CH821-section 3
Aspects of Molecular Organization and chemistry in organic solid state
S. S. Talwar, Phone X 7556 , Rm 214 A , Dept. of Physics, [email protected]
Gen. Information
Lecture slides for each lecture will be put up on Monday following each lecture.
Additional material may also be displayed from time to time relevant to the course.
Please check it at least once a week.
Note : Information given in these slides about the subject is only to be seen as
complimentary to discussion in the Lecture. It is telegraphic write up only.
Evaluation for this section
Insem. assignment : 10 , Mid sem. 6, End sem. 17
Nature of insem. assignment: Read an original work reported in lit. in the last 7 years
about any relevant area of interest to you and relevant to the broad theme of the
course. Write brief report on the paper in your words and make a presentation to the
class. Presentations will be held after the insem. examination Schedule will be worked
out later.
You can send me your questions about subject material by mail.
Bibliography:
Books
1.Molecular Crystals, J. D. Wright, Cambridge University Press , London 1987provides an introductory overview of properties and reactions of organic crystals,
Available in our library (A), Chapters 1,2,7 are of relevance to the topics being discussed
2.Organic Solid State Chemistry , G .Desiraju, Ed. (1987)(A)
3.Collected Works of GMJ Schmidt, D.Ginsburg Ed. (A)
4. Organic solid state reactions, Fumio Toda, Ed. Kluwer , 1991(A),
A survey of recent developments in Organic solid reactions ,
useful for checking the synthetic potential.
References:
5. A Givezotti and M. Simometta, Crystal Chemistry In Organic Solids, Chem. Reviews, 82,
1982,1-13 (A)
6. D.O. Cowan et.al Organic Solid State – opportunities and challenges, Chem. Eng. News,
1986(A)
7. M.D.Cohen and B.S.Green, Organic Chemistry In Solid State’ Chemistry In Britain, 1973,
490. (A)
8. M.D.Cohen, The Photochemistry of Organic Solids, Angewanndte Chemie, int. ed.,1975,
386 (A)
9. V. Ramamurthy,and K.Venkatesan, Photochemical Reactions in Organic Crystals, Chem.
Rev.1987 ,87, 433-481 (A)
10. J.M.Thomas et.al., Topochemical Phenomena , Advances in Physical Organic Chemistry,
105,
The fun slide of the day
Dr. Ram Sabnis who developed the dye that disappeared on
the bubble burst and passionate toy inventor who worked for
eleven years to develop colored soap bubbles
•To read more on soap bubbles and colored soap bubbles
follow links on Wikipedia.com
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About the course
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Introduction: In this set of lectures I propose to deal with aspects of
molecular organization and chemistry in the organic solid state.
• The properties of a substance are intimately related to molecules
that constitute a substance and also how these molecules are
structured within the substance. It is therefore desirable to
understand the structure of materials both at the molecular level and
how the molecules are organized in a specific substance. From such
studies an understanding of the correlation of properties and the
structure can emerge. Such an understanding is a key to then
designing and synthesis of new molecular entities , their
organization into defined structures with the aim of developing
materials and structures with desirable functional chemical and
physical properties. Last few decades has seen much advance in
organization methodology and thereby control of the properties of
organic solid state materials.
• Due to almost infinite potential of building organic molecules
provides a possibility of fine modulation of properties, organic solid
state has been seen as source of new materials with potential
application in number of futuristic technologies. Till a few decades
ago major type of organic solid materials , namely classical
polymers, were used primarily as insulating materials and as
materials of .construction. However in the last three decades or so,
large range of functional materials for applications in optics,
electronics , smart materials, displays etc, . have been evolved. The
cartoon taken from Cowan (1986)* in the next slide emphasizes the
variety of functional properties associated with organic solid state
materials. New materials in general and organic solid state materials
is a new frontier which possess interesting challenges. to chemists
and material scientist. Many new materials have been added to this
list in recent years, which hold great promise i.e. carbon nanotubes,
smart materials, photonic crystals etc.
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Reference 6
Carbon nano tubes,
smart crystals
Photonic crystals
Ref. 6
• Focus will be on• an overview of chemistry observed in the organic crystalline state,
underlying principles governing reactivity in crystalline state
• a brief introduction to properties of interesting classes of functional
organic solid state materials.
• overview of structural organization motifs of covalent molecules,
molecular and structural factors determinants in organized motifs
and
• experimental methodologies of generating organized solid state
structures through self assembly and examine some basic
characteristics of these structures.
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Aggregation of molecules, size of aggregates and structures
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Atoms → molecules → molecular aggregates in gas phase→ bigger molecular
aggregates in gas phase → organized structural aggregates in solution or liquid state
→ organized structures in solid
Size/level of aggregation
few molecules < 1-10 nm
100-1000 molecule10-200nm
few microns microscopic
Bulk
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Structural possiblities
Crystalline 3-D order
Partly crystalline
Liquid crystals-2D
Self assembled structures
Monolayers, bilayers, vesicles ,liposome
Unstructured – no long range order-amorphous
Properties are function of size and the structure
Methodologies for preparing aggregates/particles of different sizes
and arranging them in patterns are quite advanced.
Factors that govern organization or aggregation of molecules–
intermolecular forces that are dominant in different type of
aggregates
• ion – ion interaction
ionic solids
• Van der Walls
non polar solids
• Polar interaction
polar solids
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Dipole- dipole
Hydrogen bonding
Donor-acceptor
•Hydrophobic effect
•Pi-Pi packing
Proteins, micelles.
Nucleic acids
• shape and symmetry of molecules
general all organized structures
crystalline state and in
Features of Organic crystals- an outline
• Most organic compounds of moderate size can be
crystallized and their crystal structure can be
established by single crystal X –ray methods.
• Molecular constituents in the crystal are held together
by relatively weak forces (such as Van der Walls, dipoledipole and, H- bonds, interactions) therefore have
• low lattice energies
• low melting points
• easy deformability under stress
• exhibit anisotropic solid state physical and chemical
properties
Features of molecular crystals-contd.
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Rigid picture of the molecules in crystals ! Is it true ?
There are considerable LARGE AMPLITUDE thermal motions in crystals even
at room temperature. These increase in amplitude at higher temperatures
These motions can be studied by X-ray crystallography and solid state NMR
Motion types which are well established experimentally
– Librations of atoms around their mean positions (reflected in thermal
ellipsoids obtained from crystal structure determinations) and librations of
molecules as a whole and parts of molecules
– Rotations of groups of atoms around single bonds such as say methyl
group in toluene. Intermolecular interactions the determine rotational
barriers which are small in many cases
– Reorientation flips in disc like molecules such as benzene, naphthalene
– Molecular rotations in globular molecules CCl4 and adamantane
– Rotations around molecular axis in cylindrical molecules such as
acetylenes etc.
– Diffusional mobility – which is highly temperature dependent almost none
at low temperatures and finite near the melting point of solids.
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Some examples from ref1 are shown in the next few slides
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See Ref. 1 for general introduction and examples
See ref. 2, pp 431 for discussion of the issues involved at more sophisticated level
Librations –Slow oscillations of the molecule
around a fixed point
(blurred)
2. Reorientation flips
O
f
of cyclopentadiene rings
Exhibit rotation around threefold axis and form a plastic phase
near melting point
Exhibit rotation around the long molecular axis
Comment: Each molecule in crystal is in a field of other molecules. Energy barrier
to any motion is. a function of the intermolecular interaction and intramolecular
interaction. Shape and free volume around the molecule determines the intensity
of the interactions.
Features of molecular crystals contd.- polymorphism
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Some substances can be crystallized in more than one crystal form , ie, the
crystal forms differ from each other in unit cell dimension, space group and
molecular packing characteristic.
This phenomena is well known for organic molecules of moderate size Each
distinct crystal form is also referred to as a Phase.
InterInter-conversion of phases is possible by application of temperature and
pressure. Phase transitions is usually marked by discontinuity in properties
Phase transition may involve complete destruction of one phase and recrystallization into another phase or there may be conversion of one phase
into the other without destruction, solid – solid phase transition.
Polymorphism has important bearing on both the chemistry and physical
properties of solid as we shall see during the rest of this course of lectures
Polymorphs differ in the solid state properties
M.pt, IR, NMR, solubility in a solvent, lattice energies, optical rotation, crystal
structure etc.
But
are Identical solution properties.
The basis of identification of solids as polymorphs of a specific molecular specis is
the difference in their solid state properties e.g powder polycrystalline XRD, but
identical solution properties.
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Conformations and polymorphism in molecular crystals?
What is the role of multiplicity of conformations of molecules in the
crystallization process, which of the various conformations is found in
a specific polymorph.
Do all molecules in specific polymorph have the same conformation or
there can be more than one conformation of molecules present in a
specific polymorph.
Thus of the two relatively stable conformations of 1,2- dichloroethane,
which conformation of the molecule is expected in the crystal of this
compound. Two conformations of this molecule are anti and the
gauche forms. They have different symmetric characteristics.
Large molecules may have several conformations
differing in
energy by small amounts and can result in polymorphs with different
molecular conformation. It is fair assumption that all molecules in
crystalline solid would have same conformation in a specific
polymorph. Another polymorph may have molecules with different
conformation of the same molecule. This is also called conformational
polymorphism.
Defects in crystals
Molecules form the lattice points in the unit cell of molecular crystals.
The macro crystal being made of stacking of the unit cells. Most crystalline
materials have defects to smaller or greater extent depending on the conditions
of crystallization. Growing defect free large crystals is a specialized field.
Some type of defects are
Point defects : These arise if one or more lattice sites are unoccupied
Line defects : These arise if a whole line of lattice points is missing partly
or fully
Impurities : presence of impurities can cause defects and modify their properties
Dislocations : molecules in the plane are oriented differently from other molecules
within the plane
A point to note is that defects are usually centres with large free volume and as will
be seen in future discussion properties, and chemistry of crystals is Influenced by
the presence and the nature of these defects.
Recommended reading on Molecular Crystals
Ref.1 chapters 1-4
• A challenging problem in crystal chemistry
are
• ‘Can we predict the crystal structure of a
substance based on its molecular structure’
• Empirically
• Through theory
• Both are extremely active fields of research some success has been achieved with each
of two approaches. We shall examine this at
a later stage
• Next few slides show real crystals and
molecular packing in crystals
Insulin crystals from Wikipedia
A huge monocrystal of potassium
dihydrogen phosphate under a cover
grown from solution by Saint-Gobain
for the mega joule laser of CEA.
Molecule of 4-IODOQUINOLINE WITH THERMAL ELLIPSOIDS. The ellipsoids
indicate the thermal motions of atoms about their mean positions at the
temperature of the XRD determination. Blue and pink are nitrogen and iodine
atoms
respectively.
T
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Packing diagram of molecules 4-iodoquinoline along a particular axis. Within each stack
the molecules are paired in a head to tail manner. The distance given by the dotted line
connecting nitrogen of a molecule from one stack to the iodine atom of the of molecule
of the adjacent stack is smaller than the sum of van der walls radii indicating attractive
interaction sometimes called nitrogen – halogen bond.