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In this contribution, we revisit the neglected and forgotten cationic, air-stable, 18-valence electron, heteroleptic sandwich complex (cycloheptatrienyl)(cyclopentadienyl)manganese, which was reported independently by Fischer and by Pauson about 50 years ago. Using advanced high-power LED photochemical synthesis, an expedient rapid access to the parent complex and to functionalized derivatives with alkyl, carboxymethyl, bromo, and amino substituents was developed. A thorough study of these "tromancenium" salts by a range of spectroscopic techniques (1H/13C/55Mn-NMR, IR, UV-vis, HRMS, XRD, XPS, EPR), cyclic voltammetry (CV), and quantum chemical calculations (DFT) shows that these manganese sandwich complexes are unique metallocenes with quite different chemical and physical properties in comparison to those of isoelectronic cobaltocenium salts or (cycloheptatrienyl)(cyclopentadienyl) sandwich complexes of the early transition metals. Electrochemically, all tromancenium ions undergo a chemically partially reversible oxidation and a chemically irreversible reduction at half-wave or peak potentials that respond to the substituents at the Cp deck. As exemplarily shown for the parent tromancenium ion, the product generated during the irreversible reduction process reverts at least partially to the starting material upon reoxidation. Quantum-chemical calculations of the parent tromancenium salt indicate that metal-ligand bonding is distinctly weaker for the cycloheptatrienyl ligand in comparison to that of the cyclopentadienyl ligand. Both the HOMO and the LUMO are metal and cycloheptatrienyl-ligand centered, indicating that chemical reactions will occur either metal-based or at the seven-membered ring, but not on the cyclopentadienyl ligand. published

In this work, a set of density-functional tight-binding (DFTB) parameters for the Zr–Zr, Zr–O, Y–Y, Y–O, and Zr–Y interactions was developed for bulk and surface simulations of ZrO2 (zirconia), Y2O3 (yttria), and yttria-stabilized zirconia (YSZ) materials. The parameterization lays the ground work for realistic simulations of zirconia-, yttria-, and YSZ-based electrolytes in solid oxide fuel cells and YSZ-based catalysts on long timescales and relevant size scales. The parameterization was validated for the zirconia and yttria polymorphs observed under standard conditions based on density functional theory calculations and experimental data. Additionally, we performed DFTB-based molecular dynamics (MD) simulations to compute structural and vibrational properties of these materials. The results show that the parameters can give a qualitatively correct phase ordering of zirconia, where the tetragonal phase is more stable than the cubic phase at a lower temperature. The lattice parameters are only slightly overestimated by 0.05–0.1 Å (2% error), still within the typical accuracy of first-principles methods. Additionally, the MD results confirm that zirconia and yttria phases are stable against transformations under standard conditions. The parameterization also predicts that vibrational spectra are within the range of 100–1000 cm–1 for zirconia and 100–800 cm–1 for yttria, which is in good agreement with predictions both from full quantum mechanics and a recently developed classical force field. To further demonstrate the advantage of the developed DFTB parameters in terms of computational resources, we conducted DFTB/MD simulations of the YSZ4 and YS12 models containing approximately 750 atoms.

To the best of our knowledge, this is the first molecular dynamics simulation study on the dimeric form of the LuxS enzyme from Vibrio cholerae to evaluate its structural and dynamical properties including the dynamics of the interface formed by the two monomeric chains of the enzyme. The dynamics of the interfacial region were investigated in terms of inter-residual contacts and the associated interface area of the enzyme in its ligand-free and ligand–bound states which produced characteristics contrast in the interfacial dynamics. Moreover, the binding patterns of the two inhibitors (RHC and KRI) to the enzyme forming two different enzyme–ligand complexes were analyzed which pointed towards a varying inhibition potential of the inhibitors as also revealed by the free energies of ligand binding. It is shown that KRI is a more potent inhibitor than RHC – a substrate analogue, showing correlation with experimental data. Moreover, the role of a loop in chain B of the enzyme was found to facilitate the binding of RHC similar to that of the substrate, while KRI demonstrates a differing binding pattern. The computation of the free energy of binding for the two ligands was also carried out via thermodynamic integration which ultimately served to correlate the dynamical properties with the inhibition potential of two different ligands against the enzyme. Furthermore, this successful study provides a rational to suggest novel LuxS inhibitors which could become promising candidates to treat the diseases caused by a broad variety of bacterial species.

For more than half a century computer simulations were developed and employed to study ensemble properties of a wide variety of atomic and molecular systems with tremendous success. Nowadays, a selection of force-fields is available that describe the interactions in such systems. A key feature of force-fields is an adequate description of the electrostatic potential (ESP). Several force-fields model the ESP via point charges positioned at the atom centers. A major shortcoming of this approach, its inability to model anisotropies in the ESP, can be mitigated using additional charge sites. It has been shown that nitrogen is the most problematic element abundant in many polymers as well as large molecules of biological origin. To tackle this issue, small organic molecules containing a single nitrogen atom were studied. In performing rigorous scans of the surroundings of these nitrogen atoms, positions where a single extra charge can enhance the ESP description the most were identified. Significant improvements are found for ammonia, amines, and amides. Interestingly, the optimal location for the extra charge does not correlate with the chemically intuitive position of the nitrogen lone pair. In fact, the placement of an extra charge in the lone-pair location does not lead to significant improvements in most cases.

To the best of our knowledge, the current study based on ab initio quantum mechanical charge field molecular dynamics (QMCF-MD) is the first to explore the difference in the hydration behavior between Mn(II)- and Mg(II)-associated porphyrins (Mn(II)-POR and Mg(II)-POR) in aqueous solution. The simulation study highlights similar and dissimilar characteristics of the structural, dynamical, and thermodynamical properties of these closely related metals bound to porphyrins in aqueous solution. The structural analysis is based on radial and angular distribution functions, coordination number distributions, and angular-radial distributions. Both hydrated systems demonstrate similar pentacoordinated structures formed via the axial coordination of one water molecule to the metal ion in addition to the four nitrogen atoms of the porphyrin ring. However, in the case of Mn(II)-POR, the formation of a distorted square pyramidal geometry was observed. It was envisaged as a weak coordination of the water molecule to the Mn(II) atom and thus higher atomic fluctuation for all atoms in contrast to that for the hydrated Mg(II)-POR. The dynamical data in terms of the mean residence times, velocity autocorrelation function, free energy, and other parameters revealed the difference in the metal binding effect because the Mn(II) atom was observed to inhibit H-bond formation more than the presence of Mg(II) atoms in the core of the porphyrin. The current study thus highlights the significant differences in the structural and dynamical properties of Mn(II)- and Mg(II)-associated porphyrin systems.

The adapted Numerov approach was extended to periodic problems and applied to the torsional tunneling splitting of six increasingly complex target systems carrying a hydroxy-group. The deviations from experiment remained on the order of 1 cm−1, except for phenol in which the exceptionally small ground-state tunneling-splitting of 0.0017 cm−1 was found in very good agreement with the experimental value of 0.0019 cm−1. Overall, the accuracy of the periodic Numerov approach for the treatment of torsional tunneling is on the same order as alternative approaches, but at a substantially reduced computational demand due to the restriction of the problem to the respective degree of freedom.

The solvation structure and dynamics of Cu2+ in 18.6 % aqueous ammonia have been investigated using an ab initio quantum mechanical charge field molecular dynamics (QMCF MD) simulation approach at the Hartree–Fock (HF) level of theory applying the LANL2DZ ECP and Dunning DZP basis sets for Cu2+, ammonia and water, respectively. During a simulation time of 20 ps, only NH3 molecules are observed within the first solvation shell of Cu2+, resulting in the formation of an octahedral [Cu(NH3)6]2+ complex. While no exchange of these ligands with the second solvation shell are observed along the simulation, the monitoring of the associated N-Ntrans distances highlight the dynamics of the associated Jahn-Teller distortions, showing on average 2 elongated axial (2.19 Å) and 4 equatorial Cu–N bonds (2.39 Å). The observed structural properties are found in excellent agreement with experimental studies. In addition, an NBO analysis was carried out, confirming the strong electrostatic character of the Cu2+–NH3 interaction.

Interfacial adsorption and dissociation of water molecules at the α-Al2O3(0001) surface were studied using a novel hybrid 2D-periodic Self-Consistent Charge Density Functional Tight-Binding/Molecular Mechanics Molecular Dynamics (SCC-DFTB/MM MD) simulation strategy. The (0001) surface of α-Al2O3 (C-plane) was considered to assess the structural and dynamical behavior of adsorbed water at the interface region. In-plane distribution profiles of oxygen and hydrogen with respect to the non-periodic z-coordinate provide detailed information on the ordering of monolayer adsorbed water molecules at the interface. Dissociation of water molecules occured on the picosecond time scale, indicated by the formation of an additional plane-H peak located at 0.056 nm. Along simulation 4.2 OH groups per nm2 were formed at the α-Al2O3(0001) surface.

An adapted formulation of the grid-based Numerov approach to solve Schrodinger’s equation has been extended to four-dimensional systems and applied to problems in vibrational spectroscopy. The advantage of this novel implementation is that no approximations or assumptions with respect to the wavefunctions are required and the achieved accuracy at a given stencil size is only limited by the selected grid-spacing. To validate this approach the vibrational eigenstates and the corresponding wavenumbers of the linear molecules CO 2 , BeH 2 and HCN were investigated. Based on a potential energy grid at CCSD(T)/cc-pVnZ (n = T, Q) level all fundamental wavenumbers could be reproduced with deviations of less than 1% of the experimental values. Furthermore, the hierarchical application of a one- to four-dimensional Numerov treatment provides detailed information about the increasing influence of inter-mode coupling in addition to the inherent account for anharmonic contributions. The associated vibrational states are eigenfunctions of the Numerov matrix eigenvalue problem. Since no vibrational basis functions have to be applied in this approach, the respective eigenstates are characterized using isosurfaces of the wavefunctions in the hyperplane x 4 = 0 . This enables the direct examination of the individual wavefunctions via suitable visualization tools and the assignment of the respective vibrational quantum numbers.

The title compound, [Co(C5H5)(C10H9N2)]PF6, was synthesized from deprotonated 1-aminopyridinium iodide, followed by microwave-assisted nucleophilic aromatic substitution of iodo-cobaltocenium iodide. After anion exchange with potassium hexafluoridophosphate, the title compound crystallizes as orange prisms in the space group Pc. This very stable pyridine nitrene adduct is the first example of a cobaltocenium derivative, formally containing a nitrene nitrogen species.

The ordering effects in anthraquinone (AQ) stacking forced by thin-film application and its influence on dimer solubility and current collector adhesion are investigated. The structural characteristics of AQ and its chemical environment are found to have a substantial influence on its electrochemical performance. Computational investigation for different charged states of AQ on a carbon substrate obtained via basin hopping global minimization provides important insights into the physicochemical thin-film properties. The results reveal the ideal stacking configurations of the individual AQ-carrier systems and show ordering effects in a periodic supercell environment. The latter reveals the transition from intermolecular hydrogen bonding toward the formation of salt bridges between the reduced AQ units and a stabilizing effect upon the dimerlike rearrangement, while the strong surface-molecular interactions in the thin-film geometries are found to be crucial for the formed dimers to remain electronically active. Both characteristics, the improved current collector adhesion and the stabilization due to dimerization, are mutual benefits of thin-film electrodes over powder-based systems. This hypothesis has been further investigated for its potential application in sodium ion batteries. Our results show that AQ thin-film electrodes exhibit significantly better specific capacities (233 vs 87 mAh g-1 in the first cycle), Coulombic efficiencies, and long-term cycling performance (80 vs 4 mAh g-1 after 100 cycles) over the AQ powder electrodes. By augmenting the experimental findings via computational investigations, we are able to suggest design strategies that may foster the performance of industrially desirable powder-based electrode materials.

In this work a newly parametrised Coulomb plus Buckingham potential formulation for cubic ZrO2, Y2O3 and yttrium-stabilised zirconia (YSZ) is presented. The density and pair distributions obtained for neat ZrO2 and Y2O3 under ambient conditions are in excellent agreement with experimental data, while the vibrational power spectra are highly similar compared to those obtained via ab initio molecular dynamics simulations at the PBEsol level. In addition, it is shown that the use of effective partial charges has several advantages compared to interaction potentials employing the oxidation states in the evaluation of the coulombic interactions: (i) the diffusion coefficient and the associated activation energy of oxygen ions evaluated for YSZn (n = 4 to 12) display the best agreement with experimental data; (ii) no unphysical reorganisation of the interface and the bulk are observed in simulations of the (110) and (111) surfaces of cubic ZrO2 and Y2O3, while due to the strong coulombic contributions in the case of the tested full-charge models a pronounced restructuring of the interface and the bulk is observed in the ZrO2 case, and (iii) the use of effective partial charges ensures compatibility with existing solvent models and force-fields for the treatment of molecular compounds.

Inspired by natural photosynthesis, features such as proton relays have been integrated into water reduction catalysts (WRC) for effective production of hydrogen. Research by DuBois et al. showed the crucial influence of these relays, largely in the form of pendant amine functions. In this work catalysts are presented containing innovative diphosphinoamine ligands: [M(ii)Cl2(PNP-C1)], [M(ii)(MeCN)2(PNP-C1)]2+, [M(ii)(PNP-C1)2]2+, and [M(ii)Cl(PNP-C2)]+ (M = Pt2+, Pd2+, Ni2+, Co2+; PNP-C1 = N,N-bis{(di(2-methoxyphenyl)phosphino)methyl}-N-alkylamine, PNP-C2 = N,N-bis{(di(2-methoxyphenyl)phosphino)ethyl}-N-alkylamine and alkyl = Me, Et, iso-Pr, Bz). Synthetic strategies and detailed characterisation are covered, including 1H-, 13C-, and 31P-NMR analysis, mass spectroscopy and single crystal X-ray diffractometry (XRD). The catalytic properties have been explored by changing the pendant amines and auxiliary methoxy coordination sites, as well as enlarging the ligand backbone. Moreover, confirmed by density functional theory (DFT) calculations based on XRD data in vacuo and solvent environment, two very different catalytic cycles are proposed. PNP-C1 shows a classical proton relay, whereas PNP-C2 allows an additional coordination of nitrogen, acting optionally like a pincer. Through new insights into efficiency and stability-increasing influences of proton relays in general, their number per metal centre, an enlarged ligand backbone and the use of solvato instead of halogenido complexes, substantial improvements have been made in catalytic performance over the DuBois et al. catalysts and recently self-made WRCs. The turnover number (TON) related to the single site of cost-efficient nickel WRCs is increased from 11.4 to 637, whereas a corresponding palladium catalyst gives TON as high as 2289.

Structure and dynamics of solvated Ca2+ in liquid ammonia have been investigated using the quantum mechanical charge field molecular dynamics simulation approach, including the ion and its entire first plus second solvation shells in the QM zone. The Ca2+-ammonia interactions were calculated using ab initio HF calculations with Def2-SVP and DZP for Ca2+ and ammonia, respectively. A labile first shell structure at 2.63 A was observed with the dominant coordination numbers being 7 and 8. A number of exchange processes of ammonia ligands occurred throughout the simulation with a first shell mean ligand residence time of12.9 ps.

Lung cancer was a second common cancer case due to the high cigarette smoking activity both in men and women. One of protein receptor which plays an important role in the growth of the tumor is Epidermal Growth Factor Receptor (EGFR). EGFR protein is the most frequent protein mutation in cancer and promising target to inhibit the cancer growth. In this work, the stability of the hydrogen bond as the main interaction in the inhibition mechanism of cancer will be evaluated using molecular dynamics simulation. There were two compounds (A1 and A2) as new potential inhibitors that were complexed against the EGFR protein. The dynamic properties of each complexed were compared with respect to erlotinib against EGFR. The result revealed that both compounds had an interaction in the main catalytic area of protein receptor which is at methionine residue. Inhibitor A1 showed additional interactions during simulation time but the interactions tend to be weak. Inhibitor A2 displayed a more stable interaction. Following dynamics simulation, binding free energy calculation was performed by two scoring techniques MM/GB(PB)SA method and gave a good correlation with the stability of the complex. Furthermore, potential inhibitor A2 had a lower binding free energy as a direct consequence of the stability of hydrogen bond interaction.

The axial-ligand properties of [Pd(NH3)4]2+ and [Pt(NH3)4]2+ in aqueous solution have been assessed via quantum mechanical charge field molecular dynamics. Due to the similar distance between the axial ligands and the second solvation shell, an angular-radial distribution analysis has been performed. The result highlight how the character of the solvent influences the interaction between the axial ligands and ion and the respective influence on the experimentally observed ligand exchange rate constant of the first solvation shell. Even though both ions are often considered identical, the current results display key differences, which originate from the individual characteristics of the solvated complex structures.

The solvation structures of Pd(II) and Pt(II) are typically reduced to the well-known square-planar structural motif, although it has been shown, in both experimental and theoretical investigations, that these solutes have a tendency to bind ligand molecules at elongated distance in axial coordination sites. In aqueous solution both ions form a tetragonally elongated octahedral first hydration shell (coordination number 6). However, a recent QM/MM MD simulation of Pd(II) in ammonia solution indicated that the properties of the axial ligands are highly sensitive with respect to the nature of the solvent. In the present study the solvation properties of these solutes in aqueous solution and pure ammonia are compared, presenting novel QM/MM MD data for Pt(II) in ammonia solution. The simulation results indicate that in the latter case the coordination sites in axial position remain unoccupied, thus indeed forming the prototype four-fold, square planar solvation structure (coordination number 4). The respective solvation properties are thoroughly evaluated and compared to experimental enthalpy and entropy of activation for the first shell ligand exchange, which similarly point towards the unique solvation of Pt(II) in ammonia solution. The observed solvation can be explained via the electrostatic potential of tetraammineplatinum(II) and -palladium(II), clearly highlighting a strongly negative potential perpendicular to the plane of solvation in the Pt(II) case. This result can be well interpreted in the rather simple context of Pearson's electronegativity and hardness, which had to be re-evaluated for Pt(II) employing novel data for the second and third ionisation potentials of elemental Pt. In contrast to earlier work these results indicate that the latter is less electronegative and softer than its Pd(II) counterpart. Together with the lower electronegativity and hardness of NH3 ligands compared to H2O the interaction between the solute and axial ligands is weakened up to a point at which the formation of a tetragonally elongated coordination is prevented.

The presented study elucidates the influence of calcium(II) counter-ions on the structure of the environmentally relevant uranyl tricarbonates using hybrid quantum mechanical/molecular mechanical (QM/MM) MD simulations. Since experimental investigations may be subject to limitations in detecting the presence of counter-ions in solution, the present study is of importance to obtain a profound understanding of the effects counter-ions may have on coordination complexes. It can be concluded from the obtained simulation data that two calcium(II) ions are essential for stabilizing the experimentally observed uranyl tricarbonate complex in aqueous solution. Including only one calcium(II) ion in the coordination sphere was found to be insufficient to form a six-fold equatorial coordination of carbonates, but a five-fold coordination is adopted similar to the counter-ion free case in aqueous solution reported in a previous study.

The feasibility of a novel approach for the hybrid quantum mechanical/molecular mechanical (QM/MM) treatment of solid-state surfaces without the requirement of artificially keeping atoms at fixed positions is explored. In order to avoid potential artifacts of the QM/MM transition near the surface, a 2d-periodic QM treatment of the system is employed. Thus, the only QM/MM interface between atoms of the solid is along the non-periodic z-dimension. It is shown for the metal oxide and metal systems MgO(100) and Be(0001) that a properly adjusted embedding potential supplemented by adequate non-Coulombic potentials (if required) enables the application of the QM/MM framework in all-atom structure optimization and molecular dynamics (MD) simulation. The commonly employed constraint to keep at least some of the embedding atoms at fixed position is not required. Two exemplary applications of H2O on MgO(100) and H2 on Be(0001) demonstrate the applicability of the framework in exemplary MD simulation studies.

The potassium pentaborate KB5O7(OH)2 reported herein crystallizes in the monoclinic space group P21 /c (no. 14) with the lattice parameters a = 904.8(2), b = 753.2(2), c = 1214.9(5) pm, β = 117.16(2)°, and V = 0.73663(5) nm3 (Z = 4). It is a disordered structural variant of an already known compound with the same composition (a = 766.90(3), b = 904.45(3), c = 1223.04(4) pm, β = 119.132(2)°, and V = 0.74101(5) nm3 (Z = 4)) reported by Wu in 2011. The disorder of the potassium cation in the single crystal structure determination of KB5O7(OH)2 presented here leads to a remarkably elongated a axis and a corresponding reduction of the length of the b axis in comparison to the ordered compound. The disordered variant was obtained through a hydrothermal synthesis from KNO3, B2O3, and Ce(NO3)3·6H2O with a molar ratio of 1:1:0.07.

The amino acid [1-(aminomethyl)cyclohexyl]acetic acid was reacted with 2-hydroxynaphthaldehyde to produce the Schiff base ligand [1-({[(Z)-(2-hydroxynaphthalen-1-yl)methylidene]amino}methyl)cyclohexyl]acetic acid (H-HMAC) which was fully characterized spectroscopically and by single crystal diffraction. It was reacted with metal ions to produce compounds with composition [M(HMAC)2] [M = Co(II), Ni(II), Cu(II) and Zn(II)], which were characterized spectroscopically, with distorted tetragonal geometries assigned based on spectroscopic and B3LYP theoretical studies. All synthesized compounds were studied for their thermal stabilities under static air. The coordination compounds were also screened for their free radical scavenging properties using DPPH free radicals and xanthine oxidase inhibitory activities. Only the zinc complex was found to be an inhibitor of the enzymatic activity with IC50 = 0.7 ± 0.01 μM ± SEM better than the standard reference drug used. The inhibitory activity was structurally rationalized by carrying out molecular modeling studies using the auto dock program.

Theoretical ab initio quantum mechanical charge field molecular dynamics (QMCF MD) has been applied in conjunction with experimental large angle X-ray scattering (LAXS) and EXAFS measurements to study structure and dynamics of the hydrated oxo chloro anions chlorite, ClO2(-), chlorate, ClO3(-), and perchlorate, ClO4(-). In addition, the structures of the hydrated hypochlorite, ClO(-), bromate, BrO3(-), iodate, IO3(-) and metaperiodate, IO4(-), ions have been determined in aqueous solution by means of LAXS. The structures of the bromate, metaperiodate, and orthoperiodate, H2IO6(3-), ions have been determined by EXAFS as solid sodium salts and in aqueous solution as well. The results show clearly that the only form of periodate present in aqueous solution is metaperiodate. The Cl-O bond distances in the hydrated oxo chloro anions as determined by LAXS and obtained in the QMCF MD simulations are in excellent agreement, being 0.01-0.02 Å longer than in solid anhydrous salts due to hydration through hydrogen bonding to water molecules. The oxo halo anions, all with unit negative charge, have low charge density making them typical structure breakers, thus the hydrogen bonds formed to the hydrating water molecules are weaker and more short-lived than those between water molecules in pure water. The water exchange mechanism of the oxo chloro anions resembles those of the oxo sulfur anions with a direct exchange at the oxygen atoms for perchlorate and sulfate. The water exchange rate for the perchlorate ion is significantly faster, τ0.5 = 1.4 ps, compared to the hydrated sulfate ion and pure water, τ0.5 = 2.6 and 1.7 ps, respectively. The angular radial distribution functions show that the chlorate and sulfite ions have a more complex water exchange mechanism. As the chlorite and chlorate ions are more weakly hydrated than the sulfite ion the spatial occupancy is less well-defined and it is not possible to follow any well-defined migration pattern as it is difficult to distinguish between hydrating water molecules and bulk water in the region close to the ions.

Ab initio QMCF-MD simulations of aqueous 18-crown-6 (18C6) and strontium(II)-18-crown-6 (18C6-Sr) were performed to gather insight into their hydration properties. Strongly different characteristics were found for the two solutes in terms of structure and dynamics such as H-bonding. They, however, have in common that their backbone shows high flexibility in aqueous medium, adopting structures significantly differing from idealized gas phase geometries. In particular, planar oxyethylene units stable in the picosecond range occurred in 18C6, while the strontium complex readily exhibits a bent structure. Detailed analysis of this high flexibility was done via two dimensional root mean square deviation plots as well as the evolution of dihedral angles and angles within the simulation trajectory. The vibrational spectra obtained from the QMCF-MD simulations are in excellent agreement with experimental data and show a pronounced blueshift upon complexation of the strontium(II) ion in 18C6.

The dissociative water potential introduced by Garofalini et al. proved to be a simple and effective description to account for proton transfer in aqueous media, enabling for instance the execution of simulation studies at different pH values. In this model the charge of each particle is represented by a point-charge surrounded by a Gaussian charge-cloud of opposite sign, thus four Coulombic terms (point-charge-point-charge, point-charge-charge-cloud, charge-cloud-point-charge and charge-cloud-charge-cloud) are required per atom pair. In this work it is demonstrated that the Gaussian charge distributions can be removed from the model after a minor modification of the overall atomic point-charges. Despite this substantial modification of the model, structural properties obtained via pair- and angle distributions remain largely unaffected and the change in dynamical properties (vibrational frequencies, proton transfer properties) was found to be minor. As an additional improvement an adjustment of the bending mode vibration was carried out by carefully evaluating the parametrization of the three-body interaction potential, thereby retaining the good agreement of the transfer properties of the aqueous excess proton reported in an earlier study. The proposed simple point-charge (SPC) type parametrization of the Coulombic interactions not only leads to a notable decrease in computational demand but generalizes the dissociative model by improving its transferability to established third-party simulation software and enabling the application of different theoretical approaches such as Ewald summation techniques not considered in the original parametrization. The outlined optimization strategy demonstrates that despite the complex and challenging formulation of the force field, various dynamical properties can be selectively adjusted without influencing other critical parameters of the simulated systems.

The ab initio quantum mechanical charge field molecular dynamics (QMCF-MD) simulation approach was successfully applied to Fe2+–P and Fe3+–P in water to evaluate their structural, dynamical and energetic properties. Based on the structural data, it was found that Fe2+–P accommodates one water molecule in the first coordination sphere of the Fe2+ ion including the four nitrogen atoms of the porphyrin system coordinating with central metal species. On the other hand, two water molecules were coordinated to Fe3+–P, thus forming a hexa-coordinated species. Comparison of dynamical properties such as the vibrational power spectrum and ligand mean residence times to other metal-free porphyrin systems demonstrate the ions' influence on the hydration structure, enabling a characterisation of the strong interaction of the ions which greatly reduces the hydrogen bonding potential of the complex. The association of water molecules with the metal ions in both solutes was quantified by computing the free energy of binding obtained via the potential of mean force. This further confirmed the strong association of water to the metal ions which was conversely weak as inferred from the energetic data for the Fe2+–P system.

Erroneous activation of the Hedgehog pathway has been linked to a great amount of cancerous diseases and therefore a large number of studies aiming at its inhibition have been carried out. One leverage point for novel therapeutic strategies targeting the proteins involved, is the prevention of complex formation between the extracellular signaling protein Sonic Hedgehog and the transmembrane protein Patched 1. In 2009 robotnikinin, a small molecule capable of binding to and inhibiting the activity of Sonic Hedgehog has been identified, however in the absence of X-ray structures of the Sonic Hedgehog-robotnikinin complex, the binding mode of this inhibitor remains unknown. In order to aid with the identification of novel Sonic Hedgehog inhibitors, the presented investigation elucidates the binding mode of robotnikinin by performing an extensive docking study, including subsequent molecular mechanical as well as quantum mechanical/molecular mechanical molecular dynamics simulations. The attained configurations enabled the identification of a number of key protein-ligand interactions, aiding complex formation and providing stabilizing contributions to the binding of the ligand. The predicted structure of the Sonic Hedgehog-robotnikinin complex is provided via a PDB file as Supplementary Material and can be used for further reference.

The structural and dynamical properties of Pd2+ in liquid ammonia have been investigated via quantum mechanical charge field molecular dynamics. Similar to the case of aqueous Pd2+, a six-fold coordination polyhedron in the form of a tetrahedrally elongated octahedron is observed with two ligands in axial positions forming an extended first shell. To highlight the difference in solvation between the aqueous and ammonia case a selection based on the angular-radial distribution with respect to the well-known square planar motif was applied also providing a detailed understanding of ligand exchange between the extended first and second shells. All structural properties resulting from this investigation compare well with the available solid-state data of various N-containing complexes. From the dynamical perspective, Pd2+ in liquid ammonia forms a more flexible complex with a higher rate of ligand exchange than that of its aqueous counterpart.

The performance of the grid-based Numerov procedure for the prediction of fundamental as well as the first vibrational overtone has been systematically probed for harmonic and anharmonic model systems. In addition to monitor the prediction with respect to the spacing of the potential grid the influence of higher order approximations to the second derivative (i.e. stencils) in Schrodingers equation is evaluated. The latter enable a significant increase of the grid-spacing to achieve results of similar accuracy obtained with smaller stencil sizes. Application to the hydroxyl vibrational mode of methanol, phenol and the natural product thymol in vacuum and carbon tetrachloride predicted wavenumbers within less than 1% of experiment. Due to the highly localised character of the OH-vibration the ad hoc construction of the associated normal mode yields results of similar accuracy than those obtained using the analytical normal modes, effectively eliminating the requirement of an analytical normal mode evaluation of the entire system. This property was shown to be of particular advantage when considering explicit solute–solvent contacts, which have been demonstrated to be superior compared to an implicit representation of solvent effects. The combination of the observed findings (i.e. enlarged grid-spacing due to the application of higher order stencils, construction of localised normal modes) is envisaged to be of particular benefit when investigating localised modes in large systems, such as OH or NH groups in large (bio)macromolecules or solid-state surfaces.

In this article the extension of the grid-based Numerov approach to probe two coupled, localised vibrational modes is assessed. The theoretically obtained wave numbers are compared to experimental results for five increasingly complex organic molecules carrying two OH groups measured in gas-phase as well as carbon tetrachloride. By using an appropriate spacing of the associated potential energy grid a deviation of the predicted wave numbers with experiment of ≤1% is achieved for both the fundamental and the first overtone bands. In particular the calculated wave numbers of aliphatic species in vacuum underline the versatility of this approach. In addition, it is demonstrated that bicubic interpolation is a viable strategy to greatly reduce the required data points and thus, the computational effort. Comparison of predicted wave numbers obtained for different conformers with experimental data enables the identification of the most relevant conformer present in solution. Since especially the accurate calculation of overtone vibrations is known to be challenging in case of strongly anharmonic potentials such as OH bonds, the presented approach provides a particularly efficient route to study the properties of the associated overtone contribution under the influence of inter-mode coupling. This is due to the fact that the Numerov approach requires no assumption about form and composition of the vibrational wave functions. In addition, the presented method also provides one of the simplest routes to access combined excitations of the considered vibrational modes.

This paper presents an ab initio quantum mechanical charge field molecular dynamics simulation study of the cyanide anion (CN(-)) in aqueous solution where hydrogen bond formation plays a dominant role in the hydration process. Preferential orientation of water hydrogens compared to oxygen atoms was quantified in terms of radial, angular as well as coordination number distributions. All structural results indicate that the water hydrogens are attracted towards CN(-) atoms, thus contributing to the formation of the hydration layer. Moreover, a clear picture of the local arrangement of water molecules around the ellipsoidal CN(-) ion is provided via angular-radial distribution and spatial distribution functions. Apart from the structural analysis, the evaluation of water dynamics in terms of ligand mean residence times and H-bond correlation functions indicates the weak structure making capacity of the CN(-) ion. The similar values of H-bond lifetimes obtained for the NHwat and CHwat bonds indicate an isokinetic behaviour of these H-bonds, since there is a very small difference in the magnitude of the lifetimes. On the other hand, the H-bond lifetimes between water molecules of the hydration shell, and between solute and solvent evidence the slightly stable hydration of the CN(-). Overall, the H-bonding dominates in the hydration process of the cyanide anion enabling it to become soluble in the aqueous environment associated to chemical and biological processes.

Immobilized metal ion affinity chromatography (IMAC) is an important chromatographic technique for biomolecules. In order to get a detailed understanding of the hydration of immobilized Fe(III), complexes of Fe(III) with methyl substituted iminodiacetate ([Fe(MSIDA)(H2O)3](+)) as well as with methyl substituted nitrilotriacetate ([Fe(MSNTA)(H2O)2]) were simulated in aqueous solutions with the quantum mechanical charge field molecular dynamics (QMCF MD) approach. The simulations were carried out at the Hartree-Fock (HF) level of theory, since cluster calculations at the HF, MP2, and B3LYP levels of theory showed that this method results in a good compromise between computational effort and accuracy. None of the coordinating water molecules were exchanged during the simulation period of 15 ps. The Fe-OH2O bond distances as well as the Fe-OH2O stretching motions differed among the coordinating water molecules, indicating different bond strengths. For the water molecules in the second hydration layer, mean residence times of 2.7 and 1.9 ps were obtained for [Fe(MSIDA)(H2O)3](+) and [Fe(MSNTA)(H2O)2], respectively. Furthermore, infrared measurements were carried out to characterize the most prominent bond features of aqueous Fe(III)-NTA and to discuss these results in conjunction with the computationally derived frequencies.

This investigation presents the characterization of structural and dynamical properties of uranyl tricarbonate in aqueous solution employing an extended hybrid quantum mechanical/molecular mechanical (QM/MM) approach. It is shown that the inclusion of explicit solvent molecules in the quantum chemical treatment is essential to mimic the complex interaction occurring in an aqueous environment. Thus, in contrast to gas phase cluster calculations on a quantum chemical level proposing a 6-fold coordination of the three carbonates, the QMCF MD simulation proposes a 5-fold coordination. An extensive comparison of the simulation results to structural and dynamical data available in the literature was found to be in excellent agreement. Furthermore, this work is the first theoretical study on a quantum chemical level of theory able to observe the conversion of carbonate (CO₃²⁻) to bicarbonate (HCO₃⁻) in the equatorial coordination sphere of the uranyl ion. From a comparison of the free energy ΔG values for the unprotonated educt [UO₂(CO₃)₃]⁴⁻ and the protonated [UO₂(CO₃)₂(HCO₃)]³⁻, it could be concluded that the reaction equilibrium is strongly shifted toward the product state confirming the benignity for the observed protonation reaction. Structural properties and the three-dimensional arrangement of carbonate ligands were analyzed via pair-, three-body, and angular distributions, the dynamical properties were evaluated by hydrogen-bond correlation functions and vibrational power spectra.

In this work, the mid-infrared spectrum of aqueous glycine is predicted by a number of computational approaches. Velocity autocorrelation functions are applied to ab initio QMCF-MD and QM/MM-MD simulations in order to obtain IR power spectra. Furthermore, continuum solvation model augmented geometry optimizations are studied by anharmonic calculations relying on the PT2-VSCF and the VPT2 formalism. In this context, the potential based EFP hydration technique is discussed and the importance of a Monte Carlo search in conjunction with PT2-VSCF calculations is critically assessed. All results are directly compared to newly recorded experimental FT-IR spectroscopic data, elucidating the qualities of the respective methodology. Moreover, the computational approaches are discussed regarding their usefulness for the interpretation of experimental spectra.

An ab initio quantum mechanical charge field molecular dynamics (QMCF-MD) study of the selenate ion in water was performed at the Hartree Fock/6-31G (d,p) level of theory. The intramolecular geometry, structure and dynamics of the hydration shell and the vibrational frequency modes calculated via velocity autocorrelation functions are presented. The resulting bond distances as well as angles and vibrational frequencies are in good agreement with experimental data. The structure and dynamics reveal the hydrogen bonding network between the ion and neighboring water molecules and exchange processes in the hydration sphere characterize the ion as a structure-forming anion.

As a consequence of the ongoing development of enhanced computational resources, theoretical chemistry has become an increasingly valuable field for the investigation of a variety of chemical systems. Simulations employing a hybrid quantum mechanical/molecular mechanical (QM/MM) molecular dynamics (MD) technique have been shown to be a particularly promising approach, whenever ultrafast (i.e., picosecond) dynamical properties are to be studied, which are in many cases difficult to access via experimental techniques. Details of the quantum mechanical charge field (QMCF) ansatz, an advanced QM/MM protocol, are discussed and simulation results for various systems ranging from simple ionic hydrates to solvated organic molecules and coordination complexes in solution are presented. A particularly challenging application is the description of proton-transfer reactions in chemical simulations, which is a prerequisite to study acidified and basic systems. The methodical requirements for a combination of the QMCF methodology with a dissociative potential model for the description of the solvent are discussed. Furthermore, the possible extension of QM/MM approaches to solid/liquid interfaces is outlined.

Theoretical ab initio quantum mechanical charge field molecular dynamics (QMCF MD) has been applied in conjunction with experimental large angle X-ray scattering (LAXS) to study the structure and dynamics of the hydrated thiosulfate ion, S2O32-, in aqueous solution. The S-O and S-C-S-T bond distances have been determined to be 1.479(5) and 2.020(6) angstrom by LAXS and to be 1.478 and 2.017 angstrom by QMCF MD simulations, which are slightly longer than the mean values found in the solid state, 1.467 and 2.002 angstrom, respectively. This is due to the hydrogen bonds formed at hydration. The water dynamics show that water molecules are exchanged at the hydrated oxygen and sulfur atoms, and that the water exchange is ca. 50% faster at the sulfur atom than at the oxygen atoms with mean residence times, tau(0.5), of 2.4 and 3.6 ps, respectively. From this point of view the water exchange dynamics mechanism resembles the sulfate ion, while it is significantly different from the sulfite ion. This shows that the lone electron-pair in the sulfite ion has a much larger impact on the water exchange dynamics than a substitution of an oxygen atom for a sulfur one. The LAXS data did give mean S-C...O-aq1 and S-C...O-aq2 distances of 3.66(2) and 4.36(10) angstrom, respectively, and S-C-O-thio and O-thio...O-aq1, S-C-S-T and S-T...O-aq2 distances of 1.479(5), 2.845(10), 2.020(6) and 3.24(5) angstrom, respectively, giving S-C-O-thio...O-aq1 and S-C-S-T...O-aq2 angles close to 110 degrees, strongly indicating a tetrahedral geometry around the terminal thiosulfate sulfur and the oxygens, and thereby, three water molecules are hydrogen bound to each of them. The hydrogen bonds between thiosulfate oxygens and the hydrating water molecules are stronger and with longer mean residence times than those between water molecules in the aqueous bulk, while the opposite is true for the hydrogen bonds between the terminal thiosulfate sulfur and the hydrating water molecules. The hydration of all oxo sulfur ions is discussed using the detailed observations for the sulfate, thiosulfate and sulfite ions, and the structure of the hydrated peroxodisulfate ion, S2O82-, in aqueous solution has been determined by means of LAXS to support the general observations. The mean S-O bond distances are 1.448(2) and 1.675(5) angstrom to the oxo and peroxo oxygens, respectively.

Ab initio QMCF-MD simulations were performed for porphyrin (POR) and magnesium-porphyrin (Mg-POR) immersed in water to study their structural and dynamical properties. The observed hydration behaviour of these solutes representing biomimetic models is in fair agreement with structural and dynamical features of their biological analogues, protoporphyrin IX (PPIX) and chlorophyll (CHl). Structural data obtained from the radial, angular and spatial distribution functions as well as the angular-radial distributions have a consensus on possessing a contrasting hydration behaviour of POR and Mg-POR. Flexibility of the ring in both solutes described by the improper torsional distribution and root mean square fluctuation showed an influence on H-bond interactions between the nitrogen atoms and water molecules that are also reflected in the respective dynamics. An axial water molecule coordinated to the Mg(ii) ion indicates the penta-coordinated Mg-POR to be stable along the simulation. It was also shown that complexation of the Mg(ii) ion to the porphyrin influences the hydration patterns significantly compared to the porphyrin itself, which is further supported by the vibrational power spectra evaluated for both solutes. Free energy of binding and solvent accessible surface area calculations also confirmed that these two solutes have distinct hydration behaviour. Detailed knowledge of the individual hydration patterns is expected to be of particular benefit.

The cis- and trans-bis(glycinato)copper(II) complexes in aqueous solution have been investigated by means of a combined theoretical and experimental approach. The conducted quantum mechanical charge field molecular dynamics (QMCF-MD) studies, being the first quantum mechanical simulations of organometallic complexes by this method, yielded accurate structural details of the investigated isomers as well as novel dynamic data, which has successfully been confirmed and extended by subsequent mid-infrared measurements. The spectroscopic results, critically assessed by adjacent multivariate data analysis, indicate an isomeric stability at ambient conditions, vanishing at elevated temperatures.

Solvation phenomena have been the focus of experimental and theoretical research for many decades. While the determination of solvation properties of mono-atomic, ionic species is already a challenging task, the associated difficulties are amplified in the case of molecular compounds. Theoretical approaches have the ability to yield manifold information of the investigated systems, providing that a reliable description of the interatomic energies and forces is employed. Hybrid quantum mechanical/molecular mechanical simulations constitute a particularly successful approach for the study of solvation phenomena, and have been employed in investigations of a variety of molecular compounds in aqueous solution. While an accurate description of these systems depends on the application of reliable, theoretical approaches, the analysis of the resulting dataset is a challenge of its own. It is outlined that standard means of analysis via pair correlation functions may yield an unspecific picture of hydration phenomena, and in some cases wrong conclusions on the hydration may be drawn. More advanced means of structural analysis are thus required as they yield manifold information on solvation phenomena since pair correlations are not sufficiently responsive in such cases. The theoretical approaches required to obtain a reliable description of the investigated systems as well as increasingly complex means of structural analysis ranging from two- and three-body correlations via angular-radial distributions and two-dimensional particle mapping to the so-called SLICE projections are discussed. The application of these analysis schemes is demonstrated for a variety of systems including mono- and polyatomic ionic solutes as well as molecular organic compounds, highlighting various aspects of the hydration of these species.

In this work, the influence of the metal ions present in vertebrate Sonic Hedgehog was assessed by a series of molecular mechanics molecular dynamics simulations with differing ionic compositions. The obtained data suggest that Ca(II) binding has a very distinct influence on the composition of the protein surface surrounding the binding site by shaping several ionic interactions with negatively charged sidechains that otherwise would be pointing towards the solvent, repelling potential ligands. Furthermore, the Ca(II) ions play an important role in the stability of the loop regions where they are coordinated. In contrast, the removal of the Zn(II) ion results in no noticeable destabilization of its chemical surrounding, however, it is shown that the destabilizing effect of removed Ca(II) ions is amplified if Zn(II) is absent as well. Furthermore, a quantum mechanical/molecular mechanical (QM/MM) molecular dynamics simulation of Sonic Hedgehog with special focus on the Zn(II) binding site has been conducted. The results indicate that QM/MM in contrast to pure MM accurately reproduces structural features also found by experimental studies and therefore is able to provide credible predictions not only of the dynamical properties of the studied system but also of protein–ligand interactions at the metal ion binding site.

We present detailed analysis of the hydration behavior of zinc and copper bound porphyrins treated via ab initio quantum mechanical charge field molecular dynamics which agrees well with available experimental data. The computed metal–water coordination in the case of zinc bound porphyrin demonstrates a strong association of water with zinc compared to the copper–water interaction which correlates well with the calculated free energy of binding. The H-bond dynamics in these hydrated systems yield weaker H-bond interactions as compared to that observed in the case of metal-free porphyrin; nevertheless, the effect of metal association with porphyrin resulted in shifts in the vibrational frequencies. These characteristic data suggest a contrasting behavior between these metalloporphyrins in solution which could also serve to correlate with the properties of biological systems.

This work optimizes the link bond description of the quantum mechanical/molecular mechanical separation of deoxynucleosides. The nucleosides are separated at the C–N bond between the nucleobase and the deoxyribose, with the former acting as the quantum mechanically described species. By using a flexible link atom-ansatz plus a harmonic potential to correct the energy deviation from a full quantum mechanical description, the potential energy well of the bond’s stretching motion is mimicked with very high accuracy.

The hydration of the Bi(III) ion was determined via an ab initio quantum mechanical charge field molecular dynamics (QMCF-MD) simulation. Ten picosecond sampling was carried out to determine structural and dynamical properties of the Bi(III) ion in aqueous solution. In the first hydration shell, the ion is 9-fold coordinated with a maximum probability of the Bi-O distance at 2.51 Å. In total, 11 exchanges were observed in the first-shell showing associative, dissociative, and interexchange character. As with the dominant existence of 9-fold coordination, the geometry of the Bi(III) ion is in between the tricapped trigonal prism and the capped square antiprism.

The previously investigated La3+-hydrate has been re-evaluated by means of the quantum mechanical charge field (QMCF) molecular dynamics (MD) approach. Improved description of the hydration characteristics has been realised by including the full second hydration shell into the quantum mechanically treated region and by introducing the influence of the surrounding bulk via an electrostatic embedding technique. Analytical tools such as the ligand angular radial distribution analysis have been employed to gain deeper insight into the structural features of the hydrate. La3+ simultaneously forms nona- and decahydrates with capped trigonal and quadratic prismatic structure, besides small amounts of an octahydrate.