Structures, vibrational absorption and vibrational circular dichroism spectra of L-alanine in aqueous solution: a density functional theory and RHF study

Frimand, Kenneth; Bohr, Henrik; Jalkanen, K. J.; Suhai, Sándor

doi:10.1016/s0301-0104(00)00069-0

Cited by 89 publications

(120 citation statements)

References 47 publications

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“…The unrealistically high amide I frequencies obtained at the HF level (Figure 3a) are partially corrected in the DFT calculations, which results in a large frequency shift (down), as is known and was expected from earlier work. 28,[72][73][74][75] An increase in polarization from 6-31G* (comparison not shown) to 6-31G** with the BPW91 functional had very little impact on the spectra in this region, for example, it caused minor changes in separation of the in-phase and outof-phase amide modes. However, adding diffuse functions, i.e., 6-31++G** (Figure 3c), does have a significant impact, lowering the amide I frequencies to a range close to that which is observed experimentally yet leaving the amide II and III about the same.…”

Section: Resultsmentioning

confidence: 97%

Ab Initio Modeling of Amide I Coupling in Antiparallel β-Sheets and the Effect of ¹³C Isotopic Labeling on Infrared Spectra

2005

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Isotopic substitution with 13 C on the amide CdO has become an important means of determining localized structural information about peptide conformations with vibrational spectroscopy. Various approaches to the modeling of the interactions between labeled amide sites, specifically for antiparallel two-stranded, -forming peptides, were investigated, including different force fields [dipole-dipole interaction vs density functional theory (DFT) treatments], basis sets, and sizes of model peptides used for ab initio calculations, as well as employing models of solvation. For these -sheet systems the effect of the relative positions of the 13 C isotopic labels in each strand on their infrared spectra was investigated. The results suggest that the interaction between labeled amide groups in different strands can be used as an indicator of local -structure formation, because coupling between close-lying CdO groups on opposing chains leads to the largest frequency shifts, yet some alternate placements can lead to intensity enhancements. The basic character of the coupling interaction between labeled modes on opposing strands is independent of changes in peptide length, water solvent environment, twisting of the sheet structure, and basis set used in the calculations, although the absolute frequencies and detailed coupling magnitudes change under each of these perturbations. In particular, two strands of three amides each contain the basic interactions needed to simulate larger sheets, with the only exception that the CdO groups forming H-bonded rings at the termini can yield different coupling values than central ones of the same structure. Spectral frequencies and intensities were modeled ab initio by DFT primarily at the BPW91/ 6-31G** level for pairs of three, four, and six amide strands. Comparison to predictions of a classical coupled oscillator model show qualitative but not quantitative agreement with these DFT results. IntroductionVibrational spectra, IR and Raman, have long been used to determine average secondary structure characteristics in peptides and proteins. 1-4 Like electronic circular dichroic (ECD) structural studies, the limited resolution of vibrational spectra normally provides sequence-averaged structural information in comparison to the localized details derivable from NMR and X-ray diffraction. Since optical spectra can provide inherently fast measures of structure and are generally applicable to all protein and peptide systems, increasing their information content is of wide interest. Vibrational spectra, in contrast to electronic spectra, have distinctive frequency shifts due to isotopic variation, which can be used to give site-specific characteristics to certain bands for selectively labeled peptides. In the past decade a number of studies have appeared where isotopic substitution was used to obtain better structural insight with IR spectra. [5][6][7][8][9][10][11][12][13][14][15][16][17][18][19][20][21] Isotopic labeling of the amide group has an important impact on vibrational spectra, be...

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Section: Resultsmentioning

confidence: 97%

Ab Initio Modeling of Amide I Coupling in Antiparallel β-Sheets and the Effect of ¹³C Isotopic Labeling on Infrared Spectra

2005

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“…16,[19][20][21][22][23][24] The zwitterionic form is not stable in vacuum and explicit or implicit solvent models have to be involved in a consistent modeling. 25 Most of observed vibrational transitions have been assigned in detail on the basis of a harmonic analysis of vibrational spectra, although some features in the spectra could not be explained in full.…”

Section: Introductionmentioning

confidence: 99%

Conformational Flexibility of l-Alanine Zwitterion Determines Shapes of Raman and Raman Optical Activity Spectral Bands

et al. 2006

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Detailed analysis of Raman and Raman optical activity (ROA) of L-alanine zwitterion (ALAZW) revealed that shapes of the spectral bands are to a large extent determined by the rotation of the NH 3 + , CO 2 -, and CH 3 groups. Aqueous solution ALAZW spectra were measured down to 100 cm -1 and compared to complex simulations based on ab initio (B3LYP/CPCM/6-31++G**) computations of molecular energies and spectral parameters. The bands exhibit different sensitivities to the motion of the rotating group; typically, for more susceptible bands the Raman signal becomes broader and the ROA intensity decreases. When these dynamical factors are taken into account in Boltzmann averaging of conformer contributions, simulated spectra not only better agree with the experiment, but shapes of the rotational potentials can be estimated. Effects of the molecular flexibility could be also demonstrated on differences in Raman spectra of the solution, crystalline, and glass (gellike) solid states of ALAZW. Experimental Raman and ROA spectra of four model dipeptides of different rigidities (Ala-Pro, Pro-Ala, Pro-Gly, and Gly-Pro) indicate that the broadening of spectral lines can be used as a general site-specific indicator of molecular rigidity or flexibility.

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“…The effect of solvation has to be included in simulations to achieve physical meaningful results 30 , especially for vibrational spectra [31][32][33][34][35][36] . Nevertheless, the trialanine zwitterion in aqueous solution still remains poorly studied.…”

Section: Research Articlementioning

confidence: 99%

Geometry Optimization and Stability of Hydrated Trialanine: FMO/EFP Study

2013

Chem Sci Trans

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Abstract:The fragment molecular orbital (FMO) method interfaced with effective fragment potentials (EFP), denoted by FMO/EFP, was developed and applied to polypeptides solvated in water. The structures of neutral and zwitterionic trialanine immersed in water layers of 3.0, 3.5, 4.0, 4.5 and 5.0 Å were investigated by performing FMO/EFP geometry optimizations at the RHF/cc-pVDZ level of theory. Using the optimized geometries, the relative stability of the hydrated zwitterionic and neutral structures is discussed structurally and in terms of energetics at the second-order Møller-Plesset theory (MP2)/cc-pVDZ level.

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Structures, vibrational absorption and vibrational circular dichroism spectra of L-alanine in aqueous solution: a density functional theory and RHF study

Cited by 89 publications

References 47 publications

Ab Initio Modeling of Amide I Coupling in Antiparallel β-Sheets and the Effect of ¹³C Isotopic Labeling on Infrared Spectra

Ab Initio Modeling of Amide I Coupling in Antiparallel β-Sheets and the Effect of ¹³C Isotopic Labeling on Infrared Spectra

Conformational Flexibility of l-Alanine Zwitterion Determines Shapes of Raman and Raman Optical Activity Spectral Bands

Geometry Optimization and Stability of Hydrated Trialanine: FMO/EFP Study

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Structures, vibrational absorption and vibrational circular dichroism spectra of L-alanine in aqueous solution: a density functional theory and RHF study

Cited by 89 publications

References 47 publications

Ab Initio Modeling of Amide I Coupling in Antiparallel β-Sheets and the Effect of 13C Isotopic Labeling on Infrared Spectra

Ab Initio Modeling of Amide I Coupling in Antiparallel β-Sheets and the Effect of 13C Isotopic Labeling on Infrared Spectra

Conformational Flexibility of l-Alanine Zwitterion Determines Shapes of Raman and Raman Optical Activity Spectral Bands

Geometry Optimization and Stability of Hydrated Trialanine: FMO/EFP Study

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Ab Initio Modeling of Amide I Coupling in Antiparallel β-Sheets and the Effect of ¹³C Isotopic Labeling on Infrared Spectra

Ab Initio Modeling of Amide I Coupling in Antiparallel β-Sheets and the Effect of ¹³C Isotopic Labeling on Infrared Spectra