Correlation of structure and vibrational spectra of the zwitterion l-alanine in the presence of water: an experimental and density functional analysis

Ellzy, Michael W.; Jensen, James O.; Hameka, Hendrik F.; Kay, Jack G.

doi:10.1016/s1386-1425(03)00036-2

Cited by 41 publications

(33 citation statements)

References 15 publications

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“…39 Ellzy computed structures of alanine with four waters and compared them to vibrational circular dichroism data. 40 Ellzy's lowest energy structure is not the global minimum found by Chuchev. However, agreement with vibrational circular dichroism does imply that there is a population of an approximately energetically degenerate state near the minimum.…”

Section: 68mentioning

confidence: 88%

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: 88%

Alanine: Then There Was Water

Mullin

Gordon

2009

J. Phys. Chem. B

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“…The effects of water on amino acid structure have been investigated using theory [48 -52], spectroscopy [52][53][54][55], and by blackbody infrared radiative dissociation (BIRD) [45,56,57]. Calculations indicate that two water molecules can make the zwitterion form of glycine a local minimum on the potential energy surface, but this structure is still ϳ12 kcal/mol higher in energy than the nonzwitterion [48].…”

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confidence: 99%

Binding energies of water to lithiated valine: Formation of solution-phase structure in vacuo

Lemoff

Williams

2004

J. Am. Soc. Mass Spectrom.

100

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Dissociation kinetics for loss of a water molecule from hydrated ions of lithiated valine, alanine ethyl ester and betaine are determined using blackbody infrared radiative dissociation at temperatures between Ϫ60 and 110°C. From master equation modeling of these data, values of the threshold dissociation energy are obtained for clusters containing one through three water molecules. By comparing the values for valine with its two isomers, one a model for the nonzwitterion structure, the other a model for the zwitterion structure, information about the structure of valine in these hydrated clusters is inferred. Structures, relative energies, and water binding energies for these ions are also calculated at the B3LYP/6-31ϩϩG** level of theory. With one water molecule, both experiment and theory indicate that valine is not a zwitterion and that the lithium ion coordinates with the amino nitrogen and the carbonyl oxygen (NO coordinated) and the water molecule interacts directly with the lithium ion. With two water molecules, the zwitterion and nonzwitterion structures are nearly isoenergetic, but the experiment clearly indicates a NO-coordinated nonzwitterion structure. With three water molecules, both the experimental data and theory indicate that the lithium ion binds to the carboxylate group of valine, i.e., valine is zwitterionic with three water molecules. The agreement between the experimentally determined and calculated binding energies is good for all the clusters, with deviations of Յ 0.12 eV. M olecular structure in solution depends on both the intrinsic properties of the molecule and on the effects of the surrounding solvent molecules. Exclusion of water from the interior of proteins influences protein folding and conformation. Similarly, lipid bilayer formation is due to differences in water interaction with the polar and hydrophobic ends of the lipid molecules. Gas-phase experiments make possible investigation of the intrinsic properties of the molecule. Differences between gas-phase and solution-phase structure can be attributed to solvent effects. Studies of gas-phase peptides indicate that ␣-helices can be stable in the absence of water and indicate that the propensity for helix formation for some amino acids differs in the gas phase and in solution [1,2]. For example, peptides with high valine content have a higher helix-forming propensity than their alanine analogues in the gas phase, but just the opposite is observed in aqueous solution [1].In the condensed phase, specific water molecules can play an important role in molecular structure. Such specific water molecules are often observed in crystal structures of proteins and other molecules. Evidence for specific water has been reported by Jarrold and coworkers for the molecule BPTI which tightly binds one water molecule in the gas phase [3,4]. Magic hydration numbers for gramicidin S at 8, 11, and 14 water molecules suggest stable solvation shells around the doubly protonated gas-phase ion [5], while a magic hydration number of 40 water molecules h...

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“…[2][3][4][5][6][7][8] There are various investigations reporting structure, stability and solvent effect on amino acid. 2,[6][7][8][9][10][11][12][13][14][15][16][17][18][19][20][21][22][23] The dielectric relaxation in aqueous solutions of some amino acids has also been reported earlier. [24][25][26][27][28][29][30][31][32][33][34][35][36][37] However, to the best of our knowledge, the dielectric relaxation in aqueous solutions of tryptophan has not been studied so far.…”

Section: Introductionmentioning

confidence: 87%

Microwave Dielectric Characterization of Aqueous Solutions of Tryptophan

2008

Journal of the Korean Chemical Society

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ABSTRACT. This paper describes dielectric relaxation in aqueous solutions of tryptophan at different temperatures and concentrations. Time Domain Reflectometry in reflection mode has been used to measure the complex reflection coefficient ρ*(ω) in the frequency range of 10 MHz to 20 GHz. Bilinear calibration method has been used to obtain complex permittivity spectra ε*(ω) from the complex reflection coefficient. Dielectric parameters i.e. static permittivity and relaxation time were obtained from the complex permittivity spectra using nonlinear least squares fit method. From the values of relaxation time, thermodynamic parameters were obtained. The values of dielectric relaxation parameters increase with an increase in molar concentration of Tryptophan.

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Correlation of structure and vibrational spectra of the zwitterion l-alanine in the presence of water: an experimental and density functional analysis

Cited by 41 publications

References 15 publications

Alanine: Then There Was Water

Alanine: Then There Was Water

Binding energies of water to lithiated valine: Formation of solution-phase structure in vacuo

Microwave Dielectric Characterization of Aqueous Solutions of Tryptophan

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