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

Accurate Vibrational and Ro-Vibrational Contributions to the Properties of Large Molecules by a New Engine Employing Curvilinear Internal Coordinates and Vibrational Perturbation Theory to Second Order

The unbiased comparison between theory and experiment requires approaches more sophisticated than the basic harmonic-oscillator rigid-rotor model, for taking into account vibrational averaging effects and ro-vibrational couplings in molecules of increasing size. Second-order vibrational perturbation theory based on curvilinear internal coordinates (ICs) offers a remarkable compromise between accuracy and computational cost, thanks to the reduction of mode-mode couplings with respect to their counterparts based on Cartesian coordinates. Therefore, we have developed, implemented, and validated a general engine employing ICs, which allows the accurate evaluation of vibrational averages and ro-vibrational couplings for molecules containing up to about 50 atoms beyond the harmonic approximation. After validation of the new tool for relatively small molecules, the effectiveness of ICs has been demonstrated for some flexible and/or quite large molecular bricks of life.

Calculating absorption and fluorescence spectra for chromophores in solution with ensemble Franck-Condon methods

Accurately modeling absorption and fluorescence spectra for molecules in solution poses a challenge due to the need to incorporate both vibronic and environmental effects, as well as the necessity of accurate excited state electronic structure calculations. Nuclear ensemble approaches capture explicit environmental effects, Franck-Condon methods capture vibronic effects, and recently introduced ensemble-Franck-Condon approaches combine the advantages of both methods. In this study, we present and analyze simulated absorption and fluorescence spectra generated with combined ensemble-Franck-Condon approaches for three chromophore-solvent systems and compare them to standard ensemble and Franck-Condon spectra, as well as to the experiment. Employing configurations obtained from ground and excited state ab initio molecular dynamics, three combined ensemble-Franck-Condon approaches are directly compared to each other to assess the accuracy and relative computational time. We find that the approach employing an average finite-temperature Franck-Condon line shape generates spectra nearly identical to the direct summation of an ensemble of Franck-Condon spectra at one-fourth of the computational cost. We analyze how the spectral simulation method, as well as the level of electronic structure theory, affects spectral line shapes and associated Stokes shifts for 7-nitrobenz-2-oxa-1,3-diazol-4-yl and Nile red in dimethyl sulfoxide and 7-methoxy coumarin-4-acetic acid in methanol. For the first time, our studies show the capability of combined ensemble-Franck-Condon methods for both absorption and fluorescence spectroscopy and provide a powerful tool for simulating linear optical spectra.

Structural and Electronic Evolution of Ethanolamine upon Microhydration: Insights from Hyperfine Resolved Rotational Spectroscopy

Ethanolamine hydrates containing from one to seven water molecules were identified via rotational spectroscopy with the aid of accurate quantum chemical methods considering anharmonic vibrational corrections. Ethanolamine undergoes significant conformational changes upon hydration to form energetically favorable hydrogen bond networks. The final structures strongly resemble the pure (H2O)3-9 complexes reported before when replacing two water molecules by ethanolamine. The 14N nuclear quadrupole coupling constants of all the ethanolamine hydrates have been determined and show a remarkable correlation with the strength of hydrogen bonds involving the amino group. After addition of the seventh water molecule, both hydrogen atoms of the amino group actively contribute to hydrogen bond formation, reinforcing the network and introducing approximately 21-27 % ionicity towards the formation of protonated amine. These findings highlight the critical role of microhydration in altering the electronic environment of ethanolamine, enhancing our understanding of amine hydration dynamics.

Accurate structures and rotational constants of bicyclic monoterpenes at DFT cost by means of the bond-corrected Pisa composite scheme (BPCS)

The structural, conformational, and spectroscopic properties in the gas phase of 20 bicyclic monoterpenes and monoterpenoids have been analyzed by a new accurate, reduced-cost computational strategy. In detail, the revDSD-PBEP86 double-hybrid functional in conjunction with the D3BJ empirical dispersion corrections and a suitable triple-zeta basis set provides accurate geometrical parameters, whence equilibrium rotational constants, which are further improved by proper account of core-valence correlation. Average deviations within 0.1% between computed and experimental rotational constants are reached when taking into account the vibrational corrections obtained by the B3LYP functional in conjunction with a double-zeta basis set in the framework of second-order vibrational perturbation theory. In addition to their intrinsic interest, the studied terpenes further extend the panel of systems for which the proposed strategy has provided accurate results at density functional theory cost. Therefore, a very accurate yet robust and user-friendly tool is now available for systematic investigations of the role of stereo-electronic effects on the properties of large systems of current technological and/or biological interest by experimentally oriented researchers.

Predicting the propene stereoselectivity on transition metal catalysts: A daunting task for density functional theory

Thanks to recent developments in hardware and software, quantum chemical methods are increasingly used for interpreting the complex mechanisms underlying polymerization reaction by homogeneous catalysis. Unfortunately, the dimensions of even the smallest realistic models are too large to permit the use of state-of-the-art composite wave function methods. Under these circumstances, density functional theory still offers the best compromise between cost and accuracy. However, comprehensive benchmarks of different functionals are not yet available for this important research field. The main aim of the present paper is to fill this gap by performing an unbiased comparison of several density functionals and continuum solvent models for the stereo-control in the propylene polymerization on prototypical catalysts inducing different reaction mechanisms. While it was not possible to define a unique computational protocol providing the best results in all the situations, the B3PW91 functional in conjunction with D3 empirical dispersions and the solvent model density solvent model performs remarkably well for three out of the four investigated catalysts. Under such circumstances, it is recommended to compare the results delivered by different models when approaching additional classes of catalysts.

Tell Machine Learning Potentials What They Are Needed For: Simulation-Oriented Training Exemplified for Glycine

Machine learning potentials (MLPs) are widely applied as an efficient alternative way to represent potential energy surfaces (PESs) in many chemical simulations. The MLPs are often evaluated with the root-mean-square errors on the test set drawn from the same distribution as the training data. Here, we systematically investigate the relationship between such test errors and the simulation accuracy with MLPs on an example of a full-dimensional, global PES for the glycine amino acid. Our results show that the errors in the test set do not unambiguously reflect the MLP performance in different simulation tasks, such as relative conformer energies, barriers, vibrational levels, and zero-point vibrational energies. We also offer an easily accessible solution for improving the MLP quality in a simulation-oriented manner, yielding the most precise relative conformer energies and barriers. This solution also passed the stringent test by diffusion Monte Carlo simulations.

Unbiased Comparison between Theoretical and Experimental Molecular Structures and Properties: Toward an Accurate Reduced-Cost Evaluation of Vibrational Contributions

The tremendous development of hardware and software is constantly increasing the role of quantum chemical (QC) computations in the assignment and interpretation of experimental results. However, an unbiased comparison between theory and experiment requires the proper account of vibrational averaging effects. In particular, high-resolution spectra in the gas phase are now available for molecules containing up to about 50 atoms, which are too large for a brute-force approach with the available QC methods of sufficient accuracy. In the present paper, we introduce hybrid approaches, which allow the accurate evaluation of vibrational averaging effects for molecules of this size beyond the harmonic approximation, with special attention being devoted to rotational constants. After the validation of new tools for relatively small molecules, the β-estradiol hormone and a prototypical molecular motor have been considered to witness the feasibility of accurate computations for large molecules.

Accurate Structures and Rotational Constants of Steroid Hormones at DFT Cost: Androsterone, Testosterone, Estrone, β-Estradiol, and Estriol

A comprehensive analysis of the structural, conformational, and spectroscopic properties in the gas phase has been performed for five prototypical steroid hormones, namely, androsterone, testosterone, estrone, β-estradiol, and estriol. The revDSD-PBEP86 double-hybrid functional in conjunction with the D3BJ empirical dispersion and a suitable triple-ζ basis set provides accurate conformational energies and equilibrium molecular structures, with the latter being further improved by proper account of core-valence correlation. Average deviations within 0.1% between computed and experimental ground state rotational constants are reached when adding to those equilibrium values vibrational corrections obtained at the cost of standard harmonic frequencies thanks to the use of a new computational tool. Together with the intrinsic interest of the studied hormones, the accuracy of the results obtained at DFT cost for molecules containing about 50 atoms paves the way toward the accurate investigations of other flexible bricks of life.

Accurate Geometries of Large Molecules by Integration of the Pisa Composite Scheme and the Templating Synthon Approach

An effective yet reliable computational workflow is proposed, which permits the computation of accurate geometrical structures for large flexible molecules at an affordable cost thanks to the integration of machine learning tools and DFT models together with reduced scaling computations of vibrational averaging effects. After validation of the different components of the overall strategy, a panel of molecules of biological interest have been analyzed. The results confirm that very accurate geometrical parameters can be obtained at reasonable cost for molecules including up to about 50 atoms, which are the largest ones for which comparison with high-resolution rotational spectra is possible. Since the whole computational workflow can be followed employing standard electronic structure codes, accurate results for large-sized molecules can be obtained at DFT cost also by nonspecialists.

Quantum chemistry meets high-resolution spectroscopy for characterizing the molecular bricks of life in the gas-phase

Computation of accurate geometrical structures and spectroscopic properties of large flexible molecules in the gas-phase is tackled at an affordable cost using a general exploration/exploitation strategy. The most distinctive feature of the approach is the careful selection of different quantum chemical models for energies, geometries and vibrational frequencies with the aim of maximizing the accuracy of the overall description while retaining a reasonable cost for all the steps. In particular, a composite wave-function method is used for energies, whereas a double-hybrid functional (with the addition of core-valence correlation) is employed for geometries and harmonic frequencies and a cheaper hybrid functional for anharmonic contributions. A thorough benchmark based on a wide range of prototypical molecular bricks of life shows that the proposed strategy is close to the accuracy of state-of-the-art composite wave-function methods, and is applicable to much larger systems. A freely available web-utility post-processes the geometries optimized by standard electronic structure codes paving the way toward the accurate yet not prohibitively expensive study of medium- to large-sized molecules by experimentally-oriented researchers.

Hunting for Complex Organic Molecules in the Interstellar Medium: The Role of Accurate Low-Cost Theoretical Geometries and Rotational Constants

A new approach to computation at affordable cost of accurate geometrical structures and rotational constants for medium-sized molecules in the gas phase is further improved and applied to a large panel of interstellar complex organic molecules. The most distinctive feature of the new model is the effective inclusion of core-valence correlation and vibrational averaging effects in the framework of density functional theory (DFT). In particular, a double-hybrid functional in conjunction with a quadruple-ζ valence/triple-ζ polarization basis set is employed for geometry optimizations, whereas a cheaper hybrid functional in conjunction with a split-valence basis set is used for the evaluation of vibrational corrections. A thorough benchmark based on a wide range of prototypical systems shows that the new scheme approaches the accuracy of state-of-the-art wave function methods with the computational cost of the standard methods (DFT or MP2) routinely employed in the interpretation of microwave spectra. Since the whole computational workflow involves the postprocessing of the output of standard electronic structure codes by a new freely available web utility, the way is paved for the accurate yet not prohibitively expensive study of medium- to large-sized molecules also by nonspecialists.

Accurate Thermochemical and Kinetic Parameters at Affordable Cost by Means of the Pisa Composite Scheme (PCS)

A new strategy for the computation at an affordable cost of geometrical structures, thermochemical parameters, and rate constants for medium-sized molecules in the gas phase is proposed. The most distinctive features of the new model are the systematic use of cc-pVnZ-F12 basis sets, the addition of MP2 core-valence correlation in geometry optimizations by a double-hybrid functional, the separate extrapolation of MP2 and post-MP2 contributions, and the inclusion of anharmonic contributions in zero-point energies and thermodynamic functions. A thorough benchmark based on a wide range of prototypical systems shows that the new scheme outperforms the most well-known model chemistries without the need for any empirical parameter. Additional tests show that the computed zero-point energies and thermal contributions can be confidently used for obtaining accurate thermochemical and kinetic parameters. Since the whole computational workflow is translated in a black-box procedure, which can be followed with standard electronic structure codes, the way is paved for the accurate yet not prohibitively expensive study of medium- to large-sized molecules also by nonspecialists.

Accurate thermochemistry at affordable cost by means of an improved version of the JunChS-F12 model chemistry

The junChS-F12 composite method has been improved by means of the latest implementation of the CCSD(F12*)(T+) ansatz and validated for the thermochemistry of molecules containing atoms of the first three rows of the periodic table. A thorough benchmark showed that this model, in conjunction with cost-effective revDSD-PBEP86-D3(BJ) reference geometries, offers an optimal compromise between accuracy and computational cost. If improved geometries are sought, the most effective option is to add MP2-F12 core-valence correlation corrections to CCSD(T)-F12b/jun-cc-pVTZ geometries without the need of performing any extrapolation to the complete basis set limit. In the same vein, CCSD(T)-F12b/jun-cc-pVTZ harmonic frequencies are remarkably accurate without any additional contribution. Pilot applications to noncovalent intermolecular interactions, conformational landscapes, and tautomeric equilibria confirm the effectiveness and reliability of the model.

DFT Meets Wave-Function Methods for Accurate Structures and Rotational Constants of Histidine, Tryptophan, and Proline

A new computational strategy has been applied to the conformational and spectroscopic properties in the gas phase of amino acids with very distinctive features, ranging from different tautomeric forms (histidine) to ring puckering (proline), and heteroaromatic structures with non-equivalent rings (tryptophan). The integration of modern double-hybrid functionals and wave-function composite methods has allowed us to obtain accurate results for a large panel of conformers with reasonable computer times. The remarkable agreement between computations and microwave experiments allows an unbiased interpretation of the latter in terms of stereoelectronic effects.

Accurate structures and spectroscopic parameters of α,α-dialkylated α-amino acids in the gas-phase: a joint venture of DFT and wave-function composite methods

Accurate computations of structural, conformational and spectroscopic properties in the gas phase have been performed for two α,α-dialkylated α-amino acids, namely aminoisobutyric acid and cyclopropylglycine. Thanks to the integration of modern double hybrid functionals and wave-function methods, several low-energy structures of the title molecules could be analyzed employing standard computer resources. The computed features of all the most stable conformers of the target amino acids closely match the corresponding spectroscopic parameters issued from microwave spectroscopic studies in the gas-phase. Together with their intrinsic interest, the accuracy of the results obtained with reasonable computer times paves the way for accurate investigations of other flexible bricks of life.

Accurate Structures and Spectroscopic Parameters of Guanine Tautomers in the Gas Phase by the Pisa Conventional and Explicitly Correlated Composite Schemes (PCS and PCS-F12)

A general strategy for the accurate computation of structural and spectroscopic properties of biomolecule building blocks in the gas phase is proposed and validated for tautomeric equilibria. The main features of the new model are the inclusion of core-valence correlation in geometry optimizations by a double hybrid functional and the systematic use of wave-function composite methods in conjunction with cc-pVnZ-F12 basis sets with separate extrapolation of MP2 and post-MP2 contributions. The resulting Pisa composite scheme employing conventional (PCS) or explicitly correlated (PCS-F12) approaches is applied to the challenging problem of guanine tautomers in the gas phase. The results are in remarkable agreement with the experimental structures, relative stabilities, and spectroscopic signatures of different tautomers. The accuracy of the results obtained at reasonable cost by means of black-box parameter-free approaches paves the way toward systematic investigations of other molecular bricks of life also by non-specialists.

DFT Meets Wave-Function Composite Methods for Characterizing Cytosine Tautomers in the Gas Phase

A general strategy for the accurate computation of structural and spectroscopic properties of biomolecule building blocks in the gas phase has been further improved and validated with a special reference to tautomeric equilibria. The main improvements concern the use of the cc-pVTZ-F12 basis set in both DFT and CCSD(T)-F12 computations, the inclusion of core-valence correlation in geometry optimizations by double hybrid functionals, and the use of the cc-pVQZ-F12 basis set for complete basis set extrapolation at the MP2-F12 level. The resulting model chemistry is applied to the challenging problem of cytosine tautomers in the gas phase. The results are in remarkable agreement with experiment concerning both rotational and vibrational spectroscopic parameters and permit their unbiased interpretation in terms of structural and thermochemical features. Together with the intrinsic interest of the studied molecule, the accuracy of the results obtained at reasonable cost without any empirical parameter suggests that the proposed composite method can be profitably employed for accurate investigations of other molecular bricks of life.

Accurate Structures and Spectroscopic Parameters of Phenylalanine and Tyrosine in the Gas Phase: A Joint Venture of DFT and Composite Wave-Function Methods

A general strategy for the accurate computation of conformational and spectroscopic properties of flexible molecules in the gas phase is applied to two representative proteinogenic amino acids with aromatic side chains, namely, phenylalanine and tyrosine. The main features of all the most stable conformers predicted by this computational strategy closely match those of the species detected in microwave and infrared experiments. Together with their intrinsic interest, the accuracy of the results obtained with reasonable computer times paves the route for accurate investigations of other flexible bricks of life.

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.