Some Common Operations in HyperChem

Before you begin working with Hyperchem, you should set some preferences in the program. First, click onSelect on the menu bar, then click on Multiple Selections. This option allows you to select more than one atom at a time. Next, click on Display on the menu bar, click on Labels… and click on the radio button next to Symbol under “Atoms”. This option turns on the display of the atomic symbol for each atom in the display window.

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Drawing Bonds

Click on the Drawing Tool button. Click and drag in the display window. To draw a bond to an existing atom, click on the atom and drag.

Deleting Atoms or Bonds

Click on the Drawing Tool button. Right-click on any atom or bond to delete it.

Changing the Atom Type

Double-click on the Drawing Tool button (a Periodic Table will appear). Select the element by clicking on it in the Periodic Table. Close the Periodic Table window. Click on any atom in the display window to change the atom to the currently selected atom type.

Changing the Number of Bonds Between Two Atoms

Click on the Drawing Tool icon. Single, double, triple and resonance-type bonds can be selected by repeated clicking on the bond.

Model Building a Structure

Double-click on the Selection Tool button. Note that this will also add hydrogen atoms to any atoms that do not have a completely filled valence.

• Note: the “model build” operation will perform a “quick” optimization of the molecular geometry based on standard bond lengths and bond angles. You should always “model build” your structure before starting any higher level geometry optimizations (such as AM1).

Selecting Atoms

First, click on Select on the Toolbar (a menu will appear). If there is no check mark next to Multiple Selections, click on Multiple Selections. Then, click on the Selection Tool button. Click on the atoms to be selected (the selected atoms will become highlighted). To select all atoms in the display window, double-click in any blank area of the workspace.

• Note: you must “deselect” any selected atoms before starting a geometry optimization.

Deselecting Atoms

Click on the Selection Tool button. Right-click on the atoms to be deselected. To deselect all selected atoms, right-click in any blank area of the workspace.

Rotating a Molecule

Click on either the XY Rotation Tool or the Z Rotation Tool button. Click and drag in the workspace to rotate the molecule.

Moving a Molecule

Click on the XY Translation Tool button. Click and drag in the workspace to move the molecule.

Resizing

Click on the Zoom Tool button. Click and drag in the workspace to resize the molecule.

Changing the Display Type

Click on Display on the menu bar (a menu will appear). Click on Rendering… Select the type of display for the molecule.

Setting a Bond Length

Click on the Selection Tool button. Click on the two atoms which are bonded (the two atoms and the bond between them will become highlighted). Click on Edit on the menu bar. Click on Set Bond Length…, and enter a value (in Angstroms) for the bond length. Click OK.

Setting a Bond Angle

Click on the Selection Tool button. Click on the three atoms which define the bond angle (the three atoms and the bonds between them will become highlighted). Click on Edit on the menu bar. Click on Set Bond Angle…, and enter a value (in degrees) for the bond angle. Click OK.

Setting a Bond Torsion Angle

Click on the Selection Tool button. Click on the four atoms which define the bond torsion angle (the four atoms and the bonds between them will become highlighted). Click on Edit on the menu bar. Click on Set Bond Torsion…, and enter a value (in degrees) for the bond torsion angle. Click OK.

Optimizing the Geometry of a Molecule Using the Molecular Mechanics Method (MM+)

Click on Setup on the menu bar. Click on Molecular Mechanics… Under “Method”, click on the radio button next to “MM+”. Click OK.

Click on Compute on the menu bar. Click on Geometry Optimization… Click on OK.

Optimizing the Geometry of a Molecule Using a Semi-Empirical Method

Click on Setup on the menu bar. Click on Semi-empirical… Under “Methods”, click on the radio button next to the method to be used (e.g., “AM1″). Click on the “Options…” button. Under “Charge and Spin”, enter the “Total charge” of the molecule or ion. Click OK. Click OK.

Click on Compute on the menu bar. Click on Geometry Optimization… Click on OK.

Calculating the Energy of a Molecule For a Specific Geometry Using a Semi-Empirical Method (Single Point)

Click on Setup on the menu bar. Click on Semi-empirical… Under “Methods”, click on the radio button next to the method to be used (e.g., “AM1″). Click on the “Options…” button. Under “Charge and Spin”, enter the “Total charge” of the molecule or ion. Click OK. Click OK.

Click on Compute on the menu bar. Click on Single Point. Click on OK.

Calculating the Orbitals of a Molecule Using a Semi-Empirical Method

Click on Compute on the menu bar. Click on Orbitals… In the orbital energy diagram, click on the orbital to be plotted (the line representing the orbital will be highlighted). Click on “Plot”.

• Note: you must perform a “single point” calculation before you can calculate the orbitals of the molecule.

Displaying the Values for Bond Lengths, Bond Angles and Bond Torsion Angles

Click on the Selection Tool button. Click on the two, three or four atoms which define the bond length, bond angle or bond torsion angle, respectively. The value (in Angstroms or degrees) will be displayed on the Status Line.

Calculating the Vibrational Spectrum of a Molecule Using a Semi-Empirical Method

Click on Compute on the menu bar. Click on Vibrations. When the calculation has finished, click onCompute on the menu bar again and then click on Vibrational Spectrum… Click on any of the lines at the top of the “Vibrational Spectrum” window (the line will become highlighted) to display the frequency of that vibration.

To animate a particular vibration, first make sure there is a check mark next to Animate vibrations in the “Vibrational Spectrum” window (if there is not, click on the check box). Then, click on the line at the top of the “Vibrational Spectrum” window which represents the vibration that you want to animate (the line will become highlighted). Click OK. Click Cancel on the menu bar to stop the animation.

Source: kasmui.blog.com

Chemistry Application Download Link

When I was browsing, I found some websites that provide download link for lot of chemistry applications. Here some of them:

1. Quantum chemistry modelling software

2. Chemistry applications for Linux

3. Chemistry freeware

4. General chemistry program

5. Free chemistry program

I hope those links will be useful for whoever reading this post :)

HyperChem

HyperChem is a molecular modelling environment that unite 3D visualization and animation with quantum chemical calculations, molecular mechanics and dynamics. As per today, the latest version is HyperChem 8.0.10. The features on HyperChem are:

A Chemical Substituent Operation

HyperChem has the ability to create a three-dimensional molecular structure by just drawing it and applying the modal builder. This involves the usual chemical idea of chemical substituents, R. In HyperChem these substituents replace any selected Hydrogen atom. Thus H->R has become a standard operation for a variety of common R-groups, including Phenyl (Ph). It is expected that a near term release of HyperChem will even allow users to define their own R groups. In any event it is now easier and faster to create molecules from standard components. Starting with H2 or CP, for example, one could create any organic molecule with a few clicks rather than having to draw the whole molecule.

Calculation of Entropies and Free Energies
Calculating entropies, of course, requires more effort than just the "simple" energy. However, with the computation of vibrational and rotational spectra comes the possibility of computing the energy (E), entropy (S), and Helmholtz free energy (A=E-TS). Temperature is now a more fundamental quantity in HyperChem than before as are the thermodynamic quantities that depend on it.

Calculation of Heat Capacities
As with Energy, Entropy, and Free Energy, it is now possible to calculate Heat Capacities. These are now routinely computed along with the other thermodynamic quantities that depend upon the temperature.

Calculation of Zero-Point Energies

At zero degrees Kelvin, the energy is the dominant quantity of interest but does not only have an electronic component. Until now vibrational analysis has not reported the zero-point energy of vibration. These now are a part of any vibrational analysis.

Computation of Rate Constants

May molecular modeling programs have little to say about rate constants which are obviously an important quantity in chemistry. HyperChem makes a start at making reactivity a mainstream molecular modeling activity. While only computing rate constants using the simplest Transition State Theory it is a beginning towards being a fundamental component of the whole of chemistry rather than only what computational chemists are best at.

HyperChem computes partition functions for reactants A and B (in biomolecular reactions) or just A (in unimolecular reactions) and then computes the partition function for the Transition State. The input to these calculations are the structure of each of these species (created in HyperChem and then stored in HIN files) as well as the energy, and vibrational and rotational spectra of the species (created in HyperChem and then stored in EXT files).

These quantities can come from external third party packages as well (as described in the Third Party Interface Section above. The partition functions simply require the vibrational spectra (frequencies only) and rotatational spectra (moments of inertia only) from an EXT file created by HyperChem or elsewhere. A calculation of the rate constant as a function of temperature is then made and becomes available as a simple plot for placing into Power Point, etc.). In addition, the Arrhenius parameters can be extracted from the variation of the rate constant as a function of temperature. If desired, and the the corresponding energies are available for the products (not just the reactants and transition state), a plot of the energy of reactants, transition state, and products is available.

Computation of Equilibrium Constants

Since free energies are now available in HyperChem, a similar simple capability for calculating equilibrium constants as a function of temperature to that described for rate constants above is now available. The Helmholtz free energy A as a function of temperature is calculated from the electronic, vibrational, rotational, and translational components of the energy and entropy. The equilibrium constant for the reaction is then just the appropriate exp(- A/kT).

New Semi-empirical Method, RM1

The RM1 method is essentially an extensive re-parameterization of AM1. The results given by this method are expected to be better than those from AM1 or PM3.   The elements available are still only those that have been available with AM1 and unfortunately are still a relatively small set of atoms not including any transition metals.

Since free energies are now available in HyperChem, a similar simple capability for calculating equilibrium constants as a function of temperature to that described for rate constants above is now available. The Helmholtz free energy A as a function of temperature is calculated from the electronic, vibrational, rotational, and translational components of the energy and entropy. The equilibrium constant for the reaction is then just the appropriate exp(- A/kT).

Further Capabilities for MP2 Perturbation Energies

HyperChem has had available the computation of second-order correlation energies via the MP2 method. These are given a more prominent position in that any single point energy used, for example, by optimization, by potential plots, by rate constants, by molecular dynamics, etc., can now include the MP2 energy as well as the SCF energy. Previously, the check box for MP2 only showed that correlation energy as a property of the SCF calculation. Now that check box will use SCF MP2 results as the energy for subsequent computations. The MP2 result is considerably more reliable in many circumstances that SCF Hartree-Fock result and with advances in desktop computation speeds it seems appropriate to give MP2 a more prominent role.

The MP2 gradients, unfortunately are still computed numerically rather than analytically so these calculations are certainly not as fast as pure SCF calculations. One also should be conscious that the check box for MP2 will be used universally and slow down what previously might have been only SCF computations.

Separation of Configuration from Single Points

In a corresponding move to that for MP2 replacing SCF, a more prominent role for Configuration Interaction (CI) is expected in the future. In addition, CI was somewhat hidden in nested dialog boxes for Single Point calculations so that it was not always clear that CI was turned on. This option has now been made explicit with a Single Point CI menu item for clarity and future additions to this capability.

Display of Line Width Envelopes for IR and UV Spectra

HyperChem has performed IR and UV computations for many years. These spectra are displayed as stick drawings with individual intensities shown on the plot. The similar display of NMR spectra over the years has had "line width" capability of assigning a line width to each spectral line (the same line width for each frequency) and then summing them up to obtain an envelope that simulates what the experimental spectrum might look like. No line widths are computed - only a slider is made available to simulate increasing global line widths. Release 8 makes this same facility available for IR and UV spectra that has been available for NMR spectra. The line width is initially set to zero but a simple slider changes the appearance of the spectra to the satisfaction of the user.

Separation of MM-QM Capabilities from Current Selection

HyperChem for many years (the first wide spread implementation) had the capability of performing MM-QM calculations, i.e. calculations that on a large system treat part of the molecule with quantum mechanics (QM) and the remaining part of the molecule with molecular mechanics (MM). This capability operated via the current selection. If a subset selection was invoked at the time a quantum calculation was requested, the selected portion of the molecule was treated via quantum mechanics and the remaining portion via molecular mechanics. That is, the charges of the MM par were included in the core Hamiltonian of the quantum part.

While convenient, this use of "current selection" has proved limiting in that "current selection" meant something different during pure MM calculations. There it meant atoms that were allowed to move rather than remain fixed in space. This also made it impossible to fix atoms in space during quantum calculations.

Vibrational Analysis for Molecular Mechanics
It is available across the board with any of the "Energy Engines" available in HyperChem. With vibrational analysis and rotational moments of inertia, it is now possible to calculate Entropies and Free Energies across the board as well.
It may still be possible to spend lots of computational time performing vibrational analysis, particularly for large molecules since second derivatives are still not computed analytically for any of the methods. It is a goal for HyperChem in the future to speed up those methods that depend upon second derivatives of the energy such as vibrational analysis. This ought to be, in principal, relatively easy for molecular mechanics.

Applied Electric Fields for Molecular Mechanics
Electric fields are now available in the workspace for any of the "Compute Engines". Previously, the ability to apply an electric field was restricted to quantum mechanical methods. In molecular mechanics, the electric field interacts with the atom charges on each of the atoms. For MM , which has options for either atom charges or bond dipoles, the electric field interacts only with the atomic charges.

Source: Hypercube

Terms Related to Computational Chemistry

1. Ab initio: computational chemistry methods based on quantum chemistry
2. Born-Oppenheimer approximation: an assumption that the electronic motion and the nuclear motion in molecules can be separated 

3. Cheminformatics: the use of computer and informational techniques, applied to a range of problems in the field of chemistry
4. Comparative molecular field analysis (CoMFA): a 3D QSAR technique based on data from known active molecules
5. Computational chemistry: a branch of chemistry that uses principles of computer science to assist in solving chemical problems

6. Computer science: the study of the theoretical foundations of information and computation. It also includes practical techniques for their implementation and application in computer systems

7. Density functional theory (DFT): quantum mechanical modelling method used in physics and chemistry to investigate the electronic structure of many-body systems

8. Hartree-Fock: an approximate method for the determination of the ground-state wave function and ground-state energy of a quantum many-body system

9. Hybrid functional: a class of approximations to the exchange-correlation energy functional in density functional theory that incorporate a portion of exact exchange from Hartree-Fock theory with exchange and correlation from other sources
10. Linear combination of atomic orbitals (LCAO): a quantum superposition of atomic orbitals and a technique for calculating molecular orbitals 

11. Molecular dynamics: a computer simulation of physical movements of atoms and molecules
12. Molecular mechanics: an empirical method used to state potential energy from molecules as a function of geometric variable
13. Molecular modelling: all theoretical methods and computational techniques used to model or mimic the behaviour of molecules
14. Monte Carlo: a class of computational algorithms that rely on repeated random sampling to compute their results
15. Mulliken population analysis: estimating partial atomic charges from calculations carried out by the methods of computational chemistry
16. Quantitative structure-activity relationship (QSAR): the process by which chemical structure is quantitatively correlated with a well defined process, such as chemical reactivity

17. Post-Hartree-Fock: the set of methods developed to improve on the Hartree-Fock, or self-consistent field method

18. Quantum chemistry composite: computational chemistry methods that aim for high accuracy by combining the results of several calculations
19. Slater-type orbitals: functions used as atomic orbitals in the linear combination of atomic orbitals molecular orbital method
20. Statistic mechanics: the mathematical way to extrapolate the thermodinamic character of materials relatively


Translator: Wanda Septa (me)
Source: Centre for Molecular and Biomolecular Informatics, Faijal Chemistry, Wikipedia

How to Do a Computational Research Project?

When using computational chemistry to answer a chemical question, the obvious problem is that you need to know how to use the software. The problem that is missed is that you need to know how good the answer is going to be. Here is a check list to follow.

What do you want to know? How accurately? Why? If you can't answer these questions, then you don't even have a research project yet.

How accurate do you predict the answer will be? In analytical chemistry, you do a number of identical measurements then work out the error from a standard deviation. With computational experiments, doing the same thing should always give exactly the same result. The way that you estimate your error is to compare a number of similar computations to the experimental answers. There are articles and compilations of these studies. If none exist, you will have to guess which method should be reasonable, based on it's assumptions then do a study yourself, before you can apply it to you unknown and have any idea how good the calculation is. When someone just tells you off the top of their head what method to use, they either have a fair amount of this type of information memorized, or they don't know what they are talking about. Beware of someone who tells you a given program is good just because it is the only one they know how to use, rather than the basing their answer on the quality of the results.

How long do you expect it to take? If the world were perfect, you would tell your PC (voice input of course) to give you the exact solution to the Schrödinger equation and go on with your life. However, often ab initio calculations would be so time consuming that it would take a decade to do a single calculation, if you even had a machine with enough memory and disk space. However, a number of methods exist because each is best for some situation. The trick is to determine which one is best for your project. Again, the answer is to look into the literature and see how long each takes. If the only thing you know is how a calculation scales, do the simplest possible calculation then use the scaling equation to estimate how long it will take to do the sort of calculation that you have predicted will give the desired accuracy.

What approximations are being made? Which are significant? This is how you avoid looking like a complete fool, when you successfully perform a calculation that is complete garbage. An example would be trying to find out about vibrational motions that are very anharmonic, when the calculation uses a harmonic oscillator approximation.

Once you have finally answered all of these questions, you are ready to actually do a calculation. Now you must determine what software is available, what it costs and how to use it. Note that two programs of the same type (i.e. ab initio) may calculate different properties, so you have to make sure the program does exactly what you want.

When you are learning how to use a program, you may try to do dozens of calculations that will fail because you constructed the input incorrectly. Do not use your project molecule to do this. Make all your mistakes with something really easy, like a water molecule. That way you don't waste enormous amounts of time.

Source: Computational Chemistry List

Jmol

Jmol is an open-source Java viewer for three-dimensional chemical structures. It is cross-platform, running on Windows, Mac OS X, and Linux/Unix systems. 

Features:

- Multi-language

- Supports all major web browsers: Internet Explorer, Mozilla and Firefox, Safari, Google Chrome, Opera, etc.

- High-performance 3D rendering with no hardware requirements

- Animations

- Surfaces

- Vibrations

- Reactions

- Orbitals

- Support for unit cell and symmetry operations

- Schematic shapes for secondary structures in biomolecules

- Measurements (distance, angle, torsion angle)

You can get the latest version of Jmol here :)

Source: SourceForge

JChemPaint

JChemPaint is a Java program for drawing 2D chemical structures. It is open source and free software. Since it is written on Java, it runs on any computing platform and operating system for which a Java Virtual Machine has been implemented (like Linux, Windows, etc). If your system does not have Java Virtual Machine, you can get it here

Features:

- Drawing and deletion of single, double, triple and stereo bonds

- Colouring of atom types, and other rendering settings

- Editing of atomic charges, isotopes and hydrogen count.

- Loading and saving of structures in Chemical Markup Language (CML) and as MDL MOL files and SDF files (loading only).

- Automated Structure Layout, also known as Structure Diagram Generation.

- Loading structures from the Internet using CAS or NSC number.

- Normalization of structures, currently limited to aromaticity detection.

- Saving bitmap pictures of the structures.

- Saving structures as graphics (PNG, BMP, Scalable Vector Graphics (SVG)).

- Postscript printing

- Translated into several languages: Dutch, French, German, Polish, Portuguese and Spanish.

You can get it here :)

Source: SourceForge