C7790 Introduction to Molecular Modelling -1C7790
Introduction to Molecular
Modelling
TSM Modelling Molecular Structures
Petr Kulhánek
kulhanek@chemi.muni.cz
National Centre for Biomolecular Research, Faculty of Science
Masaryk University, Kamenice 5, CZ-62500 Brno
PS/2021 Present Form of Teaching: Rev2
Lesson 4
Phenomenological thermodynamics (spontaneity of processes)
C7790 Introduction to Molecular Modelling -2-
Overview
C7790 Introduction to Molecular Modelling -3-
Thermodynamics
Or what you should already know….
C7790 Introduction to Molecular Modelling -4The
system and its environment
system
environment
system - the part of space and its material contents, which is the subject of
thermodynamic consideration
the system is separated from the
environment by real or fictional walls
System types Description
isolated system walls protects exchange of matter and energy with the
environment
closed system walls protects exchange of matter to the environment, but it can
exchange energy with it
open system it can exchange matter and energy with the environment
C7790 Introduction to Molecular Modelling -5System
state and its properties
System state can be described by properties (mass, volume, temperature, pressure,
etc.), which are needed for the full state description.
Thermodynamic properties are state functions. The state functions ​​do not depend on the
way how the system got into the given state.
Heat and work are NOT state functions.
Thermodynamic properties can be divided into two groups:
Extensive properties: depend on the mass of the system and are additive. The value of the
extensive property is equal to the sum of individual parts of which the
system is composed. Examples are weight, energy, volume.
Intensive properties: do not depend on the size or mass of the system and are therefore
non-additive. Examples are temperature, pressure, concentration.
C7790 Introduction to Molecular Modelling -6Thermodynamic
process and equilibrium
Thermodynamic process corresponds to system state change. It can represent a change in
volume, temperature, pressure, or change in composition as a result of
chemical reaction.
Thermodynamic equilibrium is a state in which no state function changes over time.
(Chemical or other transformations may still take place in the system.
However, these must take place in conjunction so that they do not affect
the state of the system as a result.)
Thermodynamic laws:
➢ 0th law about thermodynamic equilibrium of multiple systems
➢ 1st law energy conservation law
➢ 2nd law about the spontaneity of events
➢ 3rd law about absolute entropy
C7790 Introduction to Molecular Modelling -7The
first law
WdQddU +=
change of internal energy
of the system
heat exchanged with the environment
(form of energy)
work done
(form of energy)
It is a generalization of the energy conservation law to dissipative systems, i.e., such
systems that exchange heat and work with their surroundings.
It postulates internal energy as a state variable, which is sum of other energy forms:
Sign convention for energy change:
+ (positive) - the system receives energy
- (negative) - the system releases energy
complete differential (U is a function of
system properties, a state function)
d
incomplete differential (Q and W are not
state functions)
d
C7790 Introduction to Molecular Modelling -8The
second law
It postulates the entropy as a state function:
T
dQ
dS rev
=
T
Qd
dS 
reversible action irreversible action (spontaneous)
The most important postulate of thermodynamics. It speaks about time flow direction
(time arrow). The direction of time is determined by the irreversible events.
For an isolated system, the direction of time is the same as the increase in entropy.
Spontaneous events are accompanied by an increase in entropy.
In an isolated system, the entropy increases until equilibrium is reached. At equilibrium,
the value of entropy is maximal and constant in time.
C7790 Introduction to Molecular Modelling -9-
Spontaneous
process
Or what you should already know….
C7790 Introduction to Molecular Modelling -10Entropy
and spontaneity
𝑑𝑆 > 0 In an isolated system, the entropy increases until
equilibrium is reached. At equilibrium, the value of
entropy is maximal and constant in time.
.
int
ext
intS
Entropy change of the internal system (int, system of
interest) is not sufficient to assess spontaneity of the
process. It is necessary to assess the entropy change
of the system including with its surroundings.
irreversible action
(spontaneous process)
C7790 Introduction to Molecular Modelling -11Free
energy and spontaneity
int
ext
Is there a property of the internal system, which can describe the entropy change of the
entire system (int+ext)?
Δ𝑆 𝑒𝑥𝑡 + Δ𝑆int > 0
Spontaneous process:
?
we can measure for given process (int change)
C7790 Introduction to Molecular Modelling -12Free
energy and spontaneity
int
ext
Δ𝑆 𝑒𝑥𝑡 =
𝑄 𝑟𝑒𝑣
𝑇
for the isothermal process
Spontaneous process:
Q
What is Q equal to?
Is there a property of the internal system, which can describe the entropy change of the
entire system (int+ext)?
we can measure for given process (int change)
we can estimate from
heat exchange between
int and ext
Δ𝑆 𝑒𝑥𝑡 + Δ𝑆int > 0
C7790 Introduction to Molecular Modelling -13Free
energy and spontaneity
int
ext
T
H
T
Q
S rev
ext
int−
==
for the isothermal and isobaric process
Spontaneous process:
int and ext are in
thermal equilibrium
• for reversible process, it is the lowest
estimate
• for irreversible process, the change will be
higher
Is there a property of the internal system, which can describe the entropy change of the
entire system (int+ext)?
we can measure for given process (int change)
Δ𝑆 𝑒𝑥𝑡 + Δ𝑆int > 0
Q
C7790 Introduction to Molecular Modelling -14Free
energy and spontaneity
int
ext
For an isolated system (second law):
Q
int and ext are in thermal equilibrium
Δ𝑆 𝑒𝑥𝑡 + Δ𝑆int > 0
Δ𝐺𝑖𝑛𝑡 = Δ𝐻𝑖𝑛𝑡 − 𝑇Δ𝑆𝑖𝑛𝑡 < 0
−
Δ𝐻𝑖𝑛𝑡
𝑇
+ Δ𝑆𝑖𝑛𝑡 > 0
reorganization
C7790 Introduction to Molecular Modelling -15Free
energy and spontaneity
0−= STHG
0=−= STHG
0−= STHG
spontaneous process
non-spontaneous process
the system is in equilibrium
The change in Gibbs free energy indicates whether the process can occur spontaneously.
However, it does not determine in what time the actual transformation will take place.
for process at constant temperature and pressure