Shared posts

13 Mar 07:31

[ASAP] Automation of Active Space Selection for Multireference Methods via Machine Learning on Chemical Bond Dissociation

by WooSeok Jeong†?, Samuel J. Stoneburner†??, Daniel King†, Ruye Li†#, Andrew Walker‡, Roland Lindh§, and Laura Gagliardi*†

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Journal of Chemical Theory and Computation
DOI: 10.1021/acs.jctc.9b01297
05 Mar 08:47

[ASAP] Tapping on the Black Box: How Is the Scoring Power of a Machine-Learning Scoring Function Dependent on the Training Set?

by Minyi Su†‡, Guoqin Feng†‡, Zhihai Liu†, Yan Li†§, and Renxiao Wang*†§?

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Journal of Chemical Information and Modeling
DOI: 10.1021/acs.jcim.9b00714
03 Feb 09:17

[ASAP] Tautobase: An Open Tautomer Database

by Oya Wahl* and Thomas Sander

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Journal of Chemical Information and Modeling
DOI: 10.1021/acs.jcim.0c00035
24 Jan 07:56

[ASAP] ChemStor: Using Formal Methods To Guarantee Safe Storage and Disposal of Chemicals

by Jason Ott†, Daniel Tan†, Tyson Loveless†, William H. Grover*‡, and Philip Brisk*†

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Journal of Chemical Information and Modeling
DOI: 10.1021/acs.jcim.9b00951
03 Jan 08:36

[ASAP] Automating the Development of High-Dimensional Reactive Potential Energy Surfaces with the robosurfer Program System

by Tibor Gyo?ri* and Ga´bor Czako´*

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Journal of Chemical Theory and Computation
DOI: 10.1021/acs.jctc.9b01006
02 Jan 08:24

[ASAP] A Robust and Unified Solution for Choosing the Phases of Adiabatic States as a Function of Geometry: Extending Parallel Transport Concepts to the Cases of Trivial and Near-Trivial Crossings

by Zeyu Zhou, Zuxin Jin, Tian Qiu, Andrew M. Rappe, and Joseph Eli Subotnik*

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Journal of Chemical Theory and Computation
DOI: 10.1021/acs.jctc.9b00952
05 Dec 15:55

Questaal: A package of electronic structure methods based on the linear muffin-tin orbital technique

Publication date: April 2020

Source: Computer Physics Communications, Volume 249

Author(s): Dimitar Pashov, Swagata Acharya, Walter R.L. Lambrecht, Jerome Jackson, Kirill D. Belashchenko, Athanasios Chantis, Francois Jamet, Mark van Schilfgaarde

02 Dec 09:12

PyProcar: A Python library for electronic structure pre/post-processing

Publication date: June 2020

Source: Computer Physics Communications, Volume 251

Author(s): Uthpala Herath, Pedram Tavadze, Xu He, Eric Bousquet, Sobhit Singh, Francisco Muñoz, Aldo H. Romero

15 Nov 08:27

Quantics: A general purpose package for Quantum molecular dynamics simulations

Publication date: March 2020

Source: Computer Physics Communications, Volume 248

Author(s): G.A. Worth

08 Nov 12:58

Simulation vs Understanding A Tension, in Quantum Chemistry and Beyond. Part C. Toward Consilience

by Roald Hoffmann, Jean-Paul Malrieu

In the last part of our essay, we outline a future of consilience, with a role both for fact‐seekers, and for searchers for understanding. We begin by looking at the surroundings of theory and simulation, their environment in fact shaped by experiment, especially in Chemistry. Experimenters ask questions both conceptual and numerical, and so bring the communities together. Two case studies show what brings the theoretician joy in this playground, and two more detailed ones make it in detail clear that computation/simulation is anyway deeply intertwined with theory‐building in what we do. From a definition of science we try to foresee how simulation and theory will interact in the AI‐dominated future ‐‐ Chemistry’s streak of creation provides in that conjoined future a link to Art, and a passage to a renewed vision of the sacred in science.

08 Nov 12:58

Simulation vs Understanding A Tension, in Quantum Chemistry and Beyond. PART B The March of Simulation, for Better or Worse

by Roald Hoffmann, Jean-Paul Malrieu

In the second part of this essay, we leave philosophy, simply describing Roald’s being trashed by simulation. This leads us to a general sketch of artificial intelligence (AI), Searle’s Chinese room, and Strevens’ account of what a go‐playing program knows. Back to our terrain ‐‐ we ask “Quantum Chemistry, † ca. 2020?” Then move to examples of Big Data, machine learning and neural networks in action, first in chemistry and then affecting social matters. trivial to scary. We argue that moral decisions are hardly to be left to a computer. And that causes are so much deeper than correlations.

08 Nov 12:58

Simulation vs. Understanding: A Tension, in Quantum Chemistry and Beyond. Part A. Stage Setting

by Roald Hoffmann, Jean-Paul Malrieu
Simulation vs. Understanding: A Tension, in Quantum Chemistry and Beyond. Part A. Stage Setting

There is a wave breaking over us —a wave of simulation and artificial intelligence. In three reflective Essays we make a case for true understanding, for scientific story‐telling, as well as a role for pleasure and the emotions within science in general and quantum chemistry in particular.


Abstract

We begin our tripartite Essay with a triangle of understanding, theory and simulation. Sketching the intimate tie between explanation and teaching, we also point to the emotional impact of understanding. As we trace the development of theory in chemistry, Dirac's characterization of what is known and what is needed for theoretical chemistry comes up, as does the role of prediction, and Thom's phrase “To predict is not to explain.” We give a typology of models, and then describe, no doubt inadequately, machine learning and neural networks. In the second part, we leave philosophy, beginning by describing Roald's being beaten by simulation. This leads us to artificial intelligence (AI), Searle's Chinese room, and Strevens’ account of what a go‐playing program knows. Back to our terrain—we ask “Quantum Chemistry, † ca. 2020?” Then move to examples of AI affecting social matters, ranging from trivial to scary. We argue that moral decisions are hardly to be left to a computer. At this point, we try to pull the reader up, giving the opposing view of an optimistic, limitless future a voice. But we don't do justice to that view—how could we? We return to questioning the ascetic dimension of scientists, their romance with black boxes. Onward: In the 3rd part of this Essay, we work our way up from pessimism. We trace (another triangle!) the special interests of experimentalists, who want the theory we love, and reliable numbers as well. We detail in our own science instances where theory gave us real joy. Two more examples‐on magnetic coupling in inorganic diradicals, and the way to think about alkali metal halides, show us the way to integrate simulation with theory. Back and forth is how it should be—between painfully‐obtained, intriguing numbers, begging for interpretation, in turn requiring new concepts, new models, new theoretically grounded tools of computation. Through such iterations understanding is formed. As our tripartite Essay ends, we outline a future of consilience, with a role both for fact‐seekers, and searchers for understanding. Chemistry's streak of creation provides in that conjoined future a passage to art and to perceiving, as we argue we must, the sacred in science.

28 Oct 08:35

[ASAP] New Basis Set Exchange: An Open, Up-to-Date Resource for the Molecular Sciences Community

by Benjamin P. Pritchard*†?, Doaa Altarawy†‡?, Brett Didier§, Tara D. Gibson§, and Theresa L. Windus†?

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Journal of Chemical Information and Modeling
DOI: 10.1021/acs.jcim.9b00725
07 Oct 07:37

Oxygen reduction reaction on TiO2 rutile (1 1 0) surface in the presence of bridging hydroxyl groups

Publication date: 15 November 2019

Source: Computational and Theoretical Chemistry, Volume 1168

Author(s): Ádám Ganyecz, Pál D. Mezei, Mihály Kállay

Abstract

The goal of this study is to provide insight into the mechanism of the oxygen reduction reaction on the TiO2 rutile (1 1 0) surface in the presence of bridging hydroxyl groups. Considering the Langmuir–Hinshelwood and Eley–Rideal mechanisms, each possible intermediate was identified using density functional theory and a cluster model along with the energy barriers of the reduction steps and the OO bond breaking. Our results show that the initial step, the O2 adsorption on the surface, is favored compared to the pure surface. At higher potentials, the oxygen reduction reaction was found to go through the formation of HO2, which can easily convert to two terminal hydroxyl groups. The rate-limiting step is the desorption of the first H2O with 0.58 eV energy requirement at zero applied potential, while at 1.23 V the reduction of the adsorbed OH to form H2O is the bottleneck with a barrier height of 1.71 eV.

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Graphical abstract for this article

07 Oct 07:35

KinBot: Automated stationary point search on potential energy surfaces

Publication date: March 2020

Source: Computer Physics Communications, Volume 248

Author(s): Ruben Van de Vijver, Judit Zádor

02 Oct 10:12

[ASAP] OpenMolcas: From Source Code to Insight

by Ignacio Fdez. Galva´n12, Morgane Vacher1, Ali Alavi3, Celestino Angeli4, Francesco Aquilante5, Jochen Autschbach6, Jie J. Bao7, Sergey I. Bokarev8, Nikolay A. Bogdanov3, Rebecca K. Carlson79, Liviu F. Chibotaru10, Joel Creutzberg1112, Nike Dattani13, Mickae¨l G. Delcey1, Sijia S. Dong714, Andreas Dreuw15, Leon Freitag16, Luis Manuel Frutos17, Laura Gagliardi7, Fre´de´ric Gendron6, Angelo Giussani1819, Leticia Gonza´lez20, Gilbert Grell8, Meiyuan Guo121, Chad E. Hoyer722, Marcus Johansson12, Sebastian Keller16, Stefan Knecht16, Goran Kovac?evic´23, Erik Ka¨llman1, Giovanni Li Manni3, Marcus Lundberg1, Yingjin Ma16, Sebastian Mai20, Joa~o Pedro Malhado24, Per Åke Malmqvist12, Philipp Marquetand20, Stefanie A. Mewes1525, Jesper Norell11, Massimo Olivucci262728, Markus Oppel20, Quan Manh Phung29, Kristine Pierloot29, Felix Plasser30, Markus Reiher16, Andrew M. Sand731, Igor Schapiro32, Prachi Sharma7, Christopher J. Stein1633, Lasse Kragh Sørensen134, Donald G. Truhlar7, Mihkel Ugandi135, Liviu Ungur36, Alessio Valentini37, Steven Vancoillie12, Valera Veryazov12, Oskar Weser3, Tomasz A. Wesolowski5, Per-Olof Widmark12, Sebastian Wouters38, Alexander Zech5, J. Patrick Zobel12, and Roland Lindh*239

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Journal of Chemical Theory and Computation
DOI: 10.1021/acs.jctc.9b00532
19 Aug 10:02

A Python Multiscale Thermochemistry Toolbox (pMuTT) for thermochemical and kinetic parameter estimation

Publication date: February 2020

Source: Computer Physics Communications, Volume 247

Author(s): Jonathan Lym, Gerhard R. Wittreich, Dionisios G. Vlachos

Abstract

Estimating the thermochemical properties of systems is important in many fields such as material science and catalysis. The Python multiscale thermochemistry toolbox (pMuTT) is a Python software library developed to streamline the conversion of ab-initio data to thermochemical properties using statistical mechanics, to perform thermodynamic analysis, and to create input files for kinetic modeling software. Its open-source implementation in Python leverages existing scientific codes, encourages users to write scripts for their needs, and allows the code to be expanded easily. The core classes developed include a statistical mechanical model in which energy modes can be included or excluded to suit the application, empirical models for rapid thermodynamic property estimation, and a reaction model to calculate kinetic parameters or changes in thermodynamic properties. In addition, pMuTT supports other features, such as Brønsted–Evans–Polanyi (BEP) relationships, coverage effects, and ab-initio phase diagrams.

Program summary

Program title: pMuTT

Program files doi: http://dx.doi.org/10.17632/b7f7d28ynd.1

Licensing provisions: MIT license (MIT)

Programming language: Python

External routines: ASE, NumPy, Pandas, SciPy, Matplotlib, Pygal, PyMongo, dnspython

Nature of problem: Conversion of ab-initio properties to thermochemical properties and rate constants is time consuming and error-prone.

Solution method: Python package with a modular approach to statistical thermodynamics and rate constant estimation.

13 Aug 09:22

[ASAP] Tios: The Internet of Simulations. Turning Molecular Dynamics into a Data Streaming Web Application

by Athina Meletiou§, James Gebbie-Rayet†, and Charles Laughton*§

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Journal of Chemical Information and Modeling
DOI: 10.1021/acs.jcim.9b00351
03 Jul 09:23

[ASAP] QMflows: A Tool Kit for Interoperable Parallel Workflows in Quantum Chemistry

by Felipe Zapata#†, Lars Ridder†, Johan Hidding†, Christoph R. Jacob‡, Ivan Infante*#§, and Lucas Visscher*#

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Journal of Chemical Information and Modeling
DOI: 10.1021/acs.jcim.9b00384
05 Jun 09:45

[ASAP] Single-State Single-Reference and Multistate Multireference Zeroth-Order Hamiltonians in MS-CASPT2 and Conical Intersections

by Jae Woo Park*

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Journal of Chemical Theory and Computation
DOI: 10.1021/acs.jctc.9b00067
03 Jun 07:50

[ASAP] Quantum Package 2.0: An Open-Source Determinant-Driven Suite of Programs

by Yann Garniron†, Thomas Applencourt‡, Kevin Gasperich‡§, Anouar Benali‡, Anthony Ferte´?, Julien Paquier?, Barthe´le´my Pradines??, Roland Assaraf?, Peter Reinhardt?, Julien Toulouse?, Pierrette Barbaresco#, Nicolas Renon#, Gre´goire David?, Jean-Paul Malrieu†, Mickae¨l Ve´ril†, Michel Caffarel†, Pierre-Franc¸ois Loos*†, Emmanuel Giner*?, and Anthony Scemama*†

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Journal of Chemical Theory and Computation
DOI: 10.1021/acs.jctc.9b00176
08 May 07:38

[ASAP] MiMiC: A Novel Framework for Multiscale Modeling in Computational Chemistry

by Jógvan Magnus Haugaard Olsen, Viacheslav Bolnykh, Simone Meloni, Emiliano Ippoliti, Martin P. Bircher, Paolo Carloni, Ursula Rothlisberger

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Journal of Chemical Theory and Computation
DOI: 10.1021/acs.jctc.9b00093
11 Mar 09:43

SLABCC: Total energy correction code for charged periodic slab models

Publication date: Available online 6 March 2019

Source: Computer Physics Communications

Author(s): Meisam Farzalipour Tabriz, Bálint Aradi, Thomas Frauenheim, Peter Deák

Abstract

The surface of solids or their interface with the gas phase is often modeled by a slab, periodic in two dimensions and repeated artificially in the third. When studying charged systems, a compensating background charge is required to avoid the divergence of the Coulomb energy. However, the interactions between the periodic images of the localized charge and between the localized charge and its neutralizing background can cause significant errors in the total energy. We have implemented the correction scheme proposed by Komsa and Pasquarello (2013), which estimates the error in the total energy by modeling the distribution of the localized extra charge with Gaussian functions at different sites, and comparing its energy in the periodic and in the isolated case. The program is user-friendly and robust, it is automated for simple cases while keeping the flexibility for the advanced users to handle non-trivial ones.

Program Summary

Program title: SLABCC

Program Files doi: http://dx.doi.org/10.17632/42zd5p8gxc.1

Licensing provisions: BSD 2-Clause

Programming language: C++

Nature of problem: The error in the total energy of charged slab models under 3D periodic boundary condition

Solution method: Reading the total charge density and total local potential including the ionic, and Hartree potential for the neutral and charged system and approximating the extra charge with several Gaussians embedded in a dielectric medium. Calculating the difference in the energy of the model between the isolated and periodic cases, and using it as correction of the total energy in the original system. Current version works with the Vienna Ab initio Simulation Package (VASP) file format.

18 Jan 10:30

[ASAP] AUTOSURF: A Freely Available Program To Construct Potential Energy Surfaces

by Ernesto Quintas-Sánchez, Richard Dawes

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Journal of Chemical Information and Modeling
DOI: 10.1021/acs.jcim.8b00784
15 Oct 07:31

i-PI 2.0: A universal force engine for advanced molecular simulations

Publication date: March 2019

Source: Computer Physics Communications, Volume 236

Author(s): Venkat Kapil, Mariana Rossi, Ondrej Marsalek, Riccardo Petraglia, Yair Litman, Thomas Spura, Bingqing Cheng, Alice Cuzzocrea, Robert H. Meißner, David M. Wilkins, Benjamin A. Helfrecht, Przemysław Juda, Sébastien P. Bienvenue, Wei Fang, Jan Kessler, Igor Poltavsky, Steven Vandenbrande, Jelle Wieme, Clemence Corminboeuf, Thomas D. Kühne

Abstract

Progress in the atomic-scale modeling of matter over the past decade has been tremendous. This progress has been brought about by improvements in methods for evaluating interatomic forces that work by either solving the electronic structure problem explicitly, or by computing accurate approximations of the solution and by the development of techniques that use the Born–Oppenheimer (BO) forces to move the atoms on the BO potential energy surface. As a consequence of these developments it is now possible to identify stable or metastable states, to sample configurations consistent with the appropriate thermodynamic ensemble, and to estimate the kinetics of reactions and phase transitions. All too often, however, progress is slowed down by the bottleneck associated with implementing new optimization algorithms and/or sampling techniques into the many existing electronic-structure and empirical-potential codes. To address this problem, we are thus releasing a new version of the i-PI software. This piece of software is an easily extensible framework for implementing advanced atomistic simulation techniques using interatomic potentials and forces calculated by an external driver code. While the original version of the code (Ceriotti et al., 2014) was developed with a focus on path integral molecular dynamics techniques, this second release of i-PI not only includes several new advanced path integral methods, but also offers other classes of algorithms. In other words, i-PI is moving towards becoming a universal force engine that is both modular and tightly coupled to the driver codes that evaluate the potential energy surface and its derivatives.

Program summary

Program Title: i-PI

Program Files doi: http://dx.doi.org/10.17632/x792grbm9g.1

Licensing provisions: GPLv3, MIT

Programming language: Python

External routines/libraries: NumPy

Nature of problem: Lowering the implementation barrier to bring state-of-the-art sampling and atomistic modeling techniques to ab initio and empirical potentials programs.

Solution method: Advanced sampling methods, including path-integral molecular dynamics techniques, are implemented in a Python interface. Any electronic structure code can be patched to receive the atomic coordinates from the Python interface, and to return the forces and energy that are used to integrate the equations of motion, optimize atomic geometries, etc.

Restrictions: This code does not compute interatomic potentials, although the distribution includes sample driver codes that can be used to test different techniques using a few simple model force fields.

04 Oct 07:56

[ASAP] The Use of Cluster Expansions To Predict the Structures and Properties of Surfaces and Nanostructured Materials

by Liang Cao, Chenyang Li, Tim Mueller

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Journal of Chemical Information and Modeling
DOI: 10.1021/acs.jcim.8b00413
01 Oct 10:48

Thousand-atom ab initio calculations of excited states at organic/organic interfaces: toward first-principles investigations of charge photogeneration

Phys. Chem. Chem. Phys., 2018, 20,26443-26452
DOI: 10.1039/C8CP05574B, Paper
Takatoshi Fujita, Md. Khorshed Alam, Takeo Hoshi
Electron and hole wave functions of low-lying and hybridized interfacial charge-transfer states across the pentacene/C60 interface.
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28 Sep 12:48

[ASAP] Grain Boundary Facilitates Photocatalytic Reaction in Rutile TiO2 Despite Fast Charge Recombination: A Time-Domain ab Initio Analysis

by Yaqing Wei, Zhaohui Zhou, Wei-Hai Fang, Run Long

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The Journal of Physical Chemistry Letters
DOI: 10.1021/acs.jpclett.8b02761
19 Sep 13:36

Reimagining of Schrödinger’s cat breaks quantum mechanics — and stumps physicists

by Davide Castelvecchi

Reimagining of Schrödinger’s cat breaks quantum mechanics — and stumps physicists

Reimagining of Schrödinger’s cat breaks quantum mechanics — and stumps physicists, Published online: 18 September 2018; doi:10.1038/d41586-018-06749-8

In a multi-‘cat’ experiment, the textbook interpretation of quantum theory seems to lead to contradictory pictures of reality, physicists claim.
06 Jul 07:45

[ASAP] Corresponding Orbitals Derived from Periodic Bloch States for Electron Transfer Calculations of Transition Metal Oxides

by Eric J. Bylaska, Kevin Rosso

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Journal of Chemical Theory and Computation
DOI: 10.1021/acs.jctc.7b01180