Ab Initio Mo and Monte Carlo Simulation Study on the Conformation Ofl-Alanine Zwitterion in Aqueous Solution

Kikuchi, Osamu; Watanabe, Takeharu; Ogawa, Yasushi; Takase, Hideto; Takahashi, Ohgi

doi:10.1002/(sici)1099-1395(199703)10:3<145::aid-poc885>3.0.co;2-b

Cited by 34 publications

(23 citation statements)

References 35 publications

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“…Continuum studies using PCM and DFT/B3LYP predict the Z isomer to be lower in energy than the N species. 28 MC simulations and generalized Born (GB) studies of the Z conformation with 212 explicit waters predict a nearly planar NCCOO moiety 32 for which the barrier to rotation of the COO is 5.9 kcal/mol and the NH 3 + rotation barrier is less than 1 kcal/ mol. The experimental observations show free NH 3 + rotation of glycine in spectroscopy of water-amino acid microjets.…”

Section: 68mentioning

confidence: 99%

Alanine: Then There Was Water

Mullin

Gordon

2009

J. Phys. Chem. B

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An ab initio study of the addition of successive water molecules to the amino acid l-alanine in both the nonionized (N) and zwitterionic (Z) forms are presented. The main focus is the number of waters needed to stabilize the Z form and how the solvent affects conformational preference. The solvent is modeled by ab initio electronic structure theory, the EFP (effective fragment potential) model, and the isotropic dielectric PCM (polarizable continuum method) bulk solvation techniques. The EFP discrete solvation model is used with a Monte Carlo algorithm to sample the configuration space to find the global minimum. Bridging structures are predicted to be the lowest energy Z minima after 3−5 discrete waters are included in the calculations, depending on the level of theory. Second-order perturbation theory and PCM stabilize the Z structures by ∼3−6 and 7 kcal/mol, respectively, relative to the N global minimum through the addition of up to 8 waters.Subsequently, the contributions of each are ∼1 kcal/mol relative to the N global minimum. The presence of 32 waters appears to be close to converging the N−Z enthalpy difference, ΔHN−Z. Disciplines Chemistry CommentsReprinted (adapted) February 17, 2009; ReVised Manuscript ReceiVed: April 12, 2009 An ab initio study of the addition of successive water molecules to the amino acid L-alanine in both the nonionized (N) and zwitterionic (Z) forms are presented. The main focus is the number of waters needed to stabilize the Z form and how the solvent affects conformational preference. The solvent is modeled by ab initio electronic structure theory, the EFP (effective fragment potential) model, and the isotropic dielectric PCM (polarizable continuum method) bulk solvation techniques. The EFP discrete solvation model is used with a Monte Carlo algorithm to sample the configuration space to find the global minimum. Bridging structures are predicted to be the lowest energy Z minima after 3-5 discrete waters are included in the calculations, depending on the level of theory. Second-order perturbation theory and PCM stabilize the Z structures by ∼3-6 and 7 kcal/mol, respectively, relative to the N global minimum through the addition of up to 8 waters. Subsequently, the contributions of each are ∼1 kcal/mol relative to the N global minimum. The presence of 32 waters appears to be close to converging the N-Z enthalpy difference, ∆H N-Z .

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Section: 68mentioning

confidence: 99%

Alanine: Then There Was Water

Mullin

Gordon

2009

J. Phys. Chem. B

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“…The starting point in the optimizations is the L-alanine crystalline zwitterionic structure from the neutron diffraction experiment of Lehmann et al (1972); there is no treatment of solvation effects; (b) the ROA studies of Nafie and coworkers (Nafie et al 1994;Yu et al 1995), which compare the experimental ROA spectrum of the aqueous L-alanine zwitterion with the theoretical spectrum computed using alanine geometry optimized with a 6-31G * basis set at the HF self-consistent reaction field (SCRF) level; SCRF theory simulates solvent effects with the Kirkwood-Onsager reaction field model, which places the molecule in a spherical cavity surrounded by a solvent continuum; (c) the ab initio computations of Kikuchi et al (1997), carried out at HF-SCF level with a 6-31++G * basis set and solvent effects accounted for using a variational form of the generalized Born equation; (d) the HF-SCF/6-31G * , HF-SCF/6-31++G * * and MP2/6-31++G * * optimizations by Sambrano et al (1998), which include solvation using SCRF theory; (e) the comparative structural, vibrational absorption (VA) and vibrational circular dichroism (VCD) studies of the aqueous L-alanine zwitterion by Suhai and co-workers (Tajkhorshid et al 1998;Frimand et al 2000). In these studies the alanine geometry is optimized using DFT with the B3LYP functional and a 6-31G * basis set; solvation is accounted for by SCRF theory and/or the inclusion of explicit water molecules.…”

Section: Optimized Aqueous Alanine Structuresmentioning

confidence: 99%

Electroweak Parity-Violating Energy Shifts of Amino Acids: The “Conformation Problem”

MacDermott

Hyde

et al. 2009

Orig Life Evol Biosph

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The preceding paper described our coupled-perturbed Hartree-Fock (CPHF) and density functional theory (DFT) methods of computing the parity-violating energy shift (PVES). This paper addresses the "conformation problem"-the difficulty determining which hand of amino acids in solution is favoured by the weak force due to the difficulty determining the solution conformation. We attempt to resolve this by using the methods of the preceding paper to compute the PVES of solution and gas-phase amino acid structures determined by other groups from high level optimizations that include solvation. We conclude that the conformational hypersensitivity of the PVES still precludes a definite conclusion as to the sign of the PVES of L-alanine in solution, but that there is no problem in the gas phase: the PVES of gas-phase L-alanine is decisively negative. We show that the PVES is very sensitive to certain torsion angles, but is not hypersensitive to bondlengths or bond angles. In determining structures for PVES computations, there is therefore no need for expensive full optimizations: one can just optimize the crucial torsion angles. We present new computations of gas-phase amino acids PVESs, using partial optimizations with small basis sets, and the results agree well with those from higher level techniques. In the following paper we apply these less costly techniques to larger amino acids. The "conformation problem" has led some to dismiss the PVES as the source of life's handedness, but we believe this is premature: we show here that amino acids are a special case because their favoured conformations are almost achiral.

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“…12,13,14,15,16 Furthermore, the rotational (microwave) spectra in solution are not resolved to give structural information directly, so that the structural parameters of alanine molecules in water come predominantly from computational studies. 17,18,19 As a result of this lack of experimental information regarding the alanine's structure in water, the experimental zwitterionic structure of alanine amino acid which is derived from solid state crystallographic data is often considered to be also valid for L-alanine in aqueous media. However, the origin for the L-alanine's zwitterionic form is different in crystal and in water.…”

mentioning

confidence: 99%

The Aqueous and Crystalline Forms of L-Alanine Zwitterion

Degtyarenko

Jalkanen

Gurtovenko³

et al. 2008

Jnl of Comp & Theo Nano

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The structural properties of L-alanine amino acid in aqueous solution and in crystalline phase have been studied by means of density-functional electronic-structure and molecular 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 -) group: in aqueous solution the C-O bond lengths appear to strongly correlate with the number of water molecules which form hydrogen bonds with the COOgroup. Furthermore, the hydrogen bond lengths are shorter and the hydrogen bond angles are larger for L-alanine in water as compared to crystal. Overall, our findings strongly suggest that the generally accepted approach of extending the structural information acquired from crystallographic data to a L-alanine molecule in aqueous solution should be used with caution.

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Ab Initio Mo and Monte Carlo Simulation Study on the Conformation Ofl-Alanine Zwitterion in Aqueous Solution

Cited by 34 publications

References 35 publications

Alanine: Then There Was Water

Alanine: Then There Was Water

Electroweak Parity-Violating Energy Shifts of Amino Acids: The “Conformation Problem”

The Aqueous and Crystalline Forms of L-Alanine Zwitterion

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