Search

We present an implementation of the Frenkel exciton model into the OpenMolcas program package enabling calculations of collective electronic excited states of molecular aggregates based on a multiconfigurational wave function description of the individual monomers. The computational protocol avoids using diabatization schemes and, thus, supermolecule calculations. Additionally, the use of the Cholesky decomposition of the twoelectron integrals entering pair interactions enhances the efficiency of the computational scheme. The application of the method is exemplified for two test systems, that is, a formaldehyde oxime and a bacteriochlorophyll-like dimer. For the sake of comparison with the dipole approximation, we restrict our considerations to situations where intermonomer exchange can be neglected. The protocol is expected to be beneficial for aggregates composed of molecules with extended pi systems, unpaired electrons such as radicals or transition metal centers, where it should outperform widely used methods based on time-dependent density functional theory.

The unconventional carbon dioxide insertion reaction of a gold-aluminyl [tBu3PAuAl(NON)] complex has been recently shown to be related to the electron-sharing character of the Au-Al bond that acts as a nucleophile and stabilizes the insertion product through a radical-like behavior. Since a gold-diarylboryl [IPrAuB(o-tol)2] complex with similar reactivity features has been recently reported, in this work we computationally investigate the reaction of carbon dioxide with [LAuX] (L = phosphine, N-heterocyclic carbene (NHC); X = Al(NON), B(o-tol)2) complexes to get insights into the Al/B anionic and gold ancillary ligand effects on the Au-Al/B bond nature, electronic structure, and reactivity of these compounds. We demonstrate that the Au-Al and Au-B bonds possess a similar electron-sharing nature, with diarylboryl complexes displaying a slightly more polarized bond as Au(δ+)-B(δ-). This feature reduces the radical-like reactivity toward CO2, and the Al/B anionic ligand effect is found to favor aluminyls over boryls, despite the greater oxophilicity of B. Remarkably, the ancillary ligand of gold has a negligible electronic trans effect on the Au-X bond and only a minor impact on the formation of the insertion product, which is slightly more stable with carbene ligands. Surprisingly, we find that the modification of the steric hindrance at the carbene site may exert a sizable control over the reaction, with more sterically hindered ligands thermodynamically disfavoring the formation of the CO2 insertion product.

Poly(delta-valerolactone) (PVL) was synthesized by ring-opening polymerization (ROP), employing tin(II) acetate (SnAcet(2)), lead(II) acetate trihydrate (PbAcet(2)center dot 3H(2)O) and cadmium(II) acetate dihydrate (CdAcet(2)center dot 2H(2)O) complexes as initiators without any co-initiator. The highest molecular weight PVL (45 438 g mol(-1), 91% yield) was obtained with CdAcet(2)center dot 2H(2)O. Characterization of the synthesized products was performed by FTIR, H-1 NMR, C-13 NMR, gel permeation chromatography (GPC), matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF/TOF MS), TGA and DSC. Electrostatic data (natural bond orbital and Hirshfeld) and lowest unoccupied molecular orbital (LUMO) of the initiators were obtained by using several density functional theory methods (B3LYP, omega B97X-D, PBEPBE, BPV86, HSEH1PBE, MPW1PW91, M06 and M062X). In addition, the initiation stage of the ROP mechanism of delta-valerolactone with these metal acetate complexes was investigated at the omega B97X-D level with a mixed basis set. It was computationally determined that the most effective initiator was also CdAcet(2). The molecular weight variation of PVLs synthesized with these initiators can be associated with the combined evaluation of atomic charge, LUMO and orbital overlap analyses. The computationally obtained reaction barriers for the initiators support this idea, also. In addition, toxicity tests carried out for PVLs synthesized with acetate complexes containing Sn, Cd and Pb revealed that the Sn and Cd complexes do not have a toxic effect on cell viability at some dilution rates. (C) 2021 Society of Industrial Chemistry., Research Foundation of Ege University, Turkey [2016 FEN 041]; Ege University Planning and Monitoring Coordination of Organizational Development; Ege University Directorate of Library and Documentation, This work was supported by the Research Foundation of Ege University, Turkey (No. 2016 FEN 041). The DFT calculations reported in this study were performed at TUBITAK ULAKBIM, High Performance and Grid Computing Center (TRUBA resources). We are grateful to Ege University Planning and Monitoring Coordination of Organizational Development and the Directorate of Library and Documentation for their support in the editing and proofreading service of this study.

Vision is initiated by the rhodopsin family of light-sensitive G protein-coupled receptors (GPCRs). A photon is absorbed by the 11-cis retinal chromophore of rhodopsin, which isomerizes within 200 femtoseconds to the all-trans conformation, thereby initiating the cellular signal transduction processes that ultimately lead to vision. However, the intramolecular mechanism by which the photoactivated retinal induces the activation events inside rhodopsin remains experimentally unclear. Here we use ultrafast time-resolved crystallography at room temperature to determine how an isomerized twisted all-trans retinal stores the photon energy that is required to initiate the protein conformational changes associated with the formation of the G protein-binding signalling state. The distorted retinal at a 1-ps time delay after photoactivation has pulled away from half of its numerous interactions with its binding pocket, and the excess of the photon energy is released through an anisotropic protein breathing motion in the direction of the extracellular space. Notably, the very early structural motions in the protein side chains of rhodopsin appear in regions that are involved in later stages of the conserved class A GPCR activation mechanism. Our study sheds light on the earliest stages of vision in vertebrates and points to fundamental aspects of the molecular mechanisms of agonist-mediated GPCR activation., 視覚に関わるタンパク質の超高速分子動画 --薄暗いところで光を感じる仕組み--. 京都大学プレスリリース. 2023-03-23.

Novel seven‐membered cyclic imine‐based 1,3‐P,N ligands were obtained by capturing a Beckmann nitrilium ion intermediate generated in situ from cyclohexanone with benzotriazole, and then displacing it by a secondary phosphane under triflic acid promotion. These “cycloiminophosphanes” possess flexible non‐isomerizable tetrahydroazepine rings with a high basicity; this sets them apart from previously reported iminophophanes. The donor strength of the ligands was investigated by using their P‐κ1‐ and P,N‐κ2‐tungsten(0) carbonyl complexes, by determining the IR frequency of the trans‐CO ligands. Complexes with [RhCp*Cl2]2 demonstrated the hemilability of the ligands, giving a dynamic equilibrium of κ1 and κ2 species; treatment with AgOTf gives full conversion to the κ2 complex. The potential for catalysis was shown in the RuII‐catalyzed, solvent‐free hydration of benzonitrile and the RuII‐ and IrI‐catalyzed transfer hydrogenation of cyclohexanone in isopropanol. Finally, to enable access to asymmetric catalysts, chiral cycloiminophosphanes were prepared from l‐menthone, as well as their P,N‐κ2‐RhIII and a P‐κ1‐RuII complexes., Complexes, chirality and catalysts: 1,3‐P,N hybrid ligands are broadly applied in cooperative catalysis, but show limited electronic variation. We report novel analogues with a high N‐basicity, based on 7‐membered cyclic imines. Their transition metal complexes demonstrated their donor strength (W), hemilabile coordination (Rh), and catalytic activity for nitrile hydration (Ru) and transfer hydrogenation (Ru, Ir). Chiral derivatives were also obtained, synthesized from l‐menthone.

Spectroscopic and computational examination of a homologous series of rhodium(I) pybox carbonyl complexes has revealed a correlation between the conformation of the flanking aryl-substituted oxazoline donors and the carbonyl stretching frequency. This relationship is also observed experimentally for octahedral rhodium(III) and ruthenium(II) variants and cannot be explained through the classical, Dewar-Chatt-Duncanson, interpretation of metal-carbonyl bonding. Instead, these findings are reconciled by local changes in the magnitude of the electric field that is projected along the metal-carbonyl vector: the internal Stark effect. ispartof: CHEMISTRY-A EUROPEAN JOURNAL vol:28 issue:69 ispartof: location:Germany status: published

Herein, we describe the synthesis, full spectroscopic characterization, DFT (density functional theory) calculations, and single-crystal X-ray diffraction analyses of a series of osmium arene sigma-germyl, germanate, sigma-stannyl, and stannate complexes, along with their cytotoxic (anticancer) investigations. The known dimer complexes [OsCl2(eta(6)-C6H6)](2) (1) and [OsCl2(eta(6)-p-cymene)](2) (2) were reacted with PPh3 to form the known mononuclear complex [OsCl2(eta(6)-p-cymene)(PPh3)] (3) and the new complex [OsCl2(eta(6)-C6H6)(PPh3)] (6); complex 3 was reacted with GeCl2 center dot(dioxane) and SnCl2 to afford, by insertion into the Os-Cl bond, the neutral sigma-germyl and stannyl complexes [OsCl(eta(6)-p-cymene)(PPh3)(GeCl3)] (7) and [OsCl(eta(6)-p-cymene)(PPh3)(SnCl3)] (11), respectively, as a mixture of enantiomers. Similarly, the reaction of complex 6 with GeCl2 center dot(dioxane) afforded [OsCl(eta(6)-C6H6)(PPh3)(GeCl3)] (9). Complex 2, upon reaction with 1,1-bis(diphenylphosphino)methane (dppm), formed a mixture of [OsCl2(eta(6)-p-cymene)(kappa(1)-dppm)] (4) and [Os(eta(6)-p-cymene)(kappa(2)-dppm)Cl]Cl-+(-) (5) when prepared in acetonitrile and a mixture of 4 and the dinudear complex [[OsCl2(eta(6) -p-cymene)](2) (mu-dppm)] (0) when prepared in dichloromethane. By utilizing either isolated 4 or a mixture of 4 and 5, the synthesis of kappa(2)-dppm germanate and stannate salts, [OsCl(eta(6)-p-cymene)(kappa(2)-dppm)]+GeCl3- (8) and [OsCl(eta(6)-p-cymene)(kappa(2)-dppm)]+SnCl3- (10), were accomplished via halide-abstracting reactions with GeCl2 center dot(dioxane) or SnCl2, respectively. All resulting complexes were characterized by means of multinuclear NMR, FT-IR, ESI-MS, and UV/Vis spectroscopy. X-ray diffraction analyses of 4, 8, 9, 10, and 11 were performed and are reported. DFT studies (B3LYP, basis set LANL2DZ for Os, and def2-TZVPP for Sn, Ge, Cl, P, C, and H) were performed on complex 9 and the benzene analogue of complex 11, 11-benzene, to evaluate the structural changes and the effects on the frontier molecular orbitals arising from the substitution of Ge for Sn. Finally, complexes 3 and 7-11 were investigated for potential anticancer activities considering cell cytotoxicity and apoptosis assays against Dalton's lymphoma (DL) and Ehrlich ascites carcinoma (EAC) malignant cancer cell lines. The complexes were also tested against healthy peripheral blood mononudear cells (PBMCs). All cell lines were also treated with the reference drug cisplatin to draw a comparison with the results obtained from the reported complexes. The study was further corroborated with in silica molecular interaction simulations and a pharmacokinetic study.

A series of neutral LM (L = [HC{(H3C)C(Dipp)N}(2)], Dipp = 2,6-(Pr2C6H3)-Pr-i, M = group 13: B-In, TM: Fe, Co, Ni, Cu) and L'M (L' = [HC{(CvCH(2))(CCH3)(DippN)(2)}], M = group 14: C-Pb) compounds including a main group 13/14 and first-row transition metal complexes were studied computationally by density functional theory (DFT). The optimised complexes were assessed in terms of structural parameters and electronic structures to find trends and characteristics that could be used to predict their reactivity towards ammonia. In addition, the differences in oxidative addition and Werner coordination complex formation depending on the identity of the central element were investigated and the Werner complexes were evaluated by QTAIM and EDA-NOCV approaches. The computational results complement the earlier experimental studies and shed light on the feasibility of isolating novel main group Werner complexes or transition metal oxidative addition products.

The nuclear quadrupole interaction (NQI) of quadrupolar nuclei in molecules in the gas phase has recently been quantified experimentally by the technique of Perturbed Angular Correlation (PAC) spectroscopy. Interpretation of the NQI data must rely on high-level electronic structure methods for the calculation of the electric field gradient (EFG). These calculations commonly omit contributions from anharmonicity, rovibrational coupling and (if applicable) decay-induced nuclear recoil to the molecular structure and the response of the EFG. Here we choose an alternative approach, conducting Born-Oppenheimer molecular dynamics (BOMD) simulations, and account for the effects of molecular motion on the EFG. We apply this approach to the analysis of PAC spectroscopic data recorded for gas phase CdI2 (Haas et al., 2021). With this methodology, we obtain a value of the nuclear quadrupole moment Q(Cd-111, 5/2(+)) = 0.656(7) b.

Binding affinity prediction by means of computer simulation has been increasingly incorporated in drug discovery projects. Its wide application, however, is limited by the prediction accuracy of the free energy calculations. The main error sources are force fields used to describe molecular interactions and incomplete sampling of the configurational space. Organic host-guest systems have been used to address force field quality because they share similar interactions found in ligands and receptors, and their rigidity facilitates configurational sampling. Here, we test the binding free energy prediction accuracy for 14 guests with an aromatic or adamantane core and the CB7 host using molecular electron density derived nonbonded force field parameters. We developed a computational workflow written in Python to derive atomic charges and Lennard-Jones parameters with the Minimal Basis Iterative Stockholder method using the polarized electron density of several configurations of each guest in the bound and unbound states. The resulting nonbonded force field parameters improve binding affinity prediction, especially for guests with an adamantane core in which repulsive exchange and dispersion interactions to the host dominate.

Using a combination of quantum chemistry and cluster size distribution dynamics, we study the heterogeneous nucleation of n-butanol and water onto sodium chloride (NaCl)(10) seeds at different butanol saturation ratios and relative humidities. We also investigate how the heterogeneous nucleation of butanol is affected by the seed size through comparing (NaCl)(5), (NaCl)(10), and ( NaCl)(25) seeds and by seed electrical charge through comparing (Na10Cl9)(+), (NaCl)(10), and (Na9Cl10)(-) seeds. Butanol is a common working fluid for condensation particle counters used in atmospheric aerosol studies, and NaCl seeds are frequently used for calibration purposes and as model systems, for example, sea spray aerosol. In general, our simulations reproduce the experimentally observed trends for the NaCl-BuOH-H2O system, such as the increase of nucleation rate with relative humidity and with temperature (at constant supersaturation of butanol). Our results also provide molecular-level insights into the vapor-seed interactions driving the first steps of the heterogeneous nucleation process. The main purpose of this work is to show that theoretical studies can provide molecular understanding of initial steps of heterogeneous nucleation and that it is possible to find cost-effective yet accurate-enough combinations of methods for configurational sampling and energy evaluation to successfully model heterogeneous nucleation of multicomponent systems. In the future, we anticipate that such simulations can also be extended to chemically more complex seeds.

The recombination ("dimerization") of peroxyl radicals (RO2 center dot) is one of the pathways suggested in the literature for the formation of peroxides (ROOR', often referred to as dimers or accretion products in the literature) in the atmosphere. It is generally accepted that these dimers play a major role in the first steps of the formation of submicron aerosol particles. However, the precise reaction pathways and energetics of RO2 center dot + R'O-2 center dot reactions are still unknown. In this work, we have studied the formation of tetroxide intermediates (RO4R'): their formation from two peroxyl radicals and their decomposition to triplet molecular oxygen (O-3(2)) and a triplet pair of alkoxyl radicals (RO center dot). We demonstrate this mechanism for several atmospherically relevant primary and secondary peroxyl radicals. The potential energy surface corresponds to an overall singlet state. The subsequent reaction channels of the alkoxyl radicals include, but are not limited to, their dimerization into ROOR'. Our work considers the multiconfigurational character of the tetroxides and the intermediate phases of the reaction, leading to reliable mechanistic insights for the formation and decomposition of the tetroxides. Despite substantial uncertainties in the computed energetics, our results demonstrate that the barrier heights along the reaction path are invariably small for these systems. This suggests that the reaction mechanism, previously validated at a multireference level only for methyl peroxyl radicals, is a plausible pathway for the formation of aerosol-relevant larger peroxides in the atmosphere.

Water and its interactions with metals are closely bound up with human life, and the reactivity of metal clusters with water is of fundamental importance for the understanding of hydrogen generation. Here a prominent hydrogen evolution reaction (HER) of single water molecule on vanadium clusters Vn+ (3 ≤ n ≤ 30) is observed in the reaction of cationic vanadium clusters with water at room temperature. The combined experimental and theoretical studies reveal that the wagging vibrations of a V-OH group give rise to readily formed V-O-V intermediate states on Vn+ (n ≥ 3) clusters and allow the terminal hydrogen to interact with an adsorbed hydrogen atom, enabling hydrogen release. The presence of three metal atoms reduces the energy barrier of the rate-determining step, giving rise to an effective production of hydrogen from single water molecules. This mechanism differs from dissociative chemisorption of multiple water molecules on aluminium cluster anions, which usually proceeds by dissociative chemisorption of at least two water molecules at multiple surface sites followed by a recombination of the adsorbed hydrogen atoms. Metal clusters are known to catalyze hydrogen evolution from water, but reaction mechanisms and reactivities are still not fully understood. Here, mass spectrometry of cationic vanadium clusters reacting with water vapor shows significant hydrogen evolution reactions for V3+, V5+ and V9+ that point to a hydrogen release mechanism from the transition metal cluster cations.

Atomic layer deposition (ALD) is a viable method for depositing functional, passivating, and encapsulating layers on top of halide perovskites. Studies in that area have only focused on metal oxides, despite a great number of materials that can be made with ALD. This work demonstrates that, in addition to oxides, other ALD processes can be compatible with the perovskites. We describe two new ALD processes for lead sulfide. These processes operate at low deposition temperatures (45-155 °C) that have been inaccessible to previous ALD PbS processes. Our processes rely on volatile and reactive lead precursors Pb(dbda) (dbda = rac-N2,N3-di-tert-butylbutane-2,3-diamide) and Pb(btsa)2 (btsa = bis(trimethylsilyl)amide) as well as H2S. These precursors produce high quality PbS thin films that are uniform, crystalline, and pure. The films exhibit p-type conductivity and good mobilities of 10-70 cm² V-1 s-1. Low deposition temperatures enable direct ALD of PbS onto a halide perovskite CH3NH3PbI3 (MAPI) without its decomposition. The stability of MAPI in ambient air is greatly improved by capping with ALD PbS. More generally, these new processes offer valuable alternatives for PbS-based devices, and we hope that this study will inspire more studies on ALD of non-oxides on halide perovskites.

The reaction of the intramolecular frustrated Lewis pair (FLP) tBu2PCH2BPh2 with the amine-boranes NH3 center dot BH3 and Me2NH center dot BH3 leads to the formation of the corresponding FLP-H2 adducts as well as novel five-membered heterocycles that result from capturing the in situ formed amino-borane by a second equivalent of FLP. The sterically more demanding tBu2PCH2BMes2 does not form such a five-membered heterocycle when reacted with Me2NH•BH3 and its H2 adduct liberates dihydrogen at elevated temperatures, promoting the metal-free catalytic dehydrogenation of amine-boranes.

The equilibrium structures and optical properties of the photolabile caged luciferin, (7-diethylaminocoumarin-4-yl)methyl caged D-luciferin (DEACM-caged D-luciferin), in aqueous solution were investigated via quantum chemical calculations. The probable conformers of DEACM-caged D-luciferin were determined by potential energy curve scans and structural optimizations. We identified 40 possible conformers of DEACM-caged D-luciferin in water by comparing the Gibbs free energy of the optimized structures. Despite the difference in their structures, the conformers were similar in terms of assignments, oscillator strengths and energies of the three low-lying excited states. From the concentrations of the conformers and their oscillator strengths, we obtained a theoretical UV/Vis spectrum of DEACM-caged D-luciferin that has two main bands of shape nearly identical to the experimental UV/Vis spectrum. The absorption bands with maxima similar to 384 and 339 nm were attributed to the electronic excitations of the caged group and the luciferin moiety, respectively, by analysis of the theoretical UV/Vis spectrum. Furthermore, the analysis showed that DEACM-caged D-luciferin is excited in the caged group only by light of wavelength ranging within 400-430 nm, which is in the long-wavelength tail of the 384 nm band. This should be tested to lower damage upon photocleavage.

A structurally new heptadentate derivative of a 15-membered pyridine-based macrocycle containing two benzimidazol-2-yl-methyl N-pendant arms (L = 3,12-bis((1H-benzimidazol-2-yl)methyl)-6,9-dioxa-3,12,18-triazabicyclo[12.3.1]octadeca-1(18),14,16-triene) was synthesized and its complexes with the general formula [M(L)](ClO4)(2)center dot 1.5CH(3)NO(2) (M = Mn-II (1), Fe-II (2), Co-II (3) and Ni-II (4)) were thoroughly investigated. X-ray crystal structures confirmed that all complexes are seven-coordinate with axially compressed pentagonal bipyramidal geometry having the largest distortion for Ni-II complex 4. Fe-II, Co-II and Ni-II complexes 2, 3 and 4 show rather large magnetic anisotropy manifested by moderate to high obtained values of the axial zero-field splitting parameter D (7.9, 40.3, and -17.2 cm(-1), respectively). Magneto-structural correlation of the Fe-II, Co-II and Ni-II complexes with L and with previously studied structurally similar ligands revealed a significant impact of the functional group in pendant arms on the magnetic anisotropy especially that of the Co-II and Ni-II complexes and some recommendations concerning the ligand-field design important for anisotropy tuning in future. Furthermore, complex 3 showed field-induced single-molecule magnet behavior described with the Raman (C = 507 K-n s(-1) for n = 2.58) relaxation process. The magnetic properties of the studied complexes were supported by theoretical calculations, which very well correspond with the experimental data of magnetic anisotropy. Electrochemical measurements revealed high positive redox potentials for M3+/2+ couples and high negative redox potentials for M2+/+ couples, which indicate the stabilization of the oxidation state +II expected for the sigma-donor/pi-acceptor ability of benzimidazole functional groups.

A generating function method was used to simulate the vibrationally resolved absorption and emission spectra of perylene, terrylene and quaterrylene. This method operates on the basis of adiabatic excitation energies and electronic ground and excited state vibrational frequencies. These parameters were calculated using density functional theory with the PBE0 functional for perylene and terrylene and with the BH-LYP functional for quaterrylene. The vertical excitation energies of the lower excited states were calculated using functionals with differing amounts of Hartree-Fock exchange. The optimal functional for each molecule was chosen by comparing these energies to literature excitation energies. Using this technique the calculated absorption spectra and the calculated emission spectrum of perylene were found to be in excellent agreement with the literature experimental spectra after introducing a shift and a scaling factor. The most prominent bands of the absorption spectra were assigned to their respective vibronic transitions.

We report on the C K-edge x-ray absorption spectra and the resonant (RXES) and non-resonant (NXES) x-ray emission spectra of ethylene, allene and butadiene in the gas phase. The RXES and NXES show clear differences for the different molecules. Overall both types of spectra are more structured for ethylene and allene, than for butadiene. Using density functional theory–restricted open shell configuration interaction single calculations, we simulate the spectra with remarkable agreement with the experiment. We identify the spectral features as being due to transitions involving localised 1s orbitals. For allene, there are distinct spectral bands that reflect transitions predominantly from either the central or terminal carbon atoms. These results are discussed in the context of ultrafast x-ray studies aimed at detecting the passage through conical intersections in polyatomic molecules.

The electronic structure and stability of M '@M-n systems is considered using DFT. The metal atom M ' is a rare earth, actinide, or a d transition metal, and M is a coinage (Group 11) metal. The sigma aromaticity along the M-n ring is emphasized. As a further indicator for it, the magnetically induced currents along the ring are studied, and found to be considerably larger than the aromatic pi currents in benzene. A name saturnenes is suggested for these atom-inside-ring systems. Attention is also called for the known analogous stick-inside-ring systems.

Structural chemistry 34(1), 203 - 213 (2023). doi:10.1007/s11224-022-02053-4, Here, we present new cryogenic infrared spectra of the (Imidazole)$_nH^+$ (n=1,2,3) ions. The data was obtained using helium tagging infrared predissociation spectroscopy. The new results were compared with the data obtained by Gerardi et al. (Chem. Phys. Lett. 501:172–178, 2011) using the same technique but with argon as a tag. Comparison of the two experiments, assisted by theoretical calculations, allowed us to evaluate the preferable attachment positions of argon to the (Imidazole)$_nH^+$ frame. Argon attaches to nitrogen-bonded hydrogen in the case of the (Imidazole)H+ ion, while in (Imidazole)$_2H^+$ and (Imidazole)$_3H^+$ the preferred docking sites for the argon are in the center of the complex. This conclusion is supported by analyzing the spectral features attributed to the N–H stretching vibrations. Symmetry adapted perturbation theory (SAPT) analysis of the non-covalent forces between argon and the (Imidazole)$_nH^+$ (n=1,2,3) frame revealed that this switch of docking preference with increasing complex size is caused by an interplay between induction and dispersion interactions., Published by Springer Science Business Media B.V., Dordrecht

Cyclo[n]carbons (n = 5, 7, 9,..., 29) composed from an odd number of carbon atoms are studied computationally at density functional theory (DFT) and ab initio complete active space self-consistent field (CASSCF) levels of theory to get insight into their electronic structure and aromaticity. DFT calculations predict a strongly delocalized carbene structure of the cyclo[n]carbons and an aromatic character for all of them. In contrast, calculations at the CASSCF level yield geometrically bent and electronically localized carbene structures leading to an alternating double aromaticity of the odd-number cyclo[n]carbons. CASSCF calculations yield a singlet electronic ground state for the studied cyclo[n]carbons except for C25, whereas at the DFT level the energy difference between the lowest singlet and triplet states depends on the employed functional. The BHandHLYP functional predicts a triplet ground state of the larger odd-number cyclo[n]carbons starting from n = 13. Current-density calculations at the BHandHLYP level using the CASSCFoptimized molecular structures show that there is a through-space delocalization in the cyclo[n]carbons. The current density avoids the carbene carbon atom, leading to an alternating double aromaticity of the oddnumber cyclo[n]carbons satisfying the antiaromatic [4k+1] and aromatic [4k+3] rules. C11, C15, and C19 are aromatic and can be prioritized in future synthesis. We predict a bond-shift phenomenon for the triplet state of the cyclo[n]carbons leading to resonance structures that have different reactivity toward dimerization. Funding Agencies|Swedish Research Council [2020-04600]; Academy of Finland [325369, 314821]; Danish Council for Independent Research [DFF4181-00206, 9040-00265]; VILLUM FONDEN [40871]; Russian Scientific Foundation [18-19-00268-Pi]

Fragmentation is an important decay mechanism for polycyclic aromatic hydrocarbons (PAHs) under harsh interstellar conditions and represents a possible formation pathway for small molecules such as H2, C2H2, C2H4. Our aim is to investigate the dissociation mechanism of superhydrogenated PAHs that undergo energetic processing and the formation pathway of small hydrocarbons. We obtain, experimentally, the mass distribution of protonated tetrahydropyrene (C16H15 , py+5H+) and protonated hexahydropyrene (C16H17+, py+7H+) upon collision induced dissociation (CID). The IR spectra of their main fragments are recorded by infrared multiple-photon dissociation (IRMPD). Extended tight-binding (GFN2-xTB) based molecular dynamics simulations are performed in order to provide the missing structure information in experiment and identify fragmentation pathways. The pathways for fragmentation are further investigated at a hybrid-density functional theory (DFT) and dispersion corrected level. A strong signal for loss of 28 mass units of py+7H+ is observed both in the CID experiment and the MD simulation, while py+5H+ shows negligible signal for the product corresponding to a mass loss of 28. The 28 mass loss from py+7H+ is assigned to the loss of ethylene (C2H4) and a good fit between the calculated and experimental IR spectrum of the resulting fragment species is obtained. Further DFT calculations show favorable kinetic pathways for loss of C2H4 from hydrogenated PAH configurations involving three consecutive CH2 molecular entities. This joint experimental and theoretical investigation proposes a chemical pathway of ethylene formation from fragmentation of superhydrogenated PAHs. This pathway is sensitive to hydrogenated edges (e.g. the degree of hydrogenation and the hydrogenated positions). The inclusion of this pathway in astrochemical models may improve the estimated abundance of ethylene., 11 pages, 6 figures

Density functional theory (DFT) is used in this work to predict the mechanism for constructing congested quaternary-quaternary carbon(sp3)-carbon(sp3) bonds in a pentanidium-catalyzed substitution reaction. Computational mechanistic studies were carried out to investigate the proposed SN2X manifold, which consists of two primary elementary steps: halogen atom transfer (XAT) and subsequent SN2. For the first calculated model on original experimental substrates, XAT reaction barriers were more kinetically competitive than an SN2 pathway and connect to thermodynamically stable intermediates. Extensive computational screening modeling was then done on various substrate combinations designed to study the steric influence and to understand the mechanistic rationale, and calculations reveal that sterically congested substrates prefer the SN2X manifold over SN2. Different halides as leaving groups were also screened, and it was found that the reactivity increases in the order of I > Br > Cl > F, in agreement with the strength of C-X bonds. However, DFT modeling suggests that chlorides can be a viable substrate for the SN2X process, which should be further explored experimentally. ONIOM calculations on the full catalyst model predicted the correct stereochemical outcome, and further catalyst screening with cationic Me4N+ and K+ predicted that pentanidium is still the choice for SN2X C-C bond formation. Ministry of Education (MOE) Nanyang Technological University We gratefully acknowledge financial support from the Australian Research Council (DE210100053, R.L.), UOW RITA Grant 2021 (H.Y. and R.L.), and a UOW Vice Chancellor's Research Fellowship (R.L.). We would also like to acknowledge Nanyang Technological University for Tier 1 grants (RG1/19 and RG2/20) and Ministry of Education (Singapore) Tier 2 grants (MOE2019-T2-1-091, C.H.T.).

Acyl glucuronide metabolites have been implicated in the toxicity of several carboxylic acid-containing drugs, and the rate of their degradation via intramolecular transacylation and hydrolysis has been associated with the degree of protein adduct formation. Although not yet proven, the formation of protein adducts in vivo - and subsequent downstream effects - has been proposed as a mechanism of toxicity for carboxylic acid-containing xenobiotics capable of forming acyl glucuronides. A structurally-related series of metabolites, the acyl glucosides, have also been shown to undergo similar degradation reactions and consequently the potential to display a similar mode of toxicity. Here we report detailed kinetic models of each transacylation and hydrolysis reaction for a series of phenylacetic acid acyl glucuronides and their analogous acyl glucosides. Differences in reactivity were observed for the individual transacylation steps between the compound series; our findings suggest that the charged carboxylate ion and neutral hydroxyl group in the glucuronide and glucoside conjugates, respectively, are responsible for these differences. The transacylation reaction was modelled using density functional theory and the calculated activation energy for this reaction showed a close correlation with the degradation rate of the 1-β anomer. Comparison of optimised geometries between the two series of conjugates revealed differences in hydrogen bonding which may further explain the differences in reactivity observed. Together, these models may find application in drug discovery for prediction of acyl glucuronide and glucoside metabolite behaviour.

Explicit-electron force fields introduce electrons or electron pairs as semiclassical particles in force fields or empirical potentials, which are suitable for molecular dynamics simulations. Even though semiclassical electrons are a drastic simplification compared to a quantum-mechanical electronic wave function, they still retain a relatively detailed electronic model compared to conventional polarizable and reactive force fields. The ability of explicit-electron models to describe chemical reactions and electronic response properties has already been demonstrated, yet the description of short-range interactions for a broad range of chemical systems remains challenging. In this work, we present the electron machine learning potential (eMLP), a new explicit electron force field in which the short-range interactions are modeled with machine learning. The electron pair particles will be located at well-defined positions, derived from localized molecular orbitals or Wannier centers, naturally imposing the correct dielectric and piezoelectric behavior of the system. The eMLP is benchmarked on two newly constructed data sets: eQM7, an extension of the QM7 data set for small molecules, and a data set for the crystalline beta-glycine. It is shown that the eMLP can predict dipole moments, polarizabilities, and IR-spectra of unseen molecules with high precision. Furthermore, a variety of response properties, for example, stiffness or piezoelectric constants, can be accurately reproduced.

A recently developed methodology for calculating, analyzing, and visualizing nuclear magnetic shielding densities is used for studying spatial contributions including ring-current contributions to 1H nuclear magnetic resonance (NMR) chemical shifts of aromatic and anti-aromatic free-base porphyrinoids. Our approach allows a visual inspection of the spatial origin of the positive (shielding) and negative (deshielding) contributions to the nuclear magnetic shielding constants. Diatropic and paratropic current-density fluxes yield both shielding and deshielding contributions implying that not merely the tropicity of the current density determines whether the contribution has a shielding or deshielding character. Instead the shielding or deshielding contribution is determined by the direction of the current-density flux with respect to the studied nucleus. A recently developed methodology for calculating, analyzing, and visualizing nuclear magnetic shielding densities is used for studying spatial contributions including ring-current contributions to 1H nuclear magnetic resonance (NMR) chemical shifts of aromatic and anti-aromatic free-base porphyrinoids. Our approach allows a visual inspection of the spatial origin of the positive (shielding) and negative (deshielding) contributions to the nuclear magnetic shielding constants. Diatropic and paratropic current-density fluxes yield both shielding and deshielding contributions implying that not merely the tropicity of the current density determines whether the contribution has a shielding or deshielding character. Instead the shielding or deshielding contribution is determined by the direction of the current-density flux with respect to the studied nucleus.

The collision complex between the ground electronic state of an organic molecule, M, and ground state oxygen, O 2(X 3Σ g −), can absorb light to produce an intermolecular charge transfer (CT) state, often represented simply as the M radical cation, M +˙, paired with the superoxide radical anion, O 2 −˙. Aspects of this transition have been the subject of numerous studies for ∼70 years, many of which address fundamental concepts in chemistry and physics. We now examine the extent to which the combination of Molecular Dynamics simulations and electronic structure response methods can model transitions to the toluene-O 2CT state. To account for the experimental spectra, we consider (a) the distribution of toluene-O 2geometries that contribute to the transitions, (b) a quantitative description of intermolecular CT, and (c) oxygen-induced local transitions in toluene that complement the CT transitions, specifically transitions that populate toluene triplet states. We find that the latter oxygen-induced local transitions play a prominent role on the long wavelength side of the spectrum commonly attributed to the intermolecular CT transition. Our calculations provide a new perspective on the seminal discussion between R. S. Mulliken and D. F. Evans on the nature of O 2-dependent transitions in organic molecules, and bode well for modeling transitions to excited states with CT character in noncovalent weakly-bonded molecular complexes.

A series of palladium complexes with C3-bridged bidentate bis(diphenylphosphino)propane ligands with substituents of varying steric bulk at the central carbon have been synthesized. The size of the gem-dialkyl substituents affects the C–C–C bond angles within the ligands and consequently the P–M–P ligand bite angles. A combination of solid-state X-ray diffraction (XRD) and density functional theory (DFT) studies has shown that an increase in substituent size results in a distortion of the 6-membered metal–ligand chair conformation toward a boat conformation, to avoid bond angle strain. The influence of the gem-dialkyl effect on the catalytic performance of the complexes in palladium-catalyzed hydroformylation of 1-octene has been investigated. While hydroformylation activity to nonanal decreases with increasing size of the gem-dialkyl substituents, a change in chemoselectivity toward nonanol via reductive hydroformylation is observed.

Using computational approaches, we qualitatively and quantitatively assess the bonding components of a series of experimentally characterized Au(I) diarylallenylidene complexes (N.Kim, R.A.Widenhoefer, Angew. Chem. Int. Ed. 2018, 57, 4722-4726). Our results clearly demonstrate that Au(I) engages only weakly in pi-backbonding, which is, however, a tunable bonding component. Computationally identified trends in bonding are clearly correlated with the substitution patterns of the aryl substituents in the Au(I) diarylallenylidene complexes and good agreement is found with the previously reported experimental data, such as IR spectra, C-13 NMR chemical shifts and rates of decomposition together with their corresponding barrier heights, further substantiating the computational findings. The description of the bonding patterns in these complexes allow predictions of their spectroscopic features, their reactivity and stability.

Two isomeric ruthenium(II)/5,10,15,20-tetraphe-nylporphyrin complexes featuring axially coordinated redox-active, low-optical gap 2- or 6-isocyanoazulene ligands have been isolated and characterized by NMR, UV-vis, and magnetic circular dichroism (MCD) spectroscopic methods, high-resolution mass spectrometry, and single-crystal X-ray crystallography. The UV-vis and MCD spectra support the presence of the low-energy, azulene-centered transitions in the Q band region of the porphyrin chromophore. The first coordination sphere in new L2RuTPP complexes reflects compressed tetragonal geometry. The redox properties of the new compounds were assessed by electrochemical and spectroelectrochemical means and correlated with the electronic structures predicted by density functional theory and CASSCF calculations. Both experimental and theoretical data are consistent with the first two reduction processes involving the axial azulenic ligands, whereas the oxidation profile (in the direction of increasing potential) is exerted by the ruthenium ion, the porphyrin core, and the axial azulenic moieties.

Monomethyl auristatin E and monomethyl auristatin F are widely used cytotoxic agents in antibody-drug conjugates (ADCs), a group of promising cancer drugs. The ADCs specifically target cancer cells, releasing the auristatins inside, which results in the prevention of mitosis. The auristatins suffer from a potentially serious flaw, however. In solution, the molecules exist in an equal mixture of two conformers, cis and trans. Only the trans-isomer is biologically active and the isomerization process, i.e., the conversion of cis to trans is slow. This significantly diminishes the efficiency of the drugs and their corresponding ADCs, and perhaps more importantly, raises concerns over drug safety. The potency of the auristatins would be enhanced by decreasing the amount of the biologically inactive isomer, either by stabilizing the transisomer or destabilizing the cis-isomer. Here, we follow the computer-aided design strategy of shifting the conformational equilibrium and employ high-level quantum chemical modeling to identify promising candidates for improved auristatins. Coupled cluster calculations predict that a simple halogenation in the norephedrine/phenylalanine residues shifts the isomer equilibrium almost completely toward the active trans-conformation, due to enhanced intramolecular interactions specific to the active isomer.