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Topic: Molecular structure

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	Molecular Structure - The rise and reemergence of atomism
		Distinct molecular structural units that have the same connectivities but varying three-dimensional arrangements are also isomers.
		Particle-based models for atomic and molecular structure soon gave way to the quantum mechanical view, in which electrons are not treated as localized, discrete particles (electrons orbiting around a nucleus), but as delocalized areas of wavelike charge, each possessing a given probability of being found in a given location near an atomic nucleus (an orbital).
		Molecular orbitals describe three-dimensional arrangements of the atomic nuclei in a molecule and the probability that any given electron of a given energy will occupy a given location with respect to those nuclei.
	www.chemistryexplained.com /Ma-Na/Molecular-Structure.html (1802 words)

	Molecular Structure & Bonding
		In the formula on the right all four 1º-carbons are structurally equivalent (remember the tetrahedral configuration of tetravalent carbon); however the central formula has two equivalent 1º-carbons (bonded to the 3º carbon on the left end) and a single, structurally different 1º-carbon (bonded to the 2º-carbon) at the right end.
		Although structural formulas are essential to the unique description of organic compounds, it is interesting and instructive to evaluate the information that may be obtained from a molecular formula alone.
		The double bonded structure is regarded as the major contributor, the middle structure a minor contributor and the right hand structure a non-contributor.
	www.cem.msu.edu /~reusch/VirtualText/intro3.htm (3607 words)

	Molecular Insight Pharmaceuticals : News
		In June, Molecular Insight and the University of Maryland reported on collaborative research demonstrating the potential of a molecule developed at the university incorporating SAAC technology to target angiogenesis in prostate cancer interchangeably with technetium-99m for diagnosis and rhenium-188 for therapy.
		Molecular Insight Pharmaceuticals, Inc. is a privately held biopharmaceutical company focused on leveraging its proprietary technology platforms in molecular medicine to develop innovative pharmaceuticals to diagnose and treat disease.
		Molecular Insight is also applying its platform technologies to develop targeted radiotherapeutics for the treatment of cancer.
	www.molecularinsight.com /pressreleases/20040721.aspx (664 words)

	Molecular Quantum Optics Temple University Physics Dept. marjatta lyyra
		However, due to the small size of typical molecular transition moments, the field of coherence effects in laser molecule interactions is still in its infancy.
		Similarly, all-optical control of molecular orientation and alignment on surfaces may turn out in the future to be a very attractive means for providing insights into mechanisms of chemical reactions on surfaces as well as helping advance the molecular-electronics approach to device fabrication.
		Molecular transitions are governed by the parity of the various states.
	www.temple.edu /molecular_optics (455 words)

	Molecular Structure Laboratory - SUNY Stony Brook (Site not responding. Last check: )
		The Molecular Structure Laboratory is located on the third floor of the Chemistry Building at Stony Brook.
		Molecular structure determinations of organic, inorganic and organometallic compounds are carried out on a routine basis.
		The structure was determined at Stony Brook by Professor Joseph W. Lauher.
	sbchem.sunysb.edu /msl/homepage.html (319 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)

	Molecular Structure
		These molecular vibrations occur because the relative positions and orientations of the atomic nuclei are not absolutely fixed within the molecule.
		The molecular rotations occur because the individual molecules are free to spin and rotate in space since they are in a gaseous state.
		Thanks to its linear structure, the rotational energy spectrum of CO has the same character as that for diatomic molecules and the rotational energy levels are thus approximated by:
	www.phy.davidson.edu /StuHome/jimn/CO2/Pages/CO2Theory.htm (698 words)

	Molecular Structure
		No structural formula seemed to satisfy the valence requirements and at the same time to account for the great stability of the compound.
		After all, the Kekule structural formulas were written two-dimensionally on the flat surface of a flboard or a piece of paper.
		Essentially, this theory held that the structural relationships between atoms did not need to be restricted to ordinary valence bonds.
	www.3rd1000.com /history/molecule.htm (4441 words)

	Graduate Program in Molecular Biology and Molecular Structure Research - UCHSC
		The tools and concepts of molecular and structural biology form the foundation for understanding the function of all biological systems.
		Cell growth, differentiation or death is the outcome of a series of signalling events that impinge upon a variety of effector pathways.
		A molecular understanding of the full range of these events provides not only a basis for understanding normal and disease processes, but also for interventions, including those of therapeutic importance.
	www.uchsc.edu /cdb/molecular-biology.htm (238 words)

	The Molecular Structure of Green Fluorescent Protein
		The protein is in the shape of a cylinder, comprising 11 strands of -sheet with an -helix inside and short helical segments on the ends of the cylinder.
		Molecular oxygen is proposed to be needed for formation of the double bond between C and C on the tyrosine to form an extended aromatic system, but oxygen must also be excluded from regular interactions with the fluorophore or else collisional quenching of the fluorescence or damaging photochemistry will occur.
		Structure of ribonuclease H phased at 2 A by MAD analysis of the seleniomethionyl protein.
	www-bioc.rice.edu /Bioch/Phillips/Papers/gfpbio.html (4825 words)

	Molecular Expressions: Images from the Microscope
		Fluorescence (Förster) Resonance Energy Transfer with Fluorescent Proteins - Fluorescent proteins are increasingly being applied as non-invasive probes in living cells due to their ability to be genetically fused to proteins of interest for investigations of localization, transport, and dynamics.
		The spectral properties of fluorescent proteins are dependent upon the structure of the fluorophore as well as the localized interactions of amino acid residues in the immediate vicinity, and in some cases, residues far removed from the fluorophore.
		Together with the scientists and programmers at Molecular Expressions, Nikon microscopists and engineers are providing the latest state-of-the-art information in microscope optics and imaging technology including specialized techniques such as fluorescence, differential interference contrast (DIC), phase contrast, reflected light microscopy, and microscopy of living cells.
	molecularexpressions.com (5812 words)

	Glossary - molecular structure
		The molecular structure is different from the molecular formula in that the molecular formula only tells what kinds of atoms are in a molecule and how many of each kind of atom.
		The molecular structure tells us how those atoms are arranged in space.
		The molecular structure of a molecule determines the properties of the material.
	www.chemheritage.org /EducationalServices/faces/glossary/chemstru.htm (96 words)

	Letter to Nature: Molecular structure of Nucleic Acids (Site not responding. Last check: )
		This structure as described is rather ill-defined, and for this reason we shall not comment on it.
		The novel feature of the structure is the manner in which the two chains are held together by the purine and pyrimidine bases.
		If it is assumed that the bases only occur in the structure in the most plausible tautomeric forms (that is, with the keto rather than the enol configurations) it is found that only specific pairs of bases can bond together.
	www.nature.com /genomics/human/watson-crick (954 words)

	Molecular Structure Help in Determining Salicylate Status of Ingredients
		This exact pattern must exist somewhere in the molecular structure of any chemical that is a member of the salicylate family.
		Not being chemists, we can't tell you whether the similar structures with the OH in an octo- position are scientifically salicylates or not.
		If the chemical finder finds the ingredient but does not have a molecular structure that implies the ingredient is a combination of chemicals, and not one single chemical, then we have to do further research to try and determine if salicylates are one of the chemicals in the ingredient.
	www.psha-inc.com /guai-support/sf/Sal-Free/Molecular_Structure.htm (1747 words)

	Geometry in Action: Molecular Modeling
		Many questions in molecular modeling can be understood geometrically in terms of arrangements of spheres in three dimensions.
		Classical molecular modeling has dealt with biological molecules which generally have a tree-like structure, but applications to nanotechnology require dealing with more complicated diamond-like structures; it is unclear to what extent this affects the relevant algorithms.
		Michel Sanner of Scripps studies algorithms for molecular modeling, and published a paper on molecular surface accessability at the 11th ACM Symp.
	www.ics.uci.edu /~eppstein/gina/molmod.html (405 words)

	Molecular Structure of Proteins
		The folded structure of a protein is actually thermodynamically less favorable because it reduces the disorder or entropy of the protein.
		This globular shape allows for the reduction in the number of nonpolar molecules being exposed to water and actually slightly increases entropy as water molecules are liberated by the burying of nonpolar molecules to the center of the globular structure.
		Time for this activity can be reduced by having molecular models prepared for students to observe, and not allowing students to build the molecules.
	www.scienceteacherprogram.org /biology/Granberry05.html (755 words)

	Cranium Paper - Molecular Knowledge Systems, Inc.
		Reasoning about a compound's molecular structure or a mixture's components, Cranium identifies the material's chemical family, selects the most accurate estimation technique, automatically dissects molecular structures into group fragments, and then estimates the material's physical property.
		Molecular structures, physical property data, and estimation techniques can all be added to Cranium in a single, consistent manner.
		These would contain their own material data, estimation techniques, molecular structures, etc. These knowledge bases can be freely distributed to other Cranium users or to non-users using a runtime package.
	www.molknow.com /Papers/Cranium/paper1.htm (2141 words)

	NCBI Structure Group
		MMDB, a database of macromolecular 3D structures, as well as tools for their visualization and comparative analysis.
		It is a component of NIH's Molecular Libraries Roadmap Initiative..
		Structure Summary pages for one/several/all of these may be retrieved.
	www.ncbi.nlm.nih.gov /Structure (211 words)

	TAPPI Website - Effects of Molecular Structure, Rheology, Morphology, and Orientation on Polyethylene Blown Film ...
		The effects and interactions of polyethylene molecular structure, rheology, morphology and molecular orientation on blown film properties were examined in detail.
		The molecular structure was examined via gel permeation chromatography (GPC), rheology via standard dynamic oscillatory shear tests, morphology via transmission electron microscopy (TEM) and molecular orientation via both wide angle x-ray scattering (WAXS) and infrared dichroism.
		The results clearly showed that the resin rheology and molecular structure profoundly affected the extent of lamellar stacking, fibril nuclei and degree of molecular orientation which in turn resulted in substantial changes in blown film properties.
	www.tappi.org /s_tappi/doc_bookstore.asp?CID=5114&DID=512745 (265 words)

	Organic Molecular Structure Models for Chemistry
		Orbit molecular model sets are well suited for studies in organic chemistry, biochemistry and lattices.
		Class molecular model set have more 2, 3, 4, 6, 8, 12 coordinate atoms to build all 7 basic structures at once and many more and larger structures.
		An excellent site with images of these and other structures can be found at: Crystal Lattice Structures is maintained by the US Navy.
	www.indigo.com /models/orbit-molecular-model-sets.html (366 words)

	2005 Biophysical Society Educational Resources - structures
		The Protein Data Bank provides a wealth of information on the structure, synthesis, and function of biological macromolecules at their education page.Content is suitable for students from middle school (advanced elementary) to college/university.
		Proteins are organized in a hierarchy of structures including primary structure (the amino acid sequence), secondary structure (a-helix and b-sheet), tertiary architecture (the specific atomic structure), and quaternary organization (arrangement of distinct polypeptide chains).
		PDBsum is “a database of the 3D structures of known proteins and nucleic acids” maintained by the Department of Biochemistry and Molecular Biology, University College, London.
	www.biophysics.org /education/structures.htm (969 words)

	Electron Configurations & The Periodic Table
		The study of organic chemistry must at some point extend to the molecular level, for the physical and chemical properties of a substance are ultimately explained in terms of the structure and bonding of molecules.
		Its location in the periodic table should not suggest a kinship to the chemistry of the alkali metals, and its role in the structure and properties of organic compounds is unlike that of any other element.
		Transfer of the lone 3s electron of a sodium atom to the half-filled 3p orbital of a chlorine atom generates a sodium cation (neon valence shell) and a chloride anion (argon valence shell).
	www.cem.msu.edu /~reusch/VirtualText/intro2.htm (2116 words)

	Molecular Modeling 1
		The simplest model is a Lewis dot structure which gives us an approximate picture of the bonding interactions that hold the polyatomic species together.
		VSEPR theory only predicts structure and cannot be used, by itself, to describe the places where electrons are allowed to be (i.
		Although you do not need to name the molecular shape for molecules and ions with more than one “central atom”, you should be able to indicate the molecular geometry about each “central atom.” Click here to review VSEPR theory.
	chemlab.truman.edu /CHEM121Labs/MolecularModeling1.htm (1416 words)

	Cn3D 4.0 Tutorial Index
		What sets Cn3D apart from other software is its ability to correlate structure and sequence information: for example, a scientist can quickly find the residues in a crystal structure that correspond to known disease mutations, or conserved active site residues from a family of sequence homologs.
		Cn3D displays structure-structure alignments along with their structure-based sequence alignments, to emphasize what regions of a group of related proteins are most conserved in structure and sequence.
		Crystal structure of the PTEN tumor suppressor: implications for its phosphoinositide phosphatase activity and membrane association.
	www.ncbi.nlm.nih.gov /Structure/CN3D/cn3dtut.shtml (613 words)

	Visible Crystals Reflect Molecular Structure
		The cubic shape of the visible crystal is directly related to the molecular arrangement of sodium and chloride ions.
		The model on the right shows the molecular arrangement of sodium and chloride ions in halite.
		Examine how the molecular arrangement in the 3-D model is related to the shape of the crystal in the photograph.
	www.classzone.com /books/earth_science/terc/content/investigations/es0506/es0506page05.cfm (102 words)

	Molecular Origami Home Page
		Molecular Origami is an outgrowth of 'Data-Driven Chemistry', a technique of teaching chemistry under development by Prof.
		Molecular Origami by Robert M. Hanson (University Science Books) is a set of actual paper models focusing on small organic and inorganic structures.
		Molecular Origami is unique because it enables you to pick and choose what groups you want to look at.
	www.stolaf.edu /people/hansonr/mo (452 words)

	DNA and Molecular Genetics
		He (unfortunately) also erroneously concluded that the proportions of bases were equal and that there was a tetranucleotide that was the repeating structure of the molecule.
		DNA is a double helix, with bases to the center (like rungs on a ladder) and sugar-phosphate units along the sides of the helix (like the sides of a twisted ladder).
		A Structure for Deoxyribose Nucleic Acid Text of the original paper that Watson and Crick published in 1953.
	www.emc.maricopa.edu /faculty/farabee/BIOBK/BioBookDNAMOLGEN.html (1834 words)

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