Quantification of Noncovalent Interactions in Azide-Pnictogen, -Chalcogen, and -Halogen Contacts

The noncovalent interactions between azides and oxygen‐containing moieties are investigated through a computational study based on experimental findings. The targeted synthesis of organic compounds with close intramolecular azide–oxygen contacts yielded six new representatives, for which X‐ray structures were determined. Two of those compounds were investigated with respect to their potential conformations in the gas phase and a possible significantly shorter azide–oxygen contact. Furthermore, a set of 44 high‐quality, gas‐phase computational model systems with intermolecular azide–pnictogen (N, P, As, Sb), –chalcogen (O, S, Se, Te), and –halogen (F, Cl, Br, I) contacts are compiled and investigated through semiempirical quantum mechanical methods, density functional approximations, and wave function theory. A local energy decomposition (LED) analysis is applied to study the nature of the noncovalent interaction. The special role of electrostatic and London dispersion interactions is discussed in detail. London dispersion is identified as a dominant factor of the azide–donor interaction with mean London dispersion energy‐interaction energy ratios of 1.3. Electrostatic contributions enhance the azide–donor coordination motif. The association energies range from −1.00 to −5.5 kcal mol⁻¹.

Molecular modeling approaches to address drug-metabolizing enzymes (DMEs) mediated chemoresistance: a review

Resistance against clinically approved anticancer drugs is the main roadblock in cancer treatment. Drug metabolizing enzymes (DMEs) that are capable of metabolizing a variety of xenobiotic get overexpressed in malignant cells, therefore, catalyzing drug inactivation. As evident from the literature reports, the levels of DMEs increase in cancer cells that ultimately lead to drug inactivation followed by drug resistance. To puzzle out this issue, several strategies inclusive of analog designing, prodrug designing, and inhibitor designing have been forged. On that front, the implementation of computational tools can be considered a fascinating approach to address the problem of chemoresistance. Various research groups have adopted different molecular modeling tools for the investigation of DMEs mediated toxicity problems. However, the utilization of these in-silico tools in maneuvering the DME mediated chemoresistance is least considered and yet to be explored. These tools can be employed in the designing of such chemotherapeutic agents that are devoid of the resistance problem. The current review canvasses various molecular modeling approaches that can be implemented to address this issue. Special focus was laid on the development of specific inhibitors of DMEs. Additionally, the strategies to bypass the DMEs mediated drug metabolism were also contemplated in this report that includes analogs and pro-drugs designing. Different strategies discussed in the review will be beneficial in designing novel chemotherapeutic agents that depreciate the resistance problem.

Excitonic and charge transfer interactions in tetracene stacked and T-shaped dimers

Extended quantum chemical calculations were performed for the tetracene dimer to provide benchmark results, analyze the excimer survival process, and explore the possibility of using long-range-corrected (LC) time-dependent second-order density functional tight-biding (DFTB2) for this system. Ground- and first-excited-state optimized geometries, vertical excitations at relevant minima, and intermonomer displacement potential energy curves (PECs) were calculated for these purposes. Ground-state geometries were optimized with the scaled-opposite-spin (SOS) second-order Møller-Plesset perturbation (MP2) theory and LC-DFT (density functional theory) and LC-DFTB2 levels. Excited-state geometries were optimized with SOS-ADC(2) (algebraic diagrammatic construction to second-order) and the time-dependent approaches for the latter two methods. Vertical excitations and PECs were compared to multireference configuration interaction DFT (DFT/MRCI). All methods predict the lowest-energy S₀ conformer to have monomers parallel and rotated relative to each other and the lowest S₁ conformer to be of a displaced-stacked type. LC-DFTB2, however, presents some relevant differences regarding other conformers for S₀. Despite some state-order inversions, overall good agreement between methods was observed in the spectral shape, state character, and PECs. Nevertheless, DFT/MRCI predicts that the S₁ state should acquire a doubly excited-state character relevant to the excimer survival process and, therefore, cannot be completely described by the single reference methods used in this work. PECs also revealed an interesting relation between dissociation energies and the intermonomer charge-transfer interactions for some states.

Magnetic Circular Dichroism of Naphthalene Derivatives: A Coupled Cluster Singles and Approximate Doubles and Time-Dependent Density Functional Theory Study

The UV-vis absorption and magnetic circular dichroism spectra of naphthalene and some of its derivatives have been simulated at the Coupled Cluster Singles and Approximate Doubles (CC2) level of theory, and at the Time-Dependent Density Functional Theory (TD-DFT) level using the B3LYP and CAM-B3LYP functionals. DFT and CC2 predict in general opposite energetic ordering of the L_b and L_a transitions (in gas phase), as previously observed in adenine. The CC2 simulations of UV and MCD spectra show the best agreement with the experimental data. Analysis of the Cartesian components of the electric dipole transition strengths and the magnetic dipole transition moment between the excited states have been considered in the interpretation of the electronic transitions and the Faraday B term inversion among the naphthalene derivatives.

Molecular Electron Affinities Using the Generalized Kohn-Sham Semicanonical Projected Random Phase Approximation

The suitability of one-particle energies from the generalized Kohn-Sham semicanonical projected random phase approximation (GKS-spRPA) method for electron affinities of molecules is investigated. It is shown that the GKS-spPRA effective potential includes exact exchange and polarizability-dependent correlation terms that are necessary for the correct description of anionic systems. An O(N4) implementation that enables fast computation of electron affinities is presented. For model systems, I show that the GKS-spRPA approach is applicable for valence and nonvalence type anions with a maximum error of 0.13 eV for valence anionic states and 0.03 eV for nonvalence anionic states compared to equation of motion coupled cluster methods. For a series of perhalobenzene molecules, C₆X₆ (X= F, Cl, Br, and I), GKS-spRPA predicts that the ground-state character changes from a nonvalence-σ* type in C₆F₆^- to valence-π* in C₆Cl₆^- and valence-σ* in C₆Br₆^- and C₆I₆^-. Experimental implications of these findings are discussed.

Efficient implementation of isotropic cubic response functions for two-photon absorption cross sections within the self-consistent field approximation

Within the self-consistent field approximation, computationally tractable expressions for the isotropic second-order hyperpolarizability have been derived and implemented for the calculation of two-photon absorption cross sections. The novel tensor average formulation presented in this work allows for the evaluation of isotropic damped cubic response functions using only ∼3.3% (one-photon off-resonance regions) and ∼10% (one-photon resonance regions) of the number of auxiliary Fock matrices required when explicitly calculating all the needed individual tensor components. Numerical examples of the two-photon absorption cross section in the one-photon off-resonance and resonance regions are provided for alanine-tryptophan and 2,5-dibromo-1,4-bis(2-(4-diphenylaminophenyl)vinyl)-benzene. Furthermore, a benchmark set of 22 additional small- and medium-sized organic molecules is considered. In all these calculations, a quantitative assessment is made of the reduced and approximate forms of the cubic response function in the one-photon off-resonance regions and results demonstrate a relative error of less than ∼5% when using the reduced expression as compared to the full form of the isotropic cubic response function.

Planar Tetracoordinated Silicon (ptSi): Room-Temperature Stable Compounds Containing Anti-van't Hoff/Le Bel Silicon

While a variety of compounds containing planar tetracoordinated carbon (ptC), the so-called anti-van't Hoff/Le Bel carbon, are known experimentally, stable systems containing planar tetracoordinated silicon (ptSi) are barely known. As part of our studies on the application of stereoelectronically well-defined transition-metal fragments to stabilize silicon in unprecedented bonding modes, we report herein the synthesis and full characterization of a series of thermally stable complexes of the general formula [Tp'(CO)₂MSiC(R¹)C(R²)M(CO)₂Tp'] (M = Mo, W; R¹ = R² = Me or R¹ = H, R² = SiMe₃, Ph; Tp' = κ³-N,N',N″-hydridotris(3,5-dimethylpyrazolyl)borate), which incorporate a ptSi atom in addition to two ptC atoms. The complexes were obtained by reacting the metallasilylidyne complexes [Tp'(CO)₂M≡Si-M(CO)₂(PMe₃)Tp'] with alkynes R¹C≡CR² and were comprehensively analyzed by experimental studies and quantum chemical calculations. The analyses revealed that the ptSi atom is embedded in a tricyclic trapezoidal core featuring one internal SiC₂ and two outer M-Si-C three-membered rings, which are fused via two Si-C bonds. The structural peculiarities evoked by the presence of an anti-van't Hoff/Le Bel ptSi center, such as the short M-Si bonds, a nearly linear M-Si-M spine, long M-C bonds, and the presence of two planar tetracoordinated carbon atoms were elucidated by a detailed analysis of the electronic structure, suggesting that one factor for the stabilization of the ptSi geometry is the aromaticity of the central SiC₂ ring having two delocalized π electrons. Remarkably, the results further indicate the existence of both anti-van't Hoff/Le Bel carbon and silicon centers next to each other in the isolated complexes.

Towards a converged strategy for including microsolvation in reaction mechanism calculations

A major part of chemical conversions is carried out in the fluid phase, where an accurate modeling of the involved reactions requires to also take into account solvation effects. Implicit solvation models often cover these effects with sufficient accuracy but can fail drastically when specific solvent-solute interactions are important. In those cases, microsolvation, i.e., the explicit inclusion of one or more solvent molecules, is a commonly used strategy. Nevertheless, microsolvation also introduces new challenges-a consistent workflow as well as strategies how to systematically improve prediction performance are not evident. For the COSMO and COSMO-RS solvation models, this work proposes a simple protocol to decide if microsolvation is needed and how the corresponding molecular model has to look like. To demonstrate the improved accuracy of the approach, specific application examples are presented and discussed, i.e., the computation of aqueous pK_a values and a mechanistic study of the methanol mediated Morita-Baylis-Hillman reaction.

Two-Substrate Glyoxalase I Mechanism: A Quantum Mechanics/Molecular Mechanics Study

Glyoxalase I (GlxI) is an important enzyme that catalyzes the detoxification of methylglyoxal (MG) with the help of glutathione (H-SG). It is currently unclear whether MG and H-SG are substrates of GlxI or whether the enzyme processes hemithioacetal (HTA), which is nonenzymatically formed from MG and H-SG. Most previous studies have concentrated on the latter mechanism. Here, we study the two-substrate reaction mechanism of GlxI from humans (HuGlxI) and corn (ZmGlxI), which are Zn(II)-active and -inactive, respectively. Hybrid quantum mechanics/molecular mechanics calculations were used to obtain geometrical structures of the stationary points along reaction paths, and big quantum mechanical systems with more than 1000 atoms and free-energy perturbations were used to improve the quality of the calculated energies. We studied, on an equal footing, all reasonable reaction paths to the S- and R-enantiomers of HTA from MG and H-SG (the latter was considered in two different binding modes). The results indicate that the MG and H-SG reaction in both enzymes can follow the same path to reach S-HTA. However, the respective overall barriers and reaction energies are different for the two enzymes (6.1 and -9.8 kcal/mol for HuGlxI and 15.7 and -2.2 kcal/mol for ZmGlxI). The first reaction step to produce S-HTA is facilitated by a crystal water molecule that forms hydrogen bonds with a Glu and a Thr residue in the active site. The two enzymes also follow similar paths to R-HTA. However, the reactions reach a deprotonated and protonated R-HTA in the human and corn enzymes, respectively. The production of deprotonated R-HTA in HuGlxI is consistent with other theoretical and experimental works. However, our calculations show a different behavior for ZmGlxI (both S- and R-HTA can be formed in the enzyme with the alcoholic proton on HTA). This implies that Glu-144 of corn GlxI is not basic enough to keep the alcoholic proton. In HuGlxI, the two binding modes of H-SG that lead to S- and R-HTA are degenerate, but the barrier leading to R-HTA is lower than the barrier to S-HTA. On the other hand, ZmGlxI prefers the binding mode, which produces S-HTA; this observation is consistent with experiments. Based on the results, we present a modification for a previously proposed two-substrate reaction mechanism for ZmGlxI.

Linear Size Contraction of Ligand Protected Ag29 Clusters by Substituting Ag with Cu

There are only a few examples of atomically precise, ligand protected, bimetallic coinage metal clusters in which molecular structure remains essentially unchanged over a wide composition range starting from the corresponding homometallic species. Such model systems are particularly useful to study the dynamics of alloy formation on the nanoscale. Here we demonstrate the unusual reactivity of solvated metalloid-superatom Ag₂₉(BDT)₁₂(PPh₃)₄ (BDT = 1,3 benzenedithiol) clusters toward semiconducting Cu₁₂S₆(DPPPT)₄ (DPPPT = bis(diphenylphosphino)pentane) clusters as an efficient way to exchange multiple copper atoms into the atomically precise silver clusters without changing overall the structure type. Concentration-dependent UV-vis absorption and online mass spectrometry shows that 14 Cu atoms can be exchanged into the silver cluster. Beyond the 14 Cu atom exchange, the cluster degrades to smaller thiolates. Information on cluster structures is obtained from high-resolution ion mobility mass spectrometry, which shows a linear decrease in collision cross section (CCS) with each Ag/Cu exchanged. Several isomeric structures are calculated by density functional theory (DFT), and their calculated collision cross sections are used to identify the most stable isomers for each Ag/Cu exchange product. Ag/Cu exchange is essentially limited to the cluster surface/shell. The core appears not to be involved.

Real-space quantum-based refinement for cryo-EM: Q|R#3

Electron cryo-microscopy (cryo-EM) is rapidly becoming a major competitor to X-ray crystallography, especially for large structures that are difficult or impossible to crystallize. While recent spectacular technological improvements have led to significantly higher resolution three-dimensional reconstructions, the average quality of cryo-EM maps is still at the low-resolution end of the range compared with crystallography. A long-standing challenge for atomic model refinement has been the production of stereochemically meaningful models for this resolution regime. Here, it is demonstrated that including accurate model geometry restraints derived from ab initio quantum-chemical calculations (HF-D3/6-31G) can improve the refinement of an example structure (chain A of PDB entry 3j63). The robustness of the procedure is tested for additional structures with up to 7000 atoms (PDB entry 3a5x and chain C of PDB entry 5fn5) using the less expensive semi-empirical (GFN1-xTB) model. The necessary algorithms enabling real-space quantum refinement have been implemented in the latest version of qr.refine and are described here.

Pinacolone-Alcohol Gas-Phase Solvation Balances as Experimental Dispersion Benchmarks

The influence of distant London dispersion forces on the docking preference of alcohols of different size between the two lone electron pairs of the carbonyl group in pinacolone was explored by infrared spectroscopy of the OH stretching fundamental in supersonic jet expansions of 1:1 solvate complexes. Experimentally, no pronounced tendency of the alcohol to switch from the methyl to the bulkier tert-butyl side with increasing size was found. In all cases, methyl docking dominates by at least a factor of two, whereas DFT-optimized structures suggest a very close balance for the larger alcohols, once corrected by CCSD(T) relative electronic energies. Together with inconsistencies when switching from a C4 to a C5 alcohol, this points at deficiencies of the investigated B3LYP and in particular TPSS functionals even after dispersion correction, which cannot be blamed on zero point energy effects. The search for density functionals which describe the harmonic frequency shift, the structural change and the energy difference between the docking isomers of larger alcohols to unsymmetric ketones in a satisfactory way is open.

Quantum refinement with multiple conformations: application to the P-cluster in nitrogenase

X-ray crystallography is the main source of atomistic information on the structure of proteins. Normal crystal structures are obtained as a compromise between the X-ray scattering data and a set of empirical restraints that ensure chemically reasonable bond lengths and angles. However, such restraints are not always available or accurate for nonstandard parts of the structure, for example substrates, inhibitors and metal sites. The method of quantum refinement, in which these empirical restraints are replaced by quantum-mechanical (QM) calculations, has previously been suggested for small but interesting parts of the protein. Here, this approach is extended to allow for multiple conformations in the QM region by performing separate QM calculations for each conformation. This approach is shown to work properly and leads to improved structures in terms of electron-density maps and real-space difference density Z-scores. It is also shown that the quality of the structures can be gauged using QM strain energies. The approach, called ComQumX-2QM, is applied to the P-cluster in two different crystal structures of the enzyme nitrogenase, i.e. an Fe8S7Cys6 cluster, used for electron transfer. One structure is at a very high resolution (1.0 Å) and shows a mixture of two different oxidation states, the fully reduced PN state (Fe82+, 20%) and the doubly oxidized P2+ state (80%). In the original crystal structure the coordinates differed for only two iron ions, but here it is shown that the two states also show differences in other atoms of up to 0.7 Å. The second structure is at a more modest resolution, 2.1 Å, and was originally suggested to show only the one-electron oxidized state, P1+. Here, it is shown that it is rather a 50/50% mixture of the P1+ and P2+ states and that many of the Fe-Fe and Fe-S distances in the original structure were quite inaccurate (by up to 0.8 Å). This shows that the new ComQumX-2QM approach can be used to sort out what is actually seen in crystal structures with dual conformations and to give locally improved coordinates.

Covalent Grafting of Polyoxometalate Hybrids onto Flat Silicon/Silicon Oxide: Insights from POMs Layers on Oxides

Immobilization of polyoxometalates (POMs) onto oxides is relevant to many applications in the fields of catalysis, energy conversion/storage, or molecular electronics. Optimization and understanding the molecule/oxide interface is crucial to rationally improve the performance of the final molecular materials. We herein describe the synthesis and covalent grafting of POM hybrids with remote carboxylic acid functions onto flat Si/SiO₂ substrates. Special attention has been paid to the characterization of the molecular layer and to the description of the POM anchoring mode at the oxide interface through the use of various characterization techniques, including ellipsometry, AFM, XPS, and FTIR. Finally, electron transport properties were probed in a vertical junction configuration and energy level diagrams have been drawn and discussed in relation with the POM molecular electronic features inferred from cyclic-voltammetry, UV-visible absorption spectra, and theoretical calculations. The electronic properties of these POM-based molecular junctions are driven by the POM LUMO (d-orbitals) whatever the nature of the tether or the anchoring group.

Rational Design of Fe2 (μ-PR2 )2 (L)6 Coordination Compounds Featuring Tailored Potential Inversion

It was recently discovered that some redox proteins can thermodynamically and spatially split two incoming electrons towards different pathways, resulting in the one-electron reduction of two different substrates, featuring reduction potential respectively higher and lower than the parent reductant. This energy conversion process, referred to as electron bifurcation, is relevant not only from a biochemical perspective, but also for the ground-breaking applications that electron-bifurcating molecular devices could have in the field of energy conversion. Natural electron-bifurcating systems contain a two-electron redox centre featuring potential inversion (PI), i. e. with second reduction easier than the first. With the aim of revealing key factors to tailor the span between first and second redox potentials, we performed a systematic density functional study of a 26-molecule set of models with the general formula Fe₂ (μ-PR₂ )₂ (L)₆ . It turned out that specific features such as i) a Fe-Fe antibonding character of the LUMO, ii) presence of electron-donor groups and iii) low steric congestion in the Fe's coordination sphere, are key ingredients for PI. In particular, the synergic effects of i)-iii) can lead to a span between first and second redox potentials larger than 700 mV. More generally, the "molecular recipes" herein described are expected to inspire the synthesis of Fe₂ P₂ systems with tailored PI, of primary relevance to the design of electron-bifurcating molecular devices.

Dioxygen Binding to all 3d, 4d, and 5d Transition Metals from Coupled-Cluster Theory

Understanding how transition metals bind and activate dioxygen (O₂ ) is limited by experimental and theoretical uncertainties, making accurate quantum mechanical descriptors of interest. Here we report coupled-cluster CCSD(T) energies with large basis sets and vibrational and relativistic corrections for 160 3d, 4d, and 5d metal-O₂ systems. We define four reaction energies (120 in total for the 30 metals) that quantify O-O activation and reveal linear relationships between metal-oxygen and O-O binding energies. The CCSD(T) data can be combined with thermochemical cycles to estimate chemisorption and physisorption energies for each metal from metal oxide embedding energies, in good correlation with atomization enthalpies (R² =0.75). Spin-geometry variations can break the linearities, of interest to circumventing the Sabatier principle. Pt, Pd, Co, and Fe form a distinct group with the weakest O₂ binding. R² up to 0.84 between surface adsorption energies and our energies for MO₂ systems indicate relevance also to real catalytic systems.

One Electron Multiple Proton Transfer in Model Organic Donor-Acceptor Systems: Implications for High Frequency EPR

EPR spectroscopy is an important spectroscopic method for identification and characterization of radical species involved in many biological reactions. The tyrosyl radical is one of the most studied amino acid radical intermediates in biology. Often in conjunction with histidine residues, it is involved in many fundamental biological electron and proton transfer processes, such as in the water oxidation in photosystem II. As biological processes are typically extremely complicated and hard to control, molecular bio-mimetic model complexes are often used to clarify the mechanisms of the biological reactions. Here we present theoretical calculations to investigate the sensitivity of magnetic resonance parameters to proton-coupled electron transfer events, as well as conformational substates of the molecular constructs which mimic the tyrosine-histidine (Tyr-His) pairs found in a large variety of proteins. Upon oxidation of the phenol, the Tyr analogue, these complexes can perform not only one-electron one-proton transfer (EPT), but also one-electron two-proton transfers (E2PT). It is shown that in aprotic environment the g_X-components of the electronic g-tensor are extremely sensitive to the first proton transfer from the phenoxyl oxygen to the imidazole nitrogen (EPT product), leading to a significant increase of the g_X-value of up to 0.003, but are not sensitive to the second proton transfer (E2PT product). In the latter case the change of the g_X-value is much smaller (ca. 0.0001), which is too small to be distinguished even by high frequency EPR. The ¹⁴N hyperfine values are also too similar to allow differentiation between the different protonation states in EPT and E2PT. The magnetic resonance parameters were also calculated as a function of the rotation angles around single bonds. It was demonstrated that rotation of the phenoxyl group results in large positive changes (>0.001) in the g_X-values. Analysis of the data reveals that the main source of these changes is related to the strength of the H-bond between phenoxyl oxygen and the proton(s) on N₁ and N₂ positions of the imidazole.

Magnetic circular dichroism spectra from resonant and damped coupled cluster response theory

A computational expression for the Faraday A term of magnetic circular dichroism (MCD) is derived within coupled cluster response theory and alternative computational expressions for the B term are discussed. Moreover, an approach to compute the (temperature-independent) MCD ellipticity in the context of coupled cluster damped response is presented, and its equivalence with the stick-spectrum approach in the limit of infinite lifetimes is demonstrated. The damped response approach has advantages for molecular systems or spectral ranges with a high density of states. Illustrative results are reported at the coupled cluster singles and doubles level and compared to time-dependent density functional theory results.

Building up Strain in One Step: Synthesis of an Edge-Fused Double Silacyclobutene from an Extensively Trichlorosilylated Butadiene Dianion

The exhaustive trichlorosilylation of hexachloro‐1,3‐butadiene was achieved in one step by using a mixture of Si₂Cl₆ and [nBu₄N]Cl (7:2 equiv) as the silylation reagent. The corresponding butadiene dianion salt [nBu₄N]₂[1] was isolated in 36 % yield after recrystallization. The negative charges of [1]²⁻ are mainly delocalized across its two carbanionic (Cl₃Si)₂C termini (α‐effect of silicon) such that the central bond possesses largely C=C double‐bond character. Upon treatment with 4 equiv of HCl, [1]²⁻ is converted into neutral 1,2,3,4‐tetrakis(trichlorosilyl)but‐2‐ene, 3. The Cl⁻ acceptor AlCl₃, induces a twofold ring‐closure reaction of [1]²⁻ to form a six‐membered bicycle 4 in which two silacyclobutene rings are fused along a shared C=C double bond (84 %). Compound 4, which was structurally characterized by X‐ray crystallography, undergoes partial ring opening to a monocyclic silacyclobutene 2 in the presence of HCl, but is thermally stable up to at least 180 °C.

Does the crystal structure of vanadium nitrogenase contain a reaction intermediate? Evidence from quantum refinement

Recently, a crystal structure of V-nitrogenase was presented, showing that one of the µ2 sulphide ions in the active site (S2B) is replaced by a lighter atom, suggested to be NH or NH2, i.e. representing a reaction intermediate. Moreover, a sulphur atom is found 7 Å from the S2B site, suggested to represent a storage site for this ion when it is displaced. We have re-evaluated this structure with quantum refinement, i.e. standard crystallographic refinement in which the empirical restraints (employed to ensure that the final structure makes chemical sense) are replaced by more accurate quantum-mechanical calculations. This allows us to test various interpretations of the structure, employing quantum-mechanical calculations to predict the ideal structure and to use crystallographic measures like the real-space Z-score and electron-density difference maps to decide which structure fits the crystallographic raw data best. We show that the structure contains an OH--bound state, rather than an N2-derived reaction intermediate. Moreover, the structure shows dual conformations in the active site with ~ 14% undissociated S2B ligand, but the storage site seems to be fully occupied, weakening the suggestion that it represents a storage site for the dissociated ligand.

N-Heterocyclic Silylenes as Ligands in Transition Metal Carbonyl Chemistry: Nature of Their Bonding and Supposed Innocence

A study on the reactivity of the N-heterocyclic silylene Dipp2 NHSi (1,3-bis(diisopropylphenyl)-1,3-diaza-2-silacyclopent-4-en-2-yliden) with the transition metal complexes [Ni(CO)4 ], [M(CO)6 ] (M=Cr, Mo, W), [Mn(CO)5 (Br)] and [(η5 -C5 H5 )Fe(CO)2 (I)] is reported. We demonstrate that N-heterocyclic silylenes, the higher homologues of the now ubiquitous NHC ligands, show a remarkably different behavior in coordination chemistry compared to NHC ligands. Calculations on the electronic features of these ligands revealed significant differences in the frontier orbital region which lead to some peculiarities of the coordination chemistry of silylenes, as demonstrated by the synthesis of the dinuclear, NHSi-bridged complex [{Ni(CO)2 (μ-Dipp2 NHSi)}2 ] (2), complexes [M(CO)5 (Dipp2 NHSi)] (M=Cr 3, Mo 4, W 5), [Mn(CO)3 (Dipp2 NHSi)2 (Br)] (9) and [(η5 -C5 H5 )Fe(CO)2 (Dipp2 NHSi-I)] (10). DFT calculations on several model systems [Ni(L)], [Ni(CO)3 (L)], and [W(CO)5 (L)] (L=NHC, NHSi) reveal that carbenes are typically the much better donor ligands with a larger intrinsic strength of the metal-ligand bond. The decrease going from the carbene to the silylene ligand is mainly caused by favorable electrostatic contributions for the NHC ligand to the total bond strength, whereas the orbital interactions were often found to be higher for the silylene complexes. Furthermore, we have demonstrated that the contribution of σ- and π-interaction depends significantly on the system under investigation. The σ-interaction is often much weaker for the NHSi ligand compared to NHC but, interestingly, the π-interaction prevails for many NHSi complexes. For the carbonyl complexes, the NHSi ligand is the better σ-donor ligand, and contributions of π-symmetry play only a minor role for the NHC and NHSi co-ligands.

Structural Characterization and Lifetimes of Triple-Stranded Helical Coinage Metal Complexes: Synthesis, Spectroscopy and Quantum Chemical Calculations

This work reports on a series of polynuclear complexes containing a trinuclear Cu, Ag, or Au core in combination with the fac-isomer of the metalloligand [Ru(pypzH)3 ](PF6 )2 (pypzH=3-(pyridin-2-yl)pyrazole). These (in case of the Ag and Au containing species) newly synthesized compounds of the general formula [{Ru(pypz)3 }2 M3 ](PF6 ) (2: M=Cu; 3: M=Ag; 4: M=Au) contain triple-stranded helical structures in which two ruthenium moieties are connected by three N-M-N (M=Cu, Ag, Au) bridges. In order to obtain a detailed description of the structure both in the electronic ground and excited states, extensive spectroscopic and quantum chemical calculations are applied. The equilateral coinage metal core triangle in the electronic ground state of 2-4 is distorted in the triplet state. Furthermore, the analyses offer a detailed description of electronic excitations. By using time-resolved IR spectroscopy from the microsecond down to the nanosecond regime, both the vibrational spectra and the lifetime of the lowest lying electronically excited triplet state can be determined. The lifetimes of these almost only non-radiative triplet states of 2-4 show an unusual effect in a way that the Au-containing complex 4 has a lifetime which is by more than a factor of five longer than in case of the Cu complex 2. Thus, the coinage metals have a significant effect on the electronically excited state, which is localized on a pypz ligand coordinated to the Ru atom indicating an unusual cooperative effect between two moieties of the complex.

ReSCoSS: a flexible quantum chemistry workflow identifying relevant solution conformers of drug-like molecules

Conformational equilibria are at the heart of drug design, yet their energetic description is often hampered by the insufficient accuracy of low-cost methods. Here we present a flexible and semi-automatic workflow based on quantum chemistry, ReSCoSS, designed to identify relevant conformers and predict their equilibria across different solvent environments in the Conductor-like Screening Model for Real Solvents (COSMO-RS) framework. We demonstrate the utility and accuracy of the workflow through conformational case studies on several drug-like molecules from literature where relevant conformations are known. We further show that including ReSCoSS conformers significantly improves COSMO-RS based predictions of physicochemical properties over single-conformation approaches. ReSCoSS has found broad adoption in the in-house drug discovery and development work streams and has contributed to establishing quantum-chemistry methods as a strategic pillar in ligand discovery.

Photoinduced Changes in Aromaticity Facilitate Electrocyclization of Dithienylbenzene Switches

The concepts of excited-state aromaticity and antiaromaticity have in recent years with increasing frequency been invoked to rationalize the photochemistry of cyclic conjugated organic compounds, with the long-term goal of using these concepts to improve the reactivities of such compounds toward different photochemical transformations. In this regard, it is of particular interest to assess how the presence of a benzene motif affects photochemical reactivity, as benzene is well-known to completely change its aromatic character in its lowest excited states. Here, we investigate how a benzene motif influences the photoinduced electrocyclization of dithienylethenes, a major class of molecular switches. Specifically, we report on the synthesis of a dithienylbenzene switch where the typical nonaromatic, ethene-like motif bridging the two thienyl units is replaced by a benzene motif, and show that this compound undergoes electrocyclization upon irradiation with UV-light. Furthermore, through a detailed quantum chemical analysis, we demonstrate that the electrocyclization is driven jointly and synergistically by the loss of aromaticity in this motif from the formation of a reactive, antiaromatic excited state during the initial photoexcitation, and by the subsequent relief of this antiaromaticity as the reaction progresses from the Franck–Condon region. Overall, we conclude that photoinduced changes in aromaticity facilitate the electrocyclization of dithienylbenzene switches.

Hole-hole Tamm-Dancoff-approximated density functional theory: A highly efficient electronic structure method incorporating dynamic and static correlation

The study of photochemical reaction dynamics requires accurate as well as computationally efficient electronic structure methods for the ground and excited states. While time-dependent density functional theory (TDDFT) is not able to capture static correlation, complete active space self-consistent field methods neglect much of the dynamic correlation. Hence, inexpensive methods that encompass both static and dynamic electron correlation effects are of high interest. Here, we revisit hole-hole Tamm-Dancoff approximated (hh-TDA) density functional theory for this purpose. The hh-TDA method is the hole-hole counterpart to the more established particle-particle TDA (pp-TDA) method, both of which are derived from the particle-particle random phase approximation (pp-RPA). In hh-TDA, the N-electron electronic states are obtained through double annihilations starting from a doubly anionic (N+2 electron) reference state. In this way, hh-TDA treats ground and excited states on equal footing, thus allowing for conical intersections to be correctly described. The treatment of dynamic correlation is introduced through the use of commonly employed density functional approximations to the exchange-correlation potential. We show that hh-TDA is a promising candidate to efficiently treat the photochemistry of organic and biochemical systems that involve several low-lying excited states-particularly those with both low-lying ππ^* and nπ^* states where inclusion of dynamic correlation is essential to describe the relative energetics. In contrast to the existing literature on pp-TDA and pp-RPA, we employ a functional-dependent choice for the response kernel in pp- and hh-TDA, which closely resembles the response kernels occurring in linear response and collinear spin-flip TDDFT.

XO-PBC: An Accurate and Efficient Method for Molecular Crystals

In this work, we propose the XO-PBC method, which combines the eXtended ONIOM method (XO) with the periodic boundary condition (PBC) for the description of molecular crystals. XO-PBC tries to embed a finite cluster cut out from the solid into the periodic environment, making it feasible to employ advanced molecular quantum chemistry methods, which are usually prohibitively expensive for direct PBC calculations. In particular, XO-PBC utilizes the results from force calculations to design the scheme to fragment the molecule when crystals are made of large molecules and to select cluster model systems automatically consisting of dimer up to tetramer interactions for embedding. By applying an appropriate theory to each model, a satisfactory accuracy for the system under study is ensured, while a high efficiency is achieved with massively parallel computing by distributing model systems onto different processors. A comparison of the XO-PBC calculations with the conventional direct PBC calculations at the B3LYP level demonstrates its accuracy at substantially low cost for the description of molecular crystals. The usefulness of the XO-PBC method is further exemplified, showing that XO-PBC is able to predict the lattice energies of various types of molecular crystals within chemical accuracy (<4 kJ/mol) when the doubly hybrid density functional XYG3 is used as the target high level and the periodic PBE as the basic low level. The XO-PBC method provides a general protocol that brings the great predictive power of advanced electronic structure methods from molecular systems to the extended solids.

Mechanistic Investigation into the Acetate-Initiated Catalytic Trimerization of Aliphatic Isocyanates: A Bicyclic Ride

The acetate-initiated aliphatic isocyanate trimerization to isocyanurate was investigated by state-of-the-art analytical and computational methods. Although the common cyclotrimerization mechanism assumes the consecutive addition of three equivalents of isocyanate to acetate prior to product formation, we found that the underlying mechanism is more complex. In this work, we demonstrate that the product, in fact, is formed via the connection of two unexpected catalytic cycles, with acetate being only the precatalyst. The initial discovery of a precatalyst activation by quantum chemical computations and the resulting first catalysis cycle were corroborated by mass spectrometric and NMR experiments, thereby additionally revealing a catalyst migration to the second catalytic cycle. These results were further confirmed by computations, completing the full mechanistic understanding of this catalytic system. Identification of a side product with undesired properties for final coating applications allows for process optimization in the chemical industry.

Characterization of a Mixed-Valence Ru(II)/Ru(III) Ion-Pair Complex. Unexpected High-Frequency Electron Paramagnetic Resonance Evidence for Ru(III)-Ru(III) Dimer Coupling

In this contribution, we report the synthesis and full characterization of the first mixed-valence Ru(II)/Ru(III) ion-pair complex, [Ru^II(bipy)₂(pic)]⁺[cis-Ru^IIICl₂(pic)₂]^-, in the solid state and in aqueous solution, where bipy = 2,2'-bipyridine and pic^- = picolinate. In addition, unexpected high-frequency electron paramagnetic resonance evidence for interactions between two neighboring Ru(III) ions, resulting in a triplet state, S = 1, was found.

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.