• atoms
  • This set of plastic atoms and bonds enables students to construct ball-and-stick as well as space-filling models of organic compounds. (carolina.com)
  • John Dalton represented compounds as aggregations of circular atoms, and although Johann Josef Loschmidt did not create physical models, his diagrams based on circles are two-dimensional analogues of later models. (wikipedia.org)
  • The concept of the chemical bond as a direct link between atoms can be modelled by linking balls (atoms) with sticks/rods (bonds). (wikipedia.org)
  • Molecular models typically describe atoms (nucleus and electrons collectively) as point charges with an associated mass. (wikipedia.org)
  • It is typically modeled using a 6-12 Lennard-Jones potential, which means that attractive forces fall off with distance as r−6 and repulsive forces as r−12, where r represents the distance between two atoms. (wikipedia.org)
  • In the field of computational chemistry, energy minimization (also called energy optimization, geometry minimization, or geometry optimization) is the process of finding an arrangement in space of a collection of atoms where, according to some computational model of chemical bonding, the net inter-atomic force on each atom is acceptably close to zero and the position on the potential energy surface (PES) is a stationary point (described later). (wikipedia.org)
  • In chemistry, the CPK coloring is a popular color convention for distinguishing atoms of different chemical elements in molecular models. (wikipedia.org)
  • Their models represented atoms by faceted hardwood balls, painted in different bright colors to indicate the respective chemical elements. (wikipedia.org)
  • AM1 is an attempt to improve the MNDO model by reducing the repulsion of atoms at close separation distances. (wikipedia.org)
  • Crick and Wa
  • Models encompass a wide range of degrees of precision and engineering: some models such as J.D. Bernal's water are conceptual, while the macromodels of Pauling and Crick and Watson were created with much greater precision. (wikipedia.org)
  • explicitly
  • An extension of AM1 is SemiChem Austin Model 1 (SAM1), which is implemented in the AMPAC program and which explicitly treats d-orbitals. (wikipedia.org)
  • spectroscopy
  • Krylov also develops many-body theories for describing metastable electronic states (resonances) and tools for spectroscopy modeling (including non-linear optical properties). (wikipedia.org)
  • initio
  • Nevertheless, in this thesis, CIS proves to be a good starting point for improved ab initio quantum chemistry methods, that build in the correct molecular orbital optimization. (upenn.edu)
  • Liu, Xinle, "Ab initio Quantum Chemistry Methods for Modeling Molecular Excited States Beyond Configuration Interaction Singles" (2015). (upenn.edu)
  • Such varying molecular geometries can also be computed, at least in principle, by employing ab initio quantum chemistry methods that can attain high accuracy for small molecules, although claims that acceptable accuracy can be also achieved for polynuclelotides, and DNA conformations, were recently made on the basis of vibrational circular dichroism (VCD) spectral data. (wikipedia.org)
  • theoretical
  • By combining computer-based techniques with experimental and theoretical structural information, the group is able to develop structures that mimic the behavior of molecules or molecular reactions. (nih.gov)
  • Professor Krylov leads the iOpenShell lab, a research group focused on theoretical modeling of open shell and electronically excited species. (wikipedia.org)
  • visualization
  • Q-Chem 4.0 comes with the new graphical interface, IQMol which includes hierarchical input generator, molecular builder, and general visualization capabilities (MOs, molecular vibrations, etc. (wikipedia.org)
  • biomolecules
  • In 1952, Corey and Pauling published a description of space-filling models of proteins and other biomolecules that they had been building at Caltech. (wikipedia.org)
  • typically
  • The dihedral or torsional terms typically have multiple minima and thus cannot be modeled as harmonic oscillators, though their specific functional form varies with the implementation. (wikipedia.org)
  • peptide
  • I am interested in molecular modeling of Antigenic peptide of M Leprae and its interaction with T cell CD4+ with the MHCII complex .I have chosen an antigenic peptide of 12k obtained from field trials in India.Is there any other proven antigenic peptide of m-lepray?If so what is the amino acid sequence? (bio.net)
  • structures
  • After the development of X-ray crystallography as a tool for determining crystal structures, many laboratories built models based on spheres. (wikipedia.org)
  • Molecular models of DNA structures are representations of the molecular geometry and topology of deoxyribonucleic acid (DNA) molecules using one of several means, with the aim of simplifying and presenting the essential, physical and chemical, properties of DNA molecular structures either in vivo or in vitro. (wikipedia.org)
  • Although such initial studies of DNA structures with the help of molecular models were essentially static, their consequences for explaining the in vivo functions of DNA were significant in the areas of protein biosynthesis and the quasi-universality of the genetic code. (wikipedia.org)
  • Supercoiling, packing with histones in chromosome structures, and other such supramolecular aspects also involve in vivo DNA topology which is even more complex than DNA molecular geometry, thus turning molecular modeling of DNA into an especially challenging problem for both molecular biologists and biotechnologists. (wikipedia.org)
  • The Molecular Modeling Database (MMDB) is a database of experimentally determined three-dimensional biomolecular structures and hosted by the National Center for Biotechnology Information. (wikipedia.org)
  • energies
  • Understanding electron and energy transfer at the molecular level is essential, since they must compete with deactivation processes back to the molecular ground state-- and deactivation releases any captured energies as wasted heat. (upenn.edu)
  • Physical Models
  • The construction of physical models is often a creative act, and many bespoke examples have been carefully created in the workshops of science departments. (wikipedia.org)
  • atom
  • In this article, " molecular model " will primarily refer to systems containing more than one atom and where nuclear structure is neglected. (primidi.com)
  • systems
  • The energy minimization method is useful to obtain a static picture for comparing between states of similar systems, while molecular dynamics provides information about the dynamic processes with the intrinsic inclusion of temperature effects. (wikipedia.org)
  • consists
  • Although DNA consists of relatively rigid, very large elongated biopolymer molecules called fibers or chains (that are made of repeating nucleotide units of four basic types, attached to deoxyribose and phosphate groups), its molecular structure in vivo undergoes dynamic configuration changes that involve dynamically attached water molecules and ions. (wikipedia.org)
  • structure
  • Is the structure of MHCII known with the coordinates so that this input can be used to model and study the interaction between the molecules?Can somebody throw some light on this? (bio.net)
  • From the very early stages of structural studies of DNA by X-ray diffraction and biochemical means, molecular models such as the Watson-Crick nucleic acid double helix model were successfully employed to solve the 'puzzle' of DNA structure, and also find how the latter relates to its key functions in living cells. (wikipedia.org)
  • The first reports of a double helix molecular model of B-DNA structure were made by James Watson and Francis Crick in 1953. (wikipedia.org)
  • essentially
  • Modeling electronic relaxation process is very challenging, however, for 2 reasons: i) Obtaining accurate potential energy surfaces (PESs) by solving the electronic Hamiltonian (only) is nontrivial, since all electrons are coupled together, which is essentially a many-body problem. (upenn.edu)
  • The importance of stereochemistry was not then recognised and the model is essentially topological (it should be a 3-dimensional tetrahedron). (wikipedia.org)
  • theory
  • The course is designed to give students in chemistry and related subjects an introduction to the theory for molecular modeling, and use of modeling as a tool in chemical research. (uio.no)