approximation methods and 6-31G basis approach ... Conclusion. Methods. Data Analysis. Table 1: Computed Densities of Pure Organic Solvents. Figure 1: The ...
Molecular Dynamic Simulations of Organic Solvents Afiqah B. Ayauf, Rajni Verma, Katie Mitchell-Koch Department of Chemistry, Wichita State University, Wichita KS 67260 Introduction
Data Analysis
The ultimate goal of this research is to study the specificity and efficiency of yqhD for its potential use in the biofuel industry, as well as other applications in biotechnology, medicine and biochemistry.
Right: An alcohol dehydrogenase of Escherichia coli of the K-12 strain (yqhD). It is NADP dependent and a Zn ion is its coenzyme. Courtesy of NCBI and NIH
Background In order to understand this specificity and its effects on the efficiency of the enzymes, the substrates were studied. The substrates studied were ethanol, isobutanol and propanol. The products of the above substrates were also studied, namely, acetaldehyde, isobutyralde-hyde and propionaldehyde.
Discussion
Table 1: Computed Densities of Pure Organic Solvents Density (This Error work) Estimation kg/m^3 (at 300 K) Acetaldehyde 829.017 23
Density (Literature/Experimental) kg/m^3 (at 290-300 K)
Ethanol
490.974
2.3
790.0*
Isobutanol
788.765
0.35
800.0*
Isobutanal
774.803
1.1
793.8*
The trends for the densities of the alcohol are increasing for both the computed and experimental values. The trends for the computed densities of the aldehydes are not quite close to the experimental values nor do the two sets of values have direct correlation. The diffusion coefficients obtained from this work are compared with diffusion coefficients obtained from available coefficient diffusion data. More studies will be conducted involving simulations to determine diffusion coefficients of these solvents in water and in the presence of the enzyme.
784.6ᵝ
Propanal
802.915
0.37
796.0&
Propanol
589.89
0.62
799.0#
Conclusion Figure 1: The comparison between the computed densities of the three alcohols and experimental ones.
Diffusion Constant (this work) (1e-5 cm^2/s)
ᵝ Smith, Thomas E. and R. F. Bonner. * Verschueren, Karel (2001). & Yaws, Carl L. (2003). # Wypych, George (2008; 2012).
Bottom: A TIFF Image of Isobutanol. Both images were constructed using Chimera and VMD.
Figure 1: The comparison between the computed densities of the three alcohols and experimental ones.
Acetaldehyde
3.4 (+/- 0.6)
Ethanol
6.1 (+/- 0.7)
Isobutanol
0.4 (+/- 0.02)
Isobutanal
2.5 (+/- 0.05)
Propanal
3.4 (+/- 0.2)
Propanol
3.8 (+/- 0.4)
Diffusion Constant (Lit. expt.) (1e-5 cm^2/s)
References 0.26# (Comp.), 1.1& (Expt)
# Kholmurodov, Kholmirzo, et al (2013). & Wang, Junmei and Tingjun Hou (2011).
Methods • Optimization was conducted with GAUSSIAN09 with DFT approximation methods and 6-31G basis approach GAUSSIAN09 is a program that performs quantum mechanics computations. • A box was constructed for each solvent before it underwent energy minimization. The simulation for each box of solvents was conducted with a GROMOS96 53a6 and 53a7 UA force field settings, with a V-scale thermostat, as well as an NPT environment. GROMACS is a program that performs molecular dynamics algorithms • GROMACS uses the Einstein equation to calculate diffusion constants using mean square distribution
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In summary, there is an approximate positive correlation between the number of carbons of an alcohol and its density, whereas for acetaldehydes, the densities are less dependent on the number of carbons and dependent on other factors, but the computational analys-is demonstrates on negative correlation. As the data for diffusion coefficients of these solvents are unavailable, more studies can follow this observation.
• Verschueren, Karel (2001). Handbook of Environmental Data on Organic Chemicals (4th Edition). John Wiley & Sons. http://app.knovel.com/hotlink/toc/id:kpHEDOCE02/handbookenvironmental • Wypych, George (2008; 2012). Knovel Solvents - A Properties Database. ChemTec Publishing. http://app.knovel.com/hotlink/toc/id:kpKSAPD005/knovel-solventsproperties • Yaws, Carl L. (2003). Yaws' Handbook of Thermodynamic and Physical Properties of Chemical Compounds. Knovel. http://app.knovel.com/hotlink/toc/id:kpYHTPPCC4/yaws-handbookthermodynamic • Smith, Thomas E. and R. F. Bonner. Acetaldehyde, Propionaldehyde and n-Butyraldehyde: Some Physical Properties. U.S. Industrial Chemicals, Inc., Baltimore, MD. • Kholmurodov, Kholmirzo, Ermuhammad Dushanov et al (2013). Structural and Diffusional Study of Pure Ethanol and Water on Pt (III) Surface Using Molecular Dynamics Simulations. European Chemical Bulletin. • Wang, Junmei and Tingjun Hou (2011). Application of molecular dynamics simulations in molecular property prediction II: Diffusion coefficient. J Comput Chem. 2011 December; 32(16): 3505–3519.
Acknowledgements Top: The TIFF images of both acetaldehyde and ethanol. Left: The TIFF image of isobutanol. All TIFF images were constructed with Chimera using files generated with GAUSSIAN 09.
This work is sponsored by the Department of Chemistry at Wichita State University, Kansas IDEA Network of Biomedical Excellence (K-INBRE), and Kansas National Science Foundation Experimental Program to Stimulate Competitive Research (Kansas NSF EPSCoR)
