Chemical Topology Research Articles

Chemical deposition and mechanical application of semiconductors thin films

Features and main technological methods of forming thin layers of semiconductor materials by methods of chemical deposition and mechanical application are analyzed. The disadvantages of thermal sputtering and cathodic sputtering of thin films in vacuum for multicomponent semiconductor compounds are indicated. Features of chemical deposition of semiconductor films from the gas (steam) phase are presented. Such deposition involves the transfer of source material from the evaporator zone with higher temperature in the form of volatile compounds to the colder surface of the substrate, where the film growth occurs as a result of reaction of transported compounds or their decomposition. It is shown that the growth of the film during chemical vapor deposition is a process of layer-by-layer condensation of atoms or molecules, with the advantageous difference that during chemical deposition the latter are formed as a result of a heterogeneous chemical reaction when there is no need for average free path length of the gas molecules to be larger than the size of the deposition chamber, i.e. no need for critical degree of vacuum. Chemical deposition of thin films from solution is characterized as a process of precipitation of solute which occurs due to the fact that the ionic product exceeds the product of solubility, i.e. it is greater than the constant value characteristic of a saturated solution in the equilibrium state. We emphasize, that chemical deposition from an water solution allows to obtain homogeneous in thickness and structure fine-grained non-textured mechanically stable polycrystalline films with good adhesion to substrates and the required set of properties. The method of pulverization with subsequent pyrolysis is described. This is deposition from intracomplex organometallic compounds, which is based on thermally stimulated reactions between clusters of atoms, chemically active substances of liquid or vapor phase. The method of electrolytic deposition on electrically conductive substrates is characterized. The method is using appropriate salt solutions by co-deposition of individual components, or by deposition on the cathode of one of the components with its subsequent interaction with others present in the solution. We also describe the method of obtaining epitaxial thin films of semiconductor deposition materials. We note that the analyzed methods or their modifications are necessary tool today to create thin-film semiconductor structures with predetermined properties. In the same time, in each particular case the features of each method of obtaining thin semiconductor films should be comprehensively evaluated and, depending on the chemical composition, structure, topology and complex of expected properties, the most effective method should be applied.

New insights in chemical reactivity from quantum chemical topology.

Based on the quantum chemical topology of the modified electron localization function ELFx , an efficient and robust mechanistic methodology designed to identify the favorable reaction pathway between two reactants is proposed. We first recall and reshape how the supermolecular interaction energy can be evaluated from only three distinct terms, namely the intermolecular coulomb energy, the intermolecular exchange-correlation energy and the intramolecular energies of reactants. Thereafter, we show that the reactivity between the reactants is driven by the first-order variation in the coulomb intermolecular energy defined in terms of the response to changes in the number of electrons. Illustrative examples with the formation of the dative bond B-N involved in the BH3 NH3 molecule and the typical formation of the hydrogen bond in the canonical water dimer are presented. For these selected systems, our approach unveils a noticeable mimicking of Edual onto the DFT intermolecular interaction energy surface calculated between the both reactants. An automated reaction-path algorithm aimed to determine the most favorable relative orientations when the two molecules approach each other is also outlined.

The effect of polyacid on the physical and biological properties of chitosan based layer-by-layer films

This study aimed to understand the structure-property relationship in chitosan (CHI) based layer-by-layer (LbL) films and to correlate the surface properties with the biological characteristics of the multilayers. LbL films of CHI were prepared using two different types of polyacids, i.e. a polyphenol, tannic acid (TA) and a polycarboxylic acid, poly(acrylic acid) (PAA). The chemical nature and topology of the polyacid was found to be critical on LbL growth, stability under physiologically related conditions, surface morphology, wettability and drug release properties of the multilayers. The differences in surface properties provided remarkably different biological properties such as anti-adhesiveness against protein adsorption and antibacterial activity for Ciprofloxacin (CIP) incorporated films against Escherichia coli (E. coli), Staphylococcus aureus (S. aureus), and Listeria monocytogenes (L. monocytogenes). Linearly growing TA/CHI films with relatively smooth surfaces resisted more against protein adsorption when the topmost layer and the protein carried like charges. On the other hand, exponentially growing PAA/CHI multilayers did not exhibit antiadhesive behaviour. Thick and loose PAA/CHI multilayers were able to release higher amount of CIP, thus presented enhanced antibacterial activity compared to thin and more intense TA/CHI films. Finally, we showed that pH affected the extent of association among the layers as well as drug release and antibacterial properties of the films. Our findings showed that TA/CHI films are more promising as antiadhesive surfaces, whereas PAA/CHI multilayers are more suitable for preparation of antibacterial surfaces. The fundamental findings of this study may form a basis for preparation of thin films for drug delivery applications and modification of biomaterial surfaces.

Diffusion Mechanism Modeling of Metformin in Human Organic Cationic Amino Acid Transporter one and Functional Impact of S189L, R206C, and G401S Mutation.

Metformin used as a first-line drug to treat Type 2 Diabetes Mellitus is transported via organic cation channels to soft tissues. Mutations in the SLC22A1 gene, such as Gly401Ser, Ser189Leu, and Arg206Cys, may affect the drug’s therapeutic effect on these patients. This study aims at proposing a potential structural model for drug interactions with the hOCT1 transporter, as well as the impact of these mutations at both topological and electronic structure levels on the channel’s surface, from a chemical point of view with, in addition to exploring the frequency distribution. To chemically understand metformin diffusion, we used an open model from the protein model database, with ID PM0080367, viewed through UCSF Chimera. The effect of the mutations was assessed using computational hybrid Quantum Mechanics/Molecular Mechanics, based on the Austin Model 1 semi-empirical method using Spartan 18’ software. The results demonstrate coupling energy for metformin with amino acids F, W, H and Y, because of the interaction between the metformin dication and the electron cloud of π orbitals. The mutations analyzed showed changes in the chemical polarity and topology of the structure. The proposed diffusion model is a possible approach to the interaction mechanism between metformin and its transporter, as well as the impacts of variants, suggesting structural changes in the action of the drug. Metformin efficacy considerably varies from one patient to another; this may be largely attributed to the presence of mutations on the SLC22A1 gene. This study aims at proposing a potential structural model for metformin-hOCT1 (SLC22A1) transporter interaction, as well as the identification of the effect of mutations G401S (rs34130495), S189L (rs34104736), and R206C (616C > T) of the SLC22A1 gene at the topological and electronic structure levels on the channel surfaces, from a chemical viewpoint. Our results demonstrated that the coupling energies for metformin with aromatic amino acids F, W, H and Y, because of the interaction between the metformin dication and the electron cloud of π orbitals. Changes in the chemical environment’s polarity and the structure’s topology were reported in the mutations assessed. The diffusion model proposed is a potential approach for the mechanism of interaction of metformin with its transporter and the effects of variants on the efficacy of the drug in the treatment of type 2 diabetes. The assessment of the frequency of these mutations in a sample of Colombian type 2 diabetes patients suggests that different SLC22A1 gene variants might be involved in reduced OCT1 activity in the Colombian population since none of these mutations were detected.

Fluorination Effects in XPhos Gold(I) Fluorothiolates

Gold phosphine derivatives such as thiolates have been recently proposed as catalysts or catalyst precursors. The relevance of the supramolecular environment on the fine-tuning of the catalytical activity on these compounds incentivizes the use of tools that are convenient to characterize in detail the non-covalent landscape of the systems. Herein, we show the molecular and supramolecular diversity caused by the changes in the fluorination pattern in a family of new XPhos goldfluorothiolate derivatives. Furthermore, we studied the supramolecular interactions around the Au centers using quantum chemical topology tools, in particular the quantum theory of atoms in molecules (QTAIM) and the non-covalent interaction index. Our results give detailed insights into the fluorination effects on the strength of intramolecular and intermolecular interactions in these systems. We have also used QTAIM delocalization indexes to define a novel hapticity indicator. Finally, we assessed the trans influence of the fluorothiolates on the phosphine in terms of the change in the δ 31P-NMR. These results show the feasibility of the use of fluorination in the modulation of the electronic properties of Buchwald phosphine gold(I) compounds, and thereby its potential catalytic activity.

Untangling knotty problems.

The synthesis of molecular knots has been a major achievement in the field of chemical topology, but only a few relatively simple ones have been made so far. A route based on a weaving approach has now been used to make a seven-crossing knot and could offer a route to more complicated structures.

Bulk Glassy GeTe2: A Missing Member of the Tetrahedral GeX2 Family and a Precursor for the Next Generation of Phase-Change Materials

Vitreous germanium disulfide GeS2 and diselenide GeSe2 belong to canonical chalcogenide glasses extensively studied over the past half century. Their high-temperature orthorhombic polymorphs are congruently melting compounds, and the tetrahedral crystal and glass structure is largely preserved in the melt. In contrast, the ditelluride counterpart is absent in the Ge–Te phase diagram, which shows only a single compound, monotelluride GeTe. Phase-change materials based on GeTe have become a technologically important class of solids, and their structure and properties are also widely studied. Surprisingly, very scarce information is available for alloys having GeTe2 stoichiometry. Using a fast quenching procedure in silica capillaries, high-energy X-ray diffraction, and Raman spectroscopy supported by first-principles simulations, we show that bulk glassy GeTe2 differs substantially from the lighter GeX2 members, revealing 46% of trigonal germanium, 31% of three-fold coordinated tellurium, and only 20% of edge-sharing tetrahedra or pyramids. The fraction of homopolar Ge–Ge bonds is low; however, the population of dominant Te–Te dimers and Ten oligomers, n ≤ 10, appears to be significant. The complex structural and chemical topology of g-GeTe2 is directly related to the thermodynamic metastability of germanium ditelluride, schematically represented by the following reaction: GeTe2 ⇄ GeTe + Te. Disproportionation is complete above liquidus in the temperature range of semiconductor–metal transition, and the dense metallic GeTe2 liquid, mostly consisting of five-fold coordinated Ge species, exhibits high fluidity, strong fragility (m = 99 ± 5), and presumably a fast structural transformation rate combined with low atomic mobility in the vicinity of the glass transition temperature, favorable for reliable long-term data retention in nonvolatile memories. The observed and predicted characteristic features make GeTe2 a promising precursor for the next generation of phase-change materials, especially coupled with additional metal doping, depolymerizing the tetrahedral interconnected glass network and accelerating (sub)nanosecond crystallization.

The nature of the intermolecular interaction in (H2X)2 (X = O, S, Se).

Hydrogen bonds (HBs) are crucial non-covalent interactions in chemistry. Recently, the occurrence of an HB in (H2S)2 has been reported (Arunan et al., Angew. Chem., Int. Ed., 2018, 57, 15199), challenging the textbook view of H2S dimers as mere van der Waals clusters. We herein try to shed light on the nature of the intermolecular interactions in the H2O, H2S, and H2Se dimers via correlated electronic structure calculations, Symmetry Adapted Perturbation Theory (SAPT) and Quantum Chemical Topology (QCT). Although (H2S)2 and (H2Se)2 meet some of the criteria for the occurrence of an HB, potential energy curves as well as SAPT and QCT analyses indicate that the nature of the interaction in (H2O)2 is substantially different (e.g. more anisotropic) from that in (H2S)2 and (H2Se)2. QCT reveals that the HB in (H2O)2 includes substantial covalent, dispersion and electrostatic contributions, while the last-mentioned component plays only a minor role in (H2S)2 and (H2Se)2. The major contributions to the interactions of the dimers of H2S and H2Se are covalency and dispersion as revealed by the exchange-correlation components of QCT energy partitions. The picture yielded by SAPT is somewhat different but compatible with that offered by QCT. Overall, our results indicate that neither (H2S)2 nor (H2Se)2 are hydrogen-bonded systems, showing how the nature of intermolecular contacts involving hydrogen atoms evolves in a group down the periodic table.

Bifunctional squaramides with benzyl-like fragments: analysis of CH⋯π interactions by a multivariate linear regression model and quantum chemical topology

A multivariate linear regression model and quantum chemical topology are used for the quantitative description of non-covalent interactions in the transition state of the Michael addition catalyzed by bifunctional squaramides.

Topological Dynamic Matter.

The principles of topology in condensed matter physics have expanded to areas such as photonics, acoustics, electronics, and mechanics. Their extension to dynamic (soft) matter could enable the control and design of topological thermodynamic (micro)states and nonreciprocal dynamics, potentially leading to paradigmatic applications in molecular and thermal waveguiding, logics, and energy management. This Perspective explores distinct topological concepts for dynamic matter and prospective function. Topological tools are exemplified and discussed for the study of nonlocal order parameters or invariants in dynamic molecular matter, toward the engineering of assemblies, reactions, and system chemistry with unconventional global properties-a scope which has the potential to push the frontiers of physical chemistry and transform chemical topology from form to function.

Radical Cyclic [3]Daisy Chains

Summary Mechanically interlocked molecules (MIMs) that undergo controllable internal motions of their component parts in more than one dimension are rare entities in the molecular world. Cyclic [2]daisy chains ([c2]DCs) are a class of MIMs that have been identified as prototypes for molecular muscles. It remains, however, a challenge to synthesize [cn]DCs with n > 2 selectively and efficiently. Herein, we report the design and synthesis of [c3]DCs employing radical and anionic templates. Two mechanically interlocked [c3]DCs with 18 positive charges were obtained in >90% yields. One [c3]DC displayed good air stability in its radical cationic form, while the other underwent reversible “co-conformational” switching between open macrocyclic and closed trisarm-shaped forms under electrochemical control. These findings provide not only two-dimensional MIMs with attractive electronic and switchable properties, but also a starting point for the design of extended molecular arrays, which could become the forerunners of adjustable molecular nets and breathable molecular membranes.

Open versus Interpenetrated: Switchable Supramolecular Trajectories in Mechanosynthesis of a Halogen-Bonded Borromean Network

Summary Precise control over topologically intricate molecular architectures remains an open challenge for chemists due to their inherent structural complexity. We report a simple solvent-free strategy to selectively prepare two multi-component supramolecular crystalline systems based on the halogen bond, endowed with either an unknot topology or a Borromean-type entanglement. Real-time in situ monitoring of the solvent-free mechanochemical synthesis of these three-component halogen-bonded ionic co-crystals reveals that the choice of milling conditions leads to a switch in the supramolecular reaction trajectory, resulting in the selective formation of an open halogen-bonded network or a halogen-bonded Borromean-type assembly.

Beyond the Classical Electron-Sharing and Dative Bond Picture: Case of the Spin-Polarized Bond.

Chemical bonds are traditionally assigned as electron‐sharing or donor‐acceptor/dative. External criteria such as the nature of the dissociation process, energy partitioning schemes, or quantum chemical topology are invoked to assess the bonding situation. However, for systems with marked multi‐reference character, this binary categorization might not be precise enough to render the bonding properties. A third scenario can be foreseen: spin polarized bonds. To illustrate this, the case of a NaBH3 − cluster is presented. According to the analysis NaBH3 − exhibits a strong diradical character and cannot be classified as either electron‐sharing or a dative bond. Elaborated upon are the common problems of popular bonding descriptions. Additionally, a simple model, based on the bond order and local spin indicators, which discriminates between all three bonding situations, is provided.

Fractionation of chain walking polyethylene and elucidation of branching, conformation and molar mass distributions

State-of-the-art liquid interaction chromatography (IC) allows separation of macromolecules according to chemical composition (CC), functionality or molecular topology in contrast to size-based approaches such as size exclusion chromatography (SEC), which has its limitations in distinguishing chemical structures. Yet, for macromolecules with multivariate molecular distributions, online identification and characterization of distinct components in bulk samples is a considerable challenge. A useful approach to narrow down the complexity of a given sample is preparative molar mass fractionation (pMMF) that provides fractions in mg or g scale, which can be subjected to further advanced analysis to elucidate the physical and structural properties of the sample. In this study, novel chain-walking polyethylenes (CWPE), which differ substantially in macromolecular architecture, are fractionated using pMMF. Using IC in temperature and solvent gradient modes (TGIC, SGIC), the pMMF fractions are separated according to branching topology. Quadruple-detector high temperature SEC is carried out to determine the physical properties and study the MM-dependent structural transformation of CWPE. A detailed branching analysis was carried out by means of nuclear magnetic resonance. Two-dimensional liquid chromatography (LC) hyphenating IC and SEC provides comprehensive bivariate correlations between MM and molecular topology.

On the many-body nature of intramolecular forces in FFLUX and its implications.

FFLUX is a biomolecular force field under construction, based on Quantum Chemical Topology (QCT) and machine learning (kriging), with a minimalistic and physically motivated design. A detailed analysis of the forces within the kriging models as treated in FFLUX is presented, taking as a test example a liquid water model. The energies of topological atoms are modeled as 3Natoms -6 dimensional potential energy surfaces, using atomic local frames to represent the internal degrees of freedom. As a result, the forces within the kriging models in FFLUX are inherently N-body in nature where N refers to Natoms . This provides a fuller picture that is closer to a true quantum mechanical representation of interactions between atoms. The presented computational example quantitatively showcases the non-negligible (as much as 9%) three-body nature of bonded forces and angular forces in a water molecule. We discuss the practical impact on the pressure calculation with N-body forces and periodic boundary conditions (PBC) in molecular dynamics, as opposed to classical force fields with two-body forces. The equivalence between the PBC-related correction terms in the general virial equation is shown mathematically.

The Na⋅⋅⋅B Bond in NaBH3−: A Different Type of Bond

AbstractA newly introduced Na−B bond in NaBH3− has been a challenge for the chemical bonding community. Here, a series of MBH3− (M=Li, Na, K) species and NaB(CN)3− are studied within the context of quantum chemical topology approaches. The analyses suggest that M–B interaction cannot be classified as an ordinary covalent, dative, or even simple ionic interaction. The interactions are controlled by coulombic forces between the metals and the substituents on boron, for example, H or CN, more than the direct M–B interaction. On the other hand, while the characteristics of the (3, −1) critical points of the bonds are comparable to weak hydrogen bonds, not covalent bonds, the metal and boron share a substantial sum of electrons. To the best of the author's knowledge, the characteristics of these bonds are unprecedented among known molecules. Considering all paradoxical properties of these bonds, they are herein described as ionic‐enforced covalent bonds.

The Na⋅⋅⋅B Bond in NaBH3 - : A Different Type of Bond.

A newly introduced Na-B bond in NaBH3 - has been a challenge for the chemical bonding community. Here, a series of MBH3 - (M=Li, Na, K) species and NaB(CN)3 - are studied within the context of quantum chemical topology approaches. The analyses suggest that M-B interaction cannot be classified as an ordinary covalent, dative, or even simple ionic interaction. The interactions are controlled by coulombic forces between the metals and the substituents on boron, for example, H or CN, more than the direct M-B interaction. On the other hand, while the characteristics of the (3, -1) critical points of the bonds are comparable to weak hydrogen bonds, not covalent bonds, the metal and boron share a substantial sum of electrons. To the best of the author's knowledge, the characteristics of these bonds are unprecedented among known molecules. Considering all paradoxical properties of these bonds, they are herein described as ionic-enforced covalent bonds.

Creating Gaussian process regression models for molecular simulations using adaptive sampling.

FFLUX is a new force field that combines the accuracy of quantum mechanics with the speed of force fields, without any link to the architecture of classical force fields. This force field is atom-focused and adopts the parameter-free topological atom from Quantum Chemical Topology (QCT). FFLUX uses Gaussian process regression (also known as kriging) models to make predictions of atomic properties, which in this work are atomic energies according to QCT's interacting quantum atom approach. Here, we report the adaptive sampling technique maximum expected prediction error to create data-compact, efficient, and accurate kriging models (sub-kJ mol-1 for water, ammonia, methane, and methanol and sub-kcal mol-1 for N-methylacetamide). The models cope with large molecular distortions and are ready for use in molecular simulation. A brand new press-one-button Python pipeline, called ICHOR, carries out the training.

The influence of polypropylene-block/graft-polycaprolactone copolymers on melt rheology, morphology, and dielectric properties of polypropylene/polycarbonate blends

The paper discusses the relationship between rheology and morphology of immiscible polypropylene (matrix))/polycarbonate (dispersed phase) blends compatibilized with novel polypropylene-polycaprolactone block and graft copolymers. Transmission electron microscopy (TEM) experiments revealed uniform droplet morphologies and a reduction of the average size of the dispersed phase upon addition of the compatibilizer. The results suggested the influence of the molecular weight distribution (MWD)/chemical composition distribution (CCD) and topology of the compatibilizer on the compatibilizing performance. Graft copolymers were found to be most effective in reducing the size of the dispersed phase, whereas the performance of block copolymers appeared to be highly dependent on the block length of PP. Small-amplitude oscillatory rheological experiments revealed an increase in elasticity at low frequencies caused by the interfacial interactions induced by the compatibilizer. The effect was quantified using the relaxation time spectrums that displayed the additional peak at longer relaxation times via Gramespacher-Meissner method. Broadband dielectric spectroscopy (BDS) revealed the influence of the copolymer architecture and molecular weight of the polypropylene blocks on the properties of the interfacial polarization, which was in line with both rheology and morphology data.

Quantum chemical topology at the spin-orbit configuration interaction level: Application to astatine compounds.

We report a methodology that allows the investigation of the consequences of the spin-orbit coupling by means of the QTAIM and ELF topological analyses performed on top of relativistic and multiconfigurational wave functions. In practice, it relies on the "state-specific" natural orbitals (NOs; expressed in a Cartesian Gaussian-type orbital basis) and their occupation numbers (ONs) for the quantum state of interest, arising from a spin-orbit configuration interaction calculation. The ground states of astatine diatomic molecules (AtX with X = AtF) and trihalide anions (IAtI- , BrAtBr- , and IAtBr- ) are studied, at exact two-component relativistic coupled cluster geometries, revealing unusual topological properties as well as a significant role of the spin-orbit coupling on these. In essence, the presented methodology can also be applied to the ground and/or excited states of any compound, with controlled validity up to including elements with active 5d, 6p, and/or 5f shells, and potential limitations starting with active 6d, 7p, and/or 6f shells bearing strong spin-orbit couplings.