Cold Snapshot of a Molecular Rotary Motor Captured by High-Resolution Rotational Spectroscopy

Toward Accurate Quantum Chemical Methods for Molecules of Increasing Dimension: The New Family of Pisa Composite Schemes

The new versions of the Pisa composite scheme introduced in the present paper are based on 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, the computation of accurate electronic energies has been further improved introducing more reliable complete basis set extrapolations and estimation of core-valence correlation, together with improved basis sets for third-row atoms. Furthermore, the reduced-cost frozen natural orbital (FNO) model has been introduced and validated for large molecules. Accurate molecular structures can be obtained avoiding complete basis set extrapolation and evaluating core-valence correlation at the MP2 level. Unfortunately, analytical gradients are not available for the FNO version of the model. Therefore, for large molecules, an accurate reduced-cost alternative is offered by evaluation of valence contributions with a double-hybrid functional in conjunction with the same MP2 contribution for core-valence correlation or by means of a one-parameter approximation. The same double-hybrid functional and basis set are employed to evaluate zero-point energies and partition functions. After the validation of the new models for small systems, a panel of molecular bricks of life has been used to analyze their performances for problems of current fundamental or technological interest. The fully black-box implementation of the computational workflow paves the way toward the accurate yet not prohibitively expensive study of medium- to large-sized molecules also by experimentally oriented researchers.

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 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.

Absolute configuration assignment of highly fluorinated carboxylic acids via VCD and MRR spectroscopy

Chiral analysis has become a crucial step in studying the stereospecific synthesis of Active Pharmaceutical Ingredients (APIs). Both Vibrational Circular Dichroism (VCD) and Molecular Rotational Resonance (MRR) spectroscopy are capable of determining absolute configurations (ACs) via comparison of experimental and calculated data. In this regard, each technique has its own caveats. In VCD analysis, accurate prediction of the normal modes as well as rigorous conformational searches of both the analyte and potential (self-)aggregation products are required to optimally match experimental spectra. In MRR analysis, chiral species are resolved through complexation with a chiral tag to prepare spectrally distinct diastereomeric complexes. Although individual complex isomers can be distinguished, spectral assignments need to be matched to unique isomer geometries for unambiguous AC assignment. In this work, the ACs of two highly fluorinated carboxylic acids were successfully assigned using VCD and MRR spectroscopy. In the VCD analysis, the M06-2X functional was demonstrated to be superior to B3LYP and B3LYP-GD3 in accurately predicting the C-F normal modes and both monomeric and dimeric spectral contributions were observed. In a similar analysis with broadband MRR, most experimentally identified geometries had more than one possible computational match. Nevertheless, careful consideration of the chiral tag, as well as additional isomer assignments, resulted in successful assignment of the AC. This comparative study demonstrates the power of contemporary VCD analysis and the unique contributions of MRR to the analytical toolbox.

The First Stages of Nanomicelle Formation Captured in the Sevoflurane Trimer

Self-aggregation of sevoflurane, an inhalable, fluorinated anesthetic, provides a challenge for current state-of-the-art high-resolution techniques due to its large mass and the variety of possible hydrogen bonds between monomers. Here we present the observation of sevoflurane trimer by chirped-pulse Fourier transform microwave spectroscopy, identified through the interplay of experimental and computational methods. The trimer (>600 Da), one of the largest molecular aggregates observed through rotational spectroscopy, does not resemble the binding (C-H···O) motif of the already characterized sevoflurane dimer, instead adapting a new binding configuration created predominantly from 17 CH···F hydrogen bonds that resembles a nanomicellar arrangement. The observation of such a heavy aggregate highlights the potential of rotational spectroscopy to study larger biochemical systems in the limit of spectroscopic congestion but also showcases the challenges ahead as the mass of the system increases.

Ultrafast dynamics of an azobenzene-containing molecular shuttle based on a rotaxane

An ultrafast spectroscopic study was carried out for a photoisomerizable, rotaxane-based molecular shuttle, in which photoisomerization of the azobenzene moiety of the thread-like guest drives a shuttling motion of a cyclodextrin host. Femtosecond upconversion and time-resolved absorption measurements revealed distinct S₁ dynamics with time constants of 1.2 and 17 ps. Both time constants are smaller when the cyclodextrin host is absent, implying that, within the S₁ state, there are mutiple barriers to the isomerization and subsequent shuttling, due to steric interference from the cyclodextrin.

Dynamic chiral self-recognition in aromatic dimers of styrene oxide revealed by rotational spectroscopy

Chiral molecular recognition is a pivotal phenomenon in biomolecular science, governed by subtle balances of intermolecular forces that are difficult to quantify. Non-covalent interactions involving aromatic moieties are particularly important in this realm, as recurring motifs in biomolecular aggregation. In this work, we use high-resolution broadband rotational spectroscopy to probe the dynamic conformational landscape enclosing the self-pairing topologies of styrene oxide, a chiral aromatic system. We reach a definite assignment of four homochiral and two heterochiral dimers using auxiliary quantum chemistry calculations as well as structure-solving methods based on experimental isotopic information. A complete picture of the dimer conformational space is obtained, and plausible routes for conformational relaxation are derived. Molecular structures are discussed in terms of conformational flexibility, the concerted effort of weak intermolecular interactions, and their role in the expression of the molecular fit.

Direct regioisomer analysis of crude reaction mixtures via molecular rotational resonance (MRR) spectroscopy

Direct analyses of crude reaction mixtures have been carried out using molecular rotational resonance (MRR) spectroscopy. Two examples are presented, a demonstration application in photocatalytic CH-arylation as well as generation of an intermediate in a natural product synthesis. In both cases, the reaction can proceed at more than one site, leading to a mixture of regioisomers that can be challenging to distinguish. MRR structural parameters were calculated for the low lying conformers for the desired compounds, and then compared to the experimental spectra of the crude mixtures to confirm the presence of these species. Next, quantitation was performed by comparing experimentally measured line intensities with simulations based on computed values for the magnitude and direction of the molecular dipole moment of each species. This identification and quantification was performed without sample purification and without isolated standards of the compounds of interest. The values obtained for MRR quantitation were in good agreement with the chromatographic values. Finally, previously unknown impurities were discovered within the photocatalytic CH-arylation work. This paper demonstrates the utility of MRR as a reaction characterization tool to simplify analytical workflows.

Nanoscale rotational dynamics of four independent rotators confined in crowded crystalline layers

We report a study where Car-Parrinello molecular dynamics simulations and variable-temperature (30-300 K) ¹H spin-lattice relaxation time experiments nicely complement each other to characterize the dynamics within a set of four crystalline 1,4-diethynylbicyclo[2.2.2]octane (BCO) rotors assembled in the metal-organic rotor, {Li⁺₄(^-CO₂-Ph-BCO-py)₄(H₂O)₈}·2DMF. The remarkable finding of this work is that, despite the individual rotational barriers of four rotors being indiscernible and superimposed in a broad relaxation process, we were able to unravel a strongly interrelated series of rotational motions involving disrotatory and conrotatory motions in pairs as well as rotational steps of single rotators, all three processes with similar, sizeable rotational barriers of 6 kcal mol^-1. It is noteworthy that DFT molecular dynamics simulations and variable-temperature (30-300 K) proton spin-lattice relaxation time experiments deliver the same high value for the rotational barriers stressing the potential of the combined use of the two techniques in understanding rotational motion at the nanoscale.

Water Docking Bias in [4]Helicene

We report on the one- and two-water clusters of [4]helicene, the smallest polycyclic aromatic hydrocarbon with a helical sense, which were captured in the gas phase using high-resolution rotational spectroscopy. The structures of the complexes are unambiguously revealed using microwave spectra of isotopically enriched species. In the one-water cluster, the apparent splitting pattern is consistent with a tunneling motion that encompasses an exchange of strongly and weakly bonded water hydrogens. This motion is "locked" in the two-water cluster. The relevant intermolecular contacts, symmetry, and aromaticity effects are unveiled for the microsolvated chiral topologies. These observations entail the first glance at the structures and internal dynamics of the water binding motifs of a chiral polycyclic aromatic hydrocarbon.

Water induces the same crown shapes as Li+ or Na+ in 15-crown-5 ether: a broadband rotational study

Complexation with water reduces the structural landscape of 15-crown-5 ether to the two forms observed for Li⁺ or Na⁺ complexes.

Competing Dispersive Interactions: From Small Energy Differences to Large Structural Effects in Methyl Jasmonate and Zingerone

Modern structural studies of biologically relevant molecules require an exhaustive interplay between experiment and theory. In this work, we present two examples where a poor choice of the theoretical method led to a misinterpretation of experimental results. We do that by performing a rotational spectroscopy study on two large and flexible biomolecules: methyl jasmonate and zingerone. The results show the enormous potential of rotational spectroscopy as a benchmark to evaluate the performance of theoretical methods.

Flexibility at the Fringes: Conformations of the Steroid Hormone β-Estradiol

We present the accurate experimental structure of the steroid hormone β-estradiol obtained with high-resolution rotational spectroscopy under the solvent free, isolated, and cold conditions of a molecular jet. This is the first time that the rotational signature of a steroid hormone is reported. β-Estradiol is a primary female sex hormone and features a rigid steroidal ring system. Three conformers could be identified in the cold environment of a supersonic molecular jet, which only differ in the orientation of the two hydroxy groups attached to the steroidal backbone. The conformers are almost isoenergetic and have very similar rotational constants but still could be clearly resolved and assigned. The high sensitivity of the technique allowed us to record and identify all singly substituted ¹³ C isotopologues in natural abundance for the dominant conformer. The additional spectroscopic constants led to an accurate determination of its experimental molecular structure. Along with a previous comparison of β-estradiol structures in the solid state and the liquid phase, this study completes the investigations in all three main phases by providing the interaction free gas-phase structure.

Static Modulation Wave of Arrays of Halogen Interactions Transduced to a Hierarchy of Nanoscale Change Stimuli of Crystalline Rotors Dynamics

Here we present a study where what can be seen as a static modulation wave encompassing four successive arrays of interacting iodine atoms in crystalline 1,4-Bis((4'-(iodoethynyl)phenyl) ethynyl)bicyclo[2,2,2]octane rotors changes the structure from one-half molecule to three-and-a-half molecules in the asymmetric unit below a phase transition at 105 K. The remarkable finding is that the total ¹H spin-lattice relaxation rate, T₁^-1, of unprecedented complexity to date in molecular rotors, is the weighted sum of the relaxation rates of the four contributing rotors relaxation rates, each with distinguishable exchange frequencies reflecting Arrhenius parameters with different activation barriers ( E_a) and attempt frequencies (τ_o^-1). This allows us to show in tandem with rotor-environment interaction energy calculations how the dynamics of molecular rotors are able to decode structural information from their surroundings with remarkable nanoscale precision.

Shapes, Dynamics, and Stability of β-Ionone and Its Two Mutants Evidenced by High-Resolution Spectroscopy in the Gas Phase

The conformational landscapes of β-ionone and two mutants (α-ionone and β-damascone) have been analyzed by means of state-of-the-art rotational spectroscopy and quantum-chemical calculations. The experiments performed at high resolution and sensitivity have provided a deep insight into their conformational spaces, assigning more than 8000 transitions corresponding to the rotational structures of 54 different species (3 isomers, 14 conformers, and 40 isotopologues). Methyl internal rotation dynamics were also observed and analyzed. The work proved the great flexibility of β-ionone due to its flatter potential energy surface. This feature confers on β-ionone a wider ability to interconvert between conformers with rather similar energies with respect to its mutants, allowing the retinal ligand to better adapt inside the binding pocket.

Asymmetric Choreography in Pairs of Orthogonal Rotors

An asymmetric mechanism for correlated motion occurring in noninteracting pairs of adjacent orthogonal 1,4-bis(carboxyethynyl)bicyclo[1.1.1]pentane (BCP) rotators 1 in the solid state is unraveled and shown to play an important role in understanding the dynamics in the crystalline rotor, Bu₄N⁺[1^-]·H₂O. Single crystal X-ray diffraction and calculation of rotor-rotor interaction energies combined with variable-temperature, variable-field ¹H spin-lattice relaxation experiments led to the identification and microscopic rationalization of two distinct relaxation processes.

Transient two-dimensional vibrational spectroscopy of an operating molecular machine

Synthetic molecular machines are promising building blocks for future nanoscopic devices. However, the details of their mechanical behaviour are in many cases still largely unknown. A deeper understanding of mechanics at the molecular level is essential for the design and construction of complex nanodevices. Here, we show that transient two-dimensional infrared (T2DIR) spectroscopy makes it possible to monitor the conformational changes of a translational molecular machine during its operation. Translation of a macrocyclic ring from one station to another on a molecular thread is initiated by a UV pulse. The arrival of the shuttling macrocycle at the final station is visible from a newly appearing cross peak between these two moieties. To eliminate spectral congestion in the T2DIR spectra, we use a subtraction method applicable to many other complex molecular systems. The T2DIR spectra indicate that the macrocycle adopts a boat-like conformation at the final station, which contrasts with the chair-like conformation at the initial station.

A deeper understanding of the mechanics of molecular machines is limited by the fast motions which are in the nanosecond or picosecond timescale. Here the authors present a real-time observation of structural changes in a rotaxane-based molecular shuttle by transient two-dimensional infrared spectroscopy.

Cold Snapshot of a Molecular Rotary Motor Captured by High-Resolution Rotational Spectroscopy

We present the first high‐resolution rotational spectrum of an artificial molecular rotary motor. By combining chirped‐pulse Fourier transform microwave spectroscopy and supersonic expansions, we captured the vibronic ground‐state conformation of a second‐generation motor based on chiral, overcrowded alkenes. The rotational constants were accurately determined by fitting more than 200 rotational transitions in the 2–4 GHz frequency range. Evidence for dissociation products allowed for the unambiguous identification and characterization of the isolated motor components. Experiment and complementary quantum‐chemical calculations provide accurate geometrical parameters for the C₂₇H₂₀ molecular motor, the largest molecule investigated by high‐resolution microwave spectroscopy to date.