Ir(I)-Bi(III) Donor-Acceptor Adducts Stabilized by Dispersion Interactions between the Metal Pincer Ligands and Their Possible Self-Assembly Forming Molecular 1D Semiconductors.

Structure, stability, and electronic properties of the bimetallic {[IrI(terpy)(Me)]-[BiIIINNN]}n monomeric, oligomeric, and polymeric structures (n = 1-3 and ∞; terpy = terpyridine; Me = methyl; BiNNN = bismuth triamide) and their derivatives (designated as (Bi·Ir)n structures) were studied theoretically by DFT cluster and periodic calculations. Stable Bi·Ir adducts (monomers) were formed with short Bi-Ir bonds (<2.7 Å) and Gibbs free binding energies larger than 20 kcal/mol for all systems. The substitution of the pincer ligands of Ir(I) and Bi(III) complexes by the electron-donating (NH2) and electron-withdrawing (NO2, F, CF3) groups, respectively, enhanced the Ir → Bi charge transfer, substantially stabilizing the Bi·Ir monomers. The monomers from the unsubstituted complexes can be considered as dispersion stabilized adducts, and they may form spontaneously (Bi·Ir)n layered oligomers/polymers with semiconducting properties. The self-assembly of monomers into oligomers/polymers is hindered by bulkier protecting groups on the Bi(III) complex, such as tBu and SiMe3.

Parametric Production of Prostheses Using the Additive Polymer Manufacturing Technology Multi Jet Fusion.

This study aims to develop a procedure for the production of 3D-printed forearm prostheses (especially hard outer sockets). The production procedure is designed in the form of a parametric workflow (CAD model), which significantly speeds up the designing process of the prosthesis. This procedure is not fixedly dependent on the software (SW) equipment and is fully transferable into another SW environment. The use of these prostheses will significantly increase the comfort of their patients' lives. It is possible to produce prostheses faster and in larger amounts and variants by the usage of additive technology. The input for the own production of the prosthesis is a model of the internal soft socket of the patient. This soft socket (soft bed) is made by a qualified prosthetist. A 3D-scanned CAD model is obtained afterward using the scanning method by an automatic laser projector. An editable, parametric external socket (modifiable in any CAD format) is generated from the obtained 3D scan using a special algorithmic model. This socket, after the necessary individual modifications, is transferred to 3D printing technology and produced using powder technology Multi Jet Fusion (HP MJF). The result of the designed and tested procedure is a quickly editable 3D-printed outer socket (main part of prosthesis), which is able to fully replace the current long-fiber composite solution. Production of current solutions is relatively time-consuming, and only one piece is produced in a given time. The newly designed technology eliminates this. This study summarized the possibilities of speeding up the production of forearm prostheses (but not only these) by creating a parametric CAD model that is applicable to different patients.

Minimizing Deformations during HP MJF 3D Printing.

(1) Background: The purpose of this study was to investigate deformations that occur during additive manufacturing by the HP (Hewlett-Packard) Multi Jet Fusion (MJF) process. These deformations affect the final properties of 3D-printed parts, and proper compensating technology has to be developed in order to minimize these deformations. (2) Methods: Parts were printed with powder composed of nylon plastic infused with glass beads (PA12GB). The HP MJF technology was used during investigations. All parts (specimens) were measured at different points over an extended period to follow the deformations at each point. Different finite element simulations were performed to compare them with real results and assess the viability of using simulations to save time. Various modules of the Digimat software, such as additive manufacturing (AM), material focused (MF), finite element (FE), and computer-aided engineering (CAE), were used to run the simulations. (3) Results: It was found that the printing position of the part in the printer had an impact on deformations. When the part was simulated in a tilted position but alone (deformation: 7.19 mm), the value of the deformation was 1.49 mm greater than when the other parts (two comparable parts) were simulated at the same time (deformation: 5.7 mm). The difference between the simulation with the three parts together (deformation: 5.7 mm) and reality (deformation: 3.44 mm) was 2.26 mm. Finally, the difference between the simulated single part (deformation: 7.19 mm) and the real part (deformation: 3.44) was 3.75 mm. (4) Conclusions: The results of this study will contribute to a better understanding of deformation mechanisms and will suggest solutions for improving the quality of printed parts. Three-dimensional printing is a rapidly growing technology that offers numerous possibilities across various fields. However, one commonly encountered issue is the deformation of printed parts. Methods for minimizing deformations were studied during the 3D printing process using HP MJF technology. Various factors contributing to deformation were investigated, and different techniques for reducing them were explored.

Injection Moulding into 3D-Printed Plastic Inserts Produced Using the Multi Jet Fusion Method.

Most injection-moulded plastics are injection moulded into moulds made from conventional materials such as steel or aluminium. The production costs of the mould are considerable. 3D printing from plastic can be used for injection moulds to save these costs. This article deals with injection moulding into a 3D-printed plastic mould. The injection insert was produced on a HP Multi Jet Fusion 4200 3D printer. The other part of the mould was made of aluminium. A custom injection mould was designed for the research. One insert was made from plastic, and one from aluminium. Both moulds were injected under the same injection conditions. A comparison of injection moulding into the plastic and aluminium inserts is made in this article. The difference when injection moulding into the plastic insert is explained using the different technological conditions. The part injected into the plastic insert was also different from the part injected into the aluminium insert. The difference is explained in this article. This article also looks at the interface between the injection-moulded part and the plastic insert using an electron microscope. The images taken clarify the differences between injection moulding into a plastic insert and an aluminium insert and the differences of the injection-moulded part from the plastic insert.

Correction to "Tuning the Reactivity and Bonding Properties of Metal Square-Planar Complexes by the Substitution(s) on the Trans-Coordinated Pyridine Ring".

[This corrects the article DOI: 10.1021/acsomega.0c01161.].

Tuning the Reactivity and Bonding Properties of Metal Square-Planar Complexes by the Substitution(s) on the Trans-Coordinated Pyridine Ring.

The kinetics of the hydration reaction on trans-[Pt(NH3)2(pyrX)Cl]+ (pyr = pyridine) complexes (X = OH-, Cl-, F-, Br-, NO2 -, NH2, SH-, CH3, C≡CH, and DMA) was studied by density functional theory calculations in the gas phase and in water solution described by the implicit polarizable continuum model method. All possible positions ortho, meta, and para of the substituent X in the pyridine ring were considered. The substitution of the pyr ligand by electron-donating X's led to the strengthening of the Pt-N1(pyrX) (Pt-NpyrX) bond and the weakening of the trans Pt-Cl or Pt-Ow bonds. The electron-withdrawing X's have exactly the opposite effect. The strengths of these bonds can be predicted from the basicity of sigma electrons on the NpyrX atom determined on the isolated pyrX ligand. As the pyrX ring was oriented perpendicularly with respect to the plane of the complex, the nature of the X···Cl electrostatic interaction was the decisive factor for the transition-state (TS) stabilization which resulted in the highest selectivity of ortho-substituted systems with respect to the reaction rate. Because of a smaller size of X's, the steric effects influenced less importantly the values of activation Gibbs energies ΔG ⧧ but caused geometry changes such as the elongation of the Pt-NpyrX bonds. Substitution in the meta position led to the highest ΔG ⧧ values for most of the X's. The changes of ΔG ⧧ because of electronic effects were the same in the gas phase and the water solvent. However, as the water solvent dampened electrostatic interactions, 2200 and 150 times differences in the reaction rate were observed between the most and the least reactive mono-substituted complexes in the gas phase and the water solvent, respectively. An additional NO2 substitution of the pyrNO2 ligand further decelerated the rate of the hydration reaction, but on the other hand, the poly-NH2 complexes were no more reactive than the fastest o-NH2 system. In the gas phase, the poly-X complexes showed the additivity of the substituent effects with respect to the Pt-ligand bond strengths and the ligand charges.

Square-Planar Pt(II) and Ir(I) Complexes as the Lewis Bases: Donor-Acceptor Adducts with Group 13 Trihalides and Trihydrides.

The stability and properties of donor-acceptor adducts of square-planar Pt(II) and Ir(I) complexes (designated as PtX, IrX, or generally MX complexes) with trihydrides and trihalides of group 13 elements of general formula YZ3 (Y = B, Al, Ga; Z = H, F, Cl, Br) were studied theoretically using DFT methodology in the gas phase. MX complexes were represented by wide range of the ligand environment which included model complexes [Ir(NH3)3X]0 and cis-[Pt(NH3)2X2]0 (X = H, CH3, F, Cl, Br) and isoelectronic complexes [Ir(NNN)(CH3)]0 and [Pt(NCN)(CH3)]0 with tridentate NNN and NCN pincer ligands. MX complexes acted as the Lewis bases donating electron density from the doubly occupied 5d z2 atomic orbital of the metal M atom to the empty valence p z orbital of Y whose evidence was clearly provided by the natural atomic orbital (NAO) analysis. This charge transfer led to the formation of pentacoordinated square pyramidal MX·(YZ3) adducts with M·Y dative bond. Binding energies were -44.7 and -75.2 kcal/mol for interaction of GaF3 as the strongest acid with PtNCN and IrNNN pincer ligands complexes. Only M·B bonds had covalent character although MX·BZ3 adducts were the least stable due to large values of Pauli repulsion and deformation energies. The highest degree of covalent character was found for adducts of BH3 in all series of structures studied. Al and Ga adducts showed remarkably similar behavior with respect to geometry and binding energies.

Surface segregation in a binary mixture of ionic liquids: Comparison between high-resolution RBS measurements and moleculardynamics simulations.

Surface structure of equimolar mixture of 1-ethyl-3-methylimidazolium bis(trifluoromethanesulfonyl)imide ([C2C1Im][Tf2N]) and 1-ethyl-3-methylimidazolium tetrafluoroborate ([C2C1Im][BF4]) is studied using high-resolution Rutherford backscattering spectroscopy (HRBS) and molecular dynamics (MD) simulations. Both HRBS and MD simulations show enrichment of [Tf2N] in the first molecular layer although the degree of enrichment observed by HRBS is more pronounced than that predicted by the MD simulation. In the subsurface region, MD simulation shows a small depletion of [Tf2N] while HRBS shows a small enrichment here. This discrepancy is partially attributed to the artifact of the MD simulations. Since the number of each ion is fixed in a finite-size simulation box, surface enrichment of particular ion results in its artificial depletion in the subsurface region.

Interactions of the "piano-stool" [ruthenium(II)(η(6) -arene)(quinolone)Cl](+) complexes with water; DFT computational study.

Full optimizations of stationary points along the reaction coordinate for the hydration of several quinolone Ru(II) half-sandwich complexes were performed in water environment using the B3PW91/6-31+G(d)/PCM/UAKS method. The role of diffuse functions (especially on oxygen) was found crucial for correct geometries along the reaction coordinate. Single-point (SP) calculations were performed at the B3LYP/6-311++G(2df,2pd)/DPCM/saled-UAKS level. In the first part, two possible reaction mechanisms-associative and dissociative were compared. It was found that the dissociative mechanism of the hydration process is kinetically slightly preferred. Another important conclusion concerns the reaction channels. It was found that substitution of chloride ligand (abbreviated in the text as dechlorination reaction) represents energetically and kinetically the most feasible pathway. In the second part the same hydration reaction was explored for reactivity comparison of the Ru(II)-complexes with several derivatives of nalidixic acid: cinoxacin, ofloxacin, and (thio)nalidixic acid. The hydration process is about four orders of magnitude faster in a basic solution compared to neutral/acidic environment with cinoxacin and nalidixic acid as the most reactive complexes in the former and latter environments, respectively. The explored hydration reaction is in all cases endergonic; nevertheless the endergonicity is substantially lower (by ∼6 kcal/mol) in basic environment. © 2016 Wiley Periodicals, Inc.

Pt···H Nonclassical Interaction in Water-Dissolved Pt(II) Complexes: Coaction of Electronic Effects with Solvent-Assisted Stabilization.

The structure of the hydration shell of cisplatin, cis-[Pt(NH3)2Cl2], and its aquated derivatives cis-[Pt(NH3)2Cl(H2O)](+), cis-[Pt(NH3)2OH(H2O)](+), and cis-[Pt(NH3)2(H2O)2](2+) were studied by a number of density functional molecular dynamics (DFT-MD) simulations (from 30 to 250 ps) in which Pt(II) complexes were immersed in a periodic box with 72 explicit water molecules. Furthermore, Pt(II) complex-water binding energy curves and full DFT optimizations of clusters derived from the lowest potential energy DFT-MD frames offered a deeper insight into the structure of the first hydration shell and electronic changes connected with the formation of a nonclassical Pt···H-O-H (Pt···Hw) hydrogen bond (inverse hydration). The probability of a Pt···Hw interaction decreases with increasing charge of the platinum complex due to disadvantageous electrostatics. The main stabilization comes from the charge transfer being followed by polarization and dispersion. Ligands form a framework for the network of H-bond interactions between the solvent molecules, which play an important role in the promotion/suppression of the formation of the Pt···Hw interactions. In the +2 charged diaqua complex the Pt···Hw interaction is still attractive but cannot compete with classical H bonds between solvent molecules. Thus, the formation of a Pt···Hw interaction is the result of a suitable solvent H-bonding network and the probability of its incidence decreases with increasing flexibility of the solvent.

Cy3 and Cy5 dyes terminally attached to 5'C end of DNA: structure, dynamics, and energetics.

Cy3 and Cy5 cyanine dyes terminally attached to the 5'C end (C1) of the DNA oligonucleotide were studied by metadynamics (MTD), molecular dynamics (MD), and density-functional methods with dispersion corrections (DFT-D). MTD simulations explored the free energy surface (FES) of the dye-DNA interactions, which included stacking and major groove binding motifs and unstacked structures. Dynamics of the stacked structures was studied by the MD simulations. All possible combinations of stacking interactions between the two indole rings of the dyes and the neighbor guanine and cytosine rings were observed. The most probable interaction included the stacking between the dye's distal indole ring and the guanine base. In ∼10% of the structures the delocalized π-electrons of the dyes' polymethine linkers played a key role in the dye-DNA dispersion interactions. The stacked conformers of the Cy3 dye were confirmed as true minima by DFT-D full optimizations. The stacked dye decreased flexibility up to two neighbor base pairs.

Exploration of various electronic properties along the reaction coordinate for hydration of Pt(II) and Ru(II) complexes; the CCSD, MPx, and DFT computational study.

In the study behavior of molecular electrostatic potential, averaged local ionization energy, and reaction electronic flux along the reaction coordinate of hydration process of three representative Ru(II) and Pt(II) complexes were explored using both post-HF and DFT quantum chemical approximations. Previously determined reaction mechanisms were explored by more detailed insight into changes of electronic properties using ωB97XD functional and MP2 method with 6-311++G(2df,2pd) basis set and CCSD/6-31(+)G(d,p) approach. The dependences of all examined properties on reaction coordinate give more detailed understanding of the hydration process.

Mechanism of the cis-[Pt(1R,2R-DACH)(H2O)2]2+ intrastrand binding to the double-stranded (pGpG)·(CpC) dinucleotide in aqueous solution: a computational DFT study.

A mechanism of the intrastrand 1,2-cross-link formation between the double-stranded pGpG·CpC dinucleotide (ds(pGpG)) and fully aquated oxaliplatin cis-[Pt(DACH)(H2O)2](2+) (DACH = cyclohexane-1R,2R-diamine) is presented. All structures of the reaction pathways including the transition states (TSs) were fully optimized in water solvent using DFT methodology with dispersion corrections. Both 5' → 3' and 3' → 5' binding directions were considered. In the first step there is a slight kinetic preference for 5'-guanine (5'G) monoadduct formation with an activation Gibbs free energy of 18.7 kcal/mol since the N7 center of the 5'G base is fully exposed to the solvent. On the other hand, the N7 atom of 3'-guanine (3'G) is sterically shielded by 5'G. The lowest energy path for formation of the 3'G monoadduct with an activation barrier of 19.3 kcal/mol is connected with a disruption of the 'DNA-like' structure of ds(pGpG). Monoadduct formation is the rate-determining process. The second step, chelate formation, is kinetically preferred in the 3' → 5' direction. The whole process of the platination is exergonic by up to -18.8 kcal/mol. Structural changes of ds(pGpG), charge transfer effects, and the influence of platination on the G·C base pair interaction strengths are also discussed in detail.

Influence of the environment on the specificity of the Mg(II) binding to uracil.

Interactions of uracil with the Mg(2+) ion were studied theoretically in the gas phase and in solution. The bare Mg(2+) prefers bidentate N-C═O binding sites stabilizing rare keto-enol forms of the base. Hydration and/or phosphate binding of the Mg(2+) ion shield its positive charge, which leads to preference of monodentate binding to the oxygen keto atoms, shifting fully the equilibrium between the tautomers back toward the canonical diketo tautomer. In solution, a direct inner-sphere metal binding to uracil is not clearly advantageous compared to the outer-sphere metal binding. Similar trends were also obtained for the Ca(2+) ion. Results are supported by the natural bond orbital (NBO) and atoms in molecule (AIM) analyses and the combined extended transition-state energy decomposition analysis and natural orbitals for chemical valence (ETS-NOCV).

Modeling the RNA 2'OH activation: possible roles of metal ion and nucleobase as catalysts in self-cleaving ribozymes.

The RNA 2'OH activation as taking place in the first chemical step of self-cleaving ribozymes is studied theoretically by DFT and MP2 methods using a continuum solvation model (CPCM). The reaction of proton transfer is studied in the presence of two kinds of catalysts: a fully hydrated metal ion (Mg(2+)) or partially hydrated nucleobase (guanine), taken separately or together leading to three different modes of activation. The metal ion is either directly bound (inner-sphere) or indirectly bound (outer-sphere) to the 2'OH group and a hydroxide ion acts as a general or specific base; the nucleobase is taken in anionic or in neutral enol-tautomeric forms playing itself the role of general base. The presence of a close metal ion (outer-sphere) lowers the pK(a) value of the 2'OH group by several log units in both metal-ion and nuleobase catalysis. The direct metal coordination to the 2'OH group (inner-sphere) further stabilizes the developing negative charge on the nucleophile. The switching from the inner-sphere to the outer-sphere coordination appears to be driven by the energy cost for reorganizing the first coordination shell rather than by the electrostatic repulsion between the ligands. The metal-ion catalysis is more effective with a specific base in the dianionic mechanism. On the other hand, the nucleobase catalysis is more effective in the monoanionic mechanism and in the presence of a metal ion acting as a cofactor through nonspecific electrostatic interactions. The results establish a baseline to study the possible roles of metal and nucleobase catalysts and their environment in more realistic models for self-cleaving ribozymes.

Comparison of hydration reactions for "piano-stool" RAPTA-B and [Ru(η6-arene)(en)Cl]+ complexes: density functional theory computational study.

The hydration process for two Ru(II) representative half-sandwich complexes: Ru(arene)(pta)Cl(2) (from the RAPTA family) and [Ru(arene)(en)Cl](+) (further labeled as Ru_en) were compared with analogous reaction of cisplatin. In the study, quantum chemical methods were employed. All the complexes were optimized at the B3LYP/6-31G(d) level using Conductor Polarizable Continuum Model (CPCM) solvent continuum model and single-point (SP) energy calculations and determination of electronic properties were performed at the B3LYP∕6-311++G(2df,2pd)/CPCM level. It was found that the hydration model works fairly well for the replacement of the first chloride by water where an acceptable agreement for both Gibbs free energies and rate constants was obtained. However, in the second hydration step worse agreement of the experimental and calculated values was achieved. In agreement with experimental values, the rate constants for the first step can be ordered as RAPTA-B > Ru_en > cisplatin. The rate constants correlate well with binding energies (BEs) of the Pt∕Ru-Cl bond in the reactant complexes. Substitution reactions on Ru_en and cisplatin complexes proceed only via pseudoassociative (associative interchange) mechanism. On the other hand in the case of RAPTA there is also possible a competitive dissociation mechanism with metastable pentacoordinated intermediate. The first hydration step is slightly endothermic for all three complexes by 3-5 kcal∕mol. Estimated BEs confirm that the benzene ligand is relatively weakly bonded assuming the fact that it occupies three coordination positions of the Ru(II) cation.

A comparative study of the binding of QSY 21 and Rhodamine 6G fluorescence probes to DNA: structure and dynamics.

Molecular dynamics (MD) simulations and ab initio quantum chemical calculations were employed to investigate the structure, dynamics and interactions of the QSY 21 nonfluorescent quencher and the fluorescence dye Rhodamine 6G bound to a B-DNA decamer. For QSY 21, two binding motifs were observed. In the first motif, the central xanthene ring is stacked on one base of the adjacent cytosine-guanine DNA base pair, whereas one of the 2,3-dihydro-1-indolyl aromatic side rings is stacked on the other base. In the second motif, the QSY 21 stacking interaction with the DNA base pair is mediated only by one of the side rings. Several transitions between the motifs are observed during a MD simulation. The ab initio calculations show that none of these motifs is energetically preferred. Two binding motifs were found also for Rhodamine 6G, with the xanthene ring stacked predominantly either on the cytosine or on the guanine. These results suggest that the side rings of QSY 21 play a crucial role in its stacking on the DNA and indicate novel binding mode absent in the case of Rhodamine 6G, which lacks aromatic side rings.

Cisplatin interaction with cysteine and methionine in aqueous solution: computational DFT/PCM study.

In this paper we explore cisplatin interactions with sulfur-containing amino acids in a polarizable continuum model. Two cisplatin hydrated complexes were considered as reactants (chloro complex, cis-[Pt(NH3)2Cl(H2O)]+; hydroxo complex, cis-[Pt(NH3)2(OH)(H2O)]+). We considered the following reaction mechanism: first step, substitution of the aqua ligand by amino acid; second step, dissociative chelate formation. For the optimized complex (at the B3LYP/6-31+G(d)/COSMO level), the energy profile was determined using the B3LYP/6-311++G(2df,2pd) level and two different PCM models-COSMO and UAKS/DPCM methods which were adapted for use on transition metal complexes. The results show thermodynamic preference for bonding by cysteine sulfur followed by the amino group nitrogen, methionine thioether sulfur, and carboxyl-group oxygen. Methionine slightly prefers the Pt-N(Met) coordination in the chloro complex, but in the hydroxo complex it prefers the Pt-S(Met) coordination. A similar trend follows from the bonding energies: BE(Pt-S(Cys)) = 80.8 kcal/mol and BE(Pt-N(Met)) = 76 kcal/mol. According to the experimental observations, the most stable structures found are kappa2(S,N) chelates. In the case of methionine, the same thermodynamic stability is predicted also for the kappa2(N,O) chelate. This differs from the gas-phase results, where kappa2(S,N) and even kappa2(S,O) were found to be more stable than kappa2(N,O) complex.

The trans effect in square-planar platinum(II) complexes--a density functional study.

The mechanism of substitution water exchange reactions in square planar trans-Pt[(NH(3))(2)T(H(2)O)](n+) complexes is studied (T = H(2)O, NH(3), OH(-), F(-), Cl(-), Br(-), H(2)S, CH(3)S(-), SCN(-), CN(-), PH(3), CO, CH(3)(-), H(-), C(2)H(4)). The trans effect is explained in terms of sigma-donation and pi-back-donation whose relative strengths are quantified by the changes of electron occupations of 5d platinum atomic orbitals. The sigma-donation strength is linearly correlated with the Pt-H(2)O (leaving ligand) bond length (trans influence). The kinetic trans effect strength correlates proportionally with the sigma-donation ability of the trans-ligand except the ligands with strong pi-back-donation ability that stabilizes transition state structure. The sigma-donation ability of the ligand is dependent on the sigma-donation strength of the ligand in the trans position. Therefore the trans effect caused by sigma-donation can be understood as a competition between the trans-ligands for the opportunity to donate electron density to the central Pt(II) atom. The influence of the trans effect on the reaction mechanism is also shown. For ligands with a very strong sigma-donation (e.g. CH(3)(-) and H(-)), the substitution proceeds by a dissociative interchange (I(d)) mechanism. Ligands with strong pi-back donation ability (e.g. C(2)H(4)) stabilize the pentacoordinated intermediate and the substitution proceeds by a two step associative mechanism. For ligands with weak sigma-donation and pi-back-donation abilities, the highest activation barriers have to be overcome and substitutions can be described by an associative interchange (I(a)) mechanism. The results are supported by the energy decomposition and the natural orbital analysis.