Accurate Biomolecular Structures by the Nano-LEGO Approach: Pick the Bricks and Build Your Geometry

The determination of accurate equilibrium molecular structures plays a fundamental role for understanding many physical–chemical properties of molecules, ranging from the precise evaluation of the electronic structure to the analysis of the role played by dynamical and environmental effects in tuning their overall behavior. For small semi-rigid systems in the gas phase, state-of-the-art quantum chemical computations rival the most sophisticated experimental (from, for example, high-resolution spectroscopy) results. For larger molecules, more effective computational approaches must be devised. To this end, we have further enlarged the compilation of available semi-experimental (SE) equilibrium structures, now covering the most important fragments containing H, B, C, N, O, F, P, S, and Cl atoms collected in the new SE100 database. Next, comparison with geometries optimized by methods rooted in the density functional theory showed that the already remarkable results delivered by PW6B95 and, especially, rev-DSDPBEP86 functionals can be further improved by a linear regression (LR) approach. Use of template fragments (taken from the SE100 library) together with LR estimates for the missing interfragment parameters paves the route toward accurate structures of large molecules, as witnessed by the very small deviations between computed and experimental rotational constants. The whole approach has been implemented in a user-friendly tool, termed nano-LEGO, and applied to a number of demanding case studies.

Vowel variability and contrast in Childhood Apraxia of Speech: acoustics and articulation

Phoneme production may be affected by limited speech motor control in Childhood Apraxia of Speech (CAS), with a general instability of acoustic targets across multiple repetitions of speech stimuli. This acoustic and Ultrasound Tongue Imaging (UTI) study shows that increased variability and reduction of contrast in vowel production is found in native Italian speakers with CAS, particularly as far as the height dimension is concerned. The data suggest that vowel production should play a major role in CAS diagnosis and treatment. Moreover, this study shows that a combined acoustic and articulatory approach allows direct observation of lingual dynamics together with an estimation of changes in the acoustic dimension. The two dimensions are shown not to correspond in a straightforward way in the speech of children with CAS, and encourage consideration of articulatory compensation strategies aimed at saving the acoustic identity of vowels.

Stacked but not Stuck: Unveiling the Role of π→π* Interactions with the Help of the Benzofuran-Formaldehyde Complex

The 1:1 benzofuran–formaldehyde complex has been chosen as model system for analyzing π→π* interactions in supramolecular organizations involving heteroaromatic rings and carbonyl groups. A joint “rotational spectroscopy–quantum chemistry” strategy unveiled the dominant role of π→π* interactions in tuning the intermolecular interactions of such adduct. The exploration of the intermolecular potential energy surface led to the identification of 14 low‐energy minima, with 4 stacked isomers being more stable than those linked by hydrogen bond or lone‐pair→π interactions. All energy minima are separated by loose transition states, thus suggesting an effective relaxation to the global minimum under the experimental conditions. This expectation has been confirmed by the experimental detection of only one species, which was unambiguously assigned owing to the computation of accurate spectroscopic parameters and the characterization of 11 isotopologues. The large number of isotopic species opened the way to the determination of the first semi‐experimental equilibrium structure for a molecular complex of such a dimension.

High Water Density at Non-Ice-Binding Surfaces Contributes to the Hyperactivity of Antifreeze Proteins

Antifreeze proteins (AFPs) can bind to ice nuclei thereby inhibiting their growth and their hydration shell is believed to play a fundamental role. Here, we use molecular dynamics simulations to characterize the hydration shell of four moderately-active and four hyperactive AFPs. The local water density around the ice-binding-surface (IBS) is found to be lower than that around the non-ice-binding surface (NIBS) and this difference correlates with the higher hydrophobicity of the former. While the water-density increase (with respect to bulk) around the IBS is similar between moderately-active and hyperactive AFPs, it differs around the NIBS, being higher for the hyperactive AFPs. We hypothesize that while the lower water density at the IBS can pave the way to protein binding to ice nuclei, irrespective of the antifreeze activity, the higher density at the NIBS of the hyperactive AFPs contribute to their enhanced ability in inhibiting ice growth around the bound AFPs.

Development and Validation of a Parameter-Free Model Chemistry for the Computation of Reliable Reaction Rates

A recently developed model chemistry (jun-Cheap) has been slightly modified and proposed as an effective, reliable, and parameter-free scheme for the computation of accurate reaction rates with special reference to astrochemical and atmospheric processes. Benchmarks with different sets of state-of-the-art energy barriers spanning a wide range of values show that, in the absence of strong multireference contributions, the proposed model outperforms the most well-known model chemistries, reaching a subchemical accuracy without any empirical parameter and with affordable computer times. Some test cases show that geometries, energy barriers, zero point energies, and thermal contributions computed at this level can be used in the framework of the master equation approach based on the ab initio transition-state theory for obtaining accurate reaction rates.

Integration of theory, simulation, artificial intelligence and virtual reality: a four-pillar approach for reconciling accuracy and interpretability in computational spectroscopy

The established pillars of computational spectroscopy are theory and computer based simulations. Recently, artificial intelligence and virtual reality are becoming the third and fourth pillars of an integrated strategy for the investigation of complex phenomena. The main goal of the present contribution is the description of some new perspectives for computational spectroscopy, in the framework of a strategy in which computational methodologies at the state of the art, high-performance computing, artificial intelligence and virtual reality tools are integrated with the aim of improving research throughput and achieving goals otherwise not possible. Some of the key tools (e.g., continuous molecular perception model and virtual multifrequency spectrometer) and theoretical developments (e.g., non-periodic boundaries, joint variational-perturbative models) are shortly sketched and their application illustrated by means of representative case studies taken from recent work by the authors. Some of the results presented are already well beyond the state of the art in the field of computational spectroscopy, thereby also providing a proof of concept for other research fields.

General Perturb-Then-Diagonalize Model for the Vibrational Frequencies and Intensities of Molecules Belonging to Abelian and Non-Abelian Symmetry Groups

In this paper, we show that the standard second-order vibrational perturbation theory (VPT2) for Abelian groups can be used also for non-Abelian groups without employing specific equations for two- or threefold degenerate vibrations but rather handling in the proper way all the degeneracy issues and deriving the peculiar spectroscopic signatures of non-Abelian groups (e.g., l -doubling) by a posteriori transformations of the eigenfunctions. Comparison with the results of previous conventional implementations shows a perfect agreement for the vibrational energies of linear and symmetric tops, thus paving the route to the transparent extension of the equations already available for asymmetric tops to the energies of spherical tops and the infrared and Raman intensities of molecules belonging to non-Abelian symmetry groups. The whole procedure has been implemented in our general engine for vibro-rotational computations beyond the rigid rotor/harmonic oscillator model and has been validated on a number of test cases.

A computational insight into the relationship between side chain IR line shapes and local environment in fibril-like structures

Infrared spectroscopy is a widely used technique to characterize protein structures and protein mediated processes. While the amide I band provides information on proteins' secondary structure, amino acid side chains are used as infrared probes for the investigation of protein reactions and local properties. In this paper, we use a hybrid quantum mechanical/classical molecular dynamical approach based on the perturbed matrix method to compute the infrared band due to the C=O stretching mode of amide-containing side chains. We calculate, at first, the infrared band of zwitterionic glutamine in water and obtain results in very good agreement with the experimental data. Then, we compute the signal arising from glutamine side chains in a microcrystal of the yeast prion Sup35-derived peptide, GNNQQNY, with a fibrillar structure. The infrared bands obtained by selective isotopic labeling of the two glutamine residues, Q4 and Q5, of each peptide were experimentally used to investigate the local hydration in the fibrillar microcrystal. The experimental spectra of the two glutamine residues, which experience different hydration environments, feature different spectral signals that are well reproduced by the corresponding calculated spectra. In addition, the analysis of the simulated spectra clarifies the molecular origin of the experimentally observed spectroscopic differences that arise from the different local electric field experienced by the two glutamine residues, which is, in turn, determined by a different hydrogen bonding pattern.

Looking for the Elusive Imine Tautomer of Creatinine: Different States of Aggregation Studied by Quantum Chemistry and Molecular Spectroscopy

New spectroscopic experiments and state-of-the-art quantum-chemical computations of creatinine in different aggregation states unequivocally unveiled a significant tuning of tautomeric equilibrium by the environment: from the exclusive presence of the amine tautomer in the solid state and aqueous solution to a mixture of amine and imine tautomers in the gas phase. Quantum-chemical calculations predict the amine species as the most stable tautomer by about 30 kJ mol^-1 in condensed phases. On the contrary, moving to the isolated forms, both Z and E imine isomers become more stable by about 7 kJ mol^-1 . Since the imine isomers and one amine tautomer are separated by significant energy barriers, all of them should be present in the gas phase. This prediction has indeed been confirmed by high-resolution rotational spectroscopy, which provides the first experimental characterization of the elusive imine tautomer. The interpretation of the complicated hyperfine structure of the rotational spectrum, originated by three ¹⁴ N nuclei, makes it possible to use the spectral signatures as a sort of fingerprint for each individual tautomer in the complex sample.

Interplay of stereo-electronic, vibronic and environmental effects in tuning the chiroptical properties of an Ir(III) cyclometalated N-heterocyclic carbene

Chiroptical spectra are among the most suitable techniques for investigating the ground and excited electronic states of chiral systems, but their interpretation is not straightforward and strongly benefits from quantum chemical simulations, provided that the employed computational model is sufficiently accurate and deals properly with stereo-electronic, vibrational averaging and environmental effects. Since the synergy among all these effects is only rarely accounted for, especially for large and flexible organometallic systems, the main aim of this contribution is to illustrate the latest developments of computational approaches rooted into the density functional theory for describing stereo-electronic effects and complemented by effective techniques to deal with vibrational modulation effects and solvatochromic shifts. In this connection, chiral iridium complexes offer an especially suitable case study in view of their bright phosphorescence, which is particularly significant for building effective light emitting diodes (OLEDs) and biomarkers and can be finely tuned by the nature of the metal ligands. For instance, a recently synthesized family of cycloiridiated complexes, KC and KD, bearing a pentahelicenic N-heterocyclic carbene (KB), has shown an enhanced long-lasting, bright phosphorescence. Deeper insights into the still unclear nature and origin of the enhancement could be gained by the interpretation of the chiroptical spectra, which is quite challenging in view of the presence of two sources of chirality, the chiral center on Ir and the chiral axis related to the helicene ligand, in addition to the relativistic effects related to the presence of the Ir center. At the same time, the large dimensions of KC and KD hamper the use of the most sophisticated (but prohibitively expensive) computational models, so that more approximate approaches must be validated on a suitable model compound. To this end, after optimizing the computational scheme on a model system devoid of the helicene moiety (KA), we have performed a comprehensive investigation of the KC and KD spectra, whose interpretation is further aided by novel graphical tools. The discussion and analysis of the results will not be focused on the theoretical background, but, rather, on practical details (specific functional, basis set, vibronic model, solvent regime) with the aim of providing general guidelines for the use of last-generation computational spectroscopy tools also by non-specialists.

4-Fluoro-Threonine: From Diastereoselective Synthesis to pH-Dependent Conformational Equilibrium in Aqueous Solution

4-Fluoro-threonine, the only fluoro amino acid of natural origin discovered so far, is an interesting target for both synthetic and theoretical investigations. In this work, we lay the foundation for spectroscopic characterization of 4-fluoro-threonine. First, we report a diastereoselective synthetic route, which is suitable to produce synthetic material for experimental characterization. The addition of the commercially available ethyl isocyanoacetate to benzyloxyacetaldehyde led to the corresponding benzyloxy-oxazoline, which was hydrolyzed and transformed into ethyl (4S*,5S*)-5-hydroxymethyl-2-oxo-4-oxazolidinecarboxylate in a few steps. Fluorination with diethylamino sulfur trifluoride (DAST) afforded ethyl (4S*,5S*)-5-fluoromethyl-2-oxo-4-oxazolidinecarboxylate, which was deprotected to give the desired diastereomerically pure 4-fluoro-threonine, in 8-10% overall yield. With the synthetic material in our hands, acid-base titrations have been carried out to determine acid dissociation constants and the isoelectric point, which is the testing ground for the theoretical analysis. We have used machine learning coupled with quantum chemistry at the state-of-the-art to analyze the conformational space of 4-fluoro-threonine, with the aim of gaining insights from the comparison of computational and experimental results. Indeed, we have demonstrated that our approach, which couples a last-generation double-hybrid density functional including empirical dispersion contributions with a model combining explicit first-shell molecules and a polarizable continuum for describing solvent effects, provides results and trends in remarkable agreement with experiments. Finally, the conformational analysis applied to fluoro amino acids represents an interesting study for the effect of fluorine on the stability and population of conformers.

Unveiling Bifunctional Hydrogen Bonding with the Help of Quantum Chemistry: The Imidazole-Water Adduct as Test Case

The ubiquitous role of water and its amphiprotic nature call for a deeper insight into the physical-chemical properties of hydrogen-bonded complexes formed with building blocks of biomolecules. In this work, the semiexperimental (SE) approach combined with the template model (TM) protocol allowed the accurate determination of the equilibrium structure of two isomeric forms of the imidazole-water complex. In this procedure, the integration of experiment (thanks to a recent rotational spectroscopy investigation) and theory is exploited, also providing the means of assessing the reliability and accuracy of different quantum-chemical approaches. Overall, this study demonstrated the robustness of the combined SE-TM approach, which can provide accurate results using affordable quantum-chemical methods. Finally, the structural and energetic characteristics of these complexes have been examined in detail and compared with those of analogous heterocycle-water adducts, also exploiting energy decomposition analyses.

Insoluble organic matter in chondrites: Archetypal melanin-like PAH-based multifunctionality at the origin of life?

An interdisciplinary review of the chemical literature that points to a unifying scenario for the origin of life, referred to as the Primordial Multifunctional organic Entity (PriME) scenario, is provided herein. In the PriME scenario it is suggested that the Insoluble Organic Matter (IOM) in carbonaceous chondrites, as well as interplanetary dust particles from meteorites and comets may have played an important role in the three most critical processes involved in the origin of life, namely 1) metabolism, via a) the provision and accumulation of molecules that are the building blocks of life, b) catalysis (e.g., by templation), and c) protection of developing life molecules against radiation by excited state deactivation; 2) compartmentalization, via adsorption of compounds on the exposed organic surfaces in fractured meteorites, and 3) replication, via deaggregation, desorption and related physical phenomena. This scenario is based on the hitherto overlooked structural and physicochemical similarities between the IOM and the dark, insoluble, multifunctional melanin polymers found in bacteria and fungi and associated with the ability of these microorganisms to survive extreme conditions, including ionizing radiation. The underlying conceptual link between these two materials is strengthened by the fact that primary precursors of bacterial and fungal melanins (collectively referred to herein as allomelanins) are hydroxylated aromatic compounds like homogentisic acid and 1,8-dihydroxynaphthalene, and that similar hydroxylated aromatic compounds, including hydroxynaphthalenes, figure prominently among possible components of the organic materials on dust grains and ices in the interstellar matter, and may be involved in the formation of IOM in meteorites. Inspired by this rationale, a vis-à-vis review of the properties of IOM from various chondrites and non-nitrogenous allomelanin pigments from bacteria and fungi is provided herein. The unrecognized similarities between these materials may pave the way for a novel scenario at the origin of life, in which IOM-related complex organic polymers delivered to the early Earth are proposed to serve as PriME and were preserved and transformed in those primitive forms of life that shared the ability to synthesize melanin polymers playing an important role in the critical processes underlying the establishment of terrestrial eukaryotes.

Isomerization and Fragmentation Reactions on the [C2SH4] Potential Energy Surface: The Metastable Thione S-Methylide Isomer

Thione S-methylide, parent species of the thiocarbonyl ylide family, is a 1,3-dipolar species on the [C₂SH₄] potential energy surface, not so much studied as its isomers, thiirane, vinyl thiol, and thioacetaldehyde. The conrotatory ring-closure reaction toward thiirane was studied in the 90s, but no complete analysis of the potential energy surface is available. In this paper, we report a computational study of the reaction scheme linking all species. We employed several computational methods (density functional theory, CCSD(T) composite schemes, and CASSCF/CASPT2 multireference procedures) to find the best description of thione S-methylide, its isomers, and transition states. The barrier from thiirane to thione S-methylide amounts to 52.2 kcal mol^-1 (against 17.6 kcal mol^-1 for the direct one), explaining why thiocarbonyl ylides cannot be prepared from thiiranes. Conversion of thiirane to vinyl thiol implies a large barrier, supporting why the reaction has been observed only at high temperatures. Fragmentations of thiirane to S(³P) or S(¹D) and ethylene as well as decomposition to hydrogen sulfide plus acetylene were also explored. Triplet and singlet open-shell species were identified as intermediates in the fragmentations, with energies lower than the transition state between thiirane and vinyl thiol, explaining the preference of the latter at low temperatures.

Looking for the bricks of the life in the interstellar medium: The fascinating world of astrochemistry

The discovery in the interstellar medium of molecules showing a certain degree of complexity, and in particular those with a prebiotic character, has attracted great interest. A complex chemistry takes place in space, but the processes that lead to the production of molecular species are a matter of intense discussion, the knowledge still being at a rather primitive stage. Debate on the origins of interstellar molecules has been further stimulated by the identification of biomolecular building blocks, such as nucleobases and amino acids, in meteorites and comets. Since many of the molecules found in space play a role in the chemistry of life, the issue of their molecular genesis and evolution might be related to the profound question of the origin of life itself. Understanding the underlying chemical processes, including the production, reactions and destruction of compounds, requires the concomitant study of spectroscopy, gas-phase reactivity, and heterogeneous processes on dust-grains. The aim of this contribution is to provide a general view of a complex and multifaceted challenge, while focusing on the role played by molecular spectroscopy and quantum-chemical computations. In particular, the derivation of the molecular spectroscopic features and the investigation of gas-phase formation routes of prebiotic species in the interstellar medium are addressed from a computational point of view.

A Journey from Thermally Tunable Synthesis to Spectroscopy of Phenylmethanimine in Gas Phase and Solution

Phenylmethanimine is an aromatic imine with a twofold relevance in chemistry: organic synthesis and astrochemistry. To tackle both aspects, a multidisciplinary strategy has been exploited and a new, easily accessible synthetic approach to generate stable imine-intermediates in the gas phase and in solution has been introduced. The combination of this formation pathway, based on the thermal decomposition of hydrobenzamide, with a state-of-the-art computational characterization of phenylmethanimine laid the foundation for its first laboratory observation by means of rotational electric resonance spectroscopy. Both E and Z isomers have been accurately characterized, thus providing a reliable basis to guide future astronomical observations. A further characterization has been carried out by nuclear magnetic resonance spectroscopy, showing the feasibility of this synthetic approach in solution. The temperature dependence as well as possible mechanisms of the thermolysis process have been examined.

Rotational Spectroscopy Meets Quantum Chemistry for Analyzing Substituent Effects on Non-Covalent Interactions: The Case of the Trifluoroacetophenone-Water Complex

The most stable isomer of the 1:1 complex formed by 2,2,2-trifluoroacetophenone and water has been characterized by combining rotational spectroscopy in supersonic expansion and state-of-the-art quantum-chemical computations. In the observed isomer, water plays the double role of proton donor and acceptor, thus forming a seven-membered ring with 2,2,2-trifluoroacetophenone. Accurate intermolecular parameters featuring one classical O-H···O hydrogen bond and one weak C-H···O hydrogen bond have been determined by means of a semi-experimental approach for equilibrium structure. Furthermore, insights on the nature of the established non-covalent interactions have been unveiled by means of different bond analyses. The comparison with the analogous complex formed by acetophenone with water points out the remarkable role played by fluorine atoms in tuning non-covalent interactions.

Accuracy Meets Interpretability for Computational Spectroscopy by Means of Hybrid and Double-Hybrid Functionals

Accuracy and interpretability are often seen as the devil and holy grail in computational spectroscopy and their reconciliation remains a primary research goal. In the last few decades, density functional theory has revolutionized the situation, paving the way to reliable yet effective models for medium size molecules, which could also be profitably used by non-specialists. In this contribution we will compare the results of some widely used hybrid and double hybrid functionals with the aim of defining the most suitable recipe for all the spectroscopic parameters of interest in rotational and vibrational spectroscopy, going beyond the rigid rotor/harmonic oscillator model. We will show that last-generation hybrid and double hybrid functionals in conjunction with partially augmented double- and triple-zeta basis sets can offer, in the framework of second order vibrational perturbation theory, a general, robust, and user-friendly tool with unprecedented accuracy for medium-size semi-rigid molecules.

Discovering the Elusive Global Minimum in a Ternary Chiral Cluster: Rotational Spectra of Propylene Oxide Trimer

The chirality controlled conformational landscape of the trimer of propylene oxide (PO), a prototypical chiral molecule, was investigated using rotational spectroscopy and a range of theoretical tools for conformational searches and for evaluating vibrational contributions to effective structures. Two sets of homochiral (PO)₃ rotational transitions were assigned and the associated conformers identified with theoretical support. One set of heterochiral (PO)₃ transitions was assigned, but no structures generated by one of the latest, advanced conformational search codes could account for them. With the aid of a Python program, the carbon atom backbone and then the heterochiral (PO)₃ structure were generated using ¹³C isotopic data. Excellent agreement between theoretical and experimental rotational constants and relative dipole moment components of all three conformers was achieved, especially after applying vibrational corrections to the rotational constants.