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

ChemPup

ChemPup is a unique software system built from Puppy Linux with numerous useful chemistry programs

Features

Office Productivity:

OpenOffice.org-3.0 - full office productivity suite compatible with MS Office
JabRef - reference manager that syncs with OOO3
Firefox - web browser


Chemistry Programs:
GElemental - periodic table packed with information on each element

Nomen - simple nomenclature tool

JChemPaint - 2D chemical structure editor

JMol - 3D chemical structure viewer and force-field minimizer

Avogadro - 3D chemical structure builder with built in force-fields and molecular dynamics simulations

OpenBabel - chemical file-type converter

SciFinder Scholar - online scientific journal database (must have site.prf file added from school administrator)
ChemTool and GNotebook - spreadsheet templates with useful chemical equations, conversions, etc.

You can get ChemPup here (requires registration)

ChemPup is built from Puppy Linux 4.2.1 which is a very small, flexible, portable and complete operating system. How is it so different and useful?

1. ChemPup loads its entire system into RAM memory.

Although this process takes slightly longer to boot (depending on hardware configurations) it ultimately runs very fast on even low-spec (old) computers.

2. You don't ever have to install ChemPup on any computer.

No installation required. Simply boot from the ChemPup CD or USB flashdrive.

3. You may install ChemPup to a hard-drive partition (advanced).

This can be done in two ways, "full" or "frugal" installation options. A "frugal" install is recommended as it may be installed on a NTFS formatted hard-drive along side MS Windows. This does require some additional working knowledge and the user is STRONGLY ENCOURAGED to consult the www.puppylinux.org documentation before considering this option. The only significant advantage is that the CD or DVD is no longer needed at boot-up if ChemPup has been installed

Source: ChemToolBox

Linux Live USB Creator

One of the advantages of using Ubuntu is that we can "try" it without installing it on our PC. This system is usually called Live system, LiveCD (via CD), or LiveUSB (using USB). Imagine that we can use it on every PC (which is compatible, for sure). And what's even cooler is that we can access files on that PC. Cool, right?

To try Ubuntu via CD or flashdisc, we have to own Linux CD or we have to make our flashdisc to be Linux-bootable. How? On this post, I want to share about a program which can help you make your flashdisc to be Linux-bootable. The name of the program is LiLi, or Linux Live USB Creator. Check the tutorial below...

What are the things that you have to prepare?

1. Flashdisc for sure, with 1GB of minimum capacity. Move all of the data from the flashdisc, because it will be formatted later

2. LiLi USB program, you can download it here. Then install it on your Windows PC

3. ISO distro Linux file. Ubuntu, for example. You can download it here. Choose the server location whiches closer with your location, to make the download process faster.

The steps for creating Ubuntu-bootable flashdisc

Open the LiLi program, this is how it looks like...

STEP 1: CHOOSE YOUR KEY

Choose your flashdisc drive

STEP 2: CHOOSE A SOURCE

Choose the ISO/IMG/ZIP icon. Then select the ISO file that you have downloaded. LiLi will correct that ISO file and show a success message if there is no mistake

ISO/IMG/ZIP

ISO Ubuntu file or another Linux

Checking first, then ready

STEP 3: PRESISTENCE

For now, just skip this step, or let it on its default settings. What is presistence? Presistence will create virtual saving media on your flashdisc. The function is for saving file when using LiveUSB. Of course this presistence also needs more space in flashdisc

STEP 4: OPTIONS

Give checklist on "Hide created files on key" and "Format the key in FAT32". Uncheck the last option "Enable Launching LinuxLive in Windows"

Give checklist on the first and second options only

Before step 5:

Recheck all the settings, if needed, from the first

STEP 5: CREATE

Click the lightning icon to begin process. LiLi will give warning if there's something wrong, don't worry

WAIT UNTIL FINISH

After finished, there will be "Your LinuxLive key is now up and ready" notice


After you have done installing, you have to restart your PC or laptop and change the main booting into USB drive or CD room. If you do not change it, it will be back again to Windows. To enter the booting menu, press the F2, F5, or F9, depends on your PC or laptop. The process will take time around 10-15 minutes. Then, it is up to you whether you only want to try or install it. 

Source: Goji's blog, Ka Febri's blog
Translator: Wanda Septa Luthfiasari (myself)

Methods Used in Computational Chemistry

A single molecular formula can represent a number of molecular isomers. Each isomer is a local minimum on the energy surface created from the total energy as a function of the coordinates of all the nuclei. A stationary point is a geometry such that the derivative of the energy with respect to all displacements of the nuclei is zero. A local (energy) minimum is a stationary point where all such displacements lead to an increase in energy. The local minimum that is lowest is called the global minimum and corresponds to the most stable isomer. If there is one particular coordinate change that leads to a decrease in the total energy in both directions, the stationary point is a transition structure and the coordinate is the reaction coordinate. This process of determining stationary points is called geometry optimization.

The determination of molecular structure by geometry optimization became routine only after efficient methods for calculating the first derivatives of the energy with respect to all atomic coordinates became available. Evaluation of the related second derivatives allows the prediction of vibrational frequencies if harmonic motion is estimated. More importantly, it allows for the characterization of stationary points. The frequencies are related to the eigenvalues of the Hessian matrix, which contains second derivatives. If the eigenvalues are all positive, then the frequencies are all real and the stationary point is a local minimum. If one eigenvalue is negative (i.e., an imaginary frequency), then the stationary point is a transition structure. If more than one eigenvalue is negative, then the stationary point is a more complex one, and is usually of little interest. When one of these is found, it is necessary to move the search away from it if the experimenter is looking solely for local minima and transition structures.

The total energy is determined by approximate solutions of the time-dependent Schrödinger equation, usually with no relativistic terms included, and by making use of the Born–Oppenheimer approximation, which allows for the separation of electronic and nuclear motions, thereby simplifying the Schrödinger equation. This leads to the evaluation of the total energy as a sum of the electronic energy at fixed nuclei positions and the repulsion energy of the nuclei. A notable exception are certain approaches called direct quantum chemistry, which treat electrons and nuclei on a common footing. Density functional methods and semi-empirical methods are variants on the major theme. For very large systems, the relative total energies can be compared using molecular mechanics. The ways of determining the total energy to predict molecular structures are:

1. Ab Initio methods

The programs used in computational chemistry are based on many different quantum-chemical methods that solve the molecular Schrödinger equation associated with the molecular Hamiltonian. Methods that do not include any empirical or semi-empirical parameters in their equations – being derived directly from theoretical principles, with no inclusion of experimental data – are called ab initio methods. This does not imply that the solution is an exact one; they are all approximate quantum mechanical calculations. It means that a particular approximation is rigorously defined on first principles (quantum theory) and then solved within an error margin that is qualitatively known beforehand. If numerical iterative methods have to be employed, the aim is to iterate until full machine accuracy is obtained

The simplest type of ab initio electronic structure calculation is the Hartree–Fock scheme, an extension of molecular orbital theory, in which the correlated electron–electron repulsion is not specifically taken into account; only its average effect is included in the calculation. As the basis set size is increased, the energy and wave function tend towards a limit called the Hartree–Fock limit. Many types of calculations (known as post-Hartree–Fock methods) begin with a Hartree–Fock calculation and subsequently correct for electron–electron repulsion, referred to also as electronic correlation. As these methods are pushed to the limit, they approach the exact solution of the non-relativistic Schrödinger equation. In order to obtain exact agreement with experiment, it is necessary to include relativistic and spin orbit terms, both of which are only really important for heavy atoms. In all of these approaches, in addition to the choice of method, it is necessary to choose a basis set. This is a set of functions, usually centered on the different atoms in the molecule, which are used to expand the molecular orbitals with the LCAO ansatz. Ab initio methods need to define a level of theory (the method) and a basis set.

The Hartree–Fock wave function is a single configuration or determinant. In some cases, particularly for bond breaking processes, this is quite inadequate, and several configurations need to be used. Here, the coefficients of the configurations and the coefficients of the basis functions are optimized together.

The total molecular energy can be evaluated as a function of the molecular geometry; in other words, the potential energy surface. Such a surface can be used for reaction dynamics. The stationary points of the surface lead to predictions of different isomers and the transition structures for conversion between isomers, but these can be determined without a full knowledge of the complete surface

2. Density functional methods

Density functional theory methods are often considered to be ab initio methods for determining the molecular electronic structure, even though many of the most common functionals use parameters derived from empirical data, or from more complex calculations. In DFT, the total energy is expressed in terms of the total one-electron density rather than the wave function. In this type of calculation, there is an approximate Hamiltonian and an approximate expression for the total electron density. DFT methods can be very accurate for little computational cost. Some methods combine the density functional exchange functional with the Hartree–Fock exchange term and are known as hybrid functional methods.

3. Semi-empirical and empirical methods

Semi-empirical quantum chemistry methods are based on the Hartree–Fock formalism, but make many approximations and obtain some parameters from empirical data. They are very important in computational chemistry for treating large molecules where the full Hartree–Fock method without the approximations is too expensive. The use of empirical parameters appears to allow some inclusion of correlation effects into the methods.

Semi-empirical methods follow what are often called empirical methods, where the two-electron part of the Hamiltonian is not explicitly included. For π-electron systems, this was the Hückel method proposed by Erich Hückel, and for all valence electron systems, the extended Hückel method proposed by Roald Hoffmann.

4. Molecular mechanics

In many cases, large molecular systems can be modeled successfully while avoiding quantum mechanical calculations entirely. Molecular mechanics simulations, for example, use a single classical expression for the energy of a compound, for instance the harmonic oscillator. All constants appearing in the equations must be obtained beforehand from experimental data or ab initio calculations.

The database of compounds used for parameterization is crucial to the success of molecular mechanics calculations. A force field parameterized against a specific class of molecules, for instance proteins, would be expected to only have any relevance when describing other molecules of the same class.

These methods can be applied to proteins and other large biological molecules, and allow studies of the approach and interaction (docking) of potential drug molecules

5. Methods for solids

Computational chemical methods can be applied to solid state physics problems. The electronic structure of a crystal is in general described by a band structure, which defines the energies of electron orbitals for each point in the Brillouin zone. Ab initio and semi-empirical calculations yield orbital energies; therefore, they can be applied to band structure calculations. Since it is time-consuming to calculate the energy for a molecule, it is even more time-consuming to calculate them for the entire list of points in the Brillouin zone.

Source: Wikipedia

Computational Chemistry Predicts Flu Mutations

Researchers in the US have shown how it might be possible to use computational chemistry to predict which mutations in a key influenza virus protein could lead to dangerous new strains of the disease.

Haemagglutinin is a protein which influenza viruses use to bind to specific sugar molecules on the surface of the host cell. It is thought that the more tightly the haemagglutinin binds, the more infective the virus could be. The avian influenza virus, for example, has a particular haemagglutinin that binds to sugar molecules found in cells in the upper respiratory tract of birds. These sugars are slightly different to those found in the cells of the human upper respiratory tract, but if bird flu haemagglutinin mutated in a way that favoured stronger binding to the 'human' sugar, it could result in a strain of the virus that could be more easily transmitted between humans. 

However, it is not known which mutations in the viral protein might cause this stronger binding. Now, Peter Kasson and colleagues at the University of Stanford in California have shown how molecular dynamics simulations might provide useful clues about which amino acids in the protein are important for binding.

Using data from x-ray crystallography of haemagglutinin bound to the bird-type sugar, the researchers carried out a series of molecular dynamics simulations to determine which amino acids in the protein had most influence on the binding event. They combined this information with data on the sequence of avian influenza haemagglutinin to pinpoint potential sites of mutation in the DNA that could result in the relevant amino acids being altered - and therefore have a possible impact on the binding.

Limited experimental data do exist which suggest that the predictive method could work, but Kasson concedes that more experimental work is needed to confirm that the method is accurate. 'Mutations that change the binding specificity from bird-type sugars to human-type sugars could be a high-risk mutation for human-to-human transmission,' Kasson says. 'If we can predict these mutations in advance it would give us much better data for surveillance and control.'

Peter Coombs, an expert on the influenza virus at the National Institute of Medical Research in the UK, says 'If computer simulations can predict mutations that might result in the virus binding more strongly to the host cell then we can create these mutations in the lab and test them.' This would provide better insights into the interaction of haemagglutinin and cell surface ligands. 'It is an interesting approach and if it comes to fruition it could be very useful. However, a lot more experimental work is needed to confirm that the method can provide useful predictions.'

Part of the haemagglutinin head with a small sugar molecule in orange. The mutation sites most strongly predicted to destabilise ligand binding by haemagglutinin are shown in yellow

Source: RSC

History of Computational Chemistry

Building on the founding discoveries and theories in the history of quantum mechanics, the first theoretical calculations in chemistry were those of Walter Heitler and Fritz London in 1927. The books that were influential in the early development of computational quantum chemistry include Linus Pauling and E. Bright Wilson's 1935 Introduction to Quantum Mechanics – with Applications to Chemistry, Eyring, Walter and Kimball's 1944 Quantum Chemistry, Heitler's 1945 Elementary Wave Mechanics – with Applications to Quantum Chemistry, and later Coulson's 1952 textbook Valence, each of which served as primary references for chemists in the decades to follow.

With the development of efficient computer technology in the 1940s, the solutions of elaborate wave equations for complex atomic systems began to be a realizable objective. In the early 1950s, the first semi-empirical atomic orbital calculations were carried out. Theoretical chemists became extensive users of the early digital computers. A very detailed account of such use in the United Kingdom is given by Smith and Sutcliffe. The first ab initio Hartree–Fock calculations on diatomic molecules were carried out in 1956 at MIT, using a basis set of Slater orbitals. For diatomic molecules, a systematic study using a minimum basis set and the first calculation with a larger basis set were published by Ransil and Nesbet respectively in 1960. The first polyatomic calculations using Gaussian orbitals were carried out in the late 1950s. The first configuration interaction calculations were carried out in Cambridge on the EDSAC computer in the 1950s using Gaussian orbitals by Boys and coworkers. By 1971, when a bibliography of ab initio calculations was published, the largest molecules included were naphthalene and azulene. Abstracts of many earlier developments in ab initio theory have been published by Schaefer

In 1964, Hückel method calculations (using a simple linear combination of atomic orbitals (LCAO) method for the determination of electron energies of molecular orbitals of π electrons in conjugated hydrocarbon systems) of molecules ranging in complexity from butadiene and benzene to ovalene, were generated on computers at Berkeley and Oxford. These empirical methods were replaced in the 1960s by semi-empirical methods such as CNDO

In the early 1970s, efficient ab initio computer programs such as ATMOL, GAUSSIAN, IBMOL, and POLYAYTOM, began to be used to speed up ab initio calculations of molecular orbitals. Of these four programs, only GAUSSIAN, now massively expanded, is still in use, but many other programs are now in use. At the same time, the methods of molecular mechanics, such as MM2, were developed, primarily by Norman Allinger

One of the first mentions of the term "computational chemistry" can be found in the 1970 book Computers and Their Role in the Physical Sciences by Sidney Fernbach and Abraham Haskell Taub, where they state "It seems, therefore, that 'computational chemistry' can finally be more and more of a reality." During the 1970s, widely different methods began to be seen as part of a new emerging discipline of computational chemistry. The Journal of Computational Chemistry was first published in 1980.


Source: Wikipedia