Simultaneous Thermal Analysis Thermodynamics

In The Name of Allah Simultaneous Thermal AnalysisThermodynamics By: Pooria Gill; PhD of Nanobiotechnology Assistant Professor at MAZUMS P.Gill@mazums.ac.ir

Definition • Thermodynamics is an impressive term that might seem more than just a little intimidating at first. • Luckily, like many things, once you get to know it a bit, it’s not as mysterious and difficult as it seemed at first. It’s really all about energy. • The word "thermodynamics" comes from Greek roots meaning heat (thermo) and energy, or power (dynamics). • So, Thermodynamics is really just the study of heat and energy, and how it relates to the matter in our universe. • Thermodynamics is used in many fields of study, such as physics and engineering, to understand physical processes. • Not surprisingly, it is also used by biochemists to understand processes and chemical reactions that occur in living organisms. • Despite all these applications, the basic tenets of thermodynamics can be stated in just a few laws. • There are three laws of thermodynamics, the first two of which are of most interest to biochemists.

1st Law of Thermodynamics • This is the law of the conservation of energy. It states that energy can neither be created, nor can it be destroyed. • This means that the total amount of energy in the universe always remains conserved, or constant. However, energy can be changed from one form to another. • There are many different forms of energy, some of which may be more useful than others for a particular process. • Electrical, chemical, and mechanical are all examples of different forms of energy. • The definition of energy is the ability to do work.

2nd Law of Thermodynamics • This is the law of increasing entropy. • It states that the entropy of the universe increases with every physical process (change) that occurs. • Entropy refers to the level of disorder, randomness, or chaos, of a system. • The higher the randomness of a system, the higher its entropy. • The more organized a system, the lower its entropy. • A "system" is the part of the world we are interested in. • It can be very small, like a single molecule, or as large as the entire universe.

Entropy at work A drop of dye placed in a cup of water will eventually result in an evenly colored solution, even if we never stir the liquid. The dye molecules distribute as evenly as possible throughout the volume of water.

Nature’s Heat Tax An example of this is the conversion of the energy in gasoline to power an automobile. Only about 20% of the energy results in motion of the vehicle, while the rest of the energy is lost as heat.

Car Efficiency This idea that entropy is always increasing can be a bit confusing. The second law states that the entropy of the universe must increase with each process. However, this is not the same as saying the entropy of a system must increase with each process. The system can become more ordered, but the price is that the surroundings must become much more disordered, so that there is still an overall increase in entropy for the universe.

Gibbs Free Energy In the previous section, we discussed that spontaneous reactions always proceed in a direction that will give the products less potential energy, or energy available to do work, than they started with. This means that in a spontaneous chemical reaction, energy is released, and the products of the reaction have less energy than the original reactants.

ΔG = ΔH – T ΔS • Let’s look at a hypothetical spontaneous chemical reaction: • The quantity of usable energy (chemical potential) in a reaction is called the Gibbs Free Energy (ΔG). ΔG is the difference between the energy contained in the products of a reaction and the reactants: • ΔG = (energy of products) - (energy of reactants) • Chemical reactions are classified as being either "exergonic" or "endergonic". That just means that a reaction can either release energy useful for work (an exergonic reaction) or requires energy to proceed (an endergonic reaction). • The spontaneous reaction above is an exergonic reaction. Note how for an exergonic reaction, ΔG will be negative. Thus, a negative ΔG value tells you that that reaction is possible.

For example, here is the reaction when the high energy compound ATP is hydrolyzed to release an inorganic phosphate molecule and energy: ATP + H2O → ADP + Pi ΔG = -30.5 kJ/mol Note that when the reaction releases energy, ΔG is negative! When the reaction is written in reverse, the sign of ΔG changes: ADP + Pi → ATP + H2O ΔG = +30.5 kJ/mol

Equilibrium Constants • All chemical reactions reach a point where they settle down and won’t go any further. • At that point, the reaction is said to be at equilibrium. • This point is not when all the reactants have been used up (this is actually rarely seen), nor when all the components of the reaction are present in equal quantities. • How much product and how much reactant are present at equilibrium depends on the specific chemical properties of each of the compounds involved. • The equilibrium constant, Keq, is a measure of the concentrations of the reactants and products when the chemical reaction has reached equilibrium.

Keq Definition • The equilibrium constant (Keq) is defined by the ratio of products to reactants when the reaction is at equilibrium. • That is, Keq is calculated from the concentrations of the reactants and products when the reaction has finished (reached equilibrium). • You can do the reaction many times, starting out with different concentrations of reactants and products each time, but at the end of the reaction, the ratio of products to reactants will always end up the same.

Relationship of the equilibrium constant to Gibbs free energy • Let’s look at our hypothetical reaction from the discussion on Keq again: • If the reaction above proceeds so that at equilibrium, the concentration of products is greater than the concentration of reactants, then the reaction is said to lie "to the right". • In that case, the concentrations of C and D will be higher than the concentrations of reactants A and B, and the Keq will be greater than 1. • Remember from our look at the Gibbs Free Energy, that if the formation of products is favored, then the ΔG is negative. • On the other hand, if the reaction is at equilibrium when there are still more reactants left over than products (lies "to the left"), then the concentrations of A and B will always be larger than the concentrations of C and D, and the Keq will be less than 1. • Again, from our look at Gibbs Free Energy, when the formation of reactants is energetically favored, the ΔG is positive. • Thus, there is a relationship between Keq and ΔG.

There is an equation that relates Gibbs Free Energy to the Equilibrium Constant: • ΔG = -2.3RT log Keq • R is a constant value (the gas constant, 8.3 J/mol/K ) • T is the temperature at which the reaction occurs (in Kelvin) • Why is all this important? The idea that there is a relationship between the concentrations of the reactants and products and the direction in which a reaction proceeds has important consequences for chemical reactions. • Many metabolic reactions in our bodies (reactions that produce energy, or create building blocks to build up our bodies) can go forward or backward, depending on the surplus of reactants, or the demand for their products.

Equal Right Let’s say there is a small store that sells products on one shore of a lake. Because it’s small, the store owner keeps extra inventory in a warehouse on the other side of the lake. If the warehouse is full but the store is empty, the boat moves from the warehouse to the store, so that there is more product to sell. This is similar to a biochemical reaction proceeding in an environment where the reactant-to-product ratio is greater than it is at equilibrium. In other words, there is too much reactant (stuff at the warehouse), and not enough product (at the store). The reaction (boat) spontaneously proceeds toward equilibrium, which in this case is "to the right".

Equal Left On the other hand, if it’s right after Christmas and suddenly there are a lot of returns, there is too much product at the store. The owner has to send some back to the warehouse. This is similar to a situation where a biochemical reaction is proceeding in an environment where the reactant-to-product ratio is smaller than at equilibrium. In other words, there is too much product while the warehouse sits empty. Again, the reaction moves spontaneously towards equilibrium, but in this case, that means the boat goes in the opposite direction, "to the left".

"Spontaneous" • One last thing to remember; the word "spontaneous" sure makes it sound like these reactions happen fast. • But the truth is, even when a reaction is thermodynamically possible, (has a negative ΔG value), it often happens very slowly. This is especially true of many biochemical reactions that occur under physiological conditions, that is, within our bodies. • Think of what would happen to our store owner if his boat were to break down. • He might try to float his packages across the lake, but it could take forever for them to get to the other side. • So, even if the warehouse is full, the store will get little or no product unless the boat moves. • Enzymes act in much the same way in biochemical reactions. • Metabolic reactions in our bodies are catalyzed, or helped along, by special proteins called enzymes. • They greatly speed up the rate at which reactions occur, so that reactions that are thermodynamically possible but very slow can now proceed at a rate that makes them useful for sustaining life.

Coupled reactions in biochemical processes/pathways • Even though the universe is continually becoming more disordered (following the second law of thermodynamics), not everything is utter chaos. • For instance, we know that our bodies are highly organized. Each of our different organs and tissues performs unique functions, and even at the cellular level molecules are partitioned into organelles and compartments. • Because they possess such highly organized structure, living organisms are said to have a relatively low amount of entropy. • To sustain life, organisms need to build up a complex body from more basic building blocks. • Complex proteins are made from long chains of amino acids, precisely and intricately folded. • DNA is similarly comprised of long chains of nucleic acids. • We know from the second law of thermodynamics that the reactions that create these molecules of life are certainly not spontaneous; energy input is required to make them go. • Organisms do not just magically assemble themselves. But how do living things deliver the needed energy to such body-building chemical reactions?

Coupled reactions in biochemical processes/pathways • We have already discussed that some reactions are exergonic (they release energy that might be useful for work), while others are endergonic (they need energy to make them go). • To get the energy to those endergonic reactions, they are paired up with energy-releasing exergonic reactions. • Like a locomotive that gets the train car over the hill, an exergonic reaction can "pull" an endergonic reaction along to its destination (products). • The reactions can be hooked together, or coupled, via a common intermediate.

Coupled reactions in biochemical processes/pathways • Thermodynamics lets us predict that the reaction will proceed if the overall ΔG of the two reactions is negative. When two reactions are coupled, the overall ΔG is the sum of the DGs of the component reactions. • For example, in the biochemical pathway that breaks down glucose for energy, two enzymes work one after the other to create a high-energy ATP molecule: • Enzyme 1+ cofactor: • (1) Glyceraldehyde-3-phosphate + Pi ↔ 1,3 bisphosphoglycerate (ΔG = 0 kJ/mol) • Enzyme 2 • (2) 1,3 bisphosphoglycerate + ADP ↔ 3-phosphoglycerate + ATP (ΔG = -16.7 kJ/mol)

Conclusions • The first and second laws of thermodynamics are useful in helping us to understand bioenergetics, the flow of energy through living systems. • They can help us determine whether a physical process, such as a biochemical reaction, is possible. Reactions that require energy input will not proceed naturally, or spontaneously. • However, such energy-requiring, endergonic reactions can be coupled to spontaneous, exergonic reactions. • This linking together of two chemical processes allows the energy-requiring reactions to proceed by "borrowing" energy from energy-releasing reactions. • We can calculate whether a reaction is spontaneous or not with the Gibbs Free Energy, ΔG. • The ΔG value and the equilibrium constant, Keq, allow us to predict whether the products or the reactants will be more abundant at equilibrium. • Understanding Keq and Le Chatelier’s Principle also allows us to predict which way the reaction will go to reach equilibrium when extra reactants or products are present. • However, Thermodynamics is not useful for determining reaction rates.

Thanks for Your Attentions! • Refernce: • http://www.wiley.com/college/boyer/0470003790/reviews/reviews.htm

Differential Scanning CalorimetryIntroduction & Definitions Pooria Gill PhD of Nanobiotechnology Assistant Professor at MAZUMS P.Gill@mazums.ac.ir

Introduction • Calorimetry is a primary technique for measuring the thermal properties of materials to establish a connection between temperature and specific physical properties of substances and is the only method for direct determination of the enthalpy associated with the process of interest. • Calorimeters are frequently used in "Chemistry" , "Biochemistry", "Cell Biology", "Biotechnology", "Pharmacology" , and recently in "Nanoscience" to measure thermodynamic properties of the biomolecules and nano-sized materials. • Amongst various types of calorimeters, differential scanning calorimeter (DSC) is a popular one, which is a thermal analysis apparatus measuring how physical properties of a sample change along with temperature against time. • In other words, the device is a thermal analysis instrument that determines the temperature and heat flow associated with material transitions as a function of time and temperature. • During a change in temperature, DSC measures a heat quantity which is excessively radiated or absorbed by the sample; on the basis of a temperature difference between the sample and the reference material. • Based on mechanism of operation, differential scanning calorimeters can be classified into two types: 1) Heat flux DSCs, and 2) Power compensated DSCs.

Introduction • In a heat flux DSC, the sample material, enclosed in a pan and an empty reference pan are placed on a thermoelectric disk surrounded by a furnace. • The furnace is heated at a linear heating rate and the heat is transferred to the sample and reference pan through thermoelectric disk. • However, owing to the heat capacity of the sample there would be a temperature difference between the sample and reference pans, which is measured by area thermocouples and the consequent heat flow is determined by the thermal equivalent of Ohm’s law: • Where q is "sample heat flow", ΔT is "temperature difference between sample and reference” and R is "resistance of thermoelectric disk".

Introduction • In a power compensated DSC, the sample and reference pans are placed in separate furnaces heated by separate heaters. • Both the sample and reference are maintained at the same temperature and the difference in thermal power required to maintain them at the same temperature is measured and plotted as a function of temperature or time. • In the last decades, various DSC-based techniques have been developed to improve the molecular measurements of biomolecules. • The best known of them are "conventional/basic DSC", "MEMS-DSC", "IR-heated DSC", "modulated temperature DSC", "gas-flow modulated DSC", "parallel-nano DSC", "pressure perturbation calorimetry", "self-reference DSC", and "high performance differential scanning calorimetry". • There are several reports of DSC applications in literature for: • Determining structural phase transition • Melting point • Heat of fusion • Percent of crystallinity • Crystallization kinetics • Phase transitions • Oxidative stability • Thermodynamical analysis of biomolecules • Curing kinetics of non-biological materials.

Definitions • Differential scanning calorimetry (DSC) is a thermodynamical tool for direct assessment of the heat energy uptake which occurs in a sample within regulated increase or decrease in temperature. The calorimetry is particularly applied to monitor the changes of phase transitions. • DSC is commonly employed for study of biochemical reactions which is named as a single-molecular transition of a molecule from one conformation to another. Thermal transition temperatures "(melting points)" of the samples are also determined in solution, solid or mixed phases like suspensions. • In a basic DSC experiment, energy is introduced simultaneously into a sample cell (which contains a solution with the molecule of interest) and a reference cell (containing only the solvent). • Temperatures of both cells are raised identically over time. The difference in the input energy required to match the temperature of the sample to that of the reference, would be the amount of excess heat either absorbed or released by the molecule in the sample (during an endothermic or exothermic process respectively). • Due to the presence of molecule of interest, more energy is required to bring the sample to the same temperature as the reference; hence the concept of heat excess comes into the picture (Fig. 1).

Figure 1 • Experimental setup for a differential scanning calorimetry experiment. • The amount of heat required to increase the temperature by the same increment (ΔT) of a sample cell (qs) is higher than that required for the reference cell (qr) by the excess heat absorbed by the molecules in the sample (Δq). • The resulting DSC scans with the reference subtracted from the sample shows how this excess heat changes as a function of temperature.

A Powerful Analytical Tool" DSC " • DSC is capable of elucidating the factors that contribute to the folding and stability of biomolecules. • Changes in the heat capacity are believed to originate from the disruption of the forces stabilizing native protein structure. • For example this includes: • "van der Waals", "hydrophobic and electrostatic interactions", "hydrogen bonds", "hydration of the exposed residues conformational entropy", "the physical environment (such as pH, buffer, ionic strength, excipients)". • Therefore, thermodynamic parameters obtained from DSC experiments, are quite sensitive to the structural state of biomolecule. • Any change in the conformation, would affect the position, sharpness and the shape of transition(s) in DSC scans.

Thermodynamic Terms • In a DSC experiment, thermodynamic parameters are associated with heat-induced macromolecular transitions. • For a typical macromolecule, the molar heat capacity is measured as a function of temperature; subsequently yielding the following thermodynamic parameters: • The partial heat capacity of a molecule • Change in enthalpy (ΔH) of the transition • Change in entropy (ΔS) of the transition • Change in heat capacity (ΔCp) of the transition • Melting point (Tm) of the transition • Absolute heat capacity

References • Gill et al., Differential Scanning Calorimetry Techniques: Applications in Biology and Nanoscience. Journal of Biomolecular Techniques 2010. • Donald et al., Calorimeters for Biotechnology. ThermochimicaActa 2006. Thanks for Your Attentions

Differential Scanning CalorimetryThermodynamical TermsBiological Applications (Introduction) Pooria Gill PhD of Nanobiotechnology Assistant Professor at MAZUMS P.Gill@mazums.ac.ir

Thermodynamic Terms • In a DSC experiment, thermodynamic parameters are associated with heat-induced macromolecular transitions. • For a typical macromolecule, the molar heat capacity is measured as a function of temperature; subsequently yielding the following thermodynamic parameters.

Partial Heat Capacity of a Molecule • The heat capacity of the solution containing a macromolecule is measured with respect to the heat capacity of buffer in the absence of macromolecules. • Hence the instrument measures only part of what could be actually measured which is the difference between sample and reference cells. • The sample could be a protein, tRNA, a protein–DNA complex, a protein–lipid complex, or something else. • The heat capacity at constant pressure is a temperature derivative of the enthalpy function (Cp = (H/T)p and thus the enthalpy function can be measured through integration of the heat capacity (H(T)= Cp(T)dT + H(T0)).

Partial Heat Capacity of a Molecule The partial molar heat capacity functions of (a) barnase (Mw=12.4kDa) and (b) ubiquitin (Mw=8.4 kDa), in solutions with different pH. The dashed lines represent the partial molar heat capacity of native and unfolded proteins. Data are adapted from "Privalov PL, Dragan AI. Microcalorimetry of biological macromolecules. Biophys Chem. 2007; 126: 16–24".

The more positive ΔG, The greater the stability • For any biomolecule in aqueous solution, there would be equilibrium between the native conformation (folded) and its denatured state (unfolded). • Stability of the native conformation is based on the extent of Gibbs free energy (ΔG) of the system, and thermodynamic relationships between changes in the enthalpy (ΔH) and entropy (ΔS). • A positive magnitude of ΔG represents higher stability of the native conformation than that of the denatured state. • During the unfolding process of a protein, forces that play key role in stabilization need to be broken. • At temperatures where entropy is the dominant factor, conformational entropy overcomes the stabilizing forces, leading to unfolding of protein.

Melting Point (Tm) • Differential scanning calorimetry measures ΔH of unfolding due to heat denaturation. • The transition midpoint Tm is considered as the temperature where 50% of the protein owns its native conformation and the rest 50% remains denatured. • Higher Tm values would be representative of more stable molecule. • During the same experiment, DSC is also capable of measuring the change in heat capacity (ΔCp). • Associated with protein unfolding process, heat capacity changes occur as a result of changes in hydration of side chains which are buried in the native conformation, but become exposed to the solvent in denatured state.

∆Hcal versus ∆HVH • Calorimetric enthalpy (∆Hcal) means the total integrated zone below the thermogram peak which indicates total heat energy uptake by the sample after suitable baseline correction affecting the transition. • Van’t Hoff enthalpy (∆HVH) is an independent measurement of the transitional enthalpy according to the model of the experiment. ∆HVH is determined through the shape analysis of an experimental graph of versus T.

Two-State & Cooperative Modes • The state of the transition is evaluated by comparing of ∆HVH and ∆Hcal. • If ∆HVH is equal to ∆Hcal, the transition occurs in a two-state mode. • In such process, manful thermodynamical results are determined through van’t Hoff measurements of equilibrium results. • When ∆HVH is more than ∆Hcal, the intermolecular cooperation is shown which is exposed for example as aggregation. • Comparison between ∆HVH and ∆Hcal also indicates the cooperative nature of the transition. Particularly, ∆HVH/ ∆Hcal ratio gives an estimation from the fraction of the structure which is melted as a thermodynamical value. The value is also named as the size of the cooperative unit.

Two-State & Cooperative Modes • Heat capacity change (∆Cp) for transitional state is obtained through the difference between pretransitional and posttransitional baselines of a DSC process. • The curve of Cp against T can be changed to versus T through dividing the raw Cp value by T and drawing the results as a function of T. • By integration, this curve results the transition entropy (∆S) which is expressed as (∆S) = ∫( ) dT. • Hence an individual DSC thermogram can result ∆H, ∆S, and ∆Cp. • After knowing the above data, transition free energy (∆G) can be given at each temperature (T) through the famous thermodynamical equation: ∆G = ∆H - T∆S • Although ∆S and ∆G can be obtained by DSC results, the values are more unreliable than the ∆H and ∆Cp values determined directly because of coupling and propagating of errors.

Absolute Heat Capacity • Apparent heat capacity can be obtained by DSC results. • It includes the contribution of water displacement by the protein in sample cell which could have even negative value. • Correction for the water displacement effect and normalization to a mole of protein offers the absolute heat capacity. • The value is obtained from doing a series of DSC measurements at different protein concentrations. • Determined absolute heat capacities by DSC could be employed to characterize long-range interactions and cooperative phenomena which have been shown to occur in denatured proteins.

DSC APPLICATIONS IN BIOLOGY • Analysis of Proteins • Differential Scanning Calorimetry of Nucleic Acids • Analysis of Lipids • Analysis of Carbohydrates • Analysis of Monoclonal Antibodies

Reference • Gill et al. Differential Scanning Calorimetry: Application in Biology and Nanoscience. J. Biomol. Tech., 2010. • Privalov PL, Dragan AI. Microcalorimetry of Biological Macromolecules. Biophys Chem., 2007. "Thanks for Your Attentions"

Simultaneous Thermal Analysis Thermodynamics