorobenzoic Acid (FBA)
The relevance of the matrix medium.... N2 matrix !..
.
Conf. 3-1
2

6912 cm-1
6914
6920 6912 cm-1
6914
6920

6934 cm-1
6942 6934 cm-1
6942

As-deposited As-deposited
The case of 2-Fluorobenzoic Acid (FBA)
The relevance of the matrix medium.... N2 matrix !..
.
Conf. 3-1
2

6912 cm-1
6914
6920 6912 cm-1
6914
6920

6934 cm-1
6942 6934 cm-1
6942

As-deposited As-deposited
The case of 2-Fluorobenzoic Acid (FBA)
The relevance of the matrix medium!... N2 matrix !..
. .

1 2

3
The case of 2-Fluorobenzoic Acid (FBA)
The relevance of the matrix medium!... N2 matrix !..
. .
1 3
~4
0

1 2

6912 cm -1
6914
6920

Stabilized by OH...F
intramolecular H-
bond
The case of 2-Fluorobenzoic Acid (FBA)
The relevance of the matrix medium!... N2 matrix !..
. .
1 3
~4
0

1 2

6912 cm -1 6934 cm -1
6914 6942
6920

3 4

Stabilized by OH...F
intramolecular H-
bond
The case of 2-Fluorobenzoic Acid (FBA)
The relevance of the matrix medium!... N2 matrix !..
. .
1 3
~4
0

1 2

4
6912 cm -1 6934 cm -1 Tunnelin
6914 6942 2
g ~2
6920 0

Small barrier

3 4

Stabilized by OH...F Stabilized by interactions

intramolecular H- with the N 2 matrix molecules
bond
The case of 2-Fluorobenzoic Acid (FBA)
The relevance of the matrix medium!... N2 matrix !..
. .
1 3
~4
0

1 2
4 44
-1 -1
6912 cm 6934 cm Tunnelin
6914 6942 2
g ~2
6920 ~ 0
4

Small barrier
C–C
Internal
rotation
3 4

Stabilized by OH...F Stabilized by interactions

intramolecular H- with the N 2 matrix molecules
bond
The case of 2-Fluorobenzoic Acid (FBA)
The relevance of the matrix medium!... N2 matrix !..
. .
1 3
~4
0

1 2
4 44
-1 -1
6912 cm 6934 cm
6914 6942 2
~2
6920 ~ 0
4

Small barrier

3 4

Stabilized by OH...F Stabilized by interactions

intramolecular H- with the N 2 matrix molecules
bond
Narrowband IR-induced
Transformations

ACT I
Scene -2
Genesis of Rare Dimers
Production of trans-cis dimers of acetic
acid

D2-CC
Δ
28
K D2-CC

cis D1-CC

cis

D1-CC

D2-CC
cis

D1-CC
Genesis of Rare Dimers
Production of trans-cis dimers of acetic
acid

D2-CC
Δ
28
K D2-CC

cis D1-CC

cis

D1-CC

D2-CC
cis

D1-CC
Genesis of Rare Dimers
Production of trans-cis dimers of acetic
acid

D2-CC
Δ
28
K D2-CC

cis D1-CC

cis

D1-CC

D2-CC
cis

D1-CC
Genesis of Rare Dimers
Production of trans-cis dimers of acetic
acid

D2-CC
NIR
D2-TC
Δ
28
K
cis D1-CC

cis
D2-TC

D2-TC
D2-TC

1733 D2-CC
D2-CC

D2-CC

D1-CC

D2-CC
Genesis of Rare Dimers
Production of trans-cis dimers of acetic
acid

D2-CC
NIR
D2-TC
Δ
28
K
cis D1-CC

cis
D2-TC

D2-TC
D2-TC

1733 D2-CC
D2-CC

D2-CC

D1-CC

D2-CC
Narrowband IR-induced
Transformations

ACT I
Scene -3
Conformational Stwitching by Excitation of a Remote NH Bond

6-methoxy
indole
Conformational Stwitching by Excitation of a Remote NH Bond

First time observation of a

conformation shift by
vibrational excitation of a
remote NH bond
in a system without
steric hindrance and
intramolecular H-bonding...
Narrowband UV/Vis-induced
Transformations

ACT II
Scene -1
Bond-Shift Isomers of 1,3-Dipolar Species (Nitrile Imine)

UV (230 nm)

5-phenyl-1H-tetrazole 5-phenyl-2H-tetrazole
Bond-Shift Isomers of 1,3-Dipolar Species (Nitrile Imine)

230
nm 1”

UV (370 nm)

4 3
230 nm Ar
2
P

230 nm Kr

5
Bond-Shift Isomers of 1,3-Dipolar Species (Nitrile Imine)

230
nm 1”

4 3
230 nm Ar

230 nm Kr

k k
1 2
5
k1 < k2
Bond-Shift Isomers of 1,3-Dipolar Species (Nitrile Imine)
370 nm

28
min k k
1 2

k1 < k2

4 min
Predicted UV absorbance spectra of 2A and 2P
Bond-Shift Isomers of 1,3-Dipolar Species (Nitrile Imine)

Comparison of phenyl- nitrile imine with

methyl- nitrile imine and H- nitrile imine
Bond-Shift Isomers of 1,3-Dipolar Species (Nitrile Imine)

330 nm, 25 min

The formed 2H-diazirine (3) can

be converted selectively to the
carbodiimide (4)
Bond-Shift Isomers of 1,3-Dipolar Species (Nitrile Imine)

k1 k
2

k1 < k2
Narrowband UV/Vis-induced
Transformations

ACT II
Scene -2
First Observation of a Nitrene Tunneling Reaction
Rearrangement of 2-Formyl Phenylnitrene to an Imino
Ketene

Phenylcarbene

2-formyl Phenylnitrene 6-imino-2,4-cyclo-

X phenylazide I hexadien-1-
ketene

Phenylnitrene
Contrasting chemistry of triplet phenylcarbene 2,1-
and triplet phenylnitrene. Benzisoxazole Phenylnitrene
II
First Observation of a Nitrene Tunneling Reaction
Rearrangement of 2-Formyl Phenylnitrene to an Imino
Ketene
TD-DFT calculations at the
B3LYP/6-311++G(d,p)
level, considering
production of imino ketene
at the cost of triplet nitrene.

Experimental
 First Observation of a Nitrene Tunneling Reaction
Rearrangement of 2-Formyl Phenylnitrene to an Imino
Ketene

~17 kcal mol-1

2-methyl phenylnitrene:

ca. ~1.7 Å ~27 kcal mol-1 and ΔE= -8 kcal mol -1

ΔE= 0.15 kcal mol -1

This is the irst report of a tunneling reaction

involving a nitrene and we believe it opens a new
chapter in the nitrene chemistry.