Search

The computational prediction of complex molecular behaviors is an essen- tial component of modern chemistry, as it provides a faster and more cost- effective way to explore molecular interactions that may be difficult or even impossible to study experimentally. Molecular dynamics (MD) simulations of- ten serve as a valuable tool for such predictions; however, their accuracy is inherently dependent on the force field (FF) parameters employed. While the general amber force field (GAFF) is designed to provide reasonable results for a broad array of small molecules, it often requires further refinement when using it for a specific small organic molecule. Especially for ligands of the oligothiophene class, the dihedral potential representing the rotatable bond between the two thiophene rings (of the SCCS type) is inadequately described. An objective of this dissertation is to refine FF parameters for producing meaningful MD trajectories that capture key molecular interactions, binding modes, and thermodynamic properties, and subsequent accurate calculations of spectroscopic properties. The refined FF parameters were first tested by comparing the dihedral potential derived from the FF method to the density functional theory (DFT) based dihedral potential. They were then validated by assessing the relative energies of conformers optimized using both FF and DFT methods, and by comparing the transition wavelengths calculated based on geometries optimized with both FF and DFT approaches. Importantly, the errors in dihedral potential were kept below 1 kcal/mol, and the discrepancies in transition energies were less than 0.1 eV for molecular transitions around 5 eV. This FF parametrization methodology was used in research studies focus- ing on two classes of supramolecular systems: host-guest chemistry related to neurodegenerative diseases, and self-assembly systems for material development. Specifically, we examine host-guest interactions involving proteins such as amyloid-b, Den beräkningsmässiga förutsägelsen av komplext molekylärt beteende är en viktig komponent i modern kemi, eftersom det ger ett snabbare och mer kostnadseffektivt sätt att utforska molekylära interaktioner som kan vara svåra eller till och med omöjliga att studera experimentellt. Molecular dynamics (MD)-simuleringar fungerar ofta som ett värdefullt verktyg för sådana förut- sägelser; deras noggrannhet är emellertid i sig beroende av de använda kraft- fältsparametrarna (FF). Medan det allmänna bärnstenskraftfältet (GAFF) är utformat för att ge rimliga resultat för ett brett spektrum av små molekyler, kräver det ofta ytterligare förfining när det används för en specifik liten or- ganisk molekyl. Speciellt för ligander av oligotiofenklassen är den dihedrala potentialen som representerar den roterbara bindningen mellan de två tiofen- ringarna (av SCCS-typ) otillräckligt beskriven. Ett syfte med denna avhandling är att förfina FF-parametrar för att pro- ducera meningsfulla MD-banor som fångar viktiga molekylära interaktioner, bindningslägen och termodynamiska egenskaper, och efterföljande noggranna beräkningar av spektroskopiska egenskaper. De förfinade FF-parametrarna testades först genom att jämföra den dihedrala potentialen härledd från FF- metoden med den densitetsfunktionella teorin (DFT)-baserade dihedrala po- tentialen. De validerades sedan genom att bedöma de relativa energierna för konformers optimerade med både FF- och DFT-metoder, och genom att jäm- föra övergångsvåglängderna som beräknats baserat på geometrier optimerade med både FF- och DFT-metoder. Viktigt är att felen i dihedrisk potential hölls under 1 kcal/mol, och avvikelserna i övergångsenergier var mindre än 0,1 eV för molekylära övergångar runt 5 eV. Denna FF-parametriseringsmetodik användes i forskningsstudier med fokus på två klasser av supramolekylära system: värd-gäst-kemi relaterad till neu- rodegenerativa sjukdomar, och

Chorismate mutase enzymes have long served as model systems for benchmarking new methods and tools in computational chemistry. Despite the enzymes' prominence in literature, the extent of the roles activation enthalpy and entropy play in catalyzing the conversion of chorismite to prephenate is still subject to debate. Knowledge of these parameters is a key piece in fully understanding the mechanism of chorismite mutases. Within this study, we utilize EVB/MD free energy perturbations at a range of temperatures, allowing us to extract activation enthalpies and entropies from an Arrhenius plot of reaction free energies of the reaction catalyzed by a monofunctional Bacillus subtilis chorismate mutase and the promiscuous enzyme isochorismate pyruvate lyase of Pseudomonas aeruginosa. In comparison to the uncatalyzed reaction, our results show that both enzyme-catalyzed reactions exhibit a substantial reduction in activation enthalpy, while the effect on activation entropy is relatively minor, demonstrating that enzyme-catalyzed chorismate mutase reactions are enthalpically-driven. Furthermore, we observe that the monofunctional chorismate mutase from B. subtilis more efficiently catalyzes this reaction than its promiscuous counterpart. This is supported by a structural analysis of the reaction pathway at the transition state, from which we identified key residues explaining the enthalpically-driven nature of the reactions, and also the difference in efficiencies between the two enzymes.

It is generally agreed amongst philosophers and neuroscientists that the main obstacle between the science of the brain and the conscious nature of the mind is rooted in an objective-subjective dichotomy. It is further common to classify natural sciences in terms of their epistemological values and their ontological existential attributes. As a result, one concludes that a computer that is useful for studying nature, such as the conscious mind, is not itself part of nature, or as phrased differently by the noted philosopher, John Searle, ‘there are no Turing Machines in nature! However, the great physicist John Archibald Wheeler, by declaring the famous dictum, ‘it from bit’, did impart a somewhat different approach to the true nature of reality. To reconcile the two contrasting portraits, a different picture, based on the principle of self-reference, will be presented, and applied to the brain-mind problem. It is demonstrated how this principle imparts a thermo-qubit syntax, i.e., ‘bit from it’, for communication between increasingly more complex physical systems. Altogether, the steady state situation produces negentropic pockets for quantification and storage of information. The communication protocol entails cognition mechanisms that display unexpected equivalences that prompts fundamental interpretations of general optical illusions such as Necker’s cube, the Rubin vase, and the Spinning Dancer. The derived syntax also embodies an interesting deconstruction of the recently observed dodecanogram brain signal, experimentally elucidated by Anirban Bandyopadhyay and his team.

Graphene Nano Ribbons (GNRs) have been studied extensively due to their potential applications in electrical transport, optical devices, etc. The Tight Binding (TB) model is a common method used to theoretically study the properties of GNRs. However, the hopping parameters of two-dimensional graphene (2DG) are often used as the hopping parameters of the TB model of GNRs, which may lead to inaccuracies in the prediction of GNRs. In this work, we calculated the site-dependent hopping parameters from density functional theory and construction of Wannier orbitals for use in a realistic TB model. It has been found that due to the edge effect, the hopping parameters of edge C atoms are markedly different from the bulk part, which is prominently observed in narrow GNRs. Compared to graphene, the change of hopping parameter of edge C atoms of zigzag GNRs (ZGNRs) and armchair GNRs (AGNRs) is as high as 0.11 and 0.08 eV, respectively. Moreover, we investigated the impact of the calculated site-dependent (SD) hopping parameters on the electronic transport properties of GNRs in the absence and presence of the perpendicular electric field and dilute charged impurities using the Green function approach, Landauer–Büttiker formalism and self-consistent Born approximation. We find an electron–hole asymmetry in the electronic structure and transport properties of ZGNRs with SD hopping parameters. Furthermore, AGNRs with SD hopping energies show a band gap regardless of their width, while AGNRs with 2DG hopping parameters exhibit metallic or semiconductor phases depending on their width. In addition, electric field-induced 4-ZGNR with SD hopping parameters undergoes a metallic to n-doped semiconducting phase transition whereas for 4-ZGNR with 2DG hopping parameters and 8-AGNRs with 2DG or SD hopping parameters, the application of an electric field opens the band gap in both conduction and valence bands simultaneously. Our findings provide evidence for the electron–hole symmetry breaki

Theoretical predictions of the solubilizing capacity of micelles and vesicles present in intestinal fluid are important for the development of new delivery techniques and bioavailability improvement. A balance between accuracy and computational cost is a key factor for an extensive study of numerous compounds in diverse environments. In this study, we aimed to determine an optimal molecular dynamics (MD) protocol to evaluate small-molecule interactions with micelles composed of bile salts and phospholipids. MD simulations were used to produce free energy profiles for three drug molecules (danazol, probucol, and prednisolone) and one surfactant molecule (sodium caprate) as a function of the distance from the colloid center of mass. To address the challenges associated with such tasks, we compared different simulation setups, including freely assembled colloids versus pre-organized spherical micelles, full free energy profiles versus only a few points of interest, and a coarse-grained model versus an all-atom model. Our findings demonstrate that combining these techniques is advantageous for achieving optimal performance and accuracy when evaluating the solubilization capacity of micelles.Graphical abstractAll-atom (AA) and coarse-grained (CG) umbrella sampling (US) simulations and point-wise free energy (FE) calculations were compared to their efficiency to computationally analyze the solubilization of active pharmaceutical ingredients in intestinal fluid colloids.

The decoherence of point defect qubits is often governed by the electron spin-nuclear spin hyperfine interaction that can be parameterized by using ab inito calculations in principle. So far most of the theoretical works have focused on the hyperfine interaction of the closest nuclear spins, while the accuracy of the predictions for distinct nuclear spins is barely discussed. Here we demonstrate for the case of the NV center in diamond that the absolute relative error of the computed hyperfine parameters can exceed 100% using an industry standards first-principles code. To overcome this issue, we implement an alternative method and report on significantly improved hyperfine values with O(1%) relative mean error at all distances. The provided accurate hyperfine data for the NV center enables high-precision simulation of NV quantum nodes for quantum information processing and positioning of nuclear spins by comparing experimental and theoretical hyperfine data., Funding Agencies|Magyar Tudomnyos Akadmia (Hungarian Academy of Sciences) [2022-2.1.1-NL-2022-00004, FK 145395]; National Research, Development and Innovation Office of Hungary (NKFIH) within the Quantum Information National Laboratory of Hungary [2018.0071]; Knut and Alice Wallenberg Foundation through the WBSQD2 project [2022-06725]; Swedish Research Council

A desired prerequisite when performing a quantum mechanical calculation is to have an initial idea of the atomic positions within an approximate crystal structure. The atomic positions combined should result in a system located in, or close to, an energy minimum. Designing low-energy structures for large multi-component systems is, however, often a challenging task as the degrees of freedom are close to infinite. The low-energy basins of (M ' x M '' 1-x ) 3 AlB 4 material systems are herein explored by combining cluster expansion and crystal structure prediction methodologies with density functional theory calculations. Low-energy structures are specifically found at the (M ' 1/3 M '' 2/3 ) 3 AlB 4 composition, and this for multiple crystal symmetries. A subsequent high-throughput phase stability search was performed considering the identified low-energy structures at the (M ' 1/3 M '' 2/3 ) 3 AlB 4 composition where M ' and M '' were alloyed with Sc, Y, Ti, Zr, Hf, V, Nb, Ta, Cr, Mo, W, Mn, Fe, and Co for both ordered and disordered structures. Nine quaternary phases were predicted stable with five of these favoring structures with M -sites in the form of a simulated solid solution., Funding Agencies|Swedish Research Council [2019-05047, 2022-06099, 2022-06725, 2018-05973]; Knut and Alice Wallenberg (KAW) Foundation [KAW 2020.0033]

Wearable electronics are some of the most promising technologies with the potential to transform many aspects of human life such as smart healthcare and intelligent communication. The design of self-powered fabrics with the ability to efficiently harvest energy from the ambient environment would not only be beneficial for their integration with textiles, but would also reduce the environmental impact of wearable technologies by eliminating their need for disposable batteries. Herein, inspired by classical Archimedean spirals, we report a metastructured fiber fabricated by scrolling followed by cold drawing of a bilayer thin film of an MXene and a solid polymer electrolyte. The obtained composite fibers with a typical spiral metastructure (SMFs) exhibit high efficiency for dispersing external stress, resulting in simultaneously high specific mechanical strength and toughness. Furthermore, the alternating layers of the MXene and polymer electrolyte form a unique, tandem ionic-electronic coupling device, enabling SMFs to generate electricity from diverse environmental parameters, such as mechanical vibrations, moisture gradients, and temperature differences. This work presents a design rule for assembling planar architectures into robust fibrous metastructures, and introduces the concept of ionic-electronic coupling fibers for efficient multimodal energy harvesting, which have great potential in the field of self-powered wearable electronics. In this work, a concept of ionic-electronic coupling fibers by integrating a 2D MXene and a polymer electrolyte to fabricate spiral metastructures is proposed to realize multimodal power generation from various sources simultaneously., Funding Agencies|Knut and Alice Wallenberg (KAW) Foundation [KAW2020.0033]; Swedish Research Council [2019-00207]; Fundamental Research Funds for the Central Universities of China [1082204112H83]; AForsk Foundation

Electrochemical doping of organic mixed ionic-electronic conductors is key for modulating their conductivity, charge storage and volume enabling high performing bioelectronic devices such as recording and stimulating electrodes, transistors-based sensors and actuators. However, electrochemical doping has not been explored to the same extent for modulating the mechanical properties of OMIECs on demand. Here, we report a qualitative and quantitative study on how the mechanical properties of a glycolated polythiophene, p(g3T2), change in situ during electrochemical doping and de-doping. The Young's modulus of p(g3T2) changes from 69 MPa in the dry state to less than 10 MPa in the hydrated state and then further decreases down to 0.4 MPa when electrochemically doped. With electrochemical doping-dedoping the Young's modulus of p(g3T2) changes by more than one order of magnitude reversibly, representing the largest modulation reported for an OMIEC. Furthermore, we show that the electrolyte concentration affects the magnitude of the change, demonstrating that in less concentrated electrolytes more water is driven into the film due to osmosis and therefore the film becomes softer. Finally, we find that the oligo ethylene glycol side chain functionality, specifically the length and asymmetry, affects the extent of modulation. Our findings show that glycolated polythiophenes are promising materials for mechanical actuators with a tunable modulus similar to the range of biological tissues, thus opening a pathway for new mechanostimulation devices. This work investigates the changes in the mechanical properties of glycolated polythiophenes induced by electrochemical addressing and by electrolyte concentration, due to its ability to stabilize water., Funding Agencies|Swedish Foundation for Strategic Research [FFL18-0101]; Swedish Research Council [VR-2020-05045]; Swedish Government Strategic Research Area in Materials Science on Advanced Functional Materials at Linkoeping University [2009-00971]

The Empirical Valence Bond (EVB) method has long been recognised as a reliable approach for the calculation of free energies of reactions in heterogeneous electrochemical environments. In spite of its established efficacy, existing implementations and protocols often pose challenges due to their tediousness or lack of transparency. This work introduces an open-source Python implementation of the EVB method, specifically designed to enhance accessibility and comprehension of the method making it highly suited for educational purposes. Recommendations are provided for integrating the methodology into the GROMACS application programming interface, to facilitate its integration into computational chemistry workflows and accellerating research. The program is demonstrated through various computations, including a short EVB study on the dissociation of \COt and tetraphenylporphyrin in the vicinity of a graphene sheet in water and dimethylformamide. Moreover, a novel analytical expression for computing the free energy profile is presented, showing promising agreement with the canonical discretised method.

The aim of this project was to investigate a potential connection between a molecule's capacity to penetrate the blood-brain barrier and its electrostatic potential on the surface of the molecule. A molecule's capacity to penetrate the blood-brain barrier is quantified by their log BB value. This was done by creating a set of 58 molecules, divided into a test set and a calibration set, in Gaussian 16. The molecules were then optimized and their quantum chemical properties were calculated by using HS-95. By using stepwise regression in both Matlab and Excel these different parameters were then used to search for a correlation between the parameters and experimental log BB values. This resulted in an equation with 10 variables with an adjusted R2 value of 0,6456. When tested against the test set the mean fault was 0,1443. Outliers were then identified and removed and stepwise regression was executed once more. This resulted in an equation with 10 variables with an adjusted R2 0,8749. When this was tested against the test set the mean fault was 0,0798. The results showed that the variables that were important were the electrostatic potential, surface area and volume.

The impact of the Tamm–Dancoff approximation (TDA) for time-dependent density functional theory (TDDFT) calculations of X-ray absorption and X-ray emission spectra (XAS and XES) is investigated, showing small discrepancies in the excitation energies and intensities. Through explicit diagonalization of the TDDFT Hessian, XES was considered by using full TDDFT with a core-hole reference state. This has previously not been possible with most TDDFT implementations as a result of the presence of negative eigenvalues. Furthermore, a core–valence separation (CVS) scheme for XES is presented, in which only elements including the core-hole are considered, resulting in a small Hessian with the dimension of the number of remaining occupied orbitals of the same spin as the core-hole (CH). The resulting spectra are in surprisingly good agreement with the full-space counterpart, illustrating the weak coupling between the valence–valence and valence–CH transitions. Complications resulting from contributions from the discretized continuum are discussed, which can occur for TDDFT calculations of XAS and XES and for TDA calculations of XAS. In conclusion, we recommend that TDA be used when calculating X-ray emission spectra, and either CVS-TDA or CVS-TDDFT can be used for X-ray absorption spectra.

We introduce a non-orthogonal configuration interaction approach to investigate nuclear quantum effects on energies and densities of confined fermionic nuclei. The Hamiltonian employed draws parallels between confined systems and many-electron atoms, where effective non-Coulombic potentials represent the interactions of the trapped particles. One advantage of this method is its generality, as it offers the potential to study the nuclear quantum effects of various confined species affected by effective isotropic or anisotropic potentials. As a first application, we analyze the quantum states of two 3He atoms encapsulated in C60. At the Hartree–Fock level, we observe the breaking of spin and spatial symmetries. To ensure wavefunctions with the correct symmetries, we mix the broken-symmetry Hartree–Fock states within the non-orthogonal configuration interaction expansion. Our proposed approach predicts singly and triply degenerate ground states for the singlet (para-3He2@C60) and triplet (ortho-3He2@C60) nuclear spin configurations, respectively. The ortho-3He2@C60 ground state is 5.69 cm−1 higher in energy than the para-3He2@C60 ground state. The nuclear densities obtained for these states exhibit the icosahedral symmetry of the C60 embedding potential. Importantly, our calculated energies for the lowest 85 states are in close agreement with perturbation theory results based on a harmonic oscillator plus rigid rotor model of 3He2@C60.

In this work, three versions of self-consistent field/Kohn-Sham density functional theory (SCF/KS-DFT) orbital optimization are described and benchmarked. The methods are a modified version of the geometry version of the direct inversion in the iterative subspace approach (which we call r-GDIIS), the modified restricted step rational function optimization method (RS-RFO), and the novel subspace gradient-enhanced Kriging method combined with restricted variance optimization (S-GEK/RVO). The modifications introduced are aimed at improving the robustness and computational scaling of the procedures. In particular, the subspace approach in S-GEK/RVO allows the application to SCF/KS-DFT optimization of a machine learning technique that has proven to be successful in geometry optimizations. The performance of the three methods is benchmarked for a large number of small- to medium-sized organic molecules, at equilibrium structures and close to a transition state, and a second set of molecules containing closed- and open-shell transition metals. The results indicate the importance of the resetting technique in boosting the performance of the r-GDIIS procedure. Moreover, it is demonstrated that already at the inception of the subspace version of GEK to optimize SCF wave functions, it displays superior and robust convergence properties as compared to those of the standard state-of-the-art SCF/KS-DFT optimization methods.

Photochemically prepared transition-metal complexes are known to be effective at cleaving the strong C–H bonds of organic molecules in room temperature solutions. There is also ample theoretical evidence that the two-way, metal to ligand (MLCT) and ligand to metal (LMCT), charge-transfer between an incoming alkane C–H group and the transition metal is the decisive interaction in the C–H activation reaction. What is missing, however, are experimental methods to directly probe these interactions in order to reveal what determines reactivity of intermediates and the rate of the reaction. Here, using quantum chemical simulations we predict and propose future time-resolved valence-to-core resonant inelastic X-ray scattering (VtC-RIXS) experiments at the transition metal L-edge as a method to provide a full account of the evolution of metal–alkane interactions during transition-metal mediated C–H activation reactions. For the model system cyclopentadienyl rhodium dicarbonyl (CpRh(CO)2), we demonstrate, by simulating the VtC-RIXS signatures of key intermediates in the C–H activation pathway, how the Rh-centered valence-excited states accessible through VtC-RIXS directly reflect changes in donation and back-donation between the alkane C–H group and the transition metal as the reaction proceeds via those intermediates. We benchmark and validate our quantum chemical simulations against experimental steady-state measurements of CpRh(CO)2 and Rh(acac)(CO)2 (where acac is acetylacetonate). Our study constitutes the first step towards establishing VtC-RIXS as a new experimental observable for probing reactivity of C–H activation reactions. More generally, the study further motivates the use of time-resolved VtC-RIXS to follow the valence electronic structure evolution along photochemical, photoinitiated and photocatalytic reactions with transition metal complexes.

The resolution-of-the-identity (RI) or density fitting (DF) approximation for the electron repulsion integrals (ERIs) has become a standard component of accelerated and reduced-scaling implementations of first-principles Gaussian-type orbital electronic-structure methods. The Cholesky decomposition (CD) of the ERIs has also become increasingly deployed across quantum chemistry packages in the last decade, even though its early applications were mostly limited to high-accuracy methods such as coupled-cluster theory and multiconfigurational approaches. Starting with a summary of the basic theory underpinning both the CD and RI/DF approximations, thus underlining the extremely close relation of the CD and RI/DF techniques, we provide a brief and largely chronological review of the evolution of the CD approach from its birth in 1977 to its current state. In addition to being a purely numerical procedure for handling ERIs, thus providing robust and computationally efficient approximations to the exact ERIs that have been found increasingly useful on modern computer platforms, CD also offers highly accurate approaches for generating auxiliary basis sets for the RI/DF approximation on the fly due to the deep mathematical connection between the two approaches. In this review, we aim to provide a concise reference of the main techniques employed in various CD approaches in electronic structure theory, to exemplify the connection between the CD and RI/DF approaches, and to clarify the state of the art to guide new implementations of CD approaches across electronic structure programs.

In high-energy molecular dynamics or Monte Carlo simulations, standard force fields optimized for simulations at ambient temperatures are inadequate. This is largely because their repulsive parts have been regarded as not very significant, even well below zero interaction energies. It is, therefore, not obvious which force fields to resort to for simulating hot gases or plasmas. A force field model that uses the electronic densities of noninteracting atoms or molecules within the pair approximation is introduced. We start by deriving a naive model that neglects any exchange and correlation effects between the electronic clouds and then correct this model by adding a term calibrated from ab initio calculations using the CCSD(T)/cc-pVTZ level of theory. The resulting expression for this term can be regarded as a simple exchange-correlation function. We compare the results for the repulsive part of the potential energy hypersurfaces with the force fields commonly used on some dimers of small molecules.

We present time-resolved X-ray absorption spectra of ionized liquid water and demonstrate that OH radicals, H3O+ ions, and solvated electrons all leave distinct X-ray-spectroscopic signatures. Particularly, this allows us to characterize the electron solvation process through a tool that focuses on the electronic response of oxygen atoms in the immediate vicinity of a solvated electron. Our experimental results, supported by ab initio calculations, confirm the formation of a cavity in which the solvated electron is trapped. We show that the solvation dynamics are governed by the magnitude of the random structural fluctuations present in water. As a consequence, the solvation time is highly sensitive to temperature and to the specific way the electron is injected into water.

Direct excitation of aromatic compounds grants access to high-energy intermediates that can be utilised in organic synthesis. Understanding and predicting the substituent effects at the excited state for aromatic molecules remains challenging for the synthetic photochemist. In this work, we present an experimental and computational investigation of the excited state of the isomeric chloroanilines, which promptly react by losing the chloride when the amino group is in para position, but are non-reactive and non-emissive in the meta and ortho isomers. XMS-CASPT2//CASSCF computations explain this apparent contradiction of the meta-ortho selectivity rule of Zimmerman, which originates from the substituent effects lowering to a different extent the barrier to populate the prefulvenic conical intersection that deactivates non-radiatively the singlet excited state of the chloroanilines. Computational chemistry allows to elucidate the observed selectivity in the photochemistry of chloroanilines. A meta-ortho effect of the substituents favours the population of the prefulvenic conical intersection which leads to rapid deactivation of the m- and o-isomers of chloroaniline, while the para derivative lives long enough to emit and populate the reactive triplet state which leads to C-Cl dissociation.+image

Charge-transfer reactions in proteins are important for life, such as in photolyases which repair DNA, but the role of structural dynamics remains unclear. Here, using femtosecond X-ray crystallography, we report the structural changes that take place while electrons transfer along a chain of four conserved tryptophans in the Drosophila melanogaster (6-4) photolyase. At femto- and picosecond delays, photoreduction of the flavin by the first tryptophan causes directed structural responses at a key asparagine, at a conserved salt bridge, and by rearrangements of nearby water molecules. We detect charge-induced structural changes close to the second tryptophan from 1 ps to 20 ps, identifying a nearby methionine as an active participant in the redox chain, and from 20 ps around the fourth tryptophan. The photolyase undergoes highly directed and carefully timed adaptations of its structure. This questions the validity of the linear solvent response approximation in Marcus theory and indicates that evolution has optimized fast protein fluctuations for optimal charge transfer.

A desired prerequisite when performing a quantum mechanical calculation is to have an initial idea of the atomic positions within an approximate crystal structure. The atomic positions combined should result in a system located in, or close to, an energy minimum. However, designing low-energy structures may be a challenging task when prior knowledge is scarce, specifically for large multi-component systems where the degrees of freedom are close to infinite. In this paper, we propose a method for identification of low-energy crystal structures within multi-component systems by combining cluster expansion and crystal structure predictions with density-functional theory calculations. Crystal structure prediction searches are applied to the Mo2AlB2 and Sc2AlB2 ternary systems to identify candidate structures, which are subsequently used to explore the quaternary (pseudo-binary) (MoxSc1-x)(2)AlB2 system through the cluster expansion formalism utilizing the ground-state search approach. Furthermore, we show that utilizing low-energy structures found within the cluster expansion ground-state search as seed structures within crystal structure predictions of (MoxSc1-x)(2)AlB2 can significantly reduce the computational demands. With this combined approach, we not only correctly identified the recently discovered Mo(4/3)Sc(2/3)AlB(2)i-MAB phase, comprised of in-plane chemical ordering of Mo and Sc and with Al in a Kagome lattice, but also predict additional low-energy structures at various concentrations. This result demonstrates that combining crystal structure prediction with cluster expansion provides a path for identifying low-energy crystal structures in multi-component systems by employing the strengths from both frameworks., Funding Agencies|Linkoeping University

The threshold carrier density, conventionally evaluated from optical pumping, is a key reference parameter towards electrically pumped lasers with the widely acknowledged assumption that optically excited charge carriers relax to the band edge through an ultrafast process. However, the characteristically slow carrier cooling in perovskites challenges this assumption. Here, we investigate the optical pumping of state-of-the-art bromide- and iodine-based perovskites. We find that the threshold decreases by one order of magnitude with decreasing excitation energy from 3.10 eV to 2.48 eV for methylammonium lead bromide perovskite (MAPbBr(3)), indicating that the low-energy photon excitation facilitates faster cooling and hence enables efficient carrier accumulation for population inversion. Our results are then interpreted due to the coupling of phonon scattering in connection with the band structure of perovskites. This effect is further verified in the two-photon pumping process, where the carriers relax to the band edge with a smaller difference in phonon momentum that speeds up the carrier cooling process. Furthermore, by extrapolating the optical pumping threshold to the band edge excitation as an analog of the electrical carrier injection to the perovskite, we obtain a critical threshold carrier density of similar to 1.9 x 10(17) cm(-3), which is one order of magnitude lower than that estimated from the conventional approach. Our work thus highlights the feasibility of metal halide perovskites for electrically pumped lasers., Funding Agencies|ERC Consolidator Grant [101045098]; Swedish Government Strategic Research Area in Materials Science on Functional Materials at Linkoping University [2009-00971]; China National Key Basic Research Program [2022YFA1404800]; National Science Foundation of China [12234007, 12221004, 91963212]; Science and Technology Commission of Shanghai Municipality [19XD1434600, 2019SHZDZX01, 19DZ225 3000, 20501110500, 21DZ1101500]; Marie Curie Fellowship [Horizon-MSCA-2021-PF, 101066960]; Horizon Europe

The recent synthesis of a new polymorph of two-dimensional (2D) germanium monochalcogenides, namely, gamma -GeSe with a four-atomic-layer-thick hexagonal lattice, has received considerable attention due to its novel properties and potential applications. This exciting advancement paves the path for extensive experimental and theoretical investigations on the family of gamma -MX crystals in which M and X are elements of group IV and VI, respectively. In this regard, herein we conduct first-principles-based calculations to explore the structural, vibrational, mechanical, electronic, and piezoelectric properties of gamma -GeX and Janus gamma -Ge2XX' (X/X' : S, Se, and Te) monolayers. We performed a detailed analysis of the suggested systems' dynamical, thermal, and mechanical stability through phonon-band-dispersion calculations, ab initio molecular dynamics (AIMD) simulations, and elastic tensor analyses, respectively, and all six possible nanosheets are found to be stable. The computed Raman spectra of the monolayers reveal that, different from binary systems, the formation of Janus monolayers results in the appearance of additional Raman active modes. The mechanical response of the proposed crystals is examined by calculating in-plane stiffness (Y2D) and the Poisson's ratio (nu) within the elastic regime, and the obtained results ascertain their flexibility. It is found that similar to their binary counterparts, Janus monolayers are indirect-band-gap semiconductors, and their valence-band maxima show a Mexican hat dispersion along the high-symmetry points of the Brillouin zone. Additionally, it is demonstrated that the construction of Janus crystals enhances the piezoelectric coefficients of gamma -GeX monolayers, both in the in-plane and out-of-plane directions. Our findings not only provide a comprehensive insight into physical and electronic properties of gamma -GeX and gamma -Ge2XX' monolayers but also reveal their promising features for various nanoelectronic a

The goal of present study is to explore how the size and functionalization of graphene quantum dots (GQDs) affect their sensing capabilities. Specifically, we investigated the adsorption of SO2, SOF2, SO2F2, and SF6 on GQDs that were functionalized with -CH3, -COCH3, and -NH2. We used density functional theory to analyse the electronic properties of these functionalized GQDs and found that the functionalization significantly altered their electronic properties. For example, the B3LYP H-L gap of pristine triangulene was 3.9eV, while the H-L gap of functionalized triangulene ranged from 2.8 eV to 3.6 eV (using the B3LYP functional). Our results indicate that -NH2 functionalized phenalenyl and triangulene provide strong interaction with SO2, with adsorption energies of-0.429 eV and-0.427 eV, respectively. These adsorption properties exhibit phys-isorption, leading to high gas sensitivity and superior recovery time. The findings of this study provide new insights into the potential use of GQDs for detecting the decomposed constituents of sulfur hexafluoride, which can be beneficial for assessing the operation status of SF6 insulated devices. Overall, our calculations suggest that functionalized GQDs can be employed in gas insulated systems for partial discharge detection.

Transference number is a key design parameter for electrolyte materials used in electrochemical energy storage systems. However, the determination of the true transference number from experiments is rather demanding. On the other hand, the Bruce-Vincent method is widely used in the lab to approximately measure transference numbers of polymer electrolytes, which becomes exact in the limit of infinite dilution. Therefore, theoretical formulations to treat the Bruce-Vincent transference number and the true transference number on an equal footing are clearly needed. Here, we show how the Bruce-Vincent transference number for concentrated electrolyte solutions can be derived in terms of the Onsager coefficients, without involving any extrathermodynamic assumptions. By demonstrating it for the case of poly(ethylene oxide)-lithium bis(trifluoromethane)sulfonimide system, this work opens the door to calibrating molecular dynamics (MD) simulations via reproducing the Bruce-Vincent transference number and using MD simulations as a predictive tool for determining the true transference number.

Conformational analysis is central to the design of bioactive molecules. It is particularly challenging for macrocycles due to noncovalent transannular interactions, steric interactions, and ring strain that are often coupled. Herein, we simulated the conformations of five macrocycles designed to express a progression of increasing complexity in environment-dependent intramolecular interactions and verified the results against NMR measurements in chloroform and dimethyl sulfoxide. Molecular dynamics using an explicit solvent model, but not the Monte Carlo method with implicit solvation, handled both solvents correctly. Refinement of conformations at the ab initio level was fundamental to reproducing the experimental observations-standard state-of-the-art molecular mechanics force fields were insufficient. Our simulations correctly predicted the intramolecular interactions between side chains and the macrocycle and revealed an unprecedented solvent-induced conformational switch of the macrocyclic ring. Our results provide a platform for the rational, prospective design of molecular chameleons that adapt to the properties of the environment., De två första författarna delar förstaförfattarskapet

Overcrowded alkene based molecular motors and switches constitute a unique class of photo-responsive systems due to their intrinsic chirality near the core C(sic )C bond, making them highly suitable candidates for the construction of light-switchable dynamic systems, i.e., for controlling molecular motion, modulation of material chiroptical properties and supramolecular assembly. However, the lack of general design principles, along with the challenging synthesis of these molecules, precludes full exploitation of their dynamic structures. Therefore, systematic investigations of the key parameters are crucial for the further development of these systems. Here we provide a facile alternative synthetic route, elucidate the influence of substituents on the photochemistry of overcrowded alkene-derived bistable chiroptical photoswitches, and show nearly quantitative bidirectional photoswitching. The established structure-property relationship constitutes a practical guideline for the design of these photochromes tailored to a specific application.

Herein, the Hirshfeld surfaces analysis of the crystalline methylone hydrochloride was performed in order to analyze NHMIDLINE HORIZONTAL ELLIPSISCl, CHMIDLINE HORIZONTAL ELLIPSISCl, and CHMIDLINE HORIZONTAL ELLIPSISO intermolecular interactions and study the formation of the NH2+-Cl- salt fragment in methylone hydrochloride crystal. There are two isomeric dimers with parallel and side-by-side orientation extracted from the crystal packing to model the IR spectrum of the crystalline methylone hydrochloride within the framework of density functional theory (DFT) and B3LYP/6-31G(d,p) method. We have assigned and interpreted all observed IR bands in the experimental spectrum of the 3,4-methylenedioxymethcathinone hydrochloride standard crystal sample that is important for forensic-medical examination. It was shown that intermolecular interactions between the NH2+ and Cl- ionic moieties occur in crystalline samples that confirm the presence of the ionized form of the methylone hydrochloride compound with the NH2+Cl- fragment.

Photochemistry and photophysics processes involve structures far from equilibrium. In these reactions, there is often strong coupling between nuclear and electronic degrees of freedom. For first-row transition metals, K beta X-ray emission spectroscopy (XES) is a sensitive probe of electronic structure due to the direct overlap between the valence orbitals and the 3p hole in the final state. Here the sensitivity of K beta mainline (K beta(1,3)) XES to structural dynamics is analyzed by simulating spectral changes along the excited state dynamics of an iron photosensitizer [Fe-II(bmip)(2)](2+) [bmip = 2,6-bis(3-methyl-imidazole-1-ylidine)-pyridine], using both restricted active space (RAS) multiconfigurational wavefunction theory and a one-electron orbital-energy approach in density-functional theory (1-DFT). Both methods predict a spectral blue-shift with increasing metal-ligand distance, which changes the emission intensity for any given detection energy. These results support the suggestion that the [Fe-II(bmip)(2)](2+) femtosecond K beta XES signal shows oscillations due to coherent wavepacket dynamics. Based on the RAS results, the sensitivity to structural dynamics is twice as high for K beta compared to K alpha, with the drawback of a lower signal-to-noise ratio. K beta sensitivity is favored by a larger spectral blue-shift with increasing metal-ligand distance and larger changes in spectral shape. Comparing the two simulations methods, 1-DFT predicts smaller energy shifts and lower sensitivity, likely due to missing final-state effects. The simulations can be used to design and interpret XES probes of non-equilibrium structures to gain mechanistic insights in photocatalysis.

Phytochromes belong to a group of photoreceptor proteins containing a covalently bound biliverdin chromophore that inter-converts between two isomeric forms upon photoexcitation. The existence and stability of the photocycle products are largely determined by the protein sequence and the presence of conserved hydrogen-bonding interactions in the vicinity of the chromophore. The vibrational signatures of biliverdin, however, are often weak and obscured under more intense protein bands, limiting spectroscopic studies of its non-transient signals. In this study, we apply isotope-labeling techniques to isolate the vibrational bands from the protein-bound chromophore of the bacterial phytochrome from Deinococcus radiodurans. We elucidate the structure and ultrafast dynamics of the chromophore with 2D infra-red (IR) spectroscopy and molecular dynamics simulations. The carbonyl stretch vibrations of the pyrrole rings show the heterogeneous distribution of hydrogen-bonding structures, which exhibit distinct ultrafast relaxation dynamics. Moreover, we resolve a previously undetected 1678 cm(-1) band that is strongly coupled to the A- and D-ring of biliverdin and demonstrate the presence of complex vibrational redistribution pathways between the biliverdin modes with relaxation-assisted measurements of 2D IR cross peaks. In summary, we expect 2D IR spectroscopy to be useful in explaining how point mutations in the protein sequence affect the hydrogen-bonding structure around the chromophore and consequently its ability to photoisomerize to the light-activated states.

In lanthanide-doped upconversion nanoparticles (UCNPs), the concentration of emitter ions, also known as activator ions, is usually limited to 1 - 5 mol% due to concentration quenching effects. This circumstance limits the luminescent efficiency of UCNPs' and their use in a variety of application areas. Earlier studies have attributed the activator concentration quenching to migration of energy to the nanoparticle surface, while indicating that cross-relaxation between activator ions had a minor role therein. In this work, we carried out comparative studies on Er3+-doped and Yb3+-Er3+ codoped UCNPs and could, in contrast to this notion, prove a general adverse effect of cross-relaxation between activator ions, here Er3+ ions, on up -conversion luminescence (UCL). The direct result of the cross-relaxation is that the energy of the excitation light is accumulated into a low-lying excited state of Er3+ in the infrared region, so forming a "low-lying excited state energy trap ". As a result, the excitation energy is used for generating down-conversion lu-minescence or for indirectly facilitating UCL channels that are directly related to the low-lying excited state energy trap. The identified effect can be used to regulate UCL channels to achieve a concentrated UCL band that is more favorable for certain applications, e.g., biological imaging., QC 20230131

The calculation of free energies from first principles enables the prediction of phase stability of materials with high accuracy; these calculations are complicated in magnetic materials by the interplay of electronic, magnetic, and vibrational degrees of freedom. In this work, we show the feasibility and accuracy of the calculation of phase stability in magnetic systems with ab initio methods and thermodynamic integration by sampling the magnetic and vibrational phase space with coupled atomistic spin dynamics-ab initio molecular dynamics simulations [Stockem et al., PRL 121, 125902 (2018)], where energies and interatomic forces are calculated with density functional theory. We employ the method to calculate the phase stability of Fe at ambient pressure from 800 up to 1800 K. The Gibbs free energy difference between fcc and bcc Fe at zero pressure is calculated with thermodynamic integration over temperature and over stress-strain variables and, for the best set of exchange interactions employed, the Gibbs free energy difference between the two structures is within 5 meV/atom from the CALPHAD estimate, corresponding to an error in transition temperature below 150 K. The present work paves the way to free energy calculations in magnetic materials from first principles with accuracy in the order of 1 meV/atom., Funding Agencies|Swedish Research Council [2018-05973, 2019-05403]; wedish Government Strategic Research Area in Materials Science on Functional Materials at Linkoeping University (Faculty Grant SFOMatLiU) [2009-00971]; Knut Alice Wallenberg Foundation (Wallenberg Scholar Grant) [KAW-2018.0194]; Swedish Foundation for Strategic Research (SSF) [FFL 15-0290]

Diffusion-driven rotation in cholesteric liquid crystals has been studied using molecular dynamics simulation. Then a chemical potential gradient parallel to the cholesteric axis induces a torque that rotates the director at a constant rate around this axis, besides driving a mass current. An equimolar mixture of Gay–Berne ellipsoids and Lennard-Jones spheres was used as the molecular model. In order to keep the system homogeneous, the color conductivity algorithm was used to apply a color field instead of a chemical potential gradient to drive a mass current. Then the particles are given a color charge that interacts with a color field in the same way as with an electric field, but these charges do not interact with each other. This algorithm is often used to calculate the mutual diffusion coefficient. In the above liquid crystal model, it was found that the color field induces a torque that rotates the director at a constant rate around the cholesteric axis in addition to driving a mass current. The phenomenon was quantified by calculating the cross-coupling coefficient between the color field and the director angular velocity. The results were cross-checked by using a director rotation algorithm to exert a torque to rotate the director at a constant rate. Besides rotation of the director, this resulted in a mass current parallel to the cholesteric axis. The cross-coupling coefficient between the torque and the mass current was equal to the cross-coupling coefficient between the color field and the director rotation rate within a statistical uncertainty of 10 percent, thus fulfilling the Onsager reciprocity relations. As a further cross-check, these cross-coupling coupling coefficients, the color conductivity, and the twist viscosity were calculated by evaluating the corresponding Green–Kubo relations. Finally, it was noted that the orientation of the cholesteric axis parallel to the color field is the one that minimizes the irreversible energy dissipation rate. T

In molecular dynamics simulations utilizing enhanced-sampling techniques, reweighting is a central component for recovering the targeted ensemble averages of the unbiased system by calculating and applying a bias-correction function c(t). We present enhanced reweighting protocols for variationally enhanced sampling (VES) simulations by exploiting a recent reweighting method, originally introduced in the metadynamics framework [Giberti et al. J. Chem. Theory Comput., 2020, 16, 100-107], which was modified and extended to multiple-walker simulations: these may be implemented either as independent walkers (associated with one unique correction function per walker) or cooperative ones that all share one correction function, which is the hitherto only explored option. When each case is combined with the two possibilities of determining c(t) by time integration up to either t or over the entire simulation period , altogether four reweighting options result. Their relative merits were assessed by well-tempered VES simulations of two model problems: locating the free-energy difference between two metastable molecular conformations of the N-acetyl-l-alanine methylamide dipeptide, and the recovery of an a priori known distribution when one water molecule in the liquid phase is perturbed by a periodic free-energy function. The most rapid convergence occurred for large cooperative walkers, regardless of the upper integration limit, but integrating up to t proved advantageous for small walker ensembles. That novel reweighting method compared favorably to the standard VES reweighting, as well as to current state-of-the-art reweighting options introduced for metadynamics simulations that estimate c(t) by integration over the collective variables. For further gains in computational speed and accuracy, we also introduce analytical solutions for c(t), as well as offering further insight into its features by approximative analytical expressions in the high-temperature regime.

The borylation of aryl and heteroaryl C–H bonds is valuable for the site-selective functionalization of C–H bonds in complex molecules. Iridium catalysts ligated by bipyridine ligands catalyze the borylation of the C–H bond that is most acidic and least sterically hindered in an arene, but predicting the site of borylation in molecules containing multiple arenes is difficult. To address this challenge, we report a hybrid computational model that predicts the Site of Borylation (SoBo) in complex molecules. The SoBo model combines density functional theory, semiempirical quantum mechanics, cheminformatics, linear regression, and machine learning to predict site selectivity and to extrapolate these predictions to new chemical space. Experimental validation of SoBo showed that the model predicts the major site of borylation of pharmaceutical intermediates with higher accuracy than prior machine-learning models or human experts, demonstrating that SoBo will be useful to guide experiments for the borylation of specific C(sp2)–H bonds during pharmaceutical development.

We present a time-dependent theory for non-resonant x-ray emission spectrum (XES) and normal Auger spectrum (NAS) calculation, based on a fully quantum description of nuclear dynamics using the vibrational wave packet concept. We compare two formulations of the time-dependent theory, either employing a two-time propagation scheme or using spectral integration over the electron energy continuum. We find that the latter formulation is more efficient for numerical simulations, providing a reasonable accuracy when the integration step is shorter than the lifetime broadening of the core-ionized state. We demonstrate our approach using the example of non-resonant x-ray emission from a water molecule, considering the lowest core-ionized K−1 and first core-ionized shake-up K−1V−1V1 intermediate states. These channels exemplify the developed theory on bound–bound, bound–continuum, continuum–bound, and continuum–continuum transitions. Our results suggest that the time-dependent approach is efficient for simulating XES involving dissociative states, whereas the time-independent approach, based on Franck–Condon factors, is more efficient for bound–bound transitions expressed as discrete frequency dependence in the energy domain. The methods and discussion have general applicability, including both NAS and more complex systems, such as liquid water.

Our skin constitutes an effective permeability barrier that protects the body from exogenous substances but concomitantly severely limits the number of pharmaceutical drugs that can be delivered transdermally. In topical formulation design, chemical permeation enhancers (PEs) are used to increase drug skin permeability. In vitro skin permeability experiments can measure net effects of PEs on transdermal drug transport, but they cannot explain the molecular mechanisms of interactions between drugs, permeation enhancers, and skin structure, which limits the possibility to rationally design better new drug formulations. Here we investigate the effect of the PEs water, lauric acid, geraniol, stearic acid, thymol, ethanol, oleic acid, and eucalyptol on the transdermal transport of metronidazole, caffeine, and naproxen. We use atomistic molecular dynamics (MD) simulations in combination with developed molecular models to calculate the free energy difference between 11 PE-containing formulations and the skin’s barrier structure. We then utilize the results to calculate the final concentration of PEs in skin. We obtain an RMSE of 0.58 log units for calculated partition coefficients from water into the barrier structure. We then use the modified PE-containing barrier structure to calculate the PEs’ permeability enhancement ratios (ERs) on transdermal metronidazole, caffeine, and naproxen transport and compare with the results obtained from in vitro experiments. We show that MD simulations are able to reproduce rankings based on ERs. However, strict quantitative correlation with experimental data needs further refinement, which is complicated by significant deviations between different measurements. Finally, we propose a model for how to use calculations of the potential of mean force of drugs across the skin’s barrier structure in a topical formulation design.

The broad range of applications for photochemical reactions is the result of light-matter interaction at the electronic level. The diverse application of photochemistry in various fields, including photovoltaic materials, molecular switches, and biological systems are due to electronic and structural transformations induced by photoexcitation as well as molecular alteration due to electron and charge transfer. An improved understanding of these photochemical events is dependent on the fundamental theoretical evaluation, to model and analyze the ultrafast processes. The studies discussed in this thesis explore such theoretical implementation in two different frontiers. In the first study, dynamic simulations are performed to model the light-induced bond dissociation of phenyl azide. The surface hopping formalism, implemented under the semiclassical molecular dynamics approach helped in tracing the time evolution of the electronic and structural levels, involved in the photodissociation. In the second study, the time-dependent density functional theory has been applied to generate XA spectra of imidazole solutions. The theoretical assessments support experimental measurements and provide more insight into the core excitations and structural influence on the absorption spectra., Fotokemiska reaktioner styrs av växelverkan mellan ljus of materia på en elektronisk nivå. I olika fält finns det vitt skilda tillämpningarna av fotokemi. Dessa inkluderar ljusinducerade processer i solceller, molekylära strömbrytare, och biologiska system. Reaktionerna beror av elektroniska och strukturella transformationer som induceras av fotoexcitationen, och kan ge upphov till energi- och laddningsöverföring. För att få utökad förståelse av fotokemiska reaktioner behövs grundläggande teoretiska studier där ultrasnabba processer modelleras och analyseras i jämförelse med experiment. Undersökningar som presenteras i denna avhandling använder sig att teoretiska modeller i två olika områden av fotokemi. I den första studien har vi genomfört dynamiska simuleringar för att modellera ljusinducerad dissociation av fenylazid. Vi have använt en semi-klassisk approximation med hopp mellan olika elektroniska tillstånd vilket gör det möjligt att följa utvecklingen i elektroniska och geometriska frihetsgrader under fotodissociationen. I den andra studien har tidsberoende täthetsfunktionalteori använts för att simulera röntgenabsorptionsspektrum för imidazol i lösning. Genom att utvärdera olika geometriska modeller med teoretiska beräkningar kan vi berika tolkningen av experimentella mätningar, och även få detaljerat insikt i innerskalsexcitationer och hur geometrin påverka röntgenspektrum.

The present work focuses on the structural properties, spectroscopic signatures, intermolecular hydrogen bonding interactions, chemical and biological activity of nicotinamide (NIC) based on its monomeric and trimeric models using density functional theory and vibrational spectroscopy. FT-IR and FT-Raman spectra were obtained using the double-side forward-backward acquisition mode under vacuum. UV-Vis absorption spectra were recorded in methanol and compared with the calculated values. Geometry optimization and vibrational wavenumbers were obtained with the aid of Gaussian 09 program packages. The structural analysis of NIC revealed that the trimeric model was in better agreement with the experimental values than the monomer due to the incorporation of nearest hydrogen bond interactions. Spectroscopic results showed that NH2 and C = O groups of NIC were involved in intermolecular interactions in the trimeric model. The natural bond orbital (NBO) and quantum theory of atoms in molecules (QTAIM) analyses determined the presence, strength as well as nature of the hydrogen bonds were partially covalent. The lesser value of the HOMO-LUMO energy gap for the trimeric model indicated higher reactivity than monomer. Moreover, chemical reactivity was calculated using molecular electrostatic potential surface (MESP) and reactivity descriptors. The docking studies for NIC with several targets explored its biological activity.

With the purpose to develop long chain-conjugated oligopyrrin-like compounds and their metal complexes, and thus achieve tunable near-infrared absorption, a dithienyl-blocked hexapyrrane S-2-P-6 was synthesized by acid-catalyzed [2+4+2] condensation, followed by oxidation with DDQ to afford dithiaoctapyrrin 1, and its mononuclear metal complexes 1-Cu and 1-Zn were synthesized by treating 1 with Cu(II) and Zn(II) acetates. All the compounds were systematically characterized by NMR/EPR, and HRMS. The crystal structures revealed that 1 adopts a double hook-like conformation. Whereas, both complexes 1-Cu and 1-Zn adopt spiral-hook hybrid conformations, showing smaller interplanar angles between the rings within the spiral part, compared with those in the hook-like counterpart of molecule 1, which is favorable for red-shifting the absorption. As expected, the absorption band edges for complexes 1-Cu and 1-Zn are red-shifted to ca. 1560 nm, compared with that of 1260 nm observed for 1.

There still is little treatment available for amyloid diseases, despite their significant impact on individuals and the social and economic implications for society. One reason for this is that the physical nature of amyloid formation is not understood sufficiently well. Therefore, fundamental research at the molecular level remains necessary to support the development of therapeutics. A few structures of short peptides from amyloid-forming proteins have been determined. These can in principle be used as scaffolds for designing aggregation inhibitors. Attempts to this end have often used the tools of computational chemistry, in particular molecular simulation. However, few simulation studies of these peptides in the crystal state have been presented so far. Hence, to validate the capability of common force fields (AMBER19SB, CHARMM36m, and OPLS-AA/M) to yield insight into the dynamics and structural stability of amyloid peptide aggregates, we have performed molecular dynamics simulations of twelve different peptide crystals at two different temperatures. From the simulations, we evaluate the hydrogen bonding patterns, the isotropic B-factors, the change in energy, the Ramachandran plots, and the unit cell parameters and compare the results with the crystal structures. Most crystals are stable in the simulations but for all force fields there is at least one that deviates from the experimental crystal, suggesting more work is needed on these models.

Electrochemical energy storage always involves the capacitive process. The prevailing electrode model used in the molecular simulation of polarizable electrode–electrolyte systems is the Siepmann–Sprik model developed for perfect metal electrodes. This model has been recently extended to study the metallicity in the electrode by including the Thomas–Fermi screening length. Nevertheless, a further extension to heterogeneous electrode models requires introducing chemical specificity, which does not have any analytical recipes. Here, we address this challenge by integrating the atomistic machine learning code (PiNN) for generating the base charge and response kernel and the classical molecular dynamics code (MetalWalls) dedicated to the modeling of electrochemical systems, and this leads to the development of the PiNNwall interface. Apart from the cases of chemically doped graphene and graphene oxide electrodes as shown in this study, the PiNNwall interface also allows us to probe polarized oxide surfaces in which both the proton charge and the electronic charge can coexist. Therefore, this work opens the door for modeling heterogeneous and complex electrode materials often found in energy storage systems.

The catalytic mechanism of N2 fixation by nitrogenase remains unre-solved in how the strong N=N bond is activated and why the reduc-tive elimination of H2 is required. Here, we use density functional theory and physiologically relevant thermal simulations to elucidate the mechanism of the complete nitrogenase catalytic cycle. Over the accumulation of four reducing equivalents, we find that protons and electrons transfer to the FeMo cofactor to weaken and break its bridge Fe-S bond, leading to temporary H2S formation that exposes the Fe sites to weakly bind N2. Remarkably, we find that subsequent H2 formation is responsible for chemical activation to an N=N dou-ble bond accompanied by a low barrier for H2 release. We empha-size that finite temperature effects smooth out mechanistic differ-ences between DFT functionals observed at 0 K, thus leading to a consistent understanding as to why H formation is an obligatory step in N2 adsorption and activation.

Highly accurate ab initio molecular dynamics (MD) methods are the gold standard for studying molecular mechanisms in the condensed phase, however, they are too expensive to capture many key properties that converge slowly with respect to simulation length and time scales. Machine learning (ML) approaches which reach the accuracy of ab initio simulation, and which are, at the same time, sufficiently affordable hold the key to bridging this gap. In this work we present a robust ML potential for the EC:EMC binary solvent, a key component of liquid electrolytes in rechargeable Li-ion batteries. We identify the necessary ingredients needed to successfully model this liquid mixture of organic molecules. In particular, we address the challenge posed by the separation of scale between intra- and inter-molecular interactions, which is a general issue in all condensed phase molecular systems.

Theoretical and experimental vibrational signatures of H2O and OH- (dissociated water) adsorbed on stoichiometric ceria{111} surfaces are compared. The experimental ones were collected from low-coverage experiments in the literature, and the theoretical anharmonic frequencies were generated using density functional theory calculations employing the optPBE-vdW functional for coverages from 0.5 to a few monolayers. It is found that (i) the experiments and our calculations overall agree well, lending credibility to both; (ii) the calculations manage to resolve the large class of H-bonded motifs into frequency classes that can guide experimental assignments; (iii) it is possible to find a geometrical H-bond definition that also captures the OH vibrational frequency downshifts well: R(H center dot center dot center dot O) <= 2.5 angstrom and the O-H center dot center dot center dot O angle theta >= 100 degrees; and (iv) the frequency vs electric field relations for water and hydroxides (i.e., dissociated water) follow different and well-separated curves.

The electronic structure and the chemical state in Am binary oxides and Am-doped UO2 were studied by means of X-ray absorption spectroscopy at shallow Am core (4d and 5d) edges. In particular, the Am 5f states were probed and the nature of their bonding to the oxygen states was analyzed. The interpretation of the experimental data was supported by the Anderson impurity model (AIM) calculations which took into account the full multiplet structure due to the interaction between 5f electrons as well as the interaction with the core hole. The sensitivity of the branching ratio of the Am 4d(3/2) and 4d(5/2)X-ray absorption lines to the chemical state of Am was shown using Am binary oxides as reference systems. The observed ratio for Am-doped UO2 suggests that at least at low Am concentrations, americium is in the Am(III) state in the UO2 lattice. To confirm the validity of the applied AIM approach, the analysis of the Am 4fX-ray photoelectron spectra of AmO2 and Am2O3 was also performed which revealed a good agreement between experiment and calculations. As a whole, AmO2 can be classified as the charge-transfer compound with the 5f occupancy (n(f)) equal to 5.73 electrons, while Am2O3 is rather a Mott-Hubbard system with n(f) = 6.05.

We introduce a protein-ligand binding database (PLBD) that presents thermodynamic and kinetic data of reversible protein interactions with small molecule compounds. The manually curated binding data are linked to protein-ligand crystal structures, enabling structure-thermodynamics correlations to be determined. The database contains over 5500 binding datasets of 556 sulfonamide compound interactions with the 12 catalytically active human carbonic anhydrase isozymes defined by fluorescent thermal shift assay, isothermal titration calorimetry, inhibition of enzymatic activity and surface plasmon resonance. In the PLBD, the intrinsic thermodynamic parameters of interactions are provided, which account for the binding-linked protonation reactions. In addition to the protein-ligand binding affinities, the database provides calorimetrically measured binding enthalpies, providing additional mechanistic understanding. The PLBD can be applied to investigations of protein-ligand recognition and could be integrated into small molecule drug design.