Mechanisms of glycine formation in cold interstellar media: a theoretical study.

The possibility of the formation of glycine (Gly) from fundamental gas molecules in cold interstellar media was studied using quantum chemical methods, transition state theory and microcanonical molecular dynamics simulations with surface hopping dynamics (NVE-MDSH). This theoretical study emphasized five photochemical pathways in the lowest singlet-excited (S 1) state, thermochemical processes after non-radiative S 1→S 0 relaxations, and photo-to-thermal energy conversion in the NVE ensemble. The optimized reaction pathways suggested that to generate a reactive singlet dihydroxy carbene (HOCOH) intermediate, photochemical pathways involving the H2O…CO van der Waals and H2O-OC hydrogen bond precursors (Ch (1)_Step (1)) possess considerably lower energy barriers than the S 0 state pathways. The Gibbs free energy barriers (∆G ǂ ) calculated after the non-radiative S 1 →S 0 relaxations indicated higher spontaneous temperatures (T s) for the formation of the HOCOH intermediate (Ch (1)_Step (1)) than for Gly formation (Ch (1)_Step (2) and Ch (4)). Although the termolecular reaction in Ch (4) possesses a low energy barrier, and is thermodynamically favourable, the high exothermic S 1 →S 0 relaxation energy leads to the separation of the weakly associated H2O…CH2NH…CO complex into single molecules. The NVE-MDSH results also confirmed that the molecular processes after the S 1 →S 0 relaxations are thermally selective, and because the non-radiative S 1 →S 0 relaxation temperatures are exceedingly higher than T s, the formation of Gly on consecutive reaction pathways is non-synergistic with low yields and several side products. Based on the theoretical results, photo-to-thermal control strategies to promote desirable photochemical products are proposed. They could be used as guidelines for future theoretical and experimental research on photochemical reactions.

Comments on "Planar Tetracoordinate Hydrogen: Pushing the Limit of Multicentre Bonding".

In a recent communication (Angew. Chem. Int. Ed. 2024, 63, e202317312), Kalita et al. studied In4H+ system within the frame of single-reference approximation (SRA) and found that the global energy minimum (1 a) adopted the singlet state and a planar tetracoordinate hydrogen (ptH), while the second lowest isomer (1 b) located 3.0 kcal/mol above 1 a and adopted the triplet state as well as non-planar structure with a quasi-ptH. They assessed the reliability of SRA by checking the T1-diagnostic values of coupled cluster calculations. However, according to our multi-configurational second-order perturbation theory calculations at the CASPT2(12,13)/aug-cc-pVQZ (aug-cc-pVQZ-PP for In) level, both 1 a and 1 b exhibit obvious multi-referential characters, as reflected by their largest reference coefficients of 0.928 (86.1 %) and 0.938 (88.0 %), respectively. Moreover, 1 b is 5.05 kcal/mol lower than 1 a at this level, that is, what can be observed in In4H+ system is the quasi-ptH.

Thermal rate constants and kinetic isotope effects of the H + H2O2 reactions: barrier height and reaction energy from single- and multireference methods.

CONTEXT: One of the more significant sub-mechanisms of H2/O2 combustion involves the reaction of hydrogen peroxide with hydrogen atoms (H + H2O2), resulting in the production of OH + H2O (R1) and H2 + HO2 (R2) paths. Previous experimental and ab initio calculations reveal some variations in the barrier height for (R1). To improve the energetics of both (R1) and (R2), single reference and multireference ab initio methods are employed, and the rate constants and H/D kinetic isotope effects (KIEs) are calculated as a function of temperature. For (R1), the best results for the barrier height and reaction energies computed with the CASPT2(15,11)/aug-cc-pV6Z are 5.2 and - 70.3 kcal.mol-1, respectively. CCSD(T)/aug-cc-pV5Z + CV (core-valence) calculations for (R2) give 9.7 and - 15.6 kcal.mol-1 to those parameters. The CVT/SCT rate constants of both paths agree well with the fitted rate constants from uncertainty-weighted statistical analysis of the 14-mechanism of H2/O2. The kinetic isotopic effect (kH/kD) for the reaction D + H2O2 → DH + HO2 was found to be 0.47, which is in excellent agreement with the experimental value of 0.43. METHODS: The structures of reactants, transition state, and products of (R1) and (R2) are calculated with the aug-cc-pVTZ basis set and M062X DFT, CCSD(T), and CASSCF methods. The barrier heights and reaction energies of (R1) and (R2) are computed using the M06-2X, CCSD(T), MRCI, and CASPT2 methods and various basis sets. The rate constants are calculated with the variational transition state theory including multidimensional tunneling corrections (VTST-MT), with potential energy surfaces built by the M06-2X/aug-cc-pVTZ approach.

Reply to the Comments on Planar Tetracoordinate Hydrogen: Pushing the Limit of Multicentre Bonding.

Recently, Huo et al. has commented on our communication (Angew. Chem. Int. Ed. 2024, 63, e202317312, DOI: 10.1002/anie.202317312), regarding the multireference character (MRC) of our proposed cluster. Their argument is based on small HOMO-LUMO gap, fractional occupation density (FOD) and CASPT2(12,13) calculations. They also proposed that the singlet planar In4H+ cluster cannot be observed. We present our calculations which reveals that some of their arguments are based on wrong interpretation of data and inadequate use of methodology. While we certainly agree with the strong physical ground of FOD, CASSF and CASPT2 methodology, we believe that such analysis for clusters is not adequate.

Photocatalytic Reduction of CO2 to HCOOH and CO by a Phosphine-Bipyridine-Phosphine Ir(III) Catalyst: Photophysics, Nonadiabatic Effects, Mechanism, and Selectivity.

Photocatalytic CO2 reduction is one of the best solutions to solve the global energy crisis and to realize carbon neutralization. The tetradentate phosphine-bipyridine (bpy)-phosphine (PNNP)-type Ir(III) photocatalyst, Mes-IrPCY2, was reported with a high HCOOH selectivity but the photocatalytic mechanism remains elusive. Herein, we employ electronic structure methods in combination with radiative, nonradiative, and electron transfer rate calculations, to explore the entire photocatalytic cycle to either HCOOH or CO, based on which a new mechanistic scenario is proposed. The catalytic reduction reaction starts from the generation of the precursor metal-to-ligand charge transfer (3 MLCT) state. Subsequently, the divergence happens from the 3 MLCT state, the single electron transfer (SET) and deprotonation process lead to the formation of one-electron-reduced species and Ir(I) species, which initiate the reduction reaction to HCOOH and CO, respectively. Interestingly, the efficient occurrence of proton or electron transfer reduces barriers of critical steps. In addition, nonadiabatic transitions play a nonnegligible role in the cycle. We suggest a lower free-energy barrier in the reaction-limiting step and the very efficient SET in 3 MLCT are cooperatively responsible for a high HCOOH selectivity. The gained mechanistic insights could help chemists to understand, regulate, and design photocatalytic CO2 reduction reaction of similar function-integrated molecular photocatalyst.

Theoretical insights into the photophysics of an unnatural base Z: A MS-CASPT2 investigation.

We have employed the highly accurate multistate complete active space second-order perturbation theory (MS-CASPT2) method to investigate the photoinduced excited state relaxation properties of one unnatural base, namely Z. Upon excitation to the S2 state of Z, the internal conversion to the S1 state would be dominant. From the S1 state, two intersystem crossing paths leading to the T2 and T1 states and one internal conversion path to the S0 state are possible. However, considering the large barrier to access the S1 /S0 conical intersection and the strong spin-orbit coupling between S1 and T2 states (>40 cm-1 ), the intersystem crossing to the triplet manifolds is predicted to be more preferred. Arriving at the T2 state, the internal conversion to the T1 state and the intersystem crossing back to the S1 state are both possible considering the S1 /T2 /T1 three-state intersection near the T2 minimum. Upon arrival at the T1 state, the deactivation to S0 can be efficient after overcoming a small barrier to access T1 /S0 crossing point, where the spin-orbit coupling (SOC) is as large as 39.7 cm-1 . Our present work not only provides in-depth insights into the photoinduced process of unnatural base Z, but can also help the future design of novel unnatural bases with better photostability.

Modus Operandi of a Pedalo-Type Molecular Switch: Insight from Dynamics and Theoretical Spectroscopy.

Molecular switches which can be triggered by light to interconvert between two or more well-defined conformation differing in their chemical or physical properties are fundamental for the development of materials with on-demand functionalities. Recently, a novel molecular switch based on a the azodicarboxamide core has been reported. It exhibits a volume-conserving conformational change upon excitation, making it a promising candidate for embedding in confined environments. In order to rationally implement and efficiently utilize the azodicarboxamide molecular switch, detailed insight into the coordinates governing the excited-state dynamics is needed. Here, we report a detailed comparative picture of the molecular motion at the atomic level in the presence and absence of explicit solvent. Our hybrid quantum mechanics/molecular mechanics (QM/MM) excited state simulations reveal that, although the energy landscape is slightly modulated by the solvation, the light-induced motion is dominated by a bending-assisted pedalo-type motion independent of the solvation. To support the predicted mechanism, we simulate time-resolved IR spectroscopy from first principles, thereby resolving fingerprints of the light-induced switching process. Our calculated time-resolved data are in good agreement with previously reported measured spectra.

Perturbing π-clouds with Substituents to Study the Effects on Reaction Dynamics of gauche-1,3-Butadiene to Bicyclobutane Electrocyclization.

The conical intersection (CI) governs the ultra-fast relaxation of excited states in a radiationless manner and are observed mainly in photochemical processes. In the current work, we investigated the effects of substituents on the reaction dynamics for the conversion of gauche-1,3-butadiene to bicyclobutane via photochemical electrocyclization. We incorporated both electron withdrawing (-F) and donating (-CH3 ) groups in the conjugated system. In our study, we optimized the minimum energy conical intersection (MECI) geometries using the multi-configurational state-averaged CASSCF approach, whereas, to study the ground state reaction pathways for the substituted derivatives, dispersion corrected, B3LYP-D3 functional was used. The non-adiabatic surface hopping molecular dynamics simulations were performed to observe the behaviour of electronic states involved throughout the photoconversion process. The results obtained from the multi-reference second-order perturbation correction of energy at the XMS-CASPT2 level of theory, topography analysis, and non-adiabatic dynamics suggest that the -CH3 substituted derivatives can undergo faster thermal conversion to the product in the ground state with a smaller activation energy barrier compared to -F substituted derivative. Our study also reveals that the GBUT to BIBUT conversion follows both conrotatory and disrotatory pathways, whereas, on substitution with -F or -CH3 , the conversion proceeds via the conrotatory pathway.

Electronic structure and physicochemical properties of the metal and semimetal oxide nanoclusters.

Clusters are physical entities composed of a few to thousands of atoms with capabilities to develop novel materials, like cluster-assembled materials. In this sense, knowing the electronic structure and physicochemical properties of the isolated clusters can be useful to understand how they interact with other chemical species by intermolecular forces, as free, embedded, and saturated clusters, and by intramolecular forces, acting as support clusters. In this way, in the present work, the electronic structure and physicochemical properties of metal oxide nanoclusters (MgO, Al2O3, SiO2, and TiO2) were studied by highly correlated molecular quantum chemistry methods. Through the electronic state's characterization, a semiconductor aspect was found for the titania oxide nanocluster (Te < 0.8 eV) while the other agglomerates showed a characteristic of insulating material (Te > 3.3 eV). From the stability index, the following stability order can be characterized: (SiO2)4 > (Al2O3)4 > (MgO)4 > (TiO2)3. Initial information of intermolecular and intramolecular forces caused by the studied clusters was calculated through the relative electrophilicity index, which classified the (MgO)4 and (TiO2)3 clusters as the more reactive ones, in which the (MgO)4 cluster was identified as a nucleophilic species, while the (TiO2)3 cluster as an electrophilic molecule.

Mechanistic Investigation of H2 O2 -dependent Chemiluminescence from Tetrabromo-1,4-Benzoquinone.

As a H2 O2 -dependent bioluminescent substrate, tetrabromo-1,4-benzoquinone (TBBQ) was first isolated from acorn worm. The mechanism of chemiluminescence (CL) corresponding to the bioluminescence (BL) of acorn worm is largely unknown, let alone the mechanism of BL. In this article, we firstly studied the chemical and physical processes, and mechanism of H2 O2 -dependent CL from TBBQ by theoretical and experimental methods. The research results indicate: the CL process is initiated by a nucleophilic substitution reaction, which leads to the formation of an anionic dioxetane through five consecutive reactions; the anionic dioxetane decomposes to the first singlet excited state (S1 ) via a conical interaction of the potential energy surfaces (PESs) between the ground (S0 ) and S1 state; the anionic S1 -state changes to its neutral form by a proton transfer from the solvent and this neutral product is assigned as the actual luminophore. Moreover, the experimental detection of CL, . OH and the identifications of 2,3-dibromo maleic acid and 2-bromo malonic acid as the major final products provide direct evidence of the theoretically suggested mechanism. Finally, this study proves that the activity of the H2 O2 -dependent CL from TBBQ is significantly lower than the one from tetrachloro-1,4-benzoquinone (TCBQ), which is caused by the weaker electron withdrawing effect and the stronger heavy atomic effect of bromine.

Modelling Photoionisation in Isocytosine: Potential Formation of Longer-Lived Excited State Cations in its Keto Form.

Studying the effects of UV and VUV radiation on non-canonical DNA/RNA nucleobases allows us to compare how they release excess energy following absorption with respect to their canonical counterparts. This has attracted much research attention in recent years because of its likely influence on the origin of our genetic lexicon in prebiotic times. Here we present a CASSCF and XMS-CASPT2 theoretical study of the photoionisation of non-canonical pyrimidine nucleobase isocytosine in both its keto and enol tautomeric forms. We analyse their lowest energy cationic excited states including 2π+ , 2nO+ and 2nN+ and compare these to the corresponding electronic states in cytosine. Investigating lower-energy decay pathways we find - unexpectedly - that keto-isocytosine+ presents a sizeable energy barrier potentially inhibiting decay to its cationic ground state, whereas enol-isocytosine+ features a barrierless and consequently ultrafast pathway analogous to the one previously found for the canonical (keto) form of cytosine+ . Dynamic electron correlation reduces the energy barrier in the keto form substantially (by ∼1 eV) but it is nevertheless still present. We additionally compute the UV/Vis absorption signals of the structures encountered along these decay channels to provide spectroscopic fingerprints to assist future experiments in monitoring these intricate photo-processes.

Hydrogen-Bond Network Determines the Early Photoisomerization Processes of Cph1 and AnPixJ Phytochromes.

Phytochrome proteins are light receptors that play a pivotal role in regulating the life cycles of plants and microorganisms. Intriguingly, while cyanobacterial phytochrome Cph1 and cyanobacteriochrome AnPixJ use the same phycocyanobilin (PCB) chromophore to absorb light, their excited-state behavior is very different. We employ multiscale calculations to rationalize the different early photoisomerization mechanisms of PCB in Cph1 and AnPixJ. We found that their electronic S1 , T1 , and S0 potential minima exhibit distinct geometric and electronic structures due to different hydrogen bond networks with the protein environment. These specific interactions influence the S1 electronic structures along the photoisomerization paths, ultimately leading to internal conversion in Cph1 but intersystem crossing in AnPixJ. This explains why the excited-state relaxation in AnPixJ is much slower (ca. 100 ns) than in Cph1 (ca. 30 ps). Further, we predict that efficient internal conversion in AnPixJ can be achieved upon protonating the carboxylic group that interacts with PCB.

[10]annulene: Electrocyclization mechanisms.

The mechanism of 6-π electrocyclization of all-cis, mono-trans, and double-trans [10]annulene to yield 4a,8a-dihydronaphthalene has been explored at various quantum-chemical methods. The mono-trans configuration cyclizes preferentially to trans-4a,8a-dihydronaphthalene, in agreement with the experimental results. The cyclization of the all-cis configuration requires firstly a bond-shifting to the naphthalene-like conformation of double-trans [10]annulene, which is the rate-limiting step, and finally its azulene-like conformation electrocyclizes quickly to cis-4a,8a-dihydronaphthalene. Its experimental rate coefficient is consistent with the computed one for the cyclization of the all-cis configuration, unlike the calculated one for the double-trans configuration. These results confirm the configurations assigned by Masamune et al. to the two isomers which they isolated.

iSPECTRON: A simulation interface for linear and nonlinear spectra with ab-initio quantum chemistry software.

We introduce iSPECTRON, a program that parses data from common quantum chemistry software (NWChem, OpenMolcas, Gaussian, Cobramm, etc.), produces the input files for the simulation of linear and nonlinear spectroscopy of molecules with the Spectron code, and analyzes the spectra with a broad range of tools. Vibronic spectra are expressed in term of the electronic eigenstates, obtained from quantum chemistry computations, and vibrational/bath effects are incorporated in the framework of the displaced harmonic oscillator model, where all required quantities are computed at the Franck-Condon point. The program capabilities are illustrated by simulating linear absorption, transient absorption and two dimensional electronic spectra of the pyrene molecule. Calculations at two levels of electronic structure theory, time-dependent density functional theory (with NWChem) and RASSCF/RASPT2 (with OpenMolcas) are presented and compared where possible. The iSPECTRON program is available online at https://github.com/ispectrongit/iSPECTRON/ and distributed open source under the terms of the Educational Community License version 2.0 (ECL 2.0).

Is either direct photolysis or photocatalysed H-shift of peroxyl radicals a competitive pathway in the troposphere?

Peroxyl radicals (RO O . ) are key intermediates in atmospheric chemistry, with relatively long lifetimes compared to most other radical species. In this study, we use multireference quantum chemical methods to investigate whether photolysis can compete with well-established RO O . sink reactions. We assume that the photolysis channel is always RO O . + hν => RO + O(3P). Our results show that the maximal value of the cross-section for this channel is σ = 1.3 × 10-18 cm2 at 240 nm for five atmospherically representative peroxyl radicals: CH3O O . , C(O)HCH2O O . , CH3CH2O O . , HC(O)O O . and CH3C(O)O O . . These values agree with experiments to within a factor of 2. The rate constant of photolysis in the troposphere is around 10-5 s-1 for all five RO O . . As the lifetime of peroxyl radicals in the troposphere is typically less than 100 s, photolysis is thus not a competitive process. Furthermore, we investigate whether or not electronic excitation to the first excited state (D1) by infrared radiation can facilitate various H-shift reactions, leading, for example, in the case of CH3O O . to formation of O . H and CH2O or HO O . and CH2 products. While the activation barriers for H-shifts in the D1 state may be lower than in the ground state (D0), we find that H-shifts are unlikely to be competitive with decay back to the D0 state through internal conversion, as this has a rate of the order of 1013 s-1 for all studied systems.

Electronic structures of NbGen -/0/+ (n = 1-3) clusters from multiconfigurational CASPT2 and density matrix renormalization group-CASPT2 calculations.

Density functional theory and multiconfigurational CASPT2 and density matrix renormalization group DMRG-CASPT2 have been employed to study the low-lying states of NbGen -/0/+ (n = 1-3) clusters. With the DMRG-CASPT2 method, the active spaces are extended to a size of 20 orbitals. For most of the states, the CASPT2 relative energies are comparable with the DMRG-CASPT2 results. The leading configuration, bond distances, vibrational frequencies, and relative energies of the low-lying states of these clusters were calculated. The ground states of these clusters were computed to be 3 Δ, 4 Φ, and 5 Φ of NbGe-/0/+ ; 3 A2 , 4 B1 , and 3 B1 of cyclic-NbGe2 -/0/+ ; and 1 A', 12 A″ and 12 A'' (2 E), and 3 A″ of tetrahedral-NbGe3 -/0/+ isomers. For NbGe cluster, our calculations proposed that the 6 ∑ is almost degenerate with the 4 Φ with the CASPT2 and DMRG-CASPT2 relative energies of 0.05 and 0.06 eV. The adiabatic detachment energies of NbGen - (n = 1-3) clusters were estimated to be 1.46, 1.55, and 2.18 eV by the CASPT2 method. The relevant detachment energies of the anionic ground state and the ionization energies of the neutral ground states are evaluated at the CASPT2 level.

Rearrangements of Aromatic Nitrile Oxides and Nitrile Ylides: Potential Ring Expansion to Cycloheptatetraene Derivatives Mimicking Arylcarbenes.

Nitrile imines, nitrile oxides and nitrile ylides are widely used in 1,3-dipolar cycloaddition reactions. They also undergo thermal and photochemical rearrangements to carbodiimides, isocyanates, and ketenimines, respectively. Calculations at DFT and CASPT2 levels of theory reveal novel, potential rearrangements, in which the aromatic 1,3-dipoles mimic phenylcarbene and undergo ring expansion to cycloheptatetraene derivatives. These rearrangements can potentially take place in both the singlet ground states and the triplet excited states, and they are accelerated by m,m'-bis(dimethylamino) substitution on the phenyl moieties. The new rearrangement becomes the energetically preferred path for m,m'-bis(dimethylamino)benzonitrile oxide in the triplet state. In the m,m'-bis(dimethylamino)benzo nitrile ylide, the cyclization to the 2-phenyl-1-azirine is favored over the ring expansion to a cycloheptatetraene by ca. 5 kcal mol-1 in the singlet state. In the bent triplet states, 1,3-hydrogen shifts interconverting nitrile ylides are potentially possible.

Insights into the Thermal and Photochemical Reaction Mechanisms of Azidoacetonitrile. Spectroscopic and MS-CASPT2 Calculations.

This work studies the photochemical and thermal decompositions of azidoacetonitrile (N3 CH2 CN) from both the experimental and theoretical points of view. The data of the photochemical experiments are taken from the literature, while the thermal decomposition have been carried out by us. In addition, we have performed ab initio calculations of the multiconfigurational type [complete active space self-consistent field (CASSCF) and the multistate multireference perturbation theory (MS-CASPT2)]. It is found that the first step of both type of decompositions is N2 elimination and formation of closed shell singlet nitrene. Afterwards, the nitrene tends to rapidly rearrange into formimidoyl cyanide (HNCHCN). As both reactions progress, the imine isomerizes into formimidoyl isocyanide (HNCHNC). The photoisomerization of the imine takes places thorough a conical intersection, while the same reaction on the ground electronic state occurs via a conventional transition state. The last step of the global reaction is decomposition of the imines into HCN and CNH. In photochemical conditions, the conjunction of the imines and its dissociation products (HCN and CNH) yields adenine.

A Unified Experimental/Theoretical Description of the Ultrafast Photophysics of Single and Double Thionated Uracils.

Photoinduced processes in thiouracil derivatives have lately attracted considerable attention due to their suitability for innovative biological and pharmacological applications. Here, sub-20 fs broadband transient absorption spectroscopy in the near-UV are combined with CASPT2/MM decay path calculations to unravel the excited-state decay channels of water solvated 2-thio and 2,4-dithiouracil. These molecules feature linear absorption spectra with overlapping ππ* bands, leading to parallel decay routes which we systematically track for the first time. The results reveal that different processes lead to the triplet states population, both directly from the ππ* absorbing state and via the intermediate nπ* dark state. Moreover, the 2,4-dithiouracil decay pathways is shown to be strongly correlated either to those of 2- or 4-thiouracil, depending on the sulfur atom on which the electronic transition localizes.

Light-Induced Control of the Spin Distribution on Cu⁻Dithiolene Complexes: A Correlated Ab Initio Study.

Metal dithiolene complexes-M(dmit)2-are key building blocks for magnetic, conducting, and optical molecular materials, with singular electronic structures resulting from the mixing of the metal and dmit ligand orbitals. Their use in the design of magnetic and conducting materials is linked to the control of the unpaired electrons and their localized/delocalized nature. It has been recently found that UV⁻Vis light can control the spin distribution of some [Cu(dmit)2]-2 salts in a direct and reversible way. In this work, we study the optical response of these salts and the origin of the differences observed in the EPR spectra under UV⁻Vis irradiation by means of wave function-based quantum chemistry methods. The low-lying states of the complex have been characterized and the electronic transitions with a non-negligible oscillator strength have been identified. The population of the corresponding excited states promoted by the UV⁻Vis absorption produces significant changes in the spin distribution, and could explain the changes observed in the system upon illumination. The interaction between neighbor [Cu(dmit)2]-2 complexes is weakly ferromagnetic, consistent with the relative orientation of the magnetic orbitals and the crystal packing, but in disagreement with previous assignments. Our results put in evidence the complex electronic structure of the [Cu(dmit)2]-2 radical and the relevance of a multideterminantal approach for an adequate analysis of their properties.