High-level Calculations Research Articles

Cooling dynamics of energized naphthalene and azulene radical cations.

Naphthalene and azulene are isomeric polycyclic aromatic hydrocarbons (PAHs) and are topical in the context of astrochemistry due to the recent discovery of substituted naphthalenes in the Taurus Molecular Cloud-1 (TMC-1). Here, the thermal- and photo-induced isomerization, dissociation, and radiative cooling dynamics of energized (vibrationally hot) naphthalene (Np+) and azulene (Az+) radical cations, occurring over the microsecond to seconds timescale, are investigated using a cryogenic electrostatic ion storage ring, affording "molecular cloud in a box" conditions. Measurement of the cooling dynamics and kinetic energy release distributions for neutrals formed through dissociation, until several seconds after hot ion formation, are consistent with the establishment of a rapid (sub-microsecond) Np+ ⇌ Az+ quasi-equilibrium. Consequently, dissociation by C2H2-elimination proceeds predominantly through common Az+ decomposition pathways. Simulation of the isomerization, dissociation, recurrent fluorescence, and infrared cooling dynamics using a coupled master equation combined with high-level potential energy surface calculations [CCSD(T)/cc-pVTZ], reproduce the trends in the measurements. The data show that radiative cooling via recurrent fluorescence, predominately through the Np+ D0 ← D2 transition, efficiently quenches dissociation for vibrational energies up to ≈1eV above dissociation thresholds. Our measurements support the suggestion that small cations, such as naphthalene, may be more abundant in space than previously thought. The strategy presented in this work could be extended to fingerprint the cooling dynamics of other PAH ions for which isomerization is predicted to precede dissociation.

Paving the way to the synthesis of PAHs in dark molecular clouds: The formation of cyclopentadienyl radical (c-C5H5)

Context. The interest of astrophysicists and astrochemists in studying polycyclic aromatic hydrocarbons (PAHs) has grown since their assignment to previously unidentified IR emission bands of dust grains. Although observations show that PAHs are present in the interstellar medium (ISM), there is still no consensus about their formation. PAH formation has been studied following two approaches: bottom-up (i.e. through the association of smaller hydrocarbons) and top-down (via the photo-dissociation or hydrogenation of larger-structures). The recent detection of simple aromatic rings in the TMC-1 molecular cloud seems to suggest the bottom-up scenario is favoured. Aims. We study the reaction between the propargyl (C3H3) radical and the vinyl radical (C2H3) under interstellar conditions, providing new kinetic parameters for the formation of PAH precursors. Methods. We used high-level quantum-chemical calculations to describe the reaction mechanism between these two radicals. We calculated the rate constant of the individual product channels in the temperature range 10–400 K and at 1 × 10−7 atm by solving the one-dimensional master equation to quantitatively understand whether this reaction is viable in the ISM. Results. Our results show that this reaction is likely to occur even in the low-density (~104 cm−3) and low-temperature (~10 K) conditions of molecular dark clouds. The main product is the cyclopentadienyl radical (C5H5). The unsaturated open-chain hydrocarbon C5H5 in the trans (trans-C5H5) and cis conformations (cis-C5H5) are also formed, but to a lesser extent. Conclusions. Our results show that the reaction of vinyl radical with propargyl radical is efficient under interstellar conditions and yields the cyclopentadienyl radical, which could be an important precursor for the formation of more complex polycyclic hydrocarbons (e.g. indene) and simple PAHs (e.g. naphthalene) in molecular dark clouds.

Quantum Chemical Study of the Pressure-dependent Phosphorescence of [Cr(ddpd)2 ]3+ in the Solid State.

The chromium(III) complex [Cr(ddpd)2 ][BF4 ]3 shows two spin-flip emission bands in the near-infrared spectral region. These bands shift bathochromically by -14.1 and -7.7 cm-1 kbar-1 under hydrostatic pressure (Angew. Chem. Int. Ed. 2018, 57, 11069). The present study elucidates the structural changes of the chromium(III) cations under pressure using density functional theory with periodic boundary conditions and the resulting effects on the excited state energies using high-level CASSCF-NEVPT2 calculations. The differences of the bands in pressure sensitivity are traced back to a different orbital occupation of the intraconfigurational excited states.

Ro-vibrational Spectrum of Linear Dialuminum Monoxide (Al2O) at 10 μm.

Dialuminum monoxide, Al2O, has been investigated in the laboratory at mid-IR wavelengths around 10 μm at high spectral resolution. The molecule was produced by laser ablation of an aluminum target with the addition of gaseous nitrous oxide, N2O. Subsequent adiabatic cooling of the gas in a supersonic beam expansion led to rotationally cold spectra. In total, 848 ro-vibrational transitions have been assigned to the fundamental asymmetric stretching mode ν3 and to five of its hot bands, originating from excited levels of the ν1 symmetric stretching mode and the ν2 bending mode. The measurements encompass 11 vibrational energy states (v1 v2l v3). The ro-vibrational transitions show spin statistical line intensity alternation of 7:5, which is caused by two identical aluminum nuclei of spin I = 5/2 at both ends of the centrosymmetric molecule of structure Al-O-Al. The less effective cooling of vibrational states in the supersonic beam expansion allowed measurement of transitions in excited vibrational states at energies of 1000 cm-1 and higher, while rotational levels within vibrational modes exhibited thermal population, with rotational temperatures around Trot = 115 K. Molecular parameters for 11 vibrational states were derived, including rotation and centrifugal distortion constants and l-type doubling constants for the states (v1 v2l v3) = (0 11 0) and (0 11 1) and an l-type resonance between the states (0 20 0) - (0 22 0) and (0 20 1) - (0 22 1). From the experimental results, rotational correction terms and the equilibrium bond length re were derived. The measurements were supported and guided by high-level quantum-chemical calculations that agree well with the derived experimental results.

Signatures of diradicals in x-ray absorption spectroscopy.

Theoretical simulations are critical to analyze and interpret the x-ray absorption spectrum of transient open-shell species. In this work, we propose a model of the many-body core-excited states of symmetric diradicals. We apply this model to analyze the carbon K-edge transitions of o-, m-, and p-benzyne, three organic diradicals with diverse and unusual electronic structures. The predictions of our model are compared with high-level multireference computations of the K-edge spectrum of the benzynes obtained with the driven similarity renormalization group truncated to third order. Our model shows the importance of a many-body treatment of the core-excited states of the benzynes and provides a theoretical framework to understand which properties of the ground state of these diradicals can be extracted from their x-ray spectrum.

Two Shared Icosahedral Metallacarboranes through Iron: A Joint Experimental and Theoretical Refinement of Mössbauer Spectrum in [Fe(1,2-C2B9H11)2]Cs.

Mössbauer and X-ray photoelectron spectroscopies (XPS) are complemented with high-level quantum-chemical computations in the study of the geometric and electronic structure of the paramagnetic salt of the metallacarborane sandwich complex [Fe(1,2-C2B9H11)2]Cs = FeSanCs. Experimental 57Fe isomer shifts and quadrupole splitting parameters are compared with the theoretical prediction, with good agreement. The appearance of two sets of Cs(3d) doublets in the XPS spectrum, separated by 2 eV, indicates that Cs has two different chemical environments due to ease of the Cs(+) cation moving around the sandwich complex with low-energy barriers, as confirmed by quantum-chemical computations. Several minimum-energy geometries of the FeSanCs structure with the corresponding energies and Mössbauer parameters are discussed, in particular the atomic charges and spin population and the surroundings of the Fe atom in the complex. The Mössbauer spectra were taken at different temperatures showing the presence of a low-spin Fe atom with S = 1/2 and thus confirming a paramagnetic FeIII species.

Discovery of two metallic cyanoacetylides in IRC +10216: HMgCCCN and NaCCCN

We report on the detection of a series of six lines in the ultra-deep Q-band integration towards IRC +10216 carried out with the Yebes 40 m telescope, which are in harmonic relation with integer quantum numbers Ju from 12 to 18. After a detailed analysis of all possible carriers, guided by high-level quantum chemical calculations, we conclude that the lines belong to HMgCCCN, named hydridomagnesium cyanoacetylide. The rotational temperature and column density derived for HMgCCCN are 17.1 ± 2.8 K and (3.0 ± 0.6) × 1012 cm−2, respectively. The observed abundance ratio between MgCCCN and HMgCCCN is approximately three. In addition, we report the discovery in space, also towards IRC +10216, of sodium cyanoacetylide, NaCCCN, for which accurate laboratory data are available. For this species we derived a rotational temperature of 13.5 ± 1.7 K and a column density of (1.2 ± 0.2) × 1011 cm−2.

The primary gas phase hydration shell of hydroxide.

The number of water molecules in hydroxide's primary hydration shell has been long debated to be three from the interpretation of experimental data and four from theoretical studies. Here, we provide direct evidence for the presence of a fourth water molecule in hydroxide's primary hydration shell from a combined study based on high-resolution cryogenic experimental photoelectron spectroscopy and high-level quantum chemical computations. Well-defined spectra of OH-(H2O)n clusters (n=2 to 5) yield accurate electron binding energies, which are, in turn, used as key signatures of the underlying molecular conformations. Although the smaller OH-(H2O)3 and OH-(H2O)4 clusters adopt close-lying conformations with similar electron binding energies that are hard to distinguish, the OH-(H2O)5 cluster clearly has a predominant conformation with a four-coordinated hydroxide binding motif, a finding that unambiguously determines the gas phase coordination number of hydroxide to be four.

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.

Analysis of the rotationally-resolved infrared spectrum of CD379Br and CD381Br between 900 and 1400 cm−1

The infrared spectrum of CD379Br and CD381Br between 900 cm−1 and 1400 cm−1 has been analyzed at high resolution. In this region, two fundamental vibrational states, v2 = 1 and v5 = 1, an overtone state, v3 = 2, and a combination state, v3 = v6 = 1, have been analyzed for both isotopologues. As found in other halomethane molecules, strong Coriolis resonances couple the v2 = 1 state to the v5 = 1 state, and similar resonances were also used to describe the coupling found between the v5 = 1 state to the v3 = 2 state. A new determination of the K-dependent constant A0 was performed for each isotopologue through the use of perturbation-allowed transitions. The values for A0 determined from the analysis are 2.6001898(26) and 2.6001905(27) for CD379Br and CD381Br, respectively. Density functional theory calculations were performed to examine the efficacy of high-level theoretical calculations to accurately predict spectroscopic constants. The density functional theory calculations had variable success with the largest errors associated with the prediction of the ΔB rotational constants of the interacting states.

Microwave measurements, calculations, and analysis for the gas phase ammonia-formic acid dimer

The gas-phase doubly hydrogen-bonded formic acid-ammonia complex was obtained by heating a sample of ammonium formate in neon. High-level DFT and MP2 calculations with various basis sets were performed and barriers for proton tunneling and internal rotation were determined. The microwave spectrum was measured in the 7–16 GHz frequency range using a Flygare-Balle type pulsed beam Fourier transform microwave (FTMW) spectrometer. Double resonance transitions were observed near 20 GHz. Rotational transitions were measured and fitted for two vibrational states to obtain the rotational constants and quadrupole coupling constants. The rotational constants were determined to have the following values: A = 12017.0(2), B = 4337.331(2), and C = 3227.279(2) for the 0+ state and A = 12017.0, B = 4302.02(1), and C = 3238.161(1) for the 0− state and have been fit to 16 transitions and 9 transitions respectively. Each state was fit to a rigid model showing quadrupole splitting and compared with computations.

Exploring the Chemical Kinetics of the First Oxygen Addition to Di-n-Propyl Ether Radicals at Low Temperatures.

Linear ethers are promising biomass fuels with high volume energy density and high cetane number that may be used directly as alternative fuels or fuel additives in internal combustion engines. In this work, the first O2 addition reaction of the di-n-propyl ether radical was investigated using high-level quantum chemical calculations combined with the Rice-Ramsperger-Kassel-Marcus theory to solve the master equation. The potential energy surfaces of di-n-propyl ether radicals (C6H13O) with O2 were constructed at the QCISD(T)/CBS//M062X/6-311++G(d, p) level, and the rate constants were calculated for the pressure range of 0.1-100 atm and the temperature range of 300-1500 K and fitted by a modified Arrhenius formula. The calculations show that the consumption of di-n-propyl ether peroxyl radicals (C6H13O3) via the five-membered ring or six-membered ring transition-state reaction channel is most favorable. In addition, the low-temperature oxidation experiments of di-n-propyl ether were validated based on the calculations of the current work, and the results showed that the calculations were a good predictor of the experimental results.

Electronic structure, cationic, and excited states of nitrogen-containing spiroborates.

This paper presents the results of the study of the electronic structure and cationic and excited states of three spiroborate complexes (2-acetylacetonato-1,3,2-benzodioxaborol, its NH- and NMe-derivatives) and three corresponding ligands (acetylacetone, 4-aminopent-3-en-2-one, and 4-methylaminopent-3-en-2-one).Materials based on spiroborates are used in medicine, for example, as a drug carrier. In industry, spiroborate anions are used in ionic liquids and as alternative high performance lubricants. Analysis of experimental and calculated data allowed determining the influence of functional groups on the parameters of the electronic structure and energy of electronic transitions. Compared to acetylacetone and its NH- and NMe-derivatives, the upper filled molecular orbitals of the corresponding spiroborates are stabilized at 0.4-1.7eV, which is due to the positive charge of the ligand due to the acceptor properties of the dioxyphenylene fragment. Among the studied compounds, when replacing the oxygen atom in the α-position with the NH- or NMe-group, a bathochromic shift of intense bands in the absorption spectra is observed, since the energy intervals between the orbitals of the π3 and π4 ligand are reduced. In addition, in a number of spiroborates, the violation of C2v symmetry when replacing an oxygen atom leads to the appearance of a low-intensity maximum in the long-wave part of the absorption spectrum, due to the π2X → π4 transition. Complexeswere studied by photoelectron spectroscopy, absorption spectroscopy, and high-level ab initio quantum chemical computations, including the algebraic diagrammatic construction method for the polarization propagator of the second order (ADC(2)), the outer-valence Green's function (OVGF), the density functional theory(DFT), the time-dependent density functional theory(TDDFT) andthe domain-based local pair natural orbital (EOM-DLPNO) methods.X-ray photoelectronic spectra of two spiroborates in the condensed state were measured using a two-chamber high-vacuum system MXPS XP (Omicron, Germany).UV-visible absorption spectra were recorded using a spectrophotometer 2550 (Shimadzu-UV, Japan).The geometry ofallstudied compounds was optimized by the DFT/B3LYP/Def2-SVP method. The energy of electron levels in the S0 state and the distribution of electron density at each MO were obtained by the DFT/CAMB3LYP/cc-pVDZ method.The energies of excited states were obtained by the TDDFT/CAMB3LYP/cc-pVDZ, ADC(2)/cc-pVDZ and EOM-DLPNO/cc-pVDZmethods.All DFT and TDDFT calculations were carried out in the GAMESS (US)software computing package. ADC(2) calculations of excited states were performed using the Orca 4.0.1software package. EOM-DLPNO and OVGFcalculations were carried out in the Gaussian 16software package.

Bonding, Thermodynamics, and Spectroscopy of the Metal Borides UB0/+/– and WB0/+/–

The bonding and spectroscopy of the UB0/+/- and WB0/+/- molecules were examined by performing high-level electronic structure calculation on their low-lying electronic states. The calculations were performed at the SO-CASPT2 level to obtain the low-lying excited states and at the FPD level to calculate the adiabatic electronic affinities (AEA), ionization energies (IE), and bond dissociation energies (BDE). Compared to UC and UN, UB has a much denser manifold of states below 1.7 eV. The ground state of UB is predicted to be 8I5/2, and that of WB is 6Π7/2. The calculated IEs of UB and WB are 6.241 and 7.314 eV, respectively, and the corresponding AEAs are 1.160 and 1.422 eV. The BDE of UB is predicted to be 223.1 kJ/mol, which is considerably lower than those predicted for UC and UN and ∼35 kJ/mol lower than the BDE of WB. NBO calculations show that the U and B are connected by two 1-electron π bonds and one 1-electron σ bond with substantial ionic character and a bond order of 1.5. There are three unpaired electrons in the 5f on U. WB has less ionic character than UB with a doubly occupied π bond and a singly occupied σ bond for a bond order of ∼1.5. The results show that the U in UB behaves more like an actinide and the W in WB more like a transition metal.

Room-Temperature Conversion of Methane to Methanediol by [FeO2]+

Inspired by the activities of P-450 enzyme and Rieske oxygenases in nature, in which the high-valent Fe-oxo complexes play a key role for oxidation of alkanes, the oxidation process of methane by the high-valent iron oxide cation [FeO2]+ has been explored by using Fourier transform-ion cyclotron resonance (FT-ICR) mass spectrometry complemented by high-level quantum chemical calculations. In contrast to the previously reported [FeO]+/CH4 and [Fe(O)OH]+/CH4 systems, which afford [FeOH]+ as the main product, the generation of Fe+ dominates the reaction of [FeO2]+ with CH4. Theoretical calculations suggest a novel "oxygen rebound" pathway for the liberation of methanediol. In particular, the inevitable valence increase of Fe prior to C-H activation is similar to the cytochrome P-450 mediated processes. To our best knowledge, this study provides the first example of methane activation by the high-valent Fe(V)-oxo species in the gas phase, which may thus bridge the gas-phase model and the condensed-phase biosystems.

Principles of DNA cleavage in CRISPR-Cas9.

At the core of the CRISPR-Cas9 genome-editing technology, the endonuclease Cas9 introduces site-specific breaks in double-stranded DNA. In this system, the catalysis of target DNA cleavage by the highly flexible HNH domain is undefined, with two possible conformations whose catalytic relevance has remained unmet. Here, extensive molecular simulations - harnessing multi-microsecond molecular dynamics, quantum mechanics and free energy approaches - are combined with solution NMR and DNA cleavage assays to establish how the HNH nuclease is activated and cleaves the target DNA. We show that the conformation of the active state is critically dependent on the presence of Mg2+, unveiling its cardinal structural role in the organization of the active site. Solution NMR, DNA cleavage assays and molecular simulations of the Mg2+-bound HNH report on the formation of this active state, and consistently show that the protonation state of catalytic H840 is strongly affected by residue mutations within the active site. Finally, quantum mechanical simulations establish that DNA cleavage occurs through the identified active state, showing that the catalysis is activated by H840 and completed by K866, in line with DNA cleavage experiments. Overall, high-level computations, supported by experimental evaluation, resolve the catalytic mechanism and which of the known HNH conformations is responsible for target DNA cleavage in CRISPR-Cas9. This information helps enhancing the catalytic efficiency of Cas9 and its specificity, furthering the development of genome-editing tools.

Fragmentation of SO2 q+ (q = 2-4) induced by 1keV electron collision.

We report an investigation on the fragmentation dynamics of SO2 q+ (q = 2-4) induced by 1keV electron collision utilizing an ion momentum imaging spectrometer. Six complete Coulomb explosion channels were observed using the time-of-flight correlation map. The kinetic energy release distributions for these channels were obtained and compared with those available in the literature. The fragmentation mechanisms of the three-body dissociation channels were analyzed by the Dalitz plots and Newton diagrams. Both concerted breakup and sequential fragmentation pathways were identified in the channel SO2 3+ → O+ + O+ + S+, whereas only the concerted breakup mechanism was confirmed for the channels SO2 4+ → O+ + O+ + S2+ and SO2 4+ → O2+ + O+ + S+. Using the Coulomb explosion model, we determined the molecular geometry from the concerted fragmentation channels, and the obtained bond lengths and angles from the higher kinetic energy release peaks are close to that of the neutral SO2 obtained by high-level quantum chemical calculation. The present results indicate that the electron impact experiment is a potential tool for the Coulomb explosion imaging of small molecules.

Low-lying electronic states of the diatomic sodium antimonide cation

We investigate structural features, electronic characters and transition properties of NaSb+, a hitherto experimentally unknown system, by using a high-level computation methodology. Information with respect to the manifold of thirteen low-lying Λ-S electronic states, associated with both Na+ + Sb and Na + Sb+ dissociation limits, which split into twenty-four Ω states through the spin-orbit coupling effect, are well determined and analyzed. Detailed analyses of the electronic structures explain the formation of each bound Λ-S states, and the extent of perturbations originated from the spin-orbit coupling effect to the Ω states are characterized through discussions on the spin-orbit matrix elements.

UDAformer: Underwater image enhancement based on dual attention transformer

Underwater images suffer from color casts and low contrast degraded due to wavelength-dependent light scatter and abortion of the underwater environment, which impacts the application of high-level computer vision tasks. Considering the characteristics of uneven degradation and loss of color channel of underwater images, a novel dual attention transformer-based underwater image enhancement method, called UDAformer, is proposed. Specifically, Dual Attention Transformer Block (DATB) combining Channel Self-Attention Transformer (CSAT) with Pixel Self-Attention Transformer is proposed for efficient encoding and decoding of underwater image features. Then, the shifted window method for the pixel self-attention (SW-PSAT) is proposed to improve computational efficiency. Finally, the underwater images are recovered through the design of residual connections based on the underwater imaging model. Experimental results demonstrate the proposed UDAformer surpasses previous state-of-the-art methods, both qualitatively and quantitatively. The code is publicly available at: https://github.com/ShenZhen0502/UDAformer.

Resolving Discrepancies between State-of-the-Art Theory and Experiment for HO2 + HO2 via Multiscale Informatics.

Recent high-level theoretical calculations predict a mild temperature dependence for HO2 + HO2 inconsistent with state-of-the-art experimental determinations that upheld the stronger temperature dependence observed in early experiments. Via MultiScale Informatics analysis of the theoretical and experimental data, we identified an alternative interpretation of the raw experimental data that uses HO2 + HO2 rate constants nearly identical to theoretical predictions─implying that the theoretical and experimental data are actually consistent, at least when considering the raw data from experimental studies. Similar analyses of typical signals from low-temperature experiments indicate that an HOOOOH intermediate─identified by recent theory but absent from earlier interpretations─yields modest effects that are smaller than, but may have contributed to, the scatter in data among different experiments. More generally, the findings demonstrate that modern chemical theories and experiments have progressed to a point where meaningful comparison requires joint consideration of their data simultaneously.