particle:   ‐ atom, atomic group

Describing many‐particle systems

‐ molecule
‐ molecular complexes, macromolecules
Prof. Judit Fidy ‐ etc.
2016, October 11 many:  6x1023

One given macrostate can be realized by numerous varieties of 

Simple example
Air molecules in the room…
What do the particles „do”, when the
V, p, T
macroscopic parameters are constant: 
V,p,T?  microstates that result in this macrostate)
microstates.  
An isolated system will spontaneously drive itself into the
macrostate that can be realized by the highest variety of 
microstates Æ which is of highest „probability”
Ludwig Eduard Boltzmann
Ω : thermodynamic probability of a macrostate (= number of 
1844-1906, Austrian physicist
 

Nitrogen: N2  ‐78%
II. Law of Thermodynamics:  in isolated systems, spontaneous
Oxygen: O2 ‐ 21% processes toward equilibrium are of increasing Entropy
Other: 1%

S = k ln Ω
Macrostate: logaritmus naturalis – e‐based logarithm
Described by parameters that characterize the whole system e ln Ω = Ω logx
lnx = loge
k=1.38x10‐23JK‐1 
(p, V, T, N) „e” natural base number: Euler‐number / Napier constant
Boltzmann constant
(1+ 1)n ⎯n⎯
→∞
⎯→e
n
Microstate:
Given by a set of the parameters of all individual particles in the e = 2,718 281 828 459 045 235 360 287 471 35…

system ( position, velocity etc. for each) III. Law of Termodynamics

Ω ⇔W
The Entropy of a chemically pure (of one component) crystalline system is 
zero at T=0 K.  Ω =1→ S = 0
Statistical definition of the
Absolute value of Entropy! Textbook p. 258 ‐ 265
 Boltzmann distribution function
Understanding the Boltzmann distribution function
Connecting the energetic macrostate and microstates of a system of a large number of particles.
E = ∑ n jε j N = ∑ nj εk −ε
− − Δε
j
j j nk kT kT
Consider N distinguishable independent particles at thermal equilibrium – total energy is constant - ,
T= 0, in a closed system,
=e =e
nj
ε Model: the individual particles may have different energetic states
ε
Populations of energy states – nk: number of particles in εk energy state
„distribution” of particles is supposed
E = ∑ n jε j N = ∑ nj εj possible energy status of one particle: 
potential or kinetic energy
T1<T2<T3

ε ,nk k j j nj number of particles having εj energies ε ,nk k −

εi − ε0
−
εi Same system of N particles
ni kT kT at different temperatures
=e =e supposing ε0=0
Macrostate: given by the number of particles at each energy level: n0
{ n1, n2, n3, ……..nk…..}
εi, ni Microstate:  which of the particles are at the individual levels εi, ni As the temperature is lowered, more and more
particles are in the energy minimum state
at T=0 all particles are there: ni=0, n0=N
Boltzmann’s statement: there is a strict order in the distribution of 
particles on the energy levels depending on the temperature
T1<T2<T3
n0 is the same

ε ,n εk −ε
Boltzmann
ε ,n
− Δε
1 1 1 1
−
factor
At a given ε k > ε 0 energy level, the relative
j
εi − ε0
ε nk kT ε −
0 ,,n0 =e = e kT 0 ,,n0
population related to the energy minimum ni
n0
=e kT
nj increases with the temperature

Valid for any (j,k) combinations of energy levels

εk > ε0
Textbook p. 52 ‐ 57

Boltzmann distribution – a general rule in nature

1. Classes of materials with structural order.
Considering the classes of materials – structural consequences 1.1. Order is based on interactions (bonds) between the constituting
atoms or molecules
1. Classes of materials with structural order.
Order is based on ‐ solid crystalline materials repulsion E = B
pot
primary bonds rm
‐ ideal crystals Æperfect, long range order
General concept of bond
‐ real crystals
m>n formation (applicable for all
Order is based on ‐ liquid crystals Æ case of imperfect, long range order
Eb kinds of interactions)
secondary bonds
‐ liquids Æ case of short range order
2.  Gasous systems attraction
E =− A
‐ideal gas -> lack of order (no binding energy) in the structure pot
rn
‐real gases
r= distance of two atoms forming the bond
ro= bond distance
Ebond= bond energy

The concrete expression for A, B and 

the values of n and m depend on the form of interactions
 Examples for the functional form of attractive interactions Atomic/molecular bond distances (ro= rA + rB) and binding energies Eb depend
on the type of interactions (functions a and b)
The distance dependence in the energy formulae
of electrostatic interactions
van
Van der
der Kovalens Ionic
Atom
Elem Z
Rends
zám
Waals
Waals
radius (nm)
Covalent
sugár
radius
Ionsugá
radius
r (nm)
(nm)
Ion
sugár (nm) (nm)
(nm)
Interaction Distance in the Magnitude of the
H 1 0,120 0,037 − H+
energy function Energy of interaction
(kJ/mól) Eb C 6 0,170 0,077 0,029 C+

ion-ion −1 200 - 300

r N 7 0,155 0,075 0,025 N+

ion – static dipole

r −2 10 - 20 O 8 0,152 0,073 0,140 O2-

great variety
static dipole – 1 -2 F 9 0,147 0,071 0,117 F-

- static dipole r −3
P 15 0,180 0,106 0,058 P3+

dipole – dipole 0.3 S2-

r −6
S 16 0,180 0,102 0,184
rA, rB atomic radii
with Brown motion of atoms A and B

dispersion r −6 2 „atomic radius”

1.2.Stabilizing binding energy and Boltzmann distribution

General concept of bond formation Boltzmann distribution allows for having broken
General concept of bond formation bonds!

nbrokenbonds nb − Δε
repulsion E
pot
= B repulsion E
pot
= B = = e kT
rm rm nint actbonds ni
Is it true that all constituting atoms Δε = Ebond
m>n are at bond distances (r0) from each other m>n
Eb all the time? Eb
The probability of breaking bonds by thermal
attraction attraction fluctuations depends on the relation:
E =− A E =− A
pot pot
rn rn
Δε kT
r= distance of two atoms forming the bond r= distance of two atoms forming the bond
ro= bond distance ro= bond distance kT ~ 0.027 eV T=310 K,
Ebond= bond energy Ebond= bond energy k=1.38x10-23JK-1 Boltzmann constant

The concrete expression for A, B and  The concrete expression for A, B and 

the values of n and m depend on the form of interactions the values of n and m depend on the form of interactions
Bond energies in materials with structural order Typical example for the variety of stabilizing energies: 
Great variety! structure of living „material” : cells, tissues, organs,…..     
electronvolt
1 eV= 23 kcal/mole ~ mitochondrion nucleus
~ 100 kJ/mól cytoskeleton Hierarchy in
Eb ~ primary bonds: covalent
ionic 2 – 10 eV/bond ‐bond strengths
metallic ‐bond distances
‐distance dependence of interaction energies
Eb ~ secondary bonds ‐binding water molecules and ions
Eb(eV) ‐structural constraint of prosthetic groups
H-bond several x 0.1 (water:0.2 eV)
hydrophobic ~ 0.1
dipole – point charge ~ 0.1-0.2
van der Waals dipole – dipole ~ 0.02 rough
dipole – induced dipole ~ 0.01 endoplasmic Golgi smooth
dispersion ~ 0.02 reticulum apparatus endoplasmic
reticulum
(temporary dipoles)

Great variety! Even 100‐times differences!

Blue: nucleus

Red: actin filament

Atoms Molecules Macromolecules
eg. proteins
H
O
C
N
S
. H-bond
. Van der Waals
. interactions

Salt-bridges
Primary 0.153 nm
S-bridges
bonds
Green: microtubular system
 What is the probability that the secondary bonds stabilizing
What is the probability that the primary bonds stabilizing the the structure of macromolecular structures would be broken at
structure of molecular building elements would be broken at body temperature? 
body temperature?  Are the H‐bonds always intact in a dsDNA? 

nbroken − Δε Example: DNA of T7 bacterophage

= e kT
nint act DNA with about 40000 base pairs Æ about 100 000 H-bonds Æ N= 100 000
Δε = Ebond
nb nb − Δε
ha nbroken << nint act ⇒ ≅ nbroken − 0.2 n
= e kT = e 0.026 = 0.00046 ≅ broken nbroken ~ 46/DNA
ni N nint act N
kT ~ 0.027 eV T=310 K,
− Δε Δε = Ebond = 0.2 eV
E
nb − bond
≅ e kT = e kT
k=1.38x10-23JK-1 Boltzmann constant time-average!
N nb ≅ N x 0.00046 = 46

Ebond
nb − The probability is still low, but the absolut number of broken bonds
e.g. Ebond= 2.7 eV Æ ≅e kT
= e −100 = 3.72 ∗10 − 44
N in one macromolecule is significant number Æ flexibility of
macromolecular complexes Æ
Probability very well zero! Possibility for ligand binding and chemical reactions
No danger that molecules would be degraded by thermal fluctuations Structural dynamics in live material

1.3.Structure of crystalline materials = ideal state of order

Particles: atoms/ions - bonds: primary bonds -> ordered structure
Single crystal microcrystalline state
(ideal) (real crystals)
Characteristics of „crystalline” state
‐anisotropy: properties depends on the direction
‐mechanical stability
‐defined volume
‐defined shape
grain
‐structure: long range order

long range order in ideal crystals

large number of atoms in periodic array grain boundary:
accumulation of
crystal defects The 14 kinds of unit cells
found in nature
NaCl

unit cells – periodic repetition Æ crystal lattice

14 kinds of units cells in nature: Bravais lattices
Si
long range order: distance of periodic repetition >> 100 times r0(=0.15nm)
 crystal defects in real crystals ? 1.4. Liquid state – case of partial (short range) and temporary order
nb − Eb
− 6.31
Considering two states of bonds – intact =e kT
≈ n = e 0.023 = e − 270 = 0
ni N Particles: molecules
‐ broken Interaction energy: Eb~ secondary bonds
ni + nb = N nb << ni
ordered and disordered regions Æ average Eb is small Æmany broken bonds
e.g. NaCl,  Eb=6.31eV,       kT(room tempr.)=0.023eV
But:  n broken Properties of liquid state
imperfections in crystal growth Primary bonds can not be broken by thermal fluctuations at ≅ 1 % - 0.05% (T = 300 K) ‐isotropy
n0 ‐deformability
room temperature
Elocal <Eb ‐it has a volume
Liquid water
‐the shape of its volume is defined by the container
physical/chemical point ‐short range order in temporary regions
− local
E

n≈e kT defects interstitium

vacancy
Crystalline water
point defects Ædiffusion to grain boundaries Æ Frenkel pair
Æline defectsÆsurface defectsÆfracture

diffusion takes time!

„fatique” Short range order: clusters of 5‐10 molecules in
continuous rearrangement

1.1.‐1.2. Mesomorphous materials – liquid crystals Practical aspects

Average interaction energy between molecules is small like in liquids 1. Thermotropy

Long range order (but not so strict) ~ like in crystals Cholesteric order Æ the distance of the ordered layers is sensitive to temperature Æ interference of diffracted light Æ
Deformability like in liquids Ædestructive interference for given λ‐component of white light Æ compensating color is observed in reflection
Constituting molecules are of special shape ~ string‐like, disc‐like Contact thermography
polarizable Color ~ T      
Anisotropy thermometers

Forms of order of string‐like molecules

smectic
Ordering: translational and orientational

.2. Lyotropic liq.crys.: membranes formed by amphiphilic molecules (like phopholipids)

Weak bond energy Æ order can be easily perturbed by
in proper solvents– lipid membranes: bi‐layers or multi‐layers
nematic
Lipid content
‐temperature (by Boltzmann distr.) 0% 100%
‐concentration , pH, polarity of solvents
‐electric field
cholesteric
Liposomes ‐ vesicules crystalline
thermotropic liotropic
classes
p. 467
 Biological –medical aspects
Biological significance: structure of the cell membrane, vesicules, enclosing subcellular
compartments Lipid membranes: combination of liotropic and thermotropic properties

Crystalline/solid/ordered state below Tm

Cell‐membrane:  lipid bilayer
T<Tm biologically non‐functional
e.g. ends of nerve cells in frozen limbs‐ numbness
Tm Liq.Cryst. state above Tm – capable of biological functioning
T>Tm
Role of cholesterol
‐T> Tm rigidity
40 – 60 % lipid
50 – 30 % protein 
‐T<Tm flexibility

Schematic figures !
Artificial membranes – liposomes – tools in therapy
Liposomes
Real structure of „parallel” lipids
Targeting of medications by attached antibodies
(cell membrane) Stealth liposomes to avoid degradation by macrophages
Boltzmann distribution allows for
flexibility of lipid chains!
(blue: transmembrane protein)
Result of computational modeling of bond breaking by Boltzmann distribution

Continuation in the next lecture:

electrooptical properties of liquid crystals
gaseous systems: ideal gas
real gas

Thank you for your attention!