Conformers of Gaseous Serine

Accurate Computation of Aqueous pKas of Biologically Relevant Organic Acids: Overcoming the Challenges Posed by Multiple Conformers, Tautomeric Equilibria, and Disparate Functional Groups with the Fully Black-Box pK-Yay Method

The use of static electronic structure calculations to compute solution-phase pKas offers a great advantage in that a macroscopic bulk property could be computed via microscopic computations involving very few molecules. There are various sources of errors in the quantum chemical calculations though. Overcoming these errors to accurately compute pKas of a plethora of acids is an active area of research in physical chemistry pursued by both computational as well as experimental chemists. We recently developed the pK-Yay method in our attempt to accurately compute aqueous pKas of strong and weak acids. The method is fully black-box, computationally inexpensive, and is very easy for even a nonexpert to use. However, the method was thus far tested on very few molecules (only 16 in all). Herein, in order to assess the future applicability of pK-Yay, we study the effect of multiple conformers, the presence of tautomers under equilibrium, and the impact of a wide variety of functional groups (derivatives of acetic acid with substituents at various positions, dicarboxylic acids, aromatic carboxylic acids, amines and amides, phenols and thiols, and fluorine bearing organic acids). Starting with more than 1000 conformers and tautomers, this study establishes that overall errors of ∼ 1.0 pKa units are routinely obtained for a majority of the molecules. Larger errors are noted in cases where multiple charges, intramolecular hydrogen bonding, and several ionizable functional groups are simultaneously present. An important conclusion to emerge from this work is that, the computed pKas are insensitive (difference <0.5) to whether we consider multiple conformers/tautomers or only choose the most stable conformer/tautomer. Further, pK-Yay captures the stereoelectronic effects arising due to differing axial vs equatorial pattern, and is useful to predict the dominant acid-base equilibrium in a system featuring several equilibria. Overall, pK-Yay may be employed in several chemical applications featuring organic molecules and biomonomers.

The multichannel i-propyl + O2 reaction system: A model of secondary alkyl radical oxidation

The i-propyl + O2 reaction mechanism has been investigated by definitive quantum chemical methods to establish this system as a benchmark for the combustion of secondary alkyl radicals. Focal point analyses extrapolating to the ab initio limit were performed based on explicit computations with electron correlation treatments through coupled cluster single, double, triple, and quadruple excitations and basis sets up to cc-pV5Z. The rigorous coupled cluster single, double, and triple excitations/cc-pVTZ level of theory was used to fully optimize all reaction species and transition states, thus, removing some substantial flaws in reference geometries existing in the literature. The vital i-propylperoxy radical (MIN1) and its concerted elimination transition state (TS1) were found 34.8 and 4.4 kcal mol-1 below the reactants, respectively. Two β-hydrogen transfer transition states (TS2, TS2') lie above the reactants by (1.4, 2.5) kcal mol-1 and display large Born-Oppenheimer diagonal corrections indicative of nearby surface crossings. An α-hydrogen transfer transition state (TS5) is discovered 5.7 kcal mol-1 above the reactants that bifurcates into equivalent α-peroxy radical hanging wells (MIN3) prior to a highly exothermic dissociation into acetone + OH. The reverse TS5 → MIN1 intrinsic reaction path also displays fascinating features, including another bifurcation and a conical intersection of potential energy surfaces. An exhaustive conformational search of two hydroperoxypropyl (QOOH) intermediates (MIN2 and MIN3) of the i-propyl + O2 system located nine rotamers within 0.9 kcal mol-1 of the corresponding lowest-energy minima.

Protonation of serine: conformers, proton affinities and gas-phase basicities at the "gold standard" and beyond

The potential energy surfaces (PESs) of serine and its protonated counterparts are investigated to determine the structures of the minima. A total of 95 neutral serine, 15 N-(amino-) and 46 O-(carbonyl-)protonated serine conformers are found. Their relative energies, geometries and harmonic vibrational frequencies are determined at the MP2/aug-cc-pVDZ level of theory. To obtain highly accurate thermodynamic values, further computations are performed: the ten conformers with the lowest relative energies from each molecule type (neutral, N- and O-protonated) are further optimized using the explicitly correlated CCSD(T)-F12a/cc-pVDZ-F12 method (for neutral serine, harmonic vibrational frequencies were also computed). In addition, auxiliary corrections were determined: basis-set effects up to CCSD(T)-F12b/cc-pVQZ-F12, electron correlation effects up to CCSDT(Q), core correlation and second-order Douglas-Kroll relativistic effects along with zero-point energy contributions. Two important thermodynamic parameters (at 298.15 K), proton affinity (PA)/gas-phase basicity (GB) are calculated considering the two different protonation sites: 218.05 ± 0.2/209.86 ± 0.6 kcal mol^-1 and 205.87 ± 0.2/196.36 ± 0.3 kcal mol^-1 for the amino and carbonyl sites, respectively. The uncertainty of the determined values was approximated based on various sources including auxiliary corrections, basis-set effects, harmonic vibrational frequencies.

Benchmark Structures and Conformational Landscapes of Amino Acids in the Gas Phase: A Joint Venture of Machine Learning, Quantum Chemistry, and Rotational Spectroscopy

The accurate characterization of prototypical bricks of life can strongly benefit from the integration of high resolution spectroscopy and quantum mechanical computations. We have selected a number of representative amino acids (glycine, alanine, serine, cysteine, threonine, aspartic acid and asparagine) to validate a new computational setup rooted in quantum-chemical computations of increasing accuracy guided by machine learning tools. Together with low-lying energy minima, the barriers ruling their interconversion are evaluated in order to unravel possible fast relaxation paths. Vibrational and thermal effects are also included in order to estimate relative free energies at the temperature of interest in the experiment. The spectroscopic parameters of all the most stable conformers predicted by this computational strategy, which do not have low-energy relaxation paths available, closely match those of the species detected in microwave experiments. Together with their intrinsic interest, these accurate results represent ideal benchmarks for more approximate methods.

Coupling and decoupling CH stretching vibration of methylene and methine in serine conformers

In the molecules of the early Earth, as a building block of proteins, serine has enormous chemical and biological significance. The vibrational spectroscopy of CH bonds plays an important role in probing biomolecules. Whether the CH stretching vibration bands can be accurately assigned will affect the accuracy of the detection results. In this study, we employed the MP2/cc-pVTZ method to calculate the Raman spectra of 85 serine conformers and the corresponding species with deuterium in the CH stretching region from 2800 cm^-1 to 3050 cm^-1 and then recorded the movement of each atom and the dihedral angles, CH bond lengths, and Raman shifts before and after deuterium for each conformer. We directly observed that the stretching vibration of two CH bonds in the methylene group decoupled to vibrate independently in some conformers, and the stretching vibrations of methylene and methine could be strongly coupled in some conformers. Those results are inconsistent with the traditional understanding, which is generally believed that the CH stretching vibrations are mutually coupled in a single methyl or methylene group to generate symmetric and antisymmetric stretching vibrations, while for different methyl, methylene or methine groups, the CH stretching vibrations cannot be mutually coupled. Through the statistical analysis between several factors, we found that the level of local coupling in serine methylene was correlated with the bond length difference between two CH bonds. Our work provides a new understanding of the vibrational modes of hydrocarbon bonds and the coupling between different hydrocarbon groups.

Benchmark ab initio proton affinity and gas-phase basicity of α-alanine based on coupled-cluster theory and statistical mechanics

We determine the proton affinity (PA) and gas-phase basicity (GB) of amino acid α-alanine at a chemically accurate level by performing explicitly-correlated CCSD(T)-F12b/aug-cc-pVDZ geometry optimizations and normal mode vibrational frequency calculations as well as CCSD(T)-F12b/aug-cc-pVTZ energy computations at the possible neutral and protonated geometries. Temperature effects at 298.15 K considering translational, rotational, and vibrational enthalpy and entropy corrections are obtained via standard statistical mechanics utilizing the molecular geometries and the harmonic vibrational energy levels. Both the amino nitrogen (N) and the carbonyl oxygen (O) atoms are proven to be potential protonation sites and a systematic conformational search reveals 3 N- and 9 O-protonated conformers in the 0.00-7.88 and 25.43-30.43 kcal/mol energy ranges at 0 K, respectively. The final computed PA and GB values at (0)298.15 K in case of N-protonation are (214.47)216.80 and 207.07 kcal/mol, respectively, whereas the corresponding values for O-protonation are (189.04)190.63 and 182.31 kcal/mol. The results of the benchmark high-level coupled-cluster computations are utilized to assess the accuracy of several lower-level cost-effective methods such as MP2 and density functional theory with various functionals (SOGGA11-X, M06-2X, PBE0, B3LYP, M06, TPSS).

Structural and Vibrational Properties of Amino Acids from Composite Schemes and Double-Hybrid DFT: Hydrogen Bonding in Serine as a Test Case

The structures, relative stabilities, and vibrational wavenumbers of the two most stable conformers of serine, stabilized by the O-H···N, O-H···O═C and N-H···O-H intramolecular hydrogen bonds, have been evaluated by means of state-of-the-art composite schemes based on coupled-cluster (CC) theory. The so-called "cheap" composite approach (CCSD(T)/(CBS+CV)^MP2) allowed determination of accurate equilibrium structures and harmonic vibrational wavenumbers, also pointing out significant corrections beyond the CCSD(T)/cc-pVTZ level. These accurate results stand as a reference for benchmarking selected hybrid and double-hybrid, dispersion-corrected DFT functionals. B2PLYP-D3 and DSDPBEP86 in conjunction with a triple-ζ basis set have been confirmed as effective methodologies for structural and spectroscopic studies of medium-sized flexible biomolecules, also showing intramolecular hydrogen bonding. These best performing double-hybrid functionals have been employed to simulate IR spectra by means of vibrational perturbation theory, also considering hybrid CC/DFT schemes. The best overall agreement with experiment, with mean absolute error of 8 cm^-1, has been obtained by combining CCSD(T)/(CBS+CV)^MP2 harmonic wavenumbers with B2PLYP-D3/maug-cc-pVTZ anharmonic corrections. Finally, a composite scheme entirely based on CCSD(T) calculations (CCSD(T)/CBS+CV) has been employed for energetics, further confirming that serine II is the most stable conformer, also when zero-point vibrational energy corrections are included.

Monomers of Glycine and Serine Have a Limited Ability to Hydrate in the Atmosphere

The role of atmospheric aerosols on climate change is one of the biggest uncertainties in most global climate models. Organic aerosols have been identified as potential cloud condensation nuclei (CCN), and amino acids are organic molecules that could serve as CCN. Amino acids make up a significant portion of the total organic material in the atmosphere, and herein we present a systematic study of hydration for two of the most common atmospheric amino acids, glycine and serine. We compute DLPNO/CCSD(T)//M08-HX/MG3S thermodynamic properties and atmospheric concentrations of Gly(H₂O)_n and Ser(H₂O)_n, where n = 1-5. We predict that serine-water clusters have higher concentrations at n = 1 and 5, while glycine-water clusters have higher concentrations at n = 2-4. However, both glycine and serine are inferred to exist primarily in their nonhydrated monomer forms in the absence of other species such as sulfuric acid.

Condensation Effects on Electron Chiral Asymmetries in the Photoionization of Serine: From Free Molecules to Nanoparticles

Structural changes at the molecular level, occurring at the onset of condensation, can be probed by angle-resolved valence photoelectron spectroscopy, which is inherently sensitive to the electronic structure. For larger condensed systems like aerosol particles, the observation of intrinsic angular anisotropies in photoemission (β parameters) is challenging due to the strong reduction of their magnitude by electron transport effects. Here, we use a less common, more sensitive observable in the form of the chiral asymmetry parameter to perform a comparative study of the VUV photoelectron spectroscopy and photoelectron circular dichroism (PECD) between pure gas phase enantiomers of the amino acid serine and their corresponding homochiral nanoparticles. We observe a relatively large (1%) and strongly kinetic energy-dependent asymmetry, discussed in terms of the emergence of local order and conformational changes potentially counterbalancing the loss of angular information due to electron transport scattering. This demonstrates the potential of PECD as a sensitive probe of the condensation effects from the gas phase to bulk-like chiral aerosol particles surpassing the potential of conventional photoemission observables such as β parameters.

Nitrogen Isotopic Reduced Partition Function Ratios of Glycine and Serine in Water

The nitrogen isotopic reduced partition function ratio (RPFR) of glycine (Gly) and serine (Ser) in water has been evaluated by a couple of methods. The experimental fact that those amino acids are present in the zwitterionic form in water has been best reproduced when trihydrated Gly and Ser molecules were treated by the discrete microsolvation method coupled with the self-consistent reaction field (SCRF) approach. The RPFR values of Gly and Ser in water at 25 °C are evaluated as 1.11152 and 1.11070, respectively, and the equilibrium constant of the nitrogen isotope exchange reaction between the two amino acids is calculated as 1.0007 ± 0.0008 at 25 °C. Equivalent results may be obtained by the SCRF method for non- and monohydrated molecules in the zwitterionic form.

The effect of surfactants on hydrate particle agglomeration in liquid hydrocarbon continuous systems: a molecular dynamics simulation study

Anti-agglomerants (AAs), both natural and commercial, are currently being considered for gas hydrate risk management of petroleum pipelines in offshore operations. However, the molecular mechanisms of the interaction between the AAs and gas hydrate surfaces and the prevention of hydrate agglomeration remain critical and complex questions that need to be addressed to advance this technology. Here, we use molecular dynamics (MD) simulations to investigate the effect of model surfactant molecules (polynuclear aromatic carboxylic acids) on the agglomeration behaviour of gas hydrate particles and disruption of the capillary liquid bridge between hydrate particles. The results show that the anti-agglomeration pathway can be divided into two processes: the spontaneous adsorption effect of surfactant molecules onto the hydrate surface and the weakening effect of the intensity of the liquid bridge between attracted hydrate particles. The MD simulation results also indicate that the anti-agglomeration effectiveness of surfactants is determined by the intrinsic nature of their molecular functional groups. Additionally, we find that surfactant molecules can affect hydrate growth, which decreases hydrate particle size and correspondingly lower the risk of hydrate agglomeration. This study provides molecular-level insights into the anti-agglomeration mechanism of surfactant molecules, which can aid in the ultimate application of natural or commercial AAs with optimal anti-agglomeration properties.

Schematic of anti-agglomeration effect of surfactants promoting gas hydrate particle dispersion.

Unbiased Determination of Absolute Configurations by vis-à-vis Comparison of Experimental and Simulated Spectra: The Challenging Case of Diplopyrone

A new experimental-computational strategy for the determination of the absolute configuration (AC) of complex chiral molecules is proposed by combining diverse experimental spectroscopies with quantum-mechanical simulations well beyond the current computational practice. Key features are the conformer search and relative stability evaluation performed by a new stochastic two-level tool followed by a vis-à-vis comparison of experimental and computed spectra without any ad hoc adjustment. The entire computational procedure is embedded in the user-friendly VMS software, and its reliability is granted by the inclusion of mechanic/electric/magnetic anharmonicity as well as ro-vibrational and vibronic couplings by means of generalized perturbation theory in conjunction with double-hybrid functionals combined with empirical dispersion contributions and suitable basis sets. To test and validate the new approach, the puzzling case of diplopyrone, a fungal phytotoxic metabolite, has been chosen: the close match between new experimental and simulated infrared absorption and vibrational circular dichroism spectra has led to the unbiased evaluation of its AC.

Theoretical investigation of the chiral transition of serine and the roles of water, hydroxyl radical and hydroxide ion

The serine chiral transition and the roles of water, hydroxyl radical and hydroxide ion as catalysts were theoretically investigated.