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
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