Materials
Science
Product Guide
Discover a digital chemistry platformgoverned by physics-based modeling,
amplified by machine learning andoptimized through team-based intelligence.

Materials

Applications
Schrödinger’s Materials Science solutions offer
unprecedented insights into the mechanisms andproperties of materials and chemical systems in awide range of technological applications:• Organic Electronics• Polymeric Materials• Consumer Packaged Goods• Catalysis & Reactive Systems• Semiconductors• Energy Capture & Storage• Complex Formulations• Metals, Alloys & Ceramics

2

Product Overview
Platform
SoftwareSimulation
Engines

MS Maestro

Molecular Modeling Environment

LiveDesign

Collaborative Enterprise Informatics

Molecular
Dynamics &Molecular
Mechanics

Quantum
Mechanics

MachineLearning

Multiscale

DesmondJaguarAutoQSAR

DesmondMacroModel

MacroModel
Jaguar
QSite

Application
Specific &Enabling
Products

MS CG
MS Morph

GA Optoelectronics
Quantum
ESPRESSO GUIMS Informatics

MS Mobility
MS Reactivity

MS Transport

MS Dielectric

MS Penetrant
Loading

AutoTS

OPLS4

Force Field
Builder3

MS Maestro
MS Maestro is a streamlined interface for structuralvisualization, cutting-edge predictive computationalmodeling and machine learning workflows forMaterials Science discovery and analysis.
MS Maestro enables users at all levels of experience
to work efficiently and produce impactful results.
Capabilities• Accesses various automated simulations poweredby quantum mechanics (QM), molecular dynamics(MD), and molecular mechanics (MM) throughunified and integrated modeling environment• Builds realistic structural models of crystals,
organometallic complexes, polymers, slabs
and interfaces, and more with advanced
structure builder• Accesses advanced machine learning andcheminformatics tools and solutions forpredictive model building and validation• Offers combinatorial chemistry solutions
with structural enumeration and automatedlibrary generation• Provides comprehensive data analysis tools
pipelined to materials modeling andsimulations through chemically-aware
spreadsheet environment• Manages large-scale computational modeling& simulation tasks on local / remote computeservers across Linux, Windows, Mac and cloud• Includes additional key features: optoelectronics
workflow solutions, advanced model building andsimulation modules for polymers and plotting &multivariate optimization tools

4LiveDesign
LiveDesign is a powerful web-based informatics
and molecular design platform that enables teams
to rapidly advance materials discovery projects bycollaborating, designing, experimenting, analyzing,
tracking, and reporting in a centralized platform.
This collaborative ideation solution enables teamsof computational, synthetic, analytical, and process
scientists, and engineers to work through problems
and share results on a unified platform.
Capabilities• Deploys powerful computational models widely
within organizations, democratizing predictivemodels for non-experts• Shares live computational and experimental
data and design ideas for rapid decision making• Leverages Machine Learning capabilities forcontinuous model refinement based on thelatest available data, and extends to customized
de novo design• Integrates cheminformatics and data sharing
for collaboration across organizations andgeographic locations• Facilitates project management and analytics,
accelerates project communication, andcollective learning

5

Molecular Dynamics &Molecular Mechanics: Engine
Desmond
Desmond is a GPU-powered high-performancemolecular dynamics (MD) engine providing highscalability, simulation throughput, and scientificaccuracy to predict bulk properties of materials,
such as thermophysical properties, elastic constants,stress/strain relationships, diffusion coefficients,
viscosity, persistence length, etc. It enables thecapability required to establish a “Materials by
Design” framework in a broad range of industries.

Capabilities• Improves computing speed by 100x on generalpurpose GPU (GPGPU) versus single CPU• Simulates single component, mixtures, andsolutions with periodic boundary conditions
using cubic, orthorhombic, truncated octahedron,rhombic dodecahedron, and arbitrary triclinic
simulation boxes• Simulates large scale features of nanometers
to micron size over time scales of picoseconds
to microseconds• Performs accurate checkpointing for continuing
or restoring simulations• Calculates electrostatic interactions withhigh accuracy• Offers simulation techniques for improved
sampling including: Replica Exchange, Metadynamics, and Simulated Annealing• Supports coarse-grained force fields (with MS CG),
incorporating all Desmond capabilities to coarsegrained modeling

MD & MM
6

MacroModel
MacroModel is a general purpose, force-field-based
molecular modeling program with applicability
to a wide range of chemical systems. It provides
researchers with multiple advanced methods to aid
the understanding of chemical structure, energetics,
and dynamics. MacroModel is routinely applied
to examine molecular conformations, molecularmotion, and intermolecular interactions for a wide
range of different materials including organic andinorganic molecules and oligomers, organometallic
complexes as well as complex biological systems.

Capabilities• Molecular mechanics engine for energy
minimization and conformational sampling ofmolecular compounds• Supports various force fields, e.g. MM2, MM3,
AMBER, AMBER94, MMFF, MMFFs, OPLS,
OPLS_2005 and OPLS4

MD & MM
7

Molecular Dynamics &Molecular Mechanics: Force Field
OPLS4
Accurate force field parameters are at the heart ofobtaining useful molecular structures and relative
energies for practical use in material design anddevelopments. OPLS4 is the latest version of
Schrödinger’s modern force field. It offers provenperformance for small molecules, organics,
polymers, OLEDs, silicates, and more, providing
coverage for numerous industries. OPLS4 provides
leading accuracy through detailed parameterization.

Capabilities• Offers commercial-grade force field for classicalMD and organic materials design• Contains small molecule torsion parametercoverage of 95% for relevant chemical space• Offers over 100k torsion types covering a wide
range of chemistries and, with the addition ofForce Field Builder, can create new or uniquechemistry automatically• Calculates heterocyclics and halogen off site
electron density• Supports Desmond, MacroModel and associatedapplication modules

MD & MM
8

Molecular Dynamics &Molecular Mechanics: Products
MS Transport
MS Transport provides access to MD simulation
workflows for calculating shear viscosity, and theisotropic and anisotropic diffusion coefficients fora particular type of atom or molecule. From thediffusion of Li+ ions in battery polymers to theviscosity of solvents, the equilibrium MD based
workflows in MS Transport provide valuable insight
into the performance of materials.

Capabilities• Leverages Desmond speed to calculate diffusionand viscosity in industrially relevant clock times• Calculates diffusion of gases throughmatrices, ions through battery polymers,
and additives in plastics with focused workflow
and analysis viewer• Predicts viscosity with latest in equilibrium
molecular dynamics approaches• Calculates transport properties at desired
temperatures and explore the temperaturedependence of diffusion and viscosity• Visualizes diffusion and viscosity plots
Associated Product: Desmond

MD & MM
9MS CG
Critical phenomena for formulation and chemistrydevelopment such as phase separation and liquids
structuring can occur at time and length scales thatare difficult to access with all atom simulation. MS
CG (Materials Science Coarse Grained Modeling)is intended for molecular dynamics simulations oflarger bulk systems over a more extended period oftime than all-atom (AA) models.
MS CG provides an infrastructure to draw CoarseGrained molecules, map from all-atom to CoarseGrained structures, and assign Coarse-Grained force
fields. Coarse-Grained dynamics are also faster withthe reduction in atomistic detail making it possible
to study behavior extending beyond the typicalatomistic simulation time.

Capabilities• Supports various coarse-grained (CG) models:– Dissipative particle dynamics (DPD)– Martini– Generalized Lennard-Jones + Coulomb• Provides flexible workflows to constructsystems of interest with sketcher andall-atom to CG mapping• Offers advanced workflows for thermophysical,
mechanical, and diffusion properties• Provides different levels of models, from simple
models with 10’s of atoms per bead to finer
grained models with 2-10 atoms per bead
• Integrates with other workflows and builders(Polymer Builder, Structured Liquid Builder, Stress
Strain, Thermophysical Properties, Polymer Chain
Analysis, Structure Factor) and MS Transport
Associated Product: Desmond

MM & MD
10

MS Penetrant Loading
MS Penetrant Loading allows simulations of theloading of a condensed system such as a polymer,
zeolite, or molecular solid by a small rigid molecule
such as water or methane. The calculation provides
a measure of the hygroscopicity or loading capacityof the condensed phase.
MS Penetrant Loading runs GCMC in Desmondallowing for the combination of Monte Carlo and MD
for substrate relaxation resulting in more realistic
loading, allowing for the quick screening of materials
for equilibrium adsorption.

Capabilities• Calculates small molecule adsorption into
solid or liquid materials using Grand CanonicalMonte Carlo combined with NVT or NPT
Molecular Dynamics• Calculates uptake of water at varying
temperatures and humidities• Views results in standard experiment formats
such as % uptake and % volume change• Provides access to high speed simulation
workflows with Desmond GPU• Considers the impact of water on properties suchas glass transition• Provides insights into the swelling of materials
during water uptake
Associated Product: Desmond

MM & MD
11

MS Morph
MS Morph predicts crystal shape for molecular
crystals based on the surface energies and Wulff’s
theorem. It provides valuable insights for crystal
growth and powder processing.

Capabilities• Utilizes MD simulations for calculation andranking of surface energies for a set of surface
Miller indices• Predicts equilibrium shape of crystallites basedon relative surface energies and Wulff’s theorem
Associated Product: Desmond

MM & MD
12

Quantum Mechanics:
EngineCapabilities

JaguarJaguar specializes in fast electronic structure
predictions for molecular systems of
medium and large size via the use of density
functional theory (DFT) based on thepseudospectral (PS) method which scales
reasonably with system size. Jaguar can also
be used for the ab initio- assisted design andhigh throughput virtual screening of newmaterials solutions with novel or enhanced
properties – made possible by Jaguar’s
industry-leading efficiency and robustness.

• Offers a wide range of types of molecular
QM calculations: geometry optimization,transition state search, thermochemical
properties, implicit solvation, spectra
prediction, etc.
• Provides a wide variety of DFT functionals
with analytic second derivatives anddispersion corrections• Offers sophisticated geometry constraints,
rigid and relaxed scans• Performs relativistic DFT calculations• Provides several times speedup at anegligible loss of accuracy with optional
pseudospectral approximation• Offers automated workflows for advanced
analysis: pKa prediction, conformationallyaveraged VCD and ECD spectroscopy,
tautomer generation and ranking, heat offormation, etc.
• Generates publication-quality 3D surfaces:
molecular orbitals, electrostatic potential
projected on isodensity, non-covalentinteractions, etc.

Ferrocene Fe(C5H5)2

HOMO-1HIGHEST OCCUPIED
MOLECULAR ORBITAL(HOMO)LOWEST UNOCCUPIED
MOLECULAR ORBITAL(LUMO)

LUMO+1

Quantum
Mechanics
13Quantum Mechanics:
Products
GA Optoelectronics
GA Optoelectronics enables optimization ofmaterials properties for optoelectronic applications
via a genetic algorithm. It allows the users to
implement efficient screening modes using the
MS Jaguar quantum mechanics engine, minimizing
computational expense while delivering valuable,
accurate data. The optoelectronics capabilities
are designed to leverage rapid screening tocomplement experimental development by
elucidating molecular properties and informing
future synthetic targets.

Capabilities• Generates a library of compounds within thetarget property space with genetic optimization• Supports optimization by QM (DFT)
calculated properties• Supports optimization by model-predicted
properties via machine learning• Supports basic molecular design constraints(number of elements, molecular weight, etc.)
Associated Product: Jaguar

Quantum
Mechanics
14

Quantum ESPRESSO GUI
Quantum ESPRESSO, developed by Quantum
ESPRESSO Foundation, is the leading highperformance, open-source quantum mechanicalsoftware package for nanoscale modeling ofmaterials. Quantum ESPRESSO implements plane
wave density-functional theory in conjunction
with periodic boundary conditions andpseudopotentials.
Quantum ESPRESSO GUI provides acomprehensive graphical user interface forstreamlined calculation set-up, job control andresults analysis, enabling ab initio modeling ofbulk materials, their surfaces and interfaces. The
tool is embedded directly into MS Maestro toprovide a simple user interface.

Capabilities• Provides predictions for bulk, surface andinterface properties• Supports Ultrasoft (US), Norm-Conserving(NC) and Projector Augmented Wave (PAW)
pseudopotentials• Performs structural optimization, polymorphism
and ab initio molecular dynamics• Simulates transition states and minimum energy
paths using Nudged Elastic Bands (NEB) method• Models linear response properties within
Density Functional Perturbation theory (DFPT)• Predicts spectroscopic properties• Predicts band structure and band gap, charge
density and density differences, phonons andfree energy, dielectric permittivity, etc.

Quantum
Mechanics
15

Multiscale:EngineQSite
QSite combines the accuracy of Quantum
Mechanics (QM) and the speed of Molecular
Mechanics (MM) into a mixed mode QM/MM
calculation. Transition metal atoms, and parts ofthe molecule undergoing chemical transformation
require superior accuracy and are typicallyunsuitable for treatment with MM. QSite processes
such molecular fragments with QM whereas therest of the molecular system is described by MM.

Capabilities• Offers a wide range of types of molecular QM
Performs QM/MM calculations for quantum
chemical treatment of large molecules (such as
crystals and proteins)• Supports a wide range of DFT functionals• Offers coordinate scans with atom constraints

Multiscale
16Multiscale:
Products
MS Mobility
MS Mobility utilizes Marcus rate theory andkinetic Monte Carlo approach to analyze factors
affecting charge mobility in amorphous andcrystalline solids.

Capabilities• Predicts charge carrier mobility for molecular
semiconductors based on Marcus rate theory
and Kinetic Monte Carlo (KMC)• Assesses impact of electric field, temperatureand charge carrier concentration• Calculates electron and hole hopping rates
based on Marcus rate theory• Analyzes mobility as function of field direction,
temperature, and charge carrier concentration• Allows visualization of percolation pathand charge traps and their relation to a
local morphology
Associated Products: Jaguar, QSite

Multiscale
17Capabilities

MS Reactivity
MS Reactivity offers a set of tools for reactivity
and catalysis. Auto Reaction Workflow (AutoRW)
facilitates the high-throughput screening of catalyst
and/or substrate derivatives using a combinationof enumeration tools, the Reaction Workflow (RW),
and machine learning (ML) descriptor generation.
The RW runs both Jaguar Density Functional Theory(DFT) and MacroModel Conformational Search(MM) for atomic scale simulations to lend criticalinsight and understanding for the prediction of
structures, chemical mechanisms, and reactionenergetics for fundamental reactions.

• Screens high-throughput reaction and catalyst
automatically for prediction of reactivity andselectivity, including additional energy andsolvation corrections• Computes rates, barriers, and ML descriptors
automatically during post processing• Identifies lowest energy starting structureswith conformational sampling using
MacroModel (OPLS4)• Optimizes geometries and energies ab initio
with Jaguar• Removes structures with unwanted frequencies
from post processing• Performs anharmonic correction tothermophysical properties• Visualizes reaction coordinate images withrelative energies for all properties• Visualizes contour plots of buried volumes
for catalysts
Associated Products: Jaguar, MacroModel

Reaction Transition State

Ligand Library

Enumerated Reactions

Multiscale18

Capabilities

MS Dielectric
MS Dielectric runs both Jaguar Density Functional
Theory (DFT) and Desmond Molecular Dynamics(MD) calculations to obtain dielectric properties
such as refractive index, electric polarizability, staticand complex dielectric constants and dielectric loss
function. With an input of a single molecule, all thefollowing system building, simulations, and analysis
are performed automatically, creating a single step
workflow for dielectric property.

• Computes dielectric properties of molecularmaterials with combined QM & MD workflows• Calculates the refractive index, Abbe number,and static dielectric• Simulates and plots complex dielectric constantwith dielectric loss versus frequency
Associated Products: Desmond, Jaguar

water: 1.32

EC: 1.42

ammonia: 1.29

acrylonitrile: 1.31

methanol: 1.31

chloroethane: 1.35

ethanol: 1.35

ethylene glycol: 1.41

Multiscale
19Capabilities

AutoTS
Locating a transition state is necessary forcomputing the activation energy of a reaction, andthereby the reaction rate. Transition states are
essential in many materials science applications:predicting reactivity, understanding reaction
mechanisms, designing and optimizing catalysts,
predicting outcomes of various competing
reactions and more. Locating a transition stateis unique to computation — meaning that thetransition state cannot be “found” in the lab.
AutoTS is an automated workflow to find transition
states, particularly for elementary reactions. AutoTS
requires only the structures of the reactants andthe products as input, and then automates thesearch process to obtain the transition state andthe reaction energetics.

• Locates a transition state (TS) between thereactant and product molecules with anautomated workflow• Optimizes reactants and products, determines
breaking and forming bonds, establishes
correspondence between atoms in the reactants
and the products, and generates a transition
state guess• Prints the potential energy surface diagram
showing the transition state barrier• Performs iterative transition state searchfinding intermediates that connect reactants
and products• Allows for frozen atoms and formally spectator
reactants (like catalytic solvent molecules)• Performs a conformational search on reactants,
products, and transition states, outputting
statistically averaged reaction energetics
Associated Products: Jaguar, MacroModel‡+

Transition State

Reactants

Products

Multiscale20

Force Field Builder
Force Field Builder is designed to provide
force-field parameters for torsions that are notexplicitly represented in the force field. The setof molecules is analyzed to locate such torsions,and then quantum mechanical calculations are
performed to obtain parameters for the torsions.
New parameters are seamlessly integrated into
the OPLS4 parameters directory for easy use in
subsequent simulations.

Capabilities• Builds and optimizes custom torsion parametersin OPLS4 force field for previously undefinedbond dihedrals• Visualizes forcefield torsion energy profile
compared to QM profile
Associated Products: Jaguar, MacroModel

Multiscale21

Machine Learning
AutoQSAR
AutoQSAR facilitates the automated creation
and application of QSPR machine learningmodels following a best practices workflow. This
best practices workflow includes generation ofdescriptors, feature selection, creation of a large
number of models from exhaustive combinationsof descriptors and multiple machine learning
methods, and these QSPR models are ranked
based on performance. Predictions can then be
made from a top ranked QSPR model or from a
consensus of the top scoring models.

Capabilities• Takes 1D, 2D, or 3D structural data as
input and a desired property to bemodeled and automatically computes
descriptors and fingerprints• Creates QSAR/QSPR models with multiple
machine learning statistical methods, evaluates
each QSAR/QSPR model for predictive accuracy,
and rank orders all the QSAR models by theirpredictive power• Supports deep neural network based predictions
and fully exploit large datasets with integrationof DeepChem

MachineLearning
22

MS Informatics
MS Informatics provides machine learning andfeaturization tools for organic / organometallic
molecular materials, polymers, and inorganic
periodic solid materials to assist informaticsoriented materials research for building highquality machine learning models.

Capabilities• Analyzes structures and diversity of a large
chemical space with cheminformatics tools• Generates advanced (2D/3D/repeat-unitbased) descriptors for organic, inorganic, andpolymeric materials• Offers featurization by QM and semiempirical
QM molecular descriptors• Provides model building tools for quantitative
structure-property relationship (QSPR)• Supports machine learning models built for
repeat-unit-based polymer representations

MachineLearning
23

Scientific andTechnical Support
Training resources designed fornovice and experts users
Vast educational materials and training courses
to make you an expert.

Expert technical and scientificsupport included
Self-help, email, and face-to-face from industryleading scientific and technical support.

Cross-platform support forLinux, Windows, Mac, andcloud-based solutions
Designed to work within yourcomputer environment.

Contact us: sales@schrodinger.com
Learn more: schrodinger.com/materials-science

Materials
Copyright © 2021 Schrödinger, Inc.