Computational molecular spectroscopy

Unraveling dynamic protein structures by two-dimensional infrared spectra with a pretrained machine learning model

Dynamic protein structures are crucial for deciphering their diverse biological functions. Two-dimensional infrared (2DIR) spectroscopy stands as an ideal tool for tracing rapid conformational evolutions in proteins. However, linking spectral characteristics to dynamic structures poses a formidable challenge. Here, we present a pretrained machine learning model based on 2DIR spectra analysis. This model has learned signal features from approximately 204,300 spectra to establish a "spectrum-structure" correlation, thereby tracing the dynamic conformations of proteins. It excels in accurately predicting the dynamic content changes of various secondary structures and demonstrates universal transferability on real folding trajectories spanning timescales from microseconds to milliseconds. Beyond exceptional predictive performance, the model offers attention-based spectral explanations of dynamic conformational changes. Our 2DIR-based pretrained model is anticipated to provide unique insights into the dynamic structural information of proteins in their native environments.

Extraction of uranyl from spent nuclear fuel wastewater via complexation-a local vibrational mode study

CONTEXT

The efficient extraction of uranyl from spent nuclear fuel wastewater for subsequent reprocessing and reuse is an essential effort toward minimization of long-lived radioactive waste. N-substituted amides and Schiff base ligands are propitious candidates, where extraction occurs via complexation with the uranyl moiety. In this study, we extensively probed chemical bonding in various uranyl complexes, utilizing the local vibrational modes theory alongside QTAIM and NBO analyses. We focused on (i) the assessment of the equatorial O-U and N-U bonding, including the question of chelation, and (ii) how the strength of the axial U = O bonds of the uranyl moiety changes upon complexation. Our results reveal that the strength of the equatorial uranium-ligand interactions correlates with their covalent character and with charge donation from O and N lone pairs into the vacant uranium orbitals. We also found an inverse relationship between the covalent character of the equatorial ligand bonds and the strength of the axial uranium-oxygen bond. In summary, our study provides valuable data for a strategic modulation of N-substituted amide and Schiff base ligands towards the maximization of uranyl extraction.

METHOD

Quantum chemistry calculations were performed under the PBE0 level of theory, paired with the relativistic NESCau Hamiltonian, currently implemented in Cologne2020 (interfaced with Gaussian16). Wave functions were expanded in the cc-pwCVTZ-X2C basis set for uranium and Dunning's cc-pVTZ for the remaining atoms. For the bonding properties, we utilized the package LModeA in the local modes analyses, AIMALL in the QTAIM calculations, and NBO 7.0 for the NBO analyses.

Introducing SpectraFit: An Open-Source Tool for Interactive Spectral Analysis

In chemistry, analyzing spectra through peak fitting is a crucial task that helps scientists extract useful quantitative information about a sample's chemical composition or electronic structure. To make this process more efficient, we have developed a new open-source software tool called SpectraFit. This tool allows users to perform quick data fitting using expressions of distribution and linear functions through the command line interface (CLI) or Jupyter Notebook, which can run on Linux, Windows, and MacOS, as well as in a Docker container. As part of our commitment to good scientific practice, we have introduced an output file-locking system to ensure the accuracy and consistency of information. This system collects input data, results data, and the initial fitting model in a single file, promoting transparency, reproducibility, collaboration, and innovation. To demonstrate SpectraFit's user-friendly interface and the advantages of its output file-locking system, we are focusing on a series of previously published iron-sulfur dimers and their XAS spectra. We will show how to analyze the XAS spectra via CLI and in a Jupyter Notebook by simultaneously fitting multiple data sets using SpectraFit. Additionally, we will demonstrate how SpectraFit can be used as a black box and white box solution, allowing users to apply their own algorithms to engineer the data further. This publication, along with its Supporting Information and the Jupyter Notebook, serves as a tutorial to guide users through each step of the process. SpectraFit will streamline the peak fitting process and provide a convenient, standardized platform for users to share fitting models, which we hope will improve transparency and reproducibility in the field of spectroscopy.

Metal-ring interactions in group 2 ansa-metallocenes: assessed with the local vibrational mode theory

Ansa-metallocenes, a vital class of organometallic compounds, have attracted significant attention due to their diverse structural motifs and their pivotal roles in catalysis and materials science. We investigated 37 distinct group 2 ansa-metallocenes at the B3LYP-D3/def2-TZVP level of theory. Utilizing local mode force constants derived from our local vibrational mode theory, including a special force constant directly targeting the metal-ring interaction, we could unveil latent structural differences between solvated and non-solvated metallocenophanes and the influence of the solvent on complex stability and structure. We could quantify the intrinsic strength of the metal-cyclopentadienyl (M-Cp) bonds and the influence of the bridging motifs on the stiffness of the Cp-M-Cp angles, another determinant of complex stability. LMA was complemented by the analysis of electronic density, utilizing the quantum theory of atoms in molecules (QTAIM), which confirmed both the impact of solvent coordination on the strength of the M-Cp bond(s) and the influence of the bridging motif on the Cp-M-Cp angles. The specific effect of the ansa-motif on the M-Cp interaction was further elucidated by a comparison with linear/bent metallocene structures. In summary, our results identify the local mode analysis as an efficient tool for unraveling the intricate molecular properties of ansa-metallocenes and their unique structural features.

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.

Unlocking a new hydrogen-bonding marker: C-O bond shortening in vicinal diols revealed by rotational spectroscopy

The conformational space of cis-1,2-cyclohexanediol, a model molecule for cyclic vicinal diols, was investigated using rotational spectroscopy and density functional theory calculations. Four low energy conformers within an energy window of 5 kJ mol-1 were identified computationally. A rotational spectrum of jet-cooled cis-1,2-cyclohexanediol was recorded with a chirped pulse Fourier transform microwave spectrometer. Two sets of rotational transitions were observed and could be assigned to conformers of cis-1,2-cyclohexanediol. The non-observation of other low energy conformers was explained by conformational conversion barrier height calculations and results from experimental spectra recorded with different carrier gases. Eight isotopologues, including those with 13C and 18O, of the lowest energy conformer were observed, allowing the determination of the semi-experimental equilibrium structure, reSE. Interestingly, the structural analysis revealed that the C-O bond length of the intramolecular hydrogen-bond donor is shorter than that of the acceptor. This appears to be a general characteristic of vicinal diols and can be used as a novel hydrogen-bond marker in such compounds.

Direct Probe of Vibrational Fingerprint and Combination Band Coupling

Vibrational fingerprints and combination bands are a direct measure of couplings that control molecular properties. However, most combination bands possess small transition dipoles. Here we use multiple, ultrafast coherent infrared pulses to resolve vibrational coupling between CH3CN fingerprint modes at 918 and 1039 cm-1 and combination bands in the 2750-6100 cm-1 region via doubly vibrationally enhanced (DOVE) coherent multidimensional spectroscopy (CMDS). This approach provides a direct probe of vibrational coupling between fingerprint modes and near-infrared combination bands of large and small transition dipoles in a molecular system over a large frequency range.

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.

The effect of machine learning predicted anharmonic frequencies on thermodynamic properties of fluid hydrogen fluoride

Anharmonic effects play a crucial role in determining thermochemical properties of liquids and gases. For such extended phases, the inclusion of anharmonicity in reliable electronic structure methods is computationally extremely demanding, and hence, anharmonic effects are often lacking in thermochemical calculations. In this study, we apply the quantum cluster equilibrium method to transfer density functional theory calculations at the cluster level to the macroscopic, liquid, and gaseous phase of hydrogen fluoride. This allows us to include anharmonicity, either via vibrational self-consistent field calculations for smaller clusters or using a regression model for larger clusters. We obtain the structural composition of the fluid phases in terms of the population of different clusters as well as isobaric heat capacities as an example for thermodynamic properties. We study the role of anharmonicities for these analyses and observe that, in particular, the dominating structural motifs are rather sensitive to the anharmonicity in vibrational frequencies. The regression model proves to be a promising way to get access to anharmonic features, and the extension to more sophisticated machine-learning models is promising.

Spin-Symmetry Breaking and Hyperfine Couplings in Transition-Metal Complexes Revisited Using Density Functionals Based on the Exact-Exchange Energy Density

A small set of mononuclear manganese complexes evaluated previously for their Mn hyperfine couplings (HFCs) has been analyzed using density functionals based on the exact-exchange energy density─in particular, the spin symmetry breaking (SSB) found previously when using hybrid functionals. Employing various strong-correlation corrected local hybrids (scLHs) and strong-correlation corrected range-separated local hybrids (scRSLHs) with or without additional corrections to their local mixing functions (LMFs) to mitigate delocalization errors (DE), the SSB and the associated dipolar HFCs of [Mn(CN)4]2-, MnO3, [Mn(CN)4N]-, and [Mn(CN)5NO]2- (the latter with cluster embedding) have been examined. Both strong-correlation (sc)-correction and DE-correction terms help to diminish SSB and correct the dipolar HFCs. The DE corrections are more effective, and the effects of the sc corrections depend on their damping factors. Interestingly, the DE-corrections reduce valence-shell spin polarization (VSSP) and thus SSB by locally enhancing exact-exchange (EXX) admixture near the metal center and thereby diminishing spin-density delocalization onto the ligand atoms. In contrast, sc corrections diminish EXX admixture locally, mostly on specific ligand atoms. This then reduces VSSP and SSB as well. The performance of scLHs and scRSLHs for the isotropic Mn HFCs has also been analyzed, with particular attention to core-shell spin-polarization contributions. Further sc-corrected functionals, such as the KP16/B13 construction and the DM21 deep-neural-network functional, have been examined.

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.

Understanding the surrounding effects on Raman optical activity signatures of a chiral cage system: Cryptophane-PP-111

Cryptophane molecules are cage-like structures consisting in two hemispheres, each made of three benzene rings. These hemispheres are bound together with three O(CH2)nOlinkers of various lengths giving rise to a plethora of cryptophane derivatives. Moreover, they are able to encapsulate neutral guests: CH2Cl2, CHCl3, …; and charged species: Cs+, Tl+, …. Finally, they exhibit chiroptical properties thanks to the anti arrangement of the linkers between the hemispheres. This work focuses on the Raman optical activity (ROA) signatures of Cryptophane-111 (n=1 for each linker). More specifically, we aim at simulating accurately its ROA spectra with and without a xenon atom inside its cavity. Experimental data (Buffeteau et al., 2017) have already demonstrated the effect of the encapsulation in the low-wavenumbers region. To generate the initial structures, we rely on the novel Conformer-Rotamer Ensemble Sampling Tool (CREST) program, developed by S. Grimme and co-workers. This is required due to the flexibility provided by the linkers. The CREST algorithm seems promising and has already been used to sample the potential energy surface (PES) of target systems before the simulation of their vibrational spectroscopies (Eikås et al., 2022). We observe large similarities between the two sets of conformers (one with and one without Xe encapsulated), demonstrating the robustness of the CREST algorithm. For corresponding structures, the presence of xenon pushed the two hemispheres slightly further apart. After optimization at the DFT level, only one unique conformer has a Boltzmann population ratio greater than 1%, pointing out the relative rigidity of the cage. Based on this unique conformer, our simulations are in good agreement with the experimental data. Regarding xenon encapsulation, the (experimental and theoretical) ROA signatures at low wavenumbers are impacted: slight shifts in wavenumbers are observed as well as a decrease in relative ROA intensity for bands around 150 cm-1. The wavenumber shifts were very well reproduced by our simulations, but the experimental decrease in the ROA intensity was unfortunately not reproduced.

First-Principles Anharmonic Infrared and Raman Vibrational Spectra of Materials: Fermi Resonance in Dry Ice

We introduce a computational tool for the quantum-mechanical simulation of anharmonic infrared and Raman vibrational spectra of materials. The approach, implemented in the CRYSTAL software, stems from Taylor's expansion of the potential energy surface (PES) on the basis of normal modes up to cubic and quartic terms. The PES can be sampled with four different numerical schemes at the level of density functional theory (DFT), with local, generalized-gradient, and hybrid density functional approximations. Anharmonic states are obtained by solving Shrödinger's nuclear equation with either the vibrational self-consistent field (VSCF) or vibrational configuration interaction (VCI) methods. Nuclear quantum effects (NQEs) are thus fully accounted for. Infrared intensities are computed numerically through a Berry phase approach or analytically through a coupled-perturbed (CP) approach. Raman intensities are computed analytically via the CP approach. A variety of anharmonic features of vibrational spectra of materials can be simulated, including band shifts, combination bands, overtones, resonances (first-order Fermi, second-order Darling-Dennison), and hot bands. We showcase the effectiveness of the approach on the description of a first-order Fermi resonance (FR) in CO2 dry ice: a challenging test-case given that the FR occurs in the Raman spectrum, requires NQEs, and involves two- and three-mode couplings. Fundamental mechanistic differences with respect to the well-known FR in molecular CO2 are addressed. This application represents the first quantum-mechanical, periodic description of FR in dry ice.

First-Principles Calculations of Excited-State Decay Rate Constants in Organic Fluorophores

In this Perspective, we discuss recent advances made to evaluate from first-principles the excited-state decay rate constants of organic fluorophores, focusing on the so-called static strategy. In this strategy, one essentially takes advantage of Fermi's golden rule (FGR) to evaluate rate constants at key points of the potential energy surfaces, a procedure that can be refined in a variety of ways. In this way, the radiative rate constant can be straightforwardly obtained by integrating the fluorescence line shape, itself determined from vibronic calculations. Likewise, FGR allows for a consistent calculation of the internal conversion (related to the non-adiabatic couplings) in the weak-coupling regime and intersystem crossing rates, therefore giving access to estimates of the emission yields when no complex photophysical phenomenon is at play. Beyond outlining the underlying theories, we summarize here the results of benchmarks performed for various types of rates, highlighting that both the quality of the vibronic calculations and the accuracy of the relative energies are crucial to reaching semiquantitative estimates. Finally, we illustrate the successes and challenges in determining the fluorescence quantum yields using a series of organic fluorophores.

Comprehensive quantum chemical analysis of the (ro)vibrational spectrum of thiirane and its deuterated isotopologue

The (ro)vibrational spectra of thiirane, c-C2H4S, and its fully deuterated isotopologue, c-C2D4S, have been studied by means of vibrational configuration interaction theory, VCI, its incremental variant, iVCI, and subsequent variational rovibrational calculations, RVCI, which rely on multidimensional potential energy surfaces of coupled-cluster quality including up to four-mode coupling terms. Accurate geometrical parameters, fundamental vibrational transitions and first overtones, rovibrational spectra and rotational spectroscopic constants have been determined from these calculations and were compared with experimental results whenever available. A number of tentative misassignments in the vibrational spectra could be resolved and most results for the deuterated thiirane are high-level predictions, which may guide experiments to come. Besides this, a new implementation of infrared intensities within the iVCI framework has been tested for the transitions of the title compounds and are compared with results obtained from standard VCI calculations.

Insights into the Molecular Structure and Spectroscopic Properties of HONCO: An Accurate Ab Initio Study

In an effort to provide the first accurate structural and spectroscopic characterization of the quasi-linear chain HONCO in its electronic ground state, state-of-the-art computational approaches mainly based on coupled-cluster (CC) theory have been employed. Equilibrium geometries have been calculated by means of a composite scheme based on CC calculations that incorporates up to the quadruple excitations and accounts for the extrapolation to the complete basis set limit and core correlation effects. This approach is proven to provide molecular structures with an accuracy better than 0.001 Å and 0.05° for bond lengths and angles, respectively. Incorporation of vibrational effects permits this level of theory to predict rotational constants with an estimated accuracy of 0.1% or better. Vibrational fundamental bands have been evaluated by means of a hybrid scheme based on harmonic frequencies computed using the CC singles, doubles, and a perturbative treatment of the triples method (CCSD(T)) in conjunction with a quadruple-ζ basis set, with all electrons being correlated, and anharmonic corrections from CCSD(T) calculations using a triple-ζ basis set, within the frozen-core approximation. Such a hybrid approach allowed us to obtain fundamental frequencies with a mean absolute error of about 1%. To complete the spectroscopic characterization, vertical electronic excitation energies have been calculated for the lowest singlet and triplet states using the internally contracted multireference configuration interaction (MRCI) method. Computations show that HONCO dissociates into OH + NCO upon the absorption of UV-vis light. In conclusion, we are confident that the highly accurate spectroscopic data provided herein can be useful for guiding future experimental investigations and supporting the characterization of this molecule in atmospheric and astrophysical media, as well as in combustion.

Hydrogen Sulfide Ligation in Hemoglobin I of Lucina pectinata─A QM/MM and Local Mode Study

In this study, we investigated the interaction between the H2S ligand and the heme pocket of hemoglobin I (HbI) of Lucina pectinata for the wild-type protein; three known mutations where distal glutamine is replaced by hydrophobic valine (Gln64Val) and hydrophilic histidine in both protonation forms (Gln64Hisϵ and Gln64Hisδ); five known mutations of the so-called phenyl cage, replacing the hydrophobic phenylalanines Phe29 and Phe43 with tyrosine (Tyr), valine (Val), or leucine (Leu); and two additional mutations, Phe68Tyr and Phe68Val, in order to complement previous studies with new insights about the binding mechanism at the molecular level. A particular focus was on the intrinsic strengths of the chemical bonds involved, utilizing local vibrational force constants based on combined quantum mechanical-molecular mechanical calculations. Wild-type protein and mutations clustered into two distinct groups: Group 1 protein systems with a proton acceptor in the distal protein pocket, close to one of the H2S bonds, and Group 2 protein systems without a hydrogen acceptor close by in the active site of the protein. According to our results, the interactions between H2S and HbI of Lucina pectinata involve two important elements, namely, binding of H2S to Fe of the heme group, followed by the proton transfer from the HS bond to the distal residue. The distal residue is additionally stabilized by a second proton transfer from the distal residue to COO- of the propionate group in heme. We could identify the FeS bond as a key player and discovered that the strength of this bond depends on two mutual factors, namely, the strength of the HS bond involved in the proton transfer and the electrostatic field of the protein pocket qualifying the FeS bond as a sensitive probe for monitoring changes in H2S ligation upon protein mutations. We hope our study will inspire and guide future experimental studies, targeting new promising mutations such as Phe68Tyr, Phe68Val, or Phe43Tyr/Phe68Val.

n → π* Interaction Enabling Transient Inversion of Chirality

This study reports the observation and characterization of two isomers of the acrolein dimer by using high-resolution rotational spectroscopy in pulsed jets. The first isomer is stabilized by two hydrogen bonds, adopting a planar configuration, and is energetically favored over the second isomer, which exhibits a dominant n → π* interaction in a nearly orthogonal arrangement. Surprisingly, the n → π* interaction was revealed to enable a concerted tunneling motion of two moieties along the carbonyl group. This motion leads to the inversion of transient chirality associated with the exchange of donor-acceptor roles, as revealed by the spectral feature of quadruplets. Inversion of transient chirality is a fundamental phenomenon in quantum mechanics and commonly observed for only inversional motions of protons. It is the first discovery, to the best of our knowledge, that such heavy moieties can also undergo chirality inversion.

Accuracy of Different Electronic Basis Set Families for Anharmonic Molecular Vibrations: A Comprehensive Benchmark Study

In this work, the accuracy and convergence of different electronic basis set families for the computation of anharmonic molecular vibrational spectroscopic calculations are benchmarked. A series of 39 different basis sets from different families following their hierarchy are assessed on VSCF and VSCF-PT2 algorithms with commonly used MP2 and DFT based B3LYP-D potentials for a set of molecular systems. Such an effort has been validated in a previous work ( J. Phys. Chem. A 2020, 124, 9203-9221) with split-valence basis sets for fundamentals and intensities. Here, fundamental transitions, vibrationally excited states, and intensities are compared with the experimental data to estimate the accuracy for a series of Jensen, Dunning, Calendar, Karlsruhe, and Sapporo basis set families. The convergence of basis sets are also compared with the large ANO basis set. Comprehensive statistical error analysis in terms of accuracy and precision was carried out to assess the performance of each basis set. It is observed that the improvement for the calculated harmonic and anharmonic values from the smaller basis sets to the medium (i.e., triple-ξ) is considerable. Beyond this, from medium to large basis sets, the convergence is slow and mostly posits nearly converged values. Basis sets with and without diffuse functions offer characteristically different accuracies and convergence patterns. Finally, recommendations are given on the choice of basis set chosen as black-box which can balance between accuracy and computational time, estimation of the errors, and their selections especially for large molecules.

Extensive Analysis of the Parameters Influencing Radiative Rates Obtained through Vibronic Calculations

Defining a theoretical model systematically delivering accurate ab initio predictions of the fluorescence quantum yields of organic dyes is highly desirable for designing improved fluorophores in a systematic rather than trial-and-error way. To this end, the first required step is to obtain reliable radiative rates (kr), as low kr typically precludes effective emission. In the present contribution, using a series of 10 substituted phenyls with known experimental kr, we analyze the impact of the computational protocol on the kr determined through the thermal vibration correlation function (TVCF) approach on the basis of time-dependent density functional theory (TD-DFT) calculations of the energies, structures, and vibrational parameters. Both the electronic structure (selected exchange-correlation functional, application or not of the Tamm-Dancoff approximation) and the vibronic parameters (line-shape formalism, coordinate system, potential energy surface model, and dipole expansion) are tackled. Considering all possible combinations yields more than 3500 cases, allowing to extract statistically-relevant information regarding the impact of each computational parameter on the magnitude of the estimated kr. It turns out that the selected vibronic model can have a significant impact on the computed kr, especially the potential energy surface model. This effect is of the same order of magnitude as the difference noted between B3LYP and CAM-B3LYP estimates. For the treated compounds, all evaluated functionals do deliver reasonable trends, fitting the experimental values.

Dissecting the Molecular Origin of g-Tensor Heterogeneity and Strain in Nitroxide Radicals in Water: Electron Paramagnetic Resonance Experiment versus Theory

Nitroxides are common EPR sensors of microenvironmental properties such as polarity, numbers of H-bonds, pH, and so forth. Their solvation in an aqueous environment is facilitated by their high propensity to form H-bonds with the surrounding water molecules. Their g- and A-tensor elements are key parameters to extracting the properties of their microenvironment. In particular, the gxx value of nitroxides is rich in information. It is known to be characterized by discrete values representing nitroxide populations previously assigned to have different H-bonds with the surrounding waters. Additionally, there is a large g-strain, that is, a broadening of g-values associated with it, which is generally correlated with environmental and structural micro-heterogeneities. The g-strain is responsible for the frequency dependence of the apparent line width of the EPR spectra, which becomes evident at high field/frequency. Here, we address the molecular origin of the gxx heterogeneity and of the g-strain of a nitroxide moiety (HMI: 2,2,3,4,5,5-hexamethylimidazolidin-1-oxyl, C9H19N2O) in water. To treat the solvation effect on the g-strain, we combined a multi-frequency experimental approach with ab initio molecular dynamics simulations for structural sampling and quantum chemical EPR property calculations at the highest realistically affordable level, including an explicitly micro-solvated HMI ensemble and the embedded cluster reference interaction site model. We could clearly identify the distinct populations of the H-bonded nitroxides responsible for the gxx heterogeneity experimentally observed, and we dissected the role of the solvation shell, H-bond formation, and structural deformation of the nitroxide in the creation of the g-strain associated with each nitroxide subensemble. Two contributions to the g-strain were identified in this study. The first contribution depends on the number of hydrogen bonds formed between the nitroxide and the solvent because this has a large and well-understood effect on the gxx-shift. This contribution can only be resolved at high resonance frequencies, where it leads to distinct peaks in the gxx region. The second contribution arises from configurational fluctuations of the nitroxide that necessarily lead to g-shift heterogeneity. These contributions cannot be resolved experimentally as distinct resonances but add to the line broadening. They can be quantitatively analyzed by studying the apparent line width as a function of microwave frequency. Interestingly, both theory and experiment confirm that this contribution is independent of the number of H-bonds. Perhaps even more surprisingly, the theoretical analysis suggests that the configurational fluctuation broadening is not induced by the solvent but is inherently present even in the gas phase. Moreover, the calculations predict that this broadening decreases upon solvation of the nitroxide.

Core-Projected Hybrids Fix Systematic Errors in Time-Dependent Density Functional Theory Predicted Core-Electron Excitations

Linear response time-dependent density functional theory (TDDFT) is widely applied to valence, Rydberg, and charge-transfer excitations but, in its current form, makes large errors for core-electron excitations. This work demonstrates that the admixture of nonlocal exact exchange in atomic core regions significantly improves TDDFT-predicted core excitations. Exact exchange admixture is accomplished using projected hybrid density functional theory [ J. Chem. Theory Comput. 2023, 19, 837-847]. Scalar relativistic TDDFT calculations using core-projected B3LYP accurately model core excitations of second-period elements C-F and third-period elements Si-Cl, without sacrificing performance for the relative shifts of core excitation energies. Predicted K-edge X-ray near absorption edge structure (XANES) of a series of sulfur standards highlight the value of this approach. Core-projected hybrids appear to be a practical solution to TDDFT's limitations for core excitations, in the way that long-range-corrected hybrids are a practical solution to TDDFT's limitations for Rydberg and charge-transfer excitations.

Chemical Transformations Can Occur during DMS Separations: Lessons Learned from Beer's Bittering Compounds

While developing a DMS-based separation method for beer's bittering compounds, we observed that the argentinated forms of humulone tautomers (i.e., [Hum + Ag]⁺) were partially resolvable in a N₂ environment seeded with 1.5 mol % of isopropyl alcohol (IPA). Attempting to improve the separation by introducing resolving gas unexpectedly caused the peaks for the cis-keto and trans-keto tautomers of [Hum + Ag]⁺ to coalesce. To understand why resolution loss occurred, we first confirmed that each of the tautomeric forms (i.e., dienol, cis-keto, and trans-keto) responsible for the three peaks in the [Hum + Ag]⁺ ionogram were assigned to the correct species by employing collision-induced dissociation, UV photodissociation spectroscopy, and hydrogen-deuterium exchange (HDX). The observation of HDX indicated that proton transfer was stimulated by dynamic clustering processes between IPA and [Hum + Ag]⁺ during DMS transit. Because IPA accretion preferentially occurs at Ag⁺, which can form pseudocovalent bonds with a suitable electron donor, solvent clustering also facilitated the formation of exceptionally stable microsolvated ions. The exceptional stability of these microsolvated configurations disproportionately impacted the compensation voltage (CV) required to elute each tautomer when the temperature within the DMS cell was varied. The disparity in CV response caused the peaks for the cis- and trans-keto species to merge when a temperature gradient was induced by the resolving gas. Moreover, simulations showed that microsolvation with IPA mediates dienol to trans-keto tautomerization during DMS transit, which, to the best of our knowledge, is the first observation of keto/enol tautomerization occurring within an ion-mobility device.

Nanointerfaces: Concepts and Strategies for Optical and X-ray Spectroscopic Characterization

Interfaces at the nanoscale, also called nanointerfaces, play a fundamental role in physics and chemistry. Probing the chemical and electronic environment at nanointerfaces is essential in order to elucidate chemical processes relevant for applications in a variety of fields. Many spectroscopic techniques have been applied for this purpose, although some approaches are more appropriate than others depending on the type of the nanointerface and the physical properties of the different phases. In this Perspective, we introduce the major concepts to be considered when characterizing nanointerfaces. In particular, the interplay between the characteristic length of the nanointerfaces, and the probing and information depths of different spectroscopy techniques is discussed. Differences between nano- and bulk interfaces are explained and illustrated with chosen examples from optical and X-ray spectroscopies, focusing on solid-liquid nanointerfaces. We hope that this Perspective will help to prepare spectroscopic characterization of nanointerfaces and stimulate interest in the development of new spectroscopic techniques adapted to the nanointerfaces.

An Expedited Route to Optical and Electronic Properties at Finite Temperature via Unsupervised Learning

Electronic properties and absorption spectra are the grounds to investigate molecular electronic states and their interactions with the environment. Modeling and computations are required for the molecular understanding and design strategies of photo-active materials and sensors. However, the interpretation of such properties demands expensive computations and dealing with the interplay of electronic excited states with the conformational freedom of the chromophores in complex matrices (i.e., solvents, biomolecules, crystals) at finite temperature. Computational protocols combining time dependent density functional theory and ab initio molecular dynamics (MD) have become very powerful in this field, although they require still a large number of computations for a detailed reproduction of electronic properties, such as band shapes. Besides the ongoing research in more traditional computational chemistry fields, data analysis and machine learning methods have been increasingly employed as complementary approaches for efficient data exploration, prediction and model development, starting from the data resulting from MD simulations and electronic structure calculations. In this work, dataset reduction capabilities by unsupervised clustering techniques applied to MD trajectories are proposed and tested for the ab initio modeling of electronic absorption spectra of two challenging case studies: a non-covalent charge-transfer dimer and a ruthenium complex in solution at room temperature. The K-medoids clustering technique is applied and is proven to be able to reduce by ∼100 times the total cost of excited state calculations on an MD sampling with no loss in the accuracy and it also provides an easier understanding of the representative structures (medoids) to be analyzed on the molecular scale.

Computational Protocol for the Identification of Candidates for Radioastronomical Detection and Its Application to the C3H3NO Family of Isomers

The C3H3NO family of isomers is relevant in astrochemistry, even though its members are still elusive in the interstellar medium. To identify the best candidate for astronomical detection within this family, we developed a new computational protocol based on the minimum-energy principle. This approach aims to identify the most stable isomer of the family and consists of three steps. The first step is an extensive investigation that characterizes the vast number of compounds having the C3H3NO chemical formula, employing density functional theory for this purpose. The second step is an energy refinement, which is used to select isomers and relies on coupled cluster theory. The last step is a structural improvement with a final energy refinement that provides improved energies and a large set of accurate spectroscopic parameters for all isomers lying within 30 kJ mol−1 above the most stable one. According to this protocol, vinylisocyanate is the most stable isomer, followed by oxazole, which is about 5 kJ mol−1 higher in energy. The other stable species are pyruvonitrile, cyanoacetaldehyde, and cyanovinylalcohol. For all of these species, new computed rotational and vibrational spectroscopic data are reported, which complement those already available in the literature or fill current gaps.

Future of computational molecular spectroscopy-from supporting interpretation to leading the innovation

Molecular spectroscopy measures transitions between discrete molecular energies which follow quantum mechanics. Structural information of a molecule is encoded in the spectra, which can be only decoded using quantum mechanics and therefore computational molecular spectroscopy becomes essential. In this review perspective, the role evolution of computational molecular spectroscopy has been discussed with several joint theory and experiment spectroscopic studies in the past decades, which includes rotational (microwave), vibrational and electronic spectroscopy (valence and core) of molecules. With the development in high resolution and computerized synchrotron sourced spectroscopy, spectral measurements and computational molecular spectroscopy need to be integrated for materials development. Contemporary computational molecular spectroscopy is, therefore, more than merely supporting interpretation but leading the innovation. Future development of molecular spectroscopy lies to identify the niche to integrate experimental and computational molecular spectroscopy. It also requires to engineer molecular spectroscopic databases that function according to the universal approaches of computing, such as those in a Turing machine, to be realized in a chemical and/or spectroscopic programable manner (digital twinning research) in the future.

Isotope Effects on Ground and Excited States of Ethyl Cation, H+(C2H4)

The structure and spectra of ethyl cation, H⁺(C₂H₄), and its deuterated analogues are investigated using diffusion Monte Carlo (DMC). These calculations all show that the ground state wave function for H⁺(C₂H₄) is localized near the minimum energy configuration in which the excess proton is in a bridging configuration, although the amplitude of the vibrational motions of the bridging proton is large. Deuteration of the bridging proton reduces the amplitude of this motion, while deuteration of only the ethylenic hydrogen atoms in H⁺(C₂D₄) has little effect on the amplitude of the motion of the bridging proton. Excited states that are accessed by spectroscopically observed transitions in H⁺(C₂H₄) are calculated using fixed-node DMC. The calculated and measured frequencies for the states with one quantum of excitation in the ethylenic CH stretching vibrations show good agreement. We also explore the excited state with one quantum of excitation in the proton transfer vibration of the bridging proton and obtain a frequency of 616 cm^-1 for H⁺(C₂H₄). This frequency increases to 629 cm^-1 in H⁺(C₂D₄). Deuteration decreases this frequency to 491 and 495 cm^-1 in D⁺(C₂H₄) and D⁺(C₂D₄), respectively. The effects of partial deuteration on the frequencies of the CH stretching vibrations, and the corresponding probability amplitudes are also explored. Finally, we report the vibrationally averaged rotational constants for the four isotopologues of ethyl cation considered in this study.

Insights into the molecular structure and infrared spectrum of the prebiotic species aminoacetonitrile

Aminoacetonitrile is an interstellar molecule with a prominent prebiotic role, already detected in the chemically-rich molecular cloud Sagittarius B2(N) and postulated to be present in the atmosphere of the largest Saturn's moon, Titan. To further support its observation in such remote environments and laboratory experiments aimed at improving our understanding of interstellar chemistry, we report a thorough spectroscopic and structural characterization of aminoacetonitrile. Equilibrium geometry, fundamental bands as well as spectroscopic and molecular parameters have been accurately computed by exploiting a composite scheme rooted in the coupled-cluster theory that accounts for the extrapolation to the complete basis set limit and core-correlation effects. In addition, a semi-experimental approach that combines ground-state rotational constants for different isotopic species and calculated vibrational corrections has been employed for the structure determination. From the experimental side, we report the analysis of the three strongest fundamental bands of aminoacetonitrile observed between 500 and 1000 cm^-1 in high-resolution infrared spectra. More generally, all computed band positions are in excellent agreement with the present and previous experiments. The only exception is the ν₁₅ band, for which we provide a revision of the experimental assignment, now in good agreement with theory.

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.

Connections between the accuracy of rotational constants and equilibrium molecular structures

Rotational spectroscopy is the technique of choice for investigating molecular structures in the gas phase. Indeed, rotational constants are strongly connected to the geometry of the molecular system under consideration. Therefore, they are powerful tools for assessing the accuracy that quantum chemical approaches can reach in structural determinations. In this review article, it is shown how it is possible to measure the accuracy of a computed equilibrium geometry based on the comparison of rotational constants. But, it is also addressed what accuracy is required by computations for providing molecular structures and thus rotational constants that are useful to experiment. Quantum chemical methodologies for obtaining the "0.1% accuracy" for rotational constants are reviewed for systems ranging in size from small molecules to small polycyclic aromatic hydrocarbons. This accuracy for systems containing two dozen or so atoms opens the way towards future applications such as the accurate characterization of non-covalent interactions, which play a key role in several biological and technological processes.

Influence of Number of Ligands and Point Group on the Electronic Structure of Co2+ Aqua-Complexes

The nucleation process of zeolitic imidazolate frameworks (ZIFs) is, to date, not yet completely understood, making the search for tailored materials very difficult. Recently, it has been shown that, during the formation process, the symmetry of the precursors is reduced by ligand elimination and substitution reactions. The octahedral precursors with simple ligands, such as water, methanol, and/or NO₃^-, are transformed to five- and finally four-coordinated complexes with imidazole ligands. This reduction of symmetry, caused both by the changing coordination environment and distortions from the perfect symmetry leading to another point group, will have a large influence on the electronic structure and more specifically on the d-orbital splitting. This, in turn, will affect the d-d electronic excitations, which can be followed using UV-vis spectroscopy and which can help to unravel the formation process. In this work, we systematically investigate how the lowering of the number of ligands affects the symmetry and thus the geometry and electronic structure of Co²⁺ complexes with six, five, and four aqua ligands. Therefore, we first resort to qualitative techniques, such as crystal field theory (CFT) and ligand field theory (LFT), which reveal that the orbital splitting is characteristic for the number of ligands. However, as these techniques are not capable of providing quantitative results without the use of experimental data as input, we perform various computational calculations. Both average of configuration (AOC) and unrestricted density functional theory (UDFT) are thoroughly investigated, and we will determine which technique is the best suited to properly describe the ground state of these systems. To investigate the dependency on the d-orbital occupation, we also investigated V²⁺, Mn²⁺, and Ni²⁺ hexa-aqua-complexes and compared them to the Co systems.

Rotational spectrum of anisole-CO2: Cooperative C···O tetrel bond and CH···O hydrogen bond

Rotational spectrum of the 1:1 anisole-CO₂ complex has been investigated using a pulsed jet Fourier transform microwave spectrometer supplemented with quantum chemical calculations. In the pulsed jet, only one isomer has been observed which is characterized by a dominant C···O tetrel bond and two CH···O_CO2 weak hydrogen bonds. Different theoretical methods predict different orders of relative energies of plausible conformations. The experimental observation is most consistent with the theoretical estimation at the B3LYP-D3(BJ)/6-311++G(d,p) level of theory. Johnson's non-covalent interaction, quantum theory of atoms in molecules and natural bond orbital analyses have been applied to better understand the nature of non-covalent interactions at play in the anisole-CO₂ complex.

Structural Dynamics of Chloromethanes through Computational Spectroscopy: Combining INS and DFT

In this work, the structural dynamics of the chloromethanes CCl₄, CHCl₃ and CH₂Cl₂ were evaluated through a computational spectroscopy approach by comparing experimental inelastic neutron scattering (INS) spectra with the corresponding simulated spectra obtained from periodic DFT calculations. The overall excellent agreement between experimental and calculated spectra allows a confident assignment of the vibrational features, including not only the molecular fundamental modes but also lattice and combination modes. In particular, an impressive overtone sequence for CHCl₃ is fully described by the simulated INS spectrum. In the CCl₄ spectrum, the splitting of the ν3 mode at ca. 765–790 cm⁻¹ is discussed on the basis of the Fermi resonance vs. crystal splitting controversy.

In silico NIR spectroscopy - A review. Molecular fingerprint, interpretation of calibration models, understanding of matrix effects and instrumental difference

Quantum mechanical calculations are routinely used as a major support in mid-infrared (MIR) and Raman spectroscopy. In contrast, practical limitations for long time formed a barrier to developing a similar synergy between near-infrared (NIR) spectroscopy and computational chemistry. Recent advances in theoretical methods suitable for calculation of NIR spectra opened the pathway to modeling NIR spectra of various molecules. Accurate theoretical reproduction of NIR spectra of molecules reaching the size of long-chain fatty acids was accomplished so far. In silico NIR spectroscopy, where the spectra are calculated ab initio, provides substantial improvement in our understanding of the overtones and combination bands that overlap in staggering numbers and create complex lineshape typical for NIR spectra. This improves the comprehension of the spectral information enabling access to rich and detail molecular footprint, essential for fundamental research and useful in routine analysis by NIR spectroscopy and chemometrics. This review article summarizes the most recent accomplishments in the emerging field with examples of simulated NIR spectra of molecules reaching long-chain fatty acids and polymers. In addition to detailed NIR band assignments and new physical insights, simulated spectra enable innovative support in applications. Understanding of the difference in the performance observed between miniaturized NIR spectrometers and chemical interpretation of the chemometric models are noteworthy here. These new elements integrated into NIR spectroscopy framework enable a knowledge-based design of the analysis with comprehension of the processed chemical information.

An Origami Paper-Based Biosensor for Allergen Detection by Chemiluminescence Immunoassay on Magnetic Microbeads

Food allergies are adverse health effects that arise from specific immune responses, occurring upon exposure to given foods, even if present in traces. Egg allergy is one of the most common food allergies, mainly caused by egg white proteins, with ovalbumin being the most abundant. As allergens can also be present in foodstuff due to unintended contamination, there is a need for analytical tools that are able to rapidly detect allergens in food products at the point-of-use. Herein, we report an origami paper-based device for detecting ovalbumin in food samples, based on a competitive immunoassay with chemiluminescence detection. In this biosensor, magnetic microbeads have been employed for easy and efficient immobilization of ovalbumin on paper. Immobilized ovalbumin competes with the ovalbumin present in the sample for a limited amount of enzyme-labelled anti-ovalbumin antibody. By exploiting the origami approach, a multistep analytical procedure could be performed using reagents preloaded on paper layers, thus providing a ready-to-use immunosensing platform. The assay provided a limit of detection (LOD) of about 1 ng mL^-1 for ovalbumin and, when tested on ovalbumin-spiked food matrices (chocolate chip cookies), demonstrated good assay specificity and accuracy, as compared with a commercial immunoassay kit.

Exploring Expansions of the Potential and Dipole Surfaces Used for Vibrational Perturbation Theory

A scheme for evaluating expansions of the potential and dipole moment surfaces for vibrational perturbation theory is described. The approach is based on numerical differentiation of the Hessian in the coordinates of interest. It is shown that performing these calculations in internal coordinates generates expansions that are transferable among isotopologues of the molecule of interest. Additionally, re-expressing the expansion of the potential in terms of functions of the internal coordinates, for example, cosines of angles or exponential functions of the bond length displacements, provides expansions that can be used for higher-order perturbation theory calculations. The approach is explored and the results are discussed for water, HOD, ammonia, isomers of HNO₃, and halogenated methane.

Unbiased disentanglement of conformational baths with the help of microwave spectroscopy, quantum chemistry and artificial intelligence: the puzzling case of homocysteine

An integrated experimental-computational strategy for the accurate characterization of the conformational landscape of flexible biomolecule building blocks is proposed. This is based on the combination of rotational spectroscopy with quantum-chemical computations guided by artificial intelligence tools. The first step of the strategy is the conformer search and relative stability evaluation performed by means of an evolutionary algorithm. In this step, last generation semiempirical methods are exploited together with hybrid and double-hybrid density functionals. Next, the barriers ruling the interconversion between the low-lying conformers are evaluated in order to unravel possible fast relaxation paths. The relative stabilities and spectroscopic parameters of the ``surviving' conformers are then refined using state-of-the-art composite schemes. The reliability of the computational procedure is further improved by the inclusion of vibrational and thermal effects. The final step of the strategy is the comparison between experiment and theory without any ad hoc adjustment, which allows an unbiased assignment of the spectroscopic features in terms of different conformers and their spectroscopic parameters. The proposed approach has been tested and validated for homocysteine, a highly flexible non-proteinogenic alpha-amino acid. The synergism of the integrated strategy allowed the characterization of five conformers stabilized by bifurcated N-H-O=C hydrogen bonds, together with an additional conformer involving a more conventional HNH-O hydrogen bond. The stability order estimated from the experimental intensities as well as the number and type of conformers observed in the gas phase are in full agreement with the theoretical predictions. Analogously, a good match has been found for the spectroscopic parameters.

Dipolar spin-spin coupling as an auxiliary tool for the structure determination of small isolated molecules

The "gold standard" for obtaining accurate equilibrium structures is the so-called semi-experimental (SE) approach, which exploits the structural information contained in rotational constants. Within the SE approach, ground-state rotational constants-accurately obtained from high-resolution spectroscopic studies-are computationally corrected in order to remove vibrational effects. The resulting SE equilibrium rotational constants for a significant set of isotopic species allow for retrieving a unique set of equilibrium bond lengths and angles for the molecule under consideration. However, in some cases, the lack of isotopic substitution hampers or even prevents a rigorous and complete structure determination. In this perspective, we introduce the use of dipolar spin-spin coupling constants as an additional source of structural information in support of the standard SE approach. As a proof-of-concept, we tested this new strategy on some prototypical species, such as water, ammonia, phosphine, and their fluorinated counterparts. Our results indicate that-even when the molecular structure can be obtained from a large set of isotopic rotational constants-the use of dipolar spin-spin coupling constants guarantees a better accuracy and reduces the correlations among the geometrical parameters. Moreover, we point out that our approach offers the possibility to fully derive the molecular structure of PF₃, a species for which any isotopic substitution is not possible.

Spectroscopic Characterization of 3-Aminoisoxazole, a Prebiotic Precursor of Ribonucleotides

The processes and reactions that led to the formation of the first biomolecules on Earth play a key role in the highly debated theme of the origin of life. Whether the first chemical building blocks were generated on Earth (endogenous synthesis) or brought from space (exogenous delivery) is still unanswered. The detection of complex organic molecules in the interstellar medium provides valuable support to the latter hypothesis. To gather more insight, here we provide the astronomers with accurate rotational frequencies to guide the interstellar search of 3-aminoisoxazole, which has been recently envisaged as a key reactive species in the scenario of the so-called RNA-world hypothesis. Relying on an accurate computational characterization, we were able to register and analyze the rotational spectrum of 3-aminoisoxazole in the 6–24 GHz and 80–320 GHz frequency ranges for the first time, exploiting a Fourier-transform microwave spectrometer and a frequency-modulated millimeter/sub-millimeter spectrometer, respectively. Due to the inversion motion of the −NH₂ group, two states arise, and both of them were characterized, with more than 1300 lines being assigned. Although the fit statistics were affected by an evident Coriolis interaction, we were able to produce accurate line catalogs for astronomical observations of 3-aminoisoxazole.

Applicability of the Thawed Gaussian Wavepacket Dynamics to the Calculation of Vibronic Spectra of Molecules with Double-Well Potential Energy Surfaces

Simulating vibrationally resolved electronic spectra of anharmonic systems, especially those involving double-well potential energy surfaces, often requires expensive quantum dynamics methods. Here, we explore the applicability and limitations of the recently proposed single-Hessian thawed Gaussian approximation for the simulation of spectra of systems with double-well potentials, including 1,2,4,5-tetrafluorobenzene, ammonia, phosphine, and arsine. This semiclassical wavepacket approach is shown to be more robust and to provide more accurate spectra than the conventional harmonic approximation. Specifically, we identify two cases in which the Gaussian wavepacket method is especially useful due to the breakdown of the harmonic approximation: (i) when the nuclear wavepacket is initially at the top of the potential barrier but delocalized over both wells, e.g., along a low-frequency mode, and (ii) when the wavepacket has enough energy to classically go over the low potential energy barrier connecting the two wells. The method is efficient and requires only a single classical ab initio molecular dynamics trajectory, in addition to the data required to compute the harmonic spectra. We also present an improved algorithm for computing the wavepacket autocorrelation function, which guarantees that the evaluated correlation function is continuous for arbitrary size of the time step.

Spectroscopic and Computational Characterization of 2-Aza-1,3-butadiene, a Molecule of Astrochemical Significance

Being N-substituted unsaturated species, azabutadienes are molecules of potential relevance in astrochemistry, ranging from the interstellar medium to Titan’s atmosphere. 2-Azabutadiene and butadiene share a similar conjugated π system, thus allowing investigation of the effects of heteroatom substitution. More interestingly, 2-azabutadiene can be used to proxy the abundance of interstellar butadiene. To enable future astronomical searches, the rotational spectrum of 2-azabutadiene has been investigated up to 330 GHz. The experimental work has been supported and guided by accurate computational characterization of the molecular structure, energetics, and spectroscopic properties of the two possible forms, trans and gauche. The trans species, more stable by about 7 kJ/mol than gauche-2-azabutadiene, has been experimentally observed, and its rotational and centrifugal distortion constants have been obtained with remarkable accuracy, while theoretical estimates of the spectroscopic parameters are reported for gauche-2-azabutadiene.

Interaction Types in C6H5(CH2)nOH-CO2 (n = 0-4) Determined by the Length of the Side Alkyl Chain

C₆H₅(CH₂)_nOH-CO₂ complexes have been investigated using rotational spectroscopy (n = 0-2) complemented by quantum chemical calculations (n = 0-4), which implies that the side alkyl chain length can determine the types of intermolecular interactions. Unlike the in-plane C···O tetrel bond in phenol-CO₂, the π*_CO2···π_aromatic interaction has been shown to link CO₂ to phenylmethanol and 2-phenylethanol, which is, to the best of our knowledge, the first time it has been demonstrated by rotational spectroscopy. Further elongations of the side alkyl chain gradually increase the energies of intramolecular hydrogen bonds in 3-phenylpropanol and 4-phenylbutanol so that CO₂ cannot break it. CO₂ will be pushed farther from the monomers and link with the -OH group through a dominating C···O tetrel bond. Our observations would allow, with the choice of the proper length of the side alkyl chain, new strategies for engineering C···π_aromatic-centered noncovalent bonding schemes for the capture, utilization, and storage of CO₂.

Ab Initio Study of Fine and Hyperfine Interactions in Triplet POH

Phosphorous-containing molecules have a great relevance in prebiotic chemistry in view of the fact that phosphorous is a fundamental constituent of biomolecules, such as RNA, DNA, and ATP. Its biogenic importance has led astrochemists to investigate the possibility that P-bearing species could have formed in the interstellar medium (ISM) and subsequently been delivered to early Earth by rocky bodies. However, only two P-bearing molecules have been detected so far in the ISM, with the chemistry of interstellar phosphorous remaining poorly understood. Here, in order to shed further light on P-carriers in space, we report a theoretical spectroscopic characterisation of the rotational spectrum of POH in its 3A″ ground electronic state. State-of-the-art coupled-cluster schemes have been employed to derive rotational constants, centrifugal distortion terms, and most of the fine and hyperfine interaction parameters, while the electron spin-spin dipolar coupling has been investigated using the multi-configuration self-consistent-field method. The computed spectroscopic parameters have been used to simulate the appearance of triplet POH rotational and ro-vibrational spectra in different conditions, from cold to warm environments, either in gas-phase experiments or in molecular clouds. Finally, we point out that the predicted hyperfine structures represent a key pattern for the recognition of POH in laboratory and interstellar spectra.

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.

Chiral Molecular Structure Determination for a Desired Compound Just from Its Molecular Formula and Vibrational Optical Activity Spectra

A novel proof-of-concept model for chiral molecular structure determination using just the molecular formula and vibrational optical activity (VOA) spectra is presented. To verify this concept, the molecular formula of a desired compound is used to generate all possible chiral structural isomers and their VOA spectra are predicted. The similarity analyses of predicted VOA spectra were then carried out in two different ways: (a) similarity between VOA spectrum of one structural isomer with those of the rest, referred to as cross-correlations; (b) similarity between VOA spectra of all chiral structural isomers with the experimental VOA spectra of the desired compound. Three different molecular formulae, C₄H₈O, C₃H₅ClO, and C₆H₁₀O, and their chiral structural isomers (6, 9, and 75 respectively), were investigated. In each case, the correct chiral molecular structure of the desired compound was identified without ambiguity. Cross-correlation analysis revealed the uniqueness of VOA spectra in deducing the chiral molecular structure solely from its molecular formula. Different chiral structural isomers associated with the molecular formula CH₃NO₂ were also found to have no significant cross-correlations between their VOA spectra, opening a pathway to detect and identify the elusive chiral N-hydroxyoxaziridine from its VOA spectra.