HYPERCUBE INC Basic Features of HYPERCUBE INC Benefits

HYPERCUBE INC. Basic Features of

HYPERCUBE INC. Benefits of Hyper. Chem l l l l Complete Package for PC Easy to Use Robust Windows Customizable Extensible Pocket, Lite, Student, or Pro

HYPERCUBE INC. DNA Strand

HYPERCUBE INC. Molecular Orbitals

HYPERCUBE INC. Architectural Features l l l Windows Focus Custom Menus Hcl/Tk Scripts Client-Server Various Licensing Schemes Third-Party Modules

HYPERCUBE INC. Summary of New 8. 0 Features l l l l Vista Compatibility Third-Party Interfaces – e. g. Gamess Batch Capabilities - disconnected Universal Double Precision Undo and Redo – make a mistake? Recent Files List – easy file open Geometric Measurement

HYPERCUBE INC. Summary of New 8. 0 Features l l l l Chemical Substitution of H Better Toolbar – C, N, O etc. Entropies and Free Energy at T Heat Capacities at T Zero-Point Energies Rate Constants – trans. state theory Equilibrium Constants at T

HYPERCUBE INC. Summary of New 8. 0 Features l l l l RM 1 Semi-Empirical Method More MP 2 Capabilities - optimize Batch Capabilities - disconnected Configuration Interaction Revised Line widths for IR, UV Spectra MM/QM and FIXED Atoms Named Vibrations for Molecular Mechanics

HYPERCUBE INC. Summary of New 8. 0 Features l Electric Fields for MM l Particle in Box Wave Functions

HYPERCUBE INC. Rate Constants and Equilibrium Constants

HYPERCUBE INC. Line-Width Envelope on Spectra Rendering of Planes

HYPERCUBE INC. Third-Party Interfaces

HYPERCUBE INC. Summary of New 7. 5 Features l l l l Full Open. GL Graphics Any Atom – Any Rendering 16 M Colors Secondary Structure Renderings Fast Protein Densities Video Tutorials Helices, Sheets, Turns, and Coils

HYPERCUBE INC. Variety of Atom Renderings

HYPERCUBE INC. Protein Densities

HYPERCUBE INC. Secondary Structures

HYPERCUBE INC. Video Tutorials

HYPERCUBE INC. Summary of New at 7 Features l l l l Density Functional Theory NMR Simulation Database Package Updated Charmm Force Field Typed Neglect of Diff Overlap. (TNDO) Magnetic Fields Optimization of Excited States

HYPERCUBE INC. NMR Spectra

HYPERCUBE INC. Wide Variety of Density Functionals

HYPERCUBE INC. Hyper. Chem’s Database

HYPERCUBE INC. Summary of New Features l l l l Optimum MP 2 Geometries Rendering of Aromatic Rings Drawing Program Interactive Parameter Editing Branched Polymer Building New Basis Sets New File Formats

HYPERCUBE INC. Drawing Annotations

HYPERCUBE INC. Editing Parameters

HYPERCUBE INC. Summary of New Features l l l l More Named Selections Molecule Names for Database Translation and Rotation Quenching Creation of New Parameter Sets Conjugate Direction Optimizer New Script Commands Updated Manuals and On-line Help

HYPERCUBE INC. Extensive Electronic or Printed Manuals

HYPERCUBE INC. New Features at Release 6 l l l l RMS Fitting Conformational Search Protein Sequence Editor Crystal Builder Polysaccharide Builder Polymer Builder QSAR Properties

HYPERCUBE INC. Builders

HYPERCUBE INC. New Features at Release 6 l l l l Script Editor Raytraced Renderings Amber 94 Amber 96 Default Parameters for Amber ESR Hyperfine Constants Electric Polarizabilities

HYPERCUBE INC. Raytracing

HYPERCUBE INC. New Features at Release 6 l l l l Static Electric Fields Spin Populations Save As HTML Potential Functions Protein Homology Operations Annotations Formal Charges

HYPERCUBE INC. New Features at Release 6 l l l l Extension of HIN File Constrained Drawing Enhanced Selection Gradient Vectors New Atom Labels Bond Labels Property Displays Execute Script During Dynamics

HYPERCUBE INC. Molecular Modeling: What is it? Molecular Modeling is an integration of visualization and computational tools designed to provide convenient access to established theoretical and computational methods.

HYPERCUBE INC. Summary of Basic Operations l l l l Create Molecular System Manipulate System Visualize System Energy, Derivative Generator Energetics Spectra Reactivity Visualize Results

HYPERCUBE INC. Create Molecular System. . . l l l l Files 2 D-Draw and Model Build Symmetry Stereochemistry Incremental Building Templates External Builders Scripting

HYPERCUBE INC. Files l l l l l Hyper. Chem (HIN File) Protein Data Bank File ISIS Sketch File MDL Mol File Mopac Z-matrix Tripos Mol 2 File Chem. Draw File XYZ File Cambridge Crystallographic File Custom DLL, Babel, etc.

HYPERCUBE INC. HIN FILE forcefield mm+ sys 0 0 1 view 40 0. 5102 55 15 1 0 0 0 1 -0. 25677 -0. 42475 -55 seed -1111 mol 1 atom 1 - O O 2 - 0 -0. 08578236 0. 104746 0. 0 2 2 s 3 s atom 2 - H HO - 0 -0. 08578236 1. 064746 0. 0 1 1 s atom 3 - H HO - 0 0. 8193156 -0. 2152505 0. 0 1 1 s endmol 1

HYPERCUBE INC. HIN Files l l Uninterpreted Records Ignored Essential Records Only Required Stores Drawing Program Objects Stores Annotations

HYPERCUBE INC. 2 D and 3 D Drawing -> Modelbuilder l l l l l What You Draw May Be What You Get Great Builder But Not Always Perfect Hydrocarbon Backbone to Final System? Draw Hydrogens if Really Want To Structure Constraints Stereochemical Constraints MB Sensitive to 3 D Incremental Building MB Sensitive to Formal Charge Rules not Energetics

HYPERCUBE INC. 1. Define the PLANE by Selection 2. Reflect Appropriate Atoms in Plane

HYPERCUBE INC. 1. Via model builder constraints 2. Inversion through POINT

HYPERCUBE INC. Model Builder – No Energetics

HYPERCUBE INC. Formal Charges

HYPERCUBE INC. Templates and Builders l Peptides l l l Nucleic Acids Crystals Polysaccharides Polymers Script to Build Arbitrary Structures

HYPERCUBE INC. Manipulate System l l l l Select Then Operate Operations Apply to Selections Nothing Selected is Everything Selected Left Button Manipulates Whole System Right Button Manipulates Selected Atoms Some Operations Require Named Selection Left Button(Viewer) - Right Button(Molecule) Left Button(Does) – Right Button(Undoes)

HYPERCUBE INC. Visualize System l l l l l Standard Ball and Stick, CPK, Etc. Raytraced Renderings Hydrogen Bonds Periodic Box Flexible Coloring Backbone and/or Ribbon Variety of Labels Hiding Atoms Aromatic rings

HYPERCUBE INC. Periodic Boundary

HYPERCUBE INC. Labels

HYPERCUBE INC. Raytracing

HYPERCUBE INC. Small Building Projects l l l l Basic Drawing Inversion Reflection Chiral Centers Incremental Drawing Alpha Helix Polymer Graphite

HYPERCUBE INC. Energy (And Derivative) Generators l l l Molecular Mechanics (Hyper. MM+) Molecular Mechanics (Hyper. Newton) Extended Huckel (Hyper. EHT) Semi-empirical QM (Hyper. NDO) Ab Initio QM (Hyper. Gauss) Density Functional Theory (Hyper. DFT)

HYPERCUBE INC. Molecular Mechanics l l l MM+ Amber OPLS Charmm Default Dreiding FF

HYPERCUBE INC. Semi-empirical Quantum Mechanics l CNDO l INDO l MINDO/3 l MNDO/d l AM 1 l RM 1 l PM 3 l ZINDO/1 l ZINDO/S l TNDO

HYPERCUBE INC. Quantum Mechanics: Ab Initio Standard Basis Sets: • Custom Basis Sets: Add diffuse, polarization STO-3 G or other basis functions 3 -21 G (s, p, d, spd) from dialog box. 6 -31 G**, etc. Edit existing basis set file to create new basis set. • Calculations: Single Point ( MP 2, CI ) and Geometry Optimization Molecular Dynamics, Vibrational and Optical Spectra

HYPERCUBE INC. Quantum Mechanics: Density Functional Theory All the Features of Ab Initio: Single Basis Set Derivatives for Dynamics, etc. Variable Integration Schemes Large Variety of Functionals. • Calculations: Single Point and Geometry Optimization Molecular Dynamics, Vibrational and Optical Spectra

HYPERCUBE INC. DFT Exchange Functionals l l l l None Slater Hartree-Fock Becke 88 Perdew-Wang 91 Gill 96 PBE 96 HCTH 98

HYPERCUBE INC. DFT Correlation Functionals l l l l None VWN Perdew-Zunger 81 Perdew 86 LYP Perdew-Wang 91 PBE 96 HCTH 98

HYPERCUBE INC. DFT Combination (Hybrid) Functionals l l l B 3 -LYP B 3 -PW 91 EDF 1 Becke 97 Any Explicit Exchange-Correlation Pair

HYPERCUBE INC. Thermodynamics l l l l l Energy or Heat of Formation Entropy and Free Energy Heat Capacities Equilibrium Structure Monte Carlo Molecular Dynamics Langevin Log P Conformational Search Equilibrium Constants

HYPERCUBE INC. Spectra l l l l Moments of Inertia Vibrational Normal Modes Electronic NMR Polarizabilities Line-Width Envelopes

HYPERCUBE INC. NMR Spectra

HYPERCUBE INC. Normal Modes

HYPERCUBE INC. Reactivity l l l l Transition States Molecular Dynamics Langevin Dynamics Electric Fields Magnetic Fields Potential Functions Electrostatic Potentials Kinetic Rate Constants

HYPERCUBE INC. Automated Potential Energy Plot

HYPERCUBE INC. Electrostatic Potential

HYPERCUBE INC. Sample Calculations l l l l Dihedral Angle Potential Function Transition State of Acetylene Isomerization Monte Carlo of Water Molecular Dynamics Orbitals of Water Vibrations of Formaldehyde Conformational Search of n-Pentane Dipole Moment of Substituted Benzenes

HYPERCUBE INC. Transition State Searching Two methods to locate “Saddle Point” l Eigenvector Following l Synchronous Transit

HYPERCUBE INC. 3 D Orbitals, Densities, Etc. l Orbital Surfaces l Charge Density l Spin Density l Electrostatic Potential l Mapped Electrostatic Potential

HYPERCUBE INC. Custom Hyper. Chem Applications • Simplify or Rearrange Menus • Add User-Defined Menu Items • Interface to Windows Applications • • – MS Word, MS Excel Interface to user programs – C/C++, VB, FORTRAN Interface to 3 -rd Party Programs

HYPERCUBE INC. Demonstration Customization and Scripting l Hcl scripts l Initialization of Hyper. Chem l Custom Menus

HYPERCUBE INC. Custom Menus l Custom Initialization ¡ Modify Hyper. Chem’s startup settings ¡ Use chem. scr l Custom Menus ¡ Script menu ¡ Changing Hyper. Chem menus

HYPERCUBE INC. Scripts l Hyper. Chem Command Language (Hcl) scripts ¡ Chemistry commands and variables ¡ e. g. do-molecular-dynamics l Tool Command Language (Tcl) scripts ¡ Control Structures (do-loops, if-statements, …) ¡ Extensible (include Hcl statements) ¡ e. g. set a [hc. Query molecule-count] for {set i 0} {$i < $a} {incr i} { …. }

HYPERCUBE INC. Adding Items to the Script Menu script-menu-caption(4) = "Quenched Dynamics" script-menu-command(4) = "read-script Quenched_Dynamics. scr" script-menu-enabled(4) = true

HYPERCUBE INC. Script to run Quenched Dynamics Calculation (excerpts) molecular-mechanics-method mm+ dynamics-heat-time 0. 1 dynamics-run-time 0. 2 dynamics-constant-temp yes dynamics-bath-relaxation-time 0. 01 ; Initiate the dynamics run do-molecular-dynamics ; Optimize the resulting structure do-optimization

HYPERCUBE INC. Script to Customize Hyper. Chem Initialization window-color blue window-width 400 window-height 300 color-element 17, green calculation-method semi-empirical configuration-interaction no semi-empirical-method AM 1 Save as chem. scr in Hyper. Chem (chem. exe) path.

HYPERCUBE INC. Elements of Hcl Scripting script = text file, “scr” extension sequence of Hcl command statements Hcl command statement can: read or write the value of HSV* variable activate a Hyper. Chem menu issue a direct “order” to Hyper. Chem

HYPERCUBE INC. Elements of Hcl Scripting (2) Hyper. Chem State Variables Define the current state of visualization and computation in Hyper. Chem. (see Help menu) window-color blue color-element 17, green calculation-method semi-empirical configuration-interaction no semi-empirical-method AM 1

HYPERCUBE INC. Elements of Hcl Scripting (3) Types of HSV arguments Boolean yes/no, true/false, 1/0 string text filename string requiring DOS filename enum string; limited number of possibilities integer floating point (decimal) number

HYPERCUBE INC. Elements of Hcl Scripting (4) Hcl Commands Compute Menu Commands do-single-point do-optimization do-vibrational-analysis do-molecular-dynamics do-langevin-dynamics do-monte-carlo append-dynamics-average append-dynamics-graph Help menu / Scripts lists Hcl commands and HSV’s

HYPERCUBE INC. Customizing Hyper. Chem’s menus Menu files: Default. mnu (excerpts) MENU "&File" ITEM "&Newt. Ctrl+N", menu-file-new ITEM "&Open. . . t. Ctrl+O", menu-file-open ITEM "&Merge. . . ", menu-file-merge ITEM "&Savet. Ctrl+S", menu-file-save ITEM "Save &As. . . t. Ctrl+A", menu-file-save-as SEPARATOR ITEM "S&tart Log. . . ", menu-file-start-log ITEM "Stop Lo&g", menu-file-stop-log ITEM "&Log Comments. . . ", menu-file-log-comments SEPARATOR

HYPERCUBE INC. Customizing Hyper. Chem’s menus (2) Menu files: Default. mnu (excerpts) …cont’d SEPARATOR ITEM "S&tart Log. . . ", menu-file-start-log ITEM "Stop Lo&g", menu-file-stop-log ITEM "&Log Comments. . . ", menu-file-log-comments SEPARATOR …etc.

HYPERCUBE INC. Customizing Hyper. Chem’s menus Procedure: 1. Edit menu file; save with mnu extension 2. Edit and save menu-load script load-user-menu new. mnu To restore default menus, run the script load-default-menu

HYPERCUBE INC. Add New Functionality: Tcl/Tk scripts ; Rotate. mnu MENU "&File" ITEM "&Newt. Ctrl+N", menu-file-new ITEM "&Open. . . t. Ctrl+O", menu-file-open ITEM "E&xit", load-default-menu END MENU "&Rotate" ITEM "&X Axis", read-tcl-script rotatex. tcl ITEM "&Y Axis", read-tcl-script rotatey. tcl ITEM "&Z Axis", read-tcl-script rotatez. tcl END MENUITEM "Ca&ncel", menu-cancel

HYPERCUBE INC. Server Clients The Client - Server Architecture: analysis tool communication protocol visualization tool computational backend An Open Architecture

HYPERCUBE INC. Hyper. Chem Command Language Sequential line-by-line execution Types of commands: A menu activator A direct command An HSV write An HSV read menu-file-save-as add-amino-acid abinitio-buffer-size=32000 query-value abinitio-mp 2 -correlation-energy

HYPERCUBE INC. Hyper. Chem State Variables HSV scalar vector array Element float integer boolean string enum or any hybrid abinitio-mp 2 -frozen-core: Variable, Type: boolean. beta-scf-eigenvector: Variable, Type: vector of float-list. coordinates: Variable, Type: array of float, float

HYPERCUBE INC. Using Tcl/Tk scripting language. “Tcl” - Tool Command Language - embeddable - used for controlling and extending applications “Tk” - Tool Kit - extension to Tcl - used for creation and manipulation of windowing applications

HYPERCUBE INC. Interfacing to Hyper. Chem Using external applications: l Visual Basic, Tcl/Tk, C++ for GUI elements l C/C++, FORTRAN for calculations Types of communication: l Direct use of DDE, TCP/IP, IPC l API calls to the Hyper. Chem API

HYPERCUBE INC. Hyper. Chem Application Programming Interface l Provides abstraction level for communication protocol l Fast, the most robust interface for Hyper. Chem l Implemented as system-wide DLL for Windows NT and Windows 95 l Provides text and binary form for communication l Implements command execution, HSV queries and notification protocol l Provides notification agent for non-event-driven applications l Basis for Chemist’s Operating System

HYPERCUBE INC. Creating Web Content With

HYPERCUBE INC. Creating Web Content l Structures with Geometry l Orbitals with Transparency l Spectra with Animations l Proteins with Ribbons

HYPERCUBE INC. Characteristics Free Plug-in l Direct 3 D – Very Fast l Microsoft or Netscape l Browser Only Solution l

HYPERCUBE INC. Orbitals With Transparency

HYPERCUBE INC. Spectra with Animations

HYPERCUBE INC. Structures With Geometry

HYPERCUBE INC. Proteins With Ribbons