BIOVIA Materials Studio Training Course Course Catalog Training Version 1.0 – 1.0 Version

Date: 01/04/2021 Date:

Table of Contents Contents of Table Materials Studio Courses ii SUMMARY M

DMol DFTB+ Conformers Advanced CASTEP CASTEP Introduction Blends Amorphous Cell Adsorption Locator Adsorption Intr QSAR QMERA Polymorph DMol Sorption in Scripting Materials Studio Reflex, Reflex ONETEP Morphology Mesodyn (DPD)Mesocite Materials Studio Collection Pipeline in (MSC Pilot PP) in GULP ForcitePlus VAMP Synthia aterials oduction to Materials Studio to oduction 3 3

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Introduction Advanced ......

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...... Studio Course Catalog Plus, X -Plus,

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...... - Cell, andReflexCell, QPA

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4 4 3 2 2 2 3 1 1 1 9 9 8 5 8 8 7 6 5 7 6

core modules in the Materials Studio suite of software. This workshop provides an introduction to STUDIO RIALS MATE TO INTRODUCTION MATERIALSSTUDIO COURSES • cancourses bedesigned tomeet team’s your We are proud tooffer avariety tomeet your ofcourses organization’s needs. Customized SUMMARY Delivery Methods: Manager for more informat ion.

• • • • • Topics

rather class thanduring time. experience.learning Inremote hands classes, or through avirtual offer classroom. Onsite courses hands Instructor Problem Using the client Scripting in Materials Studio Materials Modeling Materials Studio − − − −

Tools Builders: polymer, crystal, nano, meso Multiscale, quantum, MM, meso, Crystal, QSAR Interfaceand sketching

- solving approaches

- Led Training: Facilitated training by this takes aninstructor, atyour place location

- server architecture

the tools and functionality available in Materials Visualizer, the

specific needs;specific

-on exercises homework,are assigned as

Prerequisites: Duration: Location: Course Duration Prerequisitesand -on exercises theto enhance

please contact yourplease Account

1 D Onsite Virtual or Classroom ay None

behavior of blends and formulations.

polymer liquid, is Blends Studio Materials BIOVIA BLENDS plastics, glasses, foods, and chemicals. range of amorphous materials. The behavior of amorphous materials is critical to products such as BIOVIA StudioMaterials Amorphous Cell is a comprehensive model building CELL AMORPHOUS system. just a few broad range of materials, including zeolites, carbon nanotubes, silica gel, and activated carbon BIOVIA StudioMaterials Adsorption Locator helps students find the most stable adsorption sites for a LOCATOR ADSORPTION • • • • Topics • • • • • • Topics • • • • • Topics

ApplicationsLimitations and Phase Diagrams Tasks and Analysis in Blends Theory in Blends Tips and Case Studies Scripting with Amorphous Cell The Packing and Confined Layer Tasks How It Works The Construction Task Introduction Comparison with Sorption Scripting Results from Adsorption Locator Computational Tasks in Adsorption Locator Theory in Adsorption Locator

–

by carrying out Monte Carlo searches of the configurational space of the substrate -

polymer, and polymer

used

- additive mixtures in order to study the structural factors affecting the

to predict phase diagrams and interaction parameters for liquid-

Materials Studio Prerequisites: Duration: Location: Course Duration Prerequisitesand Materials Studio Prerequisites: Materials Studio Prerequisites: Duration: Location: Prerequisites Course Duration and Duration: Location: Prerequisites Course Duration and

2 Hours Onsite Virtual or Classroom

2 Hours ½ D tool for creating a wide Onsite Virtual or Classroom Onsite Virtual or Classroom Introduction to

ay Introduction to Introduction to

- adsorbate –

to name

system without the need for any experimental input. researchers to investigate the nature and origin of the electronic, optical, and structural properties of a materials classes such as ceramics, semiconductors, and metals. First principle calculations Functional Theory (DFT) to simulate the properties of solids, interfaces, and surfaces for a wide range of

NMR, STM, phonon spectra, core The CASTEP advanced course offers detailed introduction to accurate prediction of electronic properties, ADVANCED CASTEP an CASTEP is Studio Materials BIOVIA INTRODUCTION CASTEP • • • Topics • • • • • Topics

Experimental Properties Electronic Properties Introduction Properties calculationsin CASTEP Chemical reactions with CASTEP: Transition state search Computational tasks in CASTEP Technical aspects of DFT calculations Introduction to Solid- Theory (DFT) − − − − − − − − − − −

Fermi surfaces Fermi Wave Functions Work Function Function Work Core Electron density difference Optical Spectroscopy Phonons, IR and Raman spectroscopy STM NMR Density of states of Density Band structure

- level Spectroscopy

State Theory and Density F

level spectra, and optical properties.

ab initio quantum mechanical program employing Density

unctional

Materials Studio Prerequisites: Materials Studio, Prerequisites: Duration: Location: Prerequisites Course Duration and Duration: Location: Course Duration and

½ D ½ D Onsite Virtual or Classroom Onsite Virtual or Classroom

ay ay Introduction to Introduction to

CASTEP Introduction CASTEP Prerequisites allow allow

DFTB+. conductors, and interactions between organic and inorganic surfaces, are practicalnow to study using took more time compute or power than most researchers have available, such as defects in semi offers unique capabilities to study and understand systems containing hundreds of atoms. Problems that Binding (DFTB) quantum simulation method for the study of electronic properties of materials. DFTB+ application in many fields including crystallization, catalysis, and polymer studies.

an is DFTB+ Studio Materials BIOVIA DFTB+ into geometric and energetic properties, and to pro searching and analysis techniques to characterize molecular conformation and flexibility, toinsight gain BIOVIA StudioMaterials Conformers provides access to a comprehensive collection of conformational CONFORMERS • • • • • • • Topics • • Topics

Case Studies Electron Transport Calculations Tool Creating Slater Properties Calculation Computational Tasks in DFTB+ Derivation of the DFTB+ Method Introduction to DFTB+ Calculation Setting and Up Output Conformers SearchMethods − − − − − −

Output Conformers Calculation Preparing the Structure Boltzmann Random Sampling Search Scan Grid Systematic

- Jump Search Koster Parameters with the Parameterization

–

Filter

improved implementation of the Density Functional

be geometry - property relationships, which have Materials Studio Prerequisites: Duration: Location: Prerequisites Course Duration and Materials Studio Prerequisites: Du Location: Prerequisites Course Duration and ration:

2 Hours

Onsite Virtual or Classroom 1 Day Onsite Virtual or Classroom

Introduction to

- based Tight -

chemical reactions, IR and Raman spectra, optical properties, and electron transport properties. pharmaceuticals, materials science, and chemical engineering, as well as solid state physics. solution, and solid environments. It is broadly applicable to research problems inemistry, ch methods to predict materials properties reliably and quickly. It predict can processes in gas phase, The DMol DMOL DMoL Studio Materials BIOVIA DMOL • • Topics • • • • Topics

Experimental Properties Properties Properties CalculationsIn Dmol Computational Tasks In Dmol Technical Aspects Of DFT Calculations Theory (DFT) Introduction To Solid State Theory and Density Functional − − − − − − − − − −

3 Atomic populations Molecular orbitals Molecular Electrostatics Electron transport Electron densities (DOS) states of Density Band structure Optical excitations and optical Vibrations and vibration spectroscopy Chemical reactions

ADVANCED INTRODUCTION 3

advanced course offers detailed introduction to accurate prediction of electronic properties, calculationsin DMol3

combines computational speed with the accuracy of quantum mechanical

spectroscopy

Materials Studio Prerequisites: Materials Studio, Prerequisites: Course Duration Prerequisitesand Duration: Location: Course Duration Prerequisitesand Duration: Location:

½ ½ Day Onsite Virtual or Classroom Onsite Virtual or Classroom Day Introduction to Introduction to

DMol 3

Introduction

forcefields, such as the shell model for simulating ionic materials. isolated defects in a bulk material. In particular performing a wide range of calculations periodicon 3D solids, 2D surfaces, gas phase clusters, and The General Utility Lattice Program, or BIOVIA StudioMaterials GULP, is a classical simulations code for GULP provides the user with great flexibility, offering a range of forcefields and charging energy calculations and reliable geometry optimization of molecules and periodic systems. ForcitePlus ForcitePlus Studio Materials BIOVIA FORCITEPLUS • • • • • • Topics • • • • • Topics

Applications Properties Surface Properties Forcefield Fitting Computational Tasks in GULP Theory in GULP Forcite in Scripting Forcefield editing Forcefield analysis Computational tasks in Forcite Introduction to Forcefield − − −

Forcefield typing and change assignment Nonbond interactions Forcefield types

Calculation

is an advanced classical molecular mechanics tool that allows fast

, GULP a large has number of materials

Materials Studio Prerequisites: Duration: Location: Prerequisites Course Duration and Materials Studio Prerequisites: Remote Training:Onsite Prerequisites Course Duration and

Training:

1 Day Onsite Virtual or Classroom

methods. Introduction to Introduction to

1 Day ½ - specific Day

equilibrium, under shear or in confined geometries cosmetics, and controlled release. Mesocite can provide structural and dynamic properties of fluids in microseconds. Such materials pervade industrial research in areas such as composites, coatings, materials at length scales ranging from nanometers to micrometers and time scale from nanoseconds to

a state is Mesocite Studio Materials BIOVIA (DPD)MESOCITE productivity that so you can spend more time on innovation and less on costly laboratory experimentation. scientific workflows. This allows for a more streamlined approach to materials discovery and improves application. Now you can integrate predictive analytics for materials properties seamlessly i utilization of Materials Studio's premier modeling capabilities within the Pipeline Pilot™ scientific authoring The BIOVIAPipeline Pilot Materials Studio COL STUDIO MATERIALS • • • • • • • Topics • • • • • • • • • Topics

Mesocite Analysis & Scripting Analysis Mesocite Mesocite Mesocite DPD Setup Mesoscale Parameter Generation (DPD) Introduction to Dissipative Particle Dynamics Meso Building Introduction to Mesocite Parallel Processing The Pipeline Pilot Connector for Materials Studio Using the Materials Toolkit Crystallization Simulation Classical Quantum Mechanics Property Calculators Manipulation Readers, Writers, Viewer, and Reporting Components

Task Setup Task

- Structures

LECTION IN PIPELINE PIPELINE IN LECTION Collection -

- the

- art coarse art

is a new is a new software solution that accessallows and

- grained simulation module for the study of PILOT (MSC IN PP) IN (MSC PILOT Materials Studio Prerequisites: Duration: Location: Course Duration Prerequisitesand Materials Studio Prerequisites: Duration: Location: Course Duration Prerequisiteand

½ Day

Onsite Virtual or Classroom 1 Day Onsite Virtual or Classroom Introduction to

Introduction to

nto your s

than possible by using conventional DFT. (where is the N total number of atoms). As a result, the program can be used to model systems larger conventional DFT methods, the where time needed for increases linearly with the number of atoms. This linear scaling approach is a vast improvement over BIOVIA StudioMaterials ONETEP is a linear scaling method, meaning the time required for a calculation ONETEP cements, and commodity and specialty chemicals. a crystal. The application areas include pharmaceuticals, BIOVIA StudioMaterials Morphology allows you to predict crystal morphology from the atomic structure of MORPHOLOGY fluid and performs time- systems, including polymer melts and blends. MesoDyn takes a coarse- MesoDyn MESODYN • • • • Topics • • • Topics • • • • • Topics

Case Studies ONETEP Properties and Analysis Setup of Theory ONETEP Problems in Surface Chemistry Tasks and Analysis in Morphology Theory in Morphology Applications Analysis of MesoDyn Calculations Set of Up MesoDyn Calculations Density Functional Theory in MesoDyn Introduction to Mesoscale Simulations − −

Crystal Graphs Predicting Morphologies

• • •

is is a dynamic simulation method for studying the long length and time behavior of complex fluid

Equilibrium morphology method Growth morphology method Bravais ONETEP Calculations

- Friedel Donnay

evolution dynamics of the density and potential fields of the system.

- Harker(BFDH) method

computation increases at a rate of much as as N3

agrochemicals, food sciences, petrochemicals,

Materials Studio Prerequisites: Duration: Location: Prerequisites Course Duration and Materials Studio Prerequisites: Materials Studio Prerequisites: Duration: Location: Prerequisites Course Duration and Duration: Location: Prerequisites Course Duration and grained description of a complex

½ Onsite or

1 Day 2 Hours Day Onsite Virtual or Classroo Onsite Virtual or Classroom

Introduction to

Introduction to Introduction to

Virtual Classroom Virtual

amorphous material. localized. Researchers can the use method to study problems in nanotubes, nanoclusters, and well particularly either molecular periodic or systems and handle can hundreds even or thousands of atoms. It is combining DFT The BIOVIAMaterials Studio QMERA module in BIOVIA Materials Studio performs simulations by QMERA groups to search for the low lying minima in lattice energy. The approach is based on the generation of possible packing arrangements in all reas from the molecular structure. It explores and ranks polymorphs of fairly rigid, non BIOVIA StudioMaterials Polymorph is used POLYMORPH • • • • • • • Topics • • • • • • Topics

Applications DMol Servers: QMERA & Analysis Tasks QMERA General Consideration for Simulations Handling of the QM/MM Boundary The QM/MM Embedding Schemes Overviewof QM/MM Applications wit Scripting Analyzing the Results Setting Polymorph Up Calculations Theory Behind Polymorph Prediction Determination of Crystal Structures

- h the Polymorph Module methods from DMol suited for modeling problems in chemical reactivity, an where

and GULP

and force field methods from GULP. QMERA be can used to model

to predict potential polymorphs of a given compound directly

Materials Studio Prerequisites: Duration: Location: Prerequisites Course Duration and Materials Studio Prerequisites: Duration: Location: Prerequisites Course Duration and

active site is chemically chemically is active site ½ Day 1 Day Onsite Virtual or Classroom Onsite Virtual or Classroom - ionic or ionic molecules.

Introduction to Introduction to

onable space

interpretation of diffraction data, and is applied to validate the results of experiment and computation. on models of crystalline materials. Reflex aids the determination of crystal structure, assists the X- simulates Reflex Studio Materials BIOVIA - REFLEX REFLEX, calculable with other modules: Forcite, VAMP, fast descriptors. becan calculated include a wide range ofperties. pro These can be supplemented by characteristics experimental information ('activity') and molecular level characteristics ('descriptors'). The descriptors that The QSAR module is a comprehensive set of tools for creating statistical regression models between QSAR • Topics • • • • • • Topics

Introduction to Reflex Tools Model Validation and Prediction Genetic Function Building Model Descriptors Initial Data Analysis Introduction to QSAR − − − − − −

Powder QPA (Quantitative Phase Analysis) Tool Separately licensed modules Powder Crystallinity Tool Powder Solve Tool Powder Refinement Tool Powder Indexing Tool Pattern Processing Tool

Approximation

PLUS,

Separately licensed modules

X -

QPA ANDREFLEX CELL,

ray, neutron, and

electron powder diffraction patterns based

Materials Studio Prerequisites: Duration: Location: Prerequisites Course Duration and Prerequisites: Duration: Location: Prerequisites Course Duration and Materials Studio

1 Day 1 Day Onsite Virtual or Classroom Onsite Virtual or Classroom

Introduction to Introduction to

level processes. phenomena. In addition, modeling can be used to rationalize sorption properties in terms of molecular sorptionas isotherms (or loading exchange. BIOVIA Materials Studio Sorption provides a means of predicting fundamental properties, such crucial in numerous applications including air separation, hydrocarbon cracking, sensors, gas and ion Molecular adsorption into microporous structures such as zeolites, aluminophosphates SORPTION selected results along with additional examples tables; to move molecules (in a zeolite and over a surface), to set up Forcite calculations,retrieve and to get information from collection documents, information from trajectory documents, information from study the Forcite Module (Calculations and Analysis). S of the Visualizer Tools, the Properties Explorer, a range of Atomistic 3D Documents, Study Tables and This workshop provides an introduction into the Perl S • • • • • • Topics • • • • Topics CRIPTING IN MATERIAL IN CRIPTING

Adsorption Locator vs. Sorption Scripting Simulation Tips Other DialogTabs: Configuration Sampling Tasks Scripting for Modules Scripting for Tools Scripting for Documents Introduction to Scripting in Materials Studio − − −

Energy, Constraints, Properties CarloMonte Methods Fixed Pressure, Fixed Adsorption Isotherm, Sorbate Location

Loading, Henry Constant,

S STUDIO curves) and Henry’s constants, needed for investigating separations

tudents write scripts to draw molecules from scratch; to - based scripting language that allows access to some Materials Studio Prerequisites: Materials Studio Prerequisites: Duration: Location: Prerequisites Course Duration and Duration: Location: Course Duration Prerequisitesand

1 Day 2 Hours Onsite Virtual or Classroom Onsite Virtual or Classroom

Introduction to Introduction to

, or polymers is polymers is , or

and is capable of rapidly calculating many physical inorganic systems. VAMP is an ideal intermediate module between forcefield and first principles methods semi a is VAMP Studio Materials BIOVIA VAMP range of properties, and allows the property prediction of copolymer blends. Property Relationships (QSPRs). It allows researchers to rapidly screen BIOVIA StudioMaterials Synthia calculates polymer properties using advanced Quantitative Structure- SYNTHIA • • • • Topics • • • • • Topics

Case Case Properties Calculations and Analysis Calculation Setting Up Theory in VAMP Simulation Tips Random Copolymers Synthia Quantitative Structure Property Relationship (QSPR) Introduction − − −

ZINDO: CNDO/1, CNDO/2, INDO/1, and INDO/2 and INDO/1, CNDO/2, CNDO/1, ZINDO: and PM6 MNDO/d, AM1*, PM3, AM1, MNDO, MNDO/C, NDDO: Donor Carbon Nanodots(CNDs): SupramolecularElectron

Study -

Connectivity Indices Methods – Acceptor Hybrids Featuring Perylenediimides

- empirical molecular orbital package for molecular organic and

and chemical molecular properties.

Materials Studio Prerequisites: Materials Studio Prerequisites: Duration: Location: Prerequisites Course Duration and Duration: Location: Course Duration Prerequisitesand candidate polymers for a wide

2 Hours 2 Hours Onsite Virtual or Classroom Onsite Virtual or Classroom

Introduction to Introduction to