
	Where results make sense

Topic: Molecular mechanics

Related Topics

Molecular modelling

Molecular dynamics

Computational chemistry

Amber

Cheminformatics

Classical mechanics

Quantum chemistry

Quantum mechanics

Monte Carlo method

Molecule

Lithuanian language

Computational chemistry

	CHE 241 Lab - Molecular Modeling
		The molecular mechanics force field is a computational model for describing the potential energy surface for all the possible movements of atoms within a molecule.
		The major distinction between the molecular mechanics method used in this experiment and quantum mechanics is that molecular mechanics does not consider the electrons in the molecule explicitly.
		Molecular mechanics treats the atoms and their associated electrons as units interconnected by the potential functions that we have described.
	web.centre.edu /muzyka/organic/lab/molecularModeling.htm (677 words)

	MOLECULAR MODELING
		In molecular mechanics the bonds of a molecule are treated as springs and the force constants of the springs are determined from experimental measurements.
		The overall molecular energy is the sum of the energies of stretching, bending and torsion (the molecular force field) for all of the bonds in the molecule.
		Molecular mechanics does not give molecular energies but can do a reasonable job of predicting which molecular arrangement is most stable.
	web.centre.edu /che/che131_lab/MolecularModeling.htm (1549 words)

	Molecular Mechanics
		The "mechanical" molecular model was developed out of a need to describe molecular structures and properties in as practical a manner as possible.
		The object of molecular mechanics is to predict the energy associated with a given conformation of a molecule.
		The torsion energy in molecular mechanics is primarily used to correct the remaining energy terms rather than to represent a physical process.
	cmm.info.nih.gov /modeling/guide_documents/molecular_mechanics_document.html (1070 words)

	Molecular simulations in heterogeneous catalysis
		Molecular mechanics methods are used to parameterize analytical expressions that describe the interaction between atoms.
		In such cases, quantum or molecular mechanics methods can be used to compute atomic-level attributes or "descriptors" for a family of materials for which experimental data have been measured.
		The molecular mechanics simulation of large systems extended over time is enhanced by the use of quantum methods to tune the parameterizations.
	pubs.acs.org /hotartcl/chemtech/99/sep/molecular.html (2663 words)

	[No title]
		Molecular mechanics calculations, also known as force field calculations, can be of considerable use in the qualitative descriptions in these cases.
		Molecular Mechanics (Vibrational Spectroscopy): The motions of the nuclei are studied and the electrons are not explicitly examined at all, but are assumed to find an optimal distribution about the nuclei.
		Present: Molecular mechanics tends to be one of the standard methods of structural chemistry.
	www.sdsc.edu /~kimb/eff.html (1538 words)

	Techniques of Molecular Modelling: Molecular Mechanics.
		Mechanics can be very reliable for geometric predictions, and is the method of choice for interfacing between 2D/3D structure sketch programs, and expensive QM programs.
		Before a mechanics calculation can be performed, much care has to be taken to ensure all the atom and bond types are correctly defined (in the structure editor, or post processing of any 3D coordinates); these cannot of course "evolve" during the course of the mechanics calculation (unlike QM).
		Molecular mechanics is in fact an excellent and very rapid probe of the conformation of such a ring.
	www.ch.ic.ac.uk /local/organic/mod/mo_3.html (2363 words)

	Molecular modelling - Wikipedia, the free encyclopedia
		Molecular modelling is a collective term that refers to theoretical methods and computational techniques to model or mimic the behaviour of molecules.
		Molecular mechanics is synonymous with molecular modelling, as it is refers to the use of classical mechanics/Newtonian mechanics to describe the physical basis behind the models.
		This function, referred to as a potential function, computes the molecular potential energy as a sum of energy terms that describe the deviation of bond lengths, bond angles and torsion angles away from equilibrium values, plus terms for non-bonded pairs of atoms describing van der Waals and electrostatic interactions.
	en.wikipedia.org /wiki/Molecular_modelling (766 words)

	JCE 1999 (76) 31 [Jan] Molecular Mechanics across Chemistry (by Anthony K. Rappé and Carla J. Casewit)
		This title covers the basics of molecular mechanics in a readable straightforward manner and it is pertinent to beginners and experienced modelers alike.
		The novice user will be exposed to the basics of molecular mechanics necessary to perform and interpret such calculations, while advanced users may find approaches to complement and amplify their ongoing studies.
		Overall, the text provides a relatively solid and effective introduction to the field of molecular mechanics and would be a useful addition to any faculty, student, or institutional library-especially in light of recent advancements in the desktop molecular modeling field, where virtually anyone can gain insight into almost any chemical system.
	jchemed.chem.wisc.edu /Journal/Issues/1999/Jan/abs31_1.html (616 words)

	Molecular Mechanics
		Unlike Molecular mechanics, which is based on empirical parameters and gives only relative strain energies, Quantum Mechanics is based on basic physical laws and gives absolute energies.
		Molecular orbitals are represented as a linear combination of atomic orbitals (LCAO).
		Molecular orbitals are another example of LCAO orbitals which describe bonds in a molecule.
	community.middlebury.edu /~chem/chemistry/class/winterm/handouts_wt97/d-Quantum_Mechanics.html (2206 words)

	Molecular mechanics - Wikipedia, the free encyclopedia
		The potential energy of all systems in molecular mechanics is calculated using force fields.
		Molecular mechanics can be used to study small molecules as well as large biological systems or material assemblies with many thousands to millions of atoms.
		Main purpose of MD is modeling of molecular motions, although it is also applied for optimization, for example using simulated annealing.
	en.wikipedia.org /wiki/Molecular_mechanics (1275 words)

	Expert: Computational Chemistry Expert
		Expert has expertise in implementing quantum mechanics, molecular mechanics, and statistical thermodynamics in tandem with molecular graphics in order to determine the energies, structures, and properties of organic and inorganic molecules.
		He uses a variety of experimental methods, such as NMR spectroscopy and atomic force microscopy, and theoretical tools, such as molecular mechanics and molecular dynamics, to explain where enantiomers bind on these surfaces and what forces are responsible for enantiodifferentiation.
		He routinely uses molecular mechanics to better understand the structures and properties of organic and inorganic molecules.
	www.intota.com /viewbio.asp?bioID=605040&perID=716621 (657 words)

	Molecular mechanics (Site not responding. Last check: 2007-11-04)
		The term molecular mechanics refers to the use of Newtonian mechanics to model molecular systems.
		Molecular mechanics approaches are widely applied in molecular structure refinement, molecular dynamics simulations, Monte Carlo simulations and ligand docking simulations.
		Typically, molecular mechanics models consist of spherical atoms connected by springs which represent bonds.
	molecular-mechanics.iqnaut.net (119 words)

	Introduction to Computational Chemistry
		In a molecular mechanics method, the data base of compounds used to parameterize the method (a set of parameters and functions is called a force field) is crucial to it's success.
		The bad side of molecular mechanics is that there are many chemical properties that are not even defined within the method, such as electronic excited states.
		Statistical mechanics is the mathematical means to extrapolate thermodynamic properties of bulk materials from a molecular description of the material.
	www.ccl.net /cca/documents/dyoung/topics-orig/compchem.html (3078 words)

	An Introduction to Molecular Modeling
		Quantum mechanics is one of the oldest mathematical formalisms of theoretical chemistry.
		As the nuclei are moved to new coordinates and molecular energies are re-calculated, a quantitative description of molecular energy is derived.
		Molecular mechanics is a mathematical formalism which attempts to reproduce molecular geometries, energies and other features by adjusting bond lengths, bond angles and torsion angles to equilibrium values that are dependent on the hybridization of an atom and its bonding scheme (this atom description is referred to as the atom type).
	www.netsci.org /Science/Compchem/feature01.html (3950 words)

	Conformational Energy Searching
		Molecular mechanics energy approximations are most valid in and around the minima.
		However, since molecular energies are not accurately computed by molecular mechanics or semiempirical quantum mechanics, and the molecular environment in the model may not be exact (e.g.
		Molecular mechanics should be used for molecules that are too large for quantum calculations or if too many starting conformations are found from sampling (i.e.
	cmm.info.nih.gov /modeling/guide_documents/conformation_document.html (2172 words)

	Molecular Modelling: Principles and Applications
		Molecular modelling used to be restricted to a small number of scientists who had access to the necessary computer hardware and software.
		Chapters 2 and 3 describe quantum mechanics and molecular mechanics, which are the two major methods used to model the interactions within a molecular system.
		Molecular modelling is a rapidly developing discipline, and has benefitted from the dramatic improvements in computer hardware and software of recent years.
	www.booksites.net /leach1/molecular (1869 words)

	Compare Prices on Molecular Quantum Mechanics at YaPrice - Books & Magazines Reviews (Site not responding. Last check: 2007-11-04)
		I cannot say that this is a strict quantum mechanics text that would be used for a quantum physics course, for the absence of core idea like operator mechanics, ladder operators and the such.
		Yet "Molecular Quantum Mechanics" definitely shines and has proven itself to be a much better (in details, explanations, readability) text than "Physical Chemistry" written by the same author.
		"Molecular Quantum Mechanics" focuses on aspects of quantum mechanics in chemistry, especially in applications on spectroscopy (infrared and Raman) which roots in the ideas of rotation, vibration, anharmonicity, and centrifugal distortion.
	www.yaprice.com /compare/prod-p500051.html (664 words)

	Molecular Mechanics
		However, quantum mechanical methods are very demanding of computer time and memory.
		Many interesting molecular systems are simply too large for quantum mechanical calculations to be practical.
		The molecular potential energy is calculated as a function of the nuclear (atomic) positions.
	www.chm.bris.ac.uk /pt/ajm/mmhtm/MM_L1p9.htm (254 words)

	Real-Time Mechanics in Molecular Modeling
		Recent increases in computer performance, visualization, and molecular mechanics algorithms now allow researchers to dock ligands or modify loops interactively while a computer continuously modifies the conformation to account for changes in energies.
		This close coupling between the user and molecular mechanics is a new paradigm in molecular modeling that is contained in the SCULPT modeling system.
		This contrasts traditional molecular modeling development which has concentrated on improved algorithms; this had the unfortunate result of often imposing a barrier between the researcher and the modeling process.
	www.netsci.org /Science/Compchem/feature05.html (1813 words)

	Molecular Structure Laboratory
		Created in 1990, the laboratory deals with all aspects of molecular structure by employing both experimental techniques, such as X-ray crystallography, and the methods of computational chemistry, including molecular mechanics, molecular dynamics and quantum chemical calculations.
		Molecular dynamics calculations (AMBER 6) were performed by Michael Keller, who is currently researching the effects of zinc (II) on the stability of various DNA hairpins.
		Molecular dynamics calculations (AMBER 5) were performed by Evan Kransdorf, presently in the MD/PhD program at the Virginia Commonwealth University School of Medicine.
	faculty.virginia.edu /molecular-structure (93 words)

	ScienceDaily: 3-D Imaging Of Motor Proteins Provides New Insights To Molecular Mechanics Of Cell Motility, Muscle ...
		Researchers Probe Mechanism Behind Heartbeat (July 22, 1997) -- Scientists at The University of Texas-Houston Medical School and the University of Alberta in Canada have determined the three-dimensional structure of cardiac troponin C (cardiac TnC), a protein...
		A New Focus For The Mechanism Of Nerve Growth (March 20, 2006) -- Researchers at Yale shed new light on the mechanism of nerve cell growth by identifying novel functions for a molecular "motor" protein, myosin-II, according to an article in the March issue of...
		Biochemistry Molecular Biology of Plants is a major contribution to the plant sciences literature, superbly edited by three distinguished scientists, Bob B. Buchanan, Wilhelm Gruissem, and Russell...
	www.sciencedaily.com /releases/2005/10/051001102026.htm (1894 words)

	The NetSci MM/MD Software Lists
		VMD (Visual Molecular Dynamics) is program for interactive display and animation of molecules; It runs on Silicon Graphics workstations and may be compiled for HP-UX workstations if the NPGL library is available.
		The molecular packing graphics (mpg) module is closely integrated with the molecular packing analysis module to give users fast, convenient, and useful graphical visualization of the results.
		TINKER molecular modeling software is a complete package for molecular mechanics and dynamics of molecules, especially polypeptides.
	www.netsci.org /Resources/Software/Modeling/MMMD/top.html (3241 words)

	Tremendous recent theoretical and experimental advances in single
		It is increasingly clear that the mechanical properties of proteins are as important to function as their binding affinities.
		My lab is using single molecule mechanics measurements to define the relationships between the chemistry and mechanical strength of single proteins or protein bonds.
		We are using a combination of single molecule force probe studies, molecular dynamics simulations, surface force measurements between membranes, and dynamic fluorescence measurements to determine how these essential molecular building blocks assemble to form strong junctions at cell-cell interfaces.
	www.scs.uiuc.edu /~leckband/Molecular_mechanics.htm (824 words)

	[No title]
		When it is of interest to study structure and bonding in very large molecular systems comprising hundreds or even thousands of atoms, many of the more sophisticated molecular modeling techniques are too demanding of computer time resources to be of general use.
		These various types of forces are described in terms of individual potential functions which in sum constitute the overall molecular potential energy or steric energy of the molecule.
		In its simplest representation, the molecular mechanics equation is
	www.sdsc.edu /~kimb/molmech.html (2917 words)

	Molecular Mechanics
		Ref.1, et al,is a simplified molecular modeling method that simplifies molecular geometry and energy calculations.
		Some force fields developed for making molecular mechanics calculations include MM2 and MMP2 force fields of Allinger, et al Ref.1, the AMBER force field of Kollman, et al Ref.2 and the CHARMM force field of Karplus, et al Ref.3.
		The ChemPen3D DREIDING molecular mechanics force field has been extended to cover the entire periodic table.
	www.chempensoftware.com /chempen3.htm (566 words)

	Chemdraw ultra: Molecular modelling, structure drawing, Semi-empirical calculations, structure display, MOPAC, ... (Site not responding. Last check: 2007-11-04)
		Spartan is an investigative laboratory tool that helps focus the power of molecular mechanics and quantum chemical methods on your chemical research.
		HyperChem is a sophisticated molecular modeling environment that is known for its quality, flexibility, and ease of use.
		Ionic, metallic, covalent and molecular crystals may be constructed using a database of all 230 space groups, with choice of cell type and unique axis where appropriate.
	www.chemistry-software.com /molecmod.htm (479 words)

	SC680 - Molecular Mechanics (Site not responding. Last check: 2007-11-04)
		Molecular mechanics calculations are a step up from classical energy calculations as they include the energy as calculated from the above potential energy functions considering only non-bonded atoms and also use mathematical techniques to yield a more realistic structure.
		This is the effect of the charges on the atoms have on molecular conformation.
		The key feature of molecular mechanics programs which distinguishes them from classical potential energy programs is that all the potentail energy functions can be used to change the original structure into a more realistic structure.
	www.chem.swin.edu.au /courses/swin/sc680/mech.html (864 words)

	Molecular modelling, structure drawing, Semi-empirical calculations, structure display, MOPAC, solvation energy, MM2 (Site not responding. Last check: 2007-11-04)
		HyperChem is a sophisticated molecular modeling program that is known for its quality, flexibility, and ease of use.
		HyperChem unites 3-D visualization and animation with quantum chemical calculations, molecular mechanics and molecular dynamics.
		Build clusters and complex molecular assemblies; move individual atoms and molecules as easily as you move groups.
	www.chemistry-software.com /modelling/hyperchem_standard.htm (1078 words)

Try your search on: Qwika (all wikis)