Thermodynamic Properties for Applications in Chemical Industry Via Classical Force fields
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20 Years of Polarizable Force Field Development
20 YEARS OF POLARIZABLE FORCEFIELDDEVELOPMENTfor biomolecular systems thor van heesch Supervised by Daan P. Geerke and Paola Gori-Giorg 1 contents 2 1 Introduction 3 2contentsForce fields: Basics, Caveats and Extensions 4 2.1 The Classical Approach . 4 2.2 The caveats of point-charge electrostatics . 8 2.3 Physical phenomenon of polarizability . 10 2.4 Common implementation methods of electronic polarization . 11 2.5 Accounting for anisotropic interactions . 14 3 Knitting the reviews and perspectives together 17 3.1 Polarizability: A smoking gun? . 17 3.2 New branches of electronic polarization . 18 3.3 Descriptions of electrostatics . 19 3.4 Solvation and polarization . 20 3.5 The rise of new challenges . 21 3.6 Parameterization or polarization? . 22 3.7 Enough response: how far away? . 23 3.8 The last perspectives . 23 3.9 A new hope: the next-generation force fields . 29 4 Learning with machines 29 4.1 Replace the functional form with machine learned force fields . 31 4.2 A different take on polarizable force fields . 33 4.3 Are transferable parameters an universal requirement? . 33 4.4 The difference between derivation and prediction . 34 4.5 From small molecules to long range interactions . 36 4.6 Enough knowledge to fold a protein? . 37 4.7 Boltzmann generators, a not so hypothetical machine anymore . 38 5 Summary: The Red Thread 41 introduction 3 In this literature study we aimed to answer the following question: What has changedabstract in the outlook on polarizable force field development during the last 20 years? The theory, history, methods, and applications of polarizable force fields have been discussed to address this question. -
Melissa Gajewski & Jonathan Mane
Melissa Gajewski & Jonathan Mane Molecular Mechanics (MM) Methods Force fields & potential energy calculations Example using noscapine Molecular Dynamics (MD) Methods Ensembles & trajectories Example using 18-crown-6 Quantum Mechanics (QM) Methods Schrödinger’s equation Semi-empirical (SE) Wave Functional Theory (WFT) Density Functional Theory (DFT) Hybrid QM/MM & MD Methods Comparison of hybrid methods 2 3 Molecular Mechanics (MM) Methods Force fields & potential energy calculations Example using noscapine Molecular Dynamics (MD) Methods Ensembles & trajectories Example using 18-crown-6 Quantum Mechanics (QM) Methods Schrödinger’s equation Semi-empirical (SE) Wave Functional Theory (WFT) Density Functional Theory (DFT) Hybrid QM/MM & MD Methods Comparison of hybrid methods 4 Useful for all system size ◦ Small molecules, proteins, material assemblies, surface science, etc … ◦ Based on Newtonian mechanics (classical mechanics) d F = (mv) dt ◦ The potential energy of the system is calculated using a force field € 5 An atom is considered as a single particle Example: H atom Particle variables: ◦ Radius (typically van der Waals radius) ◦ Polarizability ◦ Net charge Obtained from experiment or QM calculations ◦ Bond interactions Equilibrium bond lengths & angles from experiment or QM calculations 6 All atom approach ◦ Provides parameters for every atom in the system (including hydrogen) Ex: In –CH3 each atom is assigned a set of data MOLDEN MOLDEN (Radius, polarizability, netMOLDENMOLDENMOLDENMOLDENMOLDEN charge, -
Bader's Theory of Atoms in Molecules
J. Chem. Sci. Vol. 128, No. 10, October 2016, pp. 1527–1536. c Indian Academy of Sciences. Special Issue on CHEMICAL BONDING DOI 10.1007/s12039-016-1172-3 PERSPECTIVE ARTICLE Bader’s Theory of Atoms in Molecules (AIM) and its Applications to Chemical Bonding P SHYAM VINOD KUMAR, V RAGHAVENDRA and V SUBRAMANIAN∗ Chemical Laboratory, CSIR-Central Leather Research Institute, Adyar, Chennai, Tamil Nadu 600 020, India e-mail: [email protected]; [email protected] MS received 22 July 2016; revised 17 August 2016; accepted 19 August 2016 Abstract. In this perspective article, the basic theory and applications of the “Quantum Theory of Atoms in Molecules” have been presented with examples from different categories of weak and hydrogen bonded molecular systems. Keywords. QTAIM; non-covalent interaction; chemical bonding; H-bonding; electron density 1. Introduction account of the bonding within a molecule or crystal. Specially, the derivative of electron density on BCP It is now possible to define the structure of molecules is zero. Bader’s group has made several seminal con- quantum mechanically with the help of Bader’s Quan- tributions to the development of the QTAIM theory tum Theory of Atoms in Molecules (QTAIM).1,2 This and its applications to unravel chemical bonding.10 13 theory has been widely applied to unravel atom-atom Popelier and coworkers have employed the QTAIM interactions in covalent and non-covalent interactions to address several issues in chemistry.14 16 Particu- in molecules,3 molecular clusters,4 small molecular larly, they have demonstrated the possibility of devel- crystals,5 proteins,6 DNA base pairing and stacking.7 oping structure-activity-relationship to predict various Basic motive of QTAIM is to exploit charge density or physico-chemical properties.17 They have used the the- electron density of molecules ρ(r; X) as a vehicle to ory of Quantum Chemical Topology (QCT), to provide study the nature of bonding in molecular systems. -
FORCE FIELDS for PROTEIN SIMULATIONS by JAY W. PONDER
FORCE FIELDS FOR PROTEIN SIMULATIONS By JAY W. PONDER* AND DAVIDA. CASEt *Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, 51. Louis, Missouri 63110, and tDepartment of Molecular Biology, The Scripps Research Institute, La Jolla, California 92037 I. Introduction. ...... .... ... .. ... .... .. .. ........ .. .... .... ........ ........ ..... .... 27 II. Protein Force Fields, 1980 to the Present.............................................. 30 A. The Am.ber Force Fields.............................................................. 30 B. The CHARMM Force Fields ..., ......... 35 C. The OPLS Force Fields............................................................... 38 D. Other Protein Force Fields ....... 39 E. Comparisons Am.ong Protein Force Fields ,... 41 III. Beyond Fixed Atomic Point-Charge Electrostatics.................................... 45 A. Limitations of Fixed Atomic Point-Charges ........ 46 B. Flexible Models for Static Charge Distributions.................................. 48 C. Including Environmental Effects via Polarization................................ 50 D. Consistent Treatment of Electrostatics............................................. 52 E. Current Status of Polarizable Force Fields........................................ 57 IV. Modeling the Solvent Environment .... 62 A. Explicit Water Models ....... 62 B. Continuum Solvent Models.......................................................... 64 C. Molecular Dynamics Simulations with the Generalized Born Model........ -
Tinker-HP : Accelerating Molecular Dynamics Simulations of Large Complex Systems with Advanced Point Dipole Polarizable Force Fields Using Gpus and Multi-Gpus Systems
Tinker-HP : Accelerating Molecular Dynamics Simulations of Large Complex Systems with Advanced Point Dipole Polarizable Force Fields using GPUs and Multi-GPUs systems Olivier Adjoua,y Louis Lagardère*,y,z Luc-Henri Jolly,z Arnaud Durocher,{ Thibaut Very,x Isabelle Dupays,x Zhi Wang,k Théo Jaffrelot Inizan,y Frédéric Célerse,y,? Pengyu Ren,# Jay W. Ponder,k and Jean-Philip Piquemal∗,y,# ySorbonne Université, LCT, UMR 7616 CNRS, F-75005, Paris, France zSorbonne Université, IP2CT, FR2622 CNRS, F-75005, Paris, France {Eolen, 37-39 Rue Boissière, 75116 Paris, France xIDRIS, CNRS, Orsay, France kDepartment of Chemistry, Washington University in Saint Louis, USA ?Sorbonne Université, CNRS, IPCM, Paris, France. #Department of Biomedical Engineering, The University of Texas at Austin, USA E-mail: [email protected],[email protected] arXiv:2011.01207v4 [physics.comp-ph] 3 Mar 2021 Abstract We present the extension of the Tinker-HP package (Lagardère et al., Chem. Sci., 2018,9, 956-972) to the use of Graphics Processing Unit (GPU) cards to accelerate molecular dynamics simulations using polarizable many-body force fields. The new high-performance module allows for an efficient use of single- and multi-GPUs archi- 1 tectures ranging from research laboratories to modern supercomputer centers. After de- tailing an analysis of our general scalable strategy that relies on OpenACC and CUDA , we discuss the various capabilities of the package. Among them, the multi-precision possibilities of the code are discussed. If an efficient double precision implementation is provided to preserve the possibility of fast reference computations, we show that a lower precision arithmetic is preferred providing a similar accuracy for molecular dynamics while exhibiting superior performances. -
Multiscale Friction Simulation of Dry Polymer Contacts: Reaching Experimental Length Scales by Coupling Molecular Dynamics and Contact Mechanics
Multiscale Friction Simulation of Dry Polymer Contacts: Reaching Experimental Length Scales by Coupling Molecular Dynamics and Contact Mechanics Daniele Savio ( [email protected] ) Freudenberg Technology Innovation SE & Co. KG https://orcid.org/0000-0003-1908-2379 Jannik Hamann Fraunhofer Institute for Mechanics of Materials: Fraunhofer-Institut fur Werkstoffmechanik IWM Pedro A. Romero Freudenberg Technology Innovation SE & Co. KG Christoph Klingshirn Freudenberg FST GmbH Ravindrakumar Bactavatchalou Freudenberg Technology Innovation SE & Co. KG Martin Dienwiebel Fraunhofer Institute for Mechanics of Materials: Fraunhofer-Institut fur Werkstoffmechanik IWM Michael Moseler Fraunhofer Institute for Mechanics of Materials: Fraunhofer-Institut fur Werkstoffmechanik IWM Research Article Keywords: Coupling Molecular Dynamics, Contact Mechanics, Multiscale Friction Posted Date: February 23rd, 2021 DOI: https://doi.org/10.21203/rs.3.rs-223573/v1 License: This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License Multiscale friction simulation of dry polymer contacts: reaching experimental length scales by coupling molecular dynamics and contact mechanics Daniele Savio1*, Jannik Hamann2, Pedro A. Romero1, Christoph Klingshirn3, Ravindrakumar Bactavatchalou1, Martin Dienwiebel2,4, Michael Moseler2,5 1 Freudenberg Technology Innovation SE & Co. KG, Weinheim, Germany 2 µTC Microtribology Center, Fraunhofer Institute for Mechanics of Materials IWM, Freiburg, Germany 3 Freudenberg FST GmbH, Weinheim, Germany 4 Karlsruhe Institute of Technology, Institute for Applied Materials, IAM-CMS, Karlsruhe, Germany 5 Institute of Physics, University of Freiburg, Freiburg, Germany *Corresponding author: [email protected] Abstract This work elucidates friction in Poly-Ether-Ether-Ketone (PEEK) sliding contacts through multiscale simulations. At the nanoscale, non-reactive classical molecular dynamics (MD) simulations of dry and water-lubricated amorphous PEEK-PEEK interfaces are performed. -
1 an Introduction to the Quantum Theory of Atoms in Molecules
1 1 An Introduction to the Quantum Theory of Atoms in Molecules Che´rif F. Matta and Russell J. Boyd 1.1 Introduction The observation that some properties attributed to atoms and functional groups are transferable from one molecule to another has played a key role in the devel- opment of chemistry. This observation provides a basis for group additivity schemes and is exemplified by the constancy of group contributions to thermody- namic and spectroscopic properties. But what is the electronic basis of this empir- ical transferability? The quantum theory of atoms in molecules (QTAIM) [1], de- veloped by Professor Richard F. W. Bader and his coworkers, relies on quantum observables such as the electron density rðrÞ and energy densities to answer such a question. Other important (related) questions addressed by QTAIM include: What is an atom in a molecule or a crystal? How can an atom or a group of atoms be transferable sometimes in very different external potentials? Can one define bonding in molecules unambiguously especially in borderline cases? This chapter contains a summary of some of the main concepts of QTAIM. A more comprehensive and mathematically elegant treatment can be found in Bader’s book [1]. (Often in this chapter, the word ‘‘molecule’’ includes extended systems such as polymers, weakly bonded molecular complexes, and molecular and ionic crystals, in addition to its more traditional meaning of a single, finite, isolated chemically bonded group of atoms. It will be clear from the context when this term is used in its traditional or in its larger sense.) 1.2 The Topology of the Electron Density The topology of the electron density is dominated by the attractive forces of the nuclei imparting it with its principal topological feature – a substantial local max- The Quantum Theory of Atoms in Molecules. -
Electronic Reprint Critical Examination of the Radial Functions in the Hansen
electronic reprint Acta Crystallographica Section A Foundations of Crystallography ISSN 0108-7673 Critical examination of the radial functions in the Hansen–Coppens multipole model through topological analysis of primary and refined theoretical densities Anatoliy Volkov and Philip Coppens Copyright © International Union of Crystallography Author(s) of this paper may load this reprint on their own web site provided that this cover page is retained. Republication of this article or its storage in electronic databases or the like is not permitted without prior permission in writing from the IUCr. Acta Cryst. (2001). A57, 395–405 Volkov and Coppens ¯ Hansen–Coppens multipole model research papers Acta Crystallographica Section A Foundations of Critical examination of the radial functions in Crystallography the Hansen±Coppens multipole model through ISSN 0108-7673 topological analysis of primary and refined theoretical densities Received 22 December 2000 Accepted 6 February 2001 Anatoliy Volkov and Philip Coppens* Department of Chemistry, State University of New York at Buffalo, Buffalo, NY 14260-3000, USA. Correspondence e-mail: [email protected] A double-zeta (DZ) multipolar model has been applied to theoretical structure factors of four organic molecular crystals as a test of the ability of the multipole model to faithfully retrieve a theoretical charge density. The DZ model leads to signi®cant improvement in the agreement with the theoretical charge density along the covalent bonds and its topological parameters, and eliminates some of the bias introduced by the limited ¯exibility of the radial functions when a theoretical density is projected into the conventional multipole formalism. The DZ model may be too detailed for analysis of experimental data sets of the # 2001 International Union of Crystallography accuracy and resolution typically achieved at present, but provides guidance for Printed in Great Britain ± all rights reserved the type of algorithms to be adapted in future studies. -
Some Notes On: What Is an Atom in a Molecule
Topological and AIM analyses beyond the Born-Oppenheimer paradigm: New opportunities Mohammad Goli and Shant Shahbazian* Faculty of Chemistry, Shahid Beheshti University, G. C. , Evin, Tehran, Iran, 19839, P.O. Box 19395-4716. Tel/Fax: 98-21-22431661 E-mail: (Shant Shahbazian) [email protected] * Corresponding author 1 Abstract The multi-component quantum theory of atoms in molecules (MC-QTAIM) analysis is done on methane, ethylene, acetylene and benzene as selected basic hydrocarbons. This is the first report on applying the MC-QTAIM analysis on polyatomic species. In order to perform the MC-QTAIM analysis, at first step the nuclear-electronic orbital method at Hartree-Fock level (NEO-HF) is used as a non-Born-Oppenheimer (nBO) ab initio computational procedure assuming both electrons and protons as quantum waves while carbon nuclei as point charges in these systems. The ab initio calculations proceed substituting all the protons of each species first with deuterons and then tritons. At the next step, the derived nBO wavefunctions are used for the "atoms in molecules" (AIM) analysis. The results of topological analysis and integration of atomic properties demonstrate that the MC-QTAIM is capable of deciphering the underlying AIM structure of all the considered species. Also, the results of the analysis for each isotopic composition are distinct and the fingerprint of the mass difference of hydrogen isotopes is clearly seen in both topological and AIM analyses. This isotopic distinction is quite unique in the MC-QTAIM and not recovered by the orthodox QTAIM that treats nuclei as clamped particles. The results of the analysis also demonstrate that each quantum nucleus that forms an atomic basin resides within its own basin. -
1.3 Structures of Covalent Compounds 13
01_BRCLoudon_pgs5-1.qxd 12/8/08 11:48 AM Page 13 1.3 STRUCTURES OF COVALENT COMPOUNDS 13 1.9 Draw an appropriate bond dipole for the carbon–magnesium bond of dimethylmagnesium. Ex- plain your reasoning. H3C Mg CH3 dimethylmagnesium 1.3 STRUCTURES OF COVALENT COMPOUNDS We know the structure of a molecule containing covalent bonds when we know its atomic con- nectivity and its molecular geometry. Atomic connectivity is the specification of how atoms in a molecule are connected. For example, we specify the atomic connectivity within the water molecule when we say that two hydrogens are bonded to an oxygen. Molecular geometry is the specification of how far apart the atoms are and how they are situated in space. Chemists learned about atomic connectivity before they learned about molecular geom- etry. The concept of covalent compounds as three-dimensional objects emerged in the latter part of the nineteenth century on the basis of indirect chemical and physical evidence. Until the early part of the twentieth century, however, no one knew whether these concepts had any physical reality, because scientists had no techniques for viewing molecules at the atomic level. By the second decade of the twentieth century, investigators could ask two questions: (1) Do organic molecules have specific geometries and, if so, what are they? (2) How can molecular geometry be predicted? A. Methods for Determining Molecular Geometry Among the greatest developments of chemical physics in the early twentieth century were the discoveries of ways to deduce the structures of molecules. Such techniques include various types of spectroscopy and mass spectrometry, which we’ll consider in Chapters 12–15. -
Chem3d 17.0 User Guide Chem3d 17.0
Chem3D 17.0 User Guide Chem3D 17.0 Table of Contents Recent Additions viii Chapter 1: About Chem3D 1 Additional computational engines 1 Serial numbers and technical support 3 About Chem3D Tutorials 3 Chapter 2: Chem3D Basics 5 Getting around 5 User interface preferences 9 Background settings 10 Sample files 10 Saving to Dropbox 10 Chapter 3: Basic Model Building 12 Default settings 12 Selecting a display mode 12 Using bond tools 13 Using the ChemDraw panel 15 Using other 2D drawing packages 15 Building from text 16 Adding fragments 18 Selecting atoms and bonds 18 Atom charges 21 Object position 23 Substructures 24 Refining models 27 Copying and printing 29 Finding structures online 32 Chapter 4: Displaying Models 35 © Copyright 1998-2017 PerkinElmer Informatics Inc., All rights reserved. ii Chem3D 17.0 Display modes 35 Atom and bond size 37 Displaying dot surfaces 38 Serial numbers 38 Displaying atoms 39 Atom symbols 40 Rotating models 41 Atom and bond properties 44 Showing hydrogen bonds 45 Hydrogens and lone pairs 46 Translating models 47 Scaling models 47 Aligning models 47 Applying color 49 Model Explorer 52 Measuring molecules 59 Comparing models by overlay 62 Molecular surfaces 63 Using stereo pairs 72 Stereo enhancement 72 Setting view focus 73 Chapter 5: Building Advanced Models 74 Dummy bonds and dummy atoms 74 Substructures 75 Bonding by proximity 78 Setting measurements 78 Atom and building types 81 Stereochemistry 85 © Copyright 1998-2017 PerkinElmer Informatics Inc., All rights reserved. iii Chem3D 17.0 Building with Cartesian -
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.