| Molecular modelling,drawing, molecular mechanics, Semi-empirical calculations, structure display |
|
||
|
||
|
||
|
HyperChemTM by HypercubeTM | ||||||||||||||||||||||||||||||||
|
HyperChem contains extensive facilities for building, manipulating, and visualizing molecules coupled to molecular mechanics and semi-empirical quantum mechanics programs that carry out simulations. You can carry out many different varieties of energy minimization (geometry optimization) and molecular dynamics calculation to obtain insight into molecular structure and flexibility. You can also compute and analyze IR and UV spectra. HyperChem makes full use of the Windows' clipboard and Dynamic Data Exchange capabilities to interact with other programs. A full set of scripting commands enables you to automate your work in a straightforward manner. Visualization and Manipulation HyperChem's sketch and build method of drawing structures is a fast way of getting realistic 3Dstructures on your screen. For peptides and nucleic acids, you can build structures one residue at a time by just clicking on the appropriate button. Beyond that, HyperChem allows you full mouse control over stereochemistry, as well as the ability to twist torsional angles and stretch bonds. Selecting rings, displaying backbones, and many more options enable you to focus on the important features of the system you are studying. Molecular Mechanics HyperChem software is a versatile tool for exploring the structure and stability of molecules. HyperChem integrates several molecular mechanics methods and an extensive suite of visualization and analysis tools to provide a powerful, easy-to-use, desktop molecular modeling program. HyperChem provides simple ways to produce 3D molecular structures on screen, a choice of four force fields, geometry optimization techniques to search for stable structures, and molecular dynamics techniques to carry out conformational searching and to investigate structural changes. Molecular Mechanics Applications HyperChem's molecular mechanics methods have many applications to the study of molecular structure and stability. Some typical applications are: Calculating relative conformational energies of a series of analogous structures. Re-optimizing a peptide after introducing a selective mutation. Refining structures prior to more rigorous quantum mechanics calculations. Assessing possible steric effects in a reactive intermediate. To simulate the effects of solvent attenuation of electrostatic interactions, HyperChem offers a distance-dependent dielectric constant option for selected force fields. Four Force Fields HyperChem includes four built-in molecular mechanics force fields: new implementations of techniques developed and published by respected research groups. MM+ Appropriate for most non-biological species. Based on the MM2(1977) force field developed by N. L. Allinger. Uses the 1991 parameter set. Extended to incorporate non-bonded cutoffs, restraints, and periodic boundary conditions. Computes default parameters for cases where MM2 parameters are not available. AMBER Appropriate for use on polypeptides and nucleic acids with all hydrogen atoms explicitly included. The AMBER force field was developed by the research group of P. A. Kollman. Includes parameters for Versions 2.0 and 3.0a of this widely-used force field. OPLS Designed for calculations on nucleic acids and peptides. The OPLS united-atom force field was developed by the research group of W. L. Jorgensen. The non-bonded interaction parameters are optimized for calculations where the solvent is explicitly included in the calculation. Appropriate for use with HyperChem software's built-in periodic water box. BIO+ Primarily designed to explore macromolecules. Implements the CHARMM force field developed in the group of Martin Karplus. Includes CHARMM parameters published for amino acids. Allows users to add other parameter sets. Adding Parameters A recurring problem in working with molecular mechanics force fields is that of insufficient parameters. HyperChem tackles the problem by providing a default scheme for the MM+ force field and by allowing users to add their own parameters. All HyperChem force fields parameters are present as text files to which new atom types and new parameters can be easily added. The user can also define rules for automatic assignment of new atom types. Quantum Mechanics HyperChem software provides versatile tools for exploring the structure, stability and properties of molecules using quantum mechanics. There are simple ways to produce 3D molecular structures onscreen. You choose from nine semi-empirical methods, and you can use geometry optimizers to search for stable structures or molecular dynamics techniques to model sample reaction trajectories. HyperChem allows you to easily add to or modify the semi-empirical quantum mechanics parameters in text files. With HyperChem, you can perform semi-empirical calculations on elements hydrogen through xenon, including transition-metals. HyperChem includes a model builder that turns a rough 2Dsketch of a molecule into 3D. HyperChem combines semi-empirical quantum mechanics and molecular mechanics methods in a single package to create a powerful tool for finding better starting geometries, substantially reducing computation time. Quantum Mechanics Applications HyperChem quantum mechanical methods have many practical applications to the study of molecular structure and properties, including: Determining frontier orbital interactions between donor and acceptor molecules as illustrated by Diels-Alder cycloaddition reactions. Obtaining partial atomic charges, using Mulliken population analysis, to predict likely sites of attack. Generating electrostatic potential contour plots to illustrate likely trajectories of approach in drug-receptor docking. Calculating unpaired spin densities to identify possible reactive sites on a molecule or for correlation with ESR data. UV-Visible Spectroscopy Predict wavelengths and intensities of electronic transitions. Predict locations of non-spectroscopically active states. IR Spectroscopy Predict wave numbers and intensities of vibrational absorption lines. Display motions of normal modes using vectors and animations. Nine Semi-Empirical Methods HyperChem includes nine semi-empirical quantum-mechanical methods that are implementations of methods developed and published by respected research groups. These methods range from the simple all-valence-electron method (Extended Hückel) to among the most sophisticated and accurate semi-empirical methods currently available (AM1 and PM3). The semi-empirical quantum mechanics methods available in HyperChem software are: Extended Hückel, developed by R. Hoffmann. CNDO and INDO, developed by the research group lead by J. A. Pople. MINDO/3, MNDO and AM1, developed by the research group of M. J. S. Dewar, PM3, developed by J. J. P. Stewart. ZINDO/1 and ZINDO/S developed by the research group led by M. Zerner. Flexible and Powerful Several options for electronic structure calculations are available: Systems with any charge and with spin multiplicity up to four can be studied. Restricted and Unrestricted Hartree-Fock (RHF/UHF)calculations on closed-shell and open-shell systems can be performed. Ground states (for each spin multiplicity), and first excited singlet state can be calculated. Configuration Interaction (CI) using orbital or energy criteria with singles only or microstate methods. The number of atoms is limited only by the memory in your PC: calculations using over 200 atomic orbitals can be carried out on a PC with 4Mb of RAM. You can obtain a variety of useful results with these calculations, including: Contour plots of molecular orbitals, charge and spin densities, and electrostatic potential. Displays of orbital energy-level diagrams. A log file of numerical data, including energies, heats of formation (for NOO methods), dipole moments, molecular orbital coefficients, and the density matrix. Plots and log file data that allow you to study chemical reactivity and heats of formation. Building, Visualizing and Manipulating Molecules HyperChem is an integrated desktop molecular modeling system. Its building, visualization and manipulation capabilities are linked to its extensive computational features. In addition to helping you better visualize 3D molecular structures, HyperChem lets you easily set up, perform and interpret results from a wide variety of simulations and computations, including geometry optimizations and molecular dynamics runs. Building Molecules HyperChem uses a simple sketch-and-build method for building molecules on the screen and offers several means of creating and modifying 3D molecular structures. Model Builder Converts a 2D sketch into a 3D structure. Defines stereochemistry before or after model building. Adds hydrogen atoms automatically. Sets bond lengths and bond angles to appropriate values. Uses sophisticated algorithms to set rings and cages to appropriate structures. Tools for peptides and nucleic acids Using HyperChem, you can easily select residues and specify secondary structures from a menu. Tools for modifying molecules Substitute an atom or change bond order with a mouse click. Mutate amino acid or nucleotide residues. Translate, rotate, reflect or invert all or part of a molecule. Files Read and write files in HyperChem INput (HIN), Brookhaven Protein Databank (PDB), Isis Sketch (SKC), MDL (MOL), OPAC Z-matrix and Tripos (MOL2) formats. Visualizing Structures Molecules can be rendered on the screen in several modes: sticks (stereo optional), dot surfaces, disks, or space-filling shaded spheres. HyperChem includes an array of visualization and manipulation tools to help you better understand molecular structures. You can: Highlight, color, or hide parts of a molecular system. Display peptide structure using ribbons. Color a DNA backbone one color throughout. Color a substrate differently from an enzyme. Highlight a particular ring in a complicated molecule. Optionally display hydrogens. View slices of molecules. Display computational results. Animate vibrational modes of molecules. Consistency Gives Ease of Use The HyperChem user interface consistently employs a select-and-operate method to simplify use. Simply select a set of atoms, residues or molecules with the mouse and then apply the desired operation or tool. Making and naming selections Selecting atoms, residues, or molecules is easy. You can select a particular ring, a specific side chain, a peptide or nucleic acid backbone, all atoms within a radius of a central atom, the shortest path between two atoms, or combine all these possibilities. Once you have made a selection, you can "name" it for future use. Named selections are stored in HIN files and can be restored by picking the name from a menu. Selections and Visualization Selections can be used to control the display. You can: Color a selection to distinguish it from the rest of a molecule. Hide a selection from view, or hide the rest of the system, to focus on a region of particular interest. Label a selection by element, type, chirality, residue name or charge. Selections and Manipulations You can apply an array of manipulation tools to selections to give complete control over molecule building. You can: Rotate and translate a selected molecule or part of a molecule apart from the rest of the system. Adjust selected bond lengths, bond angles and torsion angles. Select a side chain in a molecule and rotate it about the connecting bond. Invert and reflect selections, controlling stereochemistry and conformation. Delete a selection, or copy and paste it using the clipboard. Selections and Measurement Selections provide a quick way to get at structural information. The atoms do not need to be bonded, so through-space measurements are easily made. Selecting a single atom reports the type and position of that atom. Selecting two atoms reports the distance between them. Selecting three atoms reports the angle connecting them. Selecting four atoms reports the dihedral angle. Selections and Calculations Selections enable restraints to be placed on molecular mechanics calculations, parts of molecules to be held frozen, and structural features to be tracked through dynamics runs. Extension and Customization HyperChem features two powerful tools that let you extend its functionality, build batch files, and customize the program: an extensive set of scripting commands, and the ability to communicate with other Windows programs via the Dynamic Data Exchange (DDE) standard protocol and the Windows Clipboard Script Commands A script command is a text instruction that tells HyperChem to carry out a task or requests information from HyperChem. A script is a text file containing a list of script commands, which are sent in sequence to HyperChem. The HyperChem documentation contains a full listing and description of more than 400 script commands. Once a script file has been created, you can execute it from the HyperChem user interface, using the Script menu. Up to ten custom commands, complete with keyboard shortcuts, can appear on the Script menu. You can then simply click on a menu item to execute the appropriate script. Scripts can be used in many ways to: Carry out batch calculations. Automate frequent tasks. Set the visualization and computation options appropriate for different tasks. Launch other programs from HyperChem. Have HyperChem automatically read a particular file (called chem.scr) on startup to initialize your settings and carry out any task you always want executed upon start-up. Ensure that a set of calculations is carried out with exactly the same settings in every case. Dynamic Data Exchange and the Windows Clipboard Windows programs can communicate by a well-defined protocol called Dynamic Data Exchange(DDE). HyperChem can also communicate using DDE, which means it can interact directly with other Windows applications. Among other things, DDE messages can send script commands to HyperChem from other applications. HyperChem can also exchange data with other Windows application through the Windows Clipboard, which allows you to copy images from HyperChem and paste them into other Windows programs. Additionally, HyperChem provides a gateway to scientific databases such as the Brookhaven Protein Data Bank and to MDL Information Systems' ISIS database. Using the link between HyperChem and ISIS, you can build a 3D model from the data (with stereochemistry retained),perform calculations and modifications and then return the structure to the database. HyperChem and Spreadsheets You can write a macro in a Windows spreadsheet program that supports DDE (for example, Microsoft Excel) and bring spreadsheet capability to HyperChem. A macro can be used to: Automatically carry out a set of calculations on a set of molecules and read the results into the spreadsheet for analysis and convenient organization of results. Automatically carry out systematic searching of dihedral angles for stable conformations. Carry out dynamics calculations and read the results into a spreadsheet for analysis. HyperChem and Word Processors Some word processors that run in Windows support DDE (for example, Microsoft Word). The combination of word processing tools and HyperChem visualization capabilities can greatly aid in the presentation of teaching and research materials. You can: Place buttons in a document containing a lesson or tutorial that instruct HyperChem to carry out simulations illustrating the points you make in the text. Cut and paste HyperChem images into documents. Copy molecular dynamics plots into a Windows graphics programs to annotate them. Paste numerical result into documents and update them automatically through dynamic data links as HyperChem produces new results. Add-on Utilities and Programs for HyperChem New intuitive and inexpensive software development tools, such as Microsoft Visual Basic, are rapidly reducing the work needed to create Windows programs. These tools help you construct programs that communicate with HyperChem and add to its functionality. The development of small utilities to carry out minor tasks as well as full-scale, add-on programs become much easier using these tools. The ChemPlus set of extensions for HyperChem are an example add-on programs that can greatly enhance the functionality of HyperChem. Sharing HyperChem Add-ons There is an electronic HyperChem discussion group on the Internet, so when you've built something that extends HyperChem capabilities, you can share it. Molecular Dynamics HyperChem provides versatile tools for exploring the structure, stability and properties of molecules using molecular mechanics and quantum mechanics. It offers simple ways to produce 3D molecular structures on screen, a choice of four molecular mechanics force fields and nine semi-empirical quantum mechanical methods, and a selection of geometry optimization techniques to search for stable structures. The graphical user interface links all of HyperChem's extensive visualization and computational capabilities, giving you the ability to run molecular dynamics calculations using either molecular mechanics or quantum mechanics methods to calculate the inter-atomic forces. Molecular Dynamics Applications Molecular Dynamics calculations simulate the behavior of molecules at specified temperatures or energies and can be used in many applications, including: Investigating conformational flexibility. Using simulated annealing (high-temperature dynamics followed by slow cooling) to search for low-energy minima. Using dynamics with restraining forces to build experimental data into your simulations. Illustrating reaction mechanisms with dynamics trajectories using potential surfaces determined by semi-empirical quantum mechanical calculations. Versatility in Molecular Dynamics Calculations HyperChem offers a range of options for setting up molecular dynamics calculations, including the ability to: Carry out molecular dynamics calculations using any of HyperChem's molecular mechanics force fields or SCF quantum mechanical methods. Run the calculations at constant energy, or keep the system close to a constant temperature. Specify the length and temperature of the heating, run and cooling phases of a dynamics run. Specify the temperature step to be used for heating and cooling phases. Carry out molecular mechanics simulations subject to restraining forces and/or with portions of the system fixed in space. Control the rate of collection, averaging, and display of data during a run. Save the end point of the run, including velocities, so that you can resume where you left off. Carry out calculations on isolated molecules or on systems solvated in a periodic box of water molecules. Plot selected energetic and structural quantities while running or playing back a simulation. Assign specific initial atomic velocities, or let HyperChem choose velocities according to a Maxwell-Boltzmann distribution with a user-specified random number seed. HyperChem uses the leap-frog integration algorithm for molecular dynamics calculations. Analysis Capabilities HyperChem also provides powerful facilities for analyzing the results of your dynamics calculations, including the ability to: Save the run in a "snapshot" file for later replay and analysis. Statistically average energetic quantities such as the total, potential, and kinetic energies and temperature. Statistically average structural quantities such as distances (bonded and non-bonded), angles and torsion angles, as calculations are carried out. Graph energetic or structural quantities. Control sampling range and frequency for averaging and graphing. Control the display while the calculation or replay is in progress, so you can rotate, translate or zoom your view of the system as it moves. NETWORK FEATURES HyperChem Release 4 has three new features that make it suitable for use on local area networks (LANs): A network installation procedure. A network license management system. The ability to run calculations remotely. These features can be used to give all users on network the ability to run HyperChem and also allow time consuming calculations to be run on powerful networked UNIX computers. Network license management requires a network version of HyperChem, and remote calculations require HyperChem UNIX back end modules. Network Installation HyperChem's network installation procedure makes it easy to become a HyperChem user. Once a master copy has been installed on a shared network disk drive, HyperChem can be quickly installed on any PC on the network without having to insert floppy disks. HyperChem files can be installed to a local hard disk or used directly from the shared network drive. License Management Network license management allows any PC on a network to run HyperChem. Instead of requiring a parallel port lock on each PC as in the standalone version of HyperChem, with the network version of HyperChem only one PC on the network needs to have a lock. The network lock and driver software can be installed on any PC on the network - they do not have to be installed on the network file server. The network version of HyperChem can be purchased with 1, 5, 10, 25, 50 or unlimited licenses. The number of licenses determines the maximum number of instances of HyperChem that can run simultaneously on PCs on the network. You can use more than one network lock and mix network and standalone locks to suit your network configuration. HyperChem's network licensed version works with local area networks which provide NetBIOS, including: Novell NetWare. Microsoft Windows for Workgroups 3.11. Microsoft LAN Manager. Lantastic. IBM LAN Server. DEC Pathworks. Banyan Vines. 3COM. On Novell networks, the security server program may be run as a Novell certified NetWare Loadable Module (NLM). The network version of HyperChem combines security with ease of use, and transparency for the user. It has been adopted by many universities, colleges, research labs and companies to allow easy access to full-featured molecular modeling on each desktop. Colleges and universities have also used it to set up cost-effective and secure molecular modeling labs. Remote Calculations If you want to be able to use faster computers for HyperChem calculations, you can now purchase UNIX HyperChem back end modules. Instead of having a back end icon pop up on your Windows screen when you start a calculation, HyperChem can seamlessly run the calculation on a UNIXcomputer. The supported UNIX computers include: DEC Alpha running OSF/1. IBM RS/6000 running AIX. Silicon Graphics running IRIX. Your PC must be connected to the UNIX computer with network software that supports the Windows Socket Standard, Version 1.1, including: Beame & Whiteside BW-TCP and BW-NFS. Microsoft TCP/IP for Windows for Workgroups. NetManage Chameleon or ChameleonNFS. Novell LAN Workplace for DOS/Windows Trumpet 1.0 and CRYNWR Packet Drivers To give an example of possible speedup, an MNDO calculation of C60 using a DEC 3000-500 for the back end runs 18 times faster than on a NEC 486DX/50. You can even have multiple HyperChems running on your PC, with each using a different UNIX computer for a back end. Iin HyperChem Release 4.5 The most significant change between version 4 and 4.5 of HyperChem is the addition of ab initio functionality. Using any basis set of s, p or d orbitals, ab initio calculations of the following kinds can be performed: SCF calculations of single points Geometry optimizations Molecular dynamics Vibrational analysis Optical spectroscopy Basis Sets A large number of basis sets are supplied, and users are also able to define their own basis sets .HyperChem uses a simple text file format to describe basis sets, making users' modifications easy. Considerable flexibility in the choice of a basis set is available, including the ability to simply select a set of atoms with the mouse and assign a basis set to those atoms only. This makes it possible to have different basis sets assigned to different atoms, or even to select an atom and interactively assign a primitive s, p, d, sp, or spd shell to that atom with the user specified exponent for the shell. It is even possible to interactively select a set of atoms and have their nuclei treated as "ghost nuclei" - HyperChem uses the basis functions but neglects their nuclear interactions. Calculations Single-point correlation energy calculations at the MP2 level can also be performed. The ab initio calculations are completely integrated into HyperChem's usual graphical support, allowing users to visualize orbital energy plots, electron densities, IR and UV spectras, etc. Chemical reactions can be explored by performing molecular dynamics with forces computed by ab initio methods. And More! Commands have been added to the scripting language to allow all the added functions to be run by scripts, or under the control of external software such as Visual Basic or Microsoft Excel via dynamic data exchange (DDE). As usual, Hypercube supplies documentation which not only shows users how to operate the software, but also provides a solid introduction to the theory of ab initio calculations. This makes HyperChem an extremely useful educational tool. Release 4.5 of HyperChem also allows users to explore isotope effects in vibrational analysis and input ChemDraw files. For comparison with other platforms and programs, a minimal basis set wavefunction calculation for a glycine dipeptide zwitterion takes about 3 minutes on a 90Mhz Pentium computer. New in Release 5:
Also available, HyperChem for the SGI (inquire). |
