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55-779: WSA may refer to: van der Waals surface area War Shipping Administration , part of the US government responsible for building cargo ships in World War II Weapon storage area , a maximum security part of an ammunition depot where nuclear weapons are stored West Allerton railway station , Liverpool, England (station code) Western Sahara Authority Western Soccer Alliance Western Sydney Airport , an international airport currently under construction Wilderness study area Windows Socket API , Microsoft's implementation of Berkeley sockets Windows Subsystem for Android ,

110-522: 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 performed in the late 1950s. The first configuration interaction calculations were performed in Cambridge on the EDSAC computer in

165-595: A liquid-gas equation of state that accounted for the non-zero volume of atoms and molecules, and on their exhibiting an attractive force when they interacted (theoretical constructions that also bear his name). van der Waals surfaces are therefore a tool used in the abstract representations of molecules, whether accessed, as they were originally, via hand calculation, or via physical wood/plastic models, or now digitally, via computational chemistry software. Practically speaking, CPK models , developed by and named for Robert Corey , Linus Pauling , and Walter Koltun , were

220-429: A Hamiltonian. Yet, the term "empirical methods", or "empirical force fields" is usually used to describe molecular mechanics. In many cases, large molecular systems can be modeled successfully while avoiding quantum mechanical calculations entirely. Molecular mechanics simulations, for example, use one classical expression for the energy of a compound, for instance, the harmonic oscillator . All constants appearing in

275-503: A compatibility layer for Android apps in Windows 11 Women's Squash Association , the governing body for the women's professional squash circuit and the women's world rankings Worker Student Alliance , a division of Students for a Democratic Society, sometimes referred to as SDS-WSA Workers' Solidarity Alliance World Service Authority World Soundtrack Awards World Summit Award WSA Process , Wet gas Sulphuric Acid

330-418: A hybrid approach, combining quantum mechanics for a portion of the system with classical mechanics for the remainder, quantum computational chemistry exclusively uses quantum computing methods to represent and process information, such as Hamiltonian operators. Conventional computational chemistry methods often struggle with the complex quantum mechanical equations, particularly due to the exponential growth of

385-500: A level of theory (the method) and a basis set. A basis set consists of functions centered on the molecule's atoms. These sets are then used to describe molecular orbitals via the linear combination of atomic orbitals (LCAO) molecular orbital method ansatz . A common type of ab initio electronic structure calculation is the Hartree–Fock method (HF), an extension of molecular orbital theory , where electron-electron repulsions in

440-412: A molecular dynamics simulation is a trajectory that describes how the position and velocity of particles varies with time. The phase point of a system described by the positions and momenta of all its particles on a previous time point will determine the next phase point in time by integrating over Newton's laws of motion. Monte Carlo (MC) generates configurations of a system by making random changes to

495-467: A quantum system's wave function. Quantum computational chemistry addresses these challenges using quantum computing methods , such as qubitization and quantum phase estimation , which are believed to offer scalable solutions. Qubitization involves adapting the Hamiltonian operator for more efficient processing on quantum computers, enhancing the simulation's efficiency. Quantum phase estimation, on

550-483: A series of post-Hartree–Fock methods and combine the results. These methods are called quantum chemistry composite methods . After the electronic and nuclear variables are separated within the Born–Oppenheimer representation), the wave packet corresponding to the nuclear degrees of freedom is propagated via the time evolution operator (physics) associated to the time-dependent Schrödinger equation (for

605-522: A single atom or molecules are arrived at by dividing the macroscopically determined volumes by the Avogadro constant . The various methods give radius values which are similar, but not identical—generally within 1–2  Å (100–200  pm ). Useful tabulated values of van der Waals radii are obtained by taking a weighted mean of a number of different experimental values, and, for this reason, different tables will be seen to present different values for

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660-429: A surface might reside for the molecule based on the hard cutoffs of van der Waals radii for individual atoms, and it represents a surface through which the molecule might be conceived as interacting with other molecules. Also referred to as a van der Waals envelope, the van der Waals surface is named for Johannes Diderik van der Waals , a Dutch theoretical physicist and thermodynamicist who developed theory to provide

715-722: A whole host of algorithms. 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, using valence bond theory . 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

770-409: Is a Wet Catalysis Process Web Services Addressing Voivodeship Administrative Court , Wojewódzki Sąd Administracyjny, referred to as WSA United Nations World Summit Awards Topics referred to by the same term [REDACTED] This disambiguation page lists articles associated with the title WSA . If an internal link led you here, you may wish to change the link to point directly to

825-400: Is a property directly related to the van der Waals radius , and is defined as the volume occupied by an individual atom, or in a combined sense, by all atoms of a molecule. It may be calculated for atoms if the van der Waals radius is known, and for molecules if its atoms radii and the inter-atomic distances and angles are known. As above, in simplest case, for a spherical monatomic gas, V w

880-541: Is a tool for analyzing catalytic systems without doing experiments. Modern electronic structure theory and density functional theory has allowed researchers to discover and understand catalysts . Computational studies apply theoretical chemistry to catalysis research. Density functional theory methods calculate the energies and orbitals of molecules to give models of those structures. Using these methods, researchers can predict values like activation energy , site reactivity and other thermodynamic properties. Data that

935-442: Is difficult to obtain experimentally can be found using computational methods to model the mechanisms of catalytic cycles. Skilled computational chemists provide predictions that are close to experimental data with proper considerations of methods and basis sets. With good computational data, researchers can predict how catalysts can be improved to lower the cost and increase the efficiency of these reactions. Computational chemistry

990-444: Is inadequate, and several configurations must be used. 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 full knowledge of

1045-469: Is often not perfect, identifying issues is often easier for calculated data than experimental. Databases also give public access to information for researchers to use. They contain data that other researchers have found and uploaded to these databases so that anyone can search for them. Researchers use these databases to find information on molecules of interest and learn what can be done with those molecules. Some publicly available chemistry databases include

1100-401: Is rigorously defined on first principles and then solved within an error margin that is qualitatively known beforehand. If numerical iterative methods must be used, 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). Ab initio methods need to define

1155-413: Is simply the computed volume of a sphere of radius equal to the van der Waals radius of the gaseous atom: For a molecule, V w is the volume enclosed by the van der Waals surface ; hence, computation of V w presumes ability to describe and compute a van der Waals surface. van der Waals volumes of molecules are always smaller than the sum of the van der Waals volumes of their constituent atoms, due to

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1210-453: Is to use higher order splitting. Usually, second order splitting is the most that is done because higher order splitting requires much more time to calculate and is not worth the cost. Higher order methods become too difficult to implement, and are not useful for solving differential equations despite the higher accuracy. Computational chemists spend much time making systems calculated with split operator technique more accurate while minimizing

1265-984: Is used in drug development to model potentially useful drug molecules and help companies save time and cost in drug development. The drug discovery process involves analyzing data, finding ways to improve current molecules, finding synthetic routes, and testing those molecules. Computational chemistry helps with this process by giving predictions of which experiments would be best to do without conducting other experiments. Computational methods can also find values that are difficult to find experimentally like pKa 's of compounds. Methods like density functional theory can be used to model drug molecules and find their properties, like their HOMO and LUMO energies and molecular orbitals. Computational chemists also help companies with developing informatics, infrastructure and designs of drugs. Aside from drug synthesis, drug carriers are also researched by computational chemists for nanomaterials . It allows researchers to simulate environments to test

1320-401: The Hartree–Fock method formalism, but make many approximations and obtain some parameters from empirical data. They were very important in computational chemistry from the 60s to the 90s, especially for treating large molecules where the full Hartree–Fock method without the approximations were too costly. The use of empirical parameters appears to allow some inclusion of correlation effects into

1375-669: The wave packet associated to the molecular geometry are: How a computational method solves quantum equations impacts the accuracy and efficiency of the method. The split operator technique is one of these methods for solving differential equations. In computational chemistry, split operator technique reduces computational costs of simulating chemical systems. Computational costs are about how much time it takes for computers to calculate these chemical systems, as it can take days for more complex systems. Quantum systems are difficult and time-consuming to solve for humans. Split operator methods help computers calculate these systems quickly by solving

1430-682: 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 to determine 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

1485-500: 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 ab initio calculations of molecular orbitals. Of these four programs, only Gaussian, now vastly 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 force field , were developed, primarily by Norman Allinger . One of

1540-544: The Reviews of Modern Physics. This paper focused largely on the "LCAO MO" approach (Linear Combination of Atomic Orbitals Molecular Orbitals). For many years, it was the second-most cited paper in that journal. A very detailed account of such use in the United Kingdom is given by Smith and Sutcliffe. The first ab initio Hartree–Fock method calculations on diatomic molecules were performed in 1956 at MIT, using

1595-564: The behavior of atomic and molecular systems under the framework of quantum mechanics, as defined by the Schrödinger equation. To obtain exact agreement with the experiment, it is necessary to include specific terms, some of which are far more important for heavy atoms than lighter ones. In most cases, the Hartree–Fock wave function occupies a single configuration or determinant. In some cases, particularly for bond-breaking processes, this

1650-416: The complete surface. A particularly important objective, called computational thermochemistry , is to calculate thermochemical quantities such as the enthalpy of formation to chemical accuracy. Chemical accuracy is the accuracy required to make realistic chemical predictions and is generally considered to be 1 kcal/mol or 4 kJ/mol. To reach that accuracy in an economic way, it is necessary to use

1705-421: The computational cost. Calculating methods is a massive challenge for many chemists trying to simulate molecules or chemical environments. Density functional theory (DFT) 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,

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1760-449: 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 performed. Theoretical chemists became extensive users of the early digital computers. One significant advancement was marked by Clemens C. J. Roothaan's 1951 paper in

1815-407: The effectiveness and stability of drug carriers. Understanding how water interacts with these nanomaterials ensures stability of the material in human bodies. These computational simulations help researchers optimize the material find the best way to structure these nanomaterials before making them. Databases are useful for both computational and non computational chemists in research and verifying

1870-464: The equations must be obtained beforehand from experimental data or ab initio calculations. The database of compounds used for parameterization, i.e. the resulting set of parameters and functions is called the force field , 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

1925-440: The fact that the interatomic distances resulting from chemical bond are less than the sum of the atomic van der Waals radii. In this sense, a van der Waals surface of a homonuclear diatomic molecule can be viewed as an pictorial overlap of the two spherical van der Waals surfaces of the individual atoms, likewise for larger molecules like methane, ammonia, etc. (see images). van der Waals radii and volumes may be determined from

1980-535: 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

2035-416: The first widely used physical molecular models based on van der Waals radii, and allowed broad pedagogical and research use of a model showing the van der Waals surfaces of molecules. Related to the title concept are the ideas of a van der Waals volume , V w , and a van der Waals surface area, abbreviated variously as A w , vdWSA, VSA, and WSA. A van der Waals surface area is an abstract conception of

2090-453: The following. 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 theory, with no inclusion of experimental data – are called ab initio methods . A theoretical approximation

2145-416: The full molecular Hamiltonian ). In the complementary energy-dependent approach, the time-independent Schrödinger equation is solved using the scattering theory formalism. The potential representing the interatomic interaction is given by the potential energy surfaces . In general, the potential energy surfaces are coupled via the vibronic coupling terms. The most popular methods for propagating

2200-483: The intended article. Retrieved from " https://en.wikipedia.org/w/index.php?title=WSA&oldid=1258158500 " Category : Disambiguation pages Hidden categories: Short description is different from Wikidata All article disambiguation pages All disambiguation pages Van der Waals surface area The van der Waals surface of a molecule is an abstract representation or model of that molecule, illustrating where, in very rough terms,

2255-483: The mechanical properties of gases (the original method, determining the van der Waals constant ), from the critical point (e.g., of a fluid), from crystallographic measurements of the spacing between pairs of unbonded atoms in crystals, or from measurements of electrical or optical properties (i.e., polarizability or molar refractivity ). In all cases, measurements are made on macroscopic samples and results are expressed as molar quantities. van der Waals volumes of

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2310-541: The methods. Primitive semi-empirical methods were designed even before, 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 . Sometimes, Hückel methods are referred to as "completely empirical" because they do not derive from

2365-578: The molecule are not specifically taken into account; only the electrons' average effect is included in the calculation. As the basis set size increases, the energy and wave function tend towards a limit called the Hartree–Fock limit. Many types of calculations begin with a Hartree–Fock calculation and subsequently correct for electron-electron repulsion, referred to also as electronic correlation . These types of calculations are termed post-Hartree–Fock methods. By continually improving these methods, scientists can get increasingly closer to perfectly predicting

2420-773: The other hand, assists in accurately determining energy eigenstates, which are critical for understanding the quantum system's behavior. While these techniques have advanced the field of computational chemistry, especially in the simulation of chemical systems, their practical application is currently limited mainly to smaller systems due to technological constraints. Nevertheless, these developments may lead to significant progress towards achieving more precise and resource-efficient quantum chemistry simulations. The computational cost and algorithmic complexity in chemistry are used to help understand and predict chemical phenomena. They help determine which algorithms/computational methods to use when solving chemical problems. This section focuses on

2475-404: The positions of its particles, together with their orientations and conformations where appropriate. It is a random sampling method, which makes use of the so-called importance sampling . Importance sampling methods are able to generate low energy states, as this enables properties to be calculated accurately. The potential energy of each configuration of the system can be calculated, together with

2530-428: 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. Molecular dynamics (MD) use either quantum mechanics , molecular mechanics or a mixture of both to calculate forces which are then used to solve Newton's laws of motion to examine the time-dependent behavior of systems. The result of

2585-410: The sub problems in a quantum differential equation . The method does this by separating the differential equation into two different equations, like when there are more than two operators. Once solved, the split equations are combined into one equation again to give an easily calculable solution. This method is used in many fields that require solving differential equations, such as biology . However,

2640-410: The surface area of atoms or molecules from a mathematical estimation, either computing it from first principles or by integrating over a corresponding van der Waals volume. In simplest case, for a spherical monatomic gas, it is simply the computed surface area of a sphere of radius equal to the van der Waals radius of the gaseous atom: The van der Waals volume , a type of atomic or molecular volume,

2695-634: The technique comes with a splitting error. For example, with the following solution for a differential equation. e h ( A + B ) {\textstyle e^{h(A+B)}} The equation can be split, but the solutions will not be exact, only similar. This is an example of first order splitting. e h ( A + B ) ≈ e h A e h B {\textstyle e^{h(A+B)}\approx e^{hA}e^{hB}} There are ways to reduce this error, which include taking an average of two split equations. Another way to increase accuracy

2750-501: 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 termed hybrid functional methods. Semi-empirical quantum chemistry methods are based on

2805-602: The usage of computer programs and additional mathematical skills in order to accurately model various chemical problems. 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. Historically, computational chemistry has had two different aspects: These aspects, along with computational chemistry's purpose, have resulted in

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2860-739: The validity of computational methods. Empirical data is used to analyze the error of computational methods against experimental data. Empirical data helps researchers with their methods and basis sets to have greater confidence in the researchers results. Computational chemistry databases are also used in testing software or hardware for computational chemistry. Databases can also use purely calculated data. Purely calculated data uses calculated values over experimental values for databases. Purely calculated data avoids dealing with these adjusting for different experimental conditions like zero-point energy. These calculations can also avoid experimental errors for difficult to test molecules. Though purely calculated data

2915-519: The values of other properties, from the positions of the atoms. QM/MM is a hybrid method that attempts to combine the accuracy of quantum mechanics with the speed of molecular mechanics. It is useful for simulating very large molecules such as enzymes . Quantum computational chemistry aims to exploit quantum computing to simulate chemical systems, distinguishing itself from the QM/MM (Quantum Mechanics/Molecular Mechanics) approach. While QM/MM uses

2970-423: The van der Waals radius of the same atom. As well, it has been argued that the van der Waals radius is not a fixed property of an atom in all circumstances, rather, that it will vary with the chemical environment of the atom. Computational chemistry Computational chemistry differs from theoretical chemistry , which involves a mathematical description of chemistry. However, computational chemistry involves

3025-774: Was first published in 1980. Computational chemistry has featured in several Nobel Prize awards, most notably in 1998 and 2013. Walter Kohn , "for his development of the density-functional theory", and John Pople , "for his development of computational methods in quantum chemistry", received the 1998 Nobel Prize in Chemistry. Martin Karplus , Michael Levitt and Arieh Warshel received the 2013 Nobel Prize in Chemistry for "the development of multiscale models for complex chemical systems". There are several fields within computational chemistry. These fields can give rise to several applications as shown below. Computational chemistry

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