Gaseous Arginine Conformers and Their Unique Intramolecular Interactions

Identifying the protonation site and the scope of non-proline cis-peptide bond conformations: a first-principles study on protonated oligopeptides

The existence of non-proline cis-peptide bond conformations of protonated triglycine proposed by us has been verified through a recent IR-IR double resonance experiment. However, the scope of such unique structures in protonated oligopeptides and whether protonation at amide oxygen is more stable than that at traditional amino nitrogen remain unsolved. In this study, the most stable conformers of a series of protonated oligopeptides were fully searched. Our findings reveal that the special cis-peptide bond structure appears with high energies for diglycine and is energetically less favored for tetra- and pentapeptides, while it acts as the global minimum only for tripeptides. To explore the formation mechanism of the cis-peptide bond, electrostatic potential analysis, and intramolecular interactions were analyzed. Advanced theoretical calculations confirmed that amino nitrogen is still preferred as the protonated site in most cases except glycylalanylglycine(GAG). The energy difference between the two protonated isomers of GAG is only 0.03 kcal mol^-1, indicating that the tripeptide is most likely to be protonated on the amide oxygen first. We also conducted chemical (infrared (IR)) and electronic (X-ray photoelectron spectra (XPS) and near-edge X-ray absorption fine structure spectra (NEXAFS)) structure calculations of these peptides to identify their notable differences unambiguously. This study thus provides valuable information for exploring the scope of cis-peptide bond conformation and the competition between two different protonated ways.

Extensive exploration of the conformational landscapes of neutral and terminally blocked prolines in the gas phase: A density functional theory study

Proline is an important amino acid that plays unique roles in the structures of peptides and proteins. The conformations of proline are searched by a thorough method, generating 3888 trial structures optimized at the B97D/6-311++G** level. A total of 23 conformations are found and their structural and energetic data are presented. All the proline conformers exhibit a coplanar feature for four of the five pyrrolidine ring atoms. The coplanar rule reduces the cost of the conformational search by a factor of 40. The theoretical composition-weighted infrared spectrum provides a good explanation of the experimental results. A conformational search of capped proline yields seven unique conformers, all with trans C-termini peptide planes. The trans C-termini rule further cuts by half the cost of the conformational search of proline-containing peptides. The theoretical composition of the cis N-termini peptide bonds at room temperature is 5.5%, agreeing with the experimental estimations of 3%–10%.

Combining classical molecular docking with self-consistent charge density-functional tight-binding computations for the efficient and quality prediction of ligand binding structure

To improve the successful prediction rate of the existing molecular docking methods, a new docking approach is proposed that consists of three steps: generating an ensemble of docked poses with a conventional docking method, performing clustering analysis of the ensemble to select the representative poses, and optimizing the representative structures with a low-cost quantum mechanics method. Three quantum mechanics methods, self-consistent charge density-functional tight-binding, ONIOM(DFT:PM6), and ONIOM(SCC-DFTB:PM6), are tested on 18 ligand-receptor bio-complexes. The rate of successful binding pose predictions by the proposed self-consistent charge density-functional tight-binding docking method is the highest, at 67%. The self-consistent charge density-functional tight-binding docking method should be useful for the structure-based drug design.

TorsiFlex: an automatic generator of torsional conformers. Application to the twenty proteinogenic amino acids

In this work, we introduce TorsiFlex, a user-friendly software written in Python 3 and designed to find all the torsional conformers of flexible acyclic molecules in an automatic fashion. For the mapping of the torsional potential energy surface, the algorithm implemented in TorsiFlex combines two searching strategies: preconditioned and stochastic. The former is a type of systematic search based on chemical knowledge and should be carried out before the stochastic (random) search. The algorithm applies several validation tests to accelerate the exploration of the torsional space. For instance, the optimized structures are stored and this information is used to prevent revisiting these points and their surroundings in future iterations. TorsiFlex operates with a dual-level strategy by which the initial search is carried out at an inexpensive electronic structure level of theory and the located conformers are reoptimized at a higher level. Additionally, the program takes advantage of conformational enantiomerism, when possible. As a case study, and in order to exemplify the effectiveness and capabilities of this program, we have employed TorsiFlex to locate the conformers of the twenty proteinogenic amino acids in their neutral canonical form. TorsiFlex has produced a number of conformers that roughly doubles the amount of the most complete work to date.

Genetic Algorithm Embedded with a Search Space Dimension Reduction Scheme for Efficient Peptide Structure Predictions

The computational determination of peptide conformations is a challenging task of finding minima in a high dimensional space. By combining the sampling efficiency of the genetic algorithm (GA) and the dimensionality reduction resulted from the backbone dihedral angle correlations, named as the path matrix (PM) method, a new searching algorithm, parallel microgenetic algorithm (PMGA), is proposed. Meanwhile, PMGA employs the density functional theory based energy as the fitness function and performs local geometry optimizations to enhance the reliability of its GA encoding strategy. Tests on peptides with up to eight amino-acid residues show PMGA is quite efficient for providing high-quality conformational coverages. The computational cost of the PMGA search increases slowly with the number of amino-acid residues in a peptide, with no sign of deterioration on the searching results for the increased length of the peptide. The PMGA method should therefore be useful for determining the conformations of oligopeptide, studying the protein-ligand interactions, and designing the peptide-based drugs.

Theoretical Spectroscopic Studies on Chemical and Electronic Structures of Selenocysteine and Pyrrolysine

The chemical and electronic structures of the 21st and 22nd proteinogenic amino acid selenocysteine (Sec), pyrrolysine (Pyl), and their derivatives (deprotonated and protonated ions) were extensively characterized for the first time. Through the fragment based step-by-step research on their potential energy surface (PES), electronic energies of the most stable conformers of Sec, Pyl and the related ions were finally determined at the advanced CBS-QB3 and DSD-PBEP86-D3(BJ)/aug-cc-pVTZ levels, respectively, with the identification of many new low-energy conformers. The infrared spectra (IR) at 298 K of the most abundant conformers in different forms were scaled by comparison with the anharmonic frequency calculations and analyzed comparing with the experimental spectra of similar molecules. The characteristic soft X-ray spectra (including X-ray photoelectron spectra (XPS) and near-edge X-ray absorption fine-structure spectra (NEXAFS)) of the most stable conformers at 498 K were also simulated. In particular, the two possible protonated configurations of Pyl can be clearly distinguished by their different spectral features. Furthermore, a small binding energy intersection appeared around 293 eV at the C 1s edge between the canonical and protonated Pyl conformers, which is different from all the previous studies. This work thus filled the gap in our knowledge by providing detailed information on the chemical and electronic structures of Sec and Pyl and will be a useful guidance for future experimental research.

SLIM Ultrahigh Resolution Ion Mobility Spectrometry Separations of Isotopologues and Isotopomers Reveal Mobility Shifts due to Mass Distribution Changes

We report on separations of ion isotopologues and isotopomers using ultrahigh-resolution traveling wave-based Structures for Lossless Ion Manipulations with serpentine ultralong path and extended routing ion mobility spectrometry coupled to mass spectrometry (SLIM SUPER IMS-MS). Mobility separations of ions from the naturally occurring ion isotopic envelopes (e.g., [M], [M+1], [M+2], ... ions) showed the first and second isotopic peaks (i.e., [M+1] and [M+2]) for various tetraalkylammonium ions could be resolved from their respective monoisotopic ion peak ([M]) after SLIM SUPER IMS with resolving powers of ∼400-600. Similar separations were obtained for other compounds (e.g., tetrapeptide ions). Greater separation was obtained using argon versus helium drift gas, as expected from the greater reduced mass contribution to ion mobility described by the Mason-Schamp relationship. To more directly explore the role of isotopic substitutions, we studied a mixture of specific isotopically substituted (15N, 13C, and 2H) protonated arginine isotopologues. While the separations in nitrogen were primarily due to their reduced mass differences, similar to the naturally occurring isotopologues, their separations in helium, where higher resolving powers could also be achieved, revealed distinct additional relative mobility shifts. These shifts appeared correlated, after correction for the reduced mass contribution, with changes in the ion center of mass due to the different locations of heavy atom substitutions. The origin of these apparent mass distribution-induced mobility shifts was then further explored using a mixture of Iodoacetyl Tandem Mass Tag (iodoTMT) isotopomers (i.e., each having the same exact mass, but with different isotopic substitution sites). Again, the observed mobility shifts appeared correlated with changes in the ion center of mass leading to multiple monoisotopic mobilities being observed for some isotopomers (up to a ∼0.04% difference in mobility). These mobility shifts thus appear to reflect details of the ion structure, derived from the changes due to ion rotation impacting collision frequency or momentum transfer, and highlight the potential for new approaches for ion structural characterization.

To Be or Not To Be a Molecular Ion: The Role of the Solvent in Photoionization of Arginine

Application of photoionization mass spectroscopy, a technique capable of assessing protonation states in complex molecules in the gas phase, is challenging for arginine due to its fragility. We report photoionization efficiencies in the valence region of aqueous aerosol particles produced from arginine solutions under various pH and vaporization conditions. By using ab initio calculations, we investigate the stability of different conformers. Our results show that neutral arginine fragments upon ionization in the gas phase but solvation stabilizes the molecular ion, resulting in different photoionization dynamics. We also report the valence-band photoelectron spectra of the aerosol solutions obtained at different pH values.

Gas-Phase Ion/Ion Chemistry as a Probe for the Presence of Carboxylate Groups in Polypeptide Cations

The reactivity of 1-hydroxybenzoyl triazole (HOBt) esters with the carboxylate functionality present in peptides is demonstrated in the gas phase with a doubly deprotonated dianion. The reaction forms an anhydride linkage at the carboxylate site. Upon ion trap collisional-induced dissociation (CID) of the modified peptide, the resulting spectrum shows a nominal loss of the mass of the reagent and a water molecule. Analogous phenomenology was also noted for model peptide cations that likely contain zwitterionic/salt-bridged motifs in reactions with a negatively charged HOBt ester. Control experiments indicate that a carboxylate group is the likely reactive site, rather than other possible nucleophilic sites present in the peptide. These observations suggest that HOBt ester chemistry may be used as a chemical probe for the presence and location of carboxylate groups in net positively charged polypeptide ions. As an illustration, deprotonated sulfobenzoyl HOBt was reacted with the [M+7H]⁷⁺ ion of ubiquitin. The ion was shown to react with the reagent and CID of the covalent reaction product yielded an abundant [M+6H-H₂O]⁶⁺ ion. Comparison of the CID product ion spectrum of this ion with that of the water loss product generated from CID of the unmodified [M+6H]⁶⁺ ion revealed the glutamic acid at residue 64 as a reactive site, suggesting that it is present in the deprotonated form. Graphical Abstract ᅟ.

Theoretical Calculation of the Thermodynamic Properties of 20 Amino Acid Ionic Liquids

The thermodynamic properties of gas-phase amino acid ionic liquids (AAILs) containing 20 amino acids ([AA]^-) and 1-ethyl-3-methylimidazolium ([Emim]⁺) are studied using a combination of the ab initio method, molecular dynamics simulations, Born-Haber (BH) cycle analysis, and isodesmic reactions. The M06-2X/TZVP method is used to explore the structure and dissociation enthalpies of [Emim][AA] by considering dispersion interaction, and the MP2/Aug-cc-pVTZ method is used to correct these enthalpies. The vaporization enthalpies of all 20 AAILs are calculated by molecular dynamics simulations, and the gas-phase formation enthalpies (Δ_f H) of the 20 [AA]^- anions and [Emim]⁺ cation are calculated by the density functional theory/M06-2X method and isodesmic reaction approaches. To obtain the Δ_f H of the AAILs, interconnections in the corresponding BH cycles are evaluated. A systematic study of the 20 [Emim][AA] ion pairs provides some initial factors contributing to the thermodynamic properties of AAILs: including length of the alkyl chain, interatomic electronic effects, steric repulsion from the cyclic group, and H-bonds formed by functional groups. Generally speaking, the results of this work provide insights into the structure-property relationships of not only ILs but also any ionic or molecular substance.

Infrared Multiple Photon Dissociation Spectroscopy of Cationized Canavanine: Side-Chain Substitution Influences Gas-Phase Zwitterion Formation†

Infrared multiple photon dissociation spectroscopy was performed on protonated and cationized canavanine (Cav), a non-protein amino acid oxy-analog of arginine. Infrared spectra in the XH stretching region (3000 - 4000 cm^-1) were obtained at the Centre Laser Infrarouge d'Orsay (CLIO) facility. Comparison of the experimental infrared spectra with scaled harmonic frequencies at the B3LYP/6-31+G(d,p) level of theory indicates that canavanine is in a canonical neutral form in CavH⁺, CavLi⁺, and CavNa⁺; therefore, these cations are charge-solvated structures. The infrared spectrum of CavK⁺ is consistent with a mixture of Cav in canonical and zwitterionic forms leading to both charge-solvated and salt-bridged cationic structures. The Cav moiety in CavCs⁺ is shown to be zwitterionic, forming a salt-bridged structure for the cation. Infrared spectra in the fingerprint region (1000 - 2000 cm^-1) obtained at the FELIX Laboratory in Nijmegen, Netherlands support these assignments. These results show that that a single oxygen atom substitution in the side chain reduces the stability of the zwitterion compared to that of the protein amino acid arginine (Arg), which has been shown previously to adopt a zwitterionic structure in ArgNa⁺ and ArgK⁺. This difference can be explained in part due to the decreased basicity of Cav (PA = 1001 kJ/mol) as compared to arginine (PA = 1051 kJ/mol), but not entirely, as lysine, which has nearly the same proton affinity as Cav, (~993 kJ/mol) forms only canonical structures with Na⁺, K⁺, and Cs⁺. A major difference between the zwitterionic forms of ArgM⁺ and CavM⁺ is that the protonation site is on the side chain for Arg and on the N-terminus for Cav. This results in systematically weaker salt bridges in the Cav zwitterions. In addition, the presence of another hydrogen-bonding acceptor atom in the side chain contributes to the stability of the canonical structures for the smaller alkali cations.

Identification of the smallest peptide with a zwitterion as the global minimum: a first-principles study on arginine-containing peptides

Zwitterions are believed to play an important role in determining the structures, properties and functions of peptides and proteins. However, the smallest peptide with a zwitterionic structure as the global minimum in the gas phase is still not yet identified. In this study, an effective step-by-step strategy has been used to characterize the stable conformers of arginine-containing peptides arginylalanine (ArgAla) and arginylserine (ArgSer). Energy calculations at the DSD-PBEP86-D3BJ/aug-cc-pVTZ level and further extrapolation to the complete basis set (CBS) limit have confirmed, for the first time, that ArgSer appears to be a promising candidate as the smallest peptide with a zwitterionic global minimum structure. First-principles simulations have been performed for near-edge X-ray absorption fine-structure (NEXAFS) spectra and X-ray photoelectron spectra (XPS) at C, N and O K-edges, as well as for infrared (IR) spectra of these arginine-containing peptides. Notable spectral differences were found which enable the unambiguous identification of different neutral forms in future experiments. Our study thus provides valuable insights into the structural stability of zwitterions with the increase of molecular size and illustrates the competition between the canonical and zwitterionic isomers.

An improved two-rotor function for conformational potential energy surfaces of 20 amino acid diamides

Predicting the three-dimensional structure of a protein from its amino acid sequence requires a complete understanding of the molecular forces that influences the protein folding process. Each possible conformation has its corresponding potential energy, which characterizes its thermodynamic stability. This is needed to identify the primary intra- and inter-molecular interactions, so that we can reduce the dimensionality of the problem, and create a relatively simple representation of the system. Investigating this problem using quantum chemical methods produces accurate results; however, this also entails large computational resources. In this study, an improved two-rotor potential energy function is proposed to represent the backbone interactions in amino acids through a linear combination of a Fourier series and a mixture of Gaussian functions. This function is applied to approximate the 20 amino acid diamide Ramachandran-type PESs, and results yielded an average RMSE of 2.36 kJ mol−1, which suggest that the mathematical model precisely captures the general topology of the conformational potential energy surface. Furthermore, this paper provides insights on the conformational preferences of amino acid diamides through local minima geometries and energy ranges, using the improved mathematical model. The proposed mathematical model presents a simpler representation that attempts to provide a framework on building polypeptide models from individual amino acid functions, and consequently, a novel method for rapid but accurate evaluation of potential energies for biomolecular simulations.

Experimental and theoretical investigations of infrared multiple photon dissociation spectra of arginine complexes with Zn2+ and Cd2+

Arginine (Arg) complexes with Zn²⁺ and Cd²⁺ were examined by infrared multiple photon dissociation (IRMPD) action spectroscopy using light from a free electron laser.

Computational study on single molecular spectroscopy of tyrosin-glycine, tryptophane-glycine and glycine-tryptophane

Quantum chemistry calculations play a fundamental role in revealing the molecular structures observed in gas-phase spectroscopic measurements. The supersonic jet cooling widely used in single molecular spectroscopy experiment is a non-equilibrium process and often causes confusion on the theoretical and experimental comparison. A computational approach is proposed here to account for the effect of the non-equilibrium cooling on the experimental spectra and applied to the cases of tyrosin-glycine (YG), tryptophane-glycine (WG) and glycine-tryptophane (GW). The low energy conformers of YG, WG and GW are obtained through thorough conformational searches. The structural features and equilibrium distributions of conformations and the energy barriers for conformer conversions are then determined. Three classes of transition energy barriers, high, medium and low, are found for the conversions among conformers with distinctly different, similar and the same structural types, respectively. The final conformation populations are determined by assuming an initial temperature of about 450 K and allowing for only the conformation conversion with a low energy barrier to occur during the rapid cooling process. The results provide a natural explanation for the numbers of YG, WG and GW conformations observed experimentally. The theoretical conformation assignments are also in good agreement with the experimental IR data.

Systematic Study on Hydrated Arginine: Clear Theoretical Evidence for the Canonical-to-Zwitterionic Structure Transition

Extensive ab initio investigations have been performed to characterize the stable conformers of hydrated arginine (Arg-H₂O). Many new low-energy canonical Arg-H₂O conformers were identified and they are more stable than previous results. The large energy differences (more than 5.00 kcal mol^-1) between the canonical and zwitterionic Arg-H₂O isomers calculated by the composite CBS-QB3 method confirmed the dominance of the zwitterions. The micro effects of corrections of the zero-point energy and the basis set superposition error on the stability of hydrated isomers were carefully examined for the first time. The infrared (IR) spectra were simulated at a recommended temperature and the notable spectral differences enable the unambiguous identification of the different hydrated forms. Further transition state calculations revealed that the canonical Arg-H₂O can be transformed to the zwitterions using the amino group as a bridge. Our study thus shows valuable insights into the hydration of large flexible molecules and provides solid theoretical evidence for the canonical-to-zwitterionic structure transition of hydrated arginine.

Isolated complexes of the amino acid arginine with polyether and polyamine macrocycles, the role of proton transfer

Protonated arginine interacts with 12-crown-4 through the guanidinium side group. In the complex with the N-substituted analog cyclen, the dominant conformation is the result of the proton transfer from the carboxylic acid group of the amino acid to the macrocycle.

Identification of the protonation site of gaseous triglycine: the cis-peptide bond conformation as the global minimum

Extensive ab initio investigations have been performed to characterize stable conformers of protonated triglycine (GGGH) in the gas phase.

Enhanced Basicity of Push-Pull Nitrogen Bases in the Gas Phase

Nitrogen bases containing one or more pushing amino-group(s) directly linked to a pulling cyano, imino, or phosphoimino group, as well as those in which the pushing and pulling moieties are separated by a conjugated spacer (C═X)_n, where X is CH or N, display an exceptionally strong basicity. The n-π conjugation between the pushing and pulling groups in such systems lowers the basicity of the pushing amino-group(s) and increases the basicity of the pulling cyano, imino, or phosphoimino group. In the gas phase, most of the so-called push-pull nitrogen bases exhibit a very high basicity. This paper presents an analysis of the exceptional gas-phase basicity, mostly in terms of experimental data, in relation with structure and conjugation of various subfamilies of push-pull nitrogen bases: nitriles, azoles, azines, amidines, guanidines, vinamidines, biguanides, and phosphazenes. The strong basicity of biomolecules containing a push-pull nitrogen substructure, such as bioamines, amino acids, and peptides containing push-pull side chains, nucleobases, and their nucleosides and nucleotides, is also analyzed. Progress and perspectives of experimental determinations of GBs and PAs of highly basic compounds, termed as "superbases", are presented and benchmarked on the basis of theoretical calculations on existing or hypothetical molecules.

Molecular thermodynamics of metabolism: quantum thermochemical calculations for key metabolites

The present work is the first of a series of papers aiming at a coherent and unified development of the thermodynamics of metabolism and the rationalization of feasibility analysis of metabolic pathways. The focus in this part is on high-level quantum chemical calculations of the thermochemical quantities of relatively heavy metabolites such as amino acids/oligopeptides, nucleosides, saccharides and their derivatives in the ideal gas state. The results of this study will be combined with the corresponding hydration/solvation results in subsequent parts of this work in order to derive the desired thermochemical quantities in aqueous solutions. The above metabolites exist in a vast conformational/isomerization space including rotational conformers, tautomers or anomers exhibiting often multiple or cooperative intramolecular hydrogen bonding. We examine the challenges posed by these features for the reliable estimation of thermochemical quantities. We discuss conformer search, conformer distribution and averaging processes. We further consider neutral metabolites as well as protonated and deprotonated metabolites. In addition to the traditional presentation of gas-phase acidities, basicities and proton affinities, we also examine heats and free energies of ionic species. We obtain simple linear relations between the thermochemical quantities of ions and the formation quantities of their neutral counterparts. Furthermore, we compare our calculations with reliable experimental measurements and predictive calculations from the literature, when available. Finally, we discuss the next steps and perspectives for this work.

Comparative density functional theory and density functional tight binding study of arginine and arginine-rich cell penetrating peptide TAT adsorption on anatase TiO2

A comparative DFT-DFTB study of geometries and electronic structures of arginine, arginine dipeptide, and arginine-rich cell penetrating peptide TAT on the surface of TiO₂.

The computational prediction of Raman and ROA spectra of charged histidine tautomers in aqueous solution

Histidine is a key component of a number of enzymatic mechanisms, and undertakes many functionalities in biochemical systems.

Theoretical spectroscopic studies on chemical and electronic structures of arginylglycine

The global minimum of the dipeptide ArgGly is found to be in the canonical form, rather than the zwitterionic form.

Comprehensive analysis of energy minima of the 20 natural amino acids

Energy minima of the 20 natural amino acids (capped by a peptide bond at both the N and the C termini, CH3-C(═O)-N(H)-(H)Cα(R)-C(═O)-N(H)-CH3), were obtained by ab initio geometry optimization. Starting with a large number of minima, quickly generated by MarvinView, geometry optimization at the HF/6-31G(d,p) level of theory reduced the number of minima, followed by further optimization at the B3LYP/apc-1 and MP2/cc-pVDZ levels, which caused some minima to disappear and some stable minima to migrate on the Ramachandran map. There is a relation between the number of minima and the size and the flexibility of the side chain. The energy minima of the 20 amino acids are mainly located in the regions of βL, γL, δL, and αL of the Ramachandran map. Multipole moments of atoms occurring in the fragment [-NH-Cα-C(═O)-] common to all 20 amino acids were calculated at the three levels of theory mentioned above. The near parallelism in behavior of these moments between levels of theory is beneficial toward estimating moments with the more expensive B3LYP and MP2 methods from data calculated with the cheaper HF method. Finally, we explored the transferability of properties between different amino acids: the bond length and angles of the common fragment [-NH-Cα(HαCβ)-C'(═O)-] in all amino acids except Gly and Pro. All bond lengths are highly transferable between different amino acids, and the standard deviations are small.

Gas-phase enthalpies of formation and enthalpies of sublimation of amino acids based on isodesmic reaction calculations

Accurate gas-phase enthalpies of formation (ΔfH298°) of 20 common α-amino acids, seven uncommon amino acids, and three small peptides were calculated by combining G4 theory calculations with an isodesmic reaction approach. The internal consistency over a set of ΔfH298°(g) values was achieved by sequential adjustment of their values through the isodesmic reactions. Four amino acids, alanine, β-alanine, sarcosine, and glycine, with reliable internally self-consistent experimental data, were chosen as the key reference compounds. These amino acids together with about 100 compounds with reliable experimental data (their accuracy was supported by G4 calculations) were used to estimate the enthalpies of formation of remaining amino acids. All of the amino acids with the previously established enthalpies of formation were later used as the reference species in the isodesmic reactions for the other amino acids. A systematic comparison was made of 14 experimentally determined enthalpies of formation with the results of calculations. The experimental enthalpies of formation for 10 amino acids were reproduced with good accuracy, but the experimental and calculated values for 4 compounds differed by 11–21 kJ/mol. For these species, the theoretical ΔfH298°(g) values were suggested as more reliable than the experimental values. On the basis of theoretical results, the recommended values for the gas-phase enthalpies of formation were also provided for amino acids for which the experimental ΔfH298°(g) were not available. The enthalpies of sublimation were evaluated for all compounds by taking into account the literature data on the solid-phase enthalpies of formation and the ΔfH298°(g) values recommended in our work. A special attention was paid to the accurate prediction of enthalpies of formation of amino acids from the atomization reactions. The problems associated with conformational flexibility of these compounds and harmonic treatment of low frequency torsional modes were discussed. The surprisingly good agreement between the ΔfH298°(g) values calculated from the atomization and isodesmic reactions is largely the result of a fortuitous mutual compensation of various corrections used in the atomization reaction procedure.

Discovery of Most Stable Structures of Neutral and Anionic Phenylalanine through Automated Scanning of Tautomeric and Conformational Spaces

We have developed a software tool for combinatorial generation of tautomers and conformers of small molecules. We have demonstrated it by performing a systematic search for the most stable structures of neutral and anionic phenylalanine (Phe) using electronic structure methods. For the neutral canonical tautomer we found out that the conformers with and without the intramolecular (O)H···NH2 hydrogen bond are similarly stable, within the error bars of our method. A unique IR signature of the conformer without the hydrogen bond has been identified. We also considered anions of Phe, both valence type and dipole-bound. We have found out that tautomers resulting from proton transfer from the carboxylic OH to the phenyl ring do support valence anions that are vertically strongly bound, with electron vertical detachment energies (VDE) in a range of 3.2-3.5 eV. The most stable conformer of these valence anions remains adiabatically unbound with respect to the canonical neutral by only 2.17 kcal/mol at the CCSD(T)/aug-cc-pVDZ level. On the basis of our past experience with valence anions of nucleic acid bases, we suggest that the valence anions of Phe identified in this report can be observed experimentally. The most stable conformer of canonical Phe is characterized by an adiabatic electron affinity of 53 meV (a dipole-bound state).