Accurate Geometries of Large Molecules at DFT Cost by Semiexperimental and Coupled Cluster Templating Fragments

Accurate geometries of small semirigid molecules in the gas phase are available thanks to high-resolution spectroscopy and accurate quantum chemical approaches. These results can be employed for validating cheaper low-level quantum chemical models or correcting the corresponding structures of large molecules. On these grounds, in this work, a large panel of semiexperimental equilibrium structures already available in the literature is used to confirm the average error (1 mÅ for bond lengths and 2 mrad for valence angles) of a version of the Pisa composite schemes (PCS2), which is applicable to molecules containing up to about 20 atoms. Then, the geometries of 30 additional medium-sized systems were optimized at the PCS2 level to cover a more balanced chemical space containing moieties poorly represented in SE compilations. The final database is available on a public domain Web site (https://www.skies-village.it/databases/) and can be employed for correcting structures of larger molecules obtained by hybrid or double-hybrid density functionals in the framework of the templating molecule approach. Several examples show that corrections based on the structures of building blocks taken from this database reduce the error of the B3LYP geometrical parameters of large molecules by nearly an order of magnitude without increasing the computational cost. Furthermore, the results of different density functional theory (DFT) or wave function (e.g., MP2) models can be improved in the same way by simply computing both the whole molecule and suitable building blocks at the chosen level. Then, whenever reference structures of some building blocks containing up to about 20 atoms are not available, they can be purposely optimized at the PCS2 level by employing reasonable computer resources. Therefore, a new DFT-cost tool is now available for the accurate characterization of large molecules by experiment-oriented scientists.

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.

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.

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.

Neutral Peptides in the Gas Phase: Conformation and Aggregation Issues

Combined IR and UV laser spectroscopic techniques in molecular beams merged with theoretical approaches have proven to be an ideal tool to elucidate intrinsic structural properties on a molecular level. It offers the possibility to analyze structural changes, in a controlled molecular environment, when successively adding aggregation partners. By this, it further makes these techniques a valuable starting point for a bottom-up approach in understanding the forces shaping larger molecular systems. This bottom-up approach was successfully applied to neutral amino acids starting around the 1990s. Ever since, experimental and theoretical methods developed further, and investigations could be extended to larger peptide systems. Against this background, the review gives an introduction to secondary structures and experimental methods as well as a summary on theoretical approaches. Vibrational frequencies being characteristic probes of molecular structure and interactions are especially addressed. Archetypal biologically relevant secondary structures investigated by molecular beam spectroscopy are described, and the influences of specific peptide residues on conformational preferences as well as the competition between secondary structures are discussed. Important influences like microsolvation or aggregation behavior are presented. Beyond the linear α-peptides, the main results of structural analysis on cyclic systems as well as on β- and γ-peptides are summarized. Overall, this contribution addresses current aspects of molecular beam spectroscopy on peptides and related species and provides molecular level insights into manifold issues of chemical and biochemical relevance.

Conformational impact of aliphatic side chains in local anaesthetics: benzocaine, butamben and isobutamben

We studied the impact of aliphatic side chains on the stability and conformational landscape of the local anaesthetics benzocaine, butamben and isobutamben, combining high-resolution rotational spectroscopy in the microwave and millimetre regions and molecular modelling. The study reveals the connections between alkyl chain flexibility and molecular conformations.

The role of dispersion and anharmonic corrections in conformational analysis of flexible molecules: the allyl group rotamerization of matrix isolated safrole

Conformational changes of the monomeric safrole (5-(2-propenyl)-1,3-benzodioxole) isolated in low temperature xenon matrices were induced thermally or using narrow-band UV radiation. The rotation of the allyl group taking place in the studied matrices was followed by FTIR spectroscopy. Safrole represents a challenging example of a flexible molecule highlighting the importance of dispersion interactions and anharmonic effects in the structural, spectroscopic and energetic analysis. Structures of the safrole conformers, their energetics and infrared spectra have been calculated using various computational methods ranging from density functional theory (DFT) to coupled cluster (CC). The best theoretical results were obtained by integrating CCSD(T) energies including complete basis set extrapolation and core-valence corrections with B2PLYP-D3 equilibrium structures and hybrid B2PLYP-D3/B3LYP-D3 anharmonic computations for IR spectra and thermodynamics.

Multiplexed characterization of complex gas-phase mixtures combining chirped-pulse Fourier transform microwave spectroscopy and VUV photoionization time-of-flight mass spectrometry

We report details of the design and operation of a single apparatus that combines Chirped-Pulse Fourier Transform Microwave (CP-FTMW) spectroscopy with vacuum ultraviolet (VUV) photoionization Time-of-Flight Mass Spectrometry (TOFMS). The supersonic expansion used for cooling samples is interrogated first by passing through the region between two microwave horns capable of broadband excitation and detection in the 2-18 GHz frequency region of the microwave. After passing through this region, the expansion is skimmed to form a molecular beam, before being probed with 118 nm (10.5 eV) single-photon VUV photoionization in a linear time-of-flight mass spectrometer. The two detection schemes are powerfully complementary to one another. CP-FTMW detects all components with significant permanent dipole moments. Rotational transitions provide high-resolution structural data. VUV TOFMS provides a gentle and general method for ionizing all components of a gas phase mixture with ionization thresholds below 10.5 eV, providing their molecular formulae. The advantages, complementarity, and limitations of the combined methods are illustrated through results on two gas-phase mixtures made up of (i) three furanic compounds, two of which are structural isomers of one another, and (ii) the effluent from a flash pyrolysis source with o-guaiacol as the precursor.

The gas-phase structure of the asymmetric, trans-dinitrogen tetroxide (N2O4), formed by dimerization of nitrogen dioxide (NO2), from rotational spectroscopy and ab initio quantum chemistry

We report the first experimental gas-phase observation of an asymmetric, trans-N₂O₄ formed by the dimerization of NO₂. In additional to the dominant ¹⁴N₂¹⁶O₄ species, rotational transitions have been observed for all species with single ¹⁵N and ¹⁸O substitutions as well as several multiply substituted isotopologues. These transitions were used to determine a complete substitution structure as well as an r₀ structure from the fitted zero-point averaged rotational constants. The determined structure is found to be that of an ON-O-NO₂ linkage with the shared oxygen atom closer to the NO₂ than the NO (1.42 vs 1.61 Å). The structure is found to be nearly planar with a trans O-N-O-N linkage. From the spectra of the ¹⁴N¹⁵NO₄ species, we were able to determine the nuclear quadrupole coupling constants for each specific nitrogen atom. The equilibrium structure determined by ab initio quantum chemistry calculations is in excellent agreement with the experimentally determined structure. No spectral evidence of the predicted asymmetric, cis-N₂O₄ was found in the spectra.

A study of the intermolecular interactions of lipid components from analogue fingerprint residues

A compositionally simplified analogue of a latent fingermark was created by combining single representatives of each major component of a natural fingermark. Further modified analogues were also produced each having one component removed. The aim of this study was to investigate the intermolecular interactions that occurred within these analogue samples using Fourier Transform Infrared (FT-IR) Microspectroscopy. FT-IR microspectroscopy showed that the absence of squalene and cholesterol significantly restricted the interactions between the other organic constituents within the analogue samples. Investigating the intermolecular interactions of organic compounds within a simplified analogue solution could indicate corresponding interactions that occur within natural fingermarks. These potential interactions could go on to be the target of further investigation of latent fingermark chemistry, and ultimately contribute to a better understanding of the aging processes and degradation mechanisms that take place post-deposition.

CC/DFT Route toward Accurate Structures and Spectroscopic Features for Observed and Elusive Conformers of Flexible Molecules: Pyruvic Acid as a Case Study

The structures and relative stabilities as well as the rotational and vibrational spectra of the three low-energy conformers of pyruvic acid (PA) have been characterized using a state-of-the-art quantum-mechanical approach designed for flexible molecules. By making use of the available experimental rotational constants for several isotopologues of the most stable PA conformer, Tc-PA, the semiexperimental equilibrium structure has been derived. The latter provides a reference for the pure theoretical determination of the equilibrium geometries for all conformers, thus confirming for these structures an accuracy of 0.001 Å and 0.1 deg for bond lengths and angles, respectively. Highly accurate relative energies of all conformers (Tc-, Tt-, and Ct-PA) and of the transition states connecting them are provided along with the thermodynamic properties at low and high temperatures, thus leading to conformational enthalpies accurate to 1 kJ mol(-1). Concerning microwave spectroscopy, rotational constants accurate to about 20 MHz are provided for the Tt- and Ct-PA conformers, together with the computed centrifugal-distortion constants and dipole moments required to simulate their rotational spectra. For Ct-PA, vibrational frequencies in the mid-infrared region accurate to 10 cm(-1) are reported along with theoretical estimates for the transitions in the near-infrared range, and the corresponding infrared spectrum including fundamental transitions, overtones, and combination bands has been simulated. In addition to the new data described above, theoretical results for the Tc- and Tt-PA conformers are compared with all available experimental data to further confirm the accuracy of the hybrid coupled-cluster/density functional theory (CC/DFT) protocol applied in the present study. Finally, we discuss in detail the accuracy of computational models fully based on double-hybrid DFT functionals (mainly at the B2PLYP/aug-cc-pVTZ level) that avoid the use of very expensive CC calculations.

Nucleic acid ion structures in the gas phase

Nucleic acids are diverse polymeric macromolecules that are essential for all life forms. These biomolecules possess a functional three-dimensional structure under aqueous physiological conditions. Mass spectrometry-based approaches have on the other hand opened the possibility to gain structural information on nucleic acids from gas-phase measurements. To correlate gas-phase structural probing results with solution structures, it is therefore important to grasp the extent to which nucleic acid structures are preserved, or altered, when transferred from the solution to a fully anhydrous environment. We will review here experimental and theoretical approaches available to characterize the structure of nucleic acids in the gas phase (with a focus on oligonucleotides and higher-order structures), and will summarize the structural features of nucleic acids that can be preserved in the gas phase on the experiment time scale.

Behind the reactivity of lactones: a computational and spectroscopic study of phenol·γ-butyrolactone

In this work, the intermolecular interaction between phenol and γ-butyrolactone (GBL) has been studied by a combination of spectroscopic and computational techniques. The electronic and vibrational transitions of phenol · GBL were measured in a supersonic jet expansion by resonant two-photon ionization (R2PI) and ion dip IR (IDIR) spectroscopy. The results obtained were compared with calculations carried out with both M06-2X and MP2 molecular orbital methods in order to characterize the intermolecular interactions. The singly detected conformer is stabilized by a relatively strong hydrogen bond in which phenol acts as a proton donor to the carbonyl group of GBL. The phenol · GBL2 cluster has also been studied, finding up to three populated conformers. Nevertheless, in the three species, the main interaction between the phenolic hydroxyl group and the GBL's carbonyl group remains similar to that of phenol · GBL. Furthermore, the C ═ O · · · H interaction is reinforced.

A direct digital synthesis chirped pulse Fourier transform microwave spectrometer

Chirped pulse Fourier transform microwave (CP-FTMW) spectrometers have become the instrument of choice for acquiring rotational spectra, due to their high sensitivity, fast acquisition rate, and large bandwidth. Here we present the design and capabilities of a recently constructed CP-FTMW spectrometer using direct digital synthesis (DDS) as a new method for chirped pulse generation, through both a suite of extensive microwave characterizations and deep averaging of the 10-14 GHz spectrum of jet-cooled acetone. The use of DDS is more suited for in situ applications of CP-FTMW spectroscopy, as it reduces the size, weight, and power consumption of the chirp generation segment of the spectrometer all by more than an order of magnitude, while matching the performance of traditional designs. The performance of the instrument was further improved by the use of a high speed digitizer with dedicated signal averaging electronics, which facilitates a data acquisition rate of 2.1 kHz.

Rotational spectroscopy meets theory

Rotational spectroscopy is known to be a technique that is widely used to infer information on molecular structure and dynamics. In the last few decades, its role in the field of atmospheric and astrophysical investigations has rapidly grown. However, several are the challenging aspects in rotational spectroscopy, since the detection and analysis of spectra as well as interpretation of obtained results are not at all straightforward. Quantum chemistry has reached such an accuracy that can be used to disentangle these challenging situations by guiding the experimental investigation, assisting in the determination of the spectroscopic parameters, and extracting information of chemical interest. This perspective provides an overview of the theoretical background and computational requirements needed for the accurate evaluation of the spectroscopic parameters of relevance to rotational spectroscopy. The role of theory in guiding and supporting experiment is detailed through a few examples, and the interplay of experiment and theory is discussed in terms of the information of physical and chemical interest that can be derived.

Frontiers in spectroscopy

We review the frontiers of spectroscopy from a historical perspective, starting with the development of atomic spectroscopy about 150 years ago, followed by some comments on selected previous Faraday Discussions. As the spectrum of frontiers at the Faraday Discussion 150 is very broad, we give only a brief survey providing a map of the various frontiers approached today. This is followed by an exemplary discussion of one particular frontier towards the spectroscopic detection of symmetry violations in fundamental physics. In particular the understanding of parity violation in chiral molecules has recently made great progress. We briefly describe the advances made in recent decades as well as the current status of theory and experiments in this exciting field of research. We conclude with an outlook on open questions and frontiers of the future in spectroscopy.