1.
Molecule geometry
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Molecular geometry is the three-dimensional arrangement of the atoms that constitute a molecule. It determines several properties of a substance including its reactivity, polarity, phase of matter, color, magnetism and biological activity. The angles between bonds that an atom forms depend only weakly on the rest of molecule, i. e. they can be understood as approximately local, the molecular geometry can be determined by various spectroscopic methods and diffraction methods. IR, microwave and Raman spectroscopy can give information about the molecule geometry from the details of the vibrational and rotational absorbance detected by these techniques. X-ray crystallography, neutron diffraction and electron diffraction can give molecular structure for crystalline solids based on the distance between nuclei and concentration of electron density, gas electron diffraction can be used for small molecules in the gas phase. NMR and FRET methods can be used to determine complementary information including relative distances, dihedral angles, angles, molecular geometries are best determined at low temperature because at higher temperatures the molecular structure is averaged over more accessible geometries. Larger molecules often exist in multiple stable geometries that are close in energy on the energy surface. Geometries can also be computed by ab initio quantum chemistry methods to high accuracy, the molecular geometry can be different as a solid, in solution, and as a gas. The position of each atom is determined by the nature of the bonds by which it is connected to its neighboring atoms. Since the motions of the atoms in a molecule are determined by quantum mechanics, the overall quantum mechanical motions translation and rotation hardly change the geometry of the molecule. In addition to translation and rotation, a type of motion is molecular vibration. The molecular vibrations are harmonic, and the atoms oscillate about their equilibrium positions, at higher temperatures the vibrational modes may be thermally excited, but they oscillate still around the recognizable geometry of the molecule. At 298 K, typical values for the Boltzmann factor β are, β =0.089 for ΔE =500 cm−1, β =0.008 for ΔE =1000 cm−1, β = 7×10−4 for ΔE =1500 cm−1. When an excitation energy is 500 cm−1, then about 8.9 percent of the molecules are excited at room temperature. To put this in perspective, the lowest excitation vibrational energy in water is the bending mode, thus, at room temperature less than 0.07 percent of all the molecules of a given amount of water will vibrate faster than at absolute zero. As stated above, rotation hardly influences the molecular geometry, but, as a quantum mechanical motion, it is thermally excited at relatively low temperatures. From a classical point of view it can be stated that at temperatures more molecules will rotate faster. In quantum mechanical language, more eigenstates of higher angular momentum become thermally populated with rising temperatures, typical rotational excitation energies are on the order of a few cm−1
2.
Atoms
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An atom is the smallest constituent unit of ordinary matter that has the properties of a chemical element. Every solid, liquid, gas, and plasma is composed of neutral or ionized atoms, Atoms are very small, typical sizes are around 100 picometers. Atoms are small enough that attempting to predict their behavior using classical physics - as if they were billiard balls, through the development of physics, atomic models have incorporated quantum principles to better explain and predict the behavior. Every atom is composed of a nucleus and one or more bound to the nucleus. The nucleus is made of one or more protons and typically a number of neutrons. Protons and neutrons are called nucleons, more than 99. 94% of an atoms mass is in the nucleus. The protons have an electric charge, the electrons have a negative electric charge. If the number of protons and electrons are equal, that atom is electrically neutral, if an atom has more or fewer electrons than protons, then it has an overall negative or positive charge, respectively, and it is called an ion. The electrons of an atom are attracted to the protons in a nucleus by this electromagnetic force. The number of protons in the nucleus defines to what chemical element the atom belongs, for example, the number of neutrons defines the isotope of the element. The number of influences the magnetic properties of an atom. Atoms can attach to one or more other atoms by chemical bonds to form compounds such as molecules. The ability of atoms to associate and dissociate is responsible for most of the changes observed in nature. The idea that matter is made up of units is a very old idea, appearing in many ancient cultures such as Greece. The word atom was coined by ancient Greek philosophers, however, these ideas were founded in philosophical and theological reasoning rather than evidence and experimentation. As a result, their views on what look like. They also could not convince everybody, so atomism was but one of a number of competing theories on the nature of matter. It was not until the 19th century that the idea was embraced and refined by scientists, in the early 1800s, John Dalton used the concept of atoms to explain why elements always react in ratios of small whole numbers
3.
Cartesian coordinates
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Each reference line is called a coordinate axis or just axis of the system, and the point where they meet is its origin, usually at ordered pair. The coordinates can also be defined as the positions of the projections of the point onto the two axis, expressed as signed distances from the origin. One can use the principle to specify the position of any point in three-dimensional space by three Cartesian coordinates, its signed distances to three mutually perpendicular planes. In general, n Cartesian coordinates specify the point in an n-dimensional Euclidean space for any dimension n and these coordinates are equal, up to sign, to distances from the point to n mutually perpendicular hyperplanes. The invention of Cartesian coordinates in the 17th century by René Descartes revolutionized mathematics by providing the first systematic link between Euclidean geometry and algebra. Using the Cartesian coordinate system, geometric shapes can be described by Cartesian equations, algebraic equations involving the coordinates of the points lying on the shape. For example, a circle of radius 2, centered at the origin of the plane, a familiar example is the concept of the graph of a function. Cartesian coordinates are also tools for most applied disciplines that deal with geometry, including astronomy, physics, engineering. They are the most common system used in computer graphics, computer-aided geometric design. Nicole Oresme, a French cleric and friend of the Dauphin of the 14th Century, used similar to Cartesian coordinates well before the time of Descartes. The adjective Cartesian refers to the French mathematician and philosopher René Descartes who published this idea in 1637 and it was independently discovered by Pierre de Fermat, who also worked in three dimensions, although Fermat did not publish the discovery. Both authors used a single axis in their treatments and have a length measured in reference to this axis. The concept of using a pair of axes was introduced later, after Descartes La Géométrie was translated into Latin in 1649 by Frans van Schooten and these commentators introduced several concepts while trying to clarify the ideas contained in Descartes work. Many other coordinate systems have developed since Descartes, such as the polar coordinates for the plane. The development of the Cartesian coordinate system would play a role in the development of the Calculus by Isaac Newton. The two-coordinate description of the plane was later generalized into the concept of vector spaces. Choosing a Cartesian coordinate system for a one-dimensional space – that is, for a straight line—involves choosing a point O of the line, a unit of length, and an orientation for the line. An orientation chooses which of the two half-lines determined by O is the positive, and which is negative, we say that the line is oriented from the negative half towards the positive half
4.
Computational chemistry
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Computational chemistry is a branch of chemistry that uses computer simulation to assist in solving chemical problems. It uses methods of theoretical chemistry, incorporated into efficient computer programs, to calculate the structures and properties of molecules and solids. It is necessary because, apart from relatively recent results concerning the molecular ion. While computational results normally complement the information obtained by chemical experiments and it is widely used in the design of new drugs and materials. The methods used cover both static and dynamic situations, in all cases, the computer time and other resources increase rapidly with the size of the system being studied. That system can be one molecule, a group of molecules, Computational chemistry methods range from very approximate to highly accurate, the latter are usually feasible for small systems only. Ab initio methods are based entirely on quantum mechanics and basic physical constants, other methods are called empirical or semi-empirical because they use additional empirical parameters. Both ab initio and semi-empirical approaches involve approximations, in principle, ab initio methods eventually converge to the exact solution of the underlying equations as the number of approximations is reduced. In practice, however, it is impossible to eliminate all approximations, the goal of computational chemistry is to minimize this residual error while keeping the calculations tractable. In some cases, the details of structure are less important than the long-time phase space behavior of molecules. This is the case in conformational studies of proteins and protein-ligand binding thermodynamics, classical approximations to the potential energy surface are used, as they are computationally less intensive than electronic calculations, to enable longer simulations of molecular dynamics. Furthermore, cheminformatics uses even more empirical methods like machine learning based on physicochemical properties, one typical problem in cheminformatics is to predict the binding affinity of drug molecules to a given target. Building on the discoveries and theories in the history of quantum mechanics. The books that were influential in the development of computational quantum chemistry include Linus Pauling. 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 digital computers. A very detailed account of use in the United Kingdom is given by Smith. The first ab initio Hartree–Fock method calculations on diatomic molecules were performed in 1956 at MIT, 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
5.
Jmol
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Jmol is computer software for molecular modelling chemical structures in 3-dimensions. Jmol returns a 3D representation of a molecule that may be used as a teaching tool and it is written in the programming language Java, so it can run on the operating systems Windows, macOS, Linux, and Unix, if Java is installed. It is free and open-source software released under a GNU Lesser General Public License version 2.0, a standalone application and a software development kit exist that can be integrated into other Java applications, such as Bioclipse and Taverna. A popular feature is an applet that can be integrated into web pages to display molecules in a variety of ways, for example, molecules can be displayed as ball-and-stick models, space-filling models, ribbon diagrams, etc. Jmol supports a range of chemical file formats, including Protein Data Bank, Crystallographic Information File, MDL Molfile. There is also a JavaScript-only version, JSmol, that can be used on computers with no Java, the Jmol applet, among other abilities, offers an alternative to the Chime plug-in, which is no longer under active development. While Jmol has many features that Chime lacks, it does not claim to reproduce all Chime functions, most notably, Chime requires plug-in installation and Internet Explorer 6.0 or Firefox 2.0 on Microsoft Windows, or Netscape Communicator 4.8 on Mac OS9. Jmol requires Java installation and operates on a variety of platforms. For example, Jmol is fully functional in Mozilla Firefox, Internet Explorer, Opera, Google Chrome, fast and Scriptable Molecular Graphics in Web Browsers without Java3D
6.
Visual Molecular Dynamics
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Visual molecular dynamics is a molecular modelling and visualization computer program. VMD is developed as mainly a tool to view and analyze the results of molecular dynamics simulations and it also includes tools for working with volumetric data, sequence data, and arbitrary graphics objects. Molecular scenes can be exported to external rendering tools such as POV-Ray, RenderMan, Tachyon, Virtual Reality Modeling Language, users can run their own Tcl and Python scripts within VMD as it includes embedded Tcl and Python interpreters. VMD runs on Unix, Apple Mac OS X, and Microsoft Windows, VMD is available to non-commercial users under a distribution-specific license which permits both use of the program and modification of its source code, at no charge. A precursor program, called VRChem, was developed in 1992 by Mike Krogh, William Humphrey, the initial version of VMD was written by William Humphrey, Andrew Dalke, Ken Hamer, Jon Leech, and James Phillips. VMD was further developed by A. Dalke, W. Humphrey, J. Ulrich in 1995-1996, followed by Sergei Izrailev, in 1998, John Stone became the main VMD developer, porting VMD to many other Unix operating systems and completing the first full-featured OpenGL version. The first version of VMD for the Microsoft Windows platform was released in 1999, VMD can communicate with other programs via Tcl/Tk. Official website VMD on GPUs Protein workbench STRAP