Photoelimination of Nitrogen from Diazoalkanes: Involvement of Higher Excited Singlet States in the Carbene Formation

Although diazoalkanes are important carbene precursors in organic synthesis, a comprehensive mechanism of photochemical formation of carbenes from diazoalkanes has not been proposed. Synergies of experiments and computations demonstrate the involvement of higher excited singlet states in the photochemistry of diazoalkanes. In all investigated diazoalkanes, excitation to S₁ results in nonreactive internal conversion to S₀. On the contrary, excitation to higher-lying singlet states (S_n, n > 1) drives the reaction toward a different segment of the S₁/S₀ conical intersection seam and results in nitrogen elimination and formation of carbenes.

eT 1.0: An open source electronic structure program with emphasis on coupled cluster and multilevel methods

The e^T program is an open source electronic structure package with emphasis on coupled cluster and multilevel methods. It includes efficient spin adapted implementations of ground and excited singlet states, as well as equation of motion oscillator strengths, for CCS, CC2, CCSD, and CC3. Furthermore, e^T provides unique capabilities such as multilevel Hartree-Fock and multilevel CC2, real-time propagation for CCS and CCSD, and efficient CC3 oscillator strengths. With a coupled cluster code based on an efficient Cholesky decomposition algorithm for the electronic repulsion integrals, e^T has similar advantages as codes using density fitting, but with strict error control. Here, we present the main features of the program and demonstrate its performance through example calculations. Because of its availability, performance, and unique capabilities, we expect e^T to become a valuable resource to the electronic structure community.

Computation of Electromagnetic Properties of Molecular Ensembles

We outline a methodology for efficiently computing the electromagnetic response of molecular ensembles. The methodology is based on the link that we establish between quantum-chemical simulations and the transfer matrix (T-matrix) approach, a common tool in physics and engineering. We exemplify and analyze the accuracy of the methodology by using the time-dependent Hartree-Fock theory simulation data of a single chiral molecule to compute the T-matrix of a cross-like arrangement of four copies of the molecule, and then computing the circular dichroism of the cross. The results are in very good agreement with full quantum-mechanical calculations on the cross. Importantly, the choice of computing circular dichroism is arbitrary: Any kind of electromagnetic response of an object can be computed from its T-matrix. We also show, by means of another example, how the methodology can be used to predict experimental measurements on a molecular material of macroscopic dimensions. This is possible because, once the T-matrices of the individual components of an ensemble are known, the electromagnetic response of the ensemble can be efficiently computed. This holds for arbitrary arrangements of a large number of molecules, as well as for periodic or aperiodic molecular arrays. We identify areas of research for further improving the accuracy of the method, as well as new fundamental and technological research avenues based on the use of the T-matrices of molecules and molecular ensembles for quantifying their degrees of symmetry breaking. We provide T-matrix-based formulas for computing traditional chiro-optical properties like (oriented) circular dichroism, and also for quantifying electromagnetic duality and electromagnetic chirality. The formulas are valid for light-matter interactions of arbitrarily-high multipolar orders.

Thermodynamics and Structure of Neptunium(V) Complexes with Formate. Spectroscopic and Theoretical Study

The temperature and ionic strength dependences of the complex formation of NpO₂⁺ with formate in aqueous solution are studied by absorption spectroscopy (I_m = 0.5-4.0 mol kg^-1, T = 20-85 °C, [Form^-]_total = 0-0.65 mol kg^-1), extended X-ray absorption fine structure spectroscopy (EXAFS) and quantum chemical methods. The complex stoichiometry and the thermodynamic functions of the complexation reactions are determined by peak deconvolution of the absorption spectra and slope analyses. Besides the solvated NpO₂⁺ ion, two NpO₂⁺ formate species (NpO₂(Form)_n^1-n; n = 1, 2) are identified. Application of the law of mass action yields the temperature dependent conditional stability constants log β'_n(T) at a given ionic strength. These data are extrapolated to IUPAC reference state conditions (I_m = 0) using the specific ion interaction theory (SIT). The results show, that log β⁰₁(20 °C) = 0.67 ± 0.04 decreases by approximately 0.1 logarithmic units with increasing temperature, log β⁰₂(20 °C) = 0.11 ± 0.11 increases by about 0.2 logarithmic units. The temperature dependence of the log β⁰_n(T) values is modeled with the integrated Van't Hoff equation yielding the standard reaction enthalpy Δ_rH⁰ and entropy Δ_rS⁰ of the complexation reactions. The results show that the formation of NpO₂(Form) is exothermic (Δ_rH⁰₁ = -2.8 ± 0.9 kJ mol^-1) whereas the formation of NpO₂(Form)₂^- is endothermic (Δ_rH⁰₂ = 6.7 ± 4.1 kJ mol^-1). Furthermore, the binary ion-ion interaction coefficients ε_T(i,k) of the formed complexes are determined in NaClO₄ and NaCl media as a function of the temperature. The coordination mode of formate toward the metal ion is investigated by EXAFS spectroscopy and quantum chemical calculations. A coordination of the ligand via only one O atom of formate to the metal ion is identified.

Quantum Chemical Calculation of Molecular and Periodic Peptide and Protein Structures

Special-purpose classical force fields (FFs) provide good accuracy at very low computational cost, but their application is limited to systems for which potential energy functions are available. This excludes most metal-containing proteins or those containing cofactors. In contrast, the GFN2-xTB semiempirical quantum chemical method is parametrized for almost the entire periodic table. The accuracy of GFN2-xTB is assessed for protein structures with respect to experimental X-ray data. Furthermore, the results are compared with those of two special-purpose FFs, HF-3c, PM6-D3H4X, and PM7. The test sets include proteins without any prosthetic groups as well as metalloproteins. Crystal packing effects are examined for a set of smaller proteins to validate the molecular approach. For the proteins without prosthetic groups, the special purpose FF OPLS-2005 yields the smallest overall RMSD to the X-ray data but GFN2-xTB provides similarly good structures with even better bond-length distributions. For the metalloproteins with up to 5000 atoms, a good overall structural agreement is obtained with GFN2-xTB. The full geometry optimizations of protein structures with on average 1000 atoms in wall-times below 1 day establishes the GFN2-xTB method as a versatile tool for the computational treatment of various biomolecules with a good accuracy/computational cost ratio.

Twisting and Turning the Sulfonamide Bond: A Synthetic, Quantum Chemical, and Crystallographic Study

Structural restriction of the sulfonamide bond was used to design sultams with abnormal geometric parameters. Based on analysis of tertiary aliphatic sulfonamides published in the Cambridge crystallographic database, Paquette's sultams (i.e., bridged bicyclic sultams with a bridgehead nitrogen atom) were outlined, and a number of these compounds (including the novel smallest representative, 2-thia-1-azabicyclo[2.1.1]hexane 2,2-dioxide) were synthesized by cyclization of the corresponding amino sulfonyl fluorides. A series of tertiary aliphatic sulfonamides was studied by crystallographic and quantum chemical methods. It was found that the s-character of the nitrogen lone pair is the most important factor defining properties of the S-N bond. Thus, going from the sp³-hybrid lone pair in common sulfonamides to the sp-like lone pair in the smallest Paquette's sultam resulted in an increase in S-N bond length by ca. 0.06 Å. The strain energy of ca. 30 kcal/mol was predicted for the latter compound, which was higher than for any existing sulfonamides studied.

N2H2 binding to the nitrogenase FeMo cluster studied by QM/MM methods

We have made a systematic combined quantum mechanical and molecular mechanical (QM/MM) investigation of possible structures of the N₂ bound state of nitrogenase. We assume that N₂ is immediately protonated to a N₂H₂ state, thereby avoiding the problem of determining the position of the protons in the cluster. We have systematically studied both end-on and side-on structures, as well as both HNNH and NNH₂ states. Our results indicate that the binding of N₂H₂ is determined more by interactions and steric clashes with the surrounding protein than by the intrinsic preferences of the ligand and the cluster. The best binding mode with both the TPSS and B3LYP density-functional theory methods has trans-HNNH terminally bound to Fe2. It is stabilised by stacking of the substrate with His-195 and Ser-278. However, several other structures come rather close in energy (within 3-35 kJ/mol) at least in some calculations: The corresponding cis-HNNH structure terminally bound to Fe2 is second best with B3LYP. A structure with HNNH₂ terminally bound to Fe6 is second most stable with TPSS (where the third proton is transferred to the substrate from the homocitrate ligand). Structures with trans-HNNH, bound to Fe4 or Fe6, or cis-HNNH bound to Fe6 are also rather stable. Finally, with the TPSS functional, a structure with cis-HNNH side-on binding to the Fe3-Fe4-Fe5-Fe7 face of the cluster is also rather low in energy, but all side-on structures are strongly disfavoured by the B3LYP method.

Synergistic effects of binary oil mixtures on the solubility of sunscreen UV absorbers

Sunscreens for the photoprotection of human skin often are prepared as emulsions, containing organic UV-absorber molecules dissolved in the oil phase. The solubility of such oil-soluble UV-absorbers can be a limiting factor when aiming for high protection against UV-radiation. Possible synergistic effects of combinations of oil components toward UV-absorber solubility are therefore of great interest. Since a multitude of different combinations of oil components are possible, it would be desirable to predict synergistic effects by computational methods. As a model system, the solubility of a hydroxyphenyl triazine type UV-absorber was studied in several binary oil mixtures, experimentally and also by using a computational procedure based on density functional theory (DFT) and the continuum solvation model COSMO-RS. We have found good agreement of experimental and computational results. Computational methods may thus be employed to predict synergistic behaviour of solubility for systems containing two or more solvents.

Performance of Electronic Structure Methods for the Description of Hückel-Möbius Interconversions in Extended π-Systems

Expanded porphyrins provide a versatile route to molecular switching devices due to their ability to shift between several π-conjugation topologies encoding distinct properties. DFT remains the workhorse for modeling such extended macrocycles, when taking into account their size and huge conformational flexibility. Nevertheless, the stability of Hückel and Möbius conformers depends on a complex interplay of different factors, such as hydrogen bonding, π···π stacking, steric effects, ring strain, and electron delocalization. As a consequence, the selection of an exchange-correlation functional for describing the energy profile of topological switches is very difficult. For these reasons, we have examined the performance of a variety of wave function methods and density functionals for describing the thermochemistry and kinetics of topology interconversions across a wide range of macrocycles. Especially for hexa- and heptaphyrins, the Möbius structures have a stronger degree of static correlation than the Hückel and twisted-Hückel structures, and as a result the relative energies of singly twisted structures are a challenging test for electronic structure methods. Comparison of limited orbital space full CI calculations with CCSD(T) calculations within the same active spaces shows that post-CCSD(T) correlation contributions to relative energies are very minor. At the same time, relative energies are weakly sensitive to further basis set expansion, as proven by the minor energy differences between the extrapolated MP2/CBS energies estimated from cc-pV{T,Q}Z, diffuse-augmented heavy-aug-cc-pV{T,Q}Z and explicitly correlated MP2-F12/cc-pVDZ-F12 calculations. Hence, our CCSD(T) reference values are reasonably well-converged in both 1-particle and n-particle spaces. While conventional MP2 and MP3 yield very poor results, SCS-MP2 and particularly SOS-MP2 and SCS-MP3 agree to better than 1 kcal mol-1 with the CCSD(T) relative energies. Regarding DFT methods, the range-separated double hybrids, such as ωB97M(2) and B2GP-PLYP, outperform other functionals with RMSDs of 0.6 and 0.8 kcal mol-1, respectively. While the original DSD-PBEP86 double hybrid performs fairly poorly for these extended π-systems, the errors drop down to 1.9 kcal mol-1 for the revised revDOD-PBEP86-NL, which eliminates the same-spin correlation energy. Minnesota meta-GGA functionals with high fractions of exact exchange (M06-2X and M08-HX) also perform reasonably well, outperforming more robust and significantly less empirically parametrized functionals like SCAN0-D3.

First-principles calculations of charge carrier mobility and conductivity in bulk semiconductors and two-dimensional materials

One of the fundamental properties of semiconductors is their ability to support highly tunable electric currents in the presence of electric fields or carrier concentration gradients. These properties are described by transport coefficients such as electron and hole mobilities. Over the last decades, our understanding of carrier mobilities has largely been shaped by experimental investigations and empirical models. Recently, advances in electronic structure methods for real materials have made it possible to study these properties with predictive accuracy and without resorting to empirical parameters. These new developments are unlocking exciting new opportunities, from exploring carrier transport in quantum matter to in silico designing new semiconductors with tailored transport properties. In this article, we review the most recent developments in the area of ab initio calculations of carrier mobilities of semiconductors. Our aim is threefold: to make this rapidly-growing research area accessible to a broad community of condensed-matter theorists and materials scientists; to identify key challenges that need to be addressed in order to increase the predictive power of these methods; and to identify new opportunities for increasing the impact of these computational methods on the science and technology of advanced materials. The review is organized in three parts. In the first part, we offer a brief historical overview of approaches to the calculation of carrier mobilities, and we establish the conceptual framework underlying modern ab initio approaches. We summarize the Boltzmann theory of carrier transport and we discuss its scope of applicability, merits, and limitations in the broader context of many-body Green's function approaches. We discuss recent implementations of the Boltzmann formalism within the context of density functional theory and many-body perturbation theory calculations, placing an emphasis on the key computational challenges and suggested solutions. In the second part of the article, we review applications of these methods to materials of current interest, from three-dimensional semiconductors to layered and two-dimensional materials. In particular, we discuss in detail recent investigations of classic materials such as silicon, diamond, gallium arsenide, gallium nitride, gallium oxide, and lead halide perovskites as well as low-dimensional semiconductors such as graphene, silicene, phosphorene, molybdenum disulfide, and indium selenide. We also review recent efforts toward high-throughput calculations of carrier transport. In the last part, we identify important classes of materials for which an ab initio study of carrier mobilities is warranted. We discuss the extension of the methodology to study topological quantum matter and materials for spintronics and we comment on the possibility of incorporating Berry-phase effects and many-body correlations beyond the standard Boltzmann formalism.

Tip-Induced Inversion of the Chirality of a Molecule's Adsorption Potential Probed by the Switching Directionality

The switching behavior of surface-supported molecular units excited by current, light, or mechanical forces is determined by the shape of the adsorption potential. The ability to tailor the energy landscape in which a molecule resides at a surface gives the possibility of imposing a desired response, which is of paramount importance for the realization of molecular electronic units. Here, by means of scanning tunneling microscopy, a triazatruxene (TAT) molecule on Ag(111) is studied, which shows a switching behavior characterized by transitions of the molecule between three states, and which is attributed to three energetically degenerate bonding configurations. Upon tunneling current injection, the system can be excited and continuously driven, showing a switching directionality close to 100%. Two surface enantiomers of TAT show opposite switching directions pointing at the chirality of the energy landscape of the adsorption potential as a key ingredient for directional switching. Further, it is shown that by tuning the tunneling parameters, the symmetry of the adsorption potential can be controllably adjusted, leading to a suppression of the directionality or an inversion of the switching direction. The findings represent a molecule-surface model system exhibiting unprecedented control of the shape of its adsorption potential.

Quantum Mechanics/Molecular Mechanics Study of the Reaction Mechanism of Glyoxalase I

Glyoxalase I (GlxI) is a member of the glyoxalase system, which is important in cell detoxification and converts hemithioacetals of methylglyoxal (a cytotoxic byproduct of sugar metabolism that may react with DNA or proteins and introduce nucleic acid strand breaks, elevated mutation frequencies, and structural or functional changes of the proteins) and glutathione into d-lactate. GlxI accepts both the S and R enantiomers of hemithioacetal, but converts them to only the S-d enantiomer of lactoylglutathione. Interestingly, the enzyme shows this unusual specificity with a rather symmetric active site (a Zn ion coordinated to two glutamate residues; Glu-99 and Glu-172), making the investigation of its reaction mechanism challenging. Herein, we have performed a series of combined quantum mechanics and molecular mechanics calculations to study the reaction mechanism of GlxI. The substrate can bind to the enzyme in two different modes, depending on the direction of its alcoholic proton (H2; toward Glu-99 or Glu-172). Our results show that the S substrate can react only if H2 is directed toward Glu-99 and the R substrate only if H2 is directed toward Glu-172. In both cases, the reactions lead to the experimentally observed S-d enantiomer of the product. In addition, the results do not show any low-energy paths to the wrong enantiomer of the product from neither the S nor the R substrate. Previous studies have presented several opposing mechanisms for the conversion of R and S enantiomers of the substrate to the correct enantiomer of the product. Our results confirm one of them for the S substrate, but propose a new one for the R substrate.

Ultrafast Backbone Protonation in Channelrhodopsin-1 Captured by Polarization Resolved Fs Vis-pump-IR-Probe Spectroscopy and Computational Methods

Channelrhodopsins (ChR) are light-gated ion-channels heavily used in optogenetics. Upon light excitation an ultrafast all-trans to 13-cis isomerization of the retinal chromophore takes place. It is still uncertain by what means this reaction leads to further protein changes and channel conductivity. Channelrhodopsin-1 in Chlamydomonas augustae exhibits a 100 fs photoisomerization and a protonated counterion complex. By polarization resolved ultrafast spectroscopy in the mid-IR we show that the initial reaction of the retinal is accompanied by changes in the protein backbone and ultrafast protonation changes at the counterion complex comprising Asp299 and Glu169. In combination with homology modelling and quantum mechanics/molecular mechanics (QM/MM) geometry optimization we assign the protonation dynamics to ultrafast deprotonation of Glu169, and transient protonation of the Glu169 backbone, followed by a proton transfer from the backbone to the carboxylate group of Asp299 on a timescale of tens of picoseconds. The second proton transfer is not related to retinal dynamics and reflects pure protein changes in the first photoproduct. We assume these protein dynamics to be the first steps in a cascade of protein-wide changes resulting in channel conductivity.

What Is the Structure of the E4 Intermediate in Nitrogenase?

Nitrogenase is the only enzyme that can cleave the strong triple bond in N₂. The active site contains a complicated MoFe₇S₉C cluster. It is believed that it needs to accept four protons and electrons, forming the E₄ state, before it can bind N₂. However, there is no consensus on the atomic structure of the E₄ state. Experimental studies indicate that it should contain two hydride ions bridging two pairs of Fe ions, and it has been suggested that both hydride ions as well as the two protons bind on the same face of the cluster. On the other hand, density functional theory (DFT) studies have indicated that it is energetically more favorable with either three hydride ions or with a triply protonated carbide ion, depending on the DFT functional. We have performed a systematic combined quantum mechanical and molecular mechanical (QM/MM) study of possible E₄ states with two bridging hydride ions. Our calculations suggest that the most favorable structure has hydride ions bridging the Fe2/6 and Fe3/7 ion pairs. In fact, such structures are 14 kJ/mol more stable than structures with three hydride ions, showing that pure DFT functionals give energetically most favorable structures in agreement with experiments. An important reason for this finding is that we have identified a new type of broken-symmetry state that involves only two Fe ions with minority spin, in contrast to the previously studied states with three Fe ions with minority spin. The energetically best structures have the two hydride ions on different faces of the FeMo cluster, whereas better agreement with ENDOR data is obtained if they are on the same face; such structures are only 6–22 kJ/mol less stable.

Interplay of Aromaticity and Antiaromaticity in N-Doped Nanographenes

The aromaticity of three nonplanar, fully conjugated aza-nanographenes built around a pyrrolo[3,2-b]pyrrole core is assessed through the application of two different computational procedures-GIMIC and NICS. We examine the calculated magnetically induced current densities (GIMIC) and nucleus-independent chemical shifts (NICS). The structural differences between these three apparently similar molecules lead to significantly different aromatic properties. GIMIC analysis indicates that the peripheral diatropic ring current of 3.9 nA/T for the studied bowl-shaped diaza-nanographene is the strongest, followed by the double [6]helicene which lacks seven-membered rings, and is practically nonexistent for the double [5]helicene possessing seven-membered rings. The biggest difference however is that in the two not-fully-fused molecules, the central pyrrole rings possess a significant diatropic current of about 4.1 nA/T, whereas there is no such current in the diaza-nanographene. Moreover, the antiaromaticity of the seven-membered rings is increasing while moving from double [5]helicene to diaza-nanographene (from -2.4 to -6.0 nA/T). The induced currents derived from NICS_π,zz-XY-scan analysis for all of the studied systems are in qualitative agreement with the GIMIC results. Subtle differences may originate from σ-electron currents in GIMIC or inaccuracy of NICS_π,zz values due to the nonplanarity of the systems, but the general picture is similar.

A minimal predictive model for better formulations of solvent phases with low viscosity

The viscosity increase of the organic phase when liquid–liquid extraction processes are intensified causes difficulties for hydrometallurgical processes on industrial scale. In this work, we have analyzed this problem for the example of N,N-dialkylamides in the presence of uranyl nitrate experimentally. Furthermore, we present a minimal model at nanoscale that allows rationalizing the experimental phenomena by connecting the molecular, mesoscopic and macroscopic scale and that allows predicting qualitative trends in viscosity. This model opens broad possibilities in optimizing constraints and is a further step towards knowledge-based formulation of extracting microemulsions formed by microstructures with low connectivity, even at high load with heavy metals.

Calculation of vibrationally resolved absorption and fluorescence spectra of the rylenes

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

Benchmarking the Performance of Time-Dependent Density Functional Theory Methods on Biochromophores

Quantum chemical calculations are important for elucidating light-capturing mechanisms in photobiological systems. The time-dependent density functional theory (TDDFT) has become a popular methodology because of its balance between accuracy and computational scaling, despite its problems in describing, for example, charge transfer states. As a step toward systematically understanding the performance of TDDFT calculations on biomolecular systems, we study here 17 commonly used density functionals, including seven long-range separated functionals, and compare the obtained results with excitation energies calculated at the approximate second order coupled-cluster theory level (CC2). The benchmarking set includes the first five singlet excited states of 11 chemical analogues of biochromophores from the green fluorescent protein, rhodopsin/bacteriorhodopsin (Rh/bR), and the photoactive yellow protein. We find that commonly used pure density functionals such as BP86, PBE, M11-L, and hybrid functionals with 20-25% of Hartree-Fock (HF) exchange (B3LYP, PBE0) have a tendency to consistently underestimate vertical excitation energies (VEEs) relative to the CC2 values, whereas hybrid density functionals with around 50% HF exchange such as BHLYP, PBE50, and M06-2X and long-range corrected functionals such as CAM-B3LYP, ωPBE, ωPBEh, ωB97X, ωB97XD, BNL, and M11 overestimate the VEEs. We observe that calculations using the CAM-B3LYP and ωPBEh functionals with 65% and 100% long-range HF exchange, respectively, lead to an overestimation of the VEEs by 0.2-0.3 eV for the benchmarking set. To reduce the systematic error, we introduce here two new empirical functionals, CAMh-B3LYP and ωhPBE0, for which we adjusted the long-range HF exchange to 50%. The introduced parameterization reduces the mean signed average (MSA) deviation to 0.07 eV and the root mean square (rms) deviation to 0.17 eV as compared to the CC2 values. In the present study, TDDFT calculations using the aug-def2-TZVP basis sets, the best performing functionals relative to CC2 are ωhPBE0 (rms = 0.17, MSA = 0.06 eV); CAMh-B3LYP (rms = 0.16, MSA = 0.07 eV); and PBE0 (rms = 0.23, MSA = -0.14 eV). For the popular range-separated CAM-B3LYP functional, we obtain an rms value of 0.31 eV and an MSA value of 0.25 eV, which can be compared with the rms and MSA values of 0.37 and -0.31 eV, respectively, as obtained at the B3LYP level.

Three-dimensional docking of alcohols to ketones: an experimental benchmark based on acetophenone solvation energy balances

The two hydrogen bond solvation sites exhibited by the carbonyl group in acetophenone are influenced by alkylation of the methyl group in both the acetophenone and in the prototype solvent methanol, largely due to London dispersion forces. Phenyl docking and alkyl docking preferences can be realized at will by appropriate substitution. In particular, cyclopropylation helps to stabilize the opposite phenyl docking site. In all cases, the energy gap is small enough to allow for a simultaneous detection even under low temperature conditions. This density functional prediction is checked experimentally by jet FTIR spectroscopy and largely confirmed. A spurious out-of-plane solvation preference predicted for cyclopropylphenylketone with tert-butyl alcohol by B3LYP-D3 calculations is not confirmed experimentally. It is unlikely that this discrepancy is due to zero-point energy effects. Instead, the second most stable alkyl-side solvation motif predicted with a more in-plane coordination is found in the jet expansion. Overall, the ability of carbonyl solvation balances to benchmark subtle electronic structure effects for non-covalent interactions without major nuclear motion corrections is supported.

GUI Implementation of VCDtools, A Program to Analyze Computed Vibrational Circular Dichroism Spectra

As computing power increases, vibrational circular dichroism (VCD) calculations on molecules of larger sizes and complexities become possible. At the same time, the spectra resulting from these computations become increasingly more cumbersome to analyze. Here, we describe the GUI implementation into the Amsterdam Density Functional (ADF) software package of VCDtools, a toolbox that provides a user-friendly means to analyze VCD spectra. Key features are the use of the generalized coupled oscillator analysis methods, as well as an easy visualization of the atomic electric and magnetic transition dipole moments which together provide detailed insight in the origin of the VCD intensity. Using several prototypical examples we demonstrate the functionalities of the program. In particular, we show how the spectra can be analyzed to detect differences between theory and experiment arising from large-amplitude motions or incorrect molecular structures and, most importantly, how the program can be used to prevent incorrect enantiomeric assignments.

Extension and evaluation of the D4 London-dispersion model for periodic systems

We present an extension of the DFT-D4 model [J. Chem. Phys., 2019, 150, 154122] for periodic systems. The main new ingredients are additional reference polarizabilities for highly-coordinated group 1-5 elements derived from pseudo-periodic electrostatically-embedded cluster calculations. To illustrate the performance of the updated method, several test cases are considered, for which we compare D4 to its predecessor D3(BJ), as well as to a comprehensive set of other dispersion-corrected methods. The largest improvements are observed for solid-state polarizabilities of 16 inorganic salts, where the D4 model achieves an unprecedented accuracy, surpassing its predecessor as well as other, computationally much more demanding approaches. For cell volumes and lattice energies of two sets of chemically diverse molecular crystals, the accuracy gain is less pronounced compared to the already excellently performing D3(BJ) method. For the challenging adsorption energies of small organic molecules on metallic as well as on ionic surfaces, DFT-D4 provides values in good agreement with experimental and/or high-level references. These results suggest the application of the proposed D4 model as a physically improved yet computationally efficient dispersion correction for standard DFT calculations as well as low-cost approaches like semi-empirical or even force-field models.

Synthesis of 5-(Fluoroalkyl)isoxazole Building Blocks by Regioselective Reactions of Functionalized Halogenoximes

A comprehensive study on the synthesis of 5-fluoroalkyl-substituted isoxazoles starting from functionalized halogenoximes is reported. One-pot metal-free [3 + 2] cycloaddition of CF3-substituted alkenes and halogenoximes bearing ester, bromo, chloromethyl, and protected amino groups was developed for the preparation of 5-trifluoromethylisoxazoles. The target 3,5-disubstituted derivatives were obtained in a regioselective manner in good to excellent yield on up to 130 g scale. 5-Fluoromethyl- and 5-difluoromethylisoxazoles were synthesized by late-stage deoxofluorination of the corresponding 5-hydroxymethyl or 5-formyl derivatives, respectively, in turn prepared via metal-free cycloaddition of halogenoximes and propargylic alcohol. An alternative approach based on nucleophilic substitution in 5-bromomethyl derivatives was found to be more convenient for the preparation of 5-fluoromethylisoxazoles. Reaction of isoxazole-5-carbaldehydes with the Ruppert-Prakash reagent was used for the preparation of (β,β,β-trifluoro-α-hydroxyethyl)isoxazoles. Utility of described approaches was shown by multigram preparation of side-chain functionalized mono-, di-, and trifluoromethylisoxazoles, for example, fluorinated analogues of ABT-418 and ESI-09.

An Allosteric Pathway in Copper, Zinc Superoxide Dismutase Unravels the Molecular Mechanism of the G93A Amyotrophic Lateral Sclerosis-Linked Mutation

Several different mutations of the protein copper, zinc superoxide dismutase (SOD1) produce the neurodegenerative disorder amyotrophic lateral sclerosis (ALS). The molecular mechanism by which the diverse mutations converge to a similar pathology is currently unknown. The electrostatic loop (EL) of SOD1 is known to be affected in all of the studied ALS-linked mutations of SOD1. In this work, we employ a multiscale simulation approach to show that this perturbation corresponds to an increased probability of the EL detaching from its native position, exposing the metal site of the protein to water. From extensive atomistic and coarse-grained molecular dynamics (MD) simulations, we identify an allosteric pathway that explains the action of the distant G93A mutation on the EL. Finally, we employ quantum mechanics/molecular mechanics MD simulations to show that the opening of the EL decreases the Zn(II) affinity of the protein. As the loss of Zn(II) is at the center of several proposed pathogenic mechanisms in SOD1-linked ALS, the structural effect identified here not only is in agreement with the experimental data but also places the opening of the electrostatic loop as the possible main pathogenic effect for a significant number of ALS-linked SOD1 mutations.

Enhancement of and interference among higher order multipole transitions in molecules near a plasmonic nanoantenna

Spontaneous emission of quantum emitters can be modified by their optical environment, such as a resonant nanoantenna. This impact is usually evaluated under assumption that each molecular transition is dominated only by one multipolar channel, commonly the electric dipole. In this article, we go beyond the electric dipole approximation and take light-matter coupling through higher-order multipoles into account. We investigate a strong enhancement of the magnetic dipole and electric quadrupole emission channels of a molecule adjacent to a plasmonic nanoantenna. Additionally, we introduce a framework to study interference effects between various transition channels in molecules by rigorous quantum-chemical calculations of their multipolar moments and a consecutive investigation of the transition rate upon coupling to a nanoantenna. We predict interference effects between these transition channels, which allow in principle for a full suppression of radiation by exploiting destructive interference, waiving limitations imposed on the emitter's coherence time by spontaneous emission.

Orientational Dependence of Cofacial Porphyrin-Quinone Electronic Interactions within the Strong Coupling Regime

We examine the relative magnitudes of electronic coupling H_DA in two face-to-face rigid and diastereomeric (porphinato)zinc(II)-quinone (PZn-Q) assemblies, 1β-ZnA and 1β-ZnB, in which the six quinonyl carbon atoms lie in virtually identical arrangements relative to the PZn plane at sub-van der Waals donor-acceptor (D-A) interplanar separations. Steady-state and time-resolved transient optical data and computational studies show that minor differences in relative D-A cofacial orientation give rise to disparate H_DA magnitudes for both photoinduced charge separation (CS) and thermal charge recombination (CR). Time-dependent density functional theory (TDDFT) computations illuminate the nature of direct charge transfer states and the electronic structural factors that give rise to these differential H_DAs. These data show more extensive mixing of locally excited (LE) and CS states in 1β-ZnA relative to 1β-ZnB and that these H_DA differences track the magnitudes of electronic coupling matrix elements determined from steady-state electronic spectral data and thermal CR rate constants measured via pump-probe spectroscopy. Collectively, this work shows that electron transfer dynamics may be manipulated in cofacial D-A systems, even at sub-van der Waals contact, provided that conformational rigidity precludes structural fluctuations that modulate D-A interactions on the charge transfer time scale.

Intermolecular Interactions in Molecular Organic Crystals upon Relaxation of Lattice Parameters

Crystal structure prediction is based on the assumption that the most thermodynamically stable structure will crystallize first. The existence of other structures such as polymorphs or from counterenantiomers requires an accurate calculation of the electronic energy. Using atom-centered Gaussian basis functions in periodic Density Functional Theory (DFT) calculations in Turbomole, the performance of two dispersion-corrected functionals, PBE-D3 and B97-D, is assessed for molecular organic crystals of the X23 benchmark set. B97-D shows a MAE (mean absolute error) of 4 kJ/mol, compared to 9 kJ/mol for PBE-D3. A strategy for the convergence of lattice energies towards the basis set limit is outlined. A simultaneous minimization of molecular structures and lattice parameters shows that both methods are able to reproduce experimental unit cell parameters to within 4–5%. Calculated lattice energies, however, deviate slightly more from the experiment, i.e., by 0.4 kJ/mol after unit cell optimization for PBE-D3 and 0.5 kJ/mol for B97-D. The accuracy of the calculated lattice energies compared to the experimental values demonstrates the ability of current DFT methods to assist in the quest for possible polymorphs and enantioselective crystallization processes.

Functional and Basis Set Dependence for Time-Dependent Density Functional Theory Trajectory Surface Hopping Molecular Dynamics: Cis-Azobenzene Photoisomerization

Within three functionals (TD-B3LYP, TD-BHandHLYP, and TD-CAM-B3LYP) in combination with four basis sets (3-21g, 6-31g, 6-31g(d), and cc-pvdz), global switching (GS) trajectory surface hopping molecular dynamics has been performed for cis-to-trans azobenzene photoisomerization up to the S₁ (nπ*) excitation. Although all the combinations show artificial double-cone structure of conical intersection between ground and first excited states, simulated quantum yields and lifetimes are in good agreement with one another; 0.6 (±5%) and 40.5 fs (±10%) by TD-B3LYP, 0.5 (±10%) and 35.5 fs (±4%) by TD-BHandHLYP, and 0.44 (±9%) and 35.2 fs (±10%) by TD-CAM-B3LYP. By analyzing distributions of excited-state population decays, hopping spots, and typical trajectories with performance of 12 functional/basis set combinations, it has been concluded that functional dependence for given basis set is slightly more sensitive than basis set dependence for given functional. The present GS on-the-fly time-dependent density functional theory (TDDFT) trajectory surface hopping simulation can provide practical benchmark guidelines for conical intersection driven excited-state molecular dynamics simulation involving in large complex system within ordinary TDDFT framework. © 2019 Wiley Periodicals, Inc.

Theoretical Study of Divalent Bis(Pentaisopropylcyclopentadienyl) Actinocenes

The existence of divalent bis(pentaisopropylcyclopentadienyl) actinocene compounds, An(Cp^iPr₅)₂ (An = Th, U, Pu, Am, Bk, No, and Lr), is assessed by density functional theory (DFT) calculations with scalar-relativistic small-core pseudopotentials. The calculations predict ground states with significant 6d occupation for Th, U, and Lr, whereas Am, Bk, and No exhibit 5f ground states. A mixed ground state with predominant 5f character is found for Pu. The complexes exhibit a linear coordination geometry and high S₁₀ symmetry except for Pu(Cp^iPr₅)₂ and Am(Cp^iPr₅)₂, which are found to be bent by 11 and 12°, respectively. Absorption spectra are simulated with time-dependent density functional theory (TD-DFT) and compared to experimental spectra of known tris(C₄H₄SiMe₃) and tris(C₅H₃(SiMe₃)₂) compounds [ J. Am. Chem. Soc. 2015 , 137 , 369 - 382 . DOI: 10.1021/ja510831n ] as well as recently synthesized divalent lanthanide analogs Dy(Cp^iPr₅)₂ and Tb(Cp^iPr₅)₂ [ J. Am. Chem. Soc. , 2019 , 141 , 12967 - 12973 . DOI: 10.1021/jacs.9b05816 ]. Thermodynamic stability is assessed by calculation of adiabatic reduction potentials of the trivalent precursors [An(Cp^iPr₅)₂]⁺, and the feasibility of further reduction to obtain as yet unknown monovalent molecular actinide complexes is discussed.

Exciton Absorption and Luminescence in i-Motif DNA

We have studied the excited-state dynamics for the i-motif form of cytosine chains (dC)10, using the ultrafast fluorescence up-conversion technique. We have also calculated vertical electronic transition energies and determined the nature of the corresponding excited states in a model tetramer i-motif structure. Quantum chemical calculations of the excitation spectrum of a tetramer i-motif structure predict a significant (0.3 eV) red shift of the lowest-energy transition in the i-motif form relative to its absorption maximum, which agrees with the experimental absorption spectrum. The lowest excitonic state in i-(dC)10 is responsible for a 2 ps red-shifted emission at 370 nm observed in the decay-associated spectra obtained on the femtosecond time-scale. This delocalized (excitonic) excited state is likely a precursor to a long-lived excimer state observed in previous studies. Another fast 310 fs component at 330 nm is assigned to a monomer-like locally excited state. Both emissive states form within less than the available time resolution of the instrument (100 fs). This work contributes to the understanding of excited-state dynamics of DNA within the first few picoseconds, which is the most interesting time range with respect to unraveling the photodamage mechanism, including the formation of the most dangerous DNA lesions such as cyclobutane pyrimidine dimers.

Ethylene-Bridged Hexadentate Bis(amidines) and Bis(amidinates) with Variable Binding Sites

Hexadentate bis(amidines) form versatile networks of hydrogen bonds both in solid state and solution, as revealed by X-ray crystallography, IR, and NMR spectroscopy. Moreover, the corresponding bis(amidinates) produce blue and green emissions in THF solution. Tethered tetradentate bis(amidines) have emerged in coordination chemistry, enantioselective catalysis, as building blocks for polyfunctional heterocycles, and in photoluminescent materials. The next generation of flexible bis(amidine)/bis(amidinate) platforms with up to six N-donor sites has now been established.

Generating Function Approach to Single Vibronic Level Fluorescence Spectra

An efficient time-dependent generating function method to compute vibronic emission and absorption spectra arising from transitions from a singly excited vibrational initial state is presented. In contrast to existing finite temperature approaches that intrinsically contain these transitions weighted by a Boltzmann factor, the current approach allows one to calculate these transitions individually. Using vibrational frequencies and normal modes computed by the second-order approximate coupled cluster (CC2) method, this formalism is used to compute the single vibronic level (SVL) fluorescence spectra of anthracene. Calculated spectra are in excellent agreement with spectra measured in jet-cooled expansion experiments. Duschinsky mixing is necessary to explain intensities of certain peaks. In a few cases, CC2, however, underestimates Duschinsky mixing, leading to too low peak intensities. An empirical correction of the Duschinsky matrix is presented. The presented method has the potential to facilitate the assignment and interpretation of SVL fluorescence spectra.

Spin adapted implementation of EOM-CCSD for triplet excited states: Probing intersystem crossings of acetylacetone at the carbon and oxygen K-edges

We present an equation of motion coupled cluster singles and doubles approach for computing transient absorption spectra from a triplet excited state. The implementation determines the left and right excitation vectors by explicitly spin-adapting the triplet excitation space. As an illustrative application, we compute transient state X-ray absorption spectra at the carbon and oxygen K-edges for the acetylacetone molecule.