High-level Quantum Calculations Research Articles

Dynamics of NO Release and Linkage Isomer Formation from S-Nitroso-Mercaptoethanol in Aqueous Solutions: Insights from Femtosecond Infrared Spectroscopy.

Understanding the photodynamics of S-nitroso-thiol (RSNO), an effective NO transporter in biological systems, is essential for its photochemical applications. S-nitroso-mercaptoethanol (MceSNO), a simple water-soluble RSNO, facilitates high-level quantum calculations. We investigated the photoexcitation dynamics of MceSNO in an aqueous solution, focusing on NO dissociation, recombination, and linkage isomerization using quantum calculations and femtosecond infrared spectroscopy. Upon excitation at 320 nm, MceSNO rapidly dissociates into NO and MceS radicals. Approximately 31 ± 3% of MceS reacts with unexcited MceSNO molecules, forming MceSSMce and releasing additional NO. The remaining MceS undergoes geminate recombination with NO, forming either MceSNO (41 ± 4%) or MceSON (28 ± 3%), the latter being a sulfur-ON linkage isomer observed for the first time in a room-temperature solution. MceSON isomerizes back to MceSNO in 470 ± 30 ps. The formation mechanism of MceSON was verified through a potential energy surface constructed at the CASPT2D(16,11)/cc-pVTZ level. The isomerization barrier was determined to be 3.3 ± 1.2 kcal/mol in water.

Spatially Resolved Near Field Spectroscopy of Vibrational Polaritons at the Small N Limit.

Vibrational polaritons, which have been primarily studied in Fabry-Pérot cavities with a large number of molecules (N ∼ 106-1010) coupled to the resonator mode, exhibit various experimentally observed effects on chemical reactions. However, the exact mechanism is elusively understood from the theoretical side, as the large number of molecules involved in an experimental strong coupling condition cannot be represented completely in simulations. This discrepancy between theory and experiment arises from computational descriptions of polariton systems typically being limited to only a few molecules, thus failing to represent the experimental conditions adequately. To address this mismatch, we used surface phonon polariton (SPhP) resonators as an alternative platform for vibrational strong coupling. SPhPs exhibit strong electromagnetic confinement on the surface and thus allow for coupling to a small number of molecules. As a result, this platform can enhance nonlinearity and slow down relaxation to the dark modes. In this study, we fabricated a pillar-shaped quartz resonator and then coated it with a thin layer of cobalt phthalocyanine (CoPc). By employing scattering-type scanning near-field optical microscopy (s-SNOM), we spatially investigated the dependency of vibrational strong coupling on the spatially varying electromagnetic field strength and demonstrated strong coupling with 38,000 molecules only-reaching to the small N limit. Through s-SNOM analysis, we found that strong coupling was observed primarily on the edge of the quartz pillar and the apex of the s-SNOM tip, where the maximum field enhancement occurs. In contrast, a weak resonance signal and lack of coupling were observed closer to the center of the pillar. This work demonstrates the importance of spatially resolved polariton systems in nanophotonic platforms and lays a foundation to explore polariton chemistry and chemical dynamics at the small N limit-one step closer to reconcile with high-level quantum calculations.

Calcium Chemistry in Carbon-rich Circumstellar Environments: The Laboratory and Astronomical Discovery of Calcium Dicarbide, CaC2 * * This work is based on observations done using the 100 m Green Bank Telescope (GBT), the Yebes 40 m telescope (projects 19A010, 20A017, 20B014, and 21A019), and the IRAM 30 m telescope. The 100 m GBT is an instrument of the Green Bank

Calcium dicarbide, CaC2, has been characterized at high resolution in the laboratory, and its main isotopologue, 40CaC2, has been assigned to 14 rotational emission lines between 14 and 115 GHz, including 12 previously unassigned lines, in the expanding molecular envelope of the evolved carbon star IRC+10216. Aided by high-level quantum calculations and measurements of multiple isotopologues, CaC2 is determined to be a T-shaped molecule with a highly ionic bond linking the metal atom to the C2 unit, very similar in structure to isovalent magnesium dicarbide (MgC2). The excitation of CaC2 is characterized by a very low rotational temperature of 5.8 ± 0.6 K and a kinetic temperature of 36 ± 16 K, similar to values derived for MgC2. On the assumption that the emission originates from a 30″ shell in IRC+10216, the column density of CaC2 is (5.6 ± 1.7) × 1011 cm−2. CaC2 is only the second Ca-bearing molecule besides CaNC and only the second metal dicarbide besides MgC2 identified in space. Owing to the similarity between the predicted ion–molecule chemistry of Ca and Mg, a comparison of the CaC2 abundance with that of MgC2 and related species permits empirical inferences about the radiative association–dissociative recombination processes postulated to yield metal-bearing molecules in IRC+10216 and similar objects.

H-shift and cyclization reactions in unsaturated alkylperoxy radicals near room temperature: propagating or terminating autoxidation?

The autoxidation of alkylperoxy radicals (RO2, where R is organic) is an important degradation pathway for organic compounds in a wide range of chemical systems including Earth's atmosphere. It is thought to proceed by internal H-shift reactions and, for unsaturated radicals, cyclization. However, experimental data on specific reactions steps for unsaturated RO2 is scarce. This work investigates the unimolecular reactions of 1-butenyl-O2, 1-pentenyl-O2, 1-hexenyl-O2, and 2-methyl-2-pentenyl-O2 radicals near room temperature (302 ± 3 K) experimentally, by monitoring the radicals directly, and theoretically. The experimental rate coefficients are in good agreement with those determined with high-level quantum calculations, confirming that cyclization can be competitive with H-shift in some cases. However, the products observed experimentally with two different mass spectrometers suggest that all the peroxy radicals studied lead to fast decomposition (k > 1 s-1) after the isomerization step. While the mechanisms for these decompositions could not be fully elucidated theoretically, they question whether these channels contribute to propagation or to termination of the autoxidation chains.

How Doping Affects the Activity of the Aluminum Oxide Support.

The performance of heteronuclear clusters [AlXO3 ]+ (X=Al, AlO4 , AlMg2 O2 , AlZnO, AlAu2 , Mg, Y, VO, NbO, TaO) in activating methane has been explored by a combination of high-level quantum calculations with reported and supplementary gas-phase experiments. With different dopants in [AlXO3 ]+ , the mechanism, reactivity and selectivity towards methane activation varies accordingly. The classic HAT competes with PCET, depending on the composition of intramolecular interactions. Although the existence of terminal oxygen radical is beneficial for classic HAT, the Alt -C interaction in the [AlXO3 ]+ clusters as enhanced by the strongly electronegative doping groups (X=Al, AlZnO, Mg, Zn, VO, NbO, TaO) favors the PCET process, facilitating C-H bond breaking. In addition, with different dopants, the destiny of the split methyl group varies accordingly. While strong interaction between Alt and CH3 results in the formation of the Alt -C bond, dopants with variable valance may promote the formation of deep-oxidation products like formaldehyde. It has been discussed in detail how to regulate the activity and selectivity of the active center of the catalyst via rational doping.

Spin-orbit coupling in molecular complexes beyond van der Waals regime: Key factors for further splitting of 2P3/2 ground state

We report a joint spectroscopic and theoretical study probing spin-orbit coupling (SOC) in a variety of molecular complexes between an iodine atom and a ligand (L) with L ranging from Ar, HF to formic/acetic acids, and glycine/N-methylated glycine derivatives. Cryogenic photoelectron spectroscopy of L·I- (L=HCOOH, CH3COOH) reveals three distinct peaks, identified as three SOC states, denoted as X(1/2), A(3/2), and B(l/2) for the corresponding neutrals. The X and A separation ΔEXA is measured to be 0.10 eV for both, whereas the X and B gap ΔEXB is 0.98 and 0.97 eV for formic and acetic acid, respectively. These new ΔEXA values are compared with the previously reported values for the molecular complexes L·I· with L=Ar, HF, glycine, and A-methylated glycines. All together these complexes encompass a diversity of intermolecular interactions, from van der Waals to weak and strong hydrogen bonding. While the ΔEXB remains similar, the ΔEXA is shown to be extremely sensitive to the type of ligands and interactions, spanning from 5 meV to 150 meV. High-level relativistic quantum calculations including explicit SOC formulism nicely reproduce all experimental SOC splitting. A direct correlation between the magnitude of ΔEXA with the intermolecular interaction strength or bond distance of the neutral complexes—the stronger interaction (shorter bond length), the greater splitting, is established.

Product Identification in the Low-Temperature Oxidation of Cyclohexane Using a Jet-Stirred Reactor in Combination with SVUV-PEPICO Analysis and Theoretical Quantum Calculations.

Cyclohexane oxidation chemistry was investigated using a near-atmospheric pressure jet-stirred reactor at T = 570 K and equivalence ratio ϕ = 0.8. Numerous intermediates including hydroperoxides and highly oxygenated molecules were detected using synchrotron vacuum ultraviolet photoelectron photoion coincidence spectroscopy. Supported by high-level quantum calculations, the analysis of photoelectron spectra allowed the firm identification of molecular species formed during the oxidation of cyclohexane. Besides, this work validates recently published gas chromatography and synchrotron vacuum ultraviolet photoionization mass spectrometry data. Unambiguous detection of characteristic hydroperoxides (e.g., γ-ketohydroperoxides) and their respective decomposition products provides support for the conventional O2 addition channels up to the third addition and their relative contribution to the cyclohexane oxidation. The results were also compared with the predictions of a recently proposed new detailed kinetic model of cyclohexane oxidation. Most of the predictions are in line with the current experimental findings, highlighting the robustness of the kinetic model. However, the analysis of the recorded slow photoelectron spectra indicating the possible presence of C5 species in the kinetic model provides hints that the substituted cyclopentyl radicals from cyclohexyl ring opening might play a minor role in cyclohexane oxidation. Potentially important missing reactions are also discussed.

Ab initio investigation of the ground and excited states of TcO+ and RhO+

High-level quantum calculations are utilized to analyze nineteen and thirteen lowest energy electronic states of TcO+ and RhO+. Their potential energy curves, equilibrium bond lengths, electronic excitation energies, harmonic vibrational frequencies, and anharmonicities are reported using quadruple-ζ and quintuple-ζ quality correlation consistent basis sets. The core electron correlation effects and equilibrium chemical bonding patterns of several low-energy electronic states are also considered. The ground state of TcO+ (11Ʃ+) (1σ21π41δ4) is triple bonded in nature, results adiabatically from the high energy Tc+(3P) + O(3P) fragments, and relates to the first excited state of TcO (2Σ+) (1σ22σ11π41δ4). The chemical bonding of TcO+(11Ʃ+) is identical to its isoelectronic RuO2+ (X1Ʃ+) ground state. The ground state of RhO+ (3Σ−) features a 1σ21π41δ42π2 electronic configuration. Moving from TcO+ to RhO+ the binding energy decreases by ∼15−20 kcal/mol, the metal-oxygen bond shortens by 0.07 Å, and the harmonic stretching frequency decreases by ∼170 cm−1. Bonding patterns and spectroscopic constants are compared for the neighboring species of RhO+ and TcO+.

Fast Pyrolysis of Hemicelluloses into Short-Chain Acids: An Investigation on Concerted Mechanisms

The nature of the main primary mechanisms involved in lignocellulosic fast pyrolysis is often assumed to be radical mechanisms. Here we demonstrate that thermal depolymerization of native hemicelluloses can undergo several primary and secondary concerted reactions leading to light oxygenates that can compete with radical mechanisms. To model these reactions at a microscopic level, we used high-level quantum calculations based on functional theory. In parallel, a set of experimental data was collected to confirm the main structural features of extracted and purified hemicelluloses and to describe chemical variations within fast pyrolysis products released from various hemicellulosic fractions at 823 K. In general, the barriers computed at 800 K for pericyclic reactions were found to be reasonably low competing with these of homolytic reactions. The critical role of hydrogen bonding and spatial arrangement on product distribution was clearly demonstrated, stabilizing effects depending greatly on temperature. We reported a useful data set of intrinsic kinetic parameters and a reaction network readily available to complete kinetic models for “primary” and “secondary” fast pyrolysis of hemicelluloses.

Striking Generic Impact of Light-Induced Non-Adiabaticity in Polyatomic Molecules.

Non-adiabaticity, i.e., the effect of mixing electronic states by nuclear motion, is a central phenomenon in molecular science. The strongest nonadiabatic effects arise due to the presence of conical intersections of electronic energy surfaces. These intersections are abundant in polyatomic molecules. Laser light can induce in a controlled manner new conical intersections, called light-induced conical intersections, which lead to strong nonadiabatic effects similar to those of the natural conical intersections. These effects are, however, controllable and may even compete with those of the natural intersections. In this work we show that the standard low-energy vibrational spectrum of the electronic ground state can change dramatically by inducing non-adiabaticity via a light-induced conical intersection. This generic effect is demonstrated for an explicit example by full-dimensional high-level quantum calculations using a pump-probe scheme with a moderate-intensity pump laser and a weak probe laser.

Universal crossed beam imaging studies of polyatomic reaction dynamics.

The marriage between high level quantum calculations and experimental advances in laser technology, quantum state control, and detection techniques have opened the door to the study of molecular collision dynamics at a new level of detail. However, one current challenge lies in adapting these powerful strategies to address questions beyond the scope of the small ground state systems that have largely been the focus of reaction dynamics investigations to-date. For molecules with intermediate or large size (more than 6 atoms), lack of spectroscopic information and spectral congestion limit quantum state preparation, control and detection for experiment, and the large number of degrees of freedom of the system makes accurate quantum dynamics calculations prohibitively expensive. Nevertheless, studies of the chemical dynamics of such systems can reveal novel aspects of reactivity not anticipated based upon the behavior of smaller model systems. This Perspective will highlight applications of soft vacuum ultraviolet photoionization at 157 nm as a universal probe in combination with crossed beams and DC slice velocity map ion imaging to study bimolecular reaction dynamics of molecules of intermediate or large size, illuminated with support of high-level ab initio calculations. Here, we report on the chemical dynamics of atomic oxygen or chlorine reactions with organic compounds: propanol isomers, alkylamines (N(CH3)3 and NH(CH3)2), and isobutene ((CH3)2CCH2) studied using this approach. The polyatomic radical products from the hydrogen abstraction process have been detected by 157 nm photoionization and their slice ion images embody translational energy and angular information that directly reflect the underlying collision dynamics. Various reaction mechanisms (such as direct abstraction and addition-elimination) along with the involvement of roaming dynamics and novel intersystem crossing pathways are presented. These demonstrate the power of this technique to reveal fundamentally new aspects of reaction dynamics that arise in larger reaction systems.

Direct Experimental Observation of in situ Dehydrogenation of an Amine-Borane System Using Gas Electron Diffraction.

In situ dehydrogenation of azetidine-BH3, which is a candidate for hydrogen storage, was observed with the parent and dehydrogenated analogue subjected to rigorous structural and thermochemical investigations. The structural analyses utilized gas electron diffraction supported by high-level quantum calculations, while the pathway for the unimolecular hydrogen release reaction in the absence and presence of BH3 as a bifunctional catalyst was predicted at the CBS-QB3 level. The catalyzed dehydrogenation pathway has a barrier lower than the predicted B-N bond dissociation energy, hence favoring the dehydrogenation process over the dissociation of the complex. The predicted enthalpy of dehydrogenation at the CCSD(T)/CBS level indicates that mild reaction conditions would be required for hydrogen release and that the compound is closer to thermoneutral than linear amine boranes. The entropy and free energy change for the dehydrogenation process show that the reaction is exergonic, energetically feasible, and will proceed spontaneously toward hydrogen release, all of which are important factors for hydrogen storage.

On-the-Fly Femtosecond Action Spectroscopy of Charged Cyanine Dyes: Electronic Structure versus Geometry.

Understanding optical properties of molecular dyes is required to drive progress in molecular photonics. This requires a fundamental comprehension of the role of electronic structure, geometry, and interactions with the environment in order to guide molecular engineering strategies. In this context, we studied charged cyanine dye molecules in the gas phase with a controlled microenvironment to unravel the origin of the spectral tuning of this class of molecules. This was performed using a new approach combining femtosecond multiple-photon action spectroscopy of on-the-fly mass-selected molecular ions and high-level quantum calculations. While arguments based on molecular geometry are often used to design new polymethine dyes, we provide experimental evidence that electronic structure is of primary importance and hence the decisive criterion as suggested by recent theoretical investigations.

Electron correlation\xa0driven non-adiabatic relaxation in molecules excited by an ultrashort extreme ultraviolet pulse

The many-body quantum nature of molecules determines their static and dynamic properties, but remains the main obstacle in their accurate description. Ultrashort extreme ultraviolet pulses offer a means to reveal molecular dynamics at ultrashort timescales. Here, we report the use of time-resolved electron-momentum imaging combined with extreme ultraviolet attosecond pulses to study highly excited organic molecules. We measure relaxation timescales that increase with the state energy. High-level quantum calculations show these dynamics are intrinsic to the time-dependent many-body molecular wavefunction, in which multi-electronic and non-Born−Oppenheimer effects are fully entangled. Hints of coherent vibronic dynamics, which persist despite the molecular complexity and high-energy excitation, are also observed. These results offer opportunities to understand the molecular dynamics of highly excited species involved in radiation damage and astrochemistry, and the role of quantum mechanical effects in these contexts.

Quantum mechanical investigation of the nature of nucleobase-urea stacking interaction, a crucial driving force in RNA unfolding in aqueous urea

Urea-assisted denaturation of protein and RNA has been shown to be a valuable tool to study their stabilities and folding phenomena. It has been shown that stacking interactions between nucleobases and urea are one of the driving forces of denaturation. In this study, the ability of urea to form unconventional stacking interactions with RNA bases is investigated by performing high-level quantum calculations (RI-MP2/aug-cc-pVDZ level) on a few thousands of model systems. Four systems were considered based on the RNA nucleobases (GUA, ADE, CYT, and URA) for the investigation. For each system, a set of models were designed to study the role of hetero-atoms/groups of the nucleobases on stacking interactions with urea moiety with respect to every possible pair. Several plane-parallel complexes were generated with urea on top of aromatic systems to exhaustively study all possible factors for urea-nucleobases stacking interactions. Energy decomposition analysis (EDA), atoms in molecules (AIM) and natural bond orbital (NBO) analysis were performed to gain better insights on non-covalent stacking interactions. Dispersion component was found to be heavily stabilizing, while the $$\hbox {E}_\mathrm{HF}$$ was found to be repulsive for all the four systems indicating lack of hydrogen bonding (HB) type interactions and presence of dispersion type interactions. Amide and carbonyl groups of urea molecule were found to play a major role in favourable stacking interactions. We demonstrate that along with functional groups present on the nucleobases, the orientation of urea molecules plays a vital role in stabilizing the urea-nucleobase non-covalent interactions. The proposed study quantifies and provides a comprehensive theoretical description of urea nucleobase unconventional stacking interactions which helps to unravel urea driven RNA unfolding mechanism. SYNOPSIS Position and orientation effects on the stacking interactions between the urea and nucleobases, the driving force in urea-induced RNA denaturation, were studied using quantum mechanical calculations. Dispersion effects, functional groups of the bases and orientation of urea molecules are the key contributing factors affecting these interactions.

Extending density functional embedding theory for covalently bonded systems

Quantum embedding theory aims to provide an efficient solution to obtain accurate electronic energies for systems too large for full-scale, high-level quantum calculations. It adopts a hierarchical approach that divides the total system into a small embedded region and a larger environment, using different levels of theory to describe each part. Previously, we developed a density-based quantum embedding theory called density functional embedding theory (DFET), which achieved considerable success in metals and semiconductors. In this work, we extend DFET into a density-matrix-based nonlocal form, enabling DFET to study the stronger quantum couplings between covalently bonded subsystems. We name this theory density-matrix functional embedding theory (DMFET), and we demonstrate its performance in several test examples that resemble various real applications in both chemistry and biochemistry. DMFET gives excellent results in all cases tested thus far, including predicting isomerization energies, proton transfer energies, and highest occupied molecular orbital-lowest unoccupied molecular orbital gaps for local chromophores. Here, we show that DMFET systematically improves the quality of the results compared with the widely used state-of-the-art methods, such as the simple capped cluster model or the widely used ONIOM method.

Experimental and Computational Thermochemical Study of Maleic Anhydride and Vinylene Carbonate.

The standard molar enthalpies of formation of maleic anhydride and vinylene carbonate in gaseous phase, at T = 298.15 K, were derived from the standard molar enthalpies of formation of the compounds in condensed phase combined with the phase transition enthalpies. The standard molar enthalpies of formation in condensed phase were obtained from the enthalpies of combustion measured using static bomb combustion calorimetry and mini-bomb combustion calorimetry for vinylene carbonate and maleic anhydride, respectively. Phase transition enthalpies were obtained by Calvet microcalorimetry. High level quantum calculations were performed at the composite G3 level of theory in order to estimate the standard molar enthalpies of formation of both compounds in gaseous phase. Good agreement was obtained between experimental and computational results. In addition, analysis of the factors affecting the relative stability of both systems has been carried out in the framework of the ab initio valence bond (VB) theory in order to clarify the aromaticity/antiaromaticity issues involving these molecular systems.

High-Level Quantum Calculations of the IR Spectra of the Eigen, Zundel, and Ring Isomers of H+(H2O)4 Find a Single Match to Experiment.

The protonated water tetramer H+(H2O)4, often written as the Eigen cluster, H3O+(H2O)3, plays a central role in studies of the hydrated proton. The cluster has been investigated spectroscopically both experimentally and theoretically with some differences and controversies. The major issue stems from the existence of higher-energy Zundel isomers of this cluster and the role these isomers might play in the IR spectra. Settling this fundamental issue is one goal of this Communication, where high-level quantum calculations of the IR spectra of the Eigen and three isomeric forms of this cluster are presented. These calculations make use of a many-body representation of the potential and dipole moment surfaces and VSCF/VCI calculations of vibrational eigenstates and the IR spectrum. The calculated spectra for the Eigen H3O+(H2O)3 and D3O+(D2O)3 isomers compare very well with experiment. The calculated spectra for the cis and trans-Zundel and ring isomers show prominent features that do not match with experiment but which can guide future experiments to search for these interesting and important isomers.

Germanium Dicarbide: Evidence for a T-Shaped Ground State Structure.

The equilibrium structure of germanium dicarbide GeC2 has been an open question since the late 1950s. Although most high-level quantum calculations predict an L-shaped geometry, a T-shaped or even a linear geometry cannot be ruled out because of the very flat potential energy surface. By recording the rotational spectrum of this dicarbide using sensitive microwave and millimeter techniques, we unambiguously establish that GeC2 adopts a vibrationally averaged T-shaped structure in its ground state. From analysis of 14 isotopologues, a precise r0 structure has been derived, yielding a Ge-C bond length of 1.952(1) Å and an apex angle of 38.7(2)°.

Gas-Phase Infrared and NMR Investigation of the Conformers of Diacetone Diperoxide (DADP).

Gas-phase infrared measurements of diacetone diperoxide (DADP) indicate a chair conformation with less than 5% of the predicted twist conformer. Vibrational frequencies are very similar to those previously measured in the solid state. Solution NMR measurements using 2D exchange spectroscopy (EXSY) also set a very low maximum limit on the equilibrium population of the twist conformer, with a room-temperature free-energy difference in excess of 14.5 kJ/mol. These experimental results are in accord with high-level quantum calculations incorporating full thermochemistry and solvation effects, which indicate a free-energy difference in the range of 14.7-17.5 kJ/mol in polar solvents.