Vibrational analysis of amino acids and short peptides in hydrated media. I. L-glycine and L-leucine

Raman scattering and Fourier-transform infrared (FT-IR) attenuated transmission reflectance (ATR) spectra of two alpha-amino acids (alpha-AAs), i.e., glycine and leucine, were measured in H2O and D2O (at neutral pH and pD). This series of observed vibrational data gave us the opportunity to analyze vibrational features of both AAs in hydrated media by density functional theory (DFT) calculations at the B3LYP/6-31++G* level. Harmonic vibrational modes calculated after geometry optimization on the clusters containing each AA and 12 surrounding water molecules, which represent primary models for hydration scheme of amino acids, allowed us to assign the main observed peaks.     

Supramolecular Recognition of Amino Acids by Twisted Cucurbit[14]uril

Binding interactions between twisted cucurbit[14]uril (tQ[14]) and twenty standard amino acids (AAs) have been investigated by NMR spectroscopy and isothermal titration calorimetry (ITC) in aqueous HCl solutions and in DMSO. The results showed that tQ[14] displays clear binding affinity for AAs with a positively charged side chain or containing an aromatic ring, but weaker binding affinity for AAs with hydrophobic or polar side chains, with the binding mode depending on the type of side chain present in the AAs.     

Molecular rotors as simple models to study amide NH-aromatic interactions and their role in the folding of peptide-like structures

The conformational behavior of designed macrocyclic naphthalenophanes (1a,b and 2a,b) derived from amino acids (Phe and Val) has been used for studying NH...pi interactions. The cycles having 16- and 17-membered rings showed a dynamic process within the NMR time scale, produced by the flipping of the aromatic naphthalene moiety with respect to the macrocyclic main plane. We used the temperature dependence of 1H NMR to obtain activation parameters of the energetic barrier for the process (variable temperature NMR and line shape analysis). The rate of the movement clearly depends on the macrocyclic ring size and, more interestingly, on the nature of the peptidomimetic side chain, the energetic barrier being higher for the compounds bearing aromatic side chains. A largely negative entropic contribution to the free energy of activation was observed, with clear differences due to the side chain nature. Molecular modeling studies suggest that the aromatic rings interact with intramolecularly H-bonded amide NH groups, protecting them from solvation and thus leading to a larger unfavorable activation entropy. This NH...pi interaction has been exploited for the preparation of new systems (1c and meso-1b) with designed conformational preferences, in which aromatic rings tend to fold over amide NH groups. Thus, these minimalistic molecular rotors have served us as simple model systems for the study of NH...pi interactions and their implication in the folding of peptide-like molecules.     

DFT studies using supercells and projector-augmented waves for structure, energetics, and dynamics of glycine, alanine, and cysteine

A large variety of gas phase conformations of the amino acids glycine, alanine, and cysteine is studied by numerically efficient semi-local gradient-corrected density functional theory calculations using a projector-augmented wave scheme and periodic boundary conditions. Equilibrium geometries, conformational energies, dipole moments, vibrational modes, and IR optical spectra are calculated from first principles. A comparison of our results with values obtained from quantum-chemistry methods with localized basis sets and nonlocal exchange-correlation functionals as well as with experimental data is made. For conformations containing strong intramolecular hydrogen bonds deviations in their energetic ordering occur, which are traced back to different treatments of spatial nonlocality in the exchange-correlation functional. However, even for these structures, the comparison of calculated and measured vibrational frequencies shows satisfying agreement.     

Energetics of low-molecular-mass products of mechanical fracture of poly(methyl methacrylate)

It is experimentally revealed that monomer and water molecules released during the fracture of PMMA have a bimodal velocity distribution. The first distribution peak for the monomer corresponds to energetic (hot) MMA molecules (0.13–0.70 eV), and the second peak is attributed to MMA molecules bearing a low energy (0.016–0.060 eV). On the basis of the results of earlier theoretical studies of the mechanically induced polymer-chain scission, it was concluded that the energetic monomer molecules are produced immediately in the event of mechanical chain rupture and are nonthermal in nature. In the bimodal velocity distribution of occluded water molecules desorbed from a subsonic crack, the first and the second peaks are attributed to “hot” and “cold” molecules with translational temperatures of 605 ± 180 K and 53 ± 5 K, respectively. A possible mechanism of the mechanically induced desorption of occluded water is discussed. The mechanodesorption of water molecules is due to the portion of vibrational energy transferred to side methyl carboxylate groups that retain water molecules by the unloading-wave front traveling along the main chain from a macromolecule scission site. Along with hot water molecules, a considerable amount of hot free hydroxyls were detected. The mechanism of formation of the latter species is associated with the double-well structure of the hydrogen bond potential and similar to the mechanism of mechanodesorption of hot molecules of water.     

Intrinsic conformational characteristics of alpha,alpha-diphenylglycine

Quantum mechanical calculations at the B3LYP/6-31+G(d,p) level have been used to investigate the intrinsic conformational preferences of alpha,alpha-diphenylglycine, a simple alpha,alpha-dialkylated amino acid bearing two phenyl substituents on the alpha-carbon, in both the gas phase and aqueous solution. Nine minimum energy conformations have been characterized for the N-acetyl-N'-methylamide derivative within a relative energy range of about 9 kcal/mol. The relative stability of these structures is largely influenced by specific backbone...side chain and side chain...side chain interactions that can be attractive (N-H...pi and C-H...pi) or repulsive (C=O...pi). On the other hand, comparison with the minimum energy conformations calculated for alpha-aminoisobutyric acid, in which the two phenyl substituents are replaced by methyl groups, revealed that the bulky aromatic rings of alpha,alpha-diphenylglycine induce strain in the internal geometry of the peptide. Finally, a set of force-field parameters for classical Molecular Mechanics calculations was developed for the investigated amino acid. Molecular Dynamics simulations in aqueous solutions have been carried out to validate the parameters obtained.     

Vibrational and photoionization spectroscopy of biomolecules: aliphatic amino acid structures

The aliphatic amino acids glycine, valine, leucine, and isoleucine are thermally placed into the gas phase and expanded into a vacuum system for access by time of flight mass spectroscopy and infrared (IR) spectroscopy in the energy range of 2500-4000 cm(-1) (CH, NH, OH, and stretching vibrations). The isolated neutral amino acids are ionized by a single photon of 10.5 eV energy (118 nm), which exceeds by less than 2 eV their reported ionization thresholds. As has been reported for many hydrogen bonded acid-base systems (e.g., water, ammonia, alcohol, acid clusters, and acid molecules), the amino acids undergo a structural rearrangement in the ion state (e.g., in simplest form, a proton transfer) that imparts sufficient excess vibrational energy to the ion to completely fragment it. No parent ions are observed. If the neutral ground state amino acids are exposed to IR radiation prior to ionization, an IR spectrum of the individual isomers for each amino acid can be determined by observation of the ion intensity of the different fragment mass channels. Both the IR spectrum and fragmentation patterns for individual isomers can be qualitatively identified and related to a particular isomer in each instance. Thus, each fragment ion detected presents an IR spectrum of its particular parent amino acid isomer. In some instances, the absorption of IR radiation by the neutral amino acid parent isomer increases a particular fragmentation mass channel intensity, while other fragmentation mass channel intensities decrease. This phenomenon can be rationalized by considering that with added energy in the molecule, the fragmentation channel populations can be modulated by the added vibrational energy in the rearranged ions. This observation also suggests that the IR absorption does not induce isomerization in the ground electronic state of these amino acids. These data are consistent with theoretical predictions for isolated amino acid secondary structures and can be related to previous IR spectra of amino acid conformers.     

Ribosomal synthesis of N-methyl peptides

N-methyl amino acids (N-Me AAs) are a common component of nonribosomal peptides (NRPs), a class of natural products from which many clinically important therapeutics are obtained. N-Me AAs confer peptides with increased conformational rigidity, membrane permeability, and protease resistance. Hence, these analogues are highly desirable building blocks in the ribosomal synthesis of unnatural peptide libraries, from which functional, NRP-like molecules may be identified. By supplementing a reconstituted Escherichia coli translation system with specifically aminoacylated total tRNA that has been chemically methylated, we have identified three N-Me AAs (N-Me Leu, N-Me Thr, and N-Me Val) that are efficiently incorporated into peptides by the ribosome. Moreover, we have demonstrated the synthesis of peptides containing up to three N-Me AAs, a number comparable to that found in many NRP drugs. With improved incorporation efficiency and translational fidelity, it may be possible to synthesize combinatorial libraries of peptides that contain multiple N-Me AAs. Such libraries could be subjected to in vitro selection methods to identify drug-like, high-affinity ligands for protein targets of interest.     

Excess electron and lithium atom solvation in water clusters at finite temperature: an ab initio molecular dynamics study of the structural, spectral, and dynamical behavior of (H2O)6- and Li(H2O)6

The roles of hydrogen bonds in the solvation of an excess electron and a lithium atom in water hexamer cluster at 150 K have been studied by means of ab initio molecular dynamics simulations. It is found that the hydrogen bonded structures of (H(2)O)(6)(-) and Li(H(2)O)(6) clusters are very different from each other and they dynamically evolve from one conformer to other along their simulation trajectories. The populations of the single acceptor, double acceptor, and free type water molecules are found to be significantly high unlike that in pure water clusters. Free hydrogens of these type of water molecules primarily capture the unbound electron density in these clusters. It is found that the binding motifs of the free electron evolve with time and the vertical detachment energy of (H(2)O)(6)(-) and vertical ionization energy of Li(H(2)O)(6) also change with time. Assignments of the observed peaks in vibrational power spectra are done, and we found direct correlations between the time-averaged population of water molecules in different hydrogen bonding states and the spectral features. The dynamical aspects of these clusters have also been studied through calculations of time correlations of instantaneous stretch frequencies of OH modes which are obtained from the simulation trajectories through a time series analysis.     

Partial molar volumes of l-alanine,dl-serine,dl-threonine,l-histidine,glycine, and glycylglycine in water,NaCl, and DMSO aqueous solutions at T = 298.15 K

The apparent molar volumes of l-alanine, dl-serine, dl-threonine, l-histidine, glycine, and glycylglycine in water and in the aqueous solutions of NaCl and DMSO with various concentrations at T = 298.15 K have been measured by the precise vibrating-tube digital densimeter. The calculated partial molar volumes at infinite dilution have been used to obtain corresponding transfer volumes from water to various solutions. The experimental results show that the standard partial molar volumes of the above amino acids and peptide at the dilute DMSO aqueous solutions are very close to those in water. However, the volumes show several types of variations with the increase of the concentrations of DMSO due to different types of side chain of amino acids, which should be discussed specifically. The NaCl changes considerably the infinite dilution standard partial molar volumes of the above amino acids and peptide in the aqueous solutions. The infinite dilution standard partial molar volumes of the each amino acids and peptide increase with the concentrations of NaCl. The experimental results have been rationalized by a cosphere overlap model.     

Density Functional Theory Investigations on Vibrational Spectra,Molecular Structure,and Properties of the L‐Serine,L‐Cysteine,and L‐Aspartic Acid Molecules

In this paper, we present a thorough investigation of the conformational space to characterize all possible gas‐phase structures of the neutral L‐serine, L‐cysteine, and L‐aspartic acid molecules. A total of 120 trial structures were generated for L‐aspartic acid and 96 trial structures for L‐serine and L‐cysteine by combining all internal single‐bond rotamers. Various combinations of the Hartree–Fock and density functional theory/B3LYP methods with different bases were used to optimize all possible trial structures. The theoretical studies on the structure, harmonic vibrational spectra, and molecular properties of these amino acids are presented. The assignments of the calculated wave numbers resulting from potential energy distributions were performed using the VEDA 4 program to allow a good interpretation of the theoretical vibrational spectra of the title compounds. The fundamental harmonic frequencies were found to be in good agreement with data in the literature. A natural bond orbital analysis was performed to investigate the charge delocalization throughout the molecules for the three test compounds. Moreover, an extensive discussion of the highest occupied molecular orbital–lowest unoccupied molecular orbital energy gap as well as other related molecular properties are reported.     

Structural and molecular properties of dipeptides containing N-terminal selenomethionine: a theoretical study

Although the genetic code encodes only 22 amino acids during protein bio-synthesis, there are more than 140 natural amino acids whose incorporation into the protein structures is vital for proper functioning of the chemical and bio-chemical machineries associated with living beings. Among these, selenium-containing amino acids are of special interest for amino acid biochemistry. During the last few decades, the structure–function relationships of proteins are being best pursued by considering amino acids, dipeptides as well as their analogs as model systems. By performing this theoretical study it is intended to investigate the influence of functional group/groups present in side chain moieties of the varying C-terminal residues on the molecular and structural features of a set of seven dipeptides, constructed by conserving selenomethionine at their N-terminal positions while the C-terminal ends are varied with one of the following amino acid residues—Val, Trp, Glu, Cys, Tyr, Arg, and Sec. Geometry optimization and vibrational frequency calculations were carried out in gas and aqueous phase using B3LYP/6-311++G(d,p) level of theory. The results furnished by this DFT study provide a good account of the role of the C-terminal residue’s identity in determining the structural features of the amide planes, values of the ψ and ф dihedrals, geometry about the α-carbon atoms, theoretical IR spectra and the number and type of intramolecular H-bond interactions existing in the dipeptides. In aqueous phase, the dipeptide geometries exhibit larger values of total dipole moments, greater HOMO–LUMO energy gaps and enhanced thermodynamic stability than those in gas phase.     

Conformational search using a molecular dynamics–minimization procedure: Applications to clusters of coulombic charges,Lennard–Jones particles,and waters

A new conformational search method, molecular dynamics–minimization (MDM), is proposed, which combines a molecular dynamics sampling strategy with energy minimizations in the search for low-energy molecular structures. This new method is applied to the search for low energy configurations of clusters of coulombic charges on a unit sphere, Lennard–Jones clusters, and water clusters. The MDM method is shown to be efficient in finding the lowest energy configurations of these clusters. A closer comparison of MDM with alternative conformational search methods on Lennard–Jones clusters shows that, although MDM is not as efficient as the Monte Carlo–minimization method in locating the global energy minima, it is more efficient than the diffusion equation method and the method of minimization from randomly generated structures. Given the versatility of the molecular dynamics sampling strategy in comparison to Monte Carlo in treating molecular complexes or molecules in explicit solution, one anticipates that the MDM method could be profitably applied to conformational search problems where the number of degrees of freedom is much greater. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 60–70, 1998     

Improving the study of proton transfers between amino acid side chains in solution: choosing appropriate DFT functionals and avoiding hidden pitfalls

We have studied the influence of implicit solvent models, inclusion of explicit water molecules, inclusion of vibrational effects, and density functionals on the quality of the predicted pK _a of small amino acid side chain models. We found that the inclusion of vibrational effects and explicit water molecules is crucial to improve the correlation between the computed and the experimental values. In these micro-solvated systems, the best agreement between DFT-computed electronic energies and benchmark values is afforded by BHHLYP and B97-2. However, approaching experimental results requires the addition of more than three explicit water molecules, which generates new problems related to the presence of multiple minima in the potential energy surface. It thus appears that a satisfactory ab initio prediction of amino acid side chain pK _a will require methods that sample the configurational space in the presence of large solvation shells, while at the same time computing vibrational contributions to the enthalpy and entropy of the system under study in all points of that surface. Pending development of efficient algorithms for those computations, we strongly suggest that whenever counterintuitive protonation states are found in a computational study (e.g., the presence of a neutral aspartate/neutral histidine dyad instead of a deprotonated aspartate/protonated histidine pair), the reaction profile should be computed under each of the different protonation micro-states by constraining the relevant N–H or O–H bonds, in order to avoid artifacts inherent to the complex nature of the factors contributing to the pK _a.     

A genetic algorithm encoded with the structural information of amino acids and dipeptides for efficient conformational searches of oligopeptides

The genetic algorithm (GA) is an intelligent approach for finding minima in a highly dimensional parametric space. However, the success of GA searches for low energy conformations of biomolecules is rather limited so far. Herein an improved GA scheme is proposed for the conformational search of oligopeptides. A systematic analysis of the backbone dihedral angles of conformations of amino acids (AAs) and dipeptides is performed. The structural information is used to design a new encoding scheme to improve the efficiency of GA search. Local geometry optimizations based on the energy calculations by the density functional theory are employed to safeguard the quality and reliability of the GA structures. The GA scheme is applied to the conformational searches of Lys, Arg, Met‐Gly, Lys‐Gly, and Phe‐Gly‐Gly representative of AAs, dipeptides, and tripeptides with complicated side chains. Comparison with the best literature results shows that the new GA method is both highly efficient and reliable by providing the most complete set of the low energy conformations. Moreover, the computational cost of the GA method increases only moderately with the complexity of the molecule. The GA scheme is valuable for the study of the conformations and properties of oligopeptides. © 2016 Wiley Periodicals, Inc.     

Conformational equilibria of terminally blocked single amino acids at the water-hexane interface. A molecular dynamics study

The conformational equilibria of the acetyl and methyl amide terminally blocked L-alanine, L-leucine and L-glutamine amino acids are examined in vacuum, in bulk water, and at the water-hexane interface, using multi-nanosecond molecular dynamics simulations. The two-dimensional probability distribution functions of finding the peptides at different dihedral angles of the backbone, phi and psi, are calculated, and free energy differences between different conformational states are determined. All three peptides are interfacially active, i.e. tend to accumulate at the interface even though they are not amphiphilic. Conformational states stable in both gas phase and water are also stable in the interfacial environment. Their populations, however, cannot be simply predicted from the knowledge of conformational equilibria in the bulk phases, indicating that the interface exerts a unique effect on the peptides. Conformational preferences in the interfacial environment arise from the interplay between electrostatic and hydrophobic effects. As in an aqueous solution, electrostatic solute-solvent interactions lead to the stabilization of more polar peptide conformations. The hydrophobic effect is manifested at the interface by a tendency to segregate polar and nonpolar moieties of the solute into the aqueous and the hexane phases, respectively. For the terminally blocked glutamine, this favors conformations for which such a segregation is compatible with the formation of strong, backbone-side chain intramolecular hydrogen bonds on the hexane side of the interface. The influence of the hydrophobic effect can be also noted in the orientational preferences of the peptides at the interface. The terminally blocked leucine is oriented such that its nonpolar side chain is buried in hexane, whereas the polar side chain of glutamine is immersed in water. The free energies of rotating the peptides along the axis parallel to the interface by more than 90 degrees are substantial. This indicates that peptide folding at interfaces is strong by driven by the tendency to adopt amphiphilic structures.     

Benchmark structures and binding energies of small water clusters with anharmonicity corrections

For (H(2)O)(n) where n = 1-10, we used a scheme combining molecular dynamics sampling with high level ab initio calculations to locate the global and many low lying local minima for each cluster. For each isomer, we extrapolated the RI-MP2 energies to their complete basis set limit, included a CCSD(T) correction using a smaller basis set and added finite temperature corrections within the rigid-rotor-harmonic-oscillator (RRHO) model using scaled and unscaled harmonic vibrational frequencies. The vibrational scaling factors were determined specifically for water clusters by comparing harmonic frequencies with VPT2 fundamental frequencies. We find the CCSD(T) correction to the RI-MP2 binding energy to be small (<1%) but still important in determining accurate conformational energies. Anharmonic corrections are found to be non-negligble; they do not alter the energetic ordering of isomers, but they do lower the free energies of formation of the water clusters by as much as 4 kcal/mol at 298.15 K.     

Conformational landscape of l-threonine in neutral,acid and basic solutions from vibrational circular dichroism spectroscopy and quantum chemical calculations

The biological relevance of amino acids is well known. They can be used as zwitterionic, cationic or anionic forms according to the pH of the medium where they are. Thus, our aim herein was to study the conformational preference of the polar amino acid l-threonine [C₄H₉NO₃, (2S,3R)-2-amino-3-hydroxybutyric acid] under different pH conditions. A conformational study in an aqueous solution of the dissociation equilibrium of the amino acid l-threonine was carried out for this purpose. We recorded, at room temperature, the Mid-IR, Far-IR, Raman and VCD spectra of l-threonine from the aqueous solutions at pH values 5.70 (zwitterionic species), 1.00 (protonated species) and 13.00 (deprotonated species). The number of conformers found with the conformational search was 9 zwitterions, 27 anions and 52 cations. Both the study of the conformational landscape and the theoretical analysis of the vibrational features were accomplished by using DFT and ab initio calculations, that is, B3LYP/6-311++G(d,p) level of theory for all the conformers obtained from the conformational search, M062X/6-311++G(d,p) and MP2/6-311++G(d,p) levels of theory for the most stable conformers. The presence of water was included with the IEF-PCM implicit hydration model. With regard to the zwitterion, the importance of the analysis of the low frequency region (700–30 cm^–1) in the Far-IR spectra should be noted, because it provides relevant information that can be used to determine the presence of the most stable structures.