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

Foldamers controlled by functional triamino acids: structural investigation of α/γ-hybrid oligopeptides

Peptide-like foldamers controlled by normal amide backbone hydrogen bonding have been extensively studied, and their folding patterns largely rely on configurational and conformational constraints induced by the steric properties of backbone substituents at appropriate positions. In contrast, opportunities to influence peptide secondary structure by functional groups forming individual hydrogen bond networks have not received much attention. Here, peptide-like foldamers consisting of alternating α,β,γ-triamino acids 3-amino-4-(aminomethyl)-2-methylpyrrolidine-3-carboxylate (AAMP) and natural amino acids glycine and alanine are reported, which were obtained by solution phase peptide synthesis. They form ordered secondary structures, which are dominated by a three-dimensional bridged triazaspiranoid-like hydrogen bond network involving the non-backbone amino groups, the backbone amide hydrogen bonds, and the relative configuration of the α,β,γ-triamino and α-amino acid building blocks. This additional stabilization leads to folding in both nonpolar organic as well as in aqueous environments. The three-dimensional arrangement of the individual foldamers is supported by X-ray crystallography, NMR spectroscopy, chiroptical methods, and molecular dynamics simulations.

Automated Quantum Chemistry-Based Calculation of Optical Rotation for Large Flexible Molecules

The calculation of optical rotation (OR, [α]_D) for nonrigid molecules was limited to small systems due to the challenging problem of generating reliable conformer ensembles, calculating accurate Boltzmann populations and the extreme sensitivity of the OR to the molecules' three-dimensional structure. Herein, we describe and release the crenso workflow for the automated computation of conformer ensembles in solution and corresponding [α]_D values for flexible molecules. A comprehensive set of 28 organic drug molecules (28-144 atoms) with experimentally determined values is used in our assessment. In all cases, the correct OR sign is obtained with an overall mean relative deviation of 72% (mean absolute deviation of 82 °[dm(g/cm³)]^-1 for experimental values in the range -160 to 287 °[dm(g/cm³)]^-1). We show that routine [α]_D computations for very flexible, biologically active molecules are both feasible and reproducible in about a day of computation time on a standard workstation computer. Furthermore, we observed that the effect of energetically higher-lying structures in the ensemble on the OR is often averaged out and that in 23 out of 28 cases, the correct OR sign is obtained by just considering only the lowest free energy conformer. In four example cases, we show that the approach can also describe the OR of pairs of flexible diastereomers properly. In summary, even very sensitive, multifactorial physicochemical properties appear reliably predictable with minimal user input from efficiently automated quantum chemical methods.

Chiroptical Properties and Conformation of Four Lasiocepsin-Related Antimicrobial Peptides: Structural Role of Disulfide Bridges

We report an investigation of the role of disulfide bridges in the 27-residue antimicrobial peptide lasiocepsin (I) containing two disulfide groups (Cys8–Cys25, Cys17–Cys27) and three its analogs lacking one (II, III) or both (IV) native disulfides. Selective alternate incorporation of one or both disulfide bridges influences symmetry, conformation and biological properties of these peptides as demonstrated in their chiroptical (particularly Raman) properties. The effect of modifying the disulfide bridge pattern on the peptide secondary structure is investigated in water and in the presence of 2,2,2-trifluoroethanol and sodium dodecyl sulphate. A combination of experimental electronic and vibrational chiroptical data shows that both disulfide groups are necessary for stabilizing lasiocepsin secondary structure. While the Cys8–Cys25 disulfide group is important for sustaining lasiocepsin tertiary structure and maintaining its biological activity, the Cys17–Cys27 disulfide bridge has a supporting function consisting in reducing peptide flexibility.

Drop coating deposition Raman spectroscopy of proteinogenic amino acids compared with their solution and crystalline state

The Raman spectra of 20 proteinogenic amino acids were recorded in the solution, glass phase (as drop coating deposition Raman (DCDR) samples) and crystalline forms in the wide spectral range of 200-3200cm^-1. The most apparent spectral differences between the Raman spectra of the crystalline forms, glass phases and aqueous solutions of amino acids were briefly discussed and described in the frame of published works. The possible density dependencies of spectral bands were noted. In some cases, a strong influence of the sample density, as well as of the organization of the water envelope, was observed. The most apparent changes were observed for Ser and Thr. Nevertheless, for the majority of amino acids, the DCDR sample form is an intermediate between the solution and crystalline forms. In contrast, aromatic amino acids have only a small sensitivity to the form of the sample. Our reference set of Raman spectra is useful for revealing discrepancies between the SERS and solid/solution spectra of amino acids. We also found that some previously published Raman spectra of polycrystalline samples resemble glassy state rather than crystalline spectra. Therefore, this reference set of spectra will find application in every branch of Raman spectroscopy where the spectra of biomolecules are collected from coatings.

Multiscale simulations for understanding the evolution and mechanism of hierarchical peptide self-assembly

Multiscale molecular simulations that combine and systematically link several hierarchies can provide insights into the evolution and dynamics of hierarchical peptide self-assembly from the molecular level to the mesoscale.

Multi-scale modeling of electronic spectra of three aromatic amino acids: importance of conformational averaging and explicit solute-solvent interactions

Electronic transitions in the ultraviolet and visible spectral range can reveal a wealth of information about biomolecular geometry and interactions, such as those involved in protein folding. However, the modeling that provides the necessary link between spectral shapes and the structure is often difficult even for seemingly simple systems. To understand as to how conformational equilibria and solute-solvent interaction influence spectral intensities, we collected absorption (UV-vis), electronic circular dichroism (ECD), and magnetic circular dichroism (MCD) spectra of phenylalanine (Phe), tyrosine (Tyr) and tryptophan (Trp) zwitterions in aqueous solutions, and compared them with quantum-chemical simulations. These aromatic amino acids provide a relatively strong signal in the accessible wavelength range. At the same time, they allow for a relatively accurate modeling. Energies and intensities of spectral bands were reproduced by the time-dependent density functional theory (TD DFT). The solvent was approximated by a continuum as well as clusters containing solvent molecules from the first hydration sphere. The ECD signal was found to be strongly dependent on molecular conformation, and the dependence was much weaker in UV-vis and MCD spectra. All spectral intensities, however, were significantly affected by the solvent approximation; especially for ECD and MCD the usual polarizable continuum solvent model did not yield satisfactory spectral shapes. On the other hand, averaging of the clusters obtained from molecular dynamics simulations provided an unprecedented agreement with the experiment. Proper modeling of the interactions with the environment thus makes the information about the molecular structure, as obtained from the electronic spectra, more accurate and reliable.

The asymmetry of (-)α-pinene as revealed from its raman optical activity spectrum

An algorithm is employed to retrieve the differential bond polarizabilities of the C-C bonds from the Raman optical activity (ROA) spectrum of (-)α-pinene. (-)α-pinene possesses two asymmetric centers (carbon atoms) and a local mirror symmetry. These differential bond polarizabilities show the characteristics of the asymmetry around the asymmetric carbons with respect to the mirror reflection. This analysis is accompanied along with the ROA mode signatures and the calculated β(G ')(2) and β(A)(2) which show the ROA coupling mechanisms involving the electric/magnetic dipoles and the electric dipole/quadrupole, respectively.

Detection of mercury-TpT dinucleotide binding by Raman spectra: a computational study

The Hg(2+) ion stabilizes the thymine-thymine mismatched base pair and provides new ways of creating various DNA structures. Recently, such T-Hg-T binding was detected by the Raman spectroscopy. In this work, detailed differences in vibrational frequencies and Raman intensity patterns in the free TpT dinucleotide and its metal-mediated complex (TpT·Hg)(2) are interpreted on the basis of quantum chemical modeling. The computations verified specific marker Raman bands indicating the effect of mercury binding to DNA. Although the B3LYP functional well-describes the Raman frequencies, a dispersion correction had to be added for all atoms including mercury to obtain realistic geometry of the (TpT·Hg)(2) dimer. Only then, the DFT complex structure agreed with those obtained with the wave function-based MP2 method. The aqueous solvent modeled as a polarizable continuum had a minor effect on the dispersion interaction, but it stabilized conformations of the sugar and phosphate parts. A generalized definition of internal coordinate force field was introduced to monitor covalent bond mechanical strengthening and weakening upon the Hg(2+) binding. Induced vibrational frequency shifts were rationalized in terms of changes in electronic structure. The simulations thus also provided reliable insight into the complex structure and stability.

Gas phase basicities of polyfunctional molecules. Part 3: Amino acids

The present article is the third part of a general overview of the gas-phase protonation thermochemistry of polyfunctional molecules (first part: Mass Spectrom. Rev., 2007, 26:775-835, second part: Mass Spectrom. Rev., 2011, in press). This review is devoted to the 20 proteinogenic amino acids and is divided in two parts. In the first one, the experimental data obtained during the last 30 years using the equilibrium, thermokinetic and kinetic methods are presented. A general re-assignment of the values originating from these various experiments has been done on the basis of the commonly accepted Hunter & Lias 1998 gas-phase basicity scale in order to provide an homogeneous set of data. In the second part, theoretical investigations on gaseous neutral and protonated amino acids are reviewed. Conformational landscapes of both types of species were examined in order to provide theoretical protonation thermochemistry based on the truly identified most stable conformers. Proton affinities computed at the presently highest levels of theory (i.e. composite methods such as Gn procedures) are presented. Estimates of thermochemical parameters calculated using a Boltzmann distribution of conformers at 298K are also included. Finally, comparison between experiment and theory is discussed and a set of evaluated proton affinities, gas-phase basicities and protonation entropies is proposed.

Theoretical Modeling of the Surface-Enhanced Raman Optical Activity

Surface-enhanced Raman optical activity (SEROA) is a new technique combining the sensitivity of the surface-enhanced Raman scattering (SERS) with the detailed information about molecular structure provided by the chiral spectroscopies. So far, experimental SEROA spectra have been reported in several studies, but the interpretation and theoretical background are rather limited. In this work, general expressions for the electromagnetic contribution to SEROA are derived using the matrix polarization theory and used to investigate the enhancement in model systems. The results not only reveal a strong dependence of the enhancement on the distance between the molecule and a metal part but also the dependence of the ratio of ROA and Raman intensities (circular intensity difference, CID) on the distance and rotational averaging. For a ribose model, an optimal molecule-colloid distance was predicted which provided the highest CIDs. However, the CID maximum disappeared after a rotational averaging. For cysteine zwitterion, the simulated SEROA and SERS spectra provided a qualitative agreement with previous experiments.

On the limited precision of transfer of molecular optical activity tensors

Transfer of molecular property tensors (force field, dipole derivatives, polarizabilities, etc.) from smaller fragments to bigger molecules is powerful tool to calculate molecular vibrational spectra. However, we found serious accuracy limits for valinomycin (Phys. Chem. Chem. Phys. 2010, 12, 11021), where the transfer of the Raman optical activity tensors (ROA) had to be avoided. Therefore, in this study, the individual polarizable group model is analyzed for a model water dimer, and the corrections stemming from mutual group polarizations neglected in the transfer are estimated ab initio. The electric dipole polarizability was found more local and less sensitive to the interaction of distant molecular parts than the optical activity tensors (G′, A), which can partially explain the error observed during the transfer. In the second part of the study, tensor derivatives are transferred from smaller fragments to model valinomycin and insulin molecules, and the resultant tensor derivatives and ROA spectra compared to benchmark computations. The results confirmed that the error is caused by mutual polarization of molecular parts, more significant in insulin than in valinomycin, and could only partially be improved by increased size of the fragments.

Vibrational Raman optical activity of 1-phenylethanol and 1-phenylethylamine: revisiting old friends

The samples used for the first observations of vibrational Raman optical activity (ROA) in 1972, namely both enantiomers of 1-phenylethanol and 1-phenylethylamine, have been revisited using a modern commercial ROA instrument together with state-of-the-art ab initio calculations. The simulated ROA spectra reveal for the first time the vibrational origins of the first reported ROA signals, which comprised similar couplets in the alcohol and amine in the spectral range approximately 280-400 cm(-1). The results demonstrate how easy and routine ROA measurements have become, and how current ab initio quantum-chemical calculations are capable of simulating experimental ROA spectra quite closely provided sufficient averaging over accessible conformations is included. Assignment of absolute configuration is, inter alia, completely secure from results of this quality. Anharmonic corrections provided small improvements in the simulated Raman and ROA spectra. The importance of conformational averaging emphasized by this and previous related work provides the underlying theoretical background to ROA studies of dynamic aspects of chiral molecular and biomolecular structure and behavior.

Structure of the alanine hydration shell as probed by NMR chemical shifts and indirect spin-spin coupling

The structure of the alanine hydration shell was modeled by Carr-Parinello molecular dynamics (CPMD) to explain subtle differences in NMR chemical shifts and indirect spin-spin coupling constants of the neutral (zwitterionic), cationic, and anionic forms of this amino acid. In comparison with classical molecular dynamics (MD), the quantum mechanical CPMD approach revealed a more structured solvent and significant differences in the radial and angular distributions of the water molecules around the solute. In particular, the solvent was predicted to be organized around the uncharged COOH and NH(2) residues to a similar degree as that for the charged ones. This was not the case with MD. For snapshot CPMD configurations, the NMR parameters were computed by density functional theory (DFT) and averaged. Obtained values were significantly closer to experimental parameters known for (15)N and (13)C isotopically labeled alanine than those calculated by the conventional implicit dielectric solvent model. The NMR results also quantitatively reflect a superiority of the CPMD over the MD explicit solvent treatment. A further improvement of the computed spin-spin coupling constants could be achieved by taking into account vibrational averaging beyond the harmonic approximation. Differently positioned water molecules in the clusters cause an unexpectedly large scattering of the NMR parameters. About 10-15 dynamics snapshots were required for a satisfactory convergence of the shifts and couplings. The NMR chemical shift was found to be much more sensitive to the molecular hydration than the coupling. The results thus indicate a large potential of the NMR spectroscopy and quantum simulations to probe not only the structure of molecules but also their interactions with the environment.

Amide I Raman optical activity of polypeptides: fragment approximation

Vibrational optical activity (VOA) is an important property used to determine the absolute configuration of a chiral molecule in condensed phases. In particular, vibrational circular dichroism and Raman optical activity (ROA) are two representative VOA measurement techniques that have been extensively used to study structures and dynamics of biomolecules. Recently, the amide I vibrational circular dichroism of polypeptides was theoretically described by using fragment approximation methods, which are based on the assumption that amide I VOA can be described as a linear combination of those of constituent fragment peptide units. Here, we develop a fragment approximation theory applicable to numerical simulations of Raman and Raman optical activity spectra for the amide I vibrations in polypeptides. For an alanine dipeptide and pentapeptide analogs, we carried out density functional theory calculations of polarizability, magnetic dipole-, and electric quadrupole-ROA tensors. Numerically simulated spectra using the fragment approximation are directly compared to density functional theory results. Furthermore, the simulated ROA spectra of alanine-based right-handed alpha-helix and polyproline II polypeptides are directly compared to the previously reported experimental results. The agreements were found to be excellent, which suggests that the fragment approximation method developed for the numerical simulation of ROA spectrum of polypeptide in solution is valid and useful.

Structures and bonding on a colloidal silver surface of the various length carboxyl terminal fragments of bombesin

Raman (RS) and surface-enhanced Raman scattering spectra (SERS) were measured for various length carboxyl terminal fragments (X-14 of amino acid sequence) of bombesin ( BN): BN13-14, BN12-14, BN11-14, BN10-14, BN9-14, and BN8-14 in silver colloidal solutions. Density functional theory (DFT) calculations of Raman wavenumbers and intensities with extended basis sets (B3LYP/6-31++G**) were performed with the aim of providing the definitive band allocations to the normal coordinates. The proposed band assignment is consistent with the assignment for similar compounds reported in the literature. The nonadsorbed and adsorbed molecular structures were deducted by detailed spectral analysis of the RS and SERS spectra, respectively. This analysis also allowed us to propose the particular surface geometry and orientation of these peptides on silver surface, and their specific interaction with the surface. For example, a SERS spectrum of BN8-14 indicates that the interaction of a thioether atom and Trp8 with the silver surface is favorable and may dictate the orientation and conformation of adsorbed peptide. One of the most prominent and common features in all of the fragments' SERS spectra is a approximately 692 cm (-1) band due to nu(C-S) accompanied by two or three bands of different C-S conformers for all, except BN8-14, which suggests that all of the above-mentioned compounds adsorb on the silver surface through the thioether atom and that the attachment of Trp8 produces limitation in a number of possible C-S conformers adopted on this surface. Our results also show clearly that His12 and CO do not interact with the colloid surface, which supports our earlier results.

Characterizing aqueous solution conformations of a peptide backbone using Raman optical activity computations

Mounting spectroscopic evidence indicates that alanine predominantly adopts extended polyproline II (PPII) conformations in short polypeptides. Here we analyze Raman optical activity (ROA) spectra of N-acetylalanine-N'-methylamide (Ala dipeptide) in H2O and D2O using density functional theory on Monte Carlo (MC) sampled geometries to examine the propensity of Ala dipeptide to adopt compact right-handed (alpha(R)) and left-handed (alpha(L)) helical conformations. The computed ROA spectra based on MC-sampled alpha(R) and PPII peptide conformations contain all the key spectral features found in the measured spectra. However, there is no significant similarity between the measured and computed ROA spectra based on the alpha(L)- and beta-conformations sampled by the MC methods. This analysis suggests that Ala dipeptide populates the alpha(R) and PPII conformations but no substantial population of alpha(L)- or beta-structures, despite sampling alpha(L)- and beta-structures in our MC simulations. Thus, ROA spectra combined with the theoretical analysis allow us to determine the dominant populated structures. Including explicit solute-solvent interactions in the theoretical analysis is essential for the success of this approach.