L-Alanyl-L-alanine in the zwitterionic state: structures determined in the presence of explicit water molecules and with continuum models using density functional theory

Interaction of chiral L-dialanine with Cu(100)

We report on the properties of the thin films of the short peptide L-dialanine grown on Cu(100) surfaces and compare them to those of L-alanine by using surface techniques like XPS, IRRAS and STM. The first dialanine monolayer, in contact with the metallic substrate, is found to consist of whole neutral molecules in the non-zwitterionic state forming a c(2 × 4) pattern with quasi-hexagonal symmetry. The peptide bond of dialanine is preserved in the adsorption state. The ordering of the L-dialanine overlayer is shown to replicate rearrangements of the atoms of the substrate around dislocations of the latter indicating a strong molecule-surface interaction. In the multilayer regime, molecules of the second and further layers are found to be in a zwitterionic state, readily desorbing even at room temperature. The first dialanine layer is tightly bound to the substrate, begins to desorb at temperatures higher than 390 K and cracks down at the surface, transforming into a new moiety, beyond 435 K.

Solvation of a chiral carboxylic acid: effects of hydrogen bonding on the IR and VCD spectra of α-methoxyphenylacetic acid

Taking the title compound as a representative example of a chiral carboxylic acid, we investigate how its VCD spectral pattern is affected by hydrogen bonding of different solvents.

Interfacial water at the trialanine hydrophilic surface: a DFT electronic structure and bottom-up investigation

A model describing a network of hydrogen bonded water-trialanine has been developed to estimate hydration effects on various conformers of the peptide.

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.

Growth, molecular structure, NBO analysis and vibrational spectral analysis of l-tartaric acid single crystal

Single crystal of l-tartaric acid (LTA) has been grown by slow evaporation technique. The experimental and theoretical studies on molecular structure, vibrational spectra, electronic absorption spectra and non-linear optical property of the crystal are studied. The FT-IR, FT-Raman and UV-Vis-NIR experimental spectra of LTA crystal have been recorded in the range 400-4000cm(-1), 100-3700cm(-1) and 190-1100nm, respectively. Density functional theory calculations with B3LYP/6-311++G(d,p) basis sets was used to determine ground state molecular geometries, vibrational frequencies, ICT interactions, Mulliken population analysis on atomic charge, HOMO-LUMO analysis, non-linear optical response properties and thermodynamic properties for LTA and the results were discussed. Vibrational analysis confirms the formation of intramolecular OH⋯O hydrogen bonding. The stability of the molecule has been analyzed using NBO analysis. The results of electronic absorptions in gas phase and water phase LTA were calculated using TD-DFT method. The third-order nonlinear absorption behaviour of LTA was studied using open aperture Z-scan technique, with 5ns laser pulses at 532nm and the nonlinear absorption coefficient of the grown crystal was measured. The predicted NLO properties, UV absorption and Z-scan studies indicate that LTA is an attractive material for laser frequency doubling and optical limiting applications.

Vibrational spectra and density functional theoretical calculations on the anti-neurodegenerative drug: Orphenadrine hydrochloride

Vibrational spectral analysis and quantum chemical computations based on density functional theory have been performed on the anti-neuro-degenerative drug Orphenadrine hydrochloride. The geometry, intermolecular hydrogen bond, and harmonic vibrational frequencies of the title molecule have been investigated with the help of B3LYP method. The calculated molecular geometry has been compared with the experimental data. The various intramolecular interactions have been exposed by natural bond orbital analysis. The distribution of Mulliken atomic charges and bending of natural hybrid orbitals also reflect the presence of intramolecular hydrogen bonding. The analysis of the electron density of HOMO and LUMO gives an idea of the delocalization and low value of energy gap indicates electron transport in the molecule and thereby bioactivity. Effective docking of the drug molecule with NMDA receptor subunit 3A also enhances its bioactive nature.

Electronic absorption and vibrational spectra and nonlinear optical properties of L-valinium succinate

FT-Raman and FTIR techniques have been applied to investigate the potential nonlinear optical material l-valinium succinate. A detailed interpretation of the vibrational spectra was carried out with the aid of potential energy distribution analysis. Density functional theory is applied to explore the nonlinear optical properties of the molecule. Good consistency is found between the calculated results and the experimental data for IR and Raman spectra. The natural bond orbital analysis confirms the occurrence of strong intramolecular N-H⋯O hydrogen bonding.

Theoretical approaches to the calculation of Raman optical activity spectra

In this article, we will give a brief account of the different approaches that have been presented in the literature for calculating Raman optical activity (ROA) spectra by ab initio methods. We will also outline the general structure of a self-consistent-field-based approach for analytic calculations of ROA spectra, including also contributions from London orbitals. The use of London orbitals ensures that the relevant ROA parameters are gauge origin independent. We will also give an outlook on the future of ab initio calculations of Raman optical activity spectra.

Analysis of vibrational spectra of L-alanylglycine based on density functional theory calculations

FT Raman and IR spectra of the crystallized biologically active molecule, L-alanylglycine (L-Ala-Gly) have been recorded and analyzed. The equilibrium geometry, bonding features and harmonic vibrational frequencies of L-Ala-Gly have been investigated with the help of B3LYP density functional theory (DFT) method. The calculated molecular geometry has been compared with the experimental data. The assignments of the vibrational spectra have been carried out with the help of normal coordinate analysis (NCA) following the scaled quantum mechanical force field methodology (SQMFF). The optimized geometry shows the non-planarity of the peptide group of the molecule. Potential energy surface (PES) scan studies has also been carried out by ab initio calculations with B3LYP/6-311+G** basis set. The red shifting of NH3+ stretching wavenumber indicates the formation of N-H...O hydrogen bonding. The change in electron density (ED) in the sigma* antibonding orbitals and E2 energies have been calculated by natural bond orbital analysis (NBO) using DFT method. The NBO analysis confirms the occurrence of strong intermolecular hydrogen bonding in the molecule.

Ab initio molecular dynamics of protonated dialanine and comparison to infrared multiphoton dissociation experiments

Finite temperature Car-Parrinello molecular dynamics simulations are performed for the protonated dialanine peptide in vacuo, in relation to infrared multiphoton dissociation experiments. The simulations emphasize the flexibility of the different torsional angles at room temperature and the dynamical exchange between different conformers which were previously identified as stable at 0 K. A proton transfer occurring spontaneously at the N-terminal side is also observed and characterized. The theoretical infrared absorption spectrum is computed from the dipole time correlation function, and, in contrast to traditional static electronic structure calculations, it accounts directly for anharmonic and finite temperature effects. The comparison to the experimental infrared multiphoton dissociation spectrum turns out very good in terms of both band positions and band shapes. It does help the identification of a predominant conformer and the attribution of the different bands. The synergy shown between the experimental and theoretical approaches opens the door to the study of the vibrational properties of complex and floppy biomolecules in the gas phase at finite temperature.

Homochiral Preference in Peptide Synthesis in Ribosome: Role of Amino Terminal, Peptidyl Terminal, and U2620

Experimental studies have shown that peptide synthesis in ribosome exhibits a homochiral preference. We present, for the first time, an analysis of the origin of the phenomenon using hybrid quantum chemical studies based on a model of peptidyl transferase center from the crystal structure of the ribosomal part of Haloarcula marismortui. The study quantitatively shows that the observed homochiral preference is due to the difference in the nonbonded interaction between amino acids at the A- and P-terminals as well as due to the difference in interaction with the U2620 residue. A major part of the discrimination comes from the variation of nonbonded interaction of rotating A-terminal during the approach of the former toward the P-terminal. The difference indicates that, during the rotatory motion between A- and P-terminals for the proximal positioning of the reactant for reaction to occur, the interaction for a L-L pair is far less repulsive compared to the same process for a D-L pair. The activation barriers for L-L and D-L pairs of the neutral state of phenylalanine leading to corresponding dipeptides are also compared. The corresponding difference in rate constants is 40-fold. The study provides an understanding of how preferred addition of L-L pairs of amino acids rather than D-L pairs leads to retention of homochirality in peptides.

Computational study of ground-state chiral induction in small peptides: comparison of the relative stability of selected amino acid dimers and oligomers in homochiral and heterochiral combinations

The relative stabilities of homochiral and heterochiral forms of selected dipeptides, AA, AS, AC, AV, AF, AD, AK, tripeptides, AAA, AVA, and an acetylpentapeptide, AcGLSFA, have been calculated using thermodynamic integration protocols and the GROMOS 53A6 force field. Integration pathways have been designed that produce minimal disturbance to the system, including the use of soft atoms, low-energy intermediates, and chiral inversion of the smaller amino acid in the peptide. Comparison of the results obtained by thermodynamic integration between the diastereomeric forms (in explicit water, at 300 K) and from exhaustive global minimum-energy searches for the individual dipeptides (implicit water, epsilon = 78, 0 K) suggests that entropic contributions to the relative stability of the chiral forms are important. This conclusion is supported by the results of explicit calculation of the effect of temperature on the relative stability of alanylvalylalanine diastereomers. The Gibbs free energy calculations predict that at ambient temperature and pressure homochiral dipeptides with small side chains or polar groups in the vicinity of the peptide backbone, AA, AS, and AD, are more stable than their heterochiral counterparts by fractions of a kJ/mol. For bigger side chains, AC, AV, AF, and AK, the heterochiral diastereomers appear to be more stable. Predicted relative stabilities are in line with observations reported in the literature for AE and YY. Excellent agreement is found for the calculated and experimentally determined relative stabilities of the diastereomers of the dipeptide AA and of all-L AcGLSFA and its diastereomer containing D-serine in the central position. Addition of counterions to the solvent box has no significant effects on charged and neutral forms. From the present findings it would appear unlikely that the intrinsic stability difference between homo- and heterochiral dipeptides has been a driving force in a primordial selection process leading to the incorporation of amino acids with a single enantiomeric configuration in natural proteins.

Interpretation of synchrotron radiation circular dichroism spectra of anionic, cationic, and zwitterionic dialanine forms

Electronic absorption and synchrotron radiation circular dichroism (SRCD) spectra of the anionic, cationic, and zwitterionic forms of L-alanyl-L-alanine (AA) in aqueous solutions were measured and interpreted by molecular dynamics (MD) and ab initio computations. Time-dependent density functional theory (TD DFT) was applied to predict the electronic excited states. The modeling enabled the assessment of the role of molecular conformation, charge, and interaction with the polar environment in the formation of the spectral shapes. Particularly, inclusion of explicit solvent molecules in the computations appeared to be imperative because of the participation of water orbitals in the amide electronic structure. Implicit dielectric continuum solvent models gave inferior results for clusters, especially at low-energy transitions. Because of the dispersion of transition energies, tens of water/AA clusters had to be averaged in order to obtain reasonable spectral shapes with a more realistic inhomogeneous broadening. The modeling explained most of the observed differences, as the anionic and zwitterionic SRCD spectra were similar and significantly different from the cationic spectrum. The greatest deviation between the experimental and theoretical curves observed for the lowest-energy negative anion signal can be explained by the limited precision of the TD DFT method, but also by the complex dynamics of the amine group. The results also indicate that differences in the experimental spectral shapes do not directly correlate with the peptide main-chain conformation. Future peptide and protein conformational studies based on circular dichroic spectroscopy can be reliable only if such effects of molecular dynamics, solvent structure, and polar solvent-solute interactions are taken into account.

Comparison of the Intermolecular Energy Surfaces of Amino Acids: Orientation-Dependent Chiral Discrimination

In the present work, we compare the intermolecular energy surfaces of the alanine molecule in its neutral and zwitterionic state using ab initio theory (HF/6-311++G) as a function of mutual orientation. Starting from the optimized structures of the nonbonded homochiral (l-l) and heterochiral (d-l) pairs of molecules, the energy surfaces are studied with rigid geometry by varying the distance and orientation. The potential energy surfaces of the l-l and d-l pairs are found to be dissimilar and reflect the underlying chirality of the homochiral pair and racemic nature of the heterochiral pair. The intermolecular energy surface of the l-l pair is more favorable than the corresponding energy surface of the d-l pair. The study, for the first time, reveals clear homochiral preference without use of parameters, which was unobserved in previous detailed simulations but predicted by theory. The electrostatic interaction further augments the chiral discrimination. The basis set superposition error (BSSE) corrected results show enhanced discrimination. Use of higher-level Møller-Plesset perturbation theory (MP2) and further BSSE correction do not change the conclusions made at the Hartree-Fock (HF) level. The major conclusions based on HF and MP2 level calculations remain unaltered when the calculations of the potential energy surfaces for the neutral and zwitterionic pairs are repeated using the density functional theory (DFT) (B3LYP/6-311++G). The observed orientation dependence has significance in the biological chiral recognition as well as peptide synthesis at the peptidyl transferase center where the amino terminal and peptidyl terminal undergo mutual rotatory motion.

The VA, VCD, Raman and ROA spectra of tri-L-serine in aqueous solution

The structures of one conformer of the nonionic neutral and zwitterionic species of L-serinyl L-serinyl L-serine (SSS or tri-L-serine), together with its cationic and anionic species and the capped N-acetyl tri-L-serine N'-methylamide analog were optimized with density functional theory with the Becke 3LYP hybrid exchange correlation (XC) functional and the PW91 GGA XC functional and the 6-31G* and aug-cc-pVDZ basis sets. Subsequently, the vibrational absorption, vibrational circular dichroism, Raman and Raman optical activity spectra were simulated in order to compare them to experimentally measured spectra. In addition, we compare to previously reported studies for both structural determination and spectral simulations and measurements. A comparison of the various ways to treat the effects of the environment and solvation on both the structure and the spectral properties is thoroughly investigated for one conformer, with the goal to determine which level of theory is appropriate to use in the systematic search of the conformational space. In addition, the effects of the counterion, here Cl- anion, are also investigated. Here we present the current state of the art in nanobiology, where the latest methods in experimental and theoretical vibrational spectroscopy are used to gain useful information about the coupling of the nuclear, electronic and magnetic degrees of freedom and structure of tri-L-serine and its capped peptide analog with the environment.

A complete set of NMR chemical shifts and spin-spin coupling constants for L-Alanyl-L-alanine zwitterion and analysis of its conformational behavior

With the aid of labeling with stable isotopes ((15)N and (13)C) a complete set of chemical shifts and indirect spin-spin coupling constants was obtained for the zwitterionic form of L-alanyl-L-alanine in aqueous solution. Different sensitivities of the NMR parameters to the molecular geometry were discussed on the basis of comparison with ab initio (DFT) calculated values. An adiabatic two-dimensional vibrational wave function was constructed and used for determination of the main chain torsion angle dispersions and conformational averaging of the NMR shifts and coupling constants. The quantum description of the conformational dynamics based on the density functional theory and a polarizable continuum solvent model agrees reasonably with classical molecular dynamics simulations using explicit solvent. The results consistently evidence the presence of a single form in the aqueous solution with equilibrium main chain torsion angle values (psi = 147 degrees, varphi = -153 degrees), close to that one found previously in an X-ray study. Under normal temperature the torsion angles can vary by about 10 degrees around their equilibrium values, which leads, however, to minor corrections of the NMR parameters only. The main chain heavy atom chemical shifts and spin-spin coupling constants involving the alpha-carbon and hydrogen atoms appear to be most useful for the peptide structural predictions.

Vibrational Spectral Simulation for Peptides of Mixed Secondary Structure: Method Comparisons with the Trpzip Model Hairpin

Infrared absorption and vibrational circular dichroism (IR and VCD) spectra of model fragments of TrpZip-style beta-hairpin structures are simulated using density functional theory (DFT) methods to estimate the influence of fragment size, end effects, conformational irregularities, peptide side chains, and solvent. Different fragmentation schemes, computing the strands and turn segments separately, were tested by varying the sizes of each and their respective overlaps. For suitably overlapping fragments, atomic property tensors were found to be reliably transferable, as tested by their ability to generate simulated spectra in good agreement with results from ab initio DFT computations for the entire peptide. This fragment approach significantly reduces computational times and opens up a wider range of systems that can be studied with a DFT-based approach as compared to previous methods based on uniform repeating sequences. However, vacuum calculations do not adequately represent the frequency dispersion of solvated molecules, and thus, some alternate strategies for solvation correction are explored for improving the simulation accuracy. Unlike for regular periodic secondary structure, the solvent significantly impacts the spectral shapes of hairpins, due to the different degrees of hydration of individual amide groups, which can be exposed to or shielded from water due to external vs internal hydrogen bonding. This is amplified by the shielding of selected amides from the solvent due to bulky side chains. The peptide plus solvent was structurally modeled with molecular dynamics methods, and then an electrostatic field-based parametrization correction was added to the force field and intensity tensors to compensate for the solvent dipolar field. The effect of the shielding and subsequent reordering of modes has a larger impact on VCD than IR band shapes.

Solvent Effects on IR and VCD Spectra of Helical Peptides: DFT-Based Static Spectral Simulations with Explicit Water

Simulations of IR and VCD spectra are carried out for model alpha-helical, 3(10)-helical, and 3(1)-helical (polyProII-like) oligopeptides, with up to 21 amide groups, and including explicit consideration of effects of directly hydrogen-bonded solvent (water). Parameters used were obtained from ab initio density functional theory (DFT) computations of force field, atomic polar and axial tensors for oligopeptides of 5 to 7 amides, whose structures were constrained in (phi,psi) to target the secondary structure type but otherwise fully optimized. By comparison with experimental data as well as with calculations for identical but isolated (gas phase) peptides, the computed effects of an inner shell of aqueous solvent on the vibrational spectra of helical oligopeptides are illustrated. The interaction with solvent causes significant frequency shifts of the amide bands, but only minor changes in the characteristic IR intensity distributions and splittings and the VCD band shapes. Better agreement with experimental band shapes is achieved for the alpha-helical amide I' (N-deuterated) VCD by inclusion of explicit solvent in the calculations. Some improvements are also observed in theoretical VCD predictions for 13C labeled alpha-helical peptides when solvated models are used. However, the qualitative isotopic splitting patterns are preserved and just shifted in frequency due to consistent, solvent independent interamide coupling constants. The critical match of experiment and theory for relative positions of transitions in peptides with specifically separated 13C=O labels, including and neglecting solvent, confirms the stability of the coupling interactions. Despite these solvation effects, the calculated VCD band shape of the amide I mode is shown to be a reliable conformational probe, since it remains basically insensitive to frequency shifts caused by environment. Thus theoretical VCD simulations, even vacuum calculations, are shown to provide useful spectral predictions for solution-phase peptides.

A directed essential dynamics simulation of peptide folding

We present a directed essential dynamics (DED) method for peptide and protein folding. DED is a molecular dynamics method based on the essential dynamics sampling and the principal component analysis. The main idea of DED is to use principal component analysis to determine the direction of the most active collective motion of peptides at short intervals of time (20 fs) during the folding process and then add an additional force along it to adjust the folding direction. This method can make the peptides avoid being trapped in the local minima for a long time and enhance the sampling efficiency in conformational space during the simulation. An S-peptide with 15 amino acids is used to demonstrate the DED method. The results show that DED can lead the S-peptide to fold quickly into the native state, whereas traditional molecular dynamics needs more time to do this.