Apr 20, 2007 The aqueous and crystalline forms of L-alanine zwitterion Ivan Degtyarenko,* ,1 Karl J. Jalkanen, 2 Andrey A. Gurtovenko 3 and Risto M. Nieminen 1 1 Laboratory of Physics, Helsinki University of Technology, P.O.B. 1100, FIN-02015 HUT, Finland. Fax: +358 9 4513116; Tel: +358 9 4513110, +358 9 45131 05; E-mail: [email protected] , [email protected]2 Nanochemistry Research Institute, Department of Applied Chemistry, Curtin University ofTechnology, G.P.O. Box U1987, Perth 6845, Western Australia. Fax: +61 8 9266 4699; Tel: +61 8 9266 7172; E-mail: [email protected]3 Computational Laboratory, Institute of Pharmaceutical Innovation, University of Bradford, Bradford, West Yorkshire, BD7 1DP, UK. Fax: +44 1274 234679; Tel: +44 1274 236114; E-mail: [email protected]Abstract The structural properties of L-alanine amino acid in aqueous solution and in crystalline phase have bee n stu die d by means of density-funct iona l elec tro nic- structure and mol ecular dynamics simulations. The solvated zwitterionic structure of L-alanine ( + NH3-C2H4-COO - ) was systematically compared to the structure of its zwitterionic crystalline analogue acquired from both computer simulations and experiments. It turns out that the structural properties of an alanine molecule in aqueous solution can differ significantly from those in crystalline phase, these differences being mainly attributed to hydrogen bonding interactions. In particular, we found that the largest difference between the two alanine forms can be seen for the orientation and bond lengths of the carboxylate (COO - ) gro up: in aqu eous sol uti on the C-O bond lengt hs appear to str ong ly correl ate with the number of water molecules which form hydrogen bonds with the COO - group. Furthermore, the hydrogen bond lengths are shorter and the hydrogen bond angles are larger for L-alanine in water as compar ed to crysta l. Overall, our finding s strongly sugge st that the genera lly accepted appro ach ofextending the structural information acquired from crystallographic data to a L-alanine molecule in aqueous solution should be used with caution. Keywords: alanine zwitterion, crystal structure, aqueous solution 1. Introduction 1
This document is posted to help you gain knowledge. Please leave a comment to let me know what you think about it! Share it to your friends and learn new things together.
Transcript
8/4/2019 L -alanine
http://slidepdf.com/reader/full/l-alanine 1/22
Apr 20, 2007
The aqueous and crystalline forms of L-alanine zwitterion
Ivan Degtyarenko,*,1 Karl J. Jalkanen,2 Andrey A. Gurtovenko3 and Risto M. Nieminen1
1 Laboratory of Physics, Helsinki University of Technology, P.O.B. 1100, FIN-02015 HUT,
Table 2. Hydrogen bonds of L-alanine zwitterion. The distances are given in Å and angles in
degrees.
crystal water
H1-O1 1.861a 1.850b (N)H3-Ow 1.74c
H2-O2 1.780 1.458 (C)O2-Hw 1.74
H3-O2 1.828 1.876
N-O1 2.853 2.874 N-Ow 2.77
N-O2 2.813 2.579 (C)O2-Ow 2.68
N-O2 2.832 2.918
<N-H1..O1 160.9 163.1 <N-H..Ow lineard
<N-H2..O2 168.1 177.5 <O..Hw-Ow linear
<N-H3..O2 163.7 172.0
a Non-optimized neutron diffraction structure at 298 K.3
b Fully optimized crystal structure.
c The nearest neighbor distances calculated from radial distribution functions.39
d Bond angles distribution obtained after applying cone correction.39
12
8/4/2019 L -alanine
http://slidepdf.com/reader/full/l-alanine 13/22
Figure 1. Ball and stick representation of L-alanine amino acid in water. Water molecules
within the first hydration shell are shown in solid. Dotted lines indicate hydrogen bonding.
13
Cβ
Cα
C'O2
O1
NHα
H3
H1
H2
H4H5
H6
8/4/2019 L -alanine
http://slidepdf.com/reader/full/l-alanine 14/22
Figure 2. L-alanine crystalline structure. Two unit cells with species constrained to periodic
boundary conditions. The system crystallizes in the P212121 space group, with four zwitterionic
molecules per unit cell. Adopted from Lehmann et al..3
14
O2
O1
H3
H1H2
O2
O1
O2
8/4/2019 L -alanine
http://slidepdf.com/reader/full/l-alanine 15/22
Figure 3. The structural differences of the L-alanine zwitterion in aqueous and crystalline
structures. The calculated (blue), experimental (silver) crystalline and solvated molecule (red)
structures. The structures are aligned along Ca-Ha bond.
15
O2
H3
Hα
H5
O1
8/4/2019 L -alanine
http://slidepdf.com/reader/full/l-alanine 16/22
Figure 4. Hydrogen bonding in crystalline L-alanine.
16
N
H1
H2 H3
O2O2
O1
8/4/2019 L -alanine
http://slidepdf.com/reader/full/l-alanine 17/22
Figure 5. Bond lengths C'-O1 and C'-O2 versus number of water molecules within the hydration
radius (3.06 Å for carboxylate group) around atoms O1 and O2 respectively. Statistical averages are
computed by integrating over a full course of the molecular dynamics trajectory. The corresponding
bond lengths in the experimental crystal structure2 and in the calculated one are marked.
17
1.15 1.20 1.25 1.30 1.351.0
1.5
2.0
2.5
nw
d/Å
C'-O2
C'-O1
exper. C'-O2
exper. C'-O1
calc. C'-O2
calc. C'-O1
8/4/2019 L -alanine
http://slidepdf.com/reader/full/l-alanine 18/22
Figure 6. Time evolution of atomic distances during molecular dynamics simulations. H1..O1
distance is shown by solid line, H2..O1 by dashed line, and N..O1 by dotted line. The running averages
are taken every 500 fs.
18
0 10 20 302.0
2.4
2.8
3.2
r/Å
time/ps
H2-O1
H1-O1
N-O1
8/4/2019 L -alanine
http://slidepdf.com/reader/full/l-alanine 19/22
Figure 7. Deformation electron density maps for L-alanine molecule in aqueous solution. The
contour map size is 6 × 6 Å, and the contour levels are at intervals of 0.05 e⋅Å-3. The planes are
selected to visualize intramolecular hydrogen bonding interactions. (a) A plane defined by H 1, N and
O1
atoms in crystalline L-alanine, (b) in aqueous L-alanine, where carboxylate is in the C'CαN plane,
and thus O1 and H1 atoms are at the shortest distance, (c) in aqueous L-alanine, with the COO-
perpendicular to C'CαN.
19
(a)
(b)
(c)
NH1..O1 crystal
NH1..O1 water
NH1..O1 water
H1N
O1
H1N
O1
O1
H1N
8/4/2019 L -alanine
http://slidepdf.com/reader/full/l-alanine 20/22
1 (a) H. J Simpson and R. E. Marsh, Acta Cryst. 20, 550 (1966); (b) J. D. Dunitz and R. R. Ryan,
Acta Cryst. 21, 617 (1966)2 R. Destro, R. E. Marsh and R. Bianchi, J. Phys. Chem. 92, 966 (1988)3 M. S. Lehmann, T. F. Koetzle and W. C. Hamilton, J. Am. Chem. Soc. 94(8), 2657 (1972)4 R. Destro, R. Bianchi, C. Gatti and F. Merati, Chem. Phys. Lett. 186(1), 47 (1991)
5 R. Destro, R. Bianchi and G. Morosi, J. Phys. Chem. 93, 447 (1989)
6 M. Barthes, H. N. Bordallo, F. Denoyer, J.-E. Lorenzo, J. Zaccaro, A. Robert and F. Zontone,
Eur. Phys. J. B 37, 375 (2004)
7 J. Bandekar, L. Genzel, F. Kremer, L. Santo, Spectrochim. Acta A 39(4), 357 (1983)
8 A. Migliori, P. M. Maxton, A. M. Clogston, E. Zirngiebl and M. Lowe, Phys. Rev. B. 38(18),
13464 (1988)
9 A. M. Micu, D. Durand, M. Quilichini, M. J. Field and J. C. Smith, J. Phys. Chem. 99, 5645
(1995)
10 (a) W. Wang, F. Yi, Y. Ni, Z. Zhao, X. Jin and Y. Tang, J. Biol. Phys. 26, 51 (2000); (b) W.-Q.
Wang, W. Min, Z. Liang, L. Y Wang, L. Chen and F. Deng, Biophys. Chem. 103, 289 (2003)
11 C. C. Wilson, D. Myles, M. Ghosh, L. N. Johnson and W. Wang, New J. Chem. 29, 1318 (2005)
12 M. Ide, Y. Maeda and H. Kitano, J. Phys. Chem. B 101, 7022 (1997)
13 (a) Y. Kameda, K. Sugawara, T. Usuki and O. Uemura, Bull. Chem. Soc. Jpn. 76, 935 (2003); (b)
Y. Kameda, M. Sasaki, M. Yaegashi, K. Tsuji, S. Oomori, S. Hino and T. Usuki, J. Solut. Chem.
33(6-7), 733 (2004)
14 M. W. Ellzy, J. O. Jensen, H. F. Hameka and J. G. Kay, Spectrochim. Acta A 59(11), 2619 (2003)
15 D. Hetch, L. Tadesse and L. Walters, J. Am. Chem. Soc. 115, 3336 (1993)
16 W. B. Fischer and H.-H. Eysel, J. Mol. Struct. 415, 249 (1997)
17 E. Tajkhorshid, K. J. Jalkanen and S. Suhai, J. Phys. Chem. B 102, 5899 (1998)
18 K. Frimand, H. Bohr, K. J. Jalkanen and S. Suhai, Chem. Phys. 255, 165 (2000)
19 O. Kikuchi, T. Watanabe, Y. Ogawa, H. Takase and O. Takahashi, J. Phys. Org. Chem. 10, 145
(1997)
20 E. Lindahl, B. Hess and D. van der Spoel, J. Mol. Model 7, 306 (2001)
21 H. J. C. Berendsen, J. P. Postma, W. F. van Gunsteren and J. Hermans, in Intermolecular Forces,
20
8/4/2019 L -alanine
http://slidepdf.com/reader/full/l-alanine 21/22
Edited by B. Pullman, Reidel, Dordrecht (1981)
22 H. J. C. Berendsen, J. P. M. Postma, W. F. van Gunsteren, A. DiNola and J. R. Haak, J. Chem.
Phys. 81, 3684 (1984)
23
(a) T. Darden, D. York and L. Pedersen J. Chem. Phys. 98, 10089 (1993); (b) U. Essman, L.Perera, M. L. Berkowitz, T. Darden, H. Lee and L. G. Pedersen, J. Chem. Phys. 103, 8577 (1995)
24 (a) P. Hohenberg and W. Kohn, Phys. Rev. 136, 864 (1964); (b) W. Kohn, L. J. Sham, Phys. Rev.
140, 1133 (1965)
25 (a) J. M. Soler, E. Artacho, J. D. Gale, A. Gárcia, J. Junquera, P. Ordejón and D. Sánchez-Portal,
J. Phys.: Condens. Matter 14, 2745 (2002); (b) P. Ordejón, E. Artacho and J. M. Soler, Phys. Rev.
B 53, 10441 (1996)
26 J. P. Perdew, K. Burke and M. Ernzerhof, Phys. Rev. Lett. 77, 3865 (1996)
27 J. Junquera, O. Paz, D. Sánchez-Portal and E. Artacho, Phys. Rev. B 64, 235111 (2001)
28 J. Ireta, J. Neugebauer and M. Schefler, J. Phys. Chem. A 108, 5692 (2004)
29 M. Ernzerhof and G. Scuseria, J. Chem. Phys. 110(11), 5029 (1999)
30 C. Adamo and V. Barone, J. Chem. Phys. 110(13), 6158 (1999)
31 (a) N. Troullier and J. L. Martins, Phys. Rev. B 43, 1993 (1991); (b) L. Kleinman and D. M.
Bylander, Phys. Rev. Lett. 48, 1425 (1982)
32 S. C. Harvey, R. K.-Z. Tan and T. E. Cheatham III, J. Comp. Chem. 19(7), 726 (1998)
33 W. Humphrey, A. Dalke and Schulten, K, J. Molec. Graphics 14, 33 (1996)
34 (a) D. Sánchez-Portal, P. Ordejón, E. Canadell, Struct. Bond. 113, 103 (2004), and references
therein; (b) I. Degtyarenko, R. M. Nieminen and C. Rovira, Biophys. J. 91(6), 2024 (2006)
35 F. H. Allen, Acta Cryst. B58, 380 (2002); (http://www.ccdc.cam.ac.uk/)
36 As a geometrical criteria were taken corresponding dihedral angles NCαC'O, HαCαNH and
HαCαCβH.
37 The dihedrals O1-C'-Cα-Hα, H5-Cβ-Cα-Hα and H3
-N-Cα-Hα are not taken into account
38 Here and after we employ geometrical criteria to assign a hydrogen bond. Bond length is within
hydration radius and angle (donor - H atom - acceptor) is more than 130 degrees. Hydration radii
are 2.37 Å and 3.04 for (N)H3-Ow and (C)O2-Ow respectively.39
21
8/4/2019 L -alanine
http://slidepdf.com/reader/full/l-alanine 22/22
39 I. M. Degtyarenko, K. J. Jalkanen, A. A. Gurtovenko and R. M. Nieminen, J. Phys. Chem. B doi:
10.1021/jp0676991
40 J. Garen, M. J. Field, G. Kneller, M. Karplus and J. C. Smith, J. Chim. Phys. 88, 2587 (1991)
41
(a) S. Blanco, A. Lessari, J. C. Lopez and J. L Alonso, J. Am. Chem. Soc. 126, 11675 (2004); (b)A. G. Császár J. Phys. Chem. 100, 3541 (1996), and references therein
42 Charge densities plotting in real space has been perfomed with Denchar utility written by J.
Junquera and P. Ordejón and distributed together with SIESTA package.
43 M. D. Newton, G. A Jeffrey and S. Takagi, J. Am. Chem. Soc. 101(8), 1997 (1979)
44 The rationale for this is that CO2- groups prefer to accept four hydrogen bonds, but NH3
+ group has
only three protons. Some sharing takes place to satisfy the strong potential of C -=O groups as
hydrogen bond acceptor. See Ref. 45 pp. 22-26 for discussion and G. A. Jeffrey, J. Mitra, J. Am.
Chem. Soc. 106(19), 5546 (1984)
45 G. A. Jeffrey, An introduction to Hydrogen Bonding, Oxford, New York (1997)
46 The linear bonds are structurally significant because of the dipole-monopole and dipole-dipole
contributions to the electrostatic energy, which has the maximum at 180 and vanishes at 90
degrees.
47 J. D. Bernal, Z. Kristallogr. 78, 363 (1931)
48 H. A. Levy and R. B. Corey J. Am. Chem. Soc. 63, 2095 (1941)