Formamide is one of the important compounds from which prebiotic molecules can be synthesized, provided that its concentration is sufficiently high. For nucleotides and short DNA strands, it has been ...shown that a high degree of accumulation in hydrothermal pores occurs, so that temperature gradients might play a role in the origin of life Baaske P, et al. (2007) Proc Natl Acad Sci USA 104(22): 9346–9351.We show that the same combination of thermophoresis and convection in hydrothermal pores leads to accumulation of formamide up to concentrations where nucleobases are formed. The thermophoretic properties of aqueous formamide solutions are studied by means of Infrared Thermal Diffusion Forced Rayleigh Scattering. These data are used in numerical finite element calculations in hydrothermal pores for various initial concentrations, ambient temperatures, and pore sizes. The high degree of formamide accumulation is due to an unusual temperature and concentration dependence of the thermophoretic behavior of formamide. The accumulation fold in part of the pores increases strongly with increasing aspect ratio of the pores, and saturates to highly concentrated aqueous formamide solutions of ∼85 wt% at large aspect ratios. Time-dependent studies show that these high concentrations are reached after 45–90 d, starting with an initial formamide weight fraction of 10−3 wt % that is typical for concentrations in shallow lakes on early Earth.
In recent years, the response of biomolecules to a temperature gradient has been utilized to monitor reactions of biomolecules, but the underlying mechanism is not well understood due to the ...complexity of the multicomponent system. To identify some underlying principles, we investigate the thermal diffusion of small amide molecules in water systematically. We re-analyze previous measurements of urea and formamide and compare the results with acetamide, N-methylformamide, and N,N-dimethylformamide, amides with a lower hydrophilicity. It turns out that less hydrophilic substances do not show the typical temperature dependence of water soluble macromolecules. Analyzing temperature and concentration dependent measurements using an empirical expression originally derived for nonpolar mixtures, we find that the so-called isotope contribution depends strongly on the hydrophilicity of the solute. This can be qualitatively understood by comparing with molecular dynamic simulations of Lennard-Jones fluids. The hydrophobic/hydrophilic balance also influences the structure in the fluid and with that the thermal expansion coefficient, which correlates with the thermal diffusion coefficient. Furthermore, we observe a clear correlation of the temperature and concentration dependence of the Soret coefficient with the hydrophilicity, which can be quantitatively described by the partition coefficient log P.
Molecular dynamics plays an important role for the biological function of proteins. For protein ligand interactions, changes of conformational entropy of protein and hydration layer are relevant for ...the binding process. Quasielastic neutron scattering (QENS) was used to investigate differences in protein dynamics and conformational entropy of ligand-bound and ligand-free streptavidin. Protein dynamics were probed both on the fast picosecond time scale using neutron time-of-flight spectroscopy and on the slower nanosecond time scale using high-resolution neutron backscattering spectroscopy. We found the internal equilibrium motions of streptavidin and the corresponding mean square displacements (MSDs) to be greatly reduced upon biotin binding. On the basis of the observed MSDs, we calculated the difference of conformational entropy ΔS conf of the protein component between ligand-bound and ligand-free streptavidin. The rather large negative ΔS conf value (−2 kJ mol–1 K–1 on the nanosecond time scale) obtained for the streptavidin tetramer seems to be counterintuitive, given the exceptionally high affinity of streptavidin–biotin binding. Literature data on the total entropy change ΔS observed upon biotin binding to streptavidin, which includes contributions from both the protein and the hydration water, suggest partial compensation of the unfavorable ΔS conf by a large positive entropy gain of the surrounding hydration layer and water molecules that are displaced during ligand binding.
One of the central questions of humankind is: which chemical and physical conditions are necessary to make life possible? In this "origin-of-life" context, formamide plays an important role, because ...it has been demonstrated that prebiotic molecules can be synthesized from concentrated formamide solutions. Recently, it could be shown, using finite-element calculations combining thermophoresis and convection processes in hydrothermal pores, that sufficiently high formamide concentrations could be accumulated to form prebiotic molecules (Niether et al. (2016)). Depending on the initial formamide concentration, the aspect ratio of the pores, and the ambient temperature, formamide concentrations up to 85 wt % could be reached. The stationary calculations show an effective accumulation, only if the aspect ratio is above a certain threshold, and the corresponding transient studies display a sudden increase of the accumulation after a certain time. Neither of the observations were explained. In this work, we derive a simple heuristic model, which explains both phenomena. The physical idea of the approach is a comparison of the time to reach the top of the pore with the time to cross from the convective upstream towards the convective downstream. If the time to reach the top of the pore is shorter than the crossing time, the formamide molecules are flushed out of the pore. If the time is long enough, the formamide molecules can reach the downstream and accumulate at the bottom of the pore. Analysing the optimal aspect ratio as function of concentration, we find that, at a weight fraction of w=0.5 , a minimal pore height is required for effective accumulation. At the same concentration, the transient calculations show a maximum of the accumulation rate.
.
Cyclodextrins are cyclic oligosaccharides which are interesting as drug delivery systems, because they can be used as containers for pharmaceutical substances. We studied the Ludwig-Soret effect of
...-,
-,
- and methyl-
-cyclodextrin in water and formamide by infrared thermal diffusion forced Rayleigh scattering (IR-TDFRS). In water the Soret coefficient,
S
T
, of
-,
- and
-cyclodextrin increases with increasing temperature and shows a sign change from negative to positive around
T
= 35
°
C
, while
S
T
of methyl-
-cyclodextrin is positive in the entire investigated temperature. In formamide
S
T
-values of all cyclodextrins coincide and show a slight decrease with temperature. We discuss the obtained results and relate the
S
T
-values to the different hydrogen bonding capabilities of the cyclodextrins and the used solvents. It turns out that the change of
S
T
with temperature correlates with the partition coefficient, log
P
, which indicates that more hydrophilic substances show a more pronounced temperature sensitivity of
S
T
. Additionally we obtained a surprising result measuring the refractive index contrast factor with temperature,
of cyclodextrins in formamide, which might be explained by a complex formation between cyclodextrins and formamide.
Graphical abstract
Thermophoretic behavior of a free protein changes upon ligand binding and gives access to information on the binding constants. The Soret effect has also been proven to be a promising tool to gain ...information on the hydration layer, as the temperature dependence of the thermodiffusion behavior is sensitive to solute-solvent interactions. In this work, we perform systematic thermophoretic measurements of the protein streptavidin (STV) and of the complex STV with biotin (B) using thermal diffusion forced Rayleigh scattering (TDFRS). Our experiments show that the temperature sensitivity of the Soret coefficient is reduced for the complex compared to the free protein. We discuss our data in comparison with recent quasi-elastic neutron scattering (QENS) measurements. As the QENS measurement has been performed in heavy water, we perform additional measurements in water/heavy water mixtures. Finally, we also elucidate the challenges arising from the quantiative thermophoretic study of complex multicomponent systems such as protein solutions.
Protein ligand interactions play an important role in biology. Increasingly the aim is to understand and influence protein ligand binding. The binding process is heavily influenced by its ...thermodynamic parameters. In order to understand how the whole system thermodynamics work it is important to characterise the individual contribution of each of the systems components. While the change in conformational entropy of the protein can be determined using QENS complementary methods are necessary in order to characterise all components. This paper will describe the challenges that can occur when combining the different methods, as well as how they can be overcome.
.
Presently, microfluidic traps are designed mimicking the environment of hydrothermal pores, where a combination of thermophoresis and convection leads to accumulation so that high concentrations of ...organic matter can be reached. Such a setup is interesting in the context of the origin of life to observe accumulation and possible further synthesis of small organic molecules or prebiotic molecules such as nucleotides or RNA-fragments, but could also be used to replicate DNA-strands. The addition of coupling agents for the activation of carboxyl or phosphate groups such as 1-Ethyl-3-(3-dimethylaminopropyl)carbodiimide (EDC) and EDC-hydrochloride (EDC-HCl) is necessary in order to speed up the process. This work characterizes the thermophoretic properties of EDC and EDC-HCl needed to optimize the design of the traps. At
p
H 4–6 spontaneous hydrolysis of EDC is observed, which also leads to a neutralisation of the
p
H. In order to evaluate the thermodiffusion measurements the rate constants were measured at 23 and
50
∘
C and the activation energy of the hydrolysis calculated.
Graphical abstract
.
Recent experiments for various amides and sugars showed a clear correlation of the temperature dependence of the Soret coefficient with the hydrophilicity, quantitatively described by the logarithm ...of the 1-octanol/water partition coefficient log
P
. This coefficient is a measure for the hydrophilicity/hydrophobicity balance of a solute and is often used to model the transport of a compound in the environment or to screen for potential pharmaceutical compounds. In order to validate whether this concept works also for other water soluble molecules we investigated systematically the thermophoresis of mono- and polyhydric alcohols. As experimental method we use a holographic grating technique called infrared Thermal Diffusion Forced Rayleigh Scattering (IR-TDFRS). Experiments showed that the temperature dependence of the Soret coefficient of polyhydric alcohols also correlates with log
P
and lies on the same master plot as amides and sugars.
Graphical abstract
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