Glycine Conformers Research Articles

Harmonic and anharmonic vibrational computations for biomolecular building blocks: Benchmarking DFT and basis sets by theoretical and experimental IR spectrum of glycine conformers.

Advanced vibrational spectroscopic experiments have reached a level of sophistication that can only be matched by numerical simulations in order to provide an unequivocal analysis, a crucial step to understand the structure-function relationship of biomolecules. While density functional theory (DFT) has become the standard method when targeting medium-size or larger systems, the problem of its reliability and accuracy are well-known and have been abundantly documented. To establish a reliable computational protocol, especially when accuracy is critical, a tailored benchmark is usually required. This is generally done over a short list of known candidates, with the basis set often fixed a priori. In this work, we present a systematic study of the performance of DFT-based hybrid and double-hybrid functionals in the prediction of vibrational energies and infrared intensities at the harmonic level and beyond, considering anharmonic effects through vibrational perturbation theory at the second order. The study is performed for the six-lowest energy glycine conformers, utilizing available "state-of-the-art" accurate theoretical and experimental data as reference. Focusing on the most intense fundamental vibrations in the mid-infrared range of glycine conformers, the role of the basis sets is also investigated considering the balance between computational cost and accuracy. Targeting larger systems, a broad range of hybrid schemes with different computational costs is also tested.

First Glycine Isomer Detected in the Interstellar Medium: Glycolamide (NH2C(O)CH2OH)

We report the first detection in the interstellar medium (ISM) of a C2H5O2N isomer: syn-glycolamide (NH2C(O)CH2OH). The exquisite sensitivity at sub-mK levels of an ultradeep spectral survey carried out with the Yebes 40 m and IRAM 30 m telescopes toward the G+0.693–0.027 molecular cloud has allowed us to unambiguously identify multiple transitions of this species. We derived a column density of (7.4 ± 0.7) × 1012 cm−2, which implies a molecular abundance with respect to H2 of 5.5 × 10−11. The other C2H5O2N isomers, including the higher-energy anti conformer of glycolamide and two conformers of glycine, were not detected. The upper limit derived for the abundance of glycine indicates that this amino acid is surely less abundant than its isomer glycolamide in the ISM. The abundances of the C2H5O2N isomers cannot be explained in terms of thermodynamic equilibrium; thus, chemical kinetics need to be invoked. While the low abundance of glycine might not be surprising, based on the relative low abundances of acids in the ISM compared to other compounds (e.g., alcohols, aldehydes, or amines), several chemical pathways can favor the formation of its isomer glycolamide. It can be formed through radical–radical reactions on the surface of dust grains. The abundances of these radicals can be significantly boosted in an environment affected by a strong ultraviolet field induced by cosmic rays, such as that expected in G+0.693–0.027. Therefore, as shown by several recent molecular detections toward this molecular cloud, it stands out as the best target to discover new species with carbon, oxygen, and nitrogen with increasing chemical complexity.

Deep search for glycine conformers in Barnard 5

ABSTRACT One of the most fundamental hypotheses in astrochemistry and astrobiology states that crucial biotic molecules like glycine (NH2CH2COOH) found in meteorites and comets are inherited from early phases of star formation. Most observational searches for glycine in the interstellar medium have focused on warm high-mass molecular cloud sources. However, recent studies suggest that it might be appropriate to shift the observational focus to cold low-mass sources. We aim to detect glycine towards the so-called methanol hotspot in the Barnard 5 dark cloud. The hotspot is a cold source (Tgas ≈ 7.5 K) with yet high abundances of complex organic molecules (COMs) and water in the gas phase. We carried out deep pointed observations with the Onsala 20 m telescope, targeting several transitions of glycine conformers I and II (Gly-I and Gly-II) in the frequency range 70.2–77.9 GHz. No glycine lines are detected towards the targeted position, but we use a line stacking procedure to derive sensitive abundance upper limits w.r.t. H2 for Gly-I and Gly-II, i.e. ≤(2–5) × 10−10 and ≤(0.7–3) × 10−11, respectively. The obtained Gly-II upper limits are the most stringent for a cold source, while the Gly-I upper limits are mostly on the same order as previously measured limits. The measured abundances w.r.t. H2 of other COMs at the B5 methanol hotspot range from 2 × 10−10 (acetaldehyde) to 2 × 10−8 (methanol). Hence, based on a total glycine upper limit of (2–5) × 10−10, we cannot rule out that glycine is present but undetected.

Elastic Electron scattering by thermal mixture of glycine conformers in gas phase

A theoretical study of electron scattering by a thermal mixture of glycine molecules in the energy range from 1 to 10 eV is performed using the UK-RMol codes which are based on the R-Matrix method. The six lowest relative Gibbs free energies glycine conformers considered, Ip, IIp, IIn, IIIp, IIIn and IVn, are significantly populated in thermal mixtures. All these conformers present similar resonance structures in the eigenphase sums: a lower-energy resonance state near 1.8 eV and another at higher-energy above 7 eV. For the six conformers the lowest resonance lies between 1.75 eV and 2.21 eV. The very large dipole moments of 6.32 D and 5.67 D for IIp and IIn, respectively, makes the magnitude of their cross sections significantly larger than other conformers, which increases the average cross sections in thermal mixtures compared with the cross sections of the lowest energy Ip conformer. Three conformer population sets are used to calculate the averaged differential and integral cross sections: two theoretical sets based on the relative Gibbs free energies and another set that aims to mimic experiment based on the observed populations. The averaged cross sections are similar for all population sets, but differ from the Ip conformer cross section. This suggests that, for large and flexible molecules, the computed average cross sections should be used when comparing with experimental data.

Dynamics and mechanisms of nonradiative photodissociation of glycine: A theoretical study

Photochemistry of small biomolecules is fundamental to understand the photochemical reactions of larger molecules, such as proteins. In this work, the dynamics and mechanisms of photodissociations of glycine conformers were studied using the DFT, TD-DFT and CASPT2 methods with the aug-cc-pVDZ basis set and microcanonical molecular dynamics simulations with surface hopping dynamics (NVE-MDSH). This study emphasized unimolecular dissociations and isomerization, nonradiative S1 → S0 relaxations that generate molecular products and the interplay between photoenergies and thermal energies. Four nonplanar conformers were suggested by the TD-DFT/B3LYP/aug-cc-pVDZ and CASPT2(8,14)/aug-cc-pVDZ methods to be stable in the S1 state. The potential energy curves obtained from the TD-DFT/B3LYP/aug-cc-pVDZ and CASPT2(8,14)/aug-cc-pVDZ methods and SA-CPMCSCF/6-31G(d) conical intersection optimizations suggested S0/S1 intersections for distorted glycine structures, Cα–N and NH dissociations and NH → OC isomerization. The NVE-MDSH results showed that although no dissociated molecular product was observed in the S1 state, isomerization-mediated dissociation and exothermic S1 → S0 relaxation temperature could lead to eight molecular product channels, in which the vertically excited Wigner-sampled structures generated eleven reactive and stable molecular products in different temperature ranges. These thermally selective reactions favored the lowest energy conformer (structure Ip) as the precursor, from which reactive and stable molecular products were formed above the threshold exothermic relaxation temperature. These theoretical results showed in detail for the first time how unimolecular photodissociations and nonradiative S1 → S0 relaxations create molecules in cold interstellar media without heat transfer from the surroundings. The results in this work could be used in future theoretical and experimental studies on the same or similar systems.

Anticancer potential of novel 5-Fluorouracil co-crystals against MCF7 breast and SW480 colon cancer cell lines along with docking studies

In the present investigation, 5-Fluorouracil co-crystals with four cyclic dimers of amino acids (Glycine, Tryptophane, Leucine and Alanine conformers are prepared via co-crystallization route, with an aim to improve its anticancer effectiveness and to minimize its associated drawbacks. The prepared co-crystals were characterized by FTIR and PXRD techniques. FTIR revealed the presence of respective functional groups in the prepared co-crystals. Frequencies (v) of NH (3416 cm−1) and carbonyl group (1671 cm−1) in the 5-Fu (FTIR) spectrum were considerably moved in all co-crystal’s spectra exhibiting the development of new interactions. 5-Fu peak at 2θ = 28.48° was visibly transformed in the co-crystal’s graphs of PXRD. MTT assays was studied on MCF7 breast and SW480 colon cancer cell lines using 0.78 to 200 μg mL−1 dose concentration. Co-crystals with Tryptophane and Leucine cyclic dimers revealed highest potential (99 % and 100 %) respectively, against colon cancer cell line Likewise Alanine and Tryptophane dimers furnished promising efficiency (100 %) against MCF7 cell line Genetic Optimization for Ligand Docking/GOLD was applied to evaluate the latent anti-tumor behaviors against the proteins [C-myc. (PDB ID: 6G6K, Thymidylate synthase (PDB ID:1HVY) and protein kinase (PDB ID: 2X18). Results revealed that the developed 5-Fluorouracil co-crystals have promising antitumor efficacy as compared to already reported 5-Fu co-crystals and 5-Fu alone.

A high level theory investigation on the lowest-lying ionization potentials of glycine (NH2CH2COOH).

In this work, an investigation on the ionization potentials (IPs) of the glycine molecule (NH2CH2COOH) is presented. IPs ranging up to ∼20 eV were probed for each of the six conformations considered, with the referred threshold being chosen based on both: (i) the observations by recent photoelectron-photoion coincidence (PEPICO) experiments and (ii) the energy range of relevance to the modeling of other photo-induced processes (e.g., photoionization). For computing the IPs, the equation-of-motion ionization potential coupled-cluster with single and double excitations method (EOMIP-CCSD) was employed with large correlation consistent aug-cc-pVXZ and aug-cc-pCVXZ (X = D, T, and Q) basis sets. Extrapolation to the complete basis set limit and consideration of core electron correlation effects were also taken into account. Subsequently, the Feller-Peterson-Dixon (FPD) approach was used for considering all the contributions and to obtain accurate IPs. In addition, coupled-cluster with single and double excitations as well as perturbative triples, CCSD(T), was also used with the aug-cc-pVTZ basis set. When compared to each other, results obtained through the use of these approaches yielded excellent agreement. In general, the outcomes from the present work provide additional information to the insights gathered from the recent PEPICO experiments as well as accurate IPs for all 6 conformations of glycine using an approach based on high levels of theory. Hence, it is expected that other investigations focusing on photo-induced processes originating from NH2CH2COOH (for instance, the computational modeling of its photoionization) will be motivated for study in the future.

Theoretical Investigation of Glycine Micro-Solvated. Energy and NMR Spin Spin Coupling Constants Calculations

Glycine in its neutral form can exist in the gas phase while its zwitterion form is more stable in water solution, but how many waters are actually necessary to stabilize the zwitterionic structure in the gas phase? Are the intramolecular isotropic spin spin coupling constants sensitive enough to accuse the change in the environment? or the conformer observed? These and related questions have been investigated by a computational study at the level of density functional theory employing the B3LYP functional and the 6-31++G**-J basis set. We found that at least two water molecules explicitly accounted for in the super-molecule structure are necessary to stabilize both conformers of glycine within a water polarizable continuum model. At least half of the SSCCs of both conformers are very stable to changes in the environment and at least four of them differ significantly between Neutral and Zwitterion conformation.

Structural and Energetic Properties of Amino Acids and Peptides Benchmarked by Accurate Theoretical and Experimental Data.

Structural, energetic, and spectroscopic data derived in this work aim at the setup of an "experimentally validated" database for amino acids and polypeptides conformers. First, the "cheap" composite scheme (ChS, CCSD(T)/(CBS+CV)MP2) is tested for evaluation of conformational energies of all eight stable conformers of glycine, by comparing to the more accurate CCSD(T)/CBS+CV computations (Phys. Chem. Chem. Phys. 2013, 15, 10094-10111 and J Mol. Model. 2020, 26, 129). The recently proposed jun-ChS (J. Chem. Theory and Comput. 2020, 16, 988-1006), employing the jun-cc-pVnZ basis set family for CCSD(T) computations and CBS extrapolation, yields conformational energies accurate to 0.2 kJ·mol-1, at reduced computational cost with respect to aug-ChS employing aug-cc-pVnZ basis sets. The jun-ChS composite scheme is further applied to derive conformational energies for three dipeptide analogues Ac-Gly-NH2, Ac-Ala-NH2, and Gly-Gly. Finally, dipeptide conformational energies and semiexperimental equilibrium rotational constants along with the CCSD(T)/(CBS+CV)MP2 structural parameters (J. Phys. Chem. Lett. 2014, 5, 534-540) stand as the reference for benchmarking of selected density functional methodologies. The double-hybrid functionals B2-PLYP-D3(BJ) and DSD-PBEP86, perform best for structural and energetic characterization of all dipeptide analogues. From hybrid functionals CAM-B3LYP-D3(BJ) and ωB97X-D3(BJ) represent promising methods applicable for larger peptide-based systems for which computations with double-hybrid functionals are not feasible.

Conformers of dehydrogenated glycine isomers.

We report a comprehensive ab initio investigation of the conformers of dehydrogenated glycine radicals using the STO-3G, 3-21G, and aug-cc-pVDZ (aVDZ) basis sets and the UHF and UMP2 (H2 N-CH-COOH and HN-CH2 -COOH) as well as MCSCF and MRCI (H2 N-CH2 -COO) methods via two different conformational search strategies generating initial structures for optimizations by (a) removing H atoms from glycine conformers and (b) scanning torsional angles describing internal rotation along the CC, CN, and CO (except for H2 N-CH2 -COO) bonds of the radicals. We find four H2 N-CH-COOH {InCH , IInCH , IIInCH , IVnCH } and seven HN-CH2 -COOH {IpNH , IIpNH , IIInNH , IVpNH VnNH , VIpNH , VIIpNH } conformers with classical(adiabatic) relative energies of {0.00(0.00), 1.57(1.55), 5.25(5.03), 9.85(9.72)} and {0.00(0.00), 0.78(1.06), 1.93(2.08), 3.34(3.16), 3.39(3.29), 5.00(4.86), 9.27(8.87)} kcal/mol, respectively, obtained with UCCSD(T)-F12b/aug-cc-pVTZ(+UCCSD(T)-F12b/aVDZ ZPE correction) and four H2 N-CH2 -COO {IpCOO , IInCOO , IIIpCOO , IVnCOO } conformers with MRCI-F12+Q/aVDZ(+MRCI/aVDZ ZPE correction) energies of {0.00(0.00), 1.65(1.64), 1.78(1.75), 2.21(2.21)} kcal/mol, where n and p denote C1 and Cs symmetry. The MRCI-F12+Q[UCCSD(T)-F12b] InCH → IpNH and InCH → IpCOO classical(adiabatic) isomerization energies are 18.51(17.32)[21.20(20.01)] and 31.88(31.66) kcal/mol, respectively.

Toward accurate prediction of amino acid derivatives structure and energetics from DFT: glycine conformers and their interconversions.

This work provides the accurate reference data for structural and energetic properties relevant for computational studies of amino acids and polypeptides. Glycine due to its small size allows for detailed theoretical explorations of its whole conformational space. The reference energies are computed at the CCSD(T)/CBS+CV level on the best estimated geometries of all local minima and the transition states. For the minima, we complete the set of reference structures reported in Phys. Chem. Chem. Phys., 2013, 15, 10094, by determining the CCSD(T)/(CBS+CV)MP2 quality geometries for the two highest energy conformers VIIp/tcc and VIIIn/gtc. These data stand as the reference to asses reliability and accuracy of less expensive computational models, with particular focus on dispersion-corrected hybrid and double-hybrid DFT approaches, considering several basis sets of double- and triple-ζ quality. Based on results for minima the B2LYP-D3(BJ)/aug-cc-pVTZ level is set as the reference for transition states geometries. Considering accuracy of both single point energies and structural parameters B2PLYP(-D3BJ) and DSDPBEP86 in conjunction with aug-cc-pVTZ basis set can be recommended for reference studies of amino-acids and small poly-peptides, while B3LYP(-D3(BJ)) shown to be the most robust from considered hybrid DFT approaches. Graphical abstract TOC: Benchmarking DFT for amino acid analogues: highly accurate characterization of energies and structures from full glycine conformational space.

High-level theoretical study of the evolution of abundances and interconversion of glycine conformers**Project supported by the Young Scientists Funds of the National Natural Science Foundation of China (Grant Nos. 11404154 and 11304136).

The relative conformer energies of glycine are evaluated by using a focal point analysis expressed as (). The conformer abundances at various temperatures (298−500 K) are calculated based on the relative energies and Boltzmann statistical thermostatistical analysis with and without considering internal hindered rotations. A comparison between the available Raman spectrum and the electron momentum spectrum confirms that the influence of rigid-rotor hindered rotation on the conformational proportions of glycine is considerable, especially for the IIIp structure. The conformational interconversions are discussed. It is found that with increasing temperature, the mole fraction of IIn keeps constant and Ip structure can convert into IVn and IIIp, leading to the decrease in the weight of Ip and the increase in the weights of IVn and IIIp conformers, which is in accordance with experimental observations.

Can THF hydrogen bond to glycine as strong as water?

Hydrogen bond complexation between glycine and THF and between glycine and water involving four lowest-energy glycine conformers have been studied. The complexes have been investigated in the gas phase at the ab initio molecular orbital theory (MP2) with aug-cc-pVDZ basis set and density functional theory (B3LYP) with aug-cc-pVTZ basis set. Bader’s theory of atoms in molecules (AIM), natural bond orbital (NBO), and symmetry adapted perturbation theory (SAPT) analyses are employed to elucidate the interaction characteristics in the complexes. The premise that the hydrogen bond donor ability of the O–H group of the carboxyl group dominates the interaction between glycine and THF and between glycine and water is confirmed. It is found that in comparison with water, THF binds more strongly to glycine. The quantum studies indicate that contribution of N–H···O and C–H···O hydrogen bonds in the complexes, although lower in magnitude to O–H···O interactions, play an important role in the stability of complexes. The blue and red shifts in the stretching frequencies of the hydrogen bond donors X–H (X = O, C, N) have also been related to stabilization energies. Decomposition of the stabilization energy based on the SAPT method clearly indicates the dominant role of the electrostatic interactions in all the complexes under study; however, induction and dispersion interaction terms are relatively higher in glycine–THF complexes.

On-the-Fly ab Initio Semiclassical Calculation of Glycine Vibrational Spectrum.

We present an on-the-fly ab initio semiclassical study of vibrational energy levels of glycine, calculated by Fourier transform of the wavepacket correlation function. It is based on a multiple coherent states approach integrated with monodromy matrix regularization for chaotic dynamics. All four lowest-energy glycine conformers are investigated by means of single-trajectory semiclassical spectra obtained upon classical evolution of on-the-fly trajectories with harmonic zero-point energy. For the most stable conformer I, direct dynamics trajectories are also run for each vibrational mode with energy equal to the first harmonic excitation. An analysis of trajectories evolved up to 50 000 atomic time units demonstrates that, in this time span, conformers II and III can be considered as isolated species, while conformers I and IV show a pretty facile interconversion. Therefore, previous perturbative studies based on the assumption of isolated conformers are often reliable but might be not completely appropriate in the case of conformer IV and conformer I for which interconversion occurs promptly.

Development and Implementation of Advanced Fitting Methods for the Calculation of Accurate Molecular Structures.

The determination of accurate equilibrium molecular structures plays a fundamental role for understanding many physical-chemical properties of molecules, ranging from the precise evaluation of the electronic structure to the analysis of dynamical and environmental effects in tuning their overall behavior. For this purpose the so-called semiexperimental approach, based on a nonlinear least-squares fit of the moments of inertia associated with a set of available isotopologues, allows one to obtain very accurate results, without the unfavorable computational cost characterizing high-level quantum chemical methods. In the present work the MSR (Molecular Structure Refinement) software for the determination of equilibrium structures by means of the semiexperimental approach is presented, and its implementation is discussed in some detail. The software, which is interfaced with a powerful graphical user interface, includes different optimization algorithms, an extended error analysis, and a number of advanced features, the most remarkable ones concerning the choice of internal coordinates and the method of predicate observations. In particular, a new black-box scheme for defining automatically a suitable set of nonredundant internal coordinates of A1 symmetry in place of the customary Z-matrix has been designed and tested. Finally, the implementation of the method of the predicate observations is discussed and validated for a set of test molecules. As an original application, the method is employed for the determination of the semiexperimental structure for the most stable conformer of glycine.

Computational studies on the interactions of glycine amino acid with graphene, h-BN and h-SiC monolayers.

In the present work, the adsorption of glycine amino acid and its zwitterionic form onto three different hexagonal sheets, namely graphene, boron-nitride (h-BN) and silicon carbide (h-SiC), has been investigated within the framework of Density Functional Theory (DFT) calculations. The energetics and geometrical parameters of the considered systems have been explored at the GGA-PBE level in combination with Grimme's empirical dispersion corrections with Becke-Johnson damping, the DFT-D3(BJ) method. Based on the obtained results, we found that both the glycine molecule and its zwitterionic conformation tend to be chemisorbed onto the surface of h-SiC (Eads ranges from -1.01 to -1.319 eV) while the types of interactions are recognized to be of non-covalent nature for the case of graphene (Eads ranges from -0.121 to -0.345 eV) and h-BN (Eads ranges from -0.103 eV to -0.325 eV) systems. Moreover, the empirical dispersion corrections applied in these calculations significantly improved the results and confirmed the crucial role of dispersion corrections in obtaining reliable geometries and adsorption energies. Our findings revealed that the electronic properties of the considered systems did not change during the adsorption process and these monolayers preserve their inherent electronic properties as they interact with the glycine molecule. Using the SMD implicit solvation model, the effect of solvation has also been evaluated by re-optimizing the structures within a medium with a dielectric constant of 78.39 (liquid water) and it has been shown that the strength of the interaction between the glycine conformers and hexagonal sheets has decreased. The accuracy of the obtained values has been evaluated by some benchmark calculations at the hybrid PW6B95 level of theory and reasonable consistency is found between the results of the PBE-D3 method and our benchmark system. In summary, h-SiC exhibited the highest affinity toward glycine conformers and gained an important edge over other monolayers. Our findings would actively encourage experimentalists to explore the potential applications of these materials in drug delivery, biofunctionalization of nanostructured monolayers as well as electronic and nanosensor devices.

A new approach to understanding structure, functions and classificasion of GABA-benzodiazepine receptor complex, a molecular target for creation of new anticonvulsants on the base of inhibitory amino acids

The GABA molecule was shown to the methods of quantum mechanic characteristics and molecular geometry has three conformational states: linear (GABA-1 conformer), cyclic (GABA-2 comformer) and bucket-like (GABA-3 conformer). The play different functions in the brain neurons: cyclic and bucket-like conformers play role of endogenous transmitters, and linear conformer participates in neuronal metabolism. The theoretical conformational analysis shows there are two types of GABA receptors in the CNS neurons: GABA-2 receptors, agonists of which are cyclic conformer of GABA, glycine and β-alanine and antagonists are bemegride, pentilentetrazol and strychnine; and GABA-3 receptors, agonists of which is bucket-like conformer of GABA and antagonists are picrotoxin and bicuculline. Anticonvulsive and other behavioral effects of derivatives of barbituric acid, benzazepine, benzodiazepine, gidantoine, succinimide and oxasolidindione are realized probably via GABA-2 receptors to switch on them the following functional centers of their structure are nessesary: α, γ and [δ-ε] for barbitirates; β, [δ-ε] and γ for carbamazepine; β and [δ-ε] for benzodiazepine derivatives, gabapentine and vigabatrine; α, β, γ and [δ-ε] for gidantoine and oxasolidindione derivatives; α, β, γ for succinimide derivatives. The power of any behavioral effect of anticonvulsants and inhibitory amino acids depends on power, location and numbers of hydrogen bounds developed between active centers of pharmacophore of anticonvulsant or inhibitory amino acids and active centers of functional skeleton of GABA-2 receptor complex, these properties determine absense of nootropic activity in anticonvulsive drugs and presense of them in inhibitory amino acids. It is concluded there are perspectives of synthesis of conpounds, pharmacophore of which should be like as cyclic conformer of GABA, glycine and β-alanine on their quantum mechanic characteristics and molecular geometry

Conformational free energy surfaces of non-ionized glycine in aqueous solution

Ab initio calculations on glycine and quantum mechanical/molecular mechanical molecular dynamics simulations (QM/MM-MD) on solvated non-ionized glycine were performed to explore the free energy landscapes of non-ionic glycine conformers in aqueous solution. Among nine different conformers of glycine, QM/MM-MD simulations found ttc and gtc conformers stable in addition to ttt, ccc, gtt, tct and gct which were well known as stable isomers in pure QM calculation. The stabilities of ttc and gtc come from a strong solvation at their carboxylic group side (–COOH) in solution. The preferred rotation along C–C (φ) as compared to C–O (θ) in both pure QM calculations and QM/MM-MD indicates the importance of intramolecular effects in determining relative free energies. On the other hand, the existence of stable ttc and gtc conformers only in solution phase clearly shows the importance of intermolecular interaction by explicit solvents. The same intermolecular interactions have a mixed effect on the free energy barriers. They reduced the barriers of A (ccc) → B (gtc) and A (ccc) → C (gct) isomerizations as compared to the ab initio or PCM results. At the same time, they also increased the barriers of B (ttc, gtc) → D (ttt, gtt). In short, the conformational free energy surfaces of non-ionized glycine in solution are largely different from the corresponding potential energy surfaces of gas phase. The fact that the initial conformer for tautomerization ccc is stable makes the N → Z tautomerization facile. However, concurrently, diverse conformational isomerizations to ccc make the tautomerization dependent on the isomerizations.

Exposing Hidden Alternative Backbone Conformations in X-ray Crystallography Using qFit.

Proteins must move between different conformations of their native ensemble to perform their functions. Crystal structures obtained from high-resolution X-ray diffraction data reflect this heterogeneity as a spatial and temporal conformational average. Although movement between natively populated alternative conformations can be critical for characterizing molecular mechanisms, it is challenging to identify these conformations within electron density maps. Alternative side chain conformations are generally well separated into distinct rotameric conformations, but alternative backbone conformations can overlap at several atomic positions. Our model building program qFit uses mixed integer quadratic programming (MIQP) to evaluate an extremely large number of combinations of sidechain conformers and backbone fragments to locally explain the electron density. Here, we describe two major modeling enhancements to qFit: peptide flips and alternative glycine conformations. We find that peptide flips fall into four stereotypical clusters and are enriched in glycine residues at the n+1 position. The potential for insights uncovered by new peptide flips and glycine conformations is exemplified by HIV protease, where different inhibitors are associated with peptide flips in the “flap” regions adjacent to the inhibitor binding site. Our results paint a picture of peptide flips as conformational switches, often enabled by glycine flexibility, that result in dramatic local rearrangements. Our results furthermore demonstrate the power of large-scale computational analysis to provide new insights into conformational heterogeneity. Overall, improved modeling of backbone heterogeneity with high-resolution X-ray data will connect dynamics to the structure-function relationship and help drive new design strategies for inhibitors of biomedically important systems.

Gas-phase lithium cation affinity of glycine.

The gas-phase lithium cation binding thermochemistry of glycine has been determined theoretically by quantum chemical calculations at the G4 level and experimentally by the extended kinetic method using electrospray ionization quadrupole time-of-flight tandem mass spectrometry. The lithium cation affinity of glycine, ∆(Li)H°(298)(GLY), i.e. the∆(Li)H°(298) of the reaction GlyLi(+)→ Gly + Li(+)) given by the G4 method is equal to 241.4 kJ.mol(-1) if only the most stable conformer of glycine is considered or to 242.3 kJ.mol(-1) if the 298K equilibrium mixture of neutral conformers is included in the calculation. The ∆(Li)H°(298)(GLY) deduced from the extended kinetic method is obviously dependent on the choice of the Li(+) affinity scale, thus∆(Li)H°(298)(GLY) is equal to 228.7±0.9(2.0) kJ.mol(- 1) if anchored to the recently re-evaluated lithium cation affinity scale but shifted to 235.4±1.0 kJ.mol(-1) if G4 computed lithium cation affinities of the reference molecules is used. This difference of 6.3 kJ.mol(-1) may originate from a compression of the experimental lithium affinity scale in the high ∆(Li)H°(298) region. The entropy change associated with the reaction GlyLi(+)→Gly + Li(+) reveals a gain of approximately 15 J.mol(-) 1.K(-1) with respect to monodentate Li(+) acceptors. The origin of this excess entropy is attributed to the bidentate interaction between the Li(+) cation and both the carbonyl oxygen and the nitrogen atoms of glycine. The computed G4 Gibbs free energy,∆(Li)G°(298)(GLY) is equal to 205.3 kJ.mol(-1), a similar result, 201.0±3.4 kJ.mol(-1), is obtained from the experiment if the∆(Li)G°(298) of the reference molecules is anchored on the G4 results.