Amino acids and small peptides as building blocks for proteins: comparative theoretical and spectroscopic studies

Unveiling the Configurational Landscape of Carbamate: Paving the Way for Designing Functional Sequence-Defined Polymers

Carbamate is an emerging class of a polymer backbone for constructing sequence-defined, abiotic polymers. It is expected that new functional materials can be de novo designed by controlling the primary polycarbamate sequence. While amino acids have been actively studied as building blocks for protein folding and peptide self-assembly, carbamates have not been widely investigated from this perspective. Here, we combined infrared (IR), vibrational circular dichroism (VCD), and nuclear magnetic resonance (NMR) spectroscopy with density functional theory (DFT) calculations to understand the conformation of carbamate monomer units in a nonpolar, aprotic environment (chloroform). Compared with amino acid building blocks, carbamates are more rigid, presumably due to the extended delocalization of π-electrons on the backbones. Cis configurations of the amide bond can be energetically stable in carbamates, whereas peptides often assume trans configurations at low energies. This study lays an essential foundation for future developments of carbamate-based sequence-defined polymer material design.

Electromagnetic bioeffects: a multiscale molecular simulation perspective

Electromagnetic bioeffects remain an enigma from both the experimental and theoretical perspectives despite the ubiquitous presence of related technologies in contemporary life. Multiscale computational modelling can provide valuable insights into biochemical systems and predict how they will be perturbed by external stimuli. At a microscopic level, it can be used to determine what (sub)molecular scale reactions various stimuli might induce; at a macroscopic level, it can be used to examine how these changes affect dynamic behaviour of essential molecules within the crowded biomolecular milieu in living tissues. In this review, we summarise and evaluate recent computational studies that examined the impact of externally applied electric and electromagnetic fields on biologically relevant molecular systems. First, we briefly outline the various methodological approaches that have been employed to study static and oscillating field effects across different time and length scales. The practical value of such modelling is then illustrated through representative case-studies that showcase the diverse effects of electric and electromagnetic field on the main physiological solvent - water, and the essential biomolecules - DNA, proteins, lipids, as well as some novel biomedically relevant nanomaterials. The implications and relevance of the theoretical multiscale modelling to practical applications in therapeutic medicine are also discussed. Finally, we summarise ongoing challenges and potential opportunities for theoretical modelling to advance the current understanding of electromagnetic bioeffects for their modulation and/or beneficial exploitation in biomedicine and industry.

Tracking the Amide I and αCOO- Terminal ν(C=O) Raman Bands in a Family of l-Glutamic Acid-Containing Peptide Fragments: A Raman and DFT Study

The E-hook of β-tubulin plays instrumental roles in cytoskeletal regulation and function. The last six C-terminal residues of the βII isotype, a peptide of amino acid sequence EGEDEA, extend from the microtubule surface and have eluded characterization with classic X-ray crystallographic techniques. The band position of the characteristic amide I vibration of small peptide fragments is heavily dependent on the length of the peptide chain, the extent of intramolecular hydrogen bonding, and the overall polarity of the fragment. The dependence of the E residue's amide I ν(C=O) and the αCOO- terminal ν(C=O) bands on the neighboring side chain, the length of the peptide fragment, and the extent of intramolecular hydrogen bonding in the structure are investigated here via the EGEDEA peptide. The hexapeptide is broken down into fragments increasing in size from dipeptides to hexapeptides, including EG, ED, EA, EGE, EDE, DEA, EGED, EDEA, EGEDE, GEDEA, and, finally, EGEDEA, which are investigated with experimental Raman spectroscopy and density functional theory (DFT) computations to model the zwitterionic crystalline solids (in vacuo). The molecular geometries and Boltzmann sum of the simulated Raman spectra for a set of energetic minima corresponding to each peptide fragment are computed with full geometry optimizations and corresponding harmonic vibrational frequency computations at the B3LYP/6-311++G(2df,2pd) level of theory. In absence of the crystal structure, geometry sampling is performed to approximate solid phase behavior. Natural bond order (NBO) analyses are performed on each energetic minimum to quantify the magnitude of the intramolecular hydrogen bonds. The extent of the intramolecular charge transfer is dependent on the overall polarity of the fragment considered, with larger and more polar fragments exhibiting the greatest extent of intramolecular charge transfer. A steady blue shift arises when considering the amide I band position moving linearly from ED to EDE to EDEA to GEDEA and, finally, to EGEDEA. However, little variation is observed in the αCOO- ν(C=O) band position in this family of fragments.

Conformational preferences of cationic β-peptide in water studied by CCSD(T), MP2, and DFT methods

The conformational preferences of the cationic nylon-3 βNM [(3R,4)-diaminobutanoic acid, dAba] dipeptide in water were explored as the first step to understand the mode of action of polymers of βNM against phylogenetically diverse and intrinsically drug-resistant pathogenic fungi. The CCSD(T), MP2, M06-2X, ωB97X-D, B2PLYP-D3BJ, and DSD-PBEP86-D3BJ levels of theory with various basis sets were assessed for relative energies of the 45 local minima of the cationic Ac-dAba-NHMe located at the SMD M06-2X/6-31+G(d) level of theory in water against the benchmark CCSD(T)/CBS-limit energies in water. The best performance was obtained at the double-hybrid DSD-PBEP86-D3BJ/def2-QZVP level of theory with RMSD = 0.12 kcal/mol in water. The M06-2X/def2-QZVP level of theory predicted reasonably the conformational preference with RMSD = 0.38 kcal/mol in water and may be an alternative level of theory with marginal deviations for the calculation of conformational energies of relatively longer cationic peptides in water. In particular, the H₁₄–helical structures appeared to be the most feasible conformations for the cationic Ac-dAba-NHMe populated at 48–64% by relative free energies in water. The hexamer built from the H₁₄–structure of the cationic Ac-dAba-NHMe adopted a left-handed 3₁₄-helix, which has a slightly narrower radius and a longer rise than the regular 3₁₄-helix of β-peptides. Hence, the 3₁₄-helices of oligomers or polymers of the cationic dAba residues are expected to be the active conformation to exhibit the ability to bridge between charged lipid head groups that might cause a local depression or invagination of the membrane of fungi.

Electric field influence on the helical structure of peptides: insights from DFT/PCM computations

The switching of the electric field with a particular directionality could be used for the healing of misfolded proteins.

Ramachandran Plot for Alanine Dipeptide as Determined from Raman Optical Activity

Accessible values of the φ and ψ torsional angles determining peptide main chain conformation are traditionally displayed in the form of Ramachandran plots. The number of experimental methods making it possible to determine such conformational distribution is limited. In the present study, Raman optical activity (ROA) spectra of Ac-Ala-NHMe were measured and fit by theoretical curves. This revealed the most favored conformers and a large part of the potential energy surface (PES) of this model dipeptide. Such experimental PES compares well to quantum chemical computations, whereas molecular dynamics (MD) modeling reproduces it less faithfully. The surface shape is consistent with the temperature dependence of the spectra, as observed experimentally and predicted by MD. Despite errors associated with spectral modeling and the measurement, the results are likely to facilitate future applications of ROA spectroscopy.

QM and QM/MM simulations of proteins

Molecular dynamics simulations of biomolecules have matured into powerful tools of structural biology. In addition to the commonly used empirical force field potentials, quantum mechanical descriptions are gaining popularity for structure optimization and dynamic simulations of peptides and proteins. In this chapter, we introduce methodological developments such as the QM/MM framework and linear-scaling QM that make efficient calculations on large biomolecules possible. We identify the most common scenarios in which quantum descriptions of peptides and proteins are employed, such as structural refinement, force field development, treatment of unusual residues, and predicting spectroscopic and exited state properties. The benefits and shortcomings of QM potentials, in comparison to classical force fields, are discussed, with special emphasis on the sampling problems of protein conformational space. Finally, recent examples of QM/MM calculations in light-sensitive membrane proteins illustrate typical applications of the reviewed methods.

Presence or absence of a novel charge-transfer complex in the base-catalyzed hydrolysis of N-ethylbenzamide or ethyl benzoate

Reaction paths of base-catalyzed hydrolyses of isoelectronic substrates, Ph–C(=O)–X–Et [X = O (ethyl benzoate) and X = NH (N-ethylbenzamide)], were traced by DFT calculations. To simulate bond interchanges accompanied by proton transfers, a cluster model of Ph–C(=O)–X–Et + OH⁻(H₂O)₁₆ was employed. For X = O, three elementary processes and for X = NH four ones were obtained. The rate-determining step of X = O is the first TS (TS1, the OH⁻ addition step), while that of X = NH is TS2. TS2 of X = NH leads to a novel Mulliken charge-transfer complex, Ph–(OH)(O=)C∙∙∙N(H₂)–Et. The superiority or inferiority between the direct nucleophilic process or the general base-catalyzed process for TS1 was examined with the model Ph–C(=O)–X–Et + OH⁻(H₂O)_n, n = 3, 5, 8, 12, 16, 24 and 32. The latter process was calculated to be more favorable regardless of the number (n, except n = 3) of water molecules. The counter ion Na⁺ works unfavorably on the ester hydrolysis, particularly on TS1. A minimal model of TS1 was proposed and was found to be insensitive to n.

Reactivity and selectivity of charged phenyl radicals toward amino acids in a Fourier transform ion cyclotron resonance mass spectrometer

The reactivity of 10 charged phenyl radicals toward several amino acids was examined in the gas phase in a dual-cell Fourier transform ion cyclotron resonance mass spectrometer. All radicals abstract a hydrogen atom from the amino acids, as expected. The most electrophilic radicals (with the greatest calculated vertical electron affinities (EA) at the radical site) also react with these amino acids via NH(2) abstraction (a nonradical nucleophilic addition-elimination reaction). Both the radical (hydrogen atom abstraction) and nonradical (NH(2) abstraction) reaction efficiencies were found to increase with the electrophilicity (EA) of the radical. However, NH(2) abstraction is more strongly influenced by EA. In contrast to an earlier report, the ionization energies of the amino acids do not appear to play a general reactivity-controlling role. Studies using several partially deuterium-labeled amino acids revealed that abstraction of a hydrogen atom from the α-carbon is only preferred for glycine; for the other amino acids, a hydrogen atom is preferentially abstracted from the side chain. The electrophilicity of the radicals does not appear to have a major influence on the site from which the hydrogen atom is abstracted. Hence, the regioselectivity of hydrogen atom abstraction appears to be independent of the structure of the radical but dependent on the structure of the amino acid. Surprisingly, abstraction of two hydrogen atoms was observed for the N-(3-nitro-5-dehydrophenyl)pyridinium radical, indicating that substituents on the radical not only influence the EA of the radical but also can be involved in the reaction. In disagreement with an earlier report, proline was found to display several unprecedented reaction pathways that likely do not proceed via a radical mechanism but rather by a nucleophilic addition-elimination mechanism. Both NH(2) and (15)NH(2) groups were abstracted from lysine labeled with (15)N on the side chain, indicating that NH(2) abstraction occurs both from the amino terminus and from the side chain. Quantum chemical calculations were employed to obtain insights into some of the reaction mechanisms.

Isolated monohydrates of a model peptide chain: effect of a first water molecule on the secondary structure of a capped phenylalanine

The formation of monohydrates of capped phenylalanine model peptides, CH(3)-CO-Phe-NH(2) and CH(3)-CO-Phe-NH-CH(3), in a supersonic expansion has been investigated using laser spectroscopy and quantum chemistry methods. Conformational distributions of the monohydrates have been revealed by IR/UV double-resonance spectroscopy and their structures assigned by comparison with DFT-D calculations. A careful analysis of the final hydrate distribution together with a detailed theoretical investigation of the potential energy surface of the monohydrates demonstrates that solvation occurs from the conformational distribution of the isolated peptide monomers. The distribution of the monohydrates appears to be strongly dependent on both the initial monomer conformation (extended or folded backbone) and the solvation site initially occupied by the water molecule. The solvation processes taking place during the cooling can be categorized as follows: (a) solvation without significant structural changes of the peptide, (b) solvation inducing significant distortions of the backbone but retaining the secondary structure, and (c) solvation triggering backbone isomerizations, leading to a modification of the peptide secondary structure. It is observed that solvation by a single water molecule can fold a β-strand into a γ-turn structure (type c) or induce a significant opening of a γ-turn characterized by an elongated C(7) hydrogen bond (type b). These structural changes can be considered as a first step toward the polyproline II condensed-phase structure, illustrating the role played by the very first water molecule in the solvation process.

Quantitative Assessment of Force Fields on Both Low-Energy Conformational Basins and Transition-State Regions of the (ϕ-ψ) Space

The free energy surfaces (FESs) of alanine dipeptide are studied to illustrate a new strategy to assess the performance of classical molecular mechanics force field on the full range of the (ϕ-ψ) conformational space. The FES is obtained from metadynamics simulations with five commonly used force fields and from ab initio density functional theory calculations in both gas phase and aqueous solution. The FESs obtained at the B3LYP/6-311+G(2d,p)//B3LYP/6-31G(d,p) level of theory are validated by comparison with previously reported MP2 and LMP2 results as well as with experimentally obtained probability distribution between the C5-β (or β-PPII) and αR states. A quantitative assessment is made for each force field in three conformational basins, LeRI (C5-β-C7eq), LeRII (β2-αR), and LeRIII(αL-C7ax-αD) as well as three transition-state regions linking the above conformational basins. The performance of each force field is evaluated in terms of the average free energy of each region in comparison with that of the ab initio results. We quantify how well a force field FES matches the ab initio FES through the calculation of the standard deviation of a free energy difference map between the two FESs. The results indicate that the performance varies largely from region to region or from force field to force field. Although not one force field is able to outperform all others in all conformational areas, the OPLSAA/L force field gives the best performance overall, followed by OPLSAA and AMBER03. For the three top performers, the average free energies differ from the corresponding ab initio values from within the error range (<0.4 kcal/mol) to ∼1.5 kcal/mol for the low-energy regions and up to ∼2.0 kcal/mol for the transition-state regions. The strategy presented and the results obtained here should be useful for improving the parametrization of force fields targeting both accuracy in the energies of conformers and the transition-state barriers.

Theoretical study on conformational preferences of ribose in 2-thiouridine--the role of the 2'OH group

Conformational changes in ribose are well-known to play a significant role in biomolecular identification. The mechanism of selectivity towards C3'-endo conformation (conformer b) in ribose of 2-thiouridine has been studied using DFT (B3LYP) and MP2 methodology, together with 6-31+G(d,p) basis set. The polarity of the C2S2 bond is enhanced due to the orientation of H2' towards the S2 atoms, which leads to a difference in the corresponding bond lengths, the atomic charges and the vO2'H2' stretch vibrations in all the conformers. NBO analysis shows that charge transfer mainly occurs in the C2N3 and C2S2 orbitals. The higher stability of conformer b is attributed to its larger orbital interaction energies within the 2-thiouracil base, and total orbital interaction energies of conformer b. Our conclusion is that the distant electrostatic rather than hydrogen bonding effects between 2'OH and the S2 atoms play the dominant role in the orbital interaction, and enhance the selectivity towards the C3'-endo conformation of ribose.

A new model for mapping the peptide backbone: predicting proton chemical shifts in proteins

This paper describes a methodology that correlates experimental chemical shifts (at the alpha proton) of proteins with their geometrical data (both dihedral angles and distances) obtained from 13 representative proteins, which are taken from the Protein Data Bank (PDB) and the BioMagRes Data Bank (BMRB). To this end, the experimentally measured proton chemical shifts of simple amides have been correlated with DFT-based calculated structures, at the B3PW91/6-31G* level. This results in a series of mathematical relationships, which are extrapolated to the above-mentioned proteins giving rise to a modified equation for such skeleta. It is relevant to note that the equation is also supported by a clear comparison with NMR data of a protein beyond the chosen set, such as insulin, even with lower errors. The model also relates the dependence of chemical shifts on hydrophobic and anisotropic effects at the amino acid residues.

When is a molecule properly solvated by a continuum model or in a cluster ansatz? A first-principles simulation of alanine hydration

In order to test the validity of the cluster ansatz approach as well as of the continuum model approach and to learn about the solvation shell, we carried out first-principles molecular dynamics simulations of the alanine hydration. Our calculations contained one alanine molecule dissolved in 60 water molecules. Dipole moments of individual molecules were derived by means of maximally localized Wannier functions. We observed an average dipole moment of about 16.0 D for alanine and of about 3.3 D for water. In particular, the average water dipole moment in proximity of alanine's COO(-) group decayed continously with increasing distance, while, surprisingly, close to the CH3 and NH3+ group, the dipole moment first rose before its value dropped. In a cluster ansatz approach, we considered snapshots of alanine surrounded by different water molecule shells. The dipole moments from the cluster approaches utilizing both maximally localized Wannier functions as well as natural population analysis served to approximate the dipole moments of the total trajectory. Sufficient convergence of the cluster ansatz approach is found for either of the two solvent shells around the polar groups and one solvent shell around the apolar groups or two solvent shells around the polar groups surrounded by a dieletric continuum.

Conformational analysis of L-prolines in water

The results of the ring conformational analysis of L-proline, N-acetyl-L-proline, and trans-4-hydroxy-L-proline by NMR combined with calculations using density functional theory (DFT) and molecular dynamics (MD) are reported. Accurate values of 1H-1H J-couplings in water and other solvents have been determined. Using a two-site equilibrium model, the Cgamma-endo conformer of L-proline in water has been identified as intermediate between gammaTdelta [twist(Cgamma-endo, Cdelta-exo)] and gammaE [envelope(Cgamma-endo)] and the Cgamma-exo conformer as betaTgamma. Both conformers were equally populated at room temperature. The N-acetyl [cis-rotamer gammaTbeta(80%)/gammaE(20%) and trans-rotamer gammaTbeta(61%)/gammaE(39%)] and 4-hydroxy (gammaEpsilon) derivatives showed significant changes in both the population and the geometries of the preferred ring conformers. The combination of NMR predicted populations with the DFT B3LYP/6-311+G(2d,p)/IEFPCM calculations proved successful, resulting in fairly accurate predictions of J-couplings. Simulations using MD were mostly in favor of the two-site equilibrium model between Cgamma-endo and Cgamma-exo conformers, similar to that used for the analysis of NMR J-couplings. Various force fields examined for MD simulations failed to reproduce the ring conformational geometries and populations of L-proline in water accurately, while significantly better agreement with NMR was found for trans-N-acetyl-L-proline using GROMOS and AMBER force fields.

Solvent effects on Raman optical activity spectra calculated using the polarizable continuum model

The integral equation formulation of the polarizable continuum model (IEFPCM) has been extended to the calculation of solvent effects on vibrational Raman optical activity spectra. Gauge-origin independence of the differential scattering intensities of right and left circularly polarized light is ensured through the use of London atomic orbitals. Density functional theory (DFT) calculations have been carried out for bromochlorofluoromethane, methyloxirane, and epichlorhydrin. The results indicate that solvent effects on the ROA differential scattering intensities can be substantial, and vary in sign and magnitude for different vibrational modes. It is demonstrated that both direct and indirect effects are important in determining the total solvent effects on the ROA differential scattering intensities. Local field effects are shown to be in general small, whereas electronic nonequilibrium solvation has a profound effect on the calculated solvent effects compared to an equilibrium solvation model. For molecules with several conformations, the changes in the relative stability of the different conformers also lead to noticeable changes in the ROA spectra.

Mid- and Near-Infrared Spectra of Conformers of H-Pro-Trp-OH

We present near- and mid-infrared-UV double resonance spectra of the natural dipeptide H-Pro-Trp-OH. Two conformers are present in the supersonic expansion: a stretched conformer with fully extended backbone and a folded conformer with an OH...OCpep hydrogen bond. Both conformers are stabilized by dispersion interaction between indole ring and peptide backbone and a NHpep/Nproline contact. The vibrational and conformational assignment is supported by DFT and MP2 calculations. An adequate description of the energetic order of different conformers requires the explicit inclusion of dispersion and geometry optimization at the MP2 level. We will address the very sensitivity of the observed conformations to the structure of the end groups.

Structure and dynamics of the homologous series of alanine peptides: a joint molecular dynamics/NMR study

The phi,psi backbone angle distribution of small homopolymeric model peptides is investigated by a joint molecular dynamics (MD) simulation and heteronuclear NMR study. Combining the accuracy of the measured scalar coupling constants and the atomistic detail of the all-atom MD simulations with explicit solvent, the thermal populations of the peptide conformational states are determined with an uncertainty of <5 %. Trialanine samples mainly ( approximately 90%) a poly-l-proline II helix-like structure, some ( approximately 10%) beta extended structure, but no alphaR helical conformations. No significant change in the distribution of conformers is observed with increasing chain length (Ala(3) to Ala(7)). Trivaline samples all three major conformations significantly. Triglycine samples the four corner regions of the Ramachandran space and exists in a slow conformational equilibrium between the cis and trans conformation of peptide bonds. The backbone angle distribution was also studied for the segment Ala3 surrounded by either three or eight amino acids on both N- and C-termini from a sequence derived from the protein hen egg white lysozyme. While the conformational distribution of the central three alanine residues in the 9mer is similar to that for the small peptides Ala(3)-Ala(7), major differences are found for the 19mer, which significantly (30-40%) samples alphaR helical stuctures.

Critical Assessment of the Performance of Density Functional Methods for Several Atomic and Molecular Properties

The reliable prediction of molecular properties is a vital task of computational chemistry. In recent years, density functional theory (DFT) has become a popular method for calculating molecular properties for a vast array of systems varying in size from small organic molecules to large biological compounds such as proteins. In this work we assess the ability of many DFT methods to accurately determine atomic and molecular properties for small molecules containing elements commonly found in proteins, DNA, and RNA. These properties include bond lengths, bond angles, ground state vibrational frequencies, electron affinities, ionization potentials, heats of formation, hydrogen bond interaction energies, conformational energies, and reaction barrier heights. Calculations are carried out with the 3-21G*, 6-31G*, 3-21+G*, 6-31+G*, 6-31++G*, cc-pVxZ, and aug-cc-pVxZ (x=D,T) basis sets, while bond distance and bond angle calculations are also done using the cc-pVQZ and aug-cc-pVQZ basis sets. Members of the popular functional classes, namely, LSDA, GGA, meta-GGA, hybrid-GGA, and hybrid-meta-GGA, are considered in this work. For the purpose of comparison, Hartree-Fock (HF) and second order many-body perturbation (MP2) methods are also assessed in terms of their ability to determine these physical properties. Ultimately, it is observed that the split valence bases of the 6-31G variety provide accuracies similar to those of the more computationally expensive Dunning type basis sets. Another conclusion from this survey is that the hybrid-meta-GGA functionals are typically among the most accurate functionals for all of the properties examined in this work.

Proline Zwitterion Dynamics in Solution, Glass, and Crystalline State

Raman and Raman optical activity spectra of L- and D-proline zwitterionic (PROZW) forms were recorded for H(2)O and D(2)O solutions in a wide frequency range and analyzed with respect to the motion of the proline ring and rotation of the carbonyl group. The solution spectra were additionally compared to Raman scattering of glass and crystalline powder proline. Solution and glass spectral band broadenings are similar and reveal information about the extent of internal molecular motion. Two distinct but equally populated flexible forms were found in the glass and the solution. The equal population is consistent with NMR data, temperature, and concentration dependencies. The molecular flexibility is reduced significantly in the crystal, however, where only one conformer is present. Consequently, the crystal bands are narrow and exhibit minor frequency shifts. The spectra were interpreted with the aid of density functional theory computations involving both continuum and explicit solvent. A two-dimensional potential energy surface pertaining to the five-member ring puckering coordinates was constructed and used for dynamical averaging of spectral properties. Comparison of the computed and experimental bandwidths suggests that the puckering is strongly correlated with the carbonyl rotation. An averaging over these two motions produces similar results. The interpretation of the Raman experiments with the aid of the simulation techniques also indicates that the environment modulates properties of the hydrophobic part of the molecule indirectly by interacting with the ionic group. Such behavior may be important for the reactivity and biological activity of proline-containing peptides and proteins.

Biomimetic facially amphiphilic antibacterial oligomers with conformationally stiff backbones

A foldamer has been designed with a conformationally stiff backbone that is facially amphiphilic. The oligomer has excellent antimicrobial activity and was found to be 18 times more active toward bacterial cells than human red blood cells. The oligomer is built from arylamide bonds around a central 4,6-dicarboxy pyrimidine ring. The conformation was studied by X-ray crystallography and solution NMR spectroscopy. Density-functional (DFT) calculations were performed to guide the design. These calculations accurately predicted the overall conformation as well as NMR chemical shifts. Antibacterial activity was demonstrated against E. coli, a gram-negative strain, and B. subtilis, a gram-positive strain. The minimal inhibitory concentration is 0.8 microg/ml.

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

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.