We present the first comprehensive study on the prediction of reactivity for propynamides. Covalent inhibitors like propynamides often show improved potency, selectivity, and unique pharmacologic properties compared to their non-covalent counterparts. In order to achieve this, it is essential to tune the reactivity of the warhead. This study shows how three different in silico methods can predict the in vitro properties of propynamides, a covalent warhead class integrated into approved drugs on the market. Whereas the electrophilicity index is only applicable to individual subclasses of substitutions, adduct formation and transition state energies have a good predictability for the in vitro reactivity with glutathione (GSH). In summary, the reported methods are well suited to estimate the reactivity of propynamides. With this knowledge, the fine tuning of the reactivity is possible which leads to a speed up of the design process of covalent drugs.

In the past decade, the pharmaceutical industry has paid closer attention to covalent drugs. Differently from standard noncovalent drugs, these compounds can exhibit peculiar properties, such as higher potency or longer duration of target inhibition with a potentially lower dosage. These properties are mainly driven by the reactive functional group present in the compound, the so-called warhead that forms a covalent bond with a specific nucleophilic amino-acid on the target. In this work, we report the possibility to combine ab initio activation energies with machine-learning to estimate covalent compound intrinsic reactivity. The idea behind this approach is to have a precise estimation of the transition state barriers, and thus of the compound reactivity, but with the speed of a machine-learning algorithm. We call this method "BIreactive". Here, we demonstrate this approach on acrylamides and 2-chloroacetamides, two warhead classes that possess different reaction mechanisms. In combination with our recently implemented truncation algorithm, we also demonstrate the possibility to use BIreactive not only for fragments but also for lead-like molecules. The generic nature of this approach allows also the extension to several other warheads. The combination of these factors makes BIreactive a valuable tool for the covalent drug discovery process in a pharmaceutical context.

Resolving the structural dynamics of the initial steps of chemical reactions is challenging. We report the femtosecond time-resolved wide-angle x-ray scattering of the photodissociation of diiodomethane in cyclohexane. The data reveal with structural detail how the molecule dissociates into radicals, how the radicals collide with the solvent, and how they form the photoisomer. We extract how translational and rotational kinetic energy is dispersed into the solvent. We also find that 85% of the primary radical pairs are confined to their original solvent cage and discuss how this influences the downstream recombination reactions.

Drug discovery is an expensive and time-consuming process. To make this process more efficient quantum chemistry methods can be employed. The electrophilicity index is one property that can be calculated by quantum chemistry methods, and if calculated correctly gives insight into the reactivity of covalent inhibitors. Herein we present the usage of the electrophilicity index on three common warheads, i.e., acrylamides, 2-chloroacetamides, and propargylamides. We thoroughly examine the properties of the electrophilicity index, show which pitfalls should be avoided, and what the requirements to successfully apply the electrophilicity index are.

Small-angle X-ray scattering (SAXS) is a widely used experimental technique, providing structural and dynamic insight into soft-matter complexes and biomolecules under near-native conditions. However, interpreting the one-dimensional scattering profiles in terms of three-dimensional structures and ensembles remains challenging, partly because it is poorly understood how structural information is encoded along the measured scattering angle. We combined all-atom SAXS-restrained ensemble simulations, simplified continuum models, and SAXS experiments of a n-dodecyl-β-d-maltoside (DDM) micelle to decipher the effects of model asymmetry, shape fluctuations, atomic disorder, and atomic details on SAXS curves. Upon interpreting the small-angle regime, we find remarkable agreement between (i) a two-component triaxial ellipsoid model fitted against the data and (ii) a SAXS-refined all-atom ensemble. However, continuum models fail at wider angles, even if they account for shape fluctuations, disorder, and asymmetry of the micelle. We conclude that modeling atomic details is mandatory for explaining SAXS curves at wider angles.

Small-angle X-ray scattering (SAXS) is a widely used experimental technique, providing structural and dynamic insight into soft-matter complexes and biomolecules under near-native conditions. However, interpreting the one-dimensional scattering profiles in terms of three-dimensional structures and ensembles remains challenging, partly because it is poorly understood how structural information is encoded along the measured scattering angle. We combined all-atom SAXS-restrained ensemble simulations, simplified continuum models, and SAXS experiments of a n-dodecyl-beta-D-maltoside (DDM) micelle to decipher the effects of model asymmetry, shape fluctuations, atomic disorder, and atomic details on SAXS curves. Upon interpreting the small-angle regime, we find remarkable agreement between (i) a two-component triaxial ellipsoid model fitted against the data and (ii) a SAXS-refined all-atom ensemble. However, continuum models fail at wider angles, even if they account for shape fluctuations, disorder, and asymmetry of the micelle. We conclude that modeling atomic details is mandatory for explaining SAXS curves at wider angles.

Small- and wide-angle X-ray scattering (SAXS/WAXS/SWAXS) have evolved to be accurate tools used to gain structural information of biomolecules in solution. However, the interpretation of SWAXS data remains challenging owing to the low information content of the data and scattering contributions from the solvent. In recent years, methods for the interpretation of SWAXS data based on explicit-solvent molecular dynamics (MD) simulations have become increasingly popular. The physicochemical information in the MD force fields complements the low-information SWAXS data, thereby greatly reducing the risk of overfitting, and the explicit-solvent models may accurately account for scattering contributions from the solvent. In this chapter, we provide a practical introduction to MD-based methods for the interpretation of SWAXS data. First, we present the back-calculation of a SWAXS curve from an MD trajectory as required to validate an MD simulation against experimental SWAXS data. Second, we present the structure refinement of an atomic model against SWAXS data using SAXS-driven MD simulations. Common technical problems together with appropriate solutions are discussed.

Small-angle X-ray scattering (SAXS) is a widely used experimental technique, providing structural and dynamic insight into soft-matter complexes and biomolecules under near-native conditions. However, interpreting the one-dimensional scattering profiles in terms of three-dimensional structures and ensembles remains challenging, partly because it is poorly understood how structural information is encoded along the measured scattering angle. We combined all-atom SAXS-restrained ensemble simulations, simplified continuum models, and SAXS experiments of a n-dodecyl-β-D-maltoside (DDM) micelle to decipher the effects of model asymmetry, shape fluctuations, atomic disorder, and atomic details on SAXS curves. Upon interpreting the small-angle regime, we find remarkable agreement between (i) a two-component tri-axial ellipsoid model fitted against the data with (ii) a SAXS-refined all-atom ensemble. However, continuum models fail at wider angles, even if they account for shape fluctuations, disorder, and asymmetry of the micelle. We conclude that modelling atomic details is mandatory for explaining the entire SAXS curve, and that SAXS-restrained ensemble simulations are a useful tool for interpreting SAXS data of soft-matter complexes in terms of both average structures and conformational heterogeneity.

Breaking down the calculated interaction energy between two or more fragments into well-defined terms enables a physically meaningful understanding of chemical bonding. Energy decomposition analysis (EDA) is a powerful method that connects the results of accurate quantum chemical calculations with the Lewis electron-pair bonding model. The combination of EDA with natural orbitals for chemical valence (NOCV) links the heuristic Lewis picture with quantitative molecular orbital theory complemented by Pauli repulsion and Coulombic interactions. The EDA-NOCV method affords results that provide a physically sound picture of chemical bonding between any atoms. We present and discuss results for the prototypical main-group diatomics H-2, N-2, CO and BF, before comparing bonding in N-2 and C2H2 with that in heavier homologues. The discussion on multiply bonded species is continued with a description of B-2 and its N-heterocyclic carbene adducts.

Intrinsically disordered proteins (IDPs) play key roles in biology and disease, rationalizing the wide interest in deriving accurate solution ensembles of IDPs. Molecular dynamics (MD) simulations of IDPs often suffer from force-field inaccuracies, suggesting that simulations must be complemented by experimental data to obtain physically correct ensembles. We present a method for integrating small-angle X-ray scattering (SAXS) data on-the-fly into MD simulations of disordered systems, with the aim to bias the conformational sampling toward agreement with ensemble-averaged SAXS data. By coupling a set of parallel replicas to the data and following the principle of maximum entropy, this method applies only a minimal bias. Using the RS peptide as a test case, we analyze the influence of (i) the number of parallel replicas, (ii) the scaling of the force constant for the SAXS-derived biasing energy with the number of parallel replicas, and (iii) the force field. The refined ensembles are cross-validated against experimental 3JHN-Hα couplings and further compared in terms of Cα distance maps and secondary structure content. Remarkably, we find that the applied force field only has a small influence on the SAXS-refined ensemble, suggesting that incorporating SAXS data into MD simulations may greatly reduce the force-field bias.

Quantum chemical calculations of the main-group compounds E[C(NHCMe )2 ]2 (E=Be, B+ , C2+ , N3+ , Mg, Al+ , Si2+ , P3+ ) have been carried out using density functional theory at the BP86/def2-TZVPP and BP86-D3(BJ)/def2-TZVPP levels of theory. The geometry optimization at BP86/def2-TZVPP gives equilibrium structures with two-coordinated species E and bending angles C-E-C between 152.5° (E=Be) and 110.5° (E=Al). Inclusion of dispersion forces at BP86-D3(BJ)/def2-TZVPP yields a three-coordinated beryllium compound Be[C(NHCMe )2 ]2 as the only energy minimum form. Three-coordinated isomers are found besides the two-coordinated energy minima for the boron and carbon cations B[C(NHCMe )2 ]2+ and C[C(NHCMe )2 ]22+ . The three-coordinated form of the boron compound is energetically lower lying than the two-coordinated form, while the opposite trend is calculated for the carbon species. The theoretically predicted bond dissociation energies suggest that all compounds are viable species for experimental studies. The X-ray structure of the benzoannelated homologue of P[C(NHCMe )2 ]23+ that was recently reported by Dordevic et al. agrees quite well with the calculated geometry of the molecule. A detailed bonding analysis using charge and energy decomposition methods shows that the two-coordinated neutral compounds Be[C(NHCMe )2 ]2 and Mg[C(NHCMe )2 ]2 possess strongly positively charged atoms Be and Mg. The carbodicarbene groups C(NHCMe )2 serve as acceptor ligands in the compounds and may be sketched with dative bonds (NHCMe )2 C←E→C(NHCMe )2 (E=Be, Mg). Dative bonds in which the carbones C(NHCMe )2 are donor ligands are suggested for the cations (NHCMe )2 C→E←C(NHCMe )2 (E=B+ , Al+ ). The dications and trications possess electron-sharing bonds in which the bonding situation is best described with the formula [(NHCMe )2 C]+ -E-[C(NHCMe )2 ]+ (E=C, Si, N+ , P+ ).

•The relevance of dative bonding in main group chemistry is discussed in the light of the progress which was made in the last decade.•The focus of the work lies on the analysis of the bonding situation using modern methods of quantum chemistry.

The formation and X‐ray structure analysis of the PtIV complex [(CH2C{PPh2C6H4}2)PtI2] is reported. The molecule possesses the orthometalated ligand (PPh3)2C→CH2, which serves via its C2 fragment as an unprecedented four‐electron σ donor.

The formation and X-ray structure analysis of the Pt-IV complex [(CH2C{PPh2C6H4}(2))PtI2] is reported. The molecule possesses the orthometalated ligand (PPh3)(2)CCH2, which serves via its C-2 fragment as an unprecedented four-electron sigma donor.

A summary of theoretical and experimental work in the area of low-coordinated compounds of boron and group-14 atoms C-Sn in the last decade is presented. The focus of the account lies on molecules EL2, E2L2 and E3L3, which possess dative bonds between one, two or three atoms E and σ-donor ligands L that stabilize the atoms E through L→E donor-acceptor interactions. The interplay between theory and experiment provides detailed insight into the bonding situation of the molecules, which serves as guideline for the synthesis of molecules that possess unusual bonding motifs.

Condensation reaction of asymmetric triamine (spermidine) with guanidine hydrochloride provides a phantom structure with selective formation of rings in the repeat unit. The intermolecular condensation between amine and guanidine hydrochloride can provide either a linear structure or six- or seven-membered rings in the repeat unit by elimination of one or three molecules of ammonia, respectively, per repeat unit. The preference of formation of rings and mechanistic aspects are studied by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry, 1D, 2D NMR, and quantum chemical calculations.

Quantum chemical calculations using the complete active space of the valence orbitals have been carried out for HnCCHn (n=0-3) and N-2. The quadratic force constants and the stretching potentials of HnCCHn have been calculated at the CASSCF/cc-pVTZ level. The bond dissociation energies of the C-C bonds of C-2 and HCCH were computed using explicitly correlated CASPT2-F12/cc-pVTZ-F12 wave functions. The bond dissociation energies and the force constants suggest that C-2 has a weaker C-C bond than acetylene. The analysis of the CASSCF wavefunctions in conjunction with the effective bond orders of the multiple bonds shows that there are four bonding components in C-2, while there are only three in acetylene and in N-2. The bonding components in C-2 consist of two weakly bonding sigma bonds and two electron-sharing bonds. The bonding situation in C-2 can be described with the sigma bonds in Be-2 that are enforced by two bonds. There is no single Lewis structure that adequately depicts the bonding situation in C-2. The assignment of quadruple bonding in C-2 is misleading, because the bond is weaker than the triple bond in HCCH.

Not the number of bonds but the strength of the total σ bonding in C2, which is suggested by several groups to be much weaker than in acetylene, is at the core of the controversy.

A combined experimental and theoretical study on the main-group tricarbonyls [B(CO)3 ] in solid noble-gas matrices and [C(CO)3 ](+) in the gas phase is presented. The molecules are identified by comparing the experimental and theoretical IR spectra and the vibrational shifts of nuclear isotopes. Quantum chemical ab initio studies suggest that the two isoelectronic species possess a tilted η(1) (μ1 -CO)-bonded carbonyl ligand, which serves as an unprecedented one-electron donor ligand. Thus, the central atoms in both complexes still retain an 8-electron configuration. A thorough analysis of the bonding situation gives quantitative information about the donor and acceptor properties of the different carbonyl ligands. The linearly bonded CO ligands are classical two-electron donors that display classical σ-donation and π-back-donation following the Dewar-Chatt-Duncanson model. The tilted CO ligand is a formal one-electron donor that is bonded by σ-donation and π-back-donation that involves the singly occupied orbital of the radical fragments [B(CO)2 ] and [C(CO)2 ](+) .

Quantum chemical calculations using density functional theory with the TPSS+D3(BJ) and M06-2X+D3(ABC) functionals have been carried out to understand the mechanisms of catalyst-free hydrogermylation/hydrostannylation reactions between the two-coordinate hydrido-tetrylenes :E(H)(L(+) ) (E=Ge or Sn, L(+) =N(Ar(+) )(SiiPr3 ); Ar(+) =C6 H2 {C(H)Ph2 }2 iPr-2,6,4) and a range of unactivated terminal (C2 H3 R, R=H, Ph, or tBu) and cyclic [(CH)2 (CH2 )2 (CH2 )n , n=1, 2, or 4] alkenes. The calculations suggest that the addition reactions of the germylenes and stannylenes to the cyclic and acyclic alkenes occur as one-step processes through formal [2+2] addition of the E-H fragment across the C-C π bond. The reactions have moderate barriers and are weakly exergonic. The steric bulk of the tetrylene amido groups has little influence on the activation barriers and on the reaction energies of the anti-Markovnikov pathway, but the Markovnikov addition is clearly disfavored by the size of the substituents. The addition of the tetrylenes to the cyclic alkenes is less exergonic than the addition to the terminal alkenes, which agrees with the experimentally observed reversibility of the former reactions. The hydrogermylation reactions have lower activation energies and are more exergonic than the stannylene addition. An energy decomposition analysis of the transition state for the hydrogermylation of cyclohexene shows that the reaction takes place with simultaneous formation of the Ge-C and (Ge)H-C' bonds. The dominant orbitals of the germylene are the σ-type lone pair MO of Ge, which serves as a donor orbital, and the vacant p(π) MO of Ge, which acts as acceptor orbital for the π* and π MOs of the olefin. Inspection of the transition states of some selected reactions suggests that the differences between the activation energies come from a delicate balance between the deformation energies of the interacting species and their interaction energies.