Chemistry with ADF

We present the theoretical and technical foundations of the Amsterdam Density Functional (ADF) program with a survey of the characteristics of the code (numerical integration, density fitting for the Coulomb potential, and STO basis functions). Recent developments enhance the efficiency of ADF (e.g., parallelization, near order‐N scaling, QM/MM) and its functionality (e.g., NMR chemical shifts, COSMO solvent effects, ZORA relativistic method, excitation energies, frequency‐dependent (hyper)polarizabilities, atomic VDD charges). In the Applications section we discuss the physical model of the electronic structure and the chemical bond, i.e., the Kohn–Sham molecular orbital (MO) theory, and illustrate the power of the Kohn–Sham MO model in conjunction with the ADF‐typical fragment approach to quantitatively understand and predict chemical phenomena. We review the “Activation‐strain TS interaction” (ATS) model of chemical reactivity as a conceptual framework for understanding how activation barriers of various types of (competing) reaction mechanisms arise and how they may be controlled, for example, in organic chemistry or homogeneous catalysis. Finally, we include a brief discussion of exemplary applications in the field of biochemistry (structure and bonding of DNA) and of time‐dependent density functional theory (TDDFT) to indicate how this development further reinforces the ADF tools for the analysis of chemical phenomena. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 931–967, 2001     

Lipophilic Multi‐walled Carbon Nanotube‐based Solid Contact Potassium Ion‐selective Electrodes with Reproducible Standard Potentials. A Comparative Study

The two most promising approaches for preparing solid contacts (SCs) for polymeric membrane based ion‐selective electrodes (ISEs) are based on the use of large surface areas conducting materials with high capacitance (e. g., various carbon nanotubes) and redox active materials (e. g. conducting polymers). While many of the essential requirements for the potential stability of SCISEs were addressed, the E⁰ reproducibility and its predictability, that would enable single use of such electrodes without calibration is still a challenge, i. e., the fabrication of electrodes with sufficiently close E⁰ and slope values to enable the characterization of large fabrication batches through the calibration of only a small number of electrodes. The most generic solution seems to be the adjustment of the E⁰ potential by polarization prior to the application of the ion‐selective membrane. This approach proved to be successful in case of conducting polymer‐based solid contacts, but has to be still explored for capacitive solid contact based ISEs, which is the purpose of this paper. We have chosen a well‐established highly lipophilic multi‐walled carbon nanotube (MWCNT), i. e. octadecane modified MWCNT (OD‐MWCNT), that is investigated in the comparative context of a similarly lipophilic conducting polymer solid contact (a perfluorinated alkanoate side chain functionalized poly(3,4‐ethylenedioxythiophene)). While, the OD‐MWCNT based SCISEs had inherently small standard deviation of their E⁰ values (less than 5 mV) this could be further improved by external polarization and short circuiting the SCISEs.     

Synthesis and electrochemical properties of novel redox‐active polymers with anthraquinone moieties by Pd‐catalyzed cyclopolymerization of dienes

Redox‐active polymers enhanced the focus of attention in the field of battery research in recent years. Anthraquinone is one of the most generic redox‐active functional compounds for battery applications, because the quinonide structure undergoes a redox reaction involving two electrons and features stable electrochemical behavior. Although various redox‐active polymers have been developed, the polymer backbone is mostly based on linear alkyl chains [e.g., poly(methacrylate)s, poly(ether)s]. Polymers featuring ring structures in the backbone are limited due to the restricted availability of suitable polymerization techniques [e.g., poly(norbornene)s by ROMP]. The cyclopolymerization of dienes with pendant redox‐active anthraquinone moieties by Pd catalysis represents a novel approach to synthesize redox‐active polymers featuring cyclic structures in the backbone. Electrochemical investigations, in particular cyclic voltammetry, of these new diene monomer, polymers and the corresponding polymer supported carbon paper composites were conducted in different organic electrolytes. © 2016 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2016 , 54, 2184–2190     

DIESEL-MP2: a new program to perform large-scale multireference-MP2 computations

This article presents a new MR‐MP2 code (Multi‐Reference Møller–Plesset 2nd order) suitable for the computation MR‐MP2 energies of extended systems with strong near degeneracy effects (e.g., open shell systems). It is based on the DIESEL program package developed by Hanrath and Engels. Due to improved algorithms the new code is able to handle systems with 400–500 basis functions and more than 100 electrons. The code is made for parallel computers with distributed memory, but can also be run on local machines. It possesses two integral interfaces (MOLCAS, TURBOMOLE). The algorithms are briefly introduced and timings for the Neocarzinostatin chromophore are presented. The efficiencies of the codes obtained with Intel or GNU compilers are compared. © 2006 Wiley Periodicals, Inc. J Comput Chem 27: 1055–1062, 2006     

Total Synthesis and Absolute Configuration Assignment of MRSA Active Garcinol and Isogarcinol

A short total synthesis of (±)‐garcinol and (±)‐isogarcinol, two endo‐type B PPAPs with reported activity against methiciline resistant Staphylococcus aureus (MRSA), is presented. The separation of framework‐constructing from framework‐decorating steps and the application of two highly regio‐ and stereoselective Pd‐catalysed allylations, that is, the Pd‐catalysed decarboxylative Tsuji–Trost allylation and the diastereoselective Pd‐catalysed allyl–allyl cross‐coupling, are key elements that allowed the total synthesis to be accomplished within 13 steps starting from acetylacetone. After separation of the enantiomers the absolute configurations of the four natural products (i.e., (?)‐garcinol, (+)‐guttiferone E (i.e., ent‐garcinol), (?)‐isogarcinol, and (+)‐isoxanthochymol (i.e., ent‐isogarcinol)) were assigned based on ECD spectroscopy.     

All‐Solid‐State Ion Selective and All‐Solid‐State Reference Electrodes

This paper is aiming to give a brief overview of recent research in the field of all‐solid‐state, internal solution free, ion‐selective electrodes and reference electrodes, employing conducting polymers or nano‐/microstructures as solid contacts beneath the polymeric, ion‐selective or reference membranes. The emphasis is on papers published in the last five years (after 2006). According to the papers published, poly(3‐octylthiophene) conducting polymer transducers offer highly reliable sensors for various applications, involving demanding analytical approaches and miniature sensors. On the other hand, the search for alternative materials continues: the sensors obtained by placing nano‐/microstructures (conducting polymers but also other materials, like, e.g., carbon nanotubes) underneath the receptor membrane are intensively tested. The recent years have also shown how useful the application of advanced instrumental methods is for the investigation of processes occurring within all‐solid‐state ion‐selective electrodes.     

The First Demonstration of the Gyroid in a Polyoxometalate‐Based Open Framework with High Proton Conductivity

The fabrication of extended open frameworks with crystalline ordering on the atomic level by following peculiar mathematical geometry (e.g. Möbius band, Klein bottle, periodic minimal surfaces, etc.) is challenging, but extremely beneficial for discovering non‐trivial structure‐dependent properties. In light of this, we herein report the first polyoxometalate‐based open framework (POM‐OF) that definitely lies on the gyroid (G)‐minimal surface, which was constructed by a rare pair of chiral POM enantiomers and zinc ions. Due to the presence of the proton carriers (i.e., water, Na⁺, [(Bu)₄N]⁺, etc.) in the resultant gyroidal channels, with pore dimensions on the order of the quasi‐mesoporous scale, this compound shows a high proton conductivity of 1.04×10^?2 S cm^?1 at a relative humidity of 75 % (80 °C), and also exhibits enormous potential in the application of electrochemical catalysis.     

Modulated molecular recognition by a temperature‐sensitive molecularly‐imprinted polymer

Modulated molecular recognition was achieved in a temperature‐sensitive molecularly‐imprinted polymer. Using PNIPA as the temperature‐sensitive element, the adenine‐imprinted polymer (i.e., MIP‐S) was prepared and characterized. The MIP‐S exhibited a temperature‐responsive molecular recognition behavior because of the thermal phase‐transition within the MIP‐S network. Specifically, below the transition temperature (e.g., 20 °C), the MIP‐S showed a highly specific recognition for the imprint species (adenine). However, the MIP‐S did not show any significant resolution for the imprint species (adenine) and its analogue (1‐methyladenine) above the transition temperature (e.g., 40 °C). Such temperature‐regulated recognition is comparable to a switch‐on and switch‐off process, thereby making tunable molecular recognition feasible. © 2009 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 47: 2352–2360, 2009     

Registry and search of chemical compounds on graphics display

The registry and substructure search component of in-house system SPHINCS (Structure /Property Handling Information Network for Chemical Substances) has been developed. For registry, a chemical structure is constructed on a graphics display by use of templates (e.g., 6N for pyridine, NH2 for amino group) and commands (e.g., BOND, EXCHANGE, DELETE). The generated connection table and atom coordinates are stored in a file. In a search, a query substructure is drawn on a graphics display. Special atom symbols (e.g., A for any atoms but hydrogen, HT for hetero atoms) can be used to represent the generic nature of a search. More than 1000 fragment codes (elements, rings, chains and augmented atoms), generated by computer analysis of connection tables, are used as primary search screens. An atom—bond—atom search program removes false drop structures. The structures retrieved are displayed in forms familiar to chemists with use of templates.     

A generalized direct-particle-deletion scheme for the calculation of chemical potential and solubilities of small- and medium-sized molecules in amorphous polymers

The development, validation, and first applications of a generalized version of an inverse Widom method are described. It permits the calculation of solubility coefficients for molecules as large as, e.g., benzene in all polymers for which reasonable forcefield parameters exist. Predicting the solubility is a key to the knowledge-based design of materials utilized to solve permeability related problems. For long time, particle insertion methods, such as the Widom method, were the only way to predict solubilities from molecular models, but they, in most cases, only worked well for rather small penetrants (e.g., H2, O2, N2). Therefore, a few years ago, a new particle deletion algorithm "DPD" was introduced by Boulougouris, Economou, and Theodorou to overcome this problem in principle. The related computer code was, however, only applicable to special, relatively simple model systems. As application examples for the generalized version described here, solubility calculations for nitrogen, oxygen, and benzene in poly(dimethyl siloxane) are presented.     

Coating for preventing nonspecific adhesion mediated biofouling in salty systems: Effect of the electrostatic and van der waals interactions

Development of anti-biofouling coating has attracted immense attention for reducing the massively detrimental effects of biofouling in systems ranging from ship hulls and surgical instruments to catheters, implants, and stents. In this paper, we propose a model to quantify the role of electrostatic and van der Waals (vdW) forces in dictating the efficacy of dielectric coating for preventing the nonspecific adhesion mediated biofouling in salty systems. The model considers a generic charged lipid-bilayer encapsulated vesicle-like structure representing the bio-organism. Also, we consider the fouling caused by the nonspecific adhesion of the bio-organism on the substrate, without accounting for the explicit structures (e.g., pili, appendages) or conditions (e.g., surface adhesins secreted by the organisms) involved in the adhesion of specific microorganism. The model is tested by considering the properties of actual coating materials and biofouling causing microorganisms (bacteria, fungi, algae). Results show that while the electrostatic-vdW effect can be significant in anti-biofouling action for cases where the salt concentration is relatively low (e.g., saline solution for surgical instruments), it might not be effective for marine environment where the salt concentration is much higher. The findings, therefore, point to a hitherto unexplored driving mechanism of anti-biofouling action of the coating. Such an identification will also enable the appropriate choices of the coating materials (e.g., possible dielectric material with volume charge) and other system parameters (e.g., salinity of the solution for storing the surgical instruments) that will significantly improve the efficiency of the coatings in preventing the nonspecific adhesion mediated biofouling.     

The development of an artificial organic networks toolkit for LabVIEW

Two of the most challenging problems that scientists and researchers face when they want to experiment with new cutting‐edge algorithms are the time‐consuming for encoding and the difficulties for linking them with other technologies and devices. In that sense, this article introduces the artificial organic networks toolkit for LabVIEW? (AON‐TL) from the implementation point of view. The toolkit is based on the framework provided by the artificial organic networks technique, giving it the potential to add new algorithms in the future based on this technique. Moreover, the toolkit inherits both the rapid prototyping and the easy‐to‐use characteristics of the LabVIEW? software (e.g., graphical programming, transparent usage of other softwares and devices, built‐in programming event‐driven for user interfaces), to make it simple for the end‐user. In fact, the article describes the global architecture of the toolkit, with particular emphasis in the software implementation of the so‐called artificial hydrocarbon networks algorithm. Lastly, the article includes two case studies for engineering purposes (i.e., sensor characterization) and chemistry applications (i.e., blood–brain barrier partitioning data model) to show the usage of the toolkit and the potential scalability of the artificial organic networks technique. © 2015 Wiley Periodicals, Inc.     

A Critical Survey of Dithiocarbamate Reversible Addition‐Fragmentation Chain Transfer (RAFT) Agents in Radical Polymerization

This article provides a critical review of the properties, synthesis, and applications of dithiocarbamates Z′Z″NC(=S)SR as mediators in reversible addition‐fragmentation chain transfer (RAFT) polymerization. These are among the most versatile RAFT agents. Through choice of substituents on nitrogen (Z′, Z″), the polymerization of most monomer types can be controlled to provide living characteristics (i.e., low dispersities, high end‐group fidelity, and access to complex architectures). These include the more activated monomers (MAMs; e.g., styrenes and acrylates) and the less activated monomers (LAMs; e.g., vinyl esters and vinylamides). Dithiocarbamates with balanced activity (e.g., 1H‐pyrazole‐1‐carbodithioates) or switchable RAFT agents [e.g., a N‐methyl‐N‐(4‐pyridinyl)dithiocarbamate] allow control MAMs and LAMs with a single RAFT agent and provide a pathway to low‐dispersity poly(MAM)‐block‐poly(LAM). © 2018 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2019 , 57, 216–227     

High‐resolution separation of monoclonal antibodies mixtures and their charge variants by an alternative and generic CZE method

The determination of mAb critical quality attributes (CQA) is crucial for their successful application in health diseases. A generic CZE method was developed for the high‐resolution separation of various mAb charge variants, which are often recognized as important CQA. A dynamic coating of the capillary was obtained with polyethylene oxide (PEO), whereas Bis‐Tris allowed the analysis of mAbs under native conditions at pH 7.0. The effect of PEO and Bis‐Tris concentrations, as well as the nature of the acidic counter ion on the method performance was systematically studied. The %RSD on migration times was below 5% on three different CE instruments using the optimized method. Additional charge variants (in particular acidic variants) were resolved for 10 out of 17 mAbs compared to a reference CZE approach involving the use of ε‐amino‐caproic acid (EACA), triethylenetetramine (TETA), and hydroxypropylmethyl cellulose (HPMC). The amount of basic and acidic charge variants of 17 Food and Drug Administration (FDA) approved mAbs covering a wide range of physico‐chemical properties, e.g., pI between 8.0 and 9.4 and different hydrophobicity, were mainly comprised between 5–15% and 15–30%, respectively. It is noteworthy that applications for the quality control in hospitals as well as for the combination of the immune checkpoint inhibitors nivolumab and ipilimumab were presented.     

Generic schemes for single-molecule kinetics. 1: Self-consistent pathway solutions for renewal processes

In this paper, we discuss a strategy for reducing a complex single molecule kinetic process to a set of generic structures (motifs) that are building blocks for a general kinetic scheme. In general, these motifs have complex kinetics (i.e., waiting time distribution functions) which are composed of fundamental kinetic steps. (1) First, we treat four different experimental single molecule measurements within both the usual kinetic framework (i.e., using the rate matrix) and the waiting time distribution function framework. The two frameworks are then shown to be equivalent and can be formulated on the basis of the first passage time distribution function of monitored single molecule events. (2) Second, to calculate this basic quantity, we decompose a complex kinetic scheme with the help of two kinetic motifs, sequential and branching, and derive self-consistent equations by convoluting waiting time distributions and first passage time distribution(s) along the reaction pathway(s). (3) As examples, two experimental systems, a chain reaction model with a special case of enzymatic reactions and a general kinetic model for fluorescence emission, are analyzed on the basis of a generic scheme composed of a monitored link, controlled link, and unknown link, each representing a possible subscheme associated with a complex waiting time distribution function. As a result, single molecule measurements of the generic scheme retain the same functional form when a kinetic link is altered within a subscheme, and different measurements can be classified and analyzed within the same framework. (4) Finally, to explore the physical reasons for nonexponential waiting time distribution, we use the example of blinking phenomena to discuss several scenarios of dynamic and static disorder and their implications for observed memory effects. The self-consistent pathway formalism is presented in this paper for renewal processes and will be generalized to nonrenewal processes with memory effects in a future publication.     

Microelectrode Applications of Pulsed Electrochemical Detection

Pulsed electrochemical detection (PED) has been applied to the direct (i.e., requires no derivatization), sensitive and reproducible detection of numerous polar aliphatic compounds (e.g., carbohydrates, amines, and thiols). These compounds, many of which have biological significance, typically have been classified as non‐electroactive for detection under constant applied potentials and have poor optical detection properties. PED exploits the electrocatalytic activity of noble metal (e.g., Au and Pt) electrode surfaces to oxidize various polar functional groups using multi‐step potential‐time waveforms to realize amperometric/coulometric detection while maintaining uniform and reproducible electrode activity. The response mechanisms in PED are dominated by the surface properties of the electrode, and as a consequence, members of each chemical class of compounds produce virtually identical voltammetric responses. Thus, the full analytical potential is achieved when combined with an a priori separation. Although popularized in combination with high performance liquid chromatography, the combination of PED with highly efficient microseparation techniques offer the analyst unique advantages. This paper reviews the fundamental aspects of PED especially at microelectrodes, and its application in microchromatographic and electrophoretic separation techniques, including microchip devices.     

Wide‐Ranging Host Capability of a PdII‐Linked M2L4 Molecular Capsule with an Anthracene Shell

This article reports that an M₂L₄ molecular capsule is capable of encapsulating various neutral molecules in quantitative yields. The capsule was obtained as a single product by mixing a small number of components; two Pd^II ions and four bent bispyridine ligands containing two anthracene panels. Detailed studies of the host capability of the Pd^II‐linked capsule revealed that spherical (e.g., paracyclophane, adamantanes, and fullerene C₆₀), planar (e.g., pyrenes and triphenylene), and bowl‐shaped molecules (e.g., corannulene) were encapsulated in the large spherical cavity, giving rise to 1:1 and 1:2 host–guest complexes, respectively. The volume of the encapsulated guest molecules ranged from 190 to 490 ų. Within the capsule, the planar guests adopt a stacked‐dimer structure and the bowl‐shaped guests formed an unprecedented concave‐to‐concave capsular structure, which are fully shielded by the anthracene shell. Competitive binding experiments of the capsule with a set of the planar guests established a preferential binding series for pyrenes≈phenanthrene>triphenylene. Furthermore, the capsule showed the selective formation of an unusual ternary complex in the case of triphenylene and corannulene.     

Morphological studies of blends of conjugated polymers and acceptor molecules using langevin dynamics simulations

We use coarse‐grained Langevin dynamics simulations of blends of generic conjugated polymers and acceptor molecules to show how architecture (e.g., side chains, backbone flexibility of oligomers) and the pair‐wise interactions between the constituents of the blend affect morphology and phase transition. Alkyl side chains on the conjugated oligomer backbones shift the liquid crystal (LC) transition temperature from that of bare conjugated backbones and the direction of the shift depends on backbone–backbone interactions. Rigid backbones and constrained side chains cause a layer‐by‐layer morphology of conjugated polymers and amorphous acceptors, whereas flexible backbones and unconstrained side chains facilitate highly ordered acceptor arrangement. Strong backbone–backbone attraction shifts LC transition to higher temperatures than weak backbone–backbone attraction, and strong acceptor–acceptor attraction increases acceptor aggregation. Pure macro‐phase separated domains form when all pair‐wise interactions in the blend are strongly attractive, whereas interconnected domains form at intermediate acceptor–acceptor attraction and strong polymer–polymer attractions. © 2012 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys, 2013     

Equation-of-motion spin-flip coupled-cluster model with single and double substitutions: Theory and application to cyclobutadiene

While the equation-of-motion coupled-cluster (EOM-CC) method is capable of describing certain multiconfigurational wave functions within a single-reference framework (e.g., open-shell type excited states, doublet radicals, etc.), it may fail in cases of more extensive degeneracy, e.g., bond breaking and polyradicals. This work presents an extension of the EOM-CC approach to these chemically important situations. In our approach, target multiconfigurational wave functions are described as spin-flipping excitations from the high-spin reference state. This enables a balanced treatment of nearly degenerate electronic configurations present in the target low-spin wave functions. The relations between the traditional spin-conserving EOM models and the EOM spin-flip method is discussed. The presentation of the formalism emphasizes the variational properties of the theory and shows that the killer condition is rigorously satisfied in single-reference EOM-CC theories. The capabilities and advantages of the new approach are demonstrated by its application to cyclobutadiene.     

Reversible Self‐Assembly of Terpyridine‐Functionalized Graphene Oxide for Energy Conversion

Terpyridine‐functionalized graphene oxides were prepared for self‐assembly into 3D architectures with various metal ions (e.g., Fe, Ru). The resulting electrode materials showed significantly improved electroactivities for efficient energy conversion and storage. They showed promise for application in the oxygen reduction reaction (ORR), photocurrent generation, and supercapacitance.