Unveiling the tartrazine binding mode with ds-DNA by UV-visible spectroscopy, electrochemical, and QM/MM methods

Here, we studied the interaction between the food colorant tartrazine (TZ) and double stranded DNA (dsDNA), using spectroscopic, electrochemical, and computational methods such as QM/MM combined with TD-DFT. Despite the UV-vis spectroscopy is widely used to study the interaction between molecules, for the case of TZ there are discrepancies in the analyses presented in the literature available, presenting both hyperchromic and hypochromic effects and consequently different rationalizations for their results. Herein we propose the combination of UV-vis experiments with the design of high-level computational models capable of reproducing the experimental behavior to finally define the proper binding mode at the molecular scale together with the rationalization of the experimental optical response due to the complex formation. To complement the UV-vis experiments, we propose the use of electrochemical measurements, to support the results obtained through UV-vis spectroscopy, as it has been successfully used for the determination of interaction modes between small molecules and biomolecules in any condition. Our UV-vis spectroscopy experiments showed only a hypochromic effect of the absorption spectra of TZ after interaction with DNA, indicative of TZ being deeply buried in the DNA structure. The effect of ionic strength in the experimental procedures led to the dissociation of TZ, thus indicating that the interaction mode was groove binding. On the other hand, the electrochemical studies showed an irreversible reduction peak of TZ, which after the interaction with DNA exhibited a positive shift in potential that can be attributed to groove binding. The binding constant for TZ-DNA was calculated as 4.45x10⁴M^-1 (UV-vis) and 5.75x10⁴M^-1 (electrochemistry), in line with other groove binder azo dyes. Finally, through the QM/MM calculations we found that the minor-groove binding mode interacting in zones rich in adenine and thymine was the model best suited to reproduce the experimental UV-vis response.

Histidine oxidation in lytic polysaccharide monooxygenase

The lytic polysaccharide monooxygenases (LPMOs) comprise a super-family of copper enzymes that boost the depolymerisation of polysaccharides by oxidatively disrupting the glycosidic bonds connecting the sugar units. Industrial use of LPMOs for cellulose depolymerisation has already begun but is still far from reaching its full potential. One issue is that the LPMOs self-oxidise and thereby deactivate. The mechanism of this self-oxidation is unknown, but histidine residues coordinating to the copper atom are the most susceptible. An unusual methyl modification of the NE2 atom in one of the coordinating histidine residues has been proposed to have a protective role. Furthermore, substrate binding is also known to reduce oxidative damage. We here for the first time investigate the mechanism of histidine oxidation with combined quantum and molecular mechanical (QM/MM) calculations, with outset in intermediates previously shown to form from a reaction with peroxide and a reduced LPMO. We show that an intermediate with a [Cu-O]⁺ moiety is sufficiently potent to oxidise the nearest C-H bond on both histidine residues, but methylation of the NE2 atom of His-1 increases the reaction barrier of this reaction. The substrate further increases the activation barrier. We also investigate a [Cu-OH]²⁺ intermediate with a deprotonated tyrosine radical. This intermediate was previously proposed to have a protective role, and we also find it to have higher barriers than the corresponding a [Cu-O]⁺ intermediate.

Reducing Exact Two-Component Theory for NMR Couplings to a One-Component Approach: Efficiency and Accuracy

The self-consistent and complex spin-orbit exact two-component (X2C) formalism for NMR spin-spin coupling constants [ J. Chem. Theory Comput. 17, 2021, 3874-3994] is reduced to a scalar one-component ansatz. This way, the first-order response term can be partitioned into the Fermi-contact (FC) and spin-dipole (SD) interactions as well as the paramagnetic spin-orbit (PSO) contribution. The FC+SD terms are real and symmetric, while the PSO term is purely imaginary and antisymmetric. The relativistic one-component approach is combined with a modern density functional treatment up to local hybrid functionals including the response of the current density. Computational demands are reduced by factors of 8-24 as shown for a large tin compound consisting of 137 atoms. Limitations of the current ansatz are critically assessed for Sn, Pb, Pd, and Pt compounds, i.e. the one-component treatment is not sufficient for tin compounds featuring a few heavy halogen atoms.

Insights into molecular cluster materials with adamantane-like core structures by considering dimer interactions

A class of adamantane-like molecular materials attracts attention because they exhibit an extreme non-linear optical response and emit a broad white-light spectrum after illumination with a continuous-wave infrared laser source. According to recent studies, not only the nature of the cluster molecules, but also the macroscopic structure of the materials determines their non-linear optical properties. Here we present a systematic study of cluster dimers of the compounds AdR₄ and [(RT)₄ S₆ ] (T = Si, Ge, Sn) with R = methyl, phenyl or 1-naphthyl to gain fundamental knowledge about the interactions in the materials. For all compounds, a similar type of dimer structures with a staggered arrangement of substituents was determined as the energetically most favorable configuration. The binding energy between the dimers, determined by including London dispersion interactions, increases with the size of the core and the substituents. The cluster interactions can be classified as substituent-substituent-dominated (small cores, large substituents) or core-core-dominated (large cores, small substituents). Among various possible dimer conformers, those with small core-core distances are energetically preferred. Trimer and tetramer clusters display similar trends regarding the minimal core-core distances and binding energies. The much lower energy barrier determined for the rotation of substituents as compared to the rotation of the cluster dimers past each other indicates that the rotation of substituents more easily leads to different conformers in the material. Thus, understanding the interaction of the cluster dimers allows an initial assessment of the interactions in the materials.

Ultrafast structural changes direct the first molecular events of vision

Vision is initiated by the rhodopsin family of light-sensitive G protein-coupled receptors (GPCRs)1. A photon is absorbed by the 11-cis retinal chromophore of rhodopsin, which isomerizes within 200 femtoseconds to the all-trans conformation2, 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 temperature3 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.

Interaction of gentamicin and gentamicin-AOT with poly-(lactide-co-glycolate) in a drug delivery system - density functional theory calculations and molecular dynamics simulation

Gentamicin is used to treat brucellosis, an infectious disease caused by the Brucella species but the drug faces several issues such as low efficacy, instability, low solubility, and toxicity. It also has a very short half-life, therefore, requiring frequent dosing. Consequently, several other antibiotics are also being used for the treatment of brucellosis as a single dose as well as in combination with other antibiotics but none of these therapies are satisfactory. Nanoparticles in particular polymer-based ones utilizing polymers that are biodegradable and biocompatible for instance PLGA are a method of choice to overcome such drug delivery issues and enable potential targeted delivery. The current study focuses on the evaluation of the structural and dynamical properties of a drug-polymer system consisting of gentamicin drug and PLGA polymer nanoparticles in the water representing a targeted drug delivery system for the treatment of brucellosis. For this purpose, all-atom molecular dynamics simulations were carried out on the drug-polymer systems in the absence and presence of the surfactant bis(2-Ethylhexyl) sulfosuccinate (AOT) to determine the structural and dynamical properties as well as the effect of the surfactant on these properties. We also investigated systems in which the polymer constituents were in the form of monomeric units toward decoupling the primary interactions of the monomer units and polymer effects. The simulation results explain the nature of the interactions between the drug and the polymer as well as transport properties in terms of drug diffusion coefficients, which characterize the molecular behavior of gentamicin-polymer nanoparticles for use in brucellosis.

Cooperativity-Driven Reactivity of a Dinuclear Copper Dimethylglyoxime Complex

In this report, we present the dinuclear copper(II) dimethylglyoxime (H₂ dmg) complex [Cu₂ (H₂ dmg)(Hdmg)(dmg)]⁺ (1), which, in contrast to its mononuclear analogue [Cu(Hdmg)₂ ] (2), is subject to a cooperativity-driven hydrolysis. The combined Lewis acidity of both copper centers increases the electrophilicity of the carbon atom in the bridging μ₂ -O-N=C-group of H₂ dmg and thus, facilitates the nucleophilic attack of H₂ O. This hydrolysis yields butane-2,3-dione monoxime (3) and NH₂ OH that, depending on the solvent, is then either oxidized or reduced. In ethanol, NH₂ OH is reduced to NH₄ ⁺ , yielding acetaldehyde as the oxidation product. In contrast, in CH₃ CN, NH₂ OH is oxidized by Cu^II to form N₂ O and [Cu(CH₃ CN)₄ ]⁺ . Herein are presented the combined synthetic, theoretical, spectroscopic and spectrometric methods that indicate and establish the reaction pathway of this solvent-dependent reaction.

XPS and quantum chemical analysis of 4Me-BODIPY derivatives

The results of a X-ray photoelectron spectroscopy (XPS) and steady-state absorption spectroscopy study of the electronic structure, and cationic and excited states of a series of 1,3,5,7-tetramethyl-substituted BODIPYs (4Me,2R-BODIPYs) are presented. The experimental data were interpreted using 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) method, the density functional (DFT) approach, and the time-dependent DFT (TD-DFT) approach. Substitution effects on the XPS and absorption spectra were determined for 2,6-positions of 4Me,2R-BODIPY pyrrole nuclei (R = H, Br, Bu, benzyl). A very satisfactory performance of the DFT Koopmans theorem analogue was demonstrated with respect to the energy intervals between the electronic levels of 4Me,2R-BODIPY above 13 eV (BHHLYP functional) and the values of the HOMO-LUMO energy gap (ωB97X functional).

Computational study of ground-state properties of μ2 -bridged group 14 porphyrinic sandwich complexes

The structural properties of μ₂ -bridged porphyrinic double-decker complexes are investigated and the influence of various ligands, metals, substituents, and bridging atoms on the dominant structural motif is elucidated. A variety of quantum chemical methods including semiempirical (SQM) methods and density functional theory (DFT) is assessed for the calculation of ecliptic and staggered conformational energies. Local coupled cluster (DLPNO-CCSD(T1)) data are generated for reference. The r² SCAN-3c composite scheme as well as the B2PLYP-D4/def2-QZVPP approach are identified as reliable methods. Energy decomposition analyses (EDA) and localized molecular orbital analyses (LMO) are used to investigate the bonding situation and the nature of the inter-ligand interaction energy underlining the crucial role of attractive London dispersion interactions. Targeted modification of the bridging atom, e.g., by replacing O^2- by S^2- is shown to drastically change the major structural features of the investigated complexes. Further, the influence of different substituents of varying size at the phthalocyanine ligand regarding the dominant conformation is described.

Machine Learning for Fast, Quantum Mechanics-Based Approximation of Drug Lipophilicity

Lipophilicity, as measured by the partition coefficient between octanol and water (log P), is a key parameter in early drug discovery research. However, measuring log P experimentally is difficult for specific compounds and log P ranges. The resulting lack of reliable experimental data impedes development of accurate in silico models for such compounds. In certain discovery projects at Novartis focused on such compounds, a quantum mechanics (QM)-based tool for log P estimation has emerged as a valuable supplement to experimental measurements and as a preferred alternative to existing empirical models. However, this QM-based approach incurs a substantial computational cost, limiting its applicability to small series and prohibiting quick, interactive ideation. This work explores a set of machine learning models (Random Forest, Lasso, XGBoost, Chemprop, and Chemprop3D) to learn calculated log P values on both a public data set and an in-house data set to obtain a computationally affordable, QM-based estimation of drug lipophilicity. The message-passing neural network model Chemprop emerged as the best performing model with mean absolute errors of 0.44 and 0.34 log units for scaffold split test sets of the public and in-house data sets, respectively. Analysis of learning curves suggests that a further decrease in the test set error can be achieved by increasing the training set size. While models directly trained on experimental data perform better at approximating experimentally determined log P values than models trained on calculated values, we discuss the potential advantages of using calculated log P values going beyond the limits of experimental quantitation. We analyze the impact of the data set splitting strategy and gain insights into model failure modes. Potential use cases for the presented models include pre-screening of large compound collections and prioritization of compounds for full QM calculations.

Full Implementation, Optimization, and Evaluation of a Range-Separated Local Hybrid Functional with Wide Accuracy for Ground and Excited States

We report the first full and efficient implementation of range-separated local hybrid functionals (RSLHs) into the TURBOMOLE program package. This enables the computation of ground-state energies and nuclear gradients as well as excitation energies. Regarding the computational effort, RSLHs scale like regular local hybrid functionals (LHs) with system or basis set size and increase timings by a factor of 2-3 in total. An advanced RSLH, ωLH22t, has been optimized for atomization energies and reaction barriers. It is an extension of the recent LH20t local hybrid and is based on short-range PBE and long-range HF exchange-energy densities, a pig2 calibration function to deal with the gauge ambiguity of exchange-energy densities, and reoptimized B95c correlation. ωLH22t has been evaluated for a wide range of ground-state and excited-state quantities. It further improves upon the already successful LH20t functional for the GMTKN55 main-group energetics test suite, and it outperforms any global hybrid while performing close to the top rung-4 functional, ωB97M-V, for these evaluations when augmented by D4 dispersion corrections. ωLH22t performs excellently for transition-metal reactivity and provides good balance between delocalization errors and left-right correlation for mixed-valence systems, with a somewhat larger bias toward localized states compared to LH20t. It approaches the accuracy of the best local hybrids to date for core, valence singlet and triplet, and Rydberg excitation energies while improving strikingly on intra- and intermolecular charge-transfer excitations, comparable to the most successful range-separated hybrids available.

Multiscale molecular simulations for the solvation of lignin in ionic liquids

Lignin, the second most abundant biopolymer found in nature, has emerged as a potential source of sustainable fuels, chemicals, and materials. Finding suitable solvents, as well as technologies for efficient and affordable lignin dissolution and depolymerization, are major obstacles in the conversion of lignin to value-added products. Certain ionic liquids (ILs) are capable of dissolving and depolymerizing lignin but designing and developing an effective IL for lignin dissolution remains quite challenging. To address this issue, the COnductor-like Screening MOdel for Real Solvents (COSMO-RS) model was used to screen 5670 ILs by computing logarithmic activity coefficients (ln(γ)) and excess enthalpies (H^E) of lignin, respectively. Based on the COSMO-RS computed thermodynamic properties (ln(γ) and H^E) of lignin, anions such as acetate, methyl carbonate, octanoate, glycinate, alaninate, and lysinate in combination with cations like tetraalkylammonium, tetraalkylphosphonium, and pyridinium are predicted to be suitable solvents for lignin dissolution. The dissolution properties such as interaction energy between anion and cation, viscosity, Hansen solubility parameters, dissociation constants, and Kamlet-Taft parameters of selected ILs were evaluated to assess their propensity for lignin dissolution. Furthermore, molecular dynamics (MD) simulations were performed to understand the structural and dynamic properties of tetrabutylammonium [TBA]⁺-based ILs and lignin mixtures and to shed light on the mechanisms involved in lignin dissolution. MD simulation results suggested [TBA]⁺-based ILs have the potential to dissolve lignin because of their higher contact probability and interaction energies with lignin when compared to cholinium lysinate.

Metal-Free C-H Difluoromethylation of Imidazoles with the Ruppert-Prakash Reagent

The reaction of trimethyl(trifluoromethyl)silane-tetrabutylammonium difluorotriphenylsilicate (CF₃SiMe₃-TBAT) with a series of imidazoles gives products of the formal difluorocarbene insertion into the C-H bond at the C-2 position (i.e., C-difluoromethylation). According to NMR spectra, the corresponding 2-(trimethylsilyl)difluoromethyl-substituted derivatives are likely formed as the intermediates in the reaction, and then, they slowly convert to 2-difluoromethyl-substituted imidazoles. Quantum chemical calculations of two plausible reaction mechanisms indicate that it proceeds through the intermediate imidazolide anion stabilized through the interaction with solvent molecules and counterions. In the first proposed mechanism, the anion reacts with difluorocarbene without an activation barrier, and then, the CF₂ moiety of the adduct attacks the CF₃SiMe₃ molecule. After the elimination of the CF₃ anion, 2-(trimethylsilyl)difluromethyl-substituted imidazole is formed. Another possible reaction pathway includes silylation of imidazolide anion at the N-3 atom, followed by the barrierless addition of difluorocarbene at the C-2 atom and then by 1,3-shift of the SiMe₃ group from N-3 to the carbon atom of the CF₂ moiety. Both proposed mechanisms do not include steps with high activation barriers.

Quantum Mechanical Calculations of Redox Potentials of the Metal Clusters in Nitrogenase

We have calculated redox potentials of the two metal clusters in Mo-nitrogenase with quantum mechanical (QM) calculations. We employ an approach calibrated for iron-sulfur clusters with 1-4 Fe ions, involving QM-cluster calculations in continuum solvent and large QM systems (400-500 atoms), based on structures from combined QM and molecular mechanics (QM/MM) geometry optimisations. Calculations on the P-cluster show that we can reproduce the experimental redox potentials within 0.33 V. This is similar to the accuracy obtained for the smaller clusters, although two of the redox reactions involve also proton transfer. The calculated P¹⁺/P^N redox potential is nearly the same independently of whether P¹⁺ is protonated or deprotonated, explaining why redox titrations do not show any pH dependence. For the FeMo cluster, the calculations clearly show that the formal oxidation state of the cluster in the resting E₀ state is MoIIIFe3IIFe4III , in agreement with previous experimental studies and QM calculations. Moreover, the redox potentials of the first five E₀-E₄ states are nearly constant, as is expected if the electrons are delivered by the same site (the P-cluster). However, the redox potentials are insensitive to the formal oxidation states of the Fe ion (i.e., whether the added protons bind to sulfide or Fe ions). Finally, we show that the later (E₄-E₈) states of the reaction mechanism have redox potential that are more positive (i.e., more exothermic) than that of the E₀/E₁ couple.

Designing a Propellane-based Nonlinear Optically Active System Absorbing in Three Different Wavelength Regions

The aim of this work is to demonstrate the possibility of using propellane in designing a molecule that can absorb in three different wavelength regions and their nonlinear optical (NLO) activity can be fine-tuned by varying the three wings. We considered 22 tailor-made propellane derivatives consisting of phenyl, naphthyl, and biphenyl wings for this purpose. Using the state-of-the-art linear and quadratic response methods within TD-DFT and RI-CC2 theories and a suitable generalized few-state model that quantifies the effect of orientation of different transition moments on NLO properties, we discussed how and why the linear and nonlinear optical activity of propellane vary when the three wings are assembled successively to construct a full-propellane.

Modeling Nonresonant X-ray Emission of Second- and Third-Period Elements without Core-Hole Reference States and Empirical Parameters

Nonresonant X-ray emission (XE) energies and oscillator strengths are obtained using the effective potential of the generalized Kohn-Sham semi-canonical projected random phase approximation (GKS-spRPA) method. XE energies are estimated as a difference between the valence and core ionization eigenvalues, while the oscillator strengths are obtained within a frozen orbital approximation. This straightforward approach provides accurate XE energies without any need for core-hole reference states, empirical shifting parameters, or tuning of density functionals. To account for relativistic corrections to the core orbitals, we have formulated a scalar relativistic (sr) GKS-spRPA approach based on the spin-free X2C one-electron Hamiltonian. The sr-GKS-spRPA method provides highly reliable XE energies using uncontracted basis-sets on atoms where the core-hole is created prior to emission. For the largest basis-sets used in our study, using completely uncontracted polarized core-valence Dunning basis-sets, the mean absolute errors (MAEs) are within 0.7 eV compared to experimental reference values for a test-set consisting of 27 valence-to-core XE energies of molecules with second- and third-period elements. Considering a balance of accuracy and computational effort, we recommend the use of s-uncontracted def2-TZVP for second-period and all-uncontracted def2-TZVP for third-period elements. For this recommended basis-set, the MAE is 0.2 eV. The analytically continued sr-GKS-spRPA approach, with an O(N4) computational cost, enables efficient computation of XE spectra of molecules such as S₈ and C₆₀ with several core-hole states.

DFT/TD-DFT study of electronic and phosphorescent properties in cycloplatinated complexes: implications for OLEDs

High level density functional and time-dependent density functional (DFT, TD-DFT) theoretical methods have been employed to investigate the photophysical properties of 5 inorganic compounds resulting from Pt(ii) and ppy (2-phenyl-pyridine) ligands. This study is intended to provide insight into the capability of the selected systems to be used in OLED devices. In addition to an exploration of their ground and excited state geometry and electronic structures, the electronic transitions responsible for their absorption and spectra, as well as other photophysical properties, have been analyzed. To this end, their charge transfer parameters, the triplet exciton generation, phosphorescence quantum yield, and radiative decay rates have been studied. Overall, the results confirm that the selected systems are promising candidates to be used in OLED devices. Moreover, the results of this study assist in understanding the photophysical properties of Pt(ii) complexes with ppy ligands.

QM/MM Study of Partial Dissociation of S2B for the E2 Intermediate of Nitrogenase

Nitrogenase is the only enzyme that can cleave the triple bond in N2, making nitrogen available for all lifeforms. Previous computational studies have given widely diverging results regarding the reaction mechanism of the enzyme. For example, some recent studies have suggested that one of the μ2-bridging sulfide ligands (S2B) may dissociate from one of the Fe ions when protonated in the doubly reduced and protonated E2 state, whereas other studies indicated that such half-dissociated states are unfavorable. We have examined how the relative energies of 26 structures of the E2 state depend on details of combined quantum mechanical and molecular mechanical (QM/MM) calculations. We show that the selection of the broken-symmetry state, the basis set, relativistic effects, the size of the QM system, relaxation of the surroundings, and the conformations of the bound protons may affect the relative energies of the various structures by up to 12, 22, 9, 20, 37, and 33 kJ/mol, respectively. However, they do not change the preferred type of structures. On the other hand, the choice of the DFT functional strongly affects the preferences. The hybrid B3LYP functional strongly prefers doubly protonation of the central carbide ion, but such a structure is not consistent with experimental EPR data. Other functionals suggest structures with a hydride ion, in agreement with the experiments, and show that the ion bridges between Fe2 and Fe6. Moreover, there are two structures of the same type that are degenerate within 1-5 kJ/mol, in agreement with the observation of two EPR signals. However, the pure generalized gradient approximation (GGA) functional TPSS favors structures with a protonated S2B also bridging Fe2 and Fe6, whereas r2SCAN (meta-GGA) and TPSSh (hybrid) prefer structures with S2B dissociated from Fe2 (but remaining bound to Fe6). The energy difference between the two types of structure is so small (7-18 kJ/mol) that both types need to be considered in future investigations of the mechanism of nitrogenase.

Acid Rain and Flue Gas: Quantum Chemical Hydrolysis of NO2

Despite decades of efforts, much is still unknown about the hydrolysis of nitrogen dioxide (NO₂ ), a reaction associated with the formation of acid rain. From the experimental point of view, quantitative analyses are hard, and without pH control the products decompose to some reagents. We resort to high-level quantum chemistry to compute Gibbs energies for a network of reactions relevant to the hydrolysis of NO₂ . With COSMO-RS solvation corrections we calculate temperature dependent thermodynamic data in liquid water. Using the computed reaction energies, we determine equilibrium concentrations for a gas-liquid system at controlled pH. For different temperatures and initial concentrations of the different species, we observe that nitrogen dioxide should be fully converted to nitric and nitrous acid. The thermodynamic data in this work can have a potential major impact for several industries with regards to the understanding of atmospheric chemistry and in the reduction of anthropomorphic pollution.

Oxygen heterocyclic Diels-Alder-Type sesquiterpenoid dimers from Vernonia anthelmintica

Eleven undescribed oxygen heterocyclic Diels-Alder-Type sesquiterpenoid dimers, vernodalidimer I-K and M-T, along with a known one, vernodalidimer B were isolated from the seeds of Vernonia anthelmintica. The structures of them were elucidated based on 1D, 2D-NMR experiments and HRESIMS. The absolute configurations of vernodalidimer I-K and M-T were determined by comparison of their experimental and calculated electronic circular dichroism spectra. Cytotoxicity of the isolates against HCT-15, PC-3, A549, and HeLa cell lines were tested. Vernodalidimer K and Q exhibited significant cytotoxic activity against HCT-15 cell line with IC₅₀ values of 9.8 ± 5.4 μM and 9.4 ± 1.3 μM, respectively.

Encapsulation Enhances the Catalytic Activity of C-N Coupling: Reaction Mechanism of a Cu(I)/Calix[8]arene Supramolecular Catalyst

Development of C-N coupling methodologies based on Earth-abundant metals is a promising strategy in homogeneous catalysis for sustainable processes. However, such systems suffer from deactivation and low catalytic activity. We here report that encapsulation of Cu(I) within the phenanthroyl-containing calix[8]arene derivative 1,5-(2,9-dimethyl-1,10-phenanthroyl)-2,3,4,6,7,8-hexamethyl-p-tert-butylcalix[8]arene (C8PhenMe6 ) significantly enhances C-N coupling activity up to 92 % yield in the reaction of aryl halides and aryl amines, with low catalyst loadings (2.5 % mol). A tailored multiscale computational protocol based on Molecular Dynamics simulations and DFT investigations revealed an oxidative addition/reductive elimination process of the supramolecular catalyst [Cu(C8PhenMe6)I]. The computational investigations uncovered the origins of the enhanced catalytic activity over its molecular analogues: Catalyst deactivation through dimerization is prevented, and product release facilitated. Capturing the dynamic profile of the macrocycle and the impact of non-covalent interactions on reactivity allows for the rationalization of the behavior of the flexible supramolecular catalysts employed.

An automated method for graph-based chemical space exploration and transition state finding

Algorithms that automatically explore the chemical space have been limited to chemical systems with a low number of atoms due to expensive involved quantum calculations and the large amount of possible reaction pathways. The method described here presents a novel solution to the problem of chemical exploration by generating reaction networks with heuristics based on chemical theory. First, a second version of the reaction network is determined through molecular graph transformations acting upon functional groups of the reacting. Only transformations that break two chemical bonds and form two new ones are considered, leading to a significant performance enhancement compared to previously presented algorithm. Second, energy barriers for this reaction network are estimated through quantum chemical calculations by a growing string method, which can also identify non-octet species missed during the previous step and further define the reaction network. The proposed algorithm has been successfully applied to five different chemical reactions, in all cases identifying the most important reaction pathways.

Unraveling the Role of the Tyrosine Tetrad from the Binding Site of the Epigenetic Writer MLL3 in the Catalytic Mechanism and Methylation Multiplicity

MLL3, also known as KMT2C, is a lysine mono-methyltransferase in charge of the writing of an epigenetic mark on lysine 4 from histone 3. The catalytic site of MLL3 is composed of four tyrosines, namely, Y44, Y69, Y128, and Y130. Tyrosine residues are highly conserved among lysine methyltransferases’ catalytic sites, although their complete function is still unclear. The exploration of how modifications on these residues from the enzymatic machinery impact the enzymatic activity of MLL3 could shed light transversally into the inner functioning of enzymes with similar characteristics. Through the use of QMMM calculations, we focus on the effect of the mutation of each tyrosine from the catalytic site on the enzymatic activity and the product specificity in the current study. While we found that the mutations of Y44 and Y128 by phenylalanine inactivated the enzyme, the mutation of Y128 by alanine reactivated the enzymatic activity of MLL3. Moreover, according to our models, the Y128A mutant was even found to be capable of di- and tri-methylate lysine 4 from histone 3, what would represent a gain of function mutation, and could be responsible for the development of diseases. Finally, we were able to establish the inactivation mechanism, which involved the use of Y130 as a water occlusion structure, whose conformation, once perturbed by its mutation or Y128 mutant, allows the access of water molecules that sequester the electron pair from lysine 4 avoiding its methylation process and, thus, increasing the barrier height.

Self-energy corrected DFT-NEGF for conductance in molecular junctions: an accurate and efficient implementation for TRANSIESTA package applied to Au electrodes

In view of the development and the importance that the studies of conductance through molecular junctions is acquiring, robust, reliable and easy-to-use theoretical tools are the most required. Here, we present an efficient implementation of the self-energy correction to density functional theory non-equilibrium Green functions method for TRANSIESTA package. We have assessed the validity of our implementation using as benchmark systems a family of acene complexes with increasing number of aromatic rings and several anchoring groups. Our theoretical results show an excellent agreement with experimentally available measurements assuring the robustness and accuracy of our implementation.

Carbon Nanodots from an In Silico Perspective

Carbon nanodots (CNDs) are the latest and most shining rising stars among photoluminescent (PL) nanomaterials. These carbon-based surface-passivated nanostructures compete with other related PL materials, including traditional semiconductor quantum dots and organic dyes, with a long list of benefits and emerging applications. Advantages of CNDs include tunable inherent optical properties and high photostability, rich possibilities for surface functionalization and doping, dispersibility, low toxicity, and viable synthesis (top-down and bottom-up) from organic materials. CNDs can be applied to biomedicine including imaging and sensing, drug-delivery, photodynamic therapy, photocatalysis but also to energy harvesting in solar cells and as LEDs. More applications are reported continuously, making this already a research field of its own. Understanding of the properties of CNDs requires one to go to the levels of electrons, atoms, molecules, and nanostructures at different scales using modern molecular modeling and to correlate it tightly with experiments. This review highlights different in silico techniques and studies, from quantum chemistry to the mesoscale, with particular reference to carbon nanodots, carbonaceous nanoparticles whose structural and photophysical properties are not fully elucidated. The role of experimental investigation is also presented. Hereby, we hope to encourage the reader to investigate CNDs and to apply virtual chemistry to obtain further insights needed to customize these amazing systems for novel prospective applications.

Modulating the Photocyclization Reactivity of Diarylethenes through Changes in the Excited-State Aromaticity of the π-Linker

Quantum chemical calculations are performed to explore if the reactivity of diarylethene switches toward photocyclization can be controlled by the excited-state aromaticity of their bridging π-linker. Using an archetypal diarylethene with a non-aromatic π-linker as a reference, completely different outcomes are found when the π-linker is allowed to become either aromatic (no reaction) or antiaromatic (fast reaction) upon photoexcitation. The results demonstrate a possibility to use the excited-state aromaticity concept for actual modulation of photochemical reactivity.

Four-Coordinate Fe N2 and Imido Complexes Supported by a Hemilabile NNC Heteroscorpionate Ligand

Inspired by mechanistic proposals for N2 reduction at the nitrogenase FeMo cofactor, we report herein a new, strongly σ-donating heteroscorpionate ligand featuring two weak-field pyrazoles and an alkyl donor. This ligand supports four-coordinate Fe(I)-N2, Fe(II)-Cl, and Fe(III)-imido complexes, which we have characterized using a variety of spectroscopic and computational methods. Structural and quantum mechanical analysis reveal the nature of the Fe-C bonds to be essentially invariant between the complexes, with conversion between the (formally) low-valent Fe-N2 and high-valent Fe-imido complexes mediated by pyrazole hemilability. This presents a useful strategy for substrate reduction at such low-coordinate centers and suggests a mechanism by which FeMoco might accommodate the binding of both π-acidic and π-basic nitrogenous substrates.

Efficient Crystal Structure Prediction for Structurally Related Molecules with Accurate and Transferable Tailor-Made Force Fields

Crystal structure prediction (CSP) his generally used to complement experimental solid form screening and applied to individual molecules in drug development. The fast development of algorithms and computing resources offers the opportunity to use CSP earlier and for a broader range of applications in the drug design cycle. This study presents a novel paradigm of CSP specifically designed for structurally related molecules, referred to as Quick-CSP. The approach prioritizes more accurate physics through robust and transferable tailor-made force fields (TMFFs), such that significant efficiency gains are achieved through the reduction of expensive ab initio calculations. The accuracy of the TMFF is increased by the introduction of electrostatic multipoles, and the fragment-based force field parameterization scheme is demonstrated to be transferable for a family of chemically related molecules. The protocol is benchmarked with structurally related compounds from the Bromodomain and Extraterminal (BET) domain inhibitors series. A new convergence criterion is introduced that aims at performing only as many ab initio optimizations of crystal structures as required to locate the bottom of the crystal energy landscape within a user-defined accuracy. The overall approach provides significant cost savings ranging from three- to eight-fold less than the full-CSP workflow. The reported advancements expand the scope and utility of the underlying CSP building blocks as well as their novel reassembly to other applications earlier in the drug design cycle to guide molecule design and selection.

INAQS, a Generic Interface for Nonadiabatic QM/MM Dynamics: Design, Implementation, and Validation for GROMACS/Q-CHEM simulations

The accurate description of large molecular systems in complex environments remains an ongoing challenge for the field of computational chemistry. This problem is even more pronounced for photoinduced processes, as multiple excited electronic states and their corresponding nonadiabatic couplings must be taken into account. Multiscale approaches such as hybrid quantum mechanics/molecular mechanics (QM/MM) offer a balanced compromise between accuracy and computational burden. Here, we introduce an open-source software package (INAQS) for nonadiabatic QM/MM simulations that bridges the sampling capabilities of the GROMACS MD package and the excited-state infrastructure of the Q-CHEM electronic structure software. The interface is simple and can be adapted easily to other MD codes. The code supports a variety of different trajectory-based molecular dynamics, ranging from Born-Oppenheimer to surface hopping dynamics. To illustrate the power of this combination, we simulate electronic absorption spectra, free-energy surfaces along a reaction coordinate, and the excited-state dynamics of 1,3-cyclohexadiene in solution.

A Theoretical Perspective on the Actinic Photochemistry of 2-Hydroperoxypropanal

The photochemical reactions triggered by the sunlight absorption of transient volatile organic compounds in the troposphere are notoriously difficult to characterize experimentally due to the unstable and short-lived nature of these organic molecules. Some members of this family of compounds are likely to exhibit a rich photochemistry given the diversity of functional groups they can bear. Even more interesting is the photochemical fate of volatile organic compounds bearing more than one functional group that can absorb light—this is the case, for example, of α-hydroperoxycarbonyls, which are formed during the oxidation of isoprene. Experimental observables characterizing the photochemistry of these molecules like photoabsorption cross-sections or photolysis quantum yields are currently missing, and we propose here to leverage a recently developed computational protocol to predict in silico the photochemical fate of 2-hydroperoxypropanal (2-HPP) in the actinic region. We combine different levels of electronic structure methods—SCS-ADC(2) and XMS-CASPT2—with the nuclear ensemble approach and trajectory surface hopping to understand the mechanistic details of the possible nonradiative processes of 2-HPP. In particular, we predict the photoabsorption cross-section and the wavelength-dependent quantum yields for the observed photolytic pathways and combine them to determine in silico photolysis rate constants. The limitations of our protocol and possible future improvements are discussed.

Ultrafast Intersystem Crossing Dynamics of 6-Selenoguanine in Water

Rationalizing the photochemistry of nucleobases where an oxygen is replaced by a heavier atom is essential for applications that exploit near-unity triplet quantum yields. Herein, we report on the ultrafast excited-state deactivation mechanism of 6-selenoguanine (6SeGua) in water by combining nonadiabatic trajectory surface-hopping dynamics with an electrostatic embedding quantum mechanics/molecular mechanics (QM/MM) scheme. We find that the predominant relaxation mechanism after irradiation starts on the bright singlet S₂ state that converts internally to the dark S₁ state, from which the population is transferred to the triplet T₂ state via intersystem crossing and finally to the lowest T₁ state. This S₂ → S₁ → T₂ → T₁ deactivation pathway is similar to that observed for the lighter 6-thioguanine (6tGua) analogue, but counterintuitively, the T₁ lifetime of the heavier 6SeGua is shorter than that of 6tGua. This fact is explained by the smaller activation barrier to reach the T₁/S₀ crossing point and the larger spin-orbit couplings of 6SeGua compared to 6tGua. From the dynamical simulations, we also calculate transient absorption spectra (TAS), which provide two time constants (τ₁ = 131 fs and τ₂ = 191 fs) that are in excellent agreement with the experimentally reported value (τ_exp = 130 ± 50 fs) (Farrel et al. J. Am. Chem. Soc. 2018, 140, 11214). Intersystem crossing itself is calculated to occur with a time scale of 452 ± 38 fs, highlighting that the TAS is the result of a complex average of signals coming from different nonradiative processes and not intersystem crossing alone.

Automated input structure generation for single-ended reaction path optimizations

The exploration of a reaction network requires highly automated workflows to avoid error-prone and time-consuming manual steps. In this respect, a major bottleneck is the search for transition-state (TS) structures, which frequently fails and, therefore, makes (manual) revision necessary. In this work, we present a technique for obtaining suitable input structures for automated TS searches based on single-ended reaction path optimization algorithms, which makes subsequent TS searches via this method significantly more robust. First, possible input structures are generated based on the spatial alignment of the reactants. The appropriate orientation of reacting groups is achieved via stepwise rotations along selected torsional degrees of freedom. Second, a ranking of the obtained structures is performed according to selected geometric criteria. The main goals are to properly align the reactive atoms, to avoid hindrance within the reaction channel and to resolve steric clashes between the reactants. The developed procedure has been carefully tested on a variety of examples and provides suitable input structures for TS searches within seconds. The method is in daily use in an industrial setting.

Paramagnetic NMR Shielding Tensors Based on Scalar Exact Two-Component and Spin-Orbit Perturbation Theory

The temperature-dependent Fermi-contact and pseudocontact terms are important contributions to the paramagnetic NMR shielding tensor. Herein, we augment the scalar-relativistic (local) exact two-component (X2C) framework with spin-orbit perturbation theory including the screened nuclear spin-orbit correction for the EPR hyperfine coupling and g tensor to compute these temperature-dependent terms. The accuracy of this perturbative ansatz is assessed with the self-consistent spin-orbit two-component and four-component treatments serving as reference. This shows that the Fermi-contact and pseudocontact interaction is sufficiently described for paramagnetic NMR shifts; however, larger deviations are found for the EPR spectra and the principle components of the EPR properties of heavy elements. The impact of the perturbative treatment is further compared to that of the density functional approximation and the basis set. Large-scale calculations are routinely possible with the multipole-accelerated resolution of the identity approximation and the seminumerical exchange approximation, as shown for [CeTi₆O₃(OiPr)₉(salicylate)₆].

Molecular Dynamics of Linear Molecules in Strong Magnetic Fields

Molecular rotations and vibrations have been extensively studied by chemists for decades, both experimentally using spectroscopic methods and theoretically with the help of quantum chemistry. However, the theoretical investigation of molecular rotations and vibrations in strong magnetic fields requires computationally more demanding tools. As such, proper calculations of rotational and vibrational spectra were not feasible up until very recently. In this work, we present rotational and vibrational spectra for two small linear molecules, H2 and LiH, in strong magnetic fields. By treating the nuclei as classical particles, trajectories for rotations and vibrations are simulated from ab initio molecular dynamics. Born-Oppenheimer potential energy surfaces are calculated at the Hartree-Fock and MP2 levels of theory, using London atomic orbitals to ensure gauge origin invariance. For the calculation of nuclear trajectories, a highly efficient Tajima propagator is introduced, incorporating the Berry curvature tensor accounting for the screening of nuclear charges.

The Role of Packing, Dispersion, Electrostatics, and Solvation in High-Affinity Complexes of Cucurbit[n]urils with Uncharged Polar Guests

The rationalization of non-covalent binding trends is both of fundamental interest and provides new design concepts for biomimetic molecular systems. Cucurbit[n]urils (CBn) are known for a long time as the strongest synthetic binders for a wide range of (bio)organic compounds in water. However, their host-guest binding mechanism remains ambiguous despite their symmetric and simple macrocyclic structure and the wealth of literature reports. We herein report experimental thermodynamic binding parameters (ΔG, ΔH, TΔS) for CB7 and CB8 with a set of hydroxylated adamantanes, di-, and triamantanes as uncharged, rigid, and spherical/ellipsoidal guests. Binding geometries and binding energy decomposition were obtained from high-level theory computations. This study reveals that neither London dispersion interactions, nor electronic energies or entropic factors are decisive, selectivity-controlling factors for CBn complexes. In contrast, peculiar host-related solvation effects were identified as the major factor for rationalizing the unique behavior and record-affinity characteristics of cucurbit[n]urils.

Computationally enhanced X-ray diffraction analysis of a gold(III) complex interacting with the human telomeric DNA G-quadruplex. Unravelling non-unique ligand positioning

The crystal structure of the human telomeric DNA Tel24 G-quadruplex (Tel24 = TAG₃(T₂AG₃)₃T) in complex with the novel [AuL] species (with L = 2,4,6-tris(2-pyrimidyl)-1,3,5-triazine - TPymT-α) was solved by a novel joint molecular mechanical (MM)/quantum mechanical (QM) innovative approach. The quantum-refinement crystallographic method (crystallographic refinement enhanced with quantum mechanical calculation) was adapted to treat the [AuL]/G-quadruplex structure, where each gold complex in the binding site was found spread over four equally occupied positions. The four positions were first determined by docking restrained to the crystallographically determined metal ions' coordinates. Then, the quantum refinement method was used to resolve the poorly defined density around the ligands and improve the crystallographic determination, revealing that the binding preferences of this metallodrug toward Tel24 G-quadruplex arise from a combined effect of pyrimidine stacking, metal-guanine interactions and charge-charge neutralizing action of the π-acid triazine. The occurrence of interaction in solution with the Tel24 G-quadruplex DNA was further proved through DNA melting experiments, which showed a slight destabilisation of the quadruplex upon adduct formation.

A Local Hybrid Exchange Functional Approximation from First Principles

Local hybrid functionals are a more flexible class of density functional approximations allowing for a position-dependent admixture of exact exchange. This additional flexibility, however, comes with a more involved mathematical form and a more complicated design. A common denominator for previously constructed local hybrid funtionals is usage of thermochemical benchmark data to construct these functionals. Herein, we design a local hybrid functional without relying on benchmark data. Instead, we construct it in a more ab initio manner, following the principles of modern meta-generalized gradient approximations and considering theoretical constrains. To achieve this, we make use of the density matrix expansion and a local mixing function based on an approximate correlation length. The accuracy of the developed density functional approximation is assessed for thermochemistry, excitation energies, polarizabilities, magnetizabilities, NMR spin-spincoupling constants, NMR shieldings and shifts, as well as EPR g-tensors and hyperfine coupling constants. Here, the new exchange functional shows a robust performance and is especially well suited for atomization energies, barrier heights, excitation energies, NMR coupling constants, and EPR properties, whereas it looses some ground for the NMR shifts.Therefore, the designed functional is a major step forwards for functionals that have been designed from first principles.

Excited State Intramolecular Proton Transfer (ESIPT) from -NH2 to the Carbon Atom of a Naphthyl Ring

Excited state intramolecular proton transfer (ESIPT) has been documented from an amino NH₂ group to a carbon atom of an adjacent aromatic ring. This finding changes the paradigm, as hitherto such processes have not been considered as plausible due to slow protonation of carbon and low (photo)acidity of the NH₂ group. The ESIPT was studied by irradiation of 2-(2-aminophenyl)naphthalene in CH₃CN-D₂O, whereupon regiospecific incorporation of deuterium takes place at the naphthalene position 1, with a quantum yield of Φ = 0.11. A synergy of experimental and computational investigations completely unraveled the mechanism of this important photochemical reaction. Upon excitation to the photoreactive S₂(L_a) state, a favorable redistribution of charge sets the stage for ESIPT to the carbon atom in naphthalene position 1. H₂O molecules are needed, as they increase the excitation energy and oscillator strength for the population of the S₂(L_a) state. The gain in energy is used to surmount a small energy barrier on the pathway from the Franck-Condon geometry to the conical intersection with the S₀, delivering aza-quinone methide.

Optimization of the r2SCAN-3c Composite Electronic-Structure Method for Use with Slater-Type Orbital Basis Sets

The "Swiss army knife" composite density functional electronic-structure method r²SCAN-3c (J. Chem. Phys. 2021, 154, 064103) is extended and optimized for the use with Slater-type orbital basis sets. The meta generalized-gradient approximation (meta-GGA) functional r²SCAN by Furness et al. is combined with a tailor-made polarized triple-ζ Slater-type atomic orbital (STO) basis set (mTZ2P), the semiclassical London dispersion correction (D4), and a geometrical counterpoise (gCP) correction. Relativistic effects are treated explicitly with the scalar-relativistic zeroth-order regular approximation (SR-ZORA). The performance of the new implementation is assessed on eight geometry and 74 energy benchmark sets, including the extensive GMTKN55 database as well as recent sets such as ROST61 and IONPI19. In geometry optimizations, the STO-based r²SCAN-3c is either on par with or more accurate than the hybrid density functional approximation M06-2X-D3(0)/TZP. In energy calculations, the overall accuracy is similar to the original implementation of r²SCAN-3c with Gaussian-type atomic orbitals (GTO), but basic properties, intermolecular noncovalent interactions, and barrier heights are better described with the STO approach, resulting in a lower weighted mean absolute deviation (WTMAD-2(STO) = 7.15 vs 7.50 kcal mol^-1 with the original method) for the GMTKN55 database. The STO-optimized r²SCAN-3c outperforms many conventional hybrid/QZ approaches in most common applications at a fraction of their cost. The reliable, robust, and accurate r²SCAN-3c implementation with STOs is a promising alternative to the original implementation with GTOs and can be generally used for a broad field of quantum chemical problems.

Conformational Energy Benchmark for Longer n-Alkane Chains

We present the first benchmark set focusing on the conformational energies of highly flexible, long n-alkane chains, termed ACONFL. Unbranched alkanes are ubiquitous building blocks in nature, so the goal is to be able to calculate their properties most accurately to improve the modeling of, e.g., complex (biological) systems. Very accurate DLPNO-CCSD(T1)/CBS reference values are provided, which allow for a statistical meaningful evaluation of even the best available density functional methods. The performance of established and modern (dispersion corrected) density functionals is comprehensively assessed. The recently introduced r²SCAN-V functional shows excellent performance, similar to efficient composite DFT methods like B97-3c and r²SCAN-3c, which provide an even better cost-accuracy ratio, while almost reaching the accuracy of much more computationally demanding hybrid or double hybrid functionals with large QZ AO basis sets. In addition, we investigated the performance of common wave function methods, where MP2/CBS surprisingly performs worse compared to the simple D4 dispersion corrected Hartree-Fock. Furthermore, we investigate the performance of several semiempirical and force field methods, which are commonly used for the generation of conformational ensembles in multilevel workflows or in large scale molecular dynamics studies. Outstanding performance is obtained by the recently introduced general force field, GFN-FF, while other commonly applied methods like the universal force field yield large errors. We recommend the ACONFL as a helpful benchmark set for parametrization of new semiempirical or force field methods and machine learning potentials as well as a meaningful validation set for newly developed DFT or dispersion methods.

Efficient Calculation of Magnetic Circular Dichroism Spectra Using Spin-Noncollinear Linear-Response Time-Dependent Density Functional Theory in Finite Magnetic Fields

Excited-state calculations in finite magnetic fields are presented in the framework of spin-noncollinear linear-response time-dependent density functional theory. To ensure gauge-origin invariance, London atomic orbitals are employed throughout. An efficient implementation into the Turbomole package, which also includes the resolution of the identity approximation, allows for the investigation of excited states of large molecular systems. The implementation is used to investigate the magnetic circular dichroism spectra of sizable organometallic molecules such as a zinc tetraazaporphyrin with two fused naphthalene units, which is a molecule with 57 atoms.

Ultrafast proton-coupled isomerization in the phototransformation of phytochrome

The biological function of phytochromes is triggered by an ultrafast photoisomerization of the tetrapyrrole chromophore biliverdin between two rings denoted C and D. The mechanism by which this process induces extended structural changes of the protein is unclear. Here we report ultrafast proton-coupled photoisomerization upon excitation of the parent state (Pfr) of bacteriophytochrome Agp2. Transient deprotonation of the chromophore's pyrrole ring D or ring C into a hydrogen-bonded water cluster, revealed by a broad continuum infrared band, is triggered by electronic excitation, coherent oscillations and the sudden electric-field change in the excited state. Subsequently, a dominant fraction of the excited population relaxes back to the Pfr state, while ~35% follows the forward reaction to the photoproduct. A combination of quantum mechanics/molecular mechanics calculations and ultrafast visible and infrared spectroscopies demonstrates how proton-coupled dynamics in the excited state of Pfr leads to a restructured hydrogen-bond environment of early Lumi-F, which is interpreted as a trigger for downstream protein structural changes.

Deciphering the Spectral Tuning Mechanism in Proteorhodopsin: The Dominant Role of Electrostatics Instead of Chromophore Geometry

Proteorhodopsin (PR) is a photoactive proton pump found in marine bacteria. There are two phenotypes of PR exhibiting an environmental adaptation to the ocean's depth which tunes their maximum absorption: blue‐absorbing proteorhodopsin (BPR) and green‐absorbing proteorhodopsin (GPR). This blue/green color‐shift is controlled by a glutamine to leucine substitution at position 105 which accounts for a 20 nm shift. Typically, spectral tuning in rhodopsins is rationalized by the external point charge model but the Q105L mutation is charge neutral. To study this tuning mechanism, we employed the hybrid QM/MM method with sampling from molecular dynamics. Our results reveal that the positive partial charge of glutamine near the C₁₄−C₁₅ bond of retinal shortens the effective conjugation length of the chromophore compared to the leucine residue. The derived mechanism can be applied to explain the color regulation in other retinal proteins and can serve as a guideline for rational design of spectral shifts.

Automated Molecular Cluster Growing for Explicit Solvation by Efficient Force Field and Tight Binding Methods

An automated and broadly applicable workflow for the description of solvation effects in an explicit manner is introduced. This method, termed quantum cluster growth (QCG), is based on the semiempirical GFN2-xTB/GFN-FF methods, enabling efficient geometry optimizations and MD simulations. Fast structure generation is provided using the intermolecular force field xTB-IFF. Additionally, the approach uses an efficient implicit solvation model for the electrostatic embedding of the growing clusters. The novel QCG procedure presents a robust cluster generation tool for subsequent application of higher-level (e.g., DFT) methods to study solvation effects on molecular geometries explicitly or to average spectroscopic properties over cluster ensembles. Furthermore, the computation of the solvation free energy with a supermolecular approach can be carried out with QCG. The underlying growing process is physically motivated by computing the leading-order solute-solvent interactions first and can account for conformational and chemical changes due to solvation for low-energy barrier processes. The conformational space is explored with the NCI-MTD algorithm as implemented in the CREST program, using a combination of metadynamics and MD simulations. QCG with GFN2-xTB yields realistic solution geometries and reasonable solvation free energies for various systems without introducing many empirical parameters. Computed IR spectra of some solutes with QCG show a better match to the experimental data compared to well-established implicit solvation models.

Structural transformation and catalytic hydrogenation activity of amidinate-protected copper hydride clusters

Copper hydrides are important hydrogenation catalysts, but their poor stability hinders the practical applications. Ligand engineering is an effective strategy to tackle this issue. An amidinate ligand, N,N'-Di(5-trifluoromethyl-2-pyridyl)formamidinate (Tf-dpf) with four N-donors has been applied as a protecting agent in the synthesis of stable copper hydride clusters: Cu₁₁H₃(Tf-dpf)₆(OAc)₂ (Cu₁₁) with three interfacial μ₅-H and [Cu₁₂H₃(Tf-dpf)₆(OAc)₂]·OAc (Cu₁₂) with three interstitial μ₆-H. A solvent-triggered reversible interconversion between Cu₁₁ and Cu₁₂ has been observed thanks to the flexibility of Tf-dpf. Cu₁₁ shows high activity in the reduction of 4-nitrophenol to 4-aminophenol, while Cu₁₂ displays very low activity. Deuteration experiments prove that the type of hydride is the key in dictating the catalytic activity, for the interfacial μ₅-H species in Cu₁₁ are involved in the catalytic cycle whereas the interstitial μ₆-H species in Cu₁₂ are not. This work highlights the role of hydrides with regard to catalytic hydrogenation activity.

Spontaneous Coassembly of the Protein Terthiophene into Fluorescent Electroactive Microfibers in 2D and 3D Cell Cultures

Protein-based microfibers are biomaterials of paramount importance in materials science, nanotechnology, and medicine. Here we describe the spontaneous in situ formation and secretion of nanostructured protein microfibers in 2D and 3D cell cultures of 3T3 fibroblasts and B104 neuroblastoma cells upon treatment with a micromolar solution of either unmodified terthiophene or terthiophene modified by mono-oxygenation (thiophene → thiophene S-oxide) or dioxygenation (thiophene → thiophene S,S-dioxide) of the inner ring. We demonstrate via metabolic cytotoxicity tests that modification to the S-oxide leads to a severe drop in cell viability. By contrast, unmodified terthiophene and the respective S,S-dioxide cause no harm to the cells and lead to the formation and secretion of fluorescent and electroactive protein-fluorophore coassembled microfibers with a large aspect ratio, a micrometer-sized length and width, and a nanometer-sized thickness, as monitored in real-time by laser scanning confocal microscopy (LSCM). With respect to the microfibers formed by unmodified terthiophene, those formed by the S,S-dioxide display markedly red-shifted fluorescence and an increased n-type character of the material, as shown by macroscopic Kelvin probe in agreement with cyclovoltammetry data. Electrophoretic analyses and Q-TOF mass spectrometry of the isolated microfibers indicate that in all cases the prevalent proteins present are vimentin and histone H4, thus revealing the capability of these fluorophores to selectively coassemble with these proteins. Finally, DFT calculations help to illuminate the fluorophore-fluorophore intermolecular interactions contributing to the formation of the microfibers.