Analytical potentials from "ab initio" computations for the interaction between biomolecules. 1. Water with amino acids

Clementi, E.; Cavallone, F.; Scordamaglia, R.

doi:10.1021/ja00459a001

Cited by 262 publications

(69 citation statements)

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“…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. 33 Discrete solvation with a small number of waters has also been explored.…”

Section: 68mentioning

confidence: 75%

“…At this highest level of theory, Z5-1 is the global minimum, and Z5-2 (3.9 kcal/ mol higher in energy than Z5-1) is also lower in energy than any N isomer. In these two Z isomers, the water molecules interact strongly with both alanine charge centers, NH 3 + and COO -. This leads to the formation of water bridges that connect the two charge centers, as noticed previously for glycine.…”

Section: Alanine(h 2 O) 5 (Figure 8)mentioning

confidence: 99%

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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: 75%

Section: Alanine(h 2 O) 5 (Figure 8)mentioning

confidence: 99%

Alanine: Then There Was Water

Mullin

Gordon

2009

J. Phys. Chem. B

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“…5 But, all the questions discussed in their papers only limited to the interactions between single cation ͑such as H ϩ or Na ϩ ͒ and single active site of a glycine molecule. As has been determined using experimental 6 and theoretical [7][8][9][10][11][12][13][14][15][16][17][18] methods, it is well known that the glycine has many conformers. For each glycine conformer, there are three active sites-N3, O4, and O5 ͑see I in Fig.…”

Section: Introductionmentioning

confidence: 99%

Structure and property of glycine’s derivatives bound by multications (H+, Li+, and Na+): A theoretical study

Han

2002

The Journal of Chemical Physics

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The calculations using several different methods (B3P86, MP2, MP3, MP4SDQ, and CCSD) and basis sets [6-31G*, 6-31+G*, and 6-311+G(2df,2pd)] have been first performed for 15 glycine derivatives (one Gly–2H+, one Gly–3H+, five Gly–H+Li+ isomers, three Gly–H+Na+ isomers, three Gly–Li+Na+ isomers, and two Gly–2Na+ isomers) formed by multications (H+, Li+ or Na+) and different active sites of a glycine molecule. These calculations yield accurate geometric structures, relative energies, bond energies, vibrational frequencies, infrared intensities, and charge distributions. The comparisons of relative energy for each isomer show that both Gly–2H+ and Gly–3H+ derived from the most stable neutral glycine hold the lowest energies among their respective corresponding isomers. For the Gly–2H+, two protons are, respectively, bound to the amino nitrogen and the syn carbonyl oxygen of the most stable neutral glycine molecule. On the basis of the Gly–2H+, the derivative Gly–3H+ can be generated when the third proton binds to the hydroxyl oxygen. For five Gly–H+Li+ isomers, three Gly–H+Na+ isomers, three Gly–Li+Na+ isomers, and two Gly–2Na+ isomers, each of their corresponding ground state possesses the structure with the heavier cation coordinated to carbonyl oxygen and the lighter one to the anti-amino nitrogen of another kinds of neutral glycine molecule. The bond energies first reveal that some of these derivatives must surmount an activation energy barrier in the course of some cation (proton) dissociating from it. The origin of these barriers are investigated and discussed. Finally characteristic frequency calculations imply that the study is very important in the search of the glycine derivatives by rotational spectroscopy, or for the identification of their isomers by their infrared bands.

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“…Indeed, for the isolated molecule of serine, like for other simple amino acids, it has been shown that the zwitterion is only obtained as a minimum energy configuration when the calculations are performed at a very low level of theory, as a result of an inadequate description of the electronic structure of the system [27][28][29]. Second, the methods available for the indispensable consideration of the solvent have not yet proved to provide results with the desired accuracy: in this case, continuum methods do not seem to be appropriate, considering the essentially specific nature of the water/serine interactions [30][31][32], and severe constraints must still be applied to use solvent discrete models to treat a system of this size, strongly limiting their predictive capabilities. In the analysis of the Raman spectra of serine and 3,3-dideutero-serine in aqueous solution presented below, a strictly empirical approach is thus used.…”

Section: Resultsmentioning

confidence: 99%