Chemical modeling apparatus
The present invention relates to an apparatus for modeling chemical structures having multiple types of bonding. In an embodiment, the present invention relates to an apparatus for modeling chemical structures having multiple types of bonding, including hydrogen bonding. In an embodiment, the invention is a molecular modeling device including a plurality of molecular components. The molecular components can include a first elemental component comprising a plurality of first magnets, a second elemental component comprising a second magnet, and a primary structural bond attaching the first elemental component to the second elemental component. The molecular components can be attached to other molecular components through secondary structural bonds, wherein the primary structural bond attaches more strongly than the secondary structural bond. In an embodiment, the first and second magnets each include first and second magnetic poles, the first magnets disposed on the exterior of the first elemental component with the first magnetic pole pointing away from the interior of the first elemental components. The second magnet can be disposed on the exterior of the second elemental component with the second magnetic pole of the second magnet pointing away from the interior of the second elemental component.
The present invention relates to an apparatus for modeling chemical structures. More specifically, the present invention relates to an apparatus for modeling chemical structures having multiple types of bonding.
BACKGROUND OF THE INVENTIONAtoms are the building blocks of all matter. Atoms can associate with other atoms through chemical bonds. A chemical bond can be said to exist between two atoms or groups of atoms when forces acting between them lead to the formation of an aggregate with sufficient stability to make it convenient for the scientist to consider it as an independent molecular species. See L. Pauling, 1960, The Nature of the Chemical Bond. Understanding the effect that chemical bonding has on molecular structure is important in many areas of study including chemistry, physics, and biology.
Chemical bonds can be broadly classified as electrostatic, covalent, and metallic. More specific classifications of bonding can be made under these three broad categories. By way of example, ionic bonds, ion-dipole bonds, and hydrogen bonds can all be thought of as electrostatic bonds, in whole or in part.
Various modeling systems for chemical structures and bonding exist. By way of example, U.S. Pat. No. 6,508,652 (Kestyn) and U.S. Pat. No. 4,099,339 (Snelson) disclose chemical modeling systems. These modeling systems can help in visualizing the structure of chemical compounds. However, such modeling systems do not allow one to visualize the effect that hydrogen bonding has on the structure of molecules or on how molecules are arranged with respect to one another. Also, such modeling systems do not allow one to see the structural effects of different types of bonding having different relative strengths, such as the difference in strength between covalent bonding and ion-dipole bonding.
Therefore, a need exists for a chemical modeling system that will model the effects of hydrogen bonding and/or ion-dipole bonding.
SUMMARY OF THE INVENTIONThe present invention relates to an apparatus for modeling chemical structures having multiple types of bonding, including ion-dipole bonding and/or dipole-dipole bonding including hydrogen bonding. In an embodiment, the invention is a molecular modeling device including a plurality of molecular components including a first elemental component comprising a plurality of first magnets and a second elemental component comprising a second magnet. A primary structural bond can attach the first elemental component to the second elemental component. In an embodiment, the primary structural bond can model a covalent bond. The molecular components can be attached to other molecular components through secondary structural bonds, wherein the primary structural bond attaches more strongly than the secondary structural bond. In an embodiment, the secondary structural bond models an ion-dipole bond. In an embodiment, the secondary structural bond models a dipole-dipole bond. In an embodiment the secondary structural bond models a hydrogen bond. In an embodiment, the first and second magnets each include first and second magnetic poles. The first magnets can be disposed on the exterior of the first elemental component with the first magnetic pole pointing away from the interior of the first elemental components. The second magnet can be disposed on the exterior of the second elemental component with the second magnetic pole of the second magnet pointing away from the interior of the second elemental component.
In an embodiment, the invention is directed to a molecular modeling device comprising a plurality of molecular components comprising a first atomic component and a second atomic component and means for attaching molecular components together to simulate both primary and secondary structure of a chemical compound.
The above summary of the present invention is not intended to describe each discussed embodiment of the present invention. This is the purpose of the figures and the detailed description that follows.
DRAWINGSThe invention may be more completely understood in connection with the following drawings, in which:
While the invention is susceptible to various modifications and alternative forms, specifics thereof have been shown by way of example and drawings, and will be described in detail. It should be understood, however, that the invention is not limited to the particular embodiments described. On the contrary, the intention is to cover modifications, equivalents, and alternatives falling within the spirit and scope of the invention.
DETAILED DESCRIPTION OF THE INVENTIONAs described more fully below, chemical bonds can broadly be classified into three main types: electrostatic, covalent, and metallic. Electrostatic bonds include ion-dipole bonds and dipole-dipole bonds, including hydrogen bonding. Ion-dipole bonding is an attractive force between an atom or molecule having a charge and an atom or molecule having a region(s) of greater or lesser electron density. An example would be the solvation of a sodium ion by a plurality of water molecules. Hydrogen bonding is a species of dipole-dipole bonding and can be described as an attractive force between opposite charges, molecules arising from the attraction between regions of greater electron density and regions of lesser electron density. Hydrogen bonding affects the structure of both molecules and complexes of molecules. By way of example, hydrogen bonding between water molecules affects the structure that complexes of water molecules take on, in both liquid and solid forms.
Both ion-dipole bonding and dipole-dipole bonding have an enormous amount of significance in understanding the structural forms assumed by molecules. In the context of biochemistry, hydrogen bonding directly affects the structure of macromolecules such as proteins. In turn, the function of a protein depends on its three-dimensional structure. For example, the catalytic activity of an enzyme depends on its three-dimensional structure. Beyond its native conformation, a given polypeptide chain can theoretically assume countless different structural conformations. However, the native conformation of a polypeptide chain is stabilized and can be favored, in part, by hydrogen bonding. Therefore, by way of example, understanding how hydrogen bonding affects molecular structure is important to understanding the structure and function of proteins.
The present invention relates to an apparatus for modeling chemical structures having multiple types of bonding, including ion-dipole bonding and/or dipole-dipole bonding such as hydrogen bonding. By way of example, the applicant has discovered that the effects of ion-dipole bonding and/or dipole-dipole can be modeled using components including magnets to simulate areas of greater or lesser electron density on an atom or molecule. In an embodiment, the invention is a molecular modeling device including a plurality of molecular components including a first elemental component comprising a plurality of first magnets and a second elemental component comprising a second magnet. A primary structural bond can attach the first elemental component to the second elemental component. In an embodiment, the primary structural bond can model a covalent bond. The molecular components can be attached to other molecular components through secondary structural bonds, wherein the primary structural bond attaches more strongly than the secondary structural bond. In an embodiment, the secondary structural bond models an ion-dipole bond. In an embodiment, the secondary structural bond models a dipole-dipole bond. In an embodiment the secondary structural bond models a hydrogen bond. In an embodiment, the first and second magnets each include first and second magnetic poles. The first magnets can be disposed on the exterior of the first elemental component with the first magnetic pole pointing away from the interior of the first elemental components. The second magnet can be disposed on the exterior of the second elemental component with the second magnetic pole of the second magnet pointing away from the interior of the second elemental component.
Chemical Bonding
Chemical bonds account for the forces uniting atoms into molecules, giving symmetry and order to substances of incredible variety and design. Linus Pauling's monograph, The Nature of the Chemical Bond, (©1938, 1940, and 1960) is a principal reference in this field, providing perspective important in many scientific fields today.
According to Pauling, chemical bonds may be classified into three general categories: electrostatic, covalent, or metallic bonds. This organization is not a rigorous one, for many chemical bonds are mixtures of these limiting arrangements. For example, particular covalent bonds have partial electrostatic or ionic character, including —OH, >CO, or >NH. The ionic character arises from a dissimilarity of atoms bonded together, a property Pauling defined as electronegativity.
Pauling's electronegativity index assigns a number to each element according one atom's ability to sequester electrons (charge) from other atoms bonded to it. For instance, the electronegativity of hydrogen (H)=2.1, carbon (C)=2.5, nitrogen (N)=3.0, and oxygen (O)=3.5. The differences when combined suggests that the carbon-hydrogen bond is not very ionic Δ(CH)=0.4, the nitrogen-hydrogen bond is moderately ionic Δ(NH)=0.9, and the oxygen-hydrogen bond yet is more ionic Δ(OH)=1.4. The electronegativity numbers have no units but are approximate indices for comparative use.
The consequences of ionic character to chemical bonds are far-ranging. They include (1) increased solubility of ionic solids (salts) in polar (ionic-covalent) solvents such as water (H2O), and (2) strong intermolecular attraction between molecules of unique orientation, particularly configurations involving a hydrogen atom bridge, the hydrogen bond.
Under certain conditions, an atom of hydrogen is attracted by rather strong forces to two atoms (such as oxygen and/or nitrogen), instead of one, so that the hydrogen may be considered to be acting as a bond between them. This is called the hydrogen bond.
The hydrogen bond often is represented by an ellipsis ( . . . ). Examples of a hydrogen bond are: between two water molecules (H2O . . . HOH) or between two peptide moieties in a protein (O . . . HN). Depending on the bond strength, the inter-atomic distance for a hydrogen bond is larger than that of a covalent OH or NH bond; typically, an O . . . H distance=1.7 Å, whereas the approximate HO covalent bond distance=1.0 Å. (the Angstrom unit of length=10−10 meters). This bond asymmetry is usually maintained throughout the process of making a hydrogen bond, or of breaking it. Hydrogen bonding can also lead to chemical change that may be instrumental to certain chemical processes or biochemical pathways. Such changes may be visualized in the mind once a three-dimensional model is held firmly in the hand.
The hydrogen bond typically is secondary in strength to that of its covalent partner. The energy to dissociate a hydrogen bond in water is about five percent of a primary O—H covalent bond, but the energy is important, indeed vital, to the function of water as a high-density liquid, having a large heat capacity and heat of vaporization, a high dielectric constant and large surface tension. The hydrogen bond also is a directed bond, imposing structure to what otherwise may be a chaotic mixture.
The example of a water molecule includes two hydrogen atoms having, on average, a net positive charge. In turn, the oxygen atom has, on average, two negative charges on the opposite side of the molecule from the two hydrogen atoms. The two negative charges are somewhat diffuse but generally positioned 109 degrees apart. Thus, water molecules generally require preferential orientation to engage in hydrogen bonding.
As stated above, embodiments of the present invention relate to an apparatus for modeling chemical structures having multiple types of bonding, including ion-dipole bonding and/or dipole-dipole bonding including hydrogen bonding. While not limiting the scope of the present invention, exemplary modeling apparatus structures will now be described.
Modeling Apparatus
Referring to
First elemental component 1 may be made from any of a variety of materials. By way of example, first elemental component 1 may include wood, cellulose fiber, polymer, glass, metal, or a composite material. Second elemental components 3, 7, may also be made from any of a variety of materials. By way of example, second elemental components 3, 7, may include wood, cellulose fiber, polymer, glass, metal, or a composite material.
Referring now to
Referring now to
Referring now to
Embodiments of the invention can include the use of magnets of different strength. By way of example, a primary structural bond can be an attachment between magnets of relatively higher strength while a secondary structural bond can be an attachment between magnets of relatively lower strength. By way of example, magnets included in a primary structural bond can be rare earth magnets such as neodymium iron boron while the magnets included in a secondary structural bond can be alnico. In this manner, the primary structural bonds can have a greater bonding strength than the secondary structural bonds.
As the magnetic force between to magnets diminishes with increasing distance, varying bond strength can also be achieved by altering the positioning of the magnets on the elemental components. By way of example, the magnets can be positioned farther below the surface of the elemental components so that the effective distance between magnets is greater. Referring now to
Referring now to
Embodiments of the present invention may be used to model many different types of molecules that may be hydrogen-bonded either intramolecularly or to other molecules. By way of example, embodiments of the present invention can model ammonia (NH3) and ammonium ion (NH4+), and the hydrogen bonding of these molecules to other molecules. Referring now to
Though embodiments of the invention have been shown in configurations for purposes of showing hydrogen bonding for molecules such as water and ammonia, one of skill in the art will appreciate that, in embodiments, the invention can also illustrate hydrogen bonding for other atoms and molecules.
Embodiments of the present invention can be used to model many different complexes. Referring now to
One of skill in the art will appreciate that there are many uses for models in accordance with the invention. By way of example, models in accordance with the invention can be used to illustrate and understand theories regarding the structure and behavior of liquid water. By way of example, in quantum mechanics, distinct conformations of pentagonal water (five-water complex) can be used to represent base states from which another more stable stationary state can be derived, which is a theory that is important to our understanding of liquid water. Further, the mixture theory of liquid water provides that as temperature changes, the concentration of components adjusts following laws of thermodynamics. By way of example, the pentagonal water conformation would decrease in concentration with increasing temperature.
Referring now to
Three second elemental components 305, simulating hydrogen atoms, are each attached to one first elemental component 301 in a manner simulating covalent bonding, but are not shown hydrogen bonding to another component, and are all pointing up. Three more second elemental components 307, simulating hydrogen atoms, are each attached to one first elemental component 301 in a manner simulating covalent bonding, and are pointing outward in a radial manner. As visible in this configuration, the model of hexagonal water can simulate lateral hydrogen bonding. Accordingly, as with real hexagonal water, the hexagonal water model structure can fit together with other hexagonal water models and fit together into a plane.
The hexagonal water model also has a capacity for vertical hydrogen bonding. Referring now to
In an embodiment, the invention can be used to model ion-dipole bonding. Referring now to
One of skill in the art will appreciate that ion dipole bonding can take on more complex forms. Referring now to
While not shown in the Figures herein, embodiments of the present invention can also be used to model the structure of clathrates (or cage compound). Clathrates are compounds in which the crystal lattice or structure of one component (the host molecule) complete encloses spaces in which a second component (the guest molecule) is located. An example would be a 20-water complex (H2O)20 forming a dodecahedron, a cage compound around guest molecules such as Ar, N2, O2, or CO2. Forming the cage compound from embodiments of the present invention is a simple matter of using components to first create a hydrogen-bonded cyclic five-water complex such as that shown in
While the present invention has been described with reference to specific poles (North and South) of a magnet pointing in specific directions, one of skill in the art will recognize that it is the relative orientation of one magnet to another that is significant and not the absolute orientation of any given magnet. That is, where one component has the North pole of a magnet facing outwardly and is configured to interact with another component that has the South pole of a magnet facing outwardly, the orientation of one magnet can be reversed so long as the orientation of the other magnet, and any other magnets configured for interaction, is also reversed.
While the present invention has been described with reference to several particular implementations, those skilled in the art will recognize that many changes may be made hereto without departing from the spirit and scope of the present invention.
Claims
1. A molecular modeling device comprising:
- a plurality of molecular components comprising a first elemental component comprising a plurality of first magnets; a second elemental component comprising a second magnet; and a primary structural bond attaching the first elemental component to the second elemental component;
- wherein molecular components are attached to other molecular components through magnetic attraction between first magnets and second magnets; wherein the primary structural bond attaches more strongly than the secondary structural bond.
2. The molecular modeling device of claim 1, the first and second magnets each having first and second magnetic poles, the first magnets disposed on the exterior of the first elemental component with the first magnetic pole pointing away from the interior of the first elemental components; the second magnet disposed on the exterior of the second elemental component with the second magnetic pole of the second magnet pointing away from the interior of the second elemental component.
3. The molecular modeling device of claim 1, the first magnetic pole comprising a South pole and the second magnetic pole comprising a North pole.
4. The molecular modeling device of claim 1, the first magnetic pole comprising a North pole and the second magnetic pole comprising a South pole.
5. The molecular modeling device of claim 1, the primary structural bond non-reversibly attaching the first elemental component to the second elemental component.
6. The molecular modeling device of claim 1, the primary structural bond comprising a fastening device.
7. The molecular modeling device of claim 3, the fastening device comprising a screw.
8. The molecular modeling device of claim 1, the primary structural bond comprising an adhesive.
9. The molecular modeling device of claim 1, the first elemental component comprising a material selected from the group consisting of wood, cellulose fiber, polymer, glass, metal, and a composite.
10. The molecular modeling device of claim 1, the second elemental component comprising a material selected from the group consisting of wood, cellulose fiber, polymer, glass, metal, and a composite.
11. The molecular modeling device of claim 1, wherein a plurality of molecular components attach to other molecular components through secondary structural bonds to model secondary structure.
12. The molecular modeling device of claim 1, wherein two second elemental components are non-reversibly attached to one first elemental component.
13. The molecular modeling device of claim 1, wherein the first and second elemental components are spherical.
14. The molecular modeling device of claim 1, the first magnets disposed on the exterior of the first elemental component in an orientation to model the charge symmetry distribution on an atom.
15. The molecular modeling device of claim 1, the first magnets disposed on the exterior of the first elemental component at a position wherein lines connecting each of the first magnets with the center of the first elemental component intersect at an angle of between 100 and 115 degrees.
16. The molecular modeling device of claim 15, the angle comprising a tetrahedral angle of about 109.5 degrees.
17. A molecular modeling device comprising:
- a plurality of molecular components comprising a first atomic component and a second atomic component; and
- means for attaching molecular components together to simulate both primary and secondary structure of a chemical compound.
18. The molecular modeling device of claim 17, wherein the means for attaching molecular components together to simulate both primary and secondary structure of a chemical compound simulates both covalent bonding and electrostatic bonding.
19. The molecular modeling device of claim 17, wherein the means for attaching molecular components together to simulate both primary and secondary structure of a chemical compound simulates both covalent bonding and hydrogen bonding.
Type: Application
Filed: Nov 9, 2004
Publication Date: May 11, 2006
Inventor: George Anderson (Minneapolis, MN)
Application Number: 10/985,346
International Classification: A63H 33/04 (20060101);