Development and Validation of the B3LYP/N07D Computational Model for Structural Parameter and Magnetic Tensors of Large Free Radicals

Polycyclic (anti)aromatic hydrocarbons: interstellar formation and spectroscopic characterization of biphenylene and benzopentalene

Formation of biphenylene (C6H4)2 and its isomer benzopentalene, C12H8, may act as a consumption route for ortho-benzyne (o-C6H4) in interstellar clouds such as TMC-1. MRCI-F12 and CCSD(T)-F12 potential energy surfaces show that o-C6H4 dimerization is possible through a C2h-symmetry single-bond association to a (C6H4)2 precursor before isomerization to (C6H4)2 and subsequently C12H8. Formation of a bimolecular product set from either species is energetically hindered, allowing (C6H4)2 and C12H8 to stabilize radiatively. To remedy the dearth of spectroscopic data for these species, anharmonic frequencies from explicitly-correlated quartic force fields (QFFs) for o-C6H4 and c-C4H4 are employed to reparameterize the semiempirical method PM6 for use in lower-cost QFFs for (C6H4)2 and C12H8. In both cases, at least one reparameterized PM6-QFF spectrum results in the prominent C-H stretch and symmetric C-H out-of-plane-bend features to be accurately predicted with respect to gas-phase experiment or the B3LYP/N07D anharmonic absorption spectrum. B3LYP/N07D accurately recreates the experimental infrared spectrum of (C6H4)2, showing the utility of this method for spectral prediction of small and midsize polycyclic hydrocarbons on the whole. For larger systems, reparameterized PM6-QFF spectra can reproduce the most important infrared features for a species. B3LYP/N07D cascade emission spectra show that the 730 cm-1 C-H symmetric out-of-plane bending feature dominates the emission spectrum of (C6H4)2, while the spectrum of C12H8 becomes characterized by the collective set of C-H out-of-plane bends. As such, infrared emission spectra of (C6H4)2 will likely be overshadowed by C2H2. Derivatives such as cyanobiphenylene are likely better targets for infrared observation.

Assessing Nonbonded Aggregates Populations: Application to the Concentration-Dependent IR O-H Band of Phenol

In this work, we present two alternative computational strategies to determine the populations of nonbonded aggregates. One approach extracts these populations from molecular dynamics (MD) simulations, while the other employs quantum mechanical partition functions for the most relevant minima of the multimolecular potential energy surfaces (PESs), identified by automated conformational sampling. In both cases, we adopt a common graph-theory-based framework, introduced in this work, for identifying aggregate conformations, which enables a consistent comparative assessment of both methodologies and provides insight into the underlying approximations. We apply both strategies to investigate phenol aggregates, up to the tetramer, at different concentrations in phenol/carbon tetrachloride mixtures. Subsequently, we simulate the concentration-dependent OH stretching IR region by averaging the harmonic Infrared (IR) spectra of aggregates using the populations predicted by each strategy. Our results indicate that the populations extracted from MD trajectories yield OH stretching signals that closely follow the experimental trends, outperforming the spectra from populations obtained by systematic conformational searches. Such a better performance of MD is attributed to a better description of the entropic contributions. Moreover, the proposed protocol not only successfully addresses a very challenging problem but also offers a benchmark to assess the accuracy of the intermolecular force fields.

Infrared Spectroscopy of Neutral and Cationic Sumanene (C21H12 & C21H12 +) in the Gas Phase: Implications for Interstellar Aromatic Infrared Bands (AIBs)

Polycyclic aromatic hydrocarbons (PAHs) are known to be omnipresent in various astronomical sources. Ever since the discovery of C60 and C70 fullerenes in a young planetary nebula in 2010, uncovering the reaction pathways between PAHs and fullerenes has been one of the primary goals in astrochemistry. Several laboratory studies have attempted to elucidate these pathways through experiments simulating top-down and bottom-up chemistry. Recently, indene (c-C9H8, a fused pentagon and hexagonal ring) has been detected in the TMC-1 molecular cloud. This is a significant finding since pentagon-bearing PAHs could be key intermediates in the formation of fullerenes in space. Spectroscopic studies of pentagon-bearing PAHs are thus essential for their detection in molecular clouds, which would eventually lead to unraveling the intermediate steps in PAH's chemistry. This work reports the infrared (IR) spectra of both neutral and cationic sumanene (C21H12 and C21H12 +): a bowl-shaped PAH containing three pentagon rings. Apart from its relevance for furthering our understanding of the chemistry of PAHs in an astronomical context, the presence of three sp3 hybridized carbons makes the vibrational spectroscopy of this molecule highly interesting also from a spectroscopic point of view, especially in the CH stretching region. The experimental IR spectra of both species are compared with quantum chemically calculated IR spectra as well as with the aromatic infrared bands (AIBs) of the photodissociation regions of the Orion Bar obtained using the James Webb Space Telescope (JWST).

EPR Spectra Hyperfine Structure of Fluorine-Containing Nitroxide Radicals in Liquid Solutions: Prediction by DFT

Spin trap method allows receiving important information about the structure of short-living intermediate radicals involved in chemical processes. Commonly, the product of a spin trap reaction with an intermediate radical is identified based on the hyperfine structure of its EPR spectrum. However, such identification can be significantly complicated for novel radicals whose spectra are unknown. In this work, we propose a semiquantitative low-cost computation method that allows predicting the hyperfine structure of EPR spectra of the α-phenyl-N-tert-butylnitrone (PBN) adducts with fluorine-containing radicals. The scheme was tested for several radicals containing from 0 to 4 fluorine atoms.

Infrared Cooling in an Anharmonic Cascade Framework: 2-Cyanoindene, the Smallest Cyano-PAH Identified in Taurus Molecular Cloud-1

Infrared (IR) cooling of polycyclic aromatic hydrocarbon (PAH) molecules is a major radiative stabilization mechanism of PAHs present in space and is the origin of the aromatic infrared bands (AIBs). Here, we report an anharmonic cascade model in a master equation framework to model IR emission rates and emission spectra of energized PAHs as a function of internal energy. The underlying (simple harmonic cascade) framework for fundamental vibrations has been developed through the modeling of cooling rates of PAH cations and other carboneaous ions measured in electrostatic ion storage ring experiments performed under "molecular cloud in a box" conditions. The anharmonic extension is necessitated because cyano-PAHs, recently identified in Taurus Molecular Cloud-1 (TMC-1), exhibit strong anharmonic couplings, which make substantial contributions to the IR emission dynamics. We report an experimental mid-IR (650-3200 cm-1) absorption spectrum of 2-cyanoindene (2CNI), which is the smallest cyano-PAH that has been identified in TMC-1 and model its IR cooling rates and emission properties. The mid-IR absorption spectrum is reasonably described by anharmonic calculations at the B3LYP/N07D level of theory that include resonance polyad matrices, although the CN-stretch mode frequency continues to be difficult to describe. The anharmonic cascade framework can be readily applied to other neutral or charged PAHs and is also readily extended to include competing processes, such as recurrent fluorescence and isomerization.

Pinpointing the CN Stretch Frequency of Neutral Cyano-Polycyclic Aromatic Hydrocarbons: A Laboratory and Quantum Chemical Spectroscopic Study of 9-Cyanoanthracene

The CN stretch frequency of neutral, gas-phase 9-cyanoanthracene is 2207 cm-1 (4.531 μm) based on high-resolution infrared absorption experiments coupled with a new hybrid anharmonic quantum chemical methodology. A broad band (full-width at half-maximum of 47 cm-1) is observed and assigned to multiple transitions, including the CN stretch fundamental and various combination bands that gather intensity from strong anharmonic coupling with the bright CN stretch. The new hybrid computational approach utilizes the harmonic force constants from the double-hybrid rev-DSDPBEP86 functional that includes MP2 electron correlation, and the cubic and quartic force constants from the B3LYP density functional. In combination, this method computes a band center of 2207 cm-1 for 9-cyanoanthracene, a direct match with experiment. Further, the hybrid method produces a difference of less than 1 cm-1 for the two isomers of cyanonaphthalene and cyanobenzene. As shown from comparison with CCSD(T)-F12b anharmonic frequency computations of cyanobenzene, inclusion of electron correlation is required to properly characterize the electronic structure of the highly electron withdrawing CN group on polycyclic aromatic hydrocarbons. In agreement with earlier studies, computation of the CN stretch of 14 small CN-PAHs produces a narrow (∼20 cm-1) band from 2207-2229 cm-1 (4.53-4.48 μm). The remainder of the spectrum below 2000 cm-1 and from 3000-3120 cm-1 shows good agreement between experiment and the hybrid theory with a mean absolute error of 16 and 14 cm-1, respectively.

Vibrational and Electronic Spectroscopy of 2-Cyanoindene Cations

2-Cyanoindene is one of the few specific aromatic or polycyclic aromatic hydrocarbon (PAH) molecules positively identified in Taurus molecular cloud-1 (TMC-1), a cold, dense molecular cloud that is considered the nearest star-forming region to Earth. We report cryogenic mid-infrared (550-3200 cm-1) and visible (16,500-20,000 cm-1, over the D 2 ← D 0 electronic transition) spectra of 2-cyanoindene radical cations (2CNI+), measured using messenger tagging (He and Ne) photodissociation spectroscopy. The infrared spectra reveal the prominence of anharmonic couplings, particularly over the fingerprint region. There is a strong CN-stretching mode at 2177 ± 1 cm-1 (4.593 μm), which may contribute to a broad plateau of CN-stretching modes across astronomical aromatic infrared band spectra. However, the activity of this mode is suppressed in the dehydrogenated (closed shell) cation, [2CNI-H]+. The IR spectral frequencies are modeled by anharmonic calculations at the B3LYP/N07D level of theory that include resonance polyad matrices, demonstrating that the CN-stretch mode remains challenging to describe with theory. The D 2 ← D 0 electronic transition of 2CNI+, which is origin dominated, occurs at 16,549 ± 5 cm-1 in vacuum (6041.8 Å in air). There are no correspondences with reported diffuse interstellar bands.

Infrared Spectroscopy of Isocyano-Polycyclic Aromatic Hydrocarbons: The NC Stretch

Anharmonic computations reveal an intense, narrow (20 cm-1, 0.043 μm) absorption feature at approximately 2160 cm-1 (4.63 μm) in the vibrational spectra of 14 prototypical singly isocyano-substituted polycyclic aromatic hydrocarbons (NC-PAHs) attributed to the NC stretching mode. The intrinsically bright NC stretching mode and strong anharmonic coupling to other states in this region of the spectrum, along with the presence of multiple isomers of each NC-PAH, creates a complex, intense band for each molecule alone, and for the group of molecules as a whole. The NC stretching feature is shifted approximately 130 cm-1 to lower frequency compared to the CN stretching feature of cyano-substituted PAHs. This shift is due to the weaker NC bond as a result of the zwitterionic character of the NC-PAHs. Advanced resonance polyad matrices are utilized in the second order vibrational perturbation treatment, providing in-depth understanding of the spectroscopic characteristics of each vibrational transition. These detailed spectroscopic data are provided for use in analysis of future laboratory experiments and the search for NC-PAHs in astronomical observations. Such data will be vital to the continued benchmarking of computational methodologies for use in exotic, substituted PAHs that have never been studied before.

Battle of the CH motions: aliphatic versus aromatic contributions to astronomical PAH emission and exploration of the aliphatic, aromatic, and ethynyl CH stretches

Strong anharmonic coupling between vibrational states in polycyclic aromatic hydrocarbons (PAH) produces highly mixed vibrational transitions that challenge the current understanding of the nature of the astronomical mid-infrared PAH emission bands. Traditionally, PAH emission bands have been characterized as either aromatic or aliphatic, and this assignment is used to determine the fraction of aliphatic carbon in astronomical sources. In reality, each of the transitions previously utilized for such an attribution is highly mixed with contributions from both aliphatic and aromatic CH motions as well as non-CH motions such as CC stretches. High-resolution gas-phase IR absorption measurements of the spectra of the aromatic molecules indene and 2-ethynyltoluene at the Canadian Light Source combined with high-level anharmonic quantum chemical computations reveal the complex nature of these transitions, implying that the use of these features as a marker for the aliphatic fraction in astronomical sources is not uniquely true or actually predictive. Further, the presence of aliphatic, aromatic, and ethynyl CH groups in 2-ethynyltoluene provides an internally consistent opportunity to simultaneously study the spectroscopy of all three astronomically important groups. Finally, this study makes an explicit connection between fundamental quantum mechanical principles and macroscopic astronomical chemical physics, an important link necessary to untangle the lifecycle of stellar and planetary systems.

Noncovalent Interactions Steer the Formation of Polycyclic Aromatic Hydrocarbons

Aromatic molecules play an important role in the chemistry of astronomical environments such as the cold interstellar medium (ISM) and (exo)planetary atmospheres. The observed abundances of (polycyclic) aromatic hydrocarbons such as benzonitrile and cyanonaphthalenes are, however, highly underestimated by astrochemical models. This demonstrates the need for more experimentally verified reaction pathways. The low-temperature ion-molecule reaction of benzonitrile•+ with acetylene is studied here using a multifaceted approach involving kinetics and spectroscopic probing of the reaction products. A fast radiative association reaction via an in situ experimentally observed prereactive complex shows the importance of noncovalent interactions in steering the pathway during cold ion-molecule reactions. Product structures of subsequent reactions are unambiguously identified using infrared action spectroscopy and reveal the formation of nitrogen-containing, linked bicyclic structures such as phenylpyridine•+ and benzo-N-pentalene+ structures. The results, contradicting earlier assumptions on the product structure, demonstrate the importance of spectroscopic probing of reaction products and emphasize the possible formation of linked bicyclic molecules and benzo-N-pentalene+ structures in astronomical environments.

Unraveling the Isotropic Hyperfine Coupling Constants of Nitroxide Radicals via Molecular Electrostatic Potential Analysis

Nitroxide radicals have wide and promising applications as organic magnetic materials. Modulating the isotropic hyperfine coupling constants (HFCCs) of these radicals through proper structural design is an effective strategy for their application as spin probes and spin labels. In the present work, density functional theory calculations were carried out to develop a robust descriptor based on the molecular electrostatic potential for nitrogen HFCCs of nitroxide radicals. Forty nitroxide radicals from five distinct classes, namely, derivatives of cyclic, acyclic, imino, nitronyl, and benzimidazole nitronyl nitroxides, were selected, and the molecular electrostatic potential (MESP) at the nitrogen atom (VN) of the NO moiety was calculated. The VN values efficiently capture the electronic changes associated with the steric and electronic nature of these systems. A significant correlation between VN values and the experimental HFCCs of nitrogen nuclei demonstrates the applicability of VN as a simple and efficient descriptor for monitoring HFCCs. Furthermore, a good correlation between VN and experimental nitrogen HFCCs for each class of nitroxide radicals indicates the use of VN in the evaluation of the magnetic nature of the nitroxide radicals. The findings in this work are expected to facilitate the design of novel nitroxide radicals with desirable magnetic properties based on MESP topology analysis.

Picking up Good Vibrations through Quartic Force Fields and Vibrational Perturbation Theory

Quartic force fields (QFFs) define sparse potential energy surfaces (compared to semiglobal surfaces) that are the cheapest and easiest means of computing anharmonic vibrational frequencies, especially when utilized with second-order vibrational perturbation theory (VPT2). However, flat and shallow potential surfaces are exceedingly difficult for QFFs to treat through a combination of numerical noise in the often numerically computed derivatives and in competing energy factors in the composite energies often utilized to provide high-level spectroscopic predictions. While some of these issues can be alleviated with analytic derivatives, hybrid QFFs, and intelligent choices in coordinate systems, the best practice is for predicting good molecular vibrations via QFFs is to understand what they cannot do, and this manuscript documents such cases where QFFs may fail.

Assigning the CH stretch overtone spectrum of benzene and naphthalene with extension to anthracene and tetracene using 2- and 3-quanta anharmonic quantum chemical computations

The CH stretch overtone region (5750-6300 cm-1) of benzene and naphthalene is assigned herein using anharmonic quantum chemical computations, and the trend of how this extends to larger polycyclic aromatic hydrocarbons (PAHs) is established. The assignment of all experimental bands to specific vibrational states is performed for the first time. Resonance polyads and the inclusion of 3-quanta vibrational states are both needed to compute accurate vibrational frequencies with the proper density-of-states to match the experimental band shape. Hundreds of 3-quanta states produce the observed band structure in naphthalene, anthracene, and tetracene, and this number is expected to increase drastically for larger PAHs. The width and shape of the main peak are consistent from naphthalene to anthracene, necessitating further exploration of this trend to confirm whether it is representative of all PAHs in the CH stretch overtone region. Understanding observations of PAH sources in the 1-3 μm region from the NIRSpec instrument aboard JWST requires new computational data, and this study provides a benchmark and foundation for their computation.

The infrared absorption spectrum of phenylacetylene and its deuterated isotopologue in the mid- to far-IR

Anharmonicity strongly influences the absorption and emission spectra of polycyclic aromatic hydrocarbon (PAH) molecules. Here, IR-UV ion-dip spectroscopy experiments together with detailed anharmonic computations reveal the presence of fundamental, overtone, as well as 2- and 3-quanta combination band transitions in the far- and mid-infrared absorption spectra of phenylacetylene and its singly deuterated isotopologue. Strong absorption features in the 400-900 cm-1 range originate from CH(D) in-plane and out-of-plane wags and bends, as well as bending motions including the C≡C and CH bonds of the acetylene substituent and the aromatic ring. For phenylacetylene, every absorption feature is assigned either directly or indirectly to a single or multiple vibrational mode(s). The measured spectrum is dense, broad, and structureless in many regions but well characterized by computations. Upon deuteration, large isotopic shifts are observed. At frequencies above 1500 cm-1 for d1-phenylacetylene, a one-to-one match is seen when comparing computations and experiments with all features assigned to combination bands and overtones. The C≡C stretch observed in phenylacetylene is not observed in d1-phenylacetylene due to a computed 40-fold drop in intensity. Overall, a careful treatment of anharmonicity that includes 2- and 3-quanta modes is found to be crucial to understand the rich details of the infrared spectrum of phenylacetylene. Based on these results, it can be expected that such an all-inclusive anharmonic treatment will also be key for unraveling the infrared spectra of PAHs in general.

Benchmarking Basis Sets for Density Functional Theory Thermochemistry Calculations: Why Unpolarized Basis Sets and the Polarized 6-311G Family Should Be Avoided

Basis sets are a crucial but often largely overlooked choice in setting up quantum chemistry calculations. The choice of the basis set can be critical in determining the accuracy and calculation time of your quantum chemistry calculations. Clear recommendations based on thorough benchmarking are essential but not readily available currently. This study investigates the relative quality of basis sets for general properties by benchmarking basis set performance for a diverse set of 139 reactions (from the diet-150-GMTKN55 data set). In our analysis, we find the distributions of errors are often significantly non-Gaussian, meaning that the joint consideration of median errors, mean absolute errors, and outlier statistics is helpful to provide a holistic understanding of basis set performance. Our direct comparison of performance between most modern basis sets provides quantitative evidence for basis set recommendations that broadly align with the established understanding of basis set experts and is evident in the design of modern basis sets. For example, while zeta is a good measure of quality, it is not the only determining factor for an accurate calculation with unpolarized double- and triple-ζ basis sets (like 6-31G and 6-311G) having very poor performance. Appropriate use of polarization functions (e.g., 6-31G*) is essential to obtain the accuracy offered by double- or triple-ζ basis sets. In our study, the best performances for double- and triple-ζ basis sets are 6-31++G** and pcseg-2, respectively. However, the performances of singly polarized double-ζ and doubly polarized triple-ζ basis sets are quite similar with one key exception: the polarized 6-311G basis set family has poor parametrization, which means its performance is more like a double-ζ than a triple-ζ basis set. All versions of the 6-311G basis set family should be avoided entirely for valence chemistry calculations moving forward.

Size distribution of polycyclic aromatic hydrocarbons in space: an old new light on the 11.2/3.3 μm intensity ratio

The intensity ratio of the 11.2/3.3 μm emission bands is considered to be a reliable tracer of the size distribution of polycyclic aromatic hydrocarbons (PAHs) in the interstellar medium (ISM). This paper describes the validation of the calculated intrinsic infrared (IR) spectra of PAHs that underlie the interpretation of the observed ratio. The comparison of harmonic calculations from the NASA Ames PAH IR spectroscopic database to gas-phase experimental absorption IR spectra reveals a consistent underestimation of the 11.2/3.3 μm intensity ratio by 34%. IR spectra based on higher level anharmonic calculations, on the other hand, are in very good agreement with the experiments. While there are indications that the 11.2/3.3 μm ratio increases systematically for PAHs in the relevant size range when using a larger basis set, it is unfortunately not yet possible to reliably calculate anharmonic spectra for large PAHs. Based on these considerations, we have adjusted the intrinsic ratio of these modes and incorporated this in an interstellar PAH emission model. This corrected model implies that typical PAH sizes in reflection nebulae such as NGC 7023 - previously inferred to be in the range of 50 to 70 carbon atoms per PAH are actually in the range of 40 to 55 carbon atoms. The higher limit of this range is close to the size of the C60 fullerene (also detected in reflection nebulae), which would be in line with the hypothesis that, under appropriate conditions, large PAHs are converted into the more stable fullerenes in the ISM.

Intra-cluster Charge Migration upon Hydration of Protonated Formic Acid Revealed by Anharmonic Analysis of Cold Ion Vibrational Spectra

The rates of many chemical reactions are accelerated when carried out in micron-sized droplets, but the molecular origin of the rate acceleration remains unclear. One example is the condensation reaction of 1,2-diaminobenzene with formic acid to yield benzimidazole. The observed rate enhancements have been rationalized by invoking enhanced acidity at the surface of methanol solvent droplets with low water content to enable protonation of formic acid to generate a cationic species (protonated formic acid or PFA) formed by attachment of a proton to the neutral acid. Because PFA is the key feature in this reaction mechanism, vibrational spectra of cryogenically cooled, microhydrated PFA·(H2O)n=1-6 were acquired to determine how the extent of charge localization depends on the degree of hydration. Analysis of these highly anharmonic spectra with path integral ab initio molecular dynamics simulations reveals the gradual displacement of the excess proton onto the water network in the microhydration regime at low temperatures with n = 3 as the tipping point for intra-cluster proton transfer.

Multimodal investigation of electronic transport in PTMA and its impact on organic radical battery performance

Organic radical batteries (ORBs) represent a viable pathway to a more sustainable energy storage technology compared to conventional Li-ion batteries. For further materials and cell development towards competitive energy and power densities, a deeper understanding of electron transport and conductivity in organic radical polymer cathodes is required. Such electron transport is characterised by electron hopping processes, which depend on the presence of closely spaced hopping sites. Using a combination of electrochemical, electron paramagnetic resonance (EPR) spectroscopic, and theoretical molecular dynamics as well as density functional theory modelling techniques, we explored how compositional characteristics of cross-linked poly(2,2,6,6-tetramethyl-1-piperidinyloxy-4-yl methacrylate) (PTMA) polymers govern electron hopping and rationalise their impact on ORB performance. Electrochemistry and EPR spectroscopy not only show a correlation between capacity and the total number of radicals in an ORB using a PTMA cathode, but also indicates that the state-of-health degrades about twice as fast if the amount of radical is reduced by 15%. The presence of up to 3% free monomer radicals did not improve fast charging capabilities. Pulsed EPR indicated that these radicals readily dissolve into the electrolyte but a direct effect on battery degradation could not be shown. However, a qualitative impact cannot be excluded either. The work further illustrates that nitroxide units have a high affinity to the carbon black conductive additive, indicating the possibility of its participation in electron hopping. At the same time, the polymers attempt to adopt a compact conformation to increase radical-radical contact. Hence, a kinetic competition exists, which might gradually be altered towards a thermodynamically more stable configuration by repeated cycling, yet further investigations are required for its characterisation.

Intermolecular hydrogen bonding of alcohols with dinitrobenzene radical anion and dianion: A combined electrochemical and DFT study

Hydrogen bonding is one of the most important inter-molecular interactions in the field of biochemistry and medicinal chemistry. Such non-covalent interactions play a vital role in self-assembly phenomena, chemical structures, material properties and enzymatic catalysis. Herein, we present hydrogen bonding phenomenon in alcohols-dinitrobenzene (DNB) radical anion/dianion systems using electrochemical and computational approaches. First, 1,3-DNB radical anion and dianion were generated through electrochemical method and then hydrogen bonding interactions with aliphatic alcohols in DMSO are studied through cyclic voltammetry (CV). CV results show that the cathodic peak potential of 1,3-Dinitrobenzene in Dimethyl sulfoxide is shifted catholically upon addition of alcohols which represent hydrogen bonding phenomenon. Theoretical investigations are performed to gain deep insight on hydrogen bonding interaction strength in DNB-alcohol systems. H-bonding interaction of all isomers of DNB (1,2-, 1,3-, 1,4-), its corresponding radical anion, and dianion with aliphatic alcohols is studied using density functional calculations. The strength of H-bonding is evaluated both qualitatively and quantitatively using interaction energies, vibrational and electronic spectroscopic analysis. Understanding of these interactions will be helpful in gaining insight into biological systems where these interactions play significant role.

Novel Orientation-Sensitive Spin Probes for Graphene Oxide Membranes Study

Spin probe EPR spectroscopy is currently the only method to quantitatively report on the orientational ordering of graphene oxide membranes. This technique is based on the analysis of EPR spectra of a membrane containing stable radicals sorbed on oxidized graphene planes. The efficiency of the method depends on the spin probe structure; therefore, it is important to find stable paramagnetic substances that are most sensitive to the alignment of graphene oxide membranes. In the present work, three novel stable nitroxide radicals containing aromatic fragments with two nitrogen atoms were tested as spin probes to study graphene oxide membranes. The spin-Hamiltonian parameters of the radicals in graphite oxide powder and orientational order parameters of the probes inside graphene oxide membrane were determined. The sensitivity of one of these radicals to membrane orientational ordering was found to be higher than for any of spin probes used previously. A likely reason for this higher sensitivity is the presence of heteroatoms which can facilitate interaction between paramagnetic molecules and oxygen-containing groups on the inner surface of the membrane. The new high-sensitivity spin probe may significantly increase the potential of EPR spectroscopy for studying the internal structure of graphene oxide membranes.

Spectroscopic and quantum mechanical study of a scavenger molecule: N,N-diethylhydroxylamine

We report a combination of quantum mechanical calculations and a range of spectroscopic measurements in the gas phase of N,N-diethylhydroxylamine, an important scavenger compound. Three conformers were observed by pulsed jet Fourier transform microwave spectroscopy in the 6.5-18.5 GHz frequency range. They are characterized by the hydroxyl hydrogen atom being in trans orientation with respect to the bisector of the CNC angle while the side alkyl chains can be both trans (global minimum, C_s symmetry, A = 7608.1078(4), B = 2020.2988(2) and C = 1760.5423(2) MHz) or one trans and the other gauche (second energy minimum, A = 5302.896(1), B = 2395.9822(4) and C = 1804.8567(3) MHz) or gauche' (third energy minimum, A = 5960.8025(6), B = 2273.6627(4) and C = 1975.8074(4) MHz). For the global minimum, the ¹³C_α,¹³C_β and ¹⁵N isotopologues were observed in natural abundance, allowing for an accurate partial structure determination. Moreover, several lines were detected by free jet absorption millimeter wave spectroscopy in the 59.6-74.4 GHz spectral range. The electron binding energies of the highest occupied molecular orbital and the next-to-highest occupied molecular orbital, determined by photoelectron spectroscopy, are 8.95 and 10.76 eV, respectively. Supporting calculations evidence that, (i) upon ionization of the HOMO, the molecular structure changes from an amine to an N-oxoammonium arrangement and (ii) the 0-0 of the HOMO-1 photoionization is 10.46 eV. The K-shell binding energies, determined by X-ray photoelectron spectroscopy, are 290.42 eV (C_β), 291.45 eV (C_α), 405.98 eV (N) and 538.75 eV (O). The Fourier transform near infrared spectrum is reported and a tentative assignment is proposed. The equilibrium wavenumber (ω̃ = 3811 cm^-1) and the anharmonicity constant (ω̃χ = -87.5 cm^-1) of the hydroxyl stretching mode were estimated using a quadratic model.

Ab initio derivation of flavin hyperfine interactions for the protein magnetosensor cryptochrome

The radicals derived from flavin adenine dinucleotide (FAD) are a corner stone of recent hypotheses about magnetoreception, including the compass of migratory songbirds. These models attribute a magnetic sense to coherent spin dynamics in radical pairs within the flavo-protein cryptochrome. The primary determinant of sensitivity and directionality of this process are the hyperfine interactions of the involved radicals. Here, we present a comprehensive computational study of the hyperfine couplings in the protonated and unprotonated FAD radicals in cryptochrome 4 from C. livia. We combine long (800 ns) molecular dynamics trajectories to accurate quantum chemistry calculations. Hyperfine parameters are derived using auxiliary density functional theory applied to cluster and hybrid QM/MM (Quantum Mechanics/Molecular Mechanics) models comprising the FAD and its significant surrounding environment, as determined by a detailed sensitivity analysis. Thanks to this protocol we elucidate the sensitivity of the hyperfine interaction parameters to structural fluctuations and the polarisation effect of the protein environment. We find that the ensemble-averaged hyperfine interactions are predominantly governed by thermally induced geometric distortions of the flavin. We discuss our results in view of the expected performance of these radicals as part of a magnetoreceptor. Our data could be used to parametrize spin Hamiltonians including not only average values but also standard deviations.

Picomolar-sensitive β-amyloid fibril fluorophores by tailoring the hydrophobicity of biannulated π-elongated dioxaborine-dyes

The pathological origin of Alzheimer's disease (AD) is still shrouded in mystery, despite intensive worldwide research efforts. The selective visualization of β-amyloid (Aβ), the most abundant proteinaceous deposit in AD, is pivotal to reveal AD pathology. To date, several small-molecule fluorophores for Aβ species have been developed, with increasing binding affinities. In the current work, two organic small-molecule dioxaborine-derived fluorophores were rationally designed through tailoring the hydrophobicity with the aim to enhance the binding affinity for Aβ1-42 fibrils -while concurrently preventing poor aqueous solubility-via biannulate donor motifs in D-π-A dyes. An unprecedented sub-nanomolar affinity was found (K d = 0.62 ± 0.33 nM) and applied to super-sensitive and red-emissive fluorescent staining of amyloid plaques in cortical brain tissue ex vivo. These fluorophores expand the dioxaborine-curcumin-based family of Aβ-sensitive fluorophores with a promising new imaging agent.

Low-Temperature Isolation of a Labile Silylated Hydrazinium-yl Radical Cation, [(Me3 Si)2 N-N(H)SiMe3 ]

The oxidation of silylated hydrazine, (Me3 Si)2 N-N(H)SiMe3 , with silver salts led to the formation of a highly labile hydrazinium-yl radical cation, [(Me3 Si)2 N-N(H)SiMe3 ].+ , at very low temperatures (decomposition > -40 °C). EPR, NMR, DFT and Raman studies revealed the formation of a nitrogen-centered radical cation along the N-N unit of the hydrazine. In the presence of the weakly coordinating anion [Al{OCH(CF3 )2 }4 ]- , crystallization and structural characterization in the solid state were achieved. The hydrazinium-yl radical cation has a significantly shortened N-N bond and a nearly planar N2 Si3 framework, in contrast to the starting material. According to DFT calculations, the shortened N-N bond has a total bond order of 1.5 with a π-bond order of 0.5. The π bond can be regarded as a three-π-electron, two-center bond.

Anharmonicity and the IR Emission Spectrum of Neutral Interstellar PAH Molecules

The characteristics of the CH stretching and out-of-plane bending modes in polycyclic aromatic hydrocarbon molecules are investigated using anharmonic density functional theory (DFT) coupled to a vibrational second-order perturbation treatment taking resonance effects into account. The results are used to calculate the infrared emission spectrum of vibrationally excited species in the collision-less environment of interstellar space. This model follows the energy cascade as the molecules relax after the absorption of a UV photon in order to calculate the detailed profiles of the infrared bands. The results are validated against elegant laboratory spectra of polycyclic aromatic hydrocarbon absorption and emission spectra obtained in molecular beams. The factors which influence the peak position, spectral detail, and relative strength of the CH stretching and out-of-plane bending modes are investigated, and detailed profiles for these modes are derived. These are compared to observations of astronomical objects in space, and the implications for our understanding of the characteristics of the molecular inventory of space are assessed.

Spectroscopic Detection of Cyano-Cyclopentadiene Ions as Dissociation Products upon Ionization of Aniline

The H-loss products (C₆H₆N⁺) from the dissociative ionization of aniline (C₆H₇N) have been studied by infrared predissociation spectroscopy in a cryogenic ion trap instrument at the free electron laser for infrared experiments (FELIX) laboratory. Broadband and narrow line width vibrational spectra in the spectral fingerprint region of 550–1800 cm^–1 have been recorded. The comparison to calculated spectra of the potential isomeric structures of the fragment ions reveals that the dominant fragments are five-membered cyano-cyclopentadiene ions. Computed C₆H₇N^•+ potential energy surfaces suggest that the dissociation path leading to H loss starts with an isomerization process, following a similar trajectory as the one leading to HNC loss. The possible presence of cyano-cyclopentadiene ions and related five-membered ring species in Titan’s atmosphere and the interstellar medium are discussed.

Probing Liquid-Ordered and Disordered Phases in Lipid Model Membranes: A Combined Theoretical and Spectroscopic Study of a Fluorescent Molecular Rotor

An integrated theoretical/experimental strategy has been applied to the study of environmental effects on the spectroscopic parameters of 4-(diphenylamino)phtalonitrile (DPAP), a fluorescent molecular rotor. The computational part starts from the development of an effective force field for the first excited electronic state of DPAP and proceeds through molecular dynamics simulations in solvents of different polarities toward the evaluation of Stokes shifts by quantum mechanics/molecular mechanics (QM/MM) approaches. The trends of the computed results closely parallel the available experimental results thus giving confidence to the interpretation of new experimental studies of the photophysics of DPAP in lipid bilayers. In this context, results show unambiguously that both flexible dihedral angles and global rotations are significantly retarded in a cholesterol/DPPC lipid matrix with respect to the DOPC matrix, thus confirming the sensitivity of DPAP to probe different environments and, therefore, its applicability as a probe for detecting different structures and levels of plasma membrane organization.

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.

A radical approach to radicals

Nitroxide radicals are characterized by a long-lived spin-unpaired electronic ground state and are strongly sensitive to their chemical surroundings. Combined with electron paramagnetic resonance spectroscopy, these electronic features have led to the widespread application of nitroxide derivatives as spin labels for use in studying protein structure and dynamics. Site-directed spin labelling requires the incorporation of nitroxides into the protein structure, leading to a new protein-ligand molecular model. However, in protein crystallographic refinement nitroxides are highly unusual molecules with an atypical chemical composition. Because macromolecular crystallography is almost entirely agnostic to chemical radicals, their structural information is generally less accurate or even erroneous. In this work, proteins that contain an example of a radical compound (Chemical Component Dictionary ID MTN) from the nitroxide family were re-refined by defining its ideal structural parameters based on quantum-chemical calculations. The refinement results show that this procedure improves the MTN ligand geometries, while at the same time retaining higher agreement with experimental data.

junChS and junChS-F12 Models: Parameter-free Efficient yet Accurate Composite Schemes for Energies and Structures of Noncovalent Complexes

A recently developed model chemistry (denoted as junChS [Alessandrini, S.; et al. J. Chem. Theory Comput. 2020, 16, 988-1006]) has been extended to the employment of explicitly correlated (F12) methods. This led us to propose a family of effective, reliable, and parameter-free schemes for the computation of accurate interaction energies of molecular complexes ruled by noncovalent interactions. A thorough benchmark based on a wide range of interactions showed that the so-called junChS-F12 model, which employs cost-effective revDSD-PBEP86-D3(BJ) reference geometries, has an improved performance with respect to its conventional counterpart and outperforms well-known model chemistries. Without employing any empirical parameter and at an affordable computational cost, junChS-F12 reaches subchemical accuracy. Accurate characterizations of molecular complexes are usually limited to energetics. To take a step forward, the conventional and F12 composite schemes developed for interaction energies have been extended to structural determinations. A benchmark study demonstrated that the most effective option is to add MP2-F12 core-valence correlation corrections to fc-CCSD(T)-F12/jun-cc-pVTZ geometries without the need of recovering the basis set superposition error and the extrapolation to the complete basis set.

IRMPD Spectroscopy of Homo- and Heterochiral Asparagine Proton-Bound Dimers in the Gas Phase

We investigate gas-phase structures of homo- and heterochiral asparagine proton-bound dimers with infrared multiphoton dissociation (IRMPD) spectroscopy and quantum-chemical calculations. Their IRMPD spectra are recorded at room temperature in the range of 500-1875 and 3000-3600 cm-1. Both varieties of asparagine dimers are found to be charge-solvated based on their IRMPD spectra. The location of the principal intramolecular H-bond is discussed in light of harmonic frequency analyses using the B3LYP functional with GD3BJ empirical dispersion. Contrary to theoretical analyses, the two spectra are very similar.

Modeling the infrared cascade spectra of small PAHs: the 11.2 μm band

The profile of the 11.2 μm feature of the infrared (IR) cascade emission spectra of polycyclic aromatic hydrocarbon (PAH) molecules is investigated using a vibrational anharmonic method. Several factors are found to affect the profile including: the energy of the initially absorbed ultraviolet (UV) photon, the density of vibrational states, the anharmonic nature of the vibrational modes, the relative intensities of the vibrational modes, the rotational temperature of the molecule, and blending with nearby features. Each of these factors is explored independently and influence either the red or blue wing of the 11.2 μm feature. The majority impact solely the red wing, with the only factor altering the blue wing being the rotational temperature.

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.

Performance of the DLPNO-CCSD and recent DFT methods in the calculation of isotropic and dipolar contributions to 14N hyperfine coupling constants of nitroxide radicals

In the present study, the performance of a set of density functionals: BP86, PBE, OLYP, BEEF, PBEpow, TPSS, SCAN, PBEGXPBE, M06L, MN15L, B3LYP, PBE0, mPW1PW, B97, BHandHLYP, mPW1PW, B98, TPSS0, PBE1KCIS, SCAN0, M06, M06-2X, MN15, CAM-B3LYP, ωB97x, B2PLYP, and the B3LYP/N07D and PBE/N07D schemes in the calculation of the ¹⁴N anisotropic hyperfine coupling (HFC) constants of a set of 23 nitroxide radicals is evaluated. The results are compared with those obtained with the DLPNO-CCSD method and experimental HFC values. Harmonic contribution to the ¹⁴N HFC vibrational correction was calculated at the revPBE0/def2-TZVPP level and included in the evaluation. With the vibrational correction, the DLPNO-CCSD method yielded HFC values in good agreement with the experiment (mean absolute deviation (MAD) = 0.3 G for the dipole-dipole contribution and MAD = 0.8 G for the contact coupling contribution). The best DFT results are obtained using the M06 functional with MAD = 0.2 G for the dipole-dipole contribution and MAD = 0.7 G for the contact coupling contribution. In general, vibrational correction significantly improved most DFT functionals' performance but did not change its overall ranking.

IR photofragmentation of the phenyl cation: spectroscopy and fragmentation pathways

We present the gas-phase infrared spectra of the phenyl cation, phenylium, in its perprotio (C₆H₅⁺) and perdeutero (C₆D₅⁺) forms, in the 260–1925 cm⁻¹ (5.2–38 μm) spectral range, and investigate the observed photofragmentation.

Multiresolution continuous wavelet transform for studying coupled solute-solvent vibrations via ab initio molecular dynamics

Vibrational analysis in solution and the theoretical determination of infrared and Raman spectra are of key importance in many fields of chemical interest. Vibrational band dynamics of molecules and their sensitivity to the environment can also be captured by these spectroscopies in their time dependent version. However, it is often difficult to provide an interpretation of the experimental data at the molecular scale, such as molecular mechanisms or the processes hidden behind them. In this work, we present a theoretical-computational protocol based on ab initio molecular dynamics simulations and a combination of normal-like (generalized) mode analysis of solute-solvent clusters with a wavelet transform, for the first time. The case study is the vibrational dynamics of N-methyl-acetamide (NMA) in water solution, a well-known model of hydration of peptides and proteins. Amide modes are typical bands of peptide and protein backbone, and their couplings with the environment are very challenging in terms of the accurate prediction of solvent induced intensity and frequency shifts. The contribution of water molecules surrounding NMA to the composition of generalized and time resolved modes is introduced in our vibrational analysis, showing unequivocally its influence on the amide mode spectra. It is also shown that such mode compositions need the inclusion of the first shell solvent molecules to be accurately described. The wavelet analysis is proven to be strongly recommended to follow the time evolution of the spectra, and to capture vibrational band couplings and frequency shifts over time, preserving at the same time a well-balanced time-frequency resolution. This peculiar feature also allows one to perform a combined structural-vibrational analysis, where the different strengths of hydrogen bond interactions can quantitatively affect the amide bands over time at finite temperature. The proposed method allows for the direct connection between vibrational modes and local structural changes, providing a link from the spectroscopic observable to the structure, in this case the peptide backbone, and its hydration layouts.

Structural investigation of doubly-dehydrogenated pyrene cations

The vibrationally resolved spectra of the pyrene cation and doubly-dehydrogenated pyrene cation (C₁₆H₁₀˙⁺; Py⁺ and C₁₆H₈˙⁺; ddPy⁺) are presented. Infrared predissociation spectroscopy is employed to measure the vibrational spectrum of both species using a cryogenically cooled 22-pole ion trap. The spectrum of Py⁺ allows a detailed comparison with harmonic and anharmonic density functional theory (DFT) calculated normal mode frequencies. The spectrum of ddPy⁺ is dominated by absorption features from two isomers (4,5-ddPy⁺ and 1,2-ddPy⁺) with, at most, minor contributions from other isomers. These findings can be extended to explore the release of hydrogen from interstellar PAH species. Our results suggest that this process favours the loss of adjacent hydrogen atoms.

Proton-Sensitive Free-Radical Dimer Evolution Is a Critical Control Point for the Synthesis of Δ2,2'-Bibenzothiazines

The mechanism of the acid-dependent interring dehydrogenation in the conversion of the single-bonded 3-phenyl-2H-1,4-benzothiazine dimer 2 to the Δ^2,2′-bi(2H-1,4-benzothiazine) scaffold of red hair pigments is disclosed herein. Integrated chemical oxidation and oxygen consumption experiments, coupled with electron paramagnetic resonance (EPR) analyses and DFT calculations, allowed the identification of a key diprotonated free-radical intermediate, which was implicated in a remarkable oxygen-dependent chain process via peroxyl radical formation and evolution to give the Δ^2,2′-bi(2H-1,4-benzothiazine) dimer 3 by interring dehydrogenation. The critical requirement for strongly acidic conditions was rationalized for the first time by the differential evolution channels of isomeric peroxyl radical intermediates at the 2- versus 3-positions. These results offer for the first time a rationale to expand the synthetic scope of the double interring dehydrogenation pathway for the preparation of novel symmetric double-bond bridged captodative heterocycles.

Liquid-phase decomposition mechanism for bis(triaminoguanidinium) azotetrazolate (TAGzT)

This work provides new insights for the liquid-phase decomposition of bis(triaminoguanidinium) azotetrazolate (TAGzT). The liquid-phase decomposition process was investigated using a combined experimental and computational approach. Sub-milligram samples of TAGzT were heated at rates of about 2000 K s-1 to a set temperature (230 to 260 °C) where liquid-phase decomposition occurred under isothermal conditions. Fourier transform infrared (FTIR) spectroscopy and time-of-flight mass spectrometry (ToFMS) were used to acquire transmittance spectra and mass spectra of the evolved gas-phase species from the rapid thermolysis, respectively. FTIR spectroscopy was also used to acquire the transmittance spectra of the condensate and residue formed from the decomposition. N2, NH3, HCN, N2H4, triaminoguanidine and 3-azido-1,2,4-triazol-4-ide anion were identified as products of liquid-phase decomposition. Quantum chemical calculations were used for confirming the identity of the species observed in experiments and for identifying elementary chemical reactions that formed these species. Based on the calculated free energy barriers of these elementary reactions, important reaction pathways were identified for the formation of each of the product species.