Multiwfn - a Multifunctional Wavefunction Analyzer
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Supporting Information
Electronic Supplementary Material (ESI) for RSC Advances. This journal is © The Royal Society of Chemistry 2020 Supporting Information How to Select Ionic Liquids as Extracting Agent Systematically? Special Case Study for Extractive Denitrification Process Shurong Gaoa,b,c,*, Jiaxin Jina,b, Masroor Abroc, Ruozhen Songc, Miao Hed, Xiaochun Chenc,* a State Key Laboratory of Alternate Electrical Power System with Renewable Energy Sources, North China Electric Power University, Beijing, 102206, China b Research Center of Engineering Thermophysics, North China Electric Power University, Beijing, 102206, China c Beijing Key Laboratory of Membrane Science and Technology & College of Chemical Engineering, Beijing University of Chemical Technology, Beijing 100029, PR China d Office of Laboratory Safety Administration, Beijing University of Technology, Beijing 100124, China * Corresponding author, Tel./Fax: +86-10-6443-3570, E-mail: [email protected], [email protected] 1 COSMO-RS Computation COSMOtherm allows for simple and efficient processing of large numbers of compounds, i.e., a database of molecular COSMO files; e.g. the COSMObase database. COSMObase is a database of molecular COSMO files available from COSMOlogic GmbH & Co KG. Currently COSMObase consists of over 2000 compounds including a large number of industrial solvents plus a wide variety of common organic compounds. All compounds in COSMObase are indexed by their Chemical Abstracts / Registry Number (CAS/RN), by a trivial name and additionally by their sum formula and molecular weight, allowing a simple identification of the compounds. We obtained the anions and cations of different ILs and the molecular structure of typical N-compounds directly from the COSMObase database in this manuscript. -
Aqueous Pka Prediction for Tautomerizable Compounds Using Equilibrium Bond Lengths
ARTICLE https://doi.org/10.1038/s42004-020-0264-7 OPEN Aqueous pKa prediction for tautomerizable compounds using equilibrium bond lengths Beth A. Caine1,2, Maddalena Bronzato3, Torquil Fraser3, Nathan Kidley3, Christophe Dardonville 4 & ✉ Paul L.A. Popelier 1,2 1234567890():,; The accurate prediction of aqueous pKa values for tautomerizable compounds is a formidable task, even for the most established in silico tools. Empirical approaches often fall short due to a lack of pre-existing knowledge of dominant tautomeric forms. In a rigorous first-principles approach, calculations for low-energy tautomers must be performed in protonated and deprotonated forms, often both in gas and solvent phases, thus representing a significant computational task. Here we report an alternative approach, predicting pKa values for her- bicide/therapeutic derivatives of 1,3-cyclohexanedione and 1,3-cyclopentanedione to within just 0.24 units. A model, using a single ab initio bond length from one protonation state, is as accurate as other more complex regression approaches using more input features, and outperforms the program Marvin. Our approach can be used for other tautomerizable spe- cies, to predict trends across congeneric series and to correct experimental pKa values. 1 Department of Chemistry, University of Manchester, Manchester, UK. 2 Manchester Institute of Biotechnology (MIB), 131 Princess Street, Manchester, UK. 3 Syngenta AG, Jealott’s Hill, Warfield, Bracknell RG42 6E7, UK. 4 Instituto de Química Médica, IQM–CSIC, C/Juan de la Cierva 3, Madrid 28006, Spain. ✉ email: [email protected] COMMUNICATIONS CHEMISTRY | (2020) 3:21 | https://doi.org/10.1038/s42004-020-0264-7 | www.nature.com/commschem 1 ARTICLE COMMUNICATIONS CHEMISTRY | https://doi.org/10.1038/s42004-020-0264-7 pproximately 21% of the compounds that make up (http://vcclab.org), Marvin (http://www.chemaxon.com) and pharmaceutical databases are said to exist in two or more Pallas (www.compudrug.com)) on 248 compounds of the Gold A 1 12 tautomeric forms . -
Popular GPU-Accelerated Applications
LIFE & MATERIALS SCIENCES GPU-ACCELERATED APPLICATIONS | CATALOG | AUG 12 LIFE & MATERIALS SCIENCES APPLICATIONS CATALOG Application Description Supported Features Expected Multi-GPU Release Status Speed Up* Support Bioinformatics BarraCUDA Sequence mapping software Alignment of short sequencing 6-10x Yes Available now reads Version 0.6.2 CUDASW++ Open source software for Smith-Waterman Parallel search of Smith- 10-50x Yes Available now protein database searches on GPUs Waterman database Version 2.0.8 CUSHAW Parallelized short read aligner Parallel, accurate long read 10x Yes Available now aligner - gapped alignments to Version 1.0.40 large genomes CATALOG GPU-BLAST Local search with fast k-tuple heuristic Protein alignment according to 3-4x Single Only Available now blastp, multi cpu threads Version 2.2.26 GPU-HMMER Parallelized local and global search with Parallel local and global search 60-100x Yes Available now profile Hidden Markov models of Hidden Markov Models Version 2.3.2 mCUDA-MEME Ultrafast scalable motif discovery algorithm Scalable motif discovery 4-10x Yes Available now based on MEME algorithm based on MEME Version 3.0.12 MUMmerGPU A high-throughput DNA sequence alignment Aligns multiple query sequences 3-10x Yes Available now LIFE & MATERIALS& LIFE SCIENCES APPLICATIONS program against reference sequence in Version 2 parallel SeqNFind A GPU Accelerated Sequence Analysis Toolset HW & SW for reference 400x Yes Available now assembly, blast, SW, HMM, de novo assembly UGENE Opensource Smith-Waterman for SSE/CUDA, Fast short -
Computer-Assisted Catalyst Development Via Automated Modelling of Conformationally Complex Molecules
www.nature.com/scientificreports OPEN Computer‑assisted catalyst development via automated modelling of conformationally complex molecules: application to diphosphinoamine ligands Sibo Lin1*, Jenna C. Fromer2, Yagnaseni Ghosh1, Brian Hanna1, Mohamed Elanany3 & Wei Xu4 Simulation of conformationally complicated molecules requires multiple levels of theory to obtain accurate thermodynamics, requiring signifcant researcher time to implement. We automate this workfow using all open‑source code (XTBDFT) and apply it toward a practical challenge: diphosphinoamine (PNP) ligands used for ethylene tetramerization catalysis may isomerize (with deleterious efects) to iminobisphosphines (PPNs), and a computational method to evaluate PNP ligand candidates would save signifcant experimental efort. We use XTBDFT to calculate the thermodynamic stability of a wide range of conformationally complex PNP ligands against isomeriation to PPN (ΔGPPN), and establish a strong correlation between ΔGPPN and catalyst performance. Finally, we apply our method to screen novel PNP candidates, saving signifcant time by ruling out candidates with non‑trivial synthetic routes and poor expected catalytic performance. Quantum mechanical methods with high energy accuracy, such as density functional theory (DFT), can opti- mize molecular input structures to a nearby local minimum, but calculating accurate reaction thermodynamics requires fnding global minimum energy structures1,2. For simple molecules, expert intuition can identify a few minima to focus study on, but an alternative approach must be considered for more complex molecules or to eventually fulfl the dream of autonomous catalyst design 3,4: the potential energy surface must be frst surveyed with a computationally efcient method; then minima from this survey must be refned using slower, more accurate methods; fnally, for molecules possessing low-frequency vibrational modes, those modes need to be treated appropriately to obtain accurate thermodynamic energies 5–7. -
Benchmarking and Application of Density Functional Methods In
BENCHMARKING AND APPLICATION OF DENSITY FUNCTIONAL METHODS IN COMPUTATIONAL CHEMISTRY by BRIAN N. PAPAS (Under Direction the of Henry F. Schaefer III) ABSTRACT Density Functional methods were applied to systems of chemical interest. First, the effects of integration grid quadrature choice upon energy precision were documented. This was done through application of DFT theory as implemented in five standard computational chemistry programs to a subset of the G2/97 test set of molecules. Subsequently, the neutral hydrogen-loss radicals of naphthalene, anthracene, tetracene, and pentacene and their anions where characterized using five standard DFT treatments. The global and local electron affinities were computed for the twelve radicals. The results for the 1- naphthalenyl and 2-naphthalenyl radicals were compared to experiment, and it was found that B3LYP appears to be the most reliable functional for this type of system. For the larger systems the predicted site specific adiabatic electron affinities of the radicals are 1.51 eV (1-anthracenyl), 1.46 eV (2-anthracenyl), 1.68 eV (9-anthracenyl); 1.61 eV (1-tetracenyl), 1.56 eV (2-tetracenyl), 1.82 eV (12-tetracenyl); 1.93 eV (14-pentacenyl), 2.01 eV (13-pentacenyl), 1.68 eV (1-pentacenyl), and 1.63 eV (2-pentacenyl). The global minimum for each radical does not have the same hydrogen removed as the global minimum for the analogous anion. With this in mind, the global (or most preferred site) adiabatic electron affinities are 1.37 eV (naphthalenyl), 1.64 eV (anthracenyl), 1.81 eV (tetracenyl), and 1.97 eV (pentacenyl). In later work, ten (scandium through zinc) homonuclear transition metal trimers were studied using one DFT 2 functional. -
TURBOMOLE: Modular Program Suite for Ab Initio Quantum-Chemical and Condensed- Matter Simulations
TURBOMOLE: Modular program suite for ab initio quantum-chemical and condensed- matter simulations Cite as: J. Chem. Phys. 152, 184107 (2020); https://doi.org/10.1063/5.0004635 Submitted: 12 February 2020 . Accepted: 07 April 2020 . Published Online: 13 May 2020 Sree Ganesh Balasubramani, Guo P. Chen, Sonia Coriani, Michael Diedenhofen, Marius S. Frank, Yannick J. Franzke, Filipp Furche, Robin Grotjahn, Michael E. Harding, Christof Hättig, Arnim Hellweg, Benjamin Helmich-Paris, Christof Holzer, Uwe Huniar, Martin Kaupp, Alireza Marefat Khah, Sarah Karbalaei Khani, Thomas Müller, Fabian Mack, Brian D. Nguyen, Shane M. Parker, Eva Perlt, Dmitrij Rappoport, Kevin Reiter, Saswata Roy, Matthias Rückert, Gunnar Schmitz, Marek Sierka, Enrico Tapavicza, David P. Tew, Christoph van Wüllen, Vamsee K. Voora, Florian Weigend, Artur Wodyński, and Jason M. Yu COLLECTIONS Paper published as part of the special topic on Electronic Structure SoftwareESS2020 ARTICLES YOU MAY BE INTERESTED IN PSI4 1.4: Open-source software for high-throughput quantum chemistry The Journal of Chemical Physics 152, 184108 (2020); https://doi.org/10.1063/5.0006002 NWChem: Past, present, and future The Journal of Chemical Physics 152, 184102 (2020); https://doi.org/10.1063/5.0004997 CP2K: An electronic structure and molecular dynamics software package - Quickstep: Efficient and accurate electronic structure calculations The Journal of Chemical Physics 152, 194103 (2020); https://doi.org/10.1063/5.0007045 J. Chem. Phys. 152, 184107 (2020); https://doi.org/10.1063/5.0004635 152, 184107 © 2020 Author(s). The Journal ARTICLE of Chemical Physics scitation.org/journal/jcp TURBOMOLE: Modular program suite for ab initio quantum-chemical and condensed-matter simulations Cite as: J. -
A Summary of ERCAP Survey of the Users of Top Chemistry Codes
A survey of codes and algorithms used in NERSC chemical science allocations Lin-Wang Wang NERSC System Architecture Team Lawrence Berkeley National Laboratory We have analyzed the codes and their usages in the NERSC allocations in chemical science category. This is done mainly based on the ERCAP NERSC allocation data. While the MPP hours are based on actually ERCAP award for each account, the time spent on each code within an account is estimated based on the user’s estimated partition (if the user provided such estimation), or based on an equal partition among the codes within an account (if the user did not provide the partition estimation). Everything is based on 2007 allocation, before the computer time of Franklin machine is allocated. Besides the ERCAP data analysis, we have also conducted a direct user survey via email for a few most heavily used codes. We have received responses from 10 users. The user survey not only provide us with the code usage for MPP hours, more importantly, it provides us with information on how the users use their codes, e.g., on which machine, on how many processors, and how long are their simulations? We have the following observations based on our analysis. (1) There are 48 accounts under chemistry category. This is only second to the material science category. The total MPP allocation for these 48 accounts is 7.7 million hours. This is about 12% of the 66.7 MPP hours annually available for the whole NERSC facility (not accounting Franklin). The allocation is very tight. The majority of the accounts are only awarded less than half of what they requested for. -
Porting the DFT Code CASTEP to Gpgpus
Porting the DFT code CASTEP to GPGPUs Toni Collis [email protected] EPCC, University of Edinburgh CASTEP and GPGPUs Outline • Why are we interested in CASTEP and Density Functional Theory codes. • Brief introduction to CASTEP underlying computational problems. • The OpenACC implementation http://www.nu-fuse.com CASTEP: a DFT code • CASTEP is a commercial and academic software package • Capable of Density Functional Theory (DFT) and plane wave basis set calculations. • Calculates the structure and motions of materials by the use of electronic structure (atom positions are dictated by their electrons). • Modern CASTEP is a re-write of the original serial code, developed by Universities of York, Durham, St. Andrews, Cambridge and Rutherford Labs http://www.nu-fuse.com CASTEP: a DFT code • DFT/ab initio software packages are one of the largest users of HECToR (UK national supercomputing service, based at University of Edinburgh). • Codes such as CASTEP, VASP and CP2K. All involve solving a Hamiltonian to explain the electronic structure. • DFT codes are becoming more complex and with more functionality. http://www.nu-fuse.com HECToR • UK National HPC Service • Currently 30- cabinet Cray XE6 system – 90,112 cores • Each node has – 2×16-core AMD Opterons (2.3GHz Interlagos) – 32 GB memory • Peak of over 800 TF and 90 TB of memory http://www.nu-fuse.com HECToR usage statistics Phase 3 statistics (Nov 2011 - Apr 2013) Ab initio codes (VASP, CP2K, CASTEP, ONETEP, NWChem, Quantum Espresso, GAMESS-US, SIESTA, GAMESS-UK, MOLPRO) GS2NEMO ChemShell 2%2% SENGA2% 3% UM Others 4% 34% MITgcm 4% CASTEP 4% GROMACS 6% DL_POLY CP2K VASP 5% 8% 19% http://www.nu-fuse.com HECToR usage statistics Phase 3 statistics (Nov 2011 - Apr 2013) 35% of the Chemistry software on HECToR is using DFT methods. -
A Tutorial for Theodore 2.0.2
A Tutorial for TheoDORE 2.0.2 Felix Plasser, Patrick Kimber Loughborough, 2019 Department of Chemistry – Loughborough University Contents 1 Before Starting3 1.1 Introduction . .3 1.2 Notation . .3 1.3 Installation . .3 2 Natural transition orbitals (Turbomole)4 2.1 Input generation . .4 2.2 Transition density matrix (1TDM) analysis . .5 2.3 Plotting of the orbitals . .6 3 Charge transfer number and exciton analysis (Turbomole)9 3.1 Input generation . .9 3.2 Transition density matrix (1TDM) analysis . 10 3.3 Electron-hole correlation plots . 11 4 Interface to the external cclib library (Gaussian 09) 12 4.1 Check the log file . 12 4.2 Input generation . 13 4.3 Transition density matrix (1TDM) analysis . 15 5 Advanced fragment input and double excitations (Columbus) 16 5.1 Fragment preparation using Avogadro . 17 5.2 Input generation . 18 5.3 Transition density matrix (1TDM) analysis . 19 6 Fragment decomposition for a transition metal complex 21 6.1 Input generation . 21 6.2 Transition density matrix analysis and decomposition . 23 7 Domain NTO and conditional density analysis 26 7.1 Input generation . 26 1 7.2 Transition density matrix analysis . 28 7.3 Plotting of the orbitals . 29 8 Attachment/detachment analysis (Molcas - natural orbitals) 31 8.1 Input generation . 31 8.2 State density matrix analysis . 32 8.3 Plotting of the orbitals . 33 9 Contact 34 TheoDORE tutorial 2 1 Before Starting 1.1 Introduction This tutorial is intended to provide an overview over the functionalities of the TheoDORE program package. Various tasks of different complexity are discussed using interfaces to dif- ferent quantum chemistry packages. -
$ GW $100: a Plane Wave Perspective for Small Molecules
GW 100: a plane wave perspective for small molecules Emanuele Maggio,1 Peitao Liu,1, 2 Michiel J. van Setten,3 and Georg Kresse1, ∗ 1University of Vienna, Faculty of Physics and Center for Computational Materials Science, Sensengasse 8/12, A-1090 Vienna, Austria 2Institute of Metal Research, Chinese Academy of Sciences, Shenyang 110016, China 3Nanoscopic Physics, Institute of Condensed Matter and Nanosciences, Universit´eCatholique de Louvain, 1348 Louvain-la-Neuve, Belgium (Dated: November 28, 2016) In a recent work, van Setten and coworkers have presented a carefully converged G0W0 study of 100 closed shell molecules [J. Chem. Theory Comput. 11, 5665 (2015)]. For two different codes they found excellent agreement to within few 10 meV if identical Gaussian basis sets were used. We inspect the same set of molecules using the projector augmented wave method and the Vienna ab initio simulation package (VASP). For the ionization potential, the basis set extrapolated plane wave results agree very well with the Gaussian basis sets, often reaching better than 50 meV agreement. In order to achieve this agreement, we correct for finite basis set errors as well as errors introduced by periodically repeated images. For electron affinities below the vacuum level differences between Gaussian basis sets and VASP are slightly larger. We attribute this to larger basis set extrapolation errors for the Gaussian basis sets. For quasi particle (QP) resonances above the vacuum level, differences between VASP and Gaussian basis sets are, however, found to be substantial. This is tentatively explained by insufficient basis set convergence of the Gaussian type orbital calculations as exemplified for selected test cases. -
DFT and QTAIM Study of the Tetra-Tert ... -.:. Michael Pittelkow
Journal of Molecular Structure 1026 (2012) 127–132 Contents lists available at SciVerse ScienceDirect Journal of Molecular Structure journal homepage: www.elsevier.com/locate/molstruc DFT and QTAIM study of the tetra-tert-butyltetraoxa[8]circulene regioisomers structure ⇑ Gleb V. Baryshnikov a, Boris F. Minaev a, , Valentina A. Minaeva a,b, Alina T. Baryshnikova a, Michael Pittelkow c a Bohdan Khmelnytsky National University, 18031 Cherkasy, Ukraine b Theoretical Chemistry, School of Biotechnology, Royal Institute of Technology, SE-10691 Stockholm, Sweden c Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen Ø, Denmark highlights " Tetra-tert-butyltetraoxa[8]circulene regioisomers were studied by DFT method. " Electronic density distribution was calculated by the QTAIM method. " The presence of stabilizing non-valence bonds is detected by X-ray experiment. " The HÁÁÁH contacts are dynamically unstable due to high ellipticity. " The energy of the HÁÁÁH and CHÁÁÁO contacts was estimated by the Espinosa equation. article info abstract Article history: The recently synthesized tetra-tert-butyltetraoxa[8]circulene regioisomers characterized by unusual Received 6 March 2012 solution-state aggregation behavior are calculated at the density functional theory (DFT) level with the Received in revised form 24 May 2012 quantum theory of atoms in molecules (QTAIMs) approach to the electron density distribution analysis. Accepted 24 May 2012 The presence of stabilizing intramolecular hydrogen bonds and hydrogen–hydrogen interactions in the Available online 31 May 2012 studied molecules is predicted and the energies of these interactions are estimated with QTAIM. Occur- rence of the CHÁÁÁO bonds is detected by the single-crystal X-ray analysis for two regioisomers, obtained Keywords: in high purity. -
Formation of Β-Cyclodextrin Complexes in an Anhydrous Environment
JMolModel (2016) 22:207 DOI 10.1007/s00894-016-3061-6 ORIGINAL PAPER Formation of β-cyclodextrin complexes in an anhydrous environment Hocine Sifaoui1 & Ali Modarressi2 & Pierre Magri2 & Anna Stachowicz-Kuśnierz3 & Jacek Korchowiec3 & Marek Rogalski2 Received: 16 December 2015 /Accepted: 3 July 2016 # The Author(s) 2016. This article is published with open access at Springerlink.com Abstract The formation of inclusion complexes of β- Keywords β-Cyclodextrin . Differential scanning cyclodextrin was studied at the melting temperature of guest calorimetry . Inclusion complexes . Polyaromatics . Organic compounds by differential scanning calorimetry. The com- acids . Molecular modeling plexes of long-chain n-alkanes, polyaromatics, and organic acids were investigated by calorimetry and IR spectroscopy. The complexation ratio of β-cyclodextrin was compared with results obtained in an aqueous environment. The stability and Introduction structure of inclusion complexes with various stoichiometries were estimated by quantum chemistry and molecular dynam- Many lipophilic drug molecules display low bioavailability ics calculations. Comparison of experimental and theoretical that hinder their efficacy [1]. Cyclodextrins, which form stable results confirmed the possible formation of multiple inclusion complexes with numerous molecules, are used to improve complexes with guest molecules capable of forming hydrogen aqueous solubility and bioavailability. β-Cyclodextrin (β- bonds. This finding gives new insight into the mechanism of CD) is composed of seven glucopyranose units forming a formation of host–guest complexes and shows that hydropho- cyclic, cone-shaped cavity with a hydrophilic outer surface bic interactions play a secondary role in this case. and a relatively hydrophobic inner surface [2]. This molecular structure of β-CD allows the formation of complexes with a large variety of organic molecules of different shape and po- larity [3–8].