TBT4135 - Biopolymerkjemi - Sideversjonshistorikk

Yasharh på 19. apr. 2016 kl. 10:48

2016-04-19T10:48:19Z

← Eldre sideversjon		Sideversjonen fra 19. apr. 2016 kl. 10:48
Linje 359:		Linje 359:
	*[http://www.ntnu.no/studieinformasjon/timeplan/h09/?emnekode=TBT4135-1 Timeplan Høst 09]		*[http://www.ntnu.no/studieinformasjon/timeplan/h09/?emnekode=TBT4135-1 Timeplan Høst 09]
	[[Kategori:Valgbare emner]]		[[Kategori:Valgbare emner]]
	[[Kategori:Fag 6. semester]]		[[Kategori:Fag 7. semester]]
	[[Kategori:Fag]]		[[Kategori:Fag]]

Vegarot: /* Light scattering */ LaTeX fix

2012-11-08T16:18:00Z

Light scattering: LaTeX fix

← Eldre sideversjon		Sideversjonen fra 8. nov. 2012 kl. 16:18
Linje 296:		Linje 296:
	For radii of gyration between <math>\lambda/20</math> and <math>\lambda/2</math> a more advanced theory is needed, because then molecules no longer can be assumed to be point scatterers. This leads to an extra factor, and gives us the final light scattering equation:		For radii of gyration between <math>\lambda/20</math> and <math>\lambda/2</math> a more advanced theory is needed, because then molecules no longer can be assumed to be point scatterers. This leads to an extra factor, and gives us the final light scattering equation:

	<math>\frac{Kc}{R_\theta}=(1+\frac{16 \pi^2 R_G^2}{3 \lambda^2}sin^2(\theta/2))(\frac{1}{M}+2 A_2 c)</math>.		<math>\frac{Kc}{R_\theta}=\left(1+\frac{16 \pi^2 R_G^2}{3 \lambda^2}\sin^2(\theta/2)\right)\left(\frac{1}{M}+2 A_2 c\right)</math>.

	The radius of gyration determined here is the z-average.		The radius of gyration determined here is the z-average.

	To estimate the parameters one follows a 4-step method.		To estimate the parameters one follows a 4-step method.
	*Plot Kc/R as a function of <math>sin^2(\theta/2)</math> for each concentration, and then extrapolate to 0 angle.		*Plot Kc/R as a function of <math>\sin^2(\theta/2)</math> for each concentration, and then extrapolate to 0 angle.
	*Plot the intercepts from above as a function of the concentration, this gives 1/M as the intercept and <math>2A_2</math> as the slope.		*Plot the intercepts from above as a function of the concentration, this gives 1/M as the intercept and <math>2A_2</math> as the slope.
	*Plot Kc/R as a function of the concentration for each angle, then extrapolate to 0 concentration.		*Plot Kc/R as a function of the concentration for each angle, then extrapolate to 0 concentration.

Vegarot: /* Viscosity */ LaTeX fix

2012-11-08T15:02:58Z

Viscosity: LaTeX fix

← Eldre sideversjon		Sideversjonen fra 8. nov. 2012 kl. 15:02
Linje 275:		Linje 275:
	For spherical molecules in solution the solution viscosity is given by <math>\eta_s=\eta_0(1+2.5 \Phi)</math>, i.e. only a function of the volume fraction, not the size. Required is that we are in a dilute solution.		For spherical molecules in solution the solution viscosity is given by <math>\eta_s=\eta_0(1+2.5 \Phi)</math>, i.e. only a function of the volume fraction, not the size. Required is that we are in a dilute solution.

	There are some other defintions: <math>\eta_r=\frac{\eta_s}{\eta_0}</math>, relative viscosity, and <math>\eta_{sp}=\eta_r-1</math>, specific viscosity. Combined with the relationship above, we get <math>\eta_{sp}=\nu \Phi</math>. We can alternatively express <math>\Phi=v_h c</math> as a function of the hydrodynamic volume and the concentration, giving the formula <math>\frac{\eta_{sp}}{c}=\nu v_h + ... \Rightarrow [\eta]=lim_{c \to 0} lim_{\dot{\gamma} \to 0} \left(\frac{\eta_{sp}}{c}\right)=\nu v_h</math> for low solution concentrations, where <math>[\eta]</math> is the intrinsic viscosity, independent of the concentration, but dependent on the solvent/biopolymer system.		There are some other defintions: <math>\eta_r=\frac{\eta_s}{\eta_0}</math>, relative viscosity, and <math>\eta_{sp}=\eta_r-1</math>, specific viscosity. Combined with the relationship above, we get <math>\eta_{sp}=\nu \Phi</math>. We can alternatively express <math>\Phi=v_h c</math> as a function of the hydrodynamic volume and the concentration, giving the formula <math>\frac{\eta_{sp}}{c}=\nu v_h + ... \Rightarrow [\eta]=\lim_{c \to 0} \lim_{\dot{\gamma} \to 0} \left(\frac{\eta_{sp}}{c}\right)=\nu v_h</math> for low solution concentrations, where <math>[\eta]</math> is the intrinsic viscosity, independent of the concentration, but dependent on the solvent/biopolymer system.

	This is the origin of the definition for critical concentration for dilute solutions, since <math>v_h c^* =1</math> means overlap, and v=2.5 for spheres. Combining the definition for intrinsic viscosity and that for the expanded specific viscosity, one obtains the important Huggins' equation:		This is the origin of the definition for critical concentration for dilute solutions, since <math>v_h c^* =1</math> means overlap, and v=2.5 for spheres. Combining the definition for intrinsic viscosity and that for the expanded specific viscosity, one obtains the important Huggins' equation:
Linje 285:		Linje 285:
	An extremely important relation is the Mark-Hoywink-Sakurada equation (MHS), which gives the relation between intrinsic viscosity molecular weight, with the general formula <math>[\eta]=KM^a</math>. As mentioned earlier for spheres the intrinsic viscosity is independent of the size of the spheres, and thus also the molecular weight, so a=0 for spheres. For stiff rods we have a=1.8. For random coils we find that <math>[\eta] \propto \frac{R_G^3}{M} \Rightarrow [\eta] = K M^{0.5-0.8}</math>.		An extremely important relation is the Mark-Hoywink-Sakurada equation (MHS), which gives the relation between intrinsic viscosity molecular weight, with the general formula <math>[\eta]=KM^a</math>. As mentioned earlier for spheres the intrinsic viscosity is independent of the size of the spheres, and thus also the molecular weight, so a=0 for spheres. For stiff rods we have a=1.8. For random coils we find that <math>[\eta] \propto \frac{R_G^3}{M} \Rightarrow [\eta] = K M^{0.5-0.8}</math>.

	The average intrinsic viscosity in a polydisperse system is given by <math>\bar{[\eta]}=K lim_{c \to 0} \frac{\sum_i M_i^a c_i}{\sum_i c_i}</math>. We see that if a=1 this gives a weight average, while for other a-values it gives other averages.		The average intrinsic viscosity in a polydisperse system is given by <math>\bar{[\eta]}=K \lim_{c \to 0} \frac{\sum_i M_i^a c_i}{\sum_i c_i}</math>. We see that if a=1 this gives a weight average, while for other a-values it gives other averages.

	=== Light scattering ===		=== Light scattering ===

Vegarot: /* Viscosity */ LaTeX fix.

2012-11-08T15:02:10Z

Viscosity: LaTeX fix.

← Eldre sideversjon		Sideversjonen fra 8. nov. 2012 kl. 15:02
Linje 275:		Linje 275:
	For spherical molecules in solution the solution viscosity is given by <math>\eta_s=\eta_0(1+2.5 \Phi)</math>, i.e. only a function of the volume fraction, not the size. Required is that we are in a dilute solution.		For spherical molecules in solution the solution viscosity is given by <math>\eta_s=\eta_0(1+2.5 \Phi)</math>, i.e. only a function of the volume fraction, not the size. Required is that we are in a dilute solution.

	There are some other defintions: <math>\eta_r=\frac{\eta_s}{\eta_0}</math>, relative viscosity, and <math>\eta_{sp}=\eta_r-1</math>, specific viscosity. Combined with the relationship above, we get <math>\eta_{sp}=\nu \Phi</math>. We can alternatively express <math>\Phi=v_h c</math> as a function of the hydrodynamic volume and the concentration, giving the formula <math>\frac{\eta_{sp}}{c}=\nu v_h + ... \Rightarrow [\eta]=lim_{c \to 0} lim_{\dot{\gamma} \to 0} (\frac{\eta_{sp}}{c})=\nu v_h</math> for low solution concentrations, where <math>[\eta]</math> is the intrinsic viscosity, independent of the concentration, but dependent on the solvent/biopolymer system.		There are some other defintions: <math>\eta_r=\frac{\eta_s}{\eta_0}</math>, relative viscosity, and <math>\eta_{sp}=\eta_r-1</math>, specific viscosity. Combined with the relationship above, we get <math>\eta_{sp}=\nu \Phi</math>. We can alternatively express <math>\Phi=v_h c</math> as a function of the hydrodynamic volume and the concentration, giving the formula <math>\frac{\eta_{sp}}{c}=\nu v_h + ... \Rightarrow [\eta]=lim_{c \to 0} lim_{\dot{\gamma} \to 0} \left(\frac{\eta_{sp}}{c}\right)=\nu v_h</math> for low solution concentrations, where <math>[\eta]</math> is the intrinsic viscosity, independent of the concentration, but dependent on the solvent/biopolymer system.

	This is the origin of the definition for critical concentration for dilute solutions, since <math>v_h c^* =1</math> means overlap, and v=2.5 for spheres. Combining the definition for intrinsic viscosity and that for the expanded specific viscosity, one obtains the important Huggins' equation:		This is the origin of the definition for critical concentration for dilute solutions, since <math>v_h c^* =1</math> means overlap, and v=2.5 for spheres. Combining the definition for intrinsic viscosity and that for the expanded specific viscosity, one obtains the important Huggins' equation:

Vegarot: /* Osmosis */ parentesfix.

2012-11-08T14:36:26Z

Osmosis: parentesfix.

← Eldre sideversjon		Sideversjonen fra 8. nov. 2012 kl. 14:36
Linje 264:		Linje 264:
	In the case when salt is added measurements can be done on polyelectrolytes too. Using the fact that charge neutrality must be maintained as well as the chemical potential is equal at equilibrium, one finds that <math>A_2=\frac{z^2}{4 M_2^2 C_{BX}}</math>. At high ionic strengths this term is small, so then an accurate estimate of the molecular weight can be done.		In the case when salt is added measurements can be done on polyelectrolytes too. Using the fact that charge neutrality must be maintained as well as the chemical potential is equal at equilibrium, one finds that <math>A_2=\frac{z^2}{4 M_2^2 C_{BX}}</math>. At high ionic strengths this term is small, so then an accurate estimate of the molecular weight can be done.

	Typical <math>A_2</math> values <math>[\frac{ml\cdot mol}{g^2}]</math>:		Typical <math>A_2</math> values <math>\left[\frac{ml\cdot mol}{g^2}\right]</math>:
	*<math>10^{-3}</math>: Coils in good solvents, polyelectrolytes, rods		*<math>10^{-3}</math>: Coils in good solvents, polyelectrolytes, rods
	*<math>10^{-5}-10^{-4}</math>: Spheres		*<math>10^{-5}-10^{-4}</math>: Spheres

Vegarot: /* Osmosis */ glemt parentes satt inn.

2012-11-08T14:30:59Z

Osmosis: glemt parentes satt inn.

← Eldre sideversjon		Sideversjonen fra 8. nov. 2012 kl. 14:30
Linje 260:		Linje 260:

	==== Osmosis ====		==== Osmosis ====
	Using the difference between chemical potential on two sides, one with pure solvent and one with solvent and solute, one can calculate <math>A_1</math> and <math>A_2</math>. We get for the pressure on the solute side: <math>\frac{\Pi}{c_2}=RT (\frac{1}{M_2}+A_2 c_2</math>. This plot can give information both on the molecular weight (number average) and the second viral coefficient. If we look at polyelectrolytes and don't add salt to the solvent, the counterions will totally dominate the osmotic pressure (remember number average, size does not matter), so measurements can not be done in this case.		Using the difference between chemical potential on two sides, one with pure solvent and one with solvent and solute, one can calculate <math>A_1</math> and <math>A_2</math>. We get for the pressure on the solute side: <math>\frac{\Pi}{c_2}=RT \left(\frac{1}{M_2}+A_2 c_2\right)</math>. This plot can give information both on the molecular weight (number average) and the second viral coefficient. If we look at polyelectrolytes and don't add salt to the solvent, the counterions will totally dominate the osmotic pressure (remember number average, size does not matter), so measurements can not be done in this case.

	In the case when salt is added measurements can be done on polyelectrolytes too. Using the fact that charge neutrality must be maintained as well as the chemical potential is equal at equilibrium, one finds that <math>A_2=\frac{z^2}{4 M_2^2 C_{BX}}</math>. At high ionic strengths this term is small, so then an accurate estimate of the molecular weight can be done.		In the case when salt is added measurements can be done on polyelectrolytes too. Using the fact that charge neutrality must be maintained as well as the chemical potential is equal at equilibrium, one finds that <math>A_2=\frac{z^2}{4 M_2^2 C_{BX}}</math>. At high ionic strengths this term is small, so then an accurate estimate of the molecular weight can be done.

Vegarot: /* Light scattering */ pynting

2012-09-18T15:50:27Z

Light scattering: pynting

← Eldre sideversjon		Sideversjonen fra 18. sep. 2012 kl. 15:50
Linje 304:		Linje 304:
	*Plot the intercepts from above as a function of the concentration, this gives 1/M as the intercept and <math>2A_2</math> as the slope.		*Plot the intercepts from above as a function of the concentration, this gives 1/M as the intercept and <math>2A_2</math> as the slope.
	*Plot Kc/R as a function of the concentration for each angle, then extrapolate to 0 concentration.		*Plot Kc/R as a function of the concentration for each angle, then extrapolate to 0 concentration.
	*Plot the intercepts as a function of <math>sin^2(\theta/2)</math>. The intercept of this line gives 1/M again, while the slope gives <math>\frac{1}{M}(\frac{16 \pi^2 R_G^2}{3\lambda^2})</math>, which allows determination of <math>R_G</math>		*Plot the intercepts as a function of <math>sin^2(\theta/2)</math>. The intercept of this line gives 1/M again, while the slope gives <math>\frac{1}{M}\left(\frac{16 \pi^2 R_G^2}{3\lambda^2}\right)</math>, which allows determination of <math>R_G</math>

	Remember that the wavelength is the effective wavelength in the solution, e.g. <math>\lambda=\lambda_0/n</math>.		Remember that the wavelength is the effective wavelength in the solution, e.g. <math>\lambda=\lambda_0/n</math>.

Vegarot: /* =Types of bonds */ fjernet overflødig =

2012-09-18T15:49:38Z

=Types of bonds: fjernet overflødig =

← Eldre sideversjon		Sideversjonen fra 18. sep. 2012 kl. 15:49
Linje 220:		Linje 220:
	As mentioned above there can be hindered rotation around certain bonds. A Ramachandran plot can be used to gain an overview over allowed angles.		As mentioned above there can be hindered rotation around certain bonds. A Ramachandran plot can be used to gain an overview over allowed angles.

	====Types of bonds===		===Types of bonds===
	The main types of bonds are: covalent bonds (200-1000 kJ/mol), ion-ion bonds (40-400 kJ/mol), ion - induced dipole and hydrogen bonds (4-40 kJ/mol) and other types of bonds (0-4 kJ/mol). In comparison the thermal energy is 2.4 kJ/mol at 25C, the bond strength must be greater than this to be stable. A hydrogen bond can when a hydrogen atom is trapped between two highly electronegative atoms, such as oxygen or nitrogen. It is covalently bound to one of them at a distance of about 1 Å, and electrostatically bound to the other at a distance of 1.8 Å. The angle also plays a role in the bond strength.		The main types of bonds are: covalent bonds (200-1000 kJ/mol), ion-ion bonds (40-400 kJ/mol), ion - induced dipole and hydrogen bonds (4-40 kJ/mol) and other types of bonds (0-4 kJ/mol). In comparison the thermal energy is 2.4 kJ/mol at 25C, the bond strength must be greater than this to be stable. A hydrogen bond can when a hydrogen atom is trapped between two highly electronegative atoms, such as oxygen or nitrogen. It is covalently bound to one of them at a distance of about 1 Å, and electrostatically bound to the other at a distance of 1.8 Å. The angle also plays a role in the bond strength.

Carlhuse på 12. des. 2009 kl. 15:40

2009-12-12T15:40:45Z

← Eldre sideversjon		Sideversjonen fra 12. des. 2009 kl. 15:40
Linje 2:		Linje 2:
	\|Fakta høst 2009		\|Fakta høst 2009
	\|*Foreleser: Kurt Ingar Draget		\|*Foreleser: Kurt Ingar Draget
	*Stud-ass: ???
	*Vurderingsform: Skriftlig eksamen (100 %)		*Vurderingsform: Skriftlig eksamen (100 %)
	*Eksamensdato: 10.12.09		*Eksamensdato: 10.12.09
Linje 9:		Linje 8:

	{{Infobox		{{Infobox
	\|Øvingsopplegg høst ~~200+~~		\|Øvingsopplegg høst 2009
	\|* Antall godkjente: 5/6		\|* Antall godkjente: 5/6
	* Innleveringssted: Instituttkontor for bioteknologi		* Innleveringssted: Instituttkontor for bioteknologi

Beckwith: /* Thermodynamics of dilute solutions */

2009-12-06T16:36:22Z

Thermodynamics of dilute solutions

← Eldre sideversjon		Sideversjonen fra 6. des. 2009 kl. 16:36
Linje 258:		Linje 258:
	For random coil we have: <math>A_2=\frac{16 \pi}{3}\frac{R^3 N_A}{M_2^2}=\frac{16 \pi}{3}\frac{N_A}{M_2^2}\gamma^3 R_G^3</math>, while spheres have <math>A_2=4 \frac{\bar{v}}{M_2}</math> and rods have <math>A_2=\frac{L \bar{v}}{d M_2}</math>		For random coil we have: <math>A_2=\frac{16 \pi}{3}\frac{R^3 N_A}{M_2^2}=\frac{16 \pi}{3}\frac{N_A}{M_2^2}\gamma^3 R_G^3</math>, while spheres have <math>A_2=4 \frac{\bar{v}}{M_2}</math> and rods have <math>A_2=\frac{L \bar{v}}{d M_2}</math>

	We can define an excluded solute volume as <math>N_A u</math>, the ideal term being <math>u=1</math> and <math>A_2=\frac{N_A u}{2 M_2^2}</math>. Leaping back a bit, we have that if we are in a <math>\theta</math>-solvent, <math>\alpha=0</math>, so u=0 and <math>A_2=0</math>. If we are in a good solvent, <math>\alpha > 1</math>, so <math>u > 0</math> and <math>A_2 > 0</math>, while a bad solvent gives <math>\alpha < 1, u < 0, A_2<0</math>		We can define an excluded solute volume as <math>N_A u</math>, the ideal term being <math>u=1</math> and <math>A_2=\frac{N_A u}{2 M_2^2}</math>. Leaping back a bit, we have that if we are in a <math>\theta</math>-solvent, <math>\alpha=1</math>, so u=0 and <math>A_2=0</math>. If we are in a good solvent, <math>\alpha > 1</math>, so <math>u > 0</math> and <math>A_2 > 0</math>, while a bad solvent gives <math>\alpha < 1, u < 0, A_2<0</math>

	==== Osmosis ====		==== Osmosis ====