Vibrational frequency scale factors for density functional theory and the polarization consistent basis sets

The Effect of Organic Semiconductor Electron Affinity on Preventing Parasitic Oxidation Reactions Limiting Performance of n-Type Organic Electrochemical Transistors

A key challenge in the development of organic mixed ionic-electronic conducting materials (OMIEC) for high performance electrochemical transistors is their stable performance in ambient. When operating in aqueous electrolyte, potential reactions of the electrochemically injected electrons with air and water could hinder their persistence, leading to a reduction in charge transport. Here, the impact of deepening the LUMO energy level of a series of electron-transporting semiconducting polymers is evaluated, and subsequently rendering the most common oxidation processes of electron polarons thermodynamically unfavorable, on organic electrochemical transistors (OECTs) performance. Employing time resolved spectroelectrochemistry with three analogous polymers having varying electron affinities (EA), it is found that an EA below the thermodynamic threshold for oxidation of its electron polarons by oxygen significantly improves electron transport and lifetime in air. A polymer with a sufficiently large EA and subsequent thermodynamically unfavorable oxidation of electron polarons is reported, which is used as the semiconducting layer in an OECT, in its neutral and N-DMBI doped form, resulting in an excellent and air-stable OECT performance. These results show a general design methodology to avoid detrimental parasitic reactions under ambient conditions, and the benefits that arise in electrical performance.

Ion Coupling, Bonding, and Transfer in Narrow Carbon Nanotubes

Narrow carbon nanotubes (nCNT) are unique mimics of biological channels with water-ion selectivity attractive for applications such as water purification and osmotic energy harvesting, yet their understanding is still incomplete. Here, an ab initio computation is employed to develop the full picture of ion transfer in nCNT including specificity and coupling between ions. The thermodynamic costs of ion transfer are computed for single ions and ion pairs and used to evaluate different local coupling scenarios including strong (pairing) and weak (free-ion) coupling as well as "electroneutrality breakdown" (EB), possible for cations only due to their chemisorption-like interaction with nCNT. The results also indicate that nCNT behaves as a highly polarizable metal-like shell, which eliminates the dielectric energy when CNT accommodates coupled cation and anion. This allows facile computation and comparison of the full transfer costs, including translation entropy, for different ions in different coupling modes to identify the dominant regime. EB transfer appears most favorable for K+, while anions strongly favor transfer as pairs, except for chloride which favors weak coupling and, at neutral pH, transfers as a trace ion coupled to both cation and OH-. The results demonstrate that, in general, observed ion permeation and conduction in nCNT, especially for anions, reflect a complex ion-specific and composition-dependent interplay between different ions.

Vibrational study of CO, O2, and H2 Adsorbed on the CoCrFeNi (110) High Entropy Alloy Surface

The vibrational properties of CO, O2, and H2 molecularly or dissociatively adsorbed on a CoCrFeNi(110) surface have been probed using high-resolution energy loss spectroscopy (HREELS) and modeled using density functional theory (DFT) calculations. Large (∼20 mm3) single-crystal, quaternary face-centered cubic CoCrFeNi was synthesized via a modified Czochralski technique. We show strong evidence that CO adsorbs primarily on bridge and on-top sites in compositionally varied local environments, which reflect the random, multielemental surface composition inherent in a high entropy alloy. A variation of adsorption sites is also found with oxygen, which exhibits two broad groups of modes. Comparison to previous photoemission and theoretical studies suggests that the higher energy modes consist primarily of local CrO x species, while the lower energy modes are due to oxygen atoms adsorbed on other metal sites. Unlike CO and O2, HREELS upon H2 adsorption shows only two much narrower modes and is consistent with atomic adsorption on 3-fold hollow sites. The hypothesized adsorption sites for all three species are directly corroborated by our DFT calculations.

Slow vibrational relaxation drives ultrafast formation of photoexcited polaron pair states in glycolated conjugated polymers

Glycol sidechains are often used to enhance the performance of organic photoconversion and electrochemical devices. Herein, we study their effects on electronic states and electronic properties. We find that polymer glycolation not only induces more disordered packing, but also results in a higher reorganisation energy due to more localised π-electron density. Transient absorption spectroscopy and femtosecond stimulated Raman spectroscopy are utilised to monitor the structural relaxation dynamics coupled to the excited state formation upon photoexcitation. Singlet excitons are initially formed, followed by polaron pair formation. The associated structural relaxation slows down in glycolated polymers (5 ps vs. 1.25 ps for alkylated), consistent with larger reorganisation energy. This slower vibrational relaxation is found to drive ultrafast formation of the polaron pair state (5 ps vs. 10 ps for alkylated). These results provide key experimental evidence demonstrating the impact of molecular structure on electronic state formation driven by strong vibrational coupling.

Potential energy surfaces and dynamic properties via ab initio composite and density functional approaches

Vibrational spectroscopy enables critical insight into the structural and dynamic properties of molecules. Presently, the majority of theoretical approaches to spectroscopy employ wavefunction-based ab initio or density functional methods that rely on the harmonic approximation. This approximation breaks down for large molecules with strongly anharmonic bonds or for molecules with large internuclear separations. An alternative to these methods involves generating molecular anharmonic potential energy surfaces (potentials) and using them to extrapolate the vibrational frequencies. This study examines the efficacy of density functional theory (DFT) and the correlation consistent Composite Approach (ccCA) in generating anharmonic frequencies from potentials of small main group molecules. Vibrational self-consistent field Theory (VSCF) and post-VSCF methods were used to calculate the fundamental frequencies of these molecules from their potentials. Functional choice, basis set selection, and mode-coupling are also examined as factors in influencing accuracy. The absolute deviations for the calculated frequencies using potentials at the ccCA level of theory were lower than the potentials at the DFT level. With DFT resulting in bending modes that are better described than those of ccCA, a multilevel DFT:ccCA approach where DFT potentials are used for single vibrational mode potentials and ccCA is used for vibrational mode-mode couplings can be utilized for larger polyatomic systems. The frequencies obtained with this multilevel approach using VCIPSI-PT2 were closer to experimental frequencies than the scaled harmonic frequencies, indicating the success of utilizing post-VSCF methods to generate more accurate representations of computed infrared spectra.

Quantum chemical pathways for the formation of 2,3,7,8-tetrachloro dibenzo-p-dioxin (TCDD) from 2,4,5-trichlorophenol: a mechanistic and thermo-kinetic study

CONTEXT

Dioxins, specifically 2,3,7,8-tetrachlorinated dibenzo-p-dioxin (TCDD), are highly toxic dioxins known for their severe health impacts and persistent environmental pollutants. This study focuses on understanding the formation pathways of TCDD from its precursor molecule 2,4,5-trichlorophenol (2,4,5-TCP). In our exploration of reaction pathways from 2,4,5-trichlorophenol (TCP), we delve into three reaction mechanisms: free-radical, direct condensation, and anionic. Our findings highlight the significance of the radical mechanism, particularly propagated by H radicals, with a notable increase in dioxin formation around 900 K. These results are consistent with experimental observations indicating an increase in the conversion of trichlorophenol from 600 to 900 K in the non-catalytic gas phase reaction. Thermodynamic parameters (∆H, ∆S, and ∆G), reaction barriers, and rate constants (k) were calculated across a temperature range of 300-1200 K to support the findings and provide insights into the optimal temperature range for controlling dioxins during the incineration process.

METHOD

In this study, quantum chemical calculations were conducted using density functional theory (DFT) with the B3LYP functional and the 6-311 +  + G(d,p) basis set in Gaussian 16 software. Stationary points, including transition states (TS), were confirmed with frequency calculations. Intrinsic reaction coordinate (IRC) calculations ensured minimum energy paths between TS and products, visualized in GaussView 6.0 Program. Single-point energy calculations utilized a more precise basis set, 6-311 +  + G(3df,2p), for enhanced energy accuracy, incorporating zero-point vibrational energy (ZPE) and other energy corrections. These calculations were repeated over a temperature range of 298.15-1200 K at 1 atm pressure. Finally, rate constant (k) expressions associated with TCDD formation were determined using transition state theory (TST).

Understanding Effects of Alkyl Side-Chain Density on Polaron Formation Via Electrochemical Doping in Thiophene Polymers

Polarons exist when charges are injected into organic semiconductors due to their strong coupling with the lattice phonons, significantly affecting electronic charge-transport properties. Understanding the formation and (de)localization of polarons is therefore critical for further developing organic semiconductors as a future electronics platform. However, there are very few studies reported in this area. In particular, there is no direct in situ monitoring of polaron formation and identification of its dependence on molecular structure and impact on electrical properties, limiting further advancement in organic electronics. Herein, how a minor modification of side-chain density in thiophene-based conjugated polymers affects the polaron formation via electrochemical doping, changing the polymers' electrical response to the surrounding dielectric environment for gas sensing, is demonstrated. It is found that the reduction in side-chain density results in a multistep polaron formation, leading to an initial formation of localized polarons in thiophene units without side chains. Reduced side-chain density also allows the formation of a high density of polarons with fewer polymer structural changes. More numerous but more localized polarons generate a stronger analyte response but without the selectivity between polar and non-polar solvents, which is different from the more delocalized polarons that show clear selectivity. The results provide important molecular understanding and design rules for the polaron formation and its impact on electrical properties.

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.

Surface-enhanced Raman database of 24 metabolites: Stable measurement of spectra, extraction and analysis of the main features

Surface-enhanced Raman spectroscopy (SERS) has been used in Raman-based metabolomics to provide abundant molecular fingerprint information in situ with extremely high sensitivity, without damaging the sample. However, poor reproducibility, caused by the randomness of the adsorption sites, and the short-range effect of SERS have hindered the development of SERS in metabolomics, resulting in very few SERS reference databases for small-molecule metabolites. In this work, our previously proposed large laser spot-swift mapping SERS method was adopted for the measurement of 24 commercially available metabolite standards, to provide reproducible and reliable references for Raman-based metabolomics study. Among these 24 metabolites, 22 contained no Raman data in PubChem. Other than the SERS spectra data, we extracted and explained the molecular vibration information of these metabolites, and combined with the density functional theory (DFT) calculations, we provided a new possibility for the fast Raman recognition of small-molecule metabolites. Accordingly, a large laser spot-swift mapping SERS database of metabolites in human serum was initially established, which contained not only the original spectral data but also other detailed feature information regarding the Raman peaks. With continuous accumulation, this database could play a promising role in Raman-based metabolomics and other Raman-related research.

A Raman spectral marker for the iso-octyl chain structure of cholesterol

Raman spectroscopy provides label-free, specific analysis of biomolecular structure and interactions. It could have a greater impact with improved characterization of complex fingerprint vibrations. Many Raman peaks have been assigned to cholesterol, for example, but the molecular vibrations associated with those peaks are not known. In this report, time-dependent density functional theory calculations of the Raman spectrum of cholesterol are compared to measurements on microcrystalline powder to identify 23 peaks in the Raman spectrum. Among them, a band of six peaks is found to be sensitive to the conformational structure of cholesterol's iso-octyl chain. Calculations on 10 conformers in this spectral band are fit to experimental spectra to probe the cholesterol chain structure in purified powder and in phospholipid vesicles. In vesicles, the chain is found to bend perpendicular to the steroid rings, supporting the case that the chain is a dynamic structure that contributes to lipid condensation and other effects of cholesterol in biomembranes. Statement of Significance: Here we use density functional theory to identify a band of six peaks in cholesterol's Raman spectrum that is sensitive to the conformational structure of cholesterol's chain. Raman spectra were analyzed to show that in fluid-phase lipid membranes, about half of the cholesterol chains point perpendicular to the steroid rings. This new method of label-free structural analysis could make significant contributions to our understanding of cholesterol's critical role in biomembrane structure and function. More broadly, the results show that computational quantum chemistry Raman spectroscopy can make significant new contributions to molecular structure when spectra are interpreted with computational quantum chemistry.

Efficient optical plasmonic tweezer-controlled single-molecule SERS characterization of pH-dependent amylin species in aqueous milieus

It is challenging to characterize single or a few biomolecules in physiological milieus without excluding the influences of surrounding environment. Here we utilize optical plasmonic trapping to construct a dynamic nanocavity, which reduces the diffraction-limited detection volume and provides reproducible electromagnetic field enhancements to achieve high-throughput single-molecule surface-enhanced Raman spectroscopy (SERS) characterizations in aqueous environments. Specifically, we study human Islet Amyloid Polypeptide (amylin, hIAPP) under different physiological pH conditions by combining spectroscopic experiments and molecular dynamics (MD) simulations. Based on a statistically significant amount of time-dependent SERS spectra, two types of low-populated transient species of hIAPP containing either turn or β-sheet structure among its predominant helix-coil monomers are characterized during the early-stage incubation at neutral condition, which play a crucial role in driving irreversible amyloid fibril developments even after a subsequent adjustment of pH to continue the prolonged incubation at acidic condition. Our results might provide profound mechanistic insight into the pH-regulated amyloidogenesis and introduce an alternative approach for investigating complex biological processes at the single-molecule level.

Infrared Ion Spectroscopic Characterization of the Gaseous [Co(15-crown-5)(H2O)]2+ Complex

We report fingerprint infrared multiple-photon dissociation spectra of the gaseous monohydrated coordination complex of cobalt(II) and the macrocycle 1,4,7,10,13-pentaoxacyclopentadecane (or 15-crown-5), [Co(15-crown-5)(H2O)]2+. The metal-ligand complexes are generated using electrospray ionization, and their IR action spectra are recorded in a quadrupole ion trap mass spectrometer using the free-electron laser FELIX. The electronic structure and chelation motif are derived from spectral comparison with computed vibrational spectra obtained at the density functional theory level. We focus here on the gas-phase structure, addressing the question of doublet versus quartet spin multiplicity and the chelation geometry. We conclude that the gas-phase complex adopts a quartet spin state, excluding contributions of doublet species, and that the chelation geometry is pseudo-octahedral with the six oxygen centers of 15-crown-5 and H2O coordinated to the metal ion. We also address the possible presence of higher-energy conformers based on the IR spectral evidence and calculated thermodynamics.

Molecular Geometries and Vibrational Contributions to Reaction Thermochemistry Are Surprisingly Insensitive to the Choice of Basis Sets

Calculation of molecular geometries and harmonic vibrational frequencies are pre-requisites for thermochemistry calculations. Contrary to conventional wisdom, this paper demonstrates that quantum chemical predictions of the thermochemistry of many gas and solution phase chemical reactions appear to be very insensitive to the choice of basis sets. For a large test set of 80 diverse organic and transition-metal-containing reactions, variations in reaction free energy based on geometries and frequencies calculated using a variety of double and triple-zeta basis sets from the Pople, Jensen, Ahlrichs, and Dunning families are typically less than 4 kJ mol^-1, especially when the quasiharmonic oscillator correction is applied to mitigate the effects of low-frequency modes. Our analysis indicates that for many organic molecules and their transition states, high-level revDSD-PBEP86-D4 and DLPNO-CCSD(T)/(aug-)cc-pVTZ single-point energies usually vary by less than 2 kJ mol^-1 on density functional theory geometries optimized using basis sets ranging from 6-31+G(d) to aug-pcseg-2 and aug-cc-pVTZ. In cases where these single-point energies vary significantly, indicating sensitivity of molecular geometries to the choice of basis set, there is often substantial cancellation of errors when the reaction energy or barrier is calculated. The study concludes that the choice of basis set for molecular geometry and frequencies, particularly those considered in this study, is not critical for the accuracy of thermochemistry calculations in the gas or solution phase.

Harmonic Vibrational Frequency Simulation of Pharmaceutical Molecules via a Novel Multi-Molecular Fragment Interception Method

By means of a computational method based on Density Functional Theory (DFT), using commercially available software, a novel method for simulating equilibrium geometry harmonic vibrational frequencies is proposed. Finasteride, Lamivudine, and Repaglinide were selected as model molecules to study the adaptability of the new method. Three molecular models, namely the single-molecular, central-molecular, and multi-molecular fragment models, were constructed and calculated by Generalized Gradient Approximations (GGAs) with the PBE functional via the Material Studio 8.0 program. Theoretical vibrational frequencies were assigned and compared to the corresponding experimental data. The results indicated that the traditional single-molecular calculation and scaled spectra with scale factor exhibited the worst similarity for all three pharmaceutical molecules among the three models. Furthermore, the central-molecular model with a configuration closer to the empirical structure resulted in a reduction of mean absolute error (MAE) and root mean squared error (RMSE) in all three pharmaceutics, including the hydrogen-bonded functional groups. However, the improvement in computational accuracy for different drug molecules using the central-molecular model for vibrational frequency calculation was unstable. Whereas, the new multi-molecular fragment interception method showed the best agreement with experimental results, exhibiting MAE and RMSE values of 8.21 cm^-1 and 18.35 cm^-1 for Finasteride, 15.95 cm^-1 and 26.46 cm^-1 for Lamivudine, and 12.10 cm^-1 and 25.82 cm^-1 for Repaglinide. Additionally, this work provides comprehensive vibrational frequency calculations and assignments for Finasteride, Lamivudine, and Repaglinide, which have never been thoroughly investigated in previous research.

Analytical harmonic vibrational frequencies with VV10-containing density functionals: Theory, efficient implementation, and benchmark assessments

VV10 is a powerful nonlocal density functional for long-range correlation that is used to include dispersion effects in many modern density functionals, such as the meta-generalized gradient approximation (mGGA), B97M-V, the hybrid GGA, ωB97X-V, and the hybrid mGGA, ωB97M-V. While energies and analytical gradients for VV10 are already widely available, this study reports the first derivation and efficient implementation of the analytical second derivatives of the VV10 energy. The additional compute cost of the VV10 contributions to analytical frequencies is shown to be small in all but the smallest basis sets for recommended grid sizes. This study also reports the assessment of VV10-containing functionals for predicting harmonic frequencies using the analytical second derivative code. The contribution of VV10 to simulating harmonic frequencies is shown to be small for small molecules but important for systems where weak interactions are important, such as water clusters. In the latter cases, B97M-V, ωB97M-V, and ωB97X-V perform very well. The convergence of frequencies with respect to the grid size and atomic orbital basis set size is studied, and recommendations are reported. Finally, scaling factors to allow comparison of scaled harmonic frequencies with experimental fundamental frequencies and to predict zero-point vibrational energy are presented for some recently developed functionals (including r2SCAN, B97M-V, ωB97X-V, M06-SX, and ωB97M-V).

IR/UV Double Resonance Study of the 2-Phenylallyl Radical and its Pyrolysis Products

Isolated 2-phenylallyl radicals (2-PA), generated by pyrolysis from a nitrite precursor, have been investigated by IR/UV ion dip spectroscopy using free electron laser radiation. 2-PA is a resonance-stabilized radical that is considered to be involved in the formation of polycyclic aromatic hydrocarbons (PAH) in combustion, but also in interstellar space. The radical is identified based on its gas-phase IR spectrum. Furthermore, a number of bimolecular reaction products are identified, showing that the self-reaction as well as reactions with unimolecular decomposition products of 2-PA form several PAH efficiently. Possible mechanisms are discussed and the chemistry of 2-PA is compared with the one of the related 2-methylallyl and phenylpropargyl radicals.

Model Chemistry Recommendations for Scaled Harmonic Frequency Calculations: A Benchmark Study

Despite the widespread popularity of scaled harmonic frequency calculations to predict experimental fundamental frequencies in chemistry, sparse benchmarking is available to guide users on the appropriate level of theory and basis set choices (model chemistry) or deep understanding of expected errors. An updated assessment of the best approach for scaling to minimize errors is also overdue. Here, we assess the performance of over 600 popular, contemporary, and robust model chemistries in the calculation of scaled harmonic frequencies, evaluating different scaling factor types and their implications in the scaled harmonic frequencies and model chemistry performance. We can summarize our results into three main findings: (1) Using model-chemistry-specific scaling factors optimized for three different frequency regions (low (<1,000 cm^-1), mid (1,000-2,000 cm^-1), and high (>2,000 cm^-1)) results in substantial improvements in the agreement between the scaled harmonic and experimental frequencies compared to other choices. (2) Larger basis sets and more robust levels of theory generally lead to superior performance; however, the particular model chemistry choice matters and poor choices lead to significantly reduced accuracies. (3) Outliers are expected in routine calculations regardless of the model chemistry choice. Our benchmarking results here do not consider the intensity of vibrational transitions; however, we draw upon previous benchmarking results for dipole moments that highlight the importance of diffuse functions (i.e., augmented basis sets) in high-quality intensity predictions. In terms of specific recommendations, overall, the highest accuracy model chemistries are double-hybrid density functional approximations with a non-Pople augmented triple-ζ basis set, which can produce median frequency errors down to 7.6 cm^-1 (DSD-PBEP86/def2-TZVPD), which is very close to the error in the harmonic approximation, i.e., the anharmonicity error. Double-ζ basis sets should not be used with double-hybrid functionals as there is no improvement compared to hybrid functional results (unlike for double-hybrid triple-ζ model chemistries). Note that 6-311G* and 6-311+G* basis sets perform like a double-ζ basis set for vibrational frequencies. After scaling, all studied hybrid functionals with non-Pople triple-ζ basis sets will produce median errors of less than 15 cm^-1, with the best result of 9.9 cm^-1 with B97-1/def2-TZVPD. Appropriate matching of double-ζ basis sets with hybrid functionals can produce high-quality results, but the precise choice of functional and basis set is more important. The B97-1, TPSS0-D3(BJ), or ωB97X-D hybrid density functionals with 6-31G*, pc-1, or pcseg-1 are recommended for fast routine calculations, all delivering median errors of 11-12 cm^-1. Note that dispersion corrections are not easily available for B97-1; given its strong performance here, we recommend these be added to major programs in coming updates.

Methylidyne Adsorption on Pt(211) Probed by Reflection Absorption Infrared Spectroscopy (RAIRS)

Methylidyne, CH(ads), adsorbed on a Pt(211) surface and its interaction with chemisorbed hydrogen atoms was studied by reflection absorption infrared spectroscopy (RAIRS). Methylidyne was formed on Pt(211) by methane dissociation from a molecular beam followed by thermal decomposition of the methane dissociation products. CH(ads) was detected by RAIRS via its symmetric C-H stretch vibration resulting in three discrete absorption peaks in the region of 2950-2970 cm^-1. While the frequencies of the three C-H stretch peaks remain fixed, their relative intensities depend on the H(ads) co-coverage. This differs markedly from what was observed previously for the RAIR spectra of CH(ads) adsorbed on Pt(111) by the group of Trenary,¹ who observed a single C-H stretch peak, which showed a continuous blue shift with increasing H(ads) coverage. Based on our experimental results and density functional theory (DFT) calculations, we propose that the three discrete absorption peaks on Pt(211) are due to the adsorption of methylidyne on the steps of Pt(211) forming one-dimensional rows of adsorbates. Depending on the H(ads) coverage, the CH(ads) species on the step sites can have either zero, one, or two neighboring H(ads) atoms, leading to three different vibrational C-H stretch frequencies and a reversible shift in relative peak intensity depending on the H(ads) coverage.

Facial vs. meridional coordination in gaseous Ni(II)-hexacyclen complexes revealed with infrared ion spectroscopy

We report fingerprint infrared multiple-photon dissociation (IRMPD) spectra of the isolated gaseous hexa-coordinated complex of the macrocycle hexa-aza-18-crown-6 (hexacyclen, 1,4,7,10,13,16-hexaazacyclooctadecane, 18-azacrown-6) with Ni2+. The metal-ligand complexes are generated using electrospray ionization (ESI) and IR action spectra are recorded in a Fourier transform ion cyclotron resonance mass spectrometer (FTICR) MS coupled to the infrared free-electron laser FELIX. We investigate geometric structure of the complexes and in particular the chelation motif, by comparison with computed vibrational spectra, obtained using density functional theory (DFT) at the B3LYP/6-31++G(d,p) level. The quasi-octahedral chelation motif of the complex has been well documented in condensed-phase studies, and we focus here on the gas-phase structure, addressing in particular the question of a facial (fac) versus a meridional (mer) octahedral chelation geometry. Based on the good agreement between calculated linear IR spectra and experimental IRMPD spectra, we conclude that the gas-phase complex adopts a mer chelation geometry and we exclude significant contribution of the fac isomer, which is computed to lie about 10 kJ mol-1 higher in energy. We also address the possible presence of both meridional diastereomers and of higher energy conformers of meridional isomers. Finally, as expected for the d8 Ni2+-ion in an octahedral ligand environment, the IR spectrum also shows that the complexes are in a high-spin electron configuration.

Insight into pyrolysis mechanism of 1,2-propylene glycol: Based on density functional theory and wavefunction analysis

The multiple thermal decomposition mechanisms of 1,2-propylene glycol are studied through theoretical calculation and experiment, including carbon chain break, dehydrogenation and dehydration mechanism. The wavefunction is employed to analyze the decomposition process from a micro perspective. DLPNO-CCSD(T)/CBS method is engaged in establishing potential energy surface. The results reveal that the dehydration and carbon chain break mechanism are the primary pyrolysis paths, and the former is the dominant pyrolysis mechanism at low temperature, while the latter is applicable at the high temperature. The pyrolysis products are mainly acetaldehyde, propanal and acetone, which is consistent with experimental results. Besides, the comparison results of 1,2-propylene glycol and glycerol pyrolysis products indicate that the increment of hydroxyls are conducive to the generation of carbonyl compounds during the polyol thermal decomposition. This work is aimed to comprehensively investigate the pyrolysis mechanism of 1,2-propylene glycol and provide the valuable thermodynamics and kinetic data for developing efficient polyol pyrolysis technology. Furthermore, it provides a reference for choosing low-toxic tobacco humectant.

Benchmarking Density Functionals, Basis Sets, and Solvent Models in Predicting Thermodynamic Hydricities of Organic Hydrides

Many renewable energy technologies, such as hydrogen gas synthesis and carbon dioxide reduction, rely on chemical reactions involving hydride anions (H^-). When selecting molecules to be used in such applications, an important quantity to consider is the thermodynamic hydricity, which is the free energy required for a species to donate a hydride anion. Theoretical calculations of thermodynamic hydricity depend on several parameters, mainly the density functional, basis set, and solvent model. In order to assess the effects of the above three parameters, we carry out hydricity calculations with different combinations of density functionals, basis sets, and solvent models for a set of organic molecules with known experimental hydricity values. The data are analyzed by comparing the R² and root-mean-squared error (RMSE) of linear fits with a fixed slope of 1 and using the Akaike Information Criterion to determine statistical significance of the RMSE rank ordering. Based on these results, we quantified the accuracy of theoretical predictions of hydricity and found that the best compromise between accuracy and computational cost was obtained by using the B3LYP-D3 density functional for the geometry optimization and free-energy corrections, either ωB97X-D3 or M06-2X-D3 for single-point energy corrections, combined with a basis set no larger than def-TZVP and the C-PCM ISWIG solvation model. At this level of theory, the RMSEs of hydricity calculations for organic molecules in acetonitrile and dimethyl sulfoxide were found to be <4 and <10 kcal/mol, respectively, for an experimental data set with a dynamic range of 20-150 kcal/mol.

DFT-based Raman spectral study of astaxanthin geometrical isomers

Astaxanthin is a carotenoid widely used in food additives, nutritional product and medicines, which shows many physiological functions such as antioxidant, anti-inflammatory, anti-hypertensive and anti-diabetic activities. It has been recognized that astaxanthin has all-trans and nine cis isomers, and these geometrical isomers have very different biological activities. The process of selective enrichment, metabolism and isomerization of astaxanthin in animals remains to be studied. Therefore, identifying isomers and obtaining their structural parameters are important for understanding the active mechanism of different molecular isomers. Although the traditional methods such as high-performance liquid chromatography (HPLC) and nuclear magnetic resonance (NMR) spectroscopy can be used to distinguish these isomers, these methods generally require considerable testing time, cost, sample volume, and hardly be applied in vivo. In this work, Raman spectroscopy combined with density functional theory (DFT) calculation was introduced to study different geometrical isomers of astaxanthin. The theoretical and experimental Raman spectra are in agreement, and we have demonstrated that all the known ten geometrical isomers of astaxanthin can be readily distinguished using this spectroscopic approach. The astaxanthin molecular vibrational modes, geometric structures, energies of ten geometric isomers are systematically scrutinized. Moreover, a lot of structural and Raman problems unsolved previously have been solved by the DFT-based spectral analysis. Therefore, this work provides an effective way for identification of different astaxanthin geometrical isomers, and may have important significance for promoting the research of astaxanthin isomers on biological property mechanisms and related applications in food molecular science.

VIBFREQ1295: A New Database for Vibrational Frequency Calculations

High-throughput approaches for producing approximate vibrational spectral data for molecules of astrochemistry interest rely on harmonic frequency calculations using computational quantum chemistry. However, model chemistry recommendations (i.e., a level of theory and basis set pair) for these calculations are not yet available and, thus, thorough benchmarking against comprehensive benchmark databases is needed. Here, we present a new database for vibrational frequency calculations (VIBFREQ1295) storing 1295 experimental fundamental frequencies and CCSD(T)(F12*)/cc-pVDZ-F12 ab initio harmonic frequencies from 141 molecules. VIBFREQ1295's experimental data was complied through a comprehensive review of contemporary experimental data, while the ab initio data was computed here. The chemical space spanned by the molecules chosen is considered in-depth and is shown to have good representation of common organic functional groups and vibrational modes. Scaling factors are routinely used to approximate the effect of anharmonicity and convert computed harmonic frequencies to predicted fundamental frequencies. With our experimental and high-level ab initio data, we find that a single global uniform scaling factor of 0.9617(3) results in median differences of 15.9(5) cm^-1. A far superior performance with a median difference of 7.5(5) cm^-1 can be obtained, however, by using separate scaling factors (SFs) for three regions: frequencies less than 1000 cm^-1 (SF = 0.987(1)), between 1000 and 2000 cm^-1 (SF = 0.9727(6)), and above 2000 cm^-1 (SF = 0.9564(4)). This sets a lower bound for the performance that could be reliably obtained using scaling of harmonic frequency calculations to predict experimental fundamental frequencies. VIBFREQ1295's most important purpose is to provide a robust database for benchmarking the performance of any vibrational frequency calculations. VIBFREQ1295 data could also be used to train machine-learning models for the prediction of vibrational spectra and as a reference and data starting point for more detailed spectroscopic modeling of particular molecules. The database can be found as part of the Supporting Information for this paper or in the Harvard DataVerse at https://doi.org/10.7910/DVN/VLVNU7.

Putting together the puzzle of ion transfer in single-digit carbon nanotubes: mean-field meets ab initio

Nature employs channel proteins to selectively pass water across cell membranes, which inspires the search for bio-mimetic analogues. Carbon nanotube porins (CNTPs) are intriguing mimics of water channels, yet ion transport in CNTPs still poses questions. As an alternative to continuum models, here we present a molecular mean-field model that transparently describes ion coupling, yet unlike continuum models, computes ab initio all required thermodynamic quantities for the KCl salt and H⁺ and OH^- ions present in water. Starting from water transfer, the model considers the transfer of free ions, along with ion-pair formation as a proxy of non-mean-field ion-ion interactions. High affinity to hydroxide, suggested by experiments, making it a dominant charge carrier in CNTPs, is revealed as an exceptionally favorable transfer of KOH pairs. Nevertheless, free ions, coexisting with less mobile ion-pairs, apparently control ion transport. The model well explains the observed effects of salt concentration and pH on conductivity, transport numbers, anion permeation and its activation energies, and current rectification. The proposed approach is extendable to other sub-nanochannels and helps design novel osmotic materials and devices.

The gas-phase infrared spectra of the 2-methylallyl radical and its high-temperature reaction products

The resonance-stabilized 2-methylallyl radical, 2-MA, is considered as a possible intermediate in the formation of polycyclic aromatic hydrocarbons (PAHs) in combustion processes. In this work, we report on its contribution to molecular growth in a high-temperature microreactor and provide mass-selective IR/UV ion dip spectra of the radical, as well as the various jet-cooled reaction products, employing free electron laser radiation in the mid-infrared region. Small (aromatic) hydrocarbons such as fulvene, benzene, styrene, or para-xylene, as well as polycyclic molecules, like (methylated) naphthalene, were identified with the aid of ab initio DFT computations. Several reaction products differ by one or more methyl groups, suggesting that molecular growth is dominated by (de)methylation in the reactor.

On the influence of water on THz vibrational spectral features of molecular crystals

The nanoscale structure of molecular assemblies plays a major role in many (μ)-biological mechanisms. Molecular crystals are one of the most simple of these assemblies and are widely used in a variety of applications from pharmaceuticals and agrochemicals, to nutraceuticals and cosmetics. The collective vibrations in such molecular crystals can be probed using terahertz spectroscopy, providing unique characteristic spectral fingerprints. However, the association of the spectral features to the crystal conformation, crystal phase and its environment is a difficult task. We present a combined computational-experimental study on the incorporation of water in lactose molecular crystals, and show how simulations can be used to associate spectral features in the THz region to crystal conformations and phases. Using periodic DFT simulations of lactose molecular crystals, the role of water in the observed lactose THz spectrum is clarified, presenting both direct and indirect contributions. A specific experimental setup is built to allow the controlled heating and corresponding dehydration of the sample, providing the monitoring of the crystal phase transformation dynamics. Besides the observation that lactose phases and phase transformation appear to be more complex than previously thought - including several crystal forms in a single phase and a non-negligible water content in the so-called anhydrous phase - we draw two main conclusions from this study. Firstly, THz modes are spread over more than one molecule and require periodic computation rather than a gas-phase one. Secondly, hydration water does not only play a perturbative role but also participates in the facilitation of the THz vibrations.

Flexible boundary layer using exchange for embedding theories. II. QM/MM dynamics of the hydrated electron

The FlexiBLE embedding method introduced in Paper I [Z. Shen and W. J. Glover, J. Chem. Phys. 155, 224112 (2021)] is applied to explore the structure and dynamics of the aqueous solvated electron at an all-electron density functional theory Quantum Mechanics/Molecular Mechanics level. Compared to a one-electron mixed quantum/classical description, we find the dynamics of the many-electron model of the hydrated electron exhibits enhanced coupling to water OH stretch modes. Natural bond orbital analysis reveals this coupling is due to significant population of water OH σ^* orbitals, reaching 20%. Based on this, we develop a minimal frontier orbital picture of the hydrated electron involving a cavity orbital and important coupling to 4-5 coordinating OH σ^* orbitals. Implications for the interpretation of the spectroscopy of this interesting species are discussed.

DFT and Raman study of all-trans astaxanthin optical isomers

Astaxanthin (AST) is a xanthophyll carotenoid widely distributed in aquatic animals, which has many physiological functions such as antioxidant, anti-inflammatory, anti-hypertensive and anti-diabetic activities. AST has three optical isomers, including a pair of enantiomers (3S,3'S and 3R,3'R) and a meso form (3R,3'S). Different optical isomers have differences in a variety of physiological functions. Traditionally, High Performance Liquid Chromatography (HPLC) has been used to distinguish these isomers. In this work, it was found that Raman spectroscopy can be employed to distinguish the three optical isomers. The intensities of two Raman bands at 1190 and 1215 cm^-1 of three isomers are different. Density Functional Theory (DFT) calculations are performed to analyze the spectral differences. The mainly occupied conformers of these three optical isomers are speculated and identified.

IRMPD Spectroscopy of [PC (4:0/4:0) + M]+ (M = H, Na, K) and Corresponding CID Fragment Ions

Glycerophospholipids (GPs) are highly abundant in eukaryotic cells and take part in numerous fundamental physiological processes such as molecular signaling. The GP composition of samples is often analyzed using mass spectrometry (MS), but identification of some structural features, for example, differentiation of stereospecific numbering (sn) isomers by well-established tandem MS (MS²) methods, is challenging. In particular, the formation of 1,3-dioxolane over 1,3-dioxane intermediates proposed to be responsible for the sn-selectivity of these tandem MS strategies has not been validated by spectroscopic methods. In this work, we present infrared multiple photon dissociation (IRMPD) spectra of phosphatidylcholine (PC) ions [PC 4:0/4:0 + H/Na/K]⁺ and [PC 4:0/4:0 + Na/K - 183]⁺ fragments generated by electrospray ionization (ESI)-MS and collision-induced dissociation (CID), respectively. IRMPD spectra of protonated, sodiated, and potassiated PC 4:0/4:0 differ in the phosphate- and ester-related bands, which are increasingly shifted to lower wavenumbers with higher adduct masses. Comparison of calculated and experimental IR spectra indicates the presence of multiple, two and one isomer(s) for [PC 4:0/4:0 + H]⁺, [PC 4:0/4:0 + Na]⁺, and [PC 4:0/4:0 + K]⁺, respectively. Isomers exhibiting pronounced sn-1 ester-ion interactions are computationally predicted to be energetically preferred for all species and are in line with experimental results. IRMPD spectra of [PC 4:0/4:0 + Na/K - 183]⁺ are presented and shed the first light on the fragment ion structures, rationalizing MS-based lipidomics strategies that aim to characterize the sn-isomerism of GPs.

Adsorption Motifs and Molecular Orientation at the Ionic Liquid/Noble Metal Interface: [C2C1Im][NTf2] on Pt(111)

In solid catalysts with ionic liquid layers (SCILLs), ionic liquid (IL) thin films are used to modify the activity and selectivity of catalytic materials. In this work, we investigated the adsorption behavior of the IL 1-ethyl-3-methyl-imidazolium bis(trifluoromethylsulfonyl)imide [C₂C₁Im][NTf₂] on Pt(111) by combining experimental and theoretical studies. Under ultrahigh vacuum (UHV) conditions, the IL was deposited onto a Pt(111) single crystal surface by physical vapor deposition (PVD) at different surface temperatures (200, 300, and 400 K). The adsorption process was monitored by in situ infrared reflection absorption spectroscopy (IRAS). Complementary to the IRAS studies, we performed density functional theory (DFT) calculations and analyzed the adsorption motifs and orientation of the IL ions. In total, we calculated four different systems: (a) [C₂C₁Im]⁺ and [NTf₂]^- ions in the gas phase; [NTf₂]^- anions in (b) small (4 × 4) and (c) large (6 × 6) Pt(111) supercells; and (d) a complete ion pair of [C₂C₁Im][NTf₂] in a (6 × 6) Pt(111) supercell. Based on DFT, we simulated IR spectra and compared them to the experimental data. Our results suggest that the binding motif and orientation of the IL is strongly dependent on the actual IL coverage. In the monolayer (ML), [NTf₂]^- interacts strongly with the metal surface and adopts a specific orientation in which it interacts with the Pt surface via the SO₂ groups. Also the [C₂C₁Im]⁺ cations adopt a preferential orientation up to coverages of 1 ML. Upon transition to the multilayer region, the specific orientation of the ions is gradually lost.

Threshold photoelectron spectroscopy of 9-methyladenine: theory and experiment

We present a combined experimental and theoretical study of single-photon ionization of 9-methyladenine (9MA) in the gas phase. In addition to tautomerism, several rotamers due to the rotation of the methyl group may exist. Computations show, however, that solely one rotamer contributes because of low population in the molecular beam and/or unfavorable Franck-Condon factors upon ionization. Experimentally, we used VUV radiation available at the DESIRS beamline of the synchrotron radiation facility SOLEIL to record the threshold photoelectron spectrum of this molecule between 8 and 11 eV. This spectrum consists of a well-resolved band assigned mainly to vibronic levels of the D₀ cationic state, plus a contribution from the D₁ state, and two large bands corresponding to the D₁, D₂ and D₃ electronically excited states. The adiabatic ionization energy of 9MA is measured at 8.097 ± 0.005 eV in close agreement with the computed value using the explicitly correlated coupled cluster approach including core valence, scalar relativistic and zero-point vibrational energy corrections. This work sheds light on the complex pattern of the lowest doublet electronic states of 9MA⁺. The comparison to canonical adenine reveals that methylation induces further electronic structure complication that may be important to understand the effects of ionizing radiation and the charge distribution in these biological entities at different time scales.

Investigation of the thermal decomposition mechanism of glycerol: the combination of a theoretical study based on the Minnesota functional and experimental support

The multiple thermal decomposition channels of glycerol are calculated at the M06-2X-D3/6-311+G(d,p) level. In addition, the CAM-B3LYP and ωB97X-D functionals are used to show the functional influence on the free energy barrier. For the highly competitive primary channels, the DLPNO-CCSD(T)/CBS method is applied for the energy calculations. The results show that the dominant paths are: (1) breakage of the C-C, C-O, and O-H bonds of glycerol successively to form carbonyl and alkene, and then generation of water, formaldehyde, and acetaldehyde; (2) glycerol undergoing an intramolecular dehydration reaction and producing 3-hydroxypropionaldehyde; it has two subsequent reactions: ① C-C bond fracture occurring to form formaldehyde, acetaldehyde, and water; and ② intramolecular dehydration forming acrolein and water. The ΔG₁ is 65.6 kcal mol^-1 while the ΔG₂ is 65.5 kcal mol^-1 at 101 kPa and 298 K, and fitted rate equations are 1.09 × 10¹³ exp[65.6 × 10³/RT] s^-1 and 8.07 × 10¹² exp[65.4 × 10³/RT] s^-1, respectively. Besides, UPLC and TG-GC/MS are applied complementarily to investigate the anaerobic pyrolysis products of glycerol at different temperatures. The experimental results are consistent with theoretical calculations.

Mechanism for the Reaction of White Phosphorus with Cp2Cr2(CO)6 Leading Ultimately to the Triple-Decker Sandwich Cp2Cr2(μ-η5,η5-P5): A Theoretical Study

The experimentally known reaction of Cp₂Cr₂(CO)₆ with white phosphorus (P₄) to give CpCr(CO)₂(η³-P₃), Cp₂Cr₂(CO)₄(μ-η,²η²-P₂), and the triple-decker sandwich Cp₂Cr₂(μ-η,⁵η⁵-P₅) is of interest since the P₄ reactant having a tetrahedral cluster of four phosphorus atoms is converted to products having P₂, P₃, and P₅ ligands. The mechanism of this obviously complicated reaction can be dissected into three stages using a coupled cluster theoretical method that has been benchmarked with the P₂, Mn(CO)₅, and CpCr(CO)₃ dimerization processes. The first stage of the Cp₂Cr₂(CO)₆/P₄ reaction mechanism generates the unsaturated singlet intermediate Cp₂Cr₂(CO)₅ that combines with the P₄ reactant. Decarbonylation of the resulting Cp₂Cr₂(CO)₅(P₄) complex provides a singlet tetracarbonyl readily fragmenting into the stable triphosphacyclopropenyl complex CpCr(CO)₂(η³-P₃) and the chromium phosphide CpCr(CO)₂(P). The isomeric triplet tetracarbonyl Cp₂Cr₂(CO)₄(P₄), readily fragments into CpCr(CO)₂(η²-P₂), which can generate the stable diphosphaacetylene complex Cp₂Cr₂(CO)₄(η,²η²-P₂) as well as the pentamer [CpCr(CO)₂]₅(P₁₀). Combination of the coordinately unsaturated CpCr(CO)(η³-P₃) with CpCr(CO)₂(η²-P₂) can lead to a ring expansion. This generates the P₅ pentagonal ligand in a Cp₂Cr₂(CO)₃(P₅) precursor to the experimentally observed carbonyl-free triple-decker sandwich Cp₂Cr₂(μ-η,⁵η⁵-P₅) after three successive decarbonylations.

Influence of Vibronic Coupling on Ultrafast Singlet Fission in a Linear Terrylenediimide Dimer

Singlet fission (SF) is a photophysical process capable of boosting the efficiency of solar cells. Recent experimental investigations into the mechanism of SF provide evidence for coherent mixing between the singlet, triplet, and charge transfer basis states. Up until now, this interpretation has largely focused on electronic interactions; however, nuclear motions resulting in vibronic coupling have been suggested to support rapid and efficient SF in organic chromophore assemblies. Further information about the complex interactions between vibronic excited states is needed to understand the potential role of this coupling in SF. Here, we report mixed singlet and correlated triplet pair states giving rise to sub-50 fs SF in a terrylene-3,4:11,12-bis(dicarboximide) (TDI) dimer in which the two TDI molecules are covalently linked by a direct N-N connection at one of their imide positions, leading to a linear dimer with perpendicular TDI π systems. We observe the transfer of low-frequency coherent wavepackets between the initial predominantly singlet states to the product triplet-dominated states. This implies a non-negligible dependence of SF on nonadiabatic coupling in this dimer. We interpret our experimental results in the framework of a modified Holstein Hamiltonian, which predicts that vibronic interactions between low-frequency singlet modes and high-frequency correlated triplet pair motions lead to mixing of the pure basis states. These results highlight how nonadiabatic mixing can shape the complex potential energy landscape underlying ultrafast SF.

Quantitative Comparison of Experimental and Computed IR-Spectra Extracted from Ab Initio Molecular Dynamics

Experimentally measured infrared spectra are often compared to their computed equivalents. However, the accordance is typically characterized by visual inspection, which is prone to subjective judgment. The primary challenge for a similarity-based analysis is that the artifacts introduced by each approach are very different and, therefore, may require preprocessing steps to determine and correct impeding irregularities. To allow for automated objective assessment, we propose a practical and comprehensive workflow involving scaling factors, a novel baseline correction scheme, and peak smoothing. The resulting spectra can then easily be compared quantitatively using similarity measures, for which we found the Pearson correlation coefficient to be the most suitable. The proposed procedure is then applied to compare the agreement of the experimental infrared spectra from the NIST Chemistry Web book with the calculated spectra using standard harmonic frequency analysis and spectra extracted from ab initio molecular dynamics simulations at different levels of theory. We conclude that the direct, quantitative comparison of calculated and measured IR spectra might become a novel, sophisticated approach to benchmark quantum-chemical methods. In the present benchmark, simulated spectra based on ab initio molecular dynamics show in general better agreement with the experiment than static calculations.

Assignment of protonated R-homocitrate in extracted FeMo-cofactor of nitrogenase via vibrational circular dichroism spectroscopies

Protonation of FeMo-cofactor is important for the process of substrate hydrogenation. Its structure has been clarified as Δ-Mo*Fe₇S₉C(R-homocit*)(cys)(Hhis) for the efforts of nearly 30 years, while it remains controversial whether FeMo-cofactor is protonated or deprotonated with chelated ≡C-O(H) homocitrate. We have used protonated molybdenum(V) lactates 1 and its enantiomer as model compounds for R-homocitrate in FeMo-cofactor of nitrogenase. Vibrational circular dichroism (VCD) spectrum of 1 at 1051 cm^-1 is attributed to ≡C-O_H vibration, and molybdenum(VI) R-lactate at 1086 cm^-1 is assigned as ≡C-O _α-alkoxy vibration. These vibrations set up labels for the protonation state of coordinated α-hydroxycarboxylates. The characteristic VCD band of NMF-extracted FeMo-cofactor is assigned to ν(C-O_H), which is based on the comparison of molybdenum(VI) R-homocitrate. Density Functional Theory calculations are in consistent with these assignments. To the best of our knowledge, this is the first time that protonated R-homocitrate in FeMo-cofactor is confirmed by VCD spectra.