tag:blogger.com,1999:blog-31679627029996909172014-10-04T20:07:57.497-07:00Computational ChemistryUmerhttp://www.blogger.com/profile/08695541556650316904noreply@blogger.comBlogger6125tag:blogger.com,1999:blog-3167962702999690917.post-12227893335574640202011-07-03T04:41:00.000-07:002011-07-03T04:41:27.434-07:00Computational chemistry<div dir="ltr" style="text-align: left;" trbidi="on"><h1 class="firstHeading" id="firstHeading">Computational chemistry</h1><div id="siteSub"><br /></div><b>Computational chemistry</b> is a branch of chemistry that uses principles of computer science to assist in solving chemical problems. It uses the results of theoretical chemistry, incorporated into efficient computer programs, to calculate the structures and properties of molecules and solids. Its necessity arises from the well-known fact that apart from relatively recent results concerning the hydrogen molecular ion (see references therein for more details), the quantum n-body problem cannot be solved analytically, much less in closed form. While its results normally complement the information obtained by chemical experiments, it can in some cases predict hitherto unobserved chemical phenomena. It is widely used in the design of new drugs and materials.<br />Examples of such properties are structure (i.e. the expected positions of the constituent atoms), absolute and relative (interaction) energies, electronic charge distributions, dipoles and higher multipole moments, vibrational frequencies, reactivity or other spectroscopic quantities, and cross sections for collision with other particles.<br />The methods employed cover both static and dynamic situations. In all cases the computer time and other resources (such as memory and disk space) increase rapidly with the size of the system being studied. That system can be a single molecule, a group of molecules, or a solid. Computational chemistry methods range from highly accurate to very approximate; highly accurate methods are typically feasible only for small systems. <i>Ab initio</i> methods are based entirely on theory from first principles. Other (typically less accurate) methods are called empirical or semi-empirical because they employ experimental results, often from acceptable models of atoms or related molecules, to approximate some elements of the underlying theory.</div>Umerhttp://www.blogger.com/profile/08695541556650316904noreply@blogger.com0tag:blogger.com,1999:blog-3167962702999690917.post-65688868518544607602011-07-03T04:39:00.000-07:002011-07-03T04:39:24.519-07:00History<div dir="ltr" style="text-align: left;" trbidi="on"><h2><span class="mw-headline" id="History">History</span></h2>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 <i>Introduction to Quantum Mechanics – with Applications to Chemistry</i>, Eyring, Walter and Kimball's 1944 <i>Quantum Chemistry</i>, Heitler's 1945 <i>Elementary Wave Mechanics – with Applications to Quantum Chemistry</i>, and later Coulson's 1952 textbook <i>Valence</i>, each of which served as primary references for chemists in the decades to follow.<br />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.<sup class="reference" id="cite_ref-0"><span>[</span>1<span>]</span></sup> The first <i>ab initio</i> 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.<sup class="reference" id="cite_ref-1"><span>[</span>2<span>]</span></sup> 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.<sup class="reference" id="cite_ref-2"><span>[</span>3<span>]</span></sup> By 1971, when a bibliography of <i>ab initio</i> calculations was published,<sup class="reference" id="cite_ref-3"><span>[</span>4<span>]</span></sup> the largest molecules included were naphthalene and azulene.<sup class="reference" id="cite_ref-4"><span>[</span>5<span>]</span></sup><sup class="reference" id="cite_ref-5"><span>[</span>6<span>]</span></sup> Abstracts of many earlier developments in <i>ab initio</i> theory have been published by Schaefer.<sup class="reference" id="cite_ref-6"><span>[</span>7<span>]</span></sup><br />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.<sup class="reference" id="cite_ref-7"><span>[</span>8<span>]</span></sup> These empirical methods were replaced in the 1960s by semi-empirical methods such as CNDO</div>Umerhttp://www.blogger.com/profile/08695541556650316904noreply@blogger.com0tag:blogger.com,1999:blog-3167962702999690917.post-39515927280552437882011-07-03T04:36:00.001-07:002011-07-03T04:36:15.218-07:00Fields of application<div dir="ltr" style="text-align: left;" trbidi="on"><h2><span class="mw-headline" id="Fields_of_application">Fields of application</span></h2>The term <i>theoretical chemistry</i> may be defined as a mathematical description of chemistry, whereas <i>computational chemistry</i> is usually used when a mathematical method is sufficiently well developed that it can be automated for implementation on a computer. In theoretical chemistry, chemists, physicists and mathematicians develop algorithms and computer programs to predict atomic and molecular properties and reaction paths for chemical reactions. Computational chemists, in contrast, may simply apply existing computer programs and methodologies to specific chemical questions.<br />There are two different aspects to computational chemistry:<br /><ul><li>Computational studies can be carried out to find a starting point for a laboratory synthesis, or to assist in understanding experimental data, such as the position and source of spectroscopic peaks.</li><li>Computational studies can be used to predict the possibility of so far entirely unknown molecules or to explore reaction mechanisms that are not readily studied by experimental means.</li></ul>Thus, computational chemistry can assist the experimental chemist or it can challenge the experimental chemist to find entirely new chemical objects.<br />Several major areas may be distinguished within computational chemistry:<br /><ul><li>The prediction of the molecular structure of molecules by the use of the simulation of forces, or more accurate quantum chemical methods, to find stationary points on the energy surface as the position of the nuclei is varied.</li><li>Storing and searching for data on chemical entities (see chemical databases).</li><li>Identifying correlations between chemical structures and properties (see QSPR and QSAR).</li><li>Computational approaches to help in the efficient synthesis of compounds.</li><li>Computational approaches to design molecules that interact in specific ways with other molecules (e.g. drug design and catalysis).</li></ul></div>Umerhttp://www.blogger.com/profile/08695541556650316904noreply@blogger.com0tag:blogger.com,1999:blog-3167962702999690917.post-50780604936067483322011-07-03T04:34:00.001-07:002011-07-03T04:34:47.928-07:00Accuracy<div dir="ltr" style="text-align: left;" trbidi="on"><h2><span class="mw-headline" id="Accuracy">Accuracy</span></h2>The words <i>exact</i> and <i>perfect</i> do not appear here, as very few aspects of chemistry can be computed exactly. However, almost every aspect of chemistry can be described in a qualitative or approximate quantitative computational scheme.<br />Molecules consist of nuclei and electrons, so the methods of quantum mechanics apply. Computational chemists often attempt to solve the non-relativistic Schrödinger equation, with relativistic corrections added, although some progress has been made in solving the fully relativistic Dirac equation. In principle, it is possible to solve the Schrödinger equation in either its time-dependent or time-independent form, as appropriate for the problem in hand; in practice, this is not possible except for very small systems. Therefore, a great number of approximate methods strive to achieve the best trade-off between accuracy and computational cost.<br />Accuracy can always be improved with greater computational cost. Significant errors can present themselves in ab initio models comprising many electrons, due to the computational expense of full relativistic-inclusive methods. This complicates the study of molecules interacting with high atomic mass unit atoms, such as transitional metals and their catalytic properties. Present algorithms in computational chemistry can routinely calculate the properties of molecules that contain up to about 40 electrons with sufficient accuracy. Errors for energies can be less than a few kJ/mol. For geometries, bond lengths can be predicted within a few picometres and bond angles within 0.5 degrees. The treatment of larger molecules that contain a few dozen electrons is computationally tractable by approximate methods such as density functional theory (DFT).</div>Umerhttp://www.blogger.com/profile/08695541556650316904noreply@blogger.com0tag:blogger.com,1999:blog-3167962702999690917.post-42511423728755058802011-07-03T04:33:00.001-07:002011-07-03T04:33:25.046-07:00Methods<div dir="ltr" style="text-align: left;" trbidi="on"><h2><span class="mw-headline" id="Methods">Methods</span></h2>A single molecular formula can represent a number of molecular isomers. Each isomer is a local minimum on the energy surface (called the potential energy surface) created from the total energy (i.e., the electronic energy, plus the repulsion energy between the nuclei) 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.<br />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.</div>Umerhttp://www.blogger.com/profile/08695541556650316904noreply@blogger.com0tag:blogger.com,1999:blog-3167962702999690917.post-76125458643128893952011-07-03T04:32:00.000-07:002011-07-03T04:32:39.866-07:00Ab initio methods<div dir="ltr" style="text-align: left;" trbidi="on"><h3><span class="mw-headline" id="Ab_initio_methods"><i>Ab initio</i> methods</span></h3><div class="rellink relarticle mainarticle">Main article: Ab initio quantum chemistry methods</div>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 <i>ab initio methods</i>. 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 best that is possible with a finite word length on the computer, and within the mathematical and/or physical approximations made).<br /><div class="separator" style="clear: both; text-align: center;"><a class="image" href="http://en.wikipedia.org/wiki/File:Electron_correlation.png" style="clear: right; float: right; margin-bottom: 1em; margin-left: 1em;"><img alt="" class="thumbimage" height="173" src="http://upload.wikimedia.org/wikipedia/commons/thumb/7/7e/Electron_correlation.png/300px-Electron_correlation.png" width="300" /></a></div><div class="thumb tright"> <div class="thumbinner" style="width: 302px;"> <div class="thumbcaption"> <div class="magnify"><a class="internal" href="http://en.wikipedia.org/wiki/File:Electron_correlation.png" title="Enlarge"><img alt="" height="11" src="http://bits.wikimedia.org/skins-1.17/common/images/magnify-clip.png" width="15" /></a></div>Diagram illustrating various <i>ab initio</i> electronic structure methods in terms of energy. Spacings are not to scale.</div></div></div>The simplest type of <i>ab initio</i> electronic structure calculation is the Hartree–Fock (HF) 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.</div>Umerhttp://www.blogger.com/profile/08695541556650316904noreply@blogger.com0