GIAO

Parameters: MM2, MM3, Sybyl

MP3

Cons: charge calculations unreproducible

substitutes for missing parameters

File Formats:

Sybyl.mol

Brookhaven.pdb

ChemDraw

HyperChem

MDL

SMILES

SciVision

Alchemy III.mol

Dimensions: 3500+ atoms

Properties:

IR spectra

Thermodynamics

dipole moment

VdW energy

steric energy

distance

angle

SciPolymer-polymer property QSPR

SciQSAR-QSPR spreadsheet tool

SciProtein-protein structure seq's & DB

SciLogP-logP QSPR

Z-Matrix editor
simulated annealing
symmetry group assignment
CHAIN
PATH
EF
ESP
AMSOL
CODESSA - QSPR tool

File Formats:

Mopac Input
Gaussian
Hyperchem

Parameters:

MINDO/3, MNDO, PM3, AM1
SAM1
MNDOC

Properties:

IR (Force) Spectra
ESR
NLO
HOMO
LUMO
Distance
Angle
charges
molar volume
molar surface area
ovality
dipole moment
UV (CI)

SM2 Basis:

AM1
aqueous

Atoms:

H
C - F
P - Cl
Br

SM5 Basis:

230 solutes
90 solvents

Acc'y: [Delta]G(transfer)+/-0.7 kcal/mol

- Editor & CAChe Translators

3-D sketch
Polymerizer
Crystal Builder
12+ search variables
Sequential search
Force Field tools

File Formats:

MDL .mol
Tripos .mol
Brookhaven .pdb
CCSDB
Chem3D (original)
Tribble
Shelx
Mopac Input
ZINDO Input

- ExtHuckel: Extended Hückel calculations

Atoms:

<=150
H - Lr

Properties:

Overlap Matrix
Total Energy
Eigenvalues
Eigenvectors
Wyberg Bond Index
Mulliken Atomic Population Array
Atomic Charges
Dipole Moment

- Mechanics: molecular mechanics calculations including energy minimization, exhaustive, and sequential search.

Augmented MM2:

H
Li - F
Na - Cl
K, Ti - Br
Rb, Zr - I
Cs, W - Bi
Nd, Sm
U

Accuracy:

(M-bonds l+/-7% a+/-9%)

Properties:

Energy
- Steric
- Strain
- Van der Waals
- H-Bond
Geometry
- Minimum
- Cartesian Coordinates
- Distance
- Angle
- Dihedral

Dimensions (heavy/light atoms):

25x40, 66x66
70x70, 150x150

Parameters:

MINDO/3, MNDO, PM3
AM1 (w/o Li?)
(w/ Cb, +, ++, -, --)

Properties:

Dipole Moment
Energy
- Enthalpy
- Entropy
- Heat Capacity
- Heat of Formation
- Electronic
- Resonance
- Total
- Zero Point
ESR
- Spin Density
Infrared
- Spectrum
- Description of Vibrations
- Frequencies/Vibrational Energy
- Transition Dipole
Ionization Potential
Geometry
- Minimum
- Cartesian Coordinates
- Saddle
- Transition State
- Twist Angle
- 1-Dimensional Polymer
- Atom distance
- Van der Waals Surface Area
Polarizability
- (Alpha)
- Finite Field
- Second Order (Beta)
- Third Order (Gamma)
Localized Orbital
Mulliken Atomic Population
Partial Atomic Charges
Valencies
Bond
- Angle
- Length
- Order
Ensemble
- Dynamic Reaction Coordinate, DRC
- Intrinsic Reaction Coordinate, IRC
- Potential Energy Profile, Grid

Parameters:

Dreiding
MNDO, PM3, AM1, INDO/S
STO-3G(*),3-21G, 4-31G,
6-31G...6-311G*, **)
Dunning-

D95: H

Li - Ne
Al - Cl

D95*: H

Li - F
Al - Cl

Properties:

Dipole Moment
Infrared
- Spectrum
- Frequencies/Vibrational Energy
- Intensity(km/mole)
Energy
- Total
- Orbital
Polarizability (Alpha)
Electrostatic Potential
Geometry
- Minimum
- Cartesian Coordinates
- Distance
- Angle
- Dihedral
Ensembles
- Intrinsic Reaction Coordinate, IRC
- Linear Synchronous Transit, LST
- Monte Carlo

- ZINDO: Zerners INDO program for semiempirical calculations

Dimensions (atoms/basis functions):

60x210, 140x490
140x490, 200x700

Parameters:

INDO/1(+ As, Br, I)
INDO/S, INDO/2
CNDO/1 ([Delta]Hfdeg.+/-200, l+/-0.2)
CNDO/2
EHT
PPP

Properties:

Dipole Moment
Electron Affinity
ESR
- Spin Density
Ionization Potential
UV/Visible
- Spectrum
- Lambda Max/Excitation Energy
- Oscillator Strength
- Transition Dipole
- Transition Moment
Energy
- Total
- Solute Polarization
- Solvent Reorganization
Geometry
- Minimum
- Transition State
Localized Orbitals
- Boys
- Fermi
- Double Projector
Orbital
- Mulliken Populations
- Natural
Geometry
- Atom distance
- Cartesian Coordinates
Partial Atomic Charges
Bond
- Angle
- Length
- Order

Spreadsheet
Self Documenting
QSPR
- CAChe logP
DIPPR Database

Properties:

Dipole Moment
- Vacuum
- Aqueous
- vector
Electron Affinity
Energy
- Enthalpy
- Entropy
- Free energy
- Heat Capacity
- Heat of Formation
- Dielectric
- Steric
- Total
Infrared
- Spectrum
- Frequencies/Vibrational Energy
- Peak Identification
- Transition Dipole
Ionization Potential
log P - octanol-water partition coefficient
logW - water solubility
Molar refractivity
Molecular Formula
Molecular Weight
Polymer - Tg
UV/Visible
- Spectrum
- Lambda Max/Excitation Energy
- Transition Dipole
- Transition Moment
Atom Count
Polarizability
- (Alpha)
- Tensor
Connectivity Index
- Chi0 (atomic)
- Chi1 (bond)
- Chi2 (path)
- valence Chi0 (atomic)
- valence Chi1 (bond)
- valence Chi2 (path)
Molecular ovality
Polymer
- Cohesive Energy
- solubility parameter, Delta
- MVol
Shape Index
- Kappa, Order1 (cycles)
- Kappa, Order2 (linearity)
- Kappa, Order3 (branching)
Surface Area
- isosurface
- Solvent Accessible
- Van der Waals
Surface Volume
- isosurface
- VdW
- Frontier Electron Density
- HOMO Energy
- LUMO Energy
- Molecular Orbital Energy
- Molecular Orbital Occupation
Superdelocalizability
- Electrophilic
- Nucleophilic
- Radical
Susceptibility
- Electrophilic
- Nucleophilic
- Radical
Atom distance
Partial Charges
Bond
- Angle
- Dihedral angle
- Length/ Atom Distance
- Order
- Strain

RHF, ROHF, UHF
MP2, MP3, MP4
CISD, CEPA, ACPE, CCD, QCISD(T)
analytical gradients w/ MP2, MP3

Properties: electronic moment

polarizability
hyperpolarizability
IR spectrum
Raman spectrum
vibrational circular dichroism
magnetizability
NMR chemical shift
Mulliken Population Analysis

protein structure from sequence

Pros: electronic MD

periodic boundary conditions
B88-P86

Cons: must recompile to run

Dreiding

UFF: (Rappe & Landis)

Basis: Organic

Inorganic
parms calc'd from basic props

Pros: full periodic table

Cons: needs charge equilibration

2-MeO -THP equatorial

OFF: H - No
MM2
CFF93
Amber

- C2*Align: aligns sets of molecules for easy comparison during the study of drug candidates using automated or manual alignment methods.

- C2*Amorphous Builder: used to build models of amorphous polymers and polymer/solvent systems. Combined with simulation and analysis functionality, this offers a powerful way to understand the relationship between amorphous structure and properties.

- C2*Analog Builder: used to specify combinatorial libraries and select fragments/reagents based on their diversity. Generate sets of congeneric analogs that can be rapidly screened to identify drug candidates.

- C2*Blends: predicts phase diagrams and interaction parameters for liquid-liquid, polymer-polymer, and polymer-additive mixtures, for studying the structural factors affecting the behavior of blends and formulations.

- C2*CASTEP: a quantum mechanics module used to simulate the properties of solids, interfaces, and surfaces for a wide range of materials classes including ceramics, semiconductors, and metals. Determine quantities such as geometric structure, energies, band-structures, and charge density.

- C2*CAVEAT: identifies molecular frameworks from which novel active lead candidates can be designed de novo. Clustering and filtering tools.

- C2*Conformers: provides conformational search algorithms and associated analysis tools, to characterize molecular conformation and flexibility, and gain insight into geometric and energetic properties.

- C2*Crystal Builder: builds and visualizse models of inorganic or molecular crystals, to understand crystalline structure and simulate the behavior of solids.

- C2*Crystal Packer: provides rigid-body energy minimization routines to construct and analyze molecular packing in organic crystals such as pigments and drugs.

- C2*DBAccess: provides direct access to structural databases (Catalyst and MDL ISIS) for use in modeling experiments. Hits can be browsed in 2D or 3D.

- C2*Descriptor+: extends the range of QSAR analysis in Cerius2 by supplying a wide range of generic descriptors. The capabilities of C2.QSAR+ and C2.GA can be applied to problems like combinatorial chemistry analysis, optimization of formulations, and the properties of polymers and blends.

- C2*Diffraction-Amorphous: simulates non-crystalline diffraction, including small angle scattering for comparison with experimental data to determine amorphous structure, polymer chain conformation, copolymer sequence structure, and orientation.

- C2*Diffraction-Crystal: simulates powder, fiber, and single crystal diffraction from crystalline models, for interpreting experimental data from molecular, inorganic, and polymeric crystalline materials.

- C2*Diffraction-Faulted: simulates powder diffraction from faulted or layered structures, for characterizing structures such as zeolites and clays.

- C2*Diversity: analyzes chemical diversity to design and evaluate compound libraries and reagent sets for combinatorial chemistry to sample all potential drug candidates so that a reduced set can be synthesized and screened.

- C2*DLS: uses geometric refinement to predict the structures of inorganic frameworks, especially zeolites, from a trial model.

- C2*Dynamics: applies molecular mechanics to study structure relaxation and investigate the behavior of a material over a time period. Properties which can be deduced include: stability, diffusion, radial distribution functions and structure factors, and velocity auto-correlation functions.

- C2*EXAFS: integrates the EXAFS analysis and refinement techniques of Daresbury's EXCURV92 with Cerius2's modeling tools, radically improving ability to interpret EXAFS data. (Jointly developed with the CCLRC Daresbury Laboratory, UK.)

- C2*FFE: (Force Field Editor) adapts force fields from the Cerius2 database or create new to apply force fields from the literature and to develop and validate in-house parameterizations.

- C2*Gaussian: interfaces to the Gaussian code to apply ab initio, semi-empirical, and density functional techniques to study the energetics, structure, and chemistry of molecules and transition states.

- C2*GA: provides the breakthrough technology of Genetic Algorithms to evolve a family of predictive models. Develop QSAR models from receptor surface and other data, leading to faster screening of drug candidates.

- C2*HRTEM: simulates High Resolution Transmission Electron Microscope images from crystals, interfaces and defect structures. Set up and interpret EM experiments that investigate technologically important materials.

- C2*Interface Builder: builds and displays models of the interface between two materials. Visualize complex structural features and provides the basis for further simulation work.

- C2*LEED/RHEED: interpret Low Energy Electron Diffraction patterns and Reflection High Energy Electron Diffraction from surfaces.

- C2*Mechanical Properties: predicts a range of ideal elastic modulii for any materials type for designing novel crystalline and amorphous polymers, ceramics, and semiconductors.

- C2*MFA: permits field-based 3D QSAR and visualization to predict the activities of new molecules based on the geometric properties of existing compounds.

- C2*Minimizer: predicts low-energy structures using molecular mechanics calculations and the power of Cerius2's Open Force Field. Increase understanding of molecular, macromolecular, amorphous, crystalline, and surface structure and properties.

- C2*MMFF: provides the Merck Molecular Force Field for accurately studying the structure, energetics, and dynamics of molecular systems in the life sciences. MMFF is broadly parameterized for organic and bio-organic systems and for the intermolecular interactions crucial to enzyme binding.

- C2*Mopac: interfaces to the popular semi-empirical quantum code MOPAC to study molecular structure and energetics, and compute properties such as molecular orbitals and charges.

- C2*Morphology: predicts and analyzes the morphology of crystals from their internal crystal structure. Relates morphological features to structure and the likely effects of solvents and growth modifying additives.

- C2*OFF: (Open Force Field) provides molecular mechanics force fields to support Cerius2's property prediction modules. Extensive database of force fields covering organics, polymers, zeolites, organometallics, and other materials types.

- C2*Polymer Builder: is used to construct models of polymer chains from monomers that may be user-defined or taken from an extensive fragment library, to understand and characterize polymer structure.

- C2*Polymer Properties: analyzes models of polymer structure by calculating properties such as the radius of gyration, end-to-end distance, order parameters, distribution of torsional states, free volume, density, and Voronoi volume.

- C2*Polymorph: predicts the polymorphs of organic crystalline materials such as drugs, pigments, or fine chemicals, from their molecular structure. Predict unsynthesized polymorphs or determine structures in combination with techniques such as Rietveld refinement.

- C2*Powder: Indexing completes a comprehensive package of software modules for crystal structure determination from powder data. Establish unit cell and symmetry information and assist Rietveld refinement or crystal structure predictions.

- C2*Protein Active Site Viewer: visualizes the key elements of protein structure and protein-ligand interactions. A Hit-List-Browser is included to review an active site, enabling you to visualize the results of a database search in the context of the protein active site.

- C2*QSAR+: provides a wide range of regression and analysis technologies integrated in a "chemically aware" molecular spreadsheet. Existing data can be used to predict the activities of novel drug candidates.

- C2*Receptor: investigates interaction of lead candidates for drug developmentwith a protein receptor site - represented as a 3D surface. Develop predictive QSAR models or rank the results of a database search by volumetric similarity.

- C2*Rietveld: performs crystal structure refinement and quantitative phase analysis using powder diffraction data and the Rietveld method. Combines refinement programs and advanced modeling tools to determining the structures of both inorganic and molecular crystals.

- C2*SDK: a software toolkit to integrate and extend applications within the Cerius2 modeling and simulation environment, eliminating the need for writing graphics, windowing, or systems-level code. Extensive library of computational and visualization subroutines.

- C2*Sorption: predicts the adsorption properties of molecules in microporous solids, such as zeolites, to predict adsorption isotherms, binding sites, adhesion energies, diffusion paths, and molecular selectivity.

- C2*Surface Builder: builds 2D periodic models to investigate surface chemistry, structure, and interactions.

- C2*Visualizer: provides a comprehensive modeling environment for building, editing and visualizing models of molecular structure as well as the core requirements for running Cerius2 applications.

- C2*X-GEN: processes X-ray diffraction data for macromolecular X-ray crystallography. Index and clean up the data from multiple detectors - making it suitable for input to refinement packages such as X-PLOR.

Basis: 18 parameter force field

Pros: biopolymers

QM-MD
GAMESS or AMPAC QM

CHARMm: H

C - O
Na - S
K - Fe
Rb
Eu

Acc'y: [Delta]Hr+/-0.9

modeling program gives chemists instant access to the 3rd Dimension. Gain insight into molecular behavior by rotating and visualizing 5000+ atom models in color. Performs real-time animation, energy minimization and molecular dynamic calculations. Build your own models in Chem3D or convert a 2D structure to 3D just copy in a structure from ChemDraw. -- CambridgeSoft

DLS
MD
Geometry Minimization
Undo

File Formats:

MDL .mol
Tripos .mol
MSI .mol
Brookhaven .pdb
CCSDB
Alchemy
Macromodel
Mopac Input

Dimensions:

700+ atoms
1 search variable

Parameters:

MM2 (w/o F, S, Cl, Sr, Te, I):

MM2+

Basis: includes [pi] calculation

multicoordinate centers

Atoms: H

Li - F
Na - Cl
K - Br
Rb - I
Cs - La, Hf - At

Properties:

Heat of Formation
Partial Charges
Bond Lengths/Distances
Bond Angles
Torsional Angles
Steric Energy
Gradient Norm

Properties:

gNMR - spectral simulation
SymApps - symmetry point groups, character tables
logP - octanol/water partition
logH - air/water partition
MR - molar refractivity

Dimensions: <=2000 atoms

Undo

File Formats:

MDL .mol
Brookhaven .pdb
Tribble
CSSR (CCSDB)
Smiles
Gaussian
GAMESS

Dimensions:

8000+ atoms
150 search variables

Parameters:

ChemX FF

Basis: organics

inorganics
peptides

Acc'y: [Delta]Hr+/-1, [Delta]HÝ+/-2

AMPAC, Mopac (60x60)
EHT
CNDO

2D to 3D conversion
strain relief
constrained searching

periodic
- NVE
- NVT
- NPT
- NST
conformational analysis
Ewald sum w/ surface correction

Parameters:

CFF91/93 (Consistent Force Field)

CVFF (Consistent Valence ForceField)

- general purpose

Basis:

Morse function stretch term
nondiagonal force field
crossterms
empirical parameterization

GENFF (generalized CVFF)

ESFF (Extensible & Systematic Force Field)

Basis:

diagonal valence
rule based:
- electronegativity
- atomic radii
- hardness
- scaling
- d-p [pi] bonding
- organics, inorganic, organometallic & biomolecules

Atoms:

H - Rn

Pros: any element

organometallic complexes

Cons: accuracy

Amber

Properties:

radial distribution function
self-diffusion coefficient
H-bonds
Energies
- interaction
- strain
- entropy
- enthalpy
IR
- modes
- intensity

Dimensions:

<=~100 atoms

Parameters:

DNP (~6-31G**):

numeric basis set

- Atoms: H, He

Li - Ne
Na - Ar
K - Kr
Rb - Xe?

- Acc'y: l+/-3%

gradient corrections

VWN
BVWN
BP
BLYP

Properties:

IR frequencies
Dipole moments
optical polarizability
EA
IP
Mulliken & Hirshfeld Populations
charge density
spin density
electrostatic potential
equilibrium geometry

Parameters:

Born Model

RHF, UHF, ROHF, GVB
MCSCF, CI, MP2
Analytical Gradients
Saddle

Parameters:

MNDO, AM1, PM3

ECPs -

- SBK, -31G splits:

Li - Ne
Na - Ar
K - Kr
Rb - Xe
Cs - Ba, Hf - Rn
La, Ce

- HW, -21 splits:

H, He
Li - Ne
Na - Ar
K - Kr
Rb - Ag
Cs - Ba, Hf - Au

STO-nG(*), n-21G(*,+):

MINI/MIDI:

H, He
Li - Ne
Na - Ar
K - Kr
Rb - Xe

n-31G(*,**,+,++)

DZV -

- DH:

H
Li - Ne
Al - Ar

BC:

Ga - Kr

TZV -

Li - Ne
Na - Ar
K - Zn

Properties:

Energy Hessian
Normal Modes
Vibrational Frequencies
IR Intensities
Intrinsic Reaction Path
Dynamic Reaction Coordinate
Radiative Transition Probabilities
Spin Orbit Coupling
Linear Polarizability
First & Second Order Polarizability
NLO Polarizability
Localized Orbitals
Self Consistent Reaction Field
Dipole, quadrupole, & octupole moments
Electrostatic Potential
Electric Field
Electric Field Gradients
Electron Density
Spin Density
Distributed Multipole Analysis

Output Sections:

MOMENTS OF INERTIA
INTERNUCLEAR DISTANCES
NUCLEAR REPULSION ENERGY
FINAL ENERGY
E CHANGE
DENSITY CHANGE
SPIN SZ
S-SQUARED
EIGENVECTORS
TOTAL ENERGY
ENERGY COMPONENTS
ONE ELECTRON ENERGY
TWO ELECTRON ENERGY
POTENTIAL ENERGY
KINETIC ENERGY
VIRIAL RATIO
PI ENERGY ANALYSIS
FOCK ENERGY
BARE H ENERGY
ELECTRONIC ENERGY
SIGMA PART
PI PART
MULLIKEN ATOMIC POPULATION
(MULLIKEN) ATOMIC SPIN POPULATION
(LOWDIN) ATOMIC SPIN POPULATION
MULLIKEN ATOMIC OVERLAP POPULATIONS
MULL.POP. CHARGE
LOW.POP. CHARGE
BOND ORDER AND VALENCE
ATOMIC SPIN DENSITY AT THE NUCLEUS
ELECTROSTATIC MOMENTS

BLYP
SCRF
GIAO

Output Sections:

Symbolic Z-matrix:
SCF DONE:
MOLECULAR ORBITAL COEFFICIENTS
DENSITY MATRIX.
Mulliken population analysis:
Total atomic charges:
Dipole moment
Quadrupole moment
Octapole moment
Hexadecapole moment

Acc'y: ([sigma] in PPM w 6-311G** perturbed HF)

P+/-32
C+6
H+6.1%

Molecular & Stochastic Dynamics
Perturbation Thermodynamics

GROMOS FF Basis:

proteins
nucleotides
sugars

Properties:

Crystal lattice energy
Entropy
Free Energy
Heat capacity
Elastic constants
Dielectric constants
Phonon frequencies
IR activities
Electric field gradients

Atoms:

B - F
Si - Cl

Properties:

Secular Determinant
Eigenvalues
Total energy
delocalization energy
Polarographic half-wave reduction potential
Eigenvectors
Charge densities
[pi]-dipole moment
Bond lengths
Electron density - bond order matrix
Atom-atom polarizabilities
Superdelocalizabilities
- Electrophilic
- Radical
- Nucleophilic
Free valences

solvent box
MD
ab initio SCF
MP2

File Formats:

MDL .mol
Tripos .mol
Brookhaven .pdb
Mopac Input
CCSDB

Dimensions:

20,000+ atoms

Parameters:

MM2
Amber
BIO+

OPPLS

Basis: liquids

solutions
ab initio calc'ns on 100 organics

EHT
MNDO (w/o Cr, Zn, Br, Sn, Hg, Pb?)
MINDO/3
AM1 (w/o Hg?)
PM3 (w/o Hg, Tl, Pb, Bi?)
CNDO
INDO/1 (w/o As, Br, I?)
INDO/S

Properties: Dipole moment
IP
IR (Force)
UV (CI)

Crystal builder
renderings
MC search
biomolecules
logP
scripts

SCF-MO
magnetic shielding (shifts)
nuclear coupling

corrected PDB database
500 descriptors

transparency
spreadsheet
"Open Interface"

- Amorphous Cell: constructs and analyzes models of bulk amorphous systems such as polymers and glasses. Investigate properties such as cohesive energy, chain dimensions, chain packing, and local dynamical behavior.

atomistic
glassy or melt
IR
cohesive energy density
self diffusion
elasticity
correlation function
solubility parameter

- Biopolymer: constructs models of peptides, proteins, carbohydrates, and nucleic acids for visualizing complex macromolecular structures and for use in further simulation work.

- CFF95: advanced Class II force field used to optimize DNA, RNA, carbohydrates, lipids, proteins, peptides, and small-molecule models, giving a high confidence level for calculations in drug discovery, protein design, genomic theraputics, NMR spectroscopy, and X-ray crystallography.

- Characterize: simulates, displays, and interprets a wide variety of analytical data: HRTEM, NMR, diffraction, IR Raman, EXAFS, and Morphology data.

XRD, ND, ED
29Si NMR
EXAFS
Crystal morphology
IR, Raman
Pore characterization

- Converter: builds 3D models from 2D structural database output.

- Crystal Cell: study and characterize crystal structure, stability, and mechanical properties.

minimize packing energy w/ MM
vibrational dispersion curve
entropy
heat capacity
mechanical properties

- DeCipher: powerful and flexible program for high-level analysis of molecular structure and the results of molecular dynamics simulations.

- DelPhi: calculates electrostatic potentials and solvation energies of both large and small molecules, including nucleic acids. Examine the effects of charge distribution, ionic strength, and dielectric constant on the electrostatic potentials of macromolecules.

- Discover: simulation program available within Insight II. It incorporates a range of well validated forcefields for dynamics simulations, minimization, and conformational searches to predict the structure, energetics and properties of organic, inorganic, organometallic, and biological systems. Implements IPC (Inter Process Communications), which allows users to instruct Discover to turn processing control over to external programs, and retrieve the results of those external processes, incorporating them into the continuing Discover computations.

- DMol: quantum mechanics module for fast, reliable, quantitative predictions of molecular structure, energetics and properties for ground and transition states. Employs advanced density functional theory. COSMO is a continuum dielectric solvation model implemented in DMol to accurately compute the structure and properties of molecules in a solvent environment using quantum mechanics.

- DSolid: provides accurate simulation of molecules, molecular crystals, and surfaces. An adaptation of the DMol program to compute structural and vibrational properties as well as electron densities and molecular orbitals for periodic solids.

- ESOCS: (Electronic Structure Of Closed-packed Solids) calculates the electronic and magnetic properties of solids, including electronic structure of defects, optical absorption and reflection spectra, and magnetic properties of materials. Applicable to metals and alloys, the pigment industry, and for optimizating and designing magnetic materials.

all purpose
periodic electronic structure

- Flexiblend: estimates polymer miscibility. Approximate but fast to screen polymer blend candidates.

miscibility w/ specific interactions

- Insight II: creates, modifies, manipulates, displays, and analyzes molecular systems and related data and provides the core requirements for all Insight II software modules.

- Interphases: calculates the conformational properties of polymers in the vicinity of an interface.

graph theory model
monolayers & bilayers

- Ludi/ACD: links the design tools of Ludi to MDL's Available Chemicals Directory with access to over 65,000 commercially available structures to search for drug candidates.

- MADSYS: provides phasing of multi-wavelength anomalous dispersion (MAD) data collected at synchrotron radiation X-ray sources.

- Miscibility: navigational aid for predicting liquid-liquid phase diagrams of polymer solutions or blends by unifying MSI*s tools for phase diagram prediction and leading through appropriate simulation strategies.

- Modeler: automatically generates a refined homology model of a protein, given only the sequence alignment to a known 3D protein structure. Excellent structural models given as little as 30% homology to known structures.

- Networks: simulates cross-linking or cure reactions to understand properties of gels, elastomers, adhesives, and coatings.

statistical & kinetic models
elasticity
gel point

- NMR Refine/DG-II: entry-level option into NMR refinement software with capabilities for generating structures from NMR-derived distance and dihedral restraints. Restraint Analysis, NMR Database and ProStat pulldown tools for generating, analyzing and verifying high resolution structures.

- Phase Diagram: calculates liquid-liquid phase diagrams for polymer solutions and blends, to optimize the properties of formulations.

binary & ternary
calculate from Chi
fit Chi to experiment

- Plane Wave: quantum mechanics module for the materials sciences to simulate solids, interfaces, and surfaces for a wide range of materials classes including ceramics and semiconductors, determining properties such as geometric structure, energies, band-structures, and charge density.

full periodic table
pseudopotentials

- PolyNMR: helps you to interpret NMR spectra for homo- and copolymers.

C-13 from RIS w/ tables

omega functions
phase equilibria

assess whether a primary sequence is compatible with the current 3D structural model. Searches a structural-motif database with a new sequence, looking for compatibility; a sequence database with an example stucture, seeking similarity; or verifies the agreement between the sequence and current model of a protein sequence/structure under study.

- QSPR: estimates the properties of a wide range of thermoplastic materials using group additivity methods.

Synthia
Van Krevelan

QM embedded in MM

- Reaction Patterns: visualizes, interprets and analyzes chemical reactivity and reactions. It combines kinetic models and the analysis of quantum mechanical energy surfaces to give insight into fundamental chemical processes.

chemical kinetics
vibrations

statistical properties of single chain

- Sketcher: draws molecules in 2D and automatically convert them to 3D models.

- Solids Adjustment: edits crystal or cluster structures, to explore new or derivative materials.

symmetry display & modifications
find cell

crystal, metal, glass
solid, surface, sheet
modify space group

Monte Carlo docking
heat of sorption
preferred binding
diffusion strategy

METAPOCS
FUNGUS
minimization w/ symmetry
dynamics w/ symmetry

lattice images
HRTEM

Visual interface to GSAS

generic ionic models
fit xtal structures to experiment

- Turbomole: calculates molecular structure, energetics, and transition states. It predicts properties including electrostatic potentials, ESP charges, molecular moments, polarizabilities, IR spectra, and NMR chemical shifts. Computations use traditional Hartree-Fock and MP2 quantum mechanics methods as well as density functional theory. TurboNMR is a component of Turbomole which uses ab initio quantum mechanical methods to predict NMR chemical shifts, to interpret solid-state NMR and magnetic relaxation experiments.

- Viscoelasticity: estimates the dynamic mechanical response of dilute polymer solutions, to relate these to polymer structure and chemistry.

dilute solutions

- Xsight: integrates all of the major computational techniques for macromolecular crystallography: analyze and interpret X-ray data, build models of protein structures and relate them to electron density, refine structure against X-ray data, analyze structures for symmetry, and visualize and validate structure.

- ZINDO: semi-empirical molecular-orbital program for studying the spectroscopic properties of molecules and complexes. Applicable to a wide range of compounds, including organic and inorganic molecules, polymers, and organometallic complexes.

Compounds for Personal Computers

<=32,000 atoms
MM2

Monte Carlo
Molecular Dynamics
Grid search
Saddle point
Transition states
Normal mode
SHAKE annealing
Free Energy Perturbation
Continuum solvent

Basis:

generalized force field shell
point charges instead of dipoles
no [pi] calculations

Parameters:

AMBER*
- Acc'y: [Delta]HÝ+/-1, [Delta]Hr+/-0.9
MM2*
- Acc'y: [Delta]HÝ+/-0.4, [Delta]Hr+/-0.5
MM3*
- Acc'y: [Delta]HÝ+/-1, [Delta]Hr+/-0.5
OPLS
- protein/DNA

Properties:

Docking
Surface Energy/Morphology

Parameters:

Born Model

organic
inorganic
polymer
Craig Plots

- BDNR minimizer
- transition state optimization
- entropy by vibrational analysis
- [pi] calculation

Geometries
Dynamics
AMBER
MNDO
AM1
<=150 atoms

- ARGOS

connection -> 2D

- Autonom

nomenclature

- MOLKIK

DB queries

MM
2D -> 3D
logP database

OVGF

Output Sections:

FINAL HEAT OF FORMATION
TOTAL ENERGY
ELECTRONIC ENERGY
CORE-CORE REPULSION
DIELECTRIC ENERGY
VAN DER WAALS AREA
GRADIENT NORM
IONIZATION POTENTIAL
DERIVATIVES
INTERNAL COORDINATE DERIVATIVES
FORCE MATRIX
ZERO POINT ENERGY
NORMAL COORDINATE ANALYSIS
MASS-WEIGHTED COORDINATE ANALYSIS
DESCRIPTION OF VIBRATIONS
FREQ.
T-DIPOLE
ENERGY CONTRIBUTION
PARTITION FUNCTION
H.O.F.
ENTHALPY
HEAT CAPACITY
ENTROPY
BOND LENGTH, BOND ANGLE, TWIST ANGLE
INTERATOMIC DISTANCES
EIGENVECTORS
ATOMIC CHARGES
DIPOLE
CARTESIAN COORDINATES
FOCK MATRIX
DENSITY MATRIX
SIGMA-PI BOND-ORDER MATRIX
BONDING CONTRIBUTION
BOND ORDERS
VALENCIES
COMPOSITION OF ORBITALS
LOCALIZED ORBITALS
ENERGY PARTITIONING
RESONANCE ENERGY
EXCHANGE ENERGY
COULOMBIC INTERACTION
SPIN DENSITIES
MULLIKEN POPULATION ANALYSIS
FINITE-FIELD POLARIZABILITIES
MOMENTS OF INERTIA
DIPOLE
POLARIZABILITY (ALPHA)
SECOND-ORDER (BETA)
THIRD-ORDER (GAMMA)

Basis:

Lewis bond input
hybrid coordinates

Pros:

avoids diagonalization

Parameters:

same as MOPAC

Dimensions:

4000 atoms

force fields (e.g., WH86, MM85, Biosym, Charmm, etc.), or the user can supply the force field. The program selects energy minimization by OREM (off-ridge eigenvector minimization), SD (steepest descents), or the NR (Newton-Raphson) method. Simulated annealing is included to aid in locating global, rather than subsidiary, energy minima. The mpg module provides fast and convenient graphical visualization of the results. -- Donald E. Williams.

building
VDW minimization
MM optimization
conformational analysis
MOPAC Interface

File Formats:

MDL .mol
Brookhaven .pdb
CCSDB
ChemDraw
Mopac Input, Archive

Dimensions:

<=125 atoms
5 search variables

Parameters:

COSMIC:

H
C - F
P - Cl
Br
I

Properties:

partial charge
Dipole moment
distance
angle

MC simulated annealing
solvent dynamics

Dimensions:

<=500 atoms
50 search variables

Parameters:

MMX: - extended MM2

- includes transition states
- [pi] calculation
Acc'y: [Delta]Hr+/-0.4

AM1
PM3
EHT
MNDO

Properties:

distance
angle
charges
dipole moment
IR (Force)

SWISSPROT, NBRF, PDB databases

- Pro-Simulate

GROMOS
Amber
BOSS

- ES CALC

electrostatics

- N-DEG

NMR analysis

- PC-PROT+

sequence analysis

- PC-TAMMO+

protein-lipid

Parameters:

GROMOS

SPARTAN'04 and SPARTAN'04 ESSENTIAL for Windows are the latest molecular modeling applications from Wavefunction supporting Windows 98 or higher. These new versions add to user interface features including builders for organic and inorganic molecules, peptides and nucleotides, with an internal database of over 60,000 molecules pre-calculated at up to 5 quantum mechanical theory levels. Offering substantial ease-of-use with internal spreadsheets and plotting tools for organizing your data, custom clipboards, and file import/export features including: SYBYL MOL and MOL2 , PDB, MacroModel, SDF, TGF, MOL files (2D), Spartan Exchange and Collection files and graphical export of BitMap, JPEG and AVI graphics files.

Spartan for Windows will determine equilibrium and transition state geometries; identify lowest energy conformers and generate conformational and Boltzmann distributions (with optional use of NOE data); align molecules and scan geometrical coordinates; generate reaction sequences and generate and follow intrinsic reaction coordinates; calculate reaction and activation energies; calculate and plot IR, NMR, and UV/vis spectra; and search the Spartan Molecular Database and the Cambridge Structural Database. These tasks elucidate a host of numerical and graphical data and properties including:

Mulliken, electrostatic-fit and natural-bond-orbital (NBO) charges

Dipole moments and higher moments

Polarizabilities and Hyperpolarizabilities

Ovality

Electronegativity and hardness

Enthalpies, entropies and free energies

Highest Occupied and Lowest Unoccupied Molecular Orbital Energies (and homo/lumo gaps)

Aqueous solvation energies

LogP

NMR Chemical shifts (Hartree-Fock only)

UV/vis excitation energies from CIS and TDDFT models

Display of molecular orbitals, electron densities, contour displays

Display spin densities and electrostatic potentials as isosurfaces

Display ionization potentials

Composite surface maps

Ribbon displays for biopolymers

Display of hydrogen bonds

Available computational methods:

SYBYL and MMFF94 molecular mechanics

MNDO, MNDO/d, AM1 and PM3 semi-empirical MO including PM3 parameters for transition metals

Hartree-Fock molecular orbital

SVWN, BP, BLYP, EDF1 and B3LYP density functional for ground and TDDFT for excited states

MP2, MP3, MP4 and LMP2

CCSD, CCSD(T), OD, and OD(T)

G2, G3 and G3 (MP2)

QCCD and QCCD(T)

QCISD and QCISD(T)

CIS and CIS(D), for excited states

STO-3G, 3-21G, 6-31G*, 6-311G*, cc-pVDZ, cc-pVTZ and cc-pVQZ all-electron basis sets

With additional polarization and/or diffuse functions - additional and custom basis sets available

Pseudopotential basis sets for calculations on molecules with heavy elements

SPARTAN'02 for Unix / Linux support Unix: SGI IRIX 6.5 or later Linux: RedHat 6.2 or later, Mandrake 7.0 or later, SuSE 6.3 or later, or Generic Linux (Kernel 2.2 Xfree86 3.3, glibc 2.1). These applications are the latest versions of the original Unix Spartan program and contain interface features including builders for organic and inorganic molecules, polypeptides and polynucleotides. Both versions offer internal spreadsheets and plotting tools for organizing data, and file import/export features including: SYBYL MOL and MOL2 , PDB, MacroModel, and Spartan Exchange files, import of FDAT crystal files, and export of JPEG and VRML graphics files.

Spartan for Unix / Linux will determine equilibrium and transition state geometries, identify lowest energy conformers and generate conformational distributions, align molecules and scan geometrical coordinates, generate reaction sequences, calculate reaction and activation energies, calculate Infrared Spectra frequencies and intensities and search the Cambridge Structural Database. These tasks elucidate a host of numerical and graphical data and properties including:

Mulliken, electrostatic-fit and natural-bond-orbital (NBO) charges

Dipole moments and higher moments

Polarizabilities and Hyperpolarizabilities

Ovality

Electronegativity and hardness

Enthalpies, entropies and free energies

Highest Occupied and Lowest Unoccupied Molecular Orbital Energies (and homo/lumo gaps)

Aqueous solvation energies

LogP

NMR Chemical shifts (Hartree-Fock only)

UV/vis excitation energies from CIS and TDDFT models

Display of molecular orbitals, electron densities, contour displays

Display spin densities and electrostatic potentials as isosurfaces

Display ionization potentials

Composite surface maps

Available computational methods:

SYBYL and MMFF94 molecular mechanics

MNDO, MNDO/d, AM1 and PM3 semi-empirical MO including PM3 parameters for transition metals

Hartree-Fock molecular orbital

SVWN, BP, BLYP, EDF1 and B3LYP density functional for ground and excited states

MP2, MP3, MP4 and LMP2

CCSD, CCSD(T), OD, and OD(T)

G2 and G3

QCCD and QCCD(T)

QCISD and QCISD(T)

CIS and CIS(D), for excited states

STO-3G, 3-21G, 6-31G*, 6-311G*, cc-pVDZ, cc-pVTZ and cc-pVQZ all-electron basis sets

With additional polarization and/or diffuse functions - additional and custom basis sets available

Pseudopotential basis sets for calculations on molecules with heavy elements

SPARTAN'02 and SPARTAN'02 ESSENTIAL for MACINTOSH are the latest molecular modeling applications from Wavefunction, Built for OSX. With a state-of-the-art Open GL interface including builders for organic and inorganic molecules, peptides and nucleotides, these programs place sophisticated molecular mechanics and quantum chemical calculations at your fingertips. Offering substantial ease-of-use with internal spreadsheets and plotting features for organizing your data, custom clipboards, and file import/export features including: SYBYL MOL and MOL2 , PDB, MacroModel and Spartan Exchange and Collection files and graphical export of PICT, PNG, JPEG and QuickTime graphics files.

Spartan for Macintosh will determine equilibrium and transition state geometries, identify lowest energy conformers and generate conformational distributions, align molecules and scan geometrical coordinates, generate reaction sequences, calculate reaction and activation energies, and calculate IR frequencies and intensities. These tasks elucidate a host of numerical and graphical data and properties including:

Mulliken, electrostatic-fit and natural-bond-orbital (NBO) charges

Dipole moments and higher moments

Polarizabilities and Hyperpolarizabilities

Ovality

Electronegativity and hardness

Enthalpies, entropies and free energies

Highest Occupied and Lowest Unoccupied Molecular Orbital Energies (and homo/lumo gaps)

Aqueous solvation energies

LogP

Display of molecular orbitals, electron densities, contour displays

Display spin densities and electrostatic potentials as isosurfaces

Display ionization potentials

Composite surface maps

Ribbon displays for biopolymers

Available computational methods:

SYBYL and MMFF94 molecular mechanics

MNDO, MNDO/d, AM1 and PM3 semi-empirical MO including PM3 parameters for transition metals

Hartree-Fock molecular orbital

SVWN, BP, BLYP, EDF1 and B3LYP density functional for ground and excited states

MP2, MP3, MP4 and LMP2

CCSD, CCSD(T), OD, and OD(T)

G2 and G3

QCCD and QCCD(T)

QCISD and QCISD(T)

CIS and CIS(D), for excited states

STO-3G, 3-21G, 6-31G*, 6-311G*, cc-pVDZ, cc-pVTZ and cc-pVQZ all-electron basis sets

With additional polarization and/or diffuse functions - additional and custom basis sets available

Pseudopotential basis sets for calculations on molecules with heavy elements

Contact:

Nathan Dacuycuy/Sean Ohlinger

Wavefunction, Inc.

18401 Von Karman Ave, Suite 370

Irvine, CA 92612

Tel: (949) 955 2120

Fax: (949) 955 2118

Email: sales@wavefun.com

Web: http://www.wavefun.com

Parameters:

MM(P)2, MM3
Sybyl- general purpose
- nonbonded attractions high
- coordination complexes

3D QSAR spreadsheet
fragment descriptor library
topological indices
statistical tools
neural net

BLYP
VWN
BP
ACM

1H, 13C, 31P, etc.
ab initio shielding tensors
GIAO (Gauge-Independent Atomic Orbital)

Acc'y:

SCF/6-31G -

[partialdiff][Delta] 1H +/-0.2
[partialdiff][Delta] 13C +/-4

SCF/6-31G

[partialdiff][Delta] 1H +/-0.1
[partialdiff][Delta] 13C +/-2

Natural Internal Coordinates
semidirect SCF, MP-2

Properties:

optimized geometry
IR
- force constants
- energies
- intensity
Dipole - hexadecapole moments
polarizability
electrostatic potential
0th order shielding
Mulliken Population Analysis
Roby-Davidson Population Analysis
Boys orbital localization
intermolecular interaction energy

Parameters:

Gaussian basis sets

DZVP
VWN
BP
ACM
BLYP

Schafer -
- SV(+P):

H, He
Li - Ne
Na - Ar
K - Kr

- DZ(+P):

H, He
Li - Ne
Na - Ar
K - Kr

- TZ(+1-2P):

H, He
Li - Ne
Na - Ar

ECPs: Hurley; K -Kr

LaJohn; Rb - Xe
Ross; Cs - La, Hf - Rn
Cundari; Ce - Lu
Ermler; Fr - Ac, Th - Pu

STO-3G, 3-21G, 6-31G( *,**)

- CADPAC: ab initio Hartree Fock calculations.

- DGauss 3.0: a molecular DFT program for studying electronic, magnetic, & structural properties of atoms, molecules, & clusters. -- developed by Cray Research

Pros: analytical gradients

analytical 2nd Derivatives
SCRF
point charge fitting
f-functions
relativistic pseudo-potentials

Cons: no search driver

"weak" TS optimizer

Parameters:

VWN
BP
BLYP
BSPP

Properties:

multipole moments
IR spectra
Raman frequencies
polarizability
NMR chemical shift
Density of States
photoelectron spectra
Population Analysis
- Mulliken
- Landis
- Nazer

SCRF
Direct MD
Ground State
analytical gradients
Transition State
CI

Parameters:

MNDO
MNDO/H, MNDOc, MNDO/d
MINDO/3
CNDO/2
AM1
PM3
MP2
BWEN

Properties:

multipole moments
IR spectra
Raman frequencies
enthalpy, entropy, heat capacity
time-correlation function
Radial Distribution Function

semiempirical QM
electrostatic potentials
Natural Atomic Orbital Point Charges
Clark Solvation Model

Properties:

ESR hyperfine coupling
C13 NMR shifts

associations. The program examines structures from the perspective of solid geometry rather than physical chemistry. -- QCPE 617

RHF, UHF, ROHF, UHFA, CI, MP2CI
Transition Dipoles and Moments
Natural Orbitals
Self Consistent Reaction Field
Localized Orbitals
- Boys
- Fermi
- Double Projector
Ionization Potentials
Electron Affinities
Transition State
Metal Configuration Mixing
CI Excitation Indicator
Transition Dipole
Transition Energy
Oscillator Strength
Geometry optimization cycle
Change of Energy
Norm of the gradient
Max component of the gradient

Output Sections:

(Total) ENERGY
BOND LENGTH MATRIX
INTERATOMIC DISTANCES
BOND ANGLES
ATOMIC BOND INDEX
OVERLAP MATRIX
COULOMB MATRIX
ONE ELECTRON MATRIX
HAMILTONIAN MATRIX
SOLUTE POLARIZATION CONTRIBUTION
SOLVENT REORGANIZATION COST
EIGENVALUES
ATOMIC DENSITIES
EIGENVECTOR MATRIX
BOND ORDER MATRIX
TOTAL DENSITY
SPIN DENSITY
FOCK MATRIX
ALPHA SPIN
ATOMIC BOND INDEX
(ZDO Basis) CHARGE
DIPOLE MOMENT
(Mulliken) ORBITAL POPULATIONS
EXCITED STATES
CONFIGURATION INTERACTION
SINGLETS, TRIPLETS
GROUND STATE DEPRESSION
EIGENVALUES
EIGENVECTORS

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3/97 Ernie Chamot / Chamot Labs / (630) 637-1559 / echamot@chamotlabs.com