Abstract
Theoretical studies on hydrogen-bonded complexes between amino acids (glycine, alanine, and leucine) and urea in gas phase have been carried out using density functional theory (DFT) and ab initio methods at the B3LYP/6-311++g** and MP2/6-311++g** theory levels. The structures, binding energy, Chelpg (charges from electrostatic potentials using a grid-based method) charge distribution, and bond characteristics of the mentioned complexes were calculated. Urea is a good H-bond donor and an excellent receptor for highly electronegative atoms like O and N, through the formation of two or more hydrogen bonds. The NH2 and COOH groups of amino acids can form several different types of H-bonds with urea molecular, as well as CαH and alkyl side chains. The calculated high binding energy also suggests multiple H-bonds formed in one complex. The OH···O contact is the strongest hydrogen bond interaction with H···O separation around 1.65 Å and its relevant angle close to 176°. The closely linear amide H-bonds NH···O and OH···N strongly stabilize the amino acid–urea complex with H···O separation between 1.89 and 2.38 Å. The weaker CH···O/N H-bonds are also discussed as significant interaction in biological systems involving amino acids.
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Grdadolnik J, Marechal Y (2002) J Mol Struct 615:177–189. doi:10.1016/S0022-2860(02)00214-4
Mountain RD, Thirumalai D (2003) J Am Chem Soc 125:1950–1957. doi:10.1021/ja020496f
Klimov DK, Straub JE, Thirumalai D (2004) Proc Natl Acad Sci USA 101:14760–14765. doi:10.1073/pnas.0404570101
Chitra R, Smith PE (2002) J Phys Chem B 106:1491–1500. doi:10.1021/jp011462h
Caballero-Herrera A, Nordstrand K, Berndt KD, Nilsson L (2005) Biophys J 89:842–857. doi:10.1529/biophysj.105.061978
Oostenbrink C, van Gunsteren WF (2005) Phys Chem Chem Phys 7:53–58. doi:10.1039/b413167c
Lee ME, van der Vegt NFA (2006) J Am Chem Soc 128:4948–4949. doi:10.1021/ja058600r
O’Brien EP, Dima RI, Brooks B, Thirumalai D (2007) J Am Chem Soc 129:7346–7353. doi:10.1021/ja069232+
Courtenay ES, Capp MW, Record TMJ (2001) Protein Sci 10:2485–2497. doi:10.1110/ps.ps.20801
Auton M, Bolen WD (2005) Proc Natl Acad Sci USA 102:15065–15068. doi:10.1073/pnas.0507053102
Moglich A, Krieger F, Kiefhaber T (2005) J Mol Biol 345:153–162. doi:10.1016/j.jmb.2004.10.036
Bennion BJ, Daggett V (2003) Proc Natl Acad Sci USA 100:5142–5147. doi:10.1073/pnas.0930122100
Tsai J, Gerstein M, Levitt MJ (1996) Chem Phys 104:9417–9430
Zou Q, Habermann-Rottinghaus SM, Murphy KP (1998) Proteins 31:107–115. doi:0.1002/(SICI)1097-0134(19980501)31:2<107::AID-PROT1>3.0.CO;2-J1
Ikeguchi M, Nakamura S, Shimizu K (2001) J Am Chem Soc 123:677–682. doi:10.1021/ja002064f
Timasheff SN, Xie G (2003) Biophys Chem 105:421–448. doi:10.1016/S0301-4622(03)00106-6
Massimo B, Laura De B, David EG, Luigi F, Maurizio L, Enrico M (2004) J Am Chem Soc 126:16507–16514. doi:10.1021/ja045936c
Martin CS, Helmut G (2007) J Am Chem Soc 129:16126–16131. doi:10.1021/ja076216j
Dror T, Ron E, Devarajan T (2003) Biopolymers 68:359–369. doi:10.1002/bip.10290
Fuqiang B, Kathryn NR, James WG, Russell JB (2002) Theor Chem Acc 108:1–11. doi:10.1007/s00214-002-0344-z
Magalhaes AL, Madail SRRS, Ramos MJ (2000) Theor Chem Acc 105:68–76. doi:10.1007/s002140000187
Loos PF, Assfeld X, Rivail JL (2007) Theor Chem Acc 118:165–171. doi:10.1007/s00214-007-0258-x
Biegler-Konig F, Bader RF (2002) AIM 2000, Version 2
Frisch MJ, Trucks GW, Schlegel HB, Scuseria GE, Robb MA, Cheeseman JR, Montgomery JA Jr, Vreven T, Kudin KN, Burant JC, Millam JM, Iyengar SS, Tomasi J, Barone V, Mennucci B, Cossi M, Scalmani G, Rega N, Petersson GA, Nakatsuji H, Hada M, Ehara M, Toyota K, Fukuda R, Hasegawa J, Ishida M, Nakajima T, Honda Y, Kitao O, Nakai H, Klene M, Li X, Knox JE, Hratchian HP, Cross JB, Adamo C, Jaramillo J, Gomperts R, Stratmann RE, Yazyev O, Austin AJ, Cammi R, Pomelli C, Ochterski JW, Ayala PY, Morokuma K, Voth GA, Salvador P, Dannenberg JJ, Zakrzewski VG, Dapprich S, Daniels AD, Strain MC, Farkas O, Malick DK, Rabuck AD, Raghavachari K, Foresman JB, Ortiz JV, Cui Q, Baboul AG, Clifford S, Cioslowski J, Stefanov BB, Liu G, Liashenko A, Piskorz P, Komaromi I, Martin RL, Fox DJ, Keith T, Al-Laham MA, Peng CY, Nanayakkara A, Challacombe M, Gill PMW, Johnson B, Chen W, Wong MW, Gonzalez C, Pople JA (2003) Gaussian03, Gaussian, Int, Pittsburgh, PA
Uwe B (2003) Prog Polym Sci 28:1049–1105. doi:10.1016/S0079-6700(02)00150-8
Robert PA, Maria B, Sarah LP (1997) J Comput Aided Mol Des 11:479–490. doi:10.1023/A:1007923124523
Bader RFW (1990) Atom in molecules: a quantum theory. International series of monographs in chemistry. Oxford University Press, Oxford
Bader RFW (1998) J Phys Chem A 102:7314. doi:10.1021/jp981794v
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Sun, YP., Ren, XH., Wang, HJ. et al. Hydrogen-bonding interaction in a complex of amino acid with urea studied by DFT calculations. Struct Chem 20, 213–220 (2009). https://doi.org/10.1007/s11224-009-9416-1
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DOI: https://doi.org/10.1007/s11224-009-9416-1