Etanol, 1_propanol ve 2_propanol yapılarının su molekülü ile oluşturdukları dimer kümelerinin teorik incelenmesi

Yıl 2022, , 676 - 686, 15.04.2022

Zafer Maşlakcı

https://doi.org/10.17714/gumusfenbil.1055375

Öz

Küçük alkoller olarak bilinen etanol, 1_propanol ve 2_propanol yapıları su molekülleri ile hidrojen bağı oluşturabilmektedirler. Etanol, 1_propanol ve 2_propanol yapılarının hidroksil grupları hem proton alıcı hem de proton verici olarak davranış göstermektedirler. Bu çalışmanın amacı, farklı dimer kümelerinde alkol yapılarının su molekülleri ile etkileşimi sonucu gelişen topolojik ve yapısal özellikleri incelemektir. QUICKSTEP (CP2K) paket programı ile BLYP seviyesinde ve QZV3P temel setinde optimizasyonları yapılmıştır. NCI teorisi ile birlikte iso-yüzeyleri belirlenmiş ve elektron yoğunlukları değişimleri incelenmiştir. Bu çalışma, belirli alkol-su dimer komplekslerinde, Ab initio hesaplamalarında daha zayıf hidrojen bağlarının uygun şekilde dikkate alınması gerektiğini göstermektedir.

Anahtar Kelimeler

Etanol, Hidrojen bağı, Topolojik, 1_propanol, 2_propanol

Teşekkür

Bu araştırmada yer alan kısmi nümerik hesaplamalar TÜBİTAK ULAKBİM, Yüksek Başarım ve Grid Hesaplama Merkezi'nde (TRUBA kaynaklarında) gerçekleştirilmiştir ve katkılarından dolayı teşekkür ederim.

Theoretical investigation of the dimer clusters formed by ethanol, 1_propanol and 2_propanol structures with water molecule

Öz

Ethanol, 1_propanol and, 2_propanol structures, known as small alcohols, can form hydrogen bonds with water molecules. The hydroxyl groups of the ethanol, 1_propanol and, 2_propanol structures act as both proton acceptors and proton donors. The aim of this study is to examine the topological and structural properties that develop as a result of the interaction of alcohol structures with water molecules in different dimer clusters. Optimizations were made with the QUICKSTEP (CP2K) package program at the BLYP level and the QZV3P basis set. The iso-surfaces and electron densities changes are studied together with NCI theory. This study shows that in certain alcohol-water dimer complexes, weaker hydrogen bonds should be properly taken into account in Ab initio calculations.

Anahtar Kelimeler

Ethanol, Hydrogen bonding, Topological, 1_propanol, 2_propanol

Kaynakça

• Alagona, G., & Tani, A. (1981). Ab initio calculations as a source of intermolecular potential functions. Ethanol-water with a minimal basis set. Journal of Chemical Physics, 74 (7), 3980-3988. https://doi.org/10.1063/1.441578
• Alavi, S., Takeya, S., Ohmura, R., Woo, T. K., & Ripmeester, J. A. (2010). Hydrogen-bonding alcohol-water interactions in binary ethanol, 1-propanol, and 2-propanol+methane structure II clathrate hydrates. Journal of Chemical Physics, 133 (7), 074505. https://doi.org/10.1063/1.3469776
• Anisimov, V. M., Vorobyov, I. V., Roux, B., & MacKerell, A. D. (2007). Polarizable empirical force field for the primary and secondary alcohol series based on the classical drude model. Journal of Chemical Theory and Computation, 3 (6), 1927-1946. doi: 10.1021/ct700100a
• Arunan, E., Desiraju, G. R., Klein, R. A., Sadlej, J., Scheiner, S., Alkorta, I., Clary, D. C., Crabtree, R. H., Dannenberg, J., Hobza, P., Kjaergaard, H. G., Legon, A. C., Mennucci, B., & Nesbitt, D. J. (2011). Definition of the hydrogen bond. Pure and Applied Chemistry, 83 (8), 1637-1641. https://doi.org/10.1351/PAC-REC-10-01-02
• Bakkas, N., Bouteiller, Y., Loutellier, A., Perchard, J. P., & Racine, S. (1993). The water–methanol complexes. I. a matrix isolation study and an ab initio calculation on the 1‐1 Species. Journal of Chemical Physics, 99 (5), 3335-3342. https://doi.org/10.1063/1.465143
• Balcı, F. M. (2007). Metantiyol hidrojen klorür dimer ve trimerleri üzerine kuantum mekaniksel bir çalışma [Yüksek Lisans Tezi Süleyman Demirel Üniversitesi Fen Bilimleri Enstitüsü].
• Curtiss, L. A., & Blander, M. (1988). Thermodynamic properties of gas-phase hydrogen-bonded complexes. Chemical Reviews, 88 (6), 827-841. https://doi.org/10.1021/cr00088a002
• Desiraju, G. R., & Steiner, T. (1999). The weak hydrogen bond in structural chemistry and biology (International Union of Crystallography Monographs on Crystallography) (1nd ed.). Oxford University Press.
• Dixit, S., Crain, J., Poon, W. C. K., Finney, J. L., & Soper, A. K. (2002). Molecular segregation observed in a concentrated alcohol-water solution. Nature, 416 (6883), 829-832. https://doi.org/10.1038/416829a
• Evangelisti, L., Gou, Q., Feng, G., Caminati, W., Mead, G. J., Finneran, I. A., Carroll, P. B., & Blake, G. A. (2017). Conformational equilibrium and internal dynamics in the iso-propanol–water dimer. Physical Chemistry Chemical Physics, 19 (1), 568-573. https://doi.org/10.1039/C6CP06315B
• Fileti, E. E., Chaudhuri, P., & Canuto, S. (2004). Relative strength of hydrogen bond interaction in alcohol–water complexes. Chemical Physics Letters, 400 (4-6), 494-499. https://doi.org/10.1016/j.cplett.2004.10.149
• Finneran, I. A., Carroll, P. B., Allodi, M. A., & Blake, G. A. (2015). Hydrogen bonding in the ethanol–water dimer. Physical Chemistry Chemical Physics, 17 (37), 24210-24214. https://doi.org/10.1039/C5CP03589A
• Franks, F., & Desnoyers, J. E. (1985). Water science reviews 1 (1nd ed.). Cambridge University Press.
• Franks, F., & Ives, D. J. G. (1966). The structural properties of alcohol–water mixtures. Quarterly Reviews, Chemical Society, 20, 1-44. https://doi.org/10.1039/QR9662000001
• Guo, J. H., Luo, Y., Augustsson, A., Kashtanov, S., Rubensson, J. E., Shuh, D. K., Agren, H., & Nordgren, J. (2003). Molecular structure of alcohol-water mixtures. Physical Review Letters, 91 (15), 157401. https://doi.org/10.1103/PhysRevLett.91.157401
• Johnson, E. R., Keinan, S., Mori-Sánchez, P., Contreras-García, J., Cohen, A. J., & Yang, W. (2010). Revealing noncovalent interactions. Journal of the American Chemical Society, 132 (18), 6498−6506. https://doi.org/10.1021/ja100936w
• Juurinen, I., Nakahara, K., Ando, N., Nishiumi, T., Seta, H., Yoshida, N., Morinaga, T., Itou, M., Ninomiya, T., Sakurai, Y., Salonen, E., Nordlund, K., Hämäläinen, K., & Hakala, M. (2011). Measurement of two solvation regimes in water-ethanol mixtures using X-ray compton scattering. Physical Review Letters, 107 (19), 197401. https://doi.org/10.1103/PhysRevLett.107.197401
• Krack, M., Mohammed, F., Parinello, M., VandeVondele, J., Chassaing, T., & Hutter, J. (2005). Quickstep: Fast and accurate density functional calculations using a mixed Gaussian and plane waves approach. Computer Physics Communications, 167 (2), 103-128. https://doi.org/10.1016/j.cpc.2004.12.014
• Masella, M., & Flament, J. P. (1998). Relation between cooperative effects in cyclic water, methanol/water, and methanol trimers and hydrogen bonds in methanol/water, ethanol/water, and dimethylether/water heterodimers. Journal of Chemical Physics, 108 (17), 7141-7151. https://doi.org/10.1063/1.476131
• Peeters, D., & Huyskens, P. (1993). Endothermicity or exothermicity of water/alcohol mixtures. Journal of Molecular Structure, 300, 539-550. https://doi.org/10.1016/0022-2860(93)87046-C
• Scheiner, S. (1997). Hydrogen bonding: A theoritical perspective (1nd ed.). Oxford University Press.
• Sum, A. K., & Sandler, S. I. (2000). Ab initio calculations of cooperativity effects on clusters of methanol, ethanol, propanol, and methanethiol. Journal of Physical Chemistry A, 104 (6), 1121-1129. https://doi.org/10.1021/jp993094b