Karol M. Langner

Bio: Karol M. Langner is an academic researcher from University of Virginia. The author has contributed to research in topics: Distributed multipole analysis & Intermolecular force. The author has an hindex of 13, co-authored 23 publications receiving 3989 citations. Previous affiliations of Karol M. Langner include Wrocław University of Technology & National Research Nuclear University MEPhI.

cclib: A library for package‐independent computational chemistry algorithms

Abstract: There are now a wide variety of packages for electronic structure calculations, each of which differs in the algorithms implemented and the output format. Many computational chemistry algorithms are only available to users of a particular package despite being generally applicable to the results of calculations by any package. Here we present cclib, a platform for the development of package-independent computational chemistry algorithms. Files from several versions of multiple electronic structure packages are automatically detected, parsed, and the extracted information converted to a standard internal representation. A number of population analysis algorithms have been implemented as a proof of principle. In addition, cclib is currently used as an input filter for two GUI applications that analyze output files: PyMOlyze and GaussSum. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2008

A public database of macromolecular diffraction experiments.

Abstract: The low reproducibility of published experimental results in many scientific disciplines has recently garnered negative attention in scientific journals and the general media Public transparency, including the availability of `raw' experimental data, will help to address growing concerns regarding scientific integrity Macromolecular X-ray crystallography has led the way in requiring the public dissemination of atomic coordinates and a wealth of experimental data, making the field one of the most reproducible in the biological sciences However, there remains no mandate for public disclosure of the original diffraction data The Integrated Resource for Reproducibility in Macromolecular Crystallography (IRRMC) has been developed to archive raw data from diffraction experiments and, equally importantly, to provide related metadata Currently, the database of our resource contains data from 2920 macromolecular diffraction experiments (5767 data sets), accounting for around 3% of all depositions in the Protein Data Bank (PDB), with their corresponding partially curated metadata IRRMC utilizes distributed storage implemented using a federated architecture of many independent storage servers, which provides both scalability and sustainability The resource, which is accessible via the web portal at http://wwwproteindiffractionorg, can be searched using various criteria All data are available for unrestricted access and download The resource serves as a proof of concept and demonstrates the feasibility of archiving raw diffraction data and associated metadata from X-ray crystallo­graphic studies of biological macromolecules The goal is to expand this resource and include data sets that failed to yield X-ray structures in order to facilitate collaborative efforts that will improve protein structure-determination methods and to ensure the availability of `orphan' data left behind for various reasons by individual investigators and/or extinct structural genomics projects

Open Data, Open Source and Open Standards in chemistry: The Blue Obelisk five years on

Abstract: The Blue Obelisk movement was established in 2005 as a response to the lack of Open Data, Open Standards and Open Source (ODOSOS) in chemistry. It aims to make it easier to carry out chemistry research by promoting interoperability between chemistry software, encouraging cooperation between Open Source developers, and developing community resources and Open Standards. This contribution looks back on the work carried out by the Blue Obelisk in the past 5 years and surveys progress and remaining challenges in the areas of Open Data, Open Standards, and Open Source in chemistry. We show that the Blue Obelisk has been very successful in bringing together researchers and developers with common interests in ODOSOS, leading to development of many useful resources freely available to the chemistry community.

Mesoscale modeling of block copolymer nanocomposites

Abstract: Nanoadditives alter the properties of pure block copolymers, through an interplay of entropic, enthalpic and kinetic factors at competing length and time scales. A fundamental understanding of these factors is considered decisive for taming block copolymer nanocomposites, since even modest changes in design parameters can impact the final material. At the same time, analytical and computational approaches have not yet reached the maturity required for an integrated study of all relevant aspects. Heterogeneity, local irregularities and dynamic behavior—these are the most challenging issues facing theory and simulations in the quest for rational design. In this review, we discuss the state of mesoscopic modeling for block copolymer nanocomposites, and cover relevant literature from at least the last five years, during which developments have taken off.

Physical nature of ethidium and proflavine interactions with nucleic acid bases in the intercalation plane.

Abstract: On the basis of the crystallographic structures of three nucleic acid intercalation complexes involving ethidium and proflavine, we have analyzed the interaction energies between intercalator chromophores and their four nearest bases, using a hybrid variation-perturbation method at the second-order Moller-Plesset theory level (MP2) with a 6-31G(d,p) basis set. A total MP2 interaction energy minimum precisely reproduces the crystallographic position of the ethidium chromophore in the intercalation plane between UA/AU bases. The electrostatic component constitutes the same fraction of the total energy for all three studied structures. The multipole electrostatic interaction energy, calculated from cumulative atomic multipole moments (CAMMs), was found to converge only after including components above the fifth order. CAMM interaction surfaces, calculated on grids in the intercalation planes of these structures, reasonably reproduce the alignment of intercalators in crystal structures; they exhibit additional minima in the direction of the DNA grooves, however, which also need to be examined at higher theory levels if no crystallographic data are given.

Open Babel: An open chemical toolbox

Abstract: A frequent problem in computational modeling is the interconversion of chemical structures between different formats. While standard interchange formats exist (for example, Chemical Markup Language) and de facto standards have arisen (for example, SMILES format), the need to interconvert formats is a continuing problem due to the multitude of different application areas for chemistry data, differences in the data stored by different formats (0D versus 3D, for example), and competition between software along with a lack of vendor-neutral formats. We discuss, for the first time, Open Babel, an open-source chemical toolbox that speaks the many languages of chemical data. Open Babel version 2.3 interconverts over 110 formats. The need to represent such a wide variety of chemical and molecular data requires a library that implements a wide range of cheminformatics algorithms, from partial charge assignment and aromaticity detection, to bond order perception and canonicalization. We detail the implementation of Open Babel, describe key advances in the 2.3 release, and outline a variety of uses both in terms of software products and scientific research, including applications far beyond simple format interconversion. Open Babel presents a solution to the proliferation of multiple chemical file formats. In addition, it provides a variety of useful utilities from conformer searching and 2D depiction, to filtering, batch conversion, and substructure and similarity searching. For developers, it can be used as a programming library to handle chemical data in areas such as organic chemistry, drug design, materials science, and computational chemistry. It is freely available under an open-source license from http://openbabel.org .

Avogadro: an advanced semantic chemical editor, visualization, and analysis platform

Abstract: The Avogadro project has developed an advanced molecule editor and visualizer designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. It offers flexible, high quality rendering, and a powerful plugin architecture. Typical uses include building molecular structures, formatting input files, and analyzing output of a wide variety of computational chemistry packages. By using the CML file format as its native document type, Avogadro seeks to enhance the semantic accessibility of chemical data types. The work presented here details the Avogadro library, which is a framework providing a code library and application programming interface (API) with three-dimensional visualization capabilities; and has direct applications to research and education in the fields of chemistry, physics, materials science, and biology. The Avogadro application provides a rich graphical interface using dynamically loaded plugins through the library itself. The application and library can each be extended by implementing a plugin module in C++ or Python to explore different visualization techniques, build/manipulate molecular structures, and interact with other programs. We describe some example extensions, one which uses a genetic algorithm to find stable crystal structures, and one which interfaces with the PackMol program to create packed, solvated structures for molecular dynamics simulations. The 1.0 release series of Avogadro is the main focus of the results discussed here. Avogadro offers a semantic chemical builder and platform for visualization and analysis. For users, it offers an easy-to-use builder, integrated support for downloading from common databases such as PubChem and the Protein Data Bank, extracting chemical data from a wide variety of formats, including computational chemistry output, and native, semantic support for the CML file format. For developers, it can be easily extended via a powerful plugin mechanism to support new features in organic chemistry, inorganic complexes, drug design, materials, biomolecules, and simulations. Avogadro is freely available under an open-source license from http://avogadro.openmolecules.net .

Do Special Noncovalent π–π Stacking Interactions Really Exist?

Abstract: Noncovalent interactions play an increasingly important role in modern chemical research, and are nowadays considered as cornerstones in supramolecular chemistry, materials science, and even biochemistry. When unsaturated organic groups are involved in noncovalent interactions, the terms “p–p stacking”, or more generally “p–p interactions” are often used. As noted recently, this classification has a quite mysterious flavor. For larger structures, p–p stacking is a phenomenon that is theoretically not well understood, although some progress has been made. From many studies of the benzene dimer and other complexes involving phenyl rings, it can be concluded that the p orbitals do not function as in conventional overlapdriven covalent bonding, although this is not common knowledge. The prototypical benzene dimer is nowadays considered a typical van der Waals complex in which the long-range dispersion interactions (dominant R 6 dependence of the interaction energy on interfragment distance) play the major role. As a consequence, the dimer is unbound at uncorrelated Hartree–Fock and many density functional theory (DFT) levels. This more sophisticated view is increasingly replacing Hunter6s model of p–p interactions, which (over)emphasises the mainly quadrupole–quadrupole electrostatic component of the interaction in benzene-type systems (see Ref. [13] for recent theoretical work on polar psystems). Because van der Waals complexes are formed by almost all neutral, closed-shell molecules, which are considered exclusively herein, what should be so special about the interaction between stacked aromatic units compared to, for example, saturated (hydrogenated) rings of about the same size. This mainly energetic difference is termed herein the p–p stacking effect (PSE). For example, benzene and cyclohexane both exist as fluids at room temperature, which indicates similar intermolecular interactions. According to accurate CCSD(T) computations, the stacked (parallel-displaced, PD) benzene dimer has an even smaller binding energy than the pentane dimer ( 2.8 vs. 3.9 kcalmol ), 14] which has the same number of electrons. These observations seem to be incompatible with the assumption of special p–p interactions. On the other hand, it is known that larger polycyclic aromatic hydrocarbons (PAHs) behave differently to large alkanes; for example, PAHs become increasingly insoluble in common organic solvents with increasing size. Thus the magnitude of the intermolecular interactions and possibly also their fundamental character is more strongly size-dependent in aromatic systems than in saturated systems. The clarification of this matter, and the question as to whether the term “p–p interaction” makes sense from a theoretical point of view, is the central topic of the work presented herein. The linear condensed acenes, from benzene (number of rings n= 1) to tetracene (n= 4), and the corresponding perhydrogenated ring systems (all trans–all anti stereoisomers) were used as models. Homo-dimers of stacked (aromatic with Ci, except for the PD benzene dimer, which has C2h symmetry, and saturated with C2h symmetry) and T-shaped orientation (aromatic only, C2v) are investigated. The Tshaped forms are important in the crystal packing of aromatic molecules, as analyzed in detail by Desiraju and Gavezzotti. For saturated dimers, no well-defined T-shaped structures could be found. Energy-minimized dimer structures for n= 1 and n= 4 are shown as an example in Figure 1.

Protein Data Bank: the single global archive for 3D macromolecular structure data

Abstract: The Protein Data Bank (PDB) is the single global archive of experimentally determined three-dimensional (3D) structure data of biological macromolecules. Since 2003, the PDB has been managed by the Worldwide Protein Data Bank (wwPDB; wwpdb.org), an international consortium that collaboratively oversees deposition, validation, biocuration, and open access dissemination of 3D macromolecular structure data. The PDB Core Archive houses 3D atomic coordinates of more than 144 000 structural models of proteins, DNA/RNA, and their complexes with metals and small molecules and related experimental data and metadata. Structure and experimental data/metadata are also stored in the PDB Core Archive using the readily extensible wwPDB PDBx/mmCIF master data format, which will continue to evolve as data/metadata from new experimental techniques and structure determination methods are incorporated by the wwPDB. Impacts of the recently developed universal wwPDB OneDep deposition/validation/biocuration system and various methods-specific wwPDB Validation Task Forces on improving the quality of structures and data housed in the PDB Core Archive are described together with current challenges and future plans.

The Role of Local Triplet Excited States and D-A Relative Orientation in Thermally Activated Delayed Fluorescence: Photophysics and Devices.

Abstract: Here, a comprehensive photophysical investigation of a the emitter molecule DPTZ-DBTO2, showing thermally activated delayed fluorescence (TADF), with near-orthogonal electron donor (D) and acceptor (A) units is reported. It is shown that DPTZ-DBTO2 has minimal singlet–triplet energy splitting due to its near-rigid molecular geometry. However, the electronic coupling between the local triplet (3LE) and the charge transfer states, singlet and triplet, (1CT, 3CT), and the effect of dynamic rocking of the D–A units about the orthogonal geometry are crucial for efficient TADF to be achieved. In solvents with low polarity, the guest emissive singlet 1CT state couples directly to the near-degenerate 3LE, efficiently harvesting the triplet states by a spin orbit coupling charge transfer mechanism (SOCT). However, in solvents with higher polarity the emissive CT state in DPTZ-DBTO2 shifts below (the static) 3LE, leading to decreased TADF efficiencies. The relatively large energy difference between the 1CT and 3LE states and the extremely low efficiency of the 1CT to 3CT hyperfine coupling is responsible for the reduction in TADF efficiency. Both the electronic coupling between 1CT and 3LE, and the (dynamic) orientation of the D–A units are thus critical elements that dictate reverse intersystem crossing processes and thus high efficiency in TADF.