Ab initio conformational analysis of alanine

Cao, Man; Newton, Susan Q.; Pranata, Julianto; Schäfer, Lothar

doi:10.1016/0166-1280(94)03943-f

Cited by 65 publications

(57 citation statements)

References 29 publications

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“…First, the G3MP2 global minima for neutral amino acids match structures inferred from microwave and other gas-phase spectrometric methods. The examples include glycine [3,5], alanine [11][12][13][14][15], isoleucine [16], leucine [17], serine [15,18], tryptophan [19], and valine [20,21]. However, there are some examples in the literature of global minima identified with the B3LYP functional that do not match experimental structures (although many do match).…”

Section: Assessment Of Theoretical Approachmentioning

confidence: 99%

A reevaluation of computed proton affinities for the common α-amino acids

Gronert

Simpson

Conner

2009

J. Am. Soc. Mass Spectrom.

109

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The proton affinities of the 20 common amino acids have been computed at the G3MP2 level using structures derived from broad conformational searches at a variety of levels including G3MP2. In some cases, the conformational surveys identified more stable species than had been used in previous studies of proton affinities, though the differences in energy are sometimes rather small. The present values are likely the most reliable measure of amino acid proton affinities in the gas phase. An analysis of differences between these values and those obtained experimentally via the kinetic method indicates that the extraction of proton affinities from kinetic method data can potentially lead to large errors linked to the estimation of relative protonation entropies. . As noted by these authors, there is substantial variation in the experimental values reported for these species. The origin of this variability is most likely related to the difficulties of completing thermodynamic measurements in the gas phase on materials with low volatility. As a result, many of the experimental values are from kinetic method measurements and are subject to errors associated with the kinetic method approximation (as well as cumulative errors associated with the development of ladder-type scales). Therefore, in these systems, high-level computational work offers an attractive means of resolving differences in the various experimental measurements.While working on a computational study of the conformational preferences of neutral, gaseous amino acids, we realized that it would be possible to improve on the accuracy of the proton affinities reported by Paizs and coworkers. First, their computational strategy relied on the B3LYP approach to identify global minima and, often, they identified conformations for the neutral amino acids that did not match with those reported in previous computational and experimental studies (apparently in some cases this was the result of the search strategy and in others the computational method). For example, Paizs and coworkers concluded that glycine prefers a structure with an internal hydrogen bond between the carboxylic acid and amine groups. Highlevel ab initio, other B3LYP data [2], and experimental data suggest a structure with a syn carboxyl group and a weak interaction between the amine hydrogens and the carbonyl [3][4][5]. While the energetic impact of this problem is generally minor, we feel it is important to report values based on the most appropriate conformations that can be obtained within a computational method. For the protonated amino acids, this problem is less pronounced because the hydrogen bonding interactions are much stronger; most computational methods identify similar structures as the global minimum. Second, values reported by Paizs and coworkers are at 0 K. We have added a correction for the thermal energy of a proton, which amounts to about 1.5 kcal/mol at 298 K, as well as for the neutral and protonated amino acid. Although these corrections cancel to some extent and while the ge...

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Section: Assessment Of Theoretical Approachmentioning

confidence: 99%

A reevaluation of computed proton affinities for the common α-amino acids

Gronert

Simpson

Conner

2009

J. Am. Soc. Mass Spectrom.

109

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“…Several conformations were already optimized and studied in the literature [27,48,[57][58][59][60][61][62][63][64][65][66][67][68][69][70][71][72][73][74][75][76] and are referenced in the Table. The species labeled S-Thr corresponds to a threonine where the chirality of the C β (which is R in the natural Thr) is reversed. By comparing Thr and S-Thr, it turns out that the CF1 conformations present the same hydrogen-bonding patterns while the CF2 ones are permuted: the H-bonding pattern of CF2 (1) in Thr corresponds to that of CF2 (2) in S-Thr and vice-versa.…”

Section: Relative Stability Of the Neutral Conformersmentioning

confidence: 99%

Vertical Ionization Energies of α-L-Amino Acids as a Function of Their Conformation: an Ab Initio Study

Dehareng

Dive

2004

IJMS

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Vertical ionization energies (IE) as a function of the conformation are determined at the quantum chemistry level for eighteen α-L-amino acids. Geometry optimization of the neutrals are performed within the Density Functional Theory (DFT) framework using the hybrid method B3LYP and the 6-31G**(5d) basis set. Few comparisons are made with wave-function-based ab initio correlated methods like MP2, QCISD or CCSD. For each amino acid, several conformations are considered that lie in the range 10-15 kJ/mol by reference to the more stable one. Their IE are calculated using the Outer-Valence-Green's-Functions (OVGF) method at the neutrals' geometry. Few comparisons are made with MP2 and QCISD IE. It turns out that the OVGF results are satisfactory but an uncertainty relative to the most stable conformer at the B3LYP level persists. Moreover, the value of the IE can largely depend on the conformation due to the fact that the ionized molecular orbitals (MO) can change a lot as a function of the nuclear structure.

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“…As the building blocks of proteins, they are molecules of biological and biochemical interest: understanding their physical behavior is an essential first step in unravelling both the biological functionality of proteins, and in expressing this functionality in terms of quantum mechanics. A body of ab initio work concerning amino acids does exist, [7][8][9][10][11] but this is concerned, in the main, with conformational analyses of only a small subset of these molecules. In this work, we apply DFPT to the amino acids alanine, leucine, isoleucine, and valine, in order to determine their dielectric and vibrational properties.…”

Section: Introductionmentioning

confidence: 99%

Dielectric and vibrational properties of amino acids

Tulip

Clark

2004

The Journal of Chemical Physics

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The full-text may be used and/or reproduced, and given to third parties in any format or medium, without prior permission or charge, for personal research or study, educational, or not-for-prot purposes provided that:• a full bibliographic reference is made to the original source • a link is made to the metadata record in DRO • the full-text is not changed in any way The full-text must not be sold in any format or medium without the formal permission of the copyright holders.Please consult the full DRO policy for further details. We calculate polarizability tensors and normal mode frequencies for the amino acids alanine, leucine, isoleucine, and valine using density functional perturbation theory implemented within the plane wave pseudopotential framework. It is found that the behavior of the electron density under external fields depends to a large extent on the geometrical structure of the molecule in question, rather than simply on the constituent functional groups. The normal modes are able to help distinguish between the different types of intramolecular hydrogen bonding present, and help to explain why leucine is found in the zwitterionic form for the gaseous phase. Calculated IR spectra show a marked difference between those obtained for zwitterionic and nonzwitterionic molecules. These differences can be attributed to the different chemical and hydrogen bonds present. Effective dynamical charges are calculated, and compared to atomic charges obtained from Mulliken population analysis. It is found that disagreement exists, largely due to the differing origins of these quantities.

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Ab initio conformational analysis of alanine

Cited by 65 publications

References 29 publications

A reevaluation of computed proton affinities for the common α-amino acids

A reevaluation of computed proton affinities for the common α-amino acids

Vertical Ionization Energies of α-L-Amino Acids as a Function of Their Conformation: an Ab Initio Study

Dielectric and vibrational properties of amino acids

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