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Journal of Physical Chemistry B
Volumn 111, Issue 7, 2007, Pages 1858-1871
Effects of hydrogen-bonding and stacking interactions with amino acids on the acidity of uracil
Author keywords

[No Author keywords available]
Indexed keywords

ACIDITY; AMINO ACIDS; BINDING ENERGY; DENSITY FUNCTIONAL THEORY; REACTION KINETICS;
EID: 84962360703     PISSN: 15206106     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp066902p     Document Type: Article
Times cited : (34)
References (133)
  • 11
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    • For reviews on the DNA glycosylases, see, for example: (a) Dodson, M. L.; Michaels, M. L.; Lloyd, R. S. J. Biol. Chem. 1994, 269, 32709-32712.
    • For reviews on the DNA glycosylases, see, for example: (a) Dodson, M. L.; Michaels, M. L.; Lloyd, R. S. J. Biol. Chem. 1994, 269, 32709-32712.
  • 60
    • 84962348838 scopus 로고    scopus 로고
    • The 6-31G*(0.25) basis set replaces the standard optimized d-exponent for heavy atoms (0.8) with a value of 0.25.
    • The 6-31G*(0.25) basis set replaces the standard optimized d-exponent for heavy atoms (0.8) with a value of 0.25.
  • 61
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    • For a review on the calculation of stacking interactions between the natural DNA nucleobases, see, for example: (a) Hobza, P.; Sponer, J. Chem. Rev. 1999, 99, 3247-3276.
    • For a review on the calculation of stacking interactions between the natural DNA nucleobases, see, for example: (a) Hobza, P.; Sponer, J. Chem. Rev. 1999, 99, 3247-3276.
  • 83
    • 84962405822 scopus 로고    scopus 로고
    • Frisch, M. J, Trucks, G. W, Schlegel, H. B, Scuseria, G. E, Robb, M. A, Cheeseman, J. R, Montgomery, J. A, Jr, Vreven, T, Kudin, K. N, Burant, J. C, Millam, J. M, Iyengar, S. S, Tomasi, J, Barone, V. Mennucci, B, Cossi, M, Scalmani, G, Rega, N, Petersson, G. A. Nakatsuji, H, Hada, M, Ehara, M, Toyota, K, Fukuda, R, Hasegawa, J. Ishida, M, Nakajima, T, Honda, Y, Kitao, O, Nakai, H, Kiene, M, Li X, Knox, J. E, Ratchian, H. P, Cross, J. B, Adamo, C, Jaramillo, J. Gomperts, R, Stratmann, R. E, Yazyev, O, Austin, A. J, Cammi, R. Pomelli, C, Ochterski, J. W, Ayala, P. Y, Morokuma, K, Voth, G. A. Salvador, P, Dannenberg, J. J, Zakrzewski, V. G, Dapprich, S, Daniels A. D, Strain, M. C, Farkas, O, Malick, D. K, Rabuck, A. D. Raghavachari, K, Foresman, J. B, Ortiz, J. V, Cui, Q, Baboul, A. G. Clifford, S, Cioslowski, J, Stefanov, B. B, Liu, G, Liashenko, A, Piskorz P, Komaromi, I, Martin, R. L, Fox, D. J, Keith, T, Al-Laham, M. A. P
    • Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Montgomery, J. A., Jr.; Vreven, T.; Kudin, K. N.; Burant, J. C.; Millam, J. M.; Iyengar, S. S.; Tomasi, J.; Barone, V. Mennucci, B.; Cossi, M.; Scalmani, G.; Rega, N.; Petersson, G. A. Nakatsuji, H.; Hada, M.; Ehara, M.; Toyota, K.; Fukuda, R.; Hasegawa, J. Ishida, M.; Nakajima, T.; Honda, Y.; Kitao, O.; Nakai, H.; Kiene, M.; Li X.; Knox, J. E.; Ratchian, H. P.; Cross, J. B.; Adamo, C.; Jaramillo, J. Gomperts, R.; Stratmann, R. E.; Yazyev, O.; Austin, A. J.; Cammi, R. Pomelli, C.; Ochterski, J. W.; Ayala, P. Y.; Morokuma, K.; Voth, G. A. Salvador, P.; Dannenberg, J. J.; Zakrzewski, V. G.; Dapprich, S.; Daniels A. D.; Strain, M. C.; Farkas, O.; Malick, D. K.; Rabuck, A. D. Raghavachari, K.; Foresman, J. B.; Ortiz, J. V.; Cui, Q.; Baboul, A. G. Clifford, S.; Cioslowski, J.; Stefanov, B. B.; Liu, G.; Liashenko, A.; Piskorz P.; Komaromi, I.; Martin, R. L.; Fox, D. J.; Keith, T.; Al-Laham, M. A. Peng, C. Y.; Nanayakkara, A.; Challacombe, M.; Gill, P. M. W.; Johnson, B.; Chen, W.; Wong, M. W.; Gonzalez, C.; Pople, J. A. Gaussian 03, revisions C.02 and D.01; Gaussian, Inc.: Wallingford, CT, 2004.
  • 106
    • 84962374419 scopus 로고    scopus 로고
    • We note that Cheng et al, ref 8) previously calculated the O2(N3) and O4(N3) binding strengths for the neutral uracil complexes at the LMP2/ 6-31G(d,p) level. Although our B3LYP/6-311+G(2d,p) binding strengths reported in Table 2 are smaller than those previously reported, binding strengths similar to Cheng's are obtained when the smaller (6-31Gd,p, basis set is implemented
    • We note that Cheng et al. (ref 8) previously calculated the O2(N3) and O4(N3) binding strengths for the neutral uracil complexes at the LMP2/ 6-31G(d,p) level. Although our B3LYP/6-311+G(2d,p) binding strengths reported in Table 2 are smaller than those previously reported, binding strengths similar to Cheng's are obtained when the smaller (6-31G(d,p)) basis set is implemented.
  • 107
    • 84962374432 scopus 로고    scopus 로고
    • -1 more stable than the trans isomer.
    • -1 more stable than the trans isomer.
  • 110
    • 84962368325 scopus 로고    scopus 로고
    • We note that several other higher-energy minima can be found, which differ in the orientation of the terminal methyl group
    • We note that several other higher-energy minima can be found, which differ in the orientation of the terminal methyl group.
  • 126
    • 84962418374 scopus 로고    scopus 로고
    • We note that the preferred angles of rotation for neutral and anionic uracil are different. Therefore, the binding strengths, and the effect of binding on the acidity, were calculated using both the optimized angle of rotation for the anion (Table S4) and the preferred angle of rotation for neutral uracil. The results for the two data sets generally differ by less than 3 kJ mol-1
    • -1.
  • 128
    • 84962473100 scopus 로고    scopus 로고
    • We note that similar binding arrangements may also be possible with other sp2 C-H donors within the Trp ring; however, we expect the results to be similar to Trp-2, and therefore we do not further pursue these binding arrangements
    • 2 C-H donors within the Trp ring; however, we expect the results to be similar to Trp-2, and therefore we do not further pursue these binding arrangements.
  • 129
    • 84962348866 scopus 로고    scopus 로고
    • We note that Alkorta et al, ref 15 modeled the protein backbone as N-formylglycinamide in the β and γ conformations. However, because the β conformation must be optimized in fixed Cs symmetry, where release of this constraint leads to the γ conformation, we only consider the γ conformation
    • s symmetry, where release of this constraint leads to the γ conformation, we only consider the γ conformation.
  • 130
    • 84962418364 scopus 로고    scopus 로고
    • Although a binding arrangement similar to that discussed for Asn(Gln)-2 (Figure 5) can be found for the backbone model, we do not consider this interaction in the present work because this binding cannot occur with the true conformation of the protein backbone
    • Although a binding arrangement similar to that discussed for Asn(Gln)-2 (Figure 5) can be found for the backbone model, we do not consider this interaction in the present work because this binding cannot occur with the true conformation of the protein backbone.

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