US20060099877A1

US20060099877A1 - Chemical modeling apparatus

Info

Publication number: US20060099877A1
Application number: US10/985,346
Authority: US
Inventors: George Anderson
Original assignee: Individual
Current assignee: Individual
Priority date: 2004-11-09
Filing date: 2004-11-09
Publication date: 2006-05-11

Abstract

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.

Description

FIELD OF THE INVENTION

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 INVENTION

Atoms 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 INVENTION

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 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.

DRAWINGS

The invention may be more completely understood in connection with the following drawings, in which:
FIG. 1 is a front schematic view of a modeling component in accordance with an embodiment of the invention modeling water (H₂O).
FIG. 2 is a back schematic view of the modeling component of FIG. 1.
FIG. 3 is a cross-sectional schematic view of a modeling component taken along lines A-A′ of FIG. 1.
FIG. 4 is a cross-sectional schematic view of the modeling component taken along lines B-B′ of FIG. 2.
FIG. 5 is a cross-sectional schematic view of an alternative embodiment of a modeling component.
FIG. 6 is cross-section schematic view of a modeling component with magnets that are disposed within channels away from the surface of the modeling component.
FIG. 7 is a schematic view of another embodiment of a modeling component in accordance with the invention.
FIG. 8 is a schematic side offset view of another embodiment of a modeling component in accordance with the invention.
FIG. 9 is a schematic view of an embodiment of the invention modeling a hydrogen-bonded cyclic five-water complex.
FIG. 10 is a schematic view of an embodiment of the invention modeling a hydrogen bonded cyclic six-water complex (primitive unit cell of hexagonal ice).
FIG. 11 is a schematic offset view of an embodiment of the invention modeling two hexagonal water complexes hydrogen bonded to each other (complete unit cell of hexagonal ice).
FIG. 12A is a schematic view of an embodiment of the invention modeling a hydroxyl ion, shown along with a model of a water molecule.
FIG. 12B is a schematic view of an embodiment of the invention modeling a hydrated hydroxyl ion, H₃O₂ ⁻.
FIG. 13A is schematic view of an embodiment of the invention modeling the formation of a hydronium ion, shown along with models of three water molecules that can hydrate the hydronium ion.
FIG. 13B is a schematic view of an embodiment of the invention modeling a hydrated hydronium ion, H₉O₄ ⁺.
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 INVENTION

As 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=10⁻¹⁰meters). 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 FIG. 1, a front schematic view of a modeling component 10 in accordance with an embodiment of the invention is shown. A first elemental component 1 is shown attached to two second elemental components 3, 7. In this view, first elemental component 1 is shown as a sphere. However, one of skill in the art will appreciate that first elemental component 1 could be made in other shapes. In an embodiment, portions of the sphere are flattened to create an irregular sphere. By way of example, in an embodiment, portions of the sphere where first elemental component 1 is attached to two second elemental components 3, 7 can be flattened so that the sphere of the first element and the spheres of the second elemental components intersect. Both of the second elemental components 3, 7, have a magnet 5, 9, disposed on their surface. Magnets 5, 9, may be attached with a screw, a nail, an adhesive, or the like. By way of example, magnet 5 may be attached to second elemental component 3 with an adhesive. The magnets 5, 9, are disposed on second elemental components 3, 7, so as to reflect positions of lesser electron density, net positive charge on the atom. In this view, the North pole of the magnets 5, 9, is shown pointing away from the first elemental component 1. Referring now to FIG. 2, a back schematic view of the modeling component 10 of FIG. 1 is shown. Magnets 11, 13 are disposed on the surface of first elemental component 1. Magnets 11, 13, may be attached with a screw, a nail, an adhesive, or the like. By way of example, magnet 11 may be attached to second elemental component 7 with an adhesive. In this view, the South pole of the magnets 11, 13, is shown pointing away from the first elemental component 1.
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 FIG. 3, a cross-sectional schematic view of a modeling component taken along lines A-A′ of FIG. 1 is shown. In this view, fastening device 15 can be seen attaching second elemental component 3 to first elemental component 1. Fastening device 17 can be seen attaching second elemental component 7 to first elemental component 1. Fastening devices 15 and 17 may be the same or different. Fastening devices 15, 17, may include wood, cellulose fiber, polymer, glass, metal, or a composite. Fastening device 15, 17, may include a screw, such as a wood screw, a nail, a dowel, an adhesive, and the like. Fastening devices may also include threaded protrusions or threaded channels. By way of example, one elemental component may include a protrusion having threads adapted and configured to fit with corresponding threads disposed in a channel on a second elemental component. In this view, the bond angle 19 between lines drawn through the center of second elemental components 3, 7, and the center 21 of the first elemental component 1 is determined from literature of chemical bonds and valance. In the case of water ice, the angle 19 is approximately 109.5 degrees. In an embodiment, the angle 19 may be between 100 and 115 degrees. FIG. 3 also shows magnets 5, 9, disposed on second elemental components 3, 7. In this view magnets 5, 9, fit into a recessed portion of second elemental components 3, 7. However, magnets 5, 9, may also be attached to second elemental components 3, 7, without being in a recessed portion. Magnets 5, 9, may be attached to second elemental components 3, 7, with a screw, a nail, an adhesive, and the like. By way of example, in an embodiment, magnet 5 is attached to second elemental component 3 with an adhesive.
Referring now to FIG. 4, a cross-sectional schematic view of a modeling component taken along lines B-B′ of FIG. 2 is shown. In this view, the angle 23 between lines drawn through the center of magnets 11, 13, and the center 21 of the first elemental component 1 is determined from literature of chemical bonds and valance. In the case of water ice, the angle 19 is approximately 109.5 degrees. In an embodiment, the angle 23 may be between 100 and 115 degrees. FIG. 4 shows magnets 11, 13, disposed on first elemental component 1. In this view, magnets 11, 13, fit into recessed portions of first elemental component 1. However, magnets 11, 13, may also be attached to first elemental component 1, without being in a recessed portion. Magnets 11, 13, may be attached to first elemental component 1, with a screw, a nail, an adhesive, and the like. By way of example, in an embodiment, magnet 11 is attached to first elemental component 1 with an adhesive.
Referring now to FIG. 5, a cross-sectional schematic view of an alternative embodiment of a modeling component 50 is shown. Second elemental component 7 is reversibly attached to first elemental component through attraction between magnet 25 and magnet 27. In this manner, the modeling system can simulate a hydroxyl ion (OH⁻) when second elemental component 7 is not attached to first elemental component 1. The unattached second elemental component 7 can then associate with and attach to a model of a water molecule as in FIG. 1 to simulate a hydronium ion (H₃O⁺) as shown in FIG. 8. Fastening device 15 attaches second elemental component 3 to first elemental component 1. Fastening device 15 may include wood, cellulose fiber, polymer, glass, metal, or a composite. Fastening device 15 may include a screw, such as a wood screw, a nail, a dowel, an adhesive, and the like. In this view, the angle 19 between lines drawn through the center of second elemental components 3, 7, and the center 21 of the first elemental component 1 is determined from literature of chemical bonds and valance. In the case of water, the angle 19 is approximately 109.5 degrees. In an embodiment, the angle 19 may be between 100 and 115 degrees. FIG. 5 also shows magnets 5, 9, disposed on second elemental components 3, 7. In this view magnets 5, 9, fit into a recessed portion of second elemental components 3, 7. However, magnets 5, 9, may also be attached to second elemental components 3, 7, without being in a recessed portion. Magnets 5, 9, may be attached to second elemental components 3, 7, with a screw, a nail, an adhesive, and the like. By way of example, in an embodiment, magnet 5 is attached to second elemental component 3 with an adhesive. In an embodiment, magnet 9 is attached to second elemental component 7 with an adhesive. Magnets of the invention may include any that can display an attractive force, or a repulsive force, great enough for the purposes contemplated herein. In an embodiment, magnets of the invention can include ceramic (ferrite), alnico (aluminum, nickel, cobalt), samarium cobalt, neodymium iron boron, and composites. Magnets of the invention can be in many different shapes. By way of example, magnets of the invention can include disk and bar magnets.
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 FIG. 6, a cross-sectional schematic view of a modeling component 70 is shown that is similar to that of FIG. 4. However, in this embodiment the magnets are positioned farther away from the surface of the elemental component. Specifically, FIG. 6 shows magnets 11, 13, disposed on first elemental component 1. In this view, magnets 11, 13, are disposed within channels 71 and 73 respectively a distance from the surface of first elemental component 1. In this manner, the magnets 11, 13 would attach to other magnets less strongly than they would if they were positioned at the very surface of first elemental component 1. Magnets 11, 13, may be attached to first elemental component 1, with a screw, a nail, an adhesive, and the like. By way of example, in an embodiment, magnet 11 is attached to first elemental component 1 with an adhesive. In an embodiment, magnets comprising primary structural bonds are disposed closer to the surface of the first elemental component than are magnets comprising secondary structural bonds.
Referring now to FIG. 7, a schematic view of another embodiment of a modeling component 100 in accordance with the invention is shown. A first elemental component 101 is shown attached to two second elemental components 103, 107. In this embodiment, first elemental component is a cube. Both of the second elemental components 103, 107, have a magnet 105, 109, disposed on their surface. Magnets 105, 109, may be attached with a screw, a nail, an adhesive, or the like. By way of example, magnet 105 can be attached to second elemental component 103 with an adhesive. The magnets 105, 109, are disposed on second elemental components 103, 107, so as to reflect positions of lesser electron density. Magnets 111, 113 are disposed on the surface of first elemental component 101. Magnets 111, 113, may be attached with a screw, a nail, an adhesive, or the like. By way of example, magnet 111 may be attached to second elemental component 107 with an adhesive.
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 FIG. 8, a first elemental component 152, representing nitrogen, is attached to three second elemental components 153, each representing a hydrogen. Together, first elemental component 152 and the three second elemental components 153 form a complex 151 modeling an ammonia molecule. Magnets 155 are disposed on each of the three second elemental components 153. Magnets 155 can attach to other magnets (not shown) on other model components to simulate the effects of hydrogen bonding. A magnet 157 is disposed on the top of first elemental component 152 in a configuration to simulate the electron or charge density on a nitrogen atom when it is in an ammonia molecule. Another second elemental component 159 is shown that is not attached to the ammonia complex 151. Second elemental component 159 has magnets 161, 163 disposed on opposite sides, in this view, top and bottom. Magnets 161 and 157 are configured so that there is an attractive force by which second elemental component 159 can attach to first elemental component 152, forming an ammonium ion.
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 FIG. 9, a schematic view of an embodiment of the invention modeling a hydrogen-bonded cyclic five-water complex 200 is shown. Five first elemental components 201, simulating oxygen atoms, are in a complex held together by five second elemental components 203, simulating hydrogen atoms, that are each attached to one first elemental component in a manner to simulate covalent bonding and attached to one first elemental component in a manner to simulate hydrogen bonding. Five more second elemental components 205, simulating hydrogen atoms, are each attached to one first elemental component 201 in a manner simulating covalent bonding, but are not shown hydrogen bonding to another component. The non-hydrogen bonded second elemental components 205 shown are all pointing up. However, one of skill in the art will appreciate that each one can point either up or down depending on the orientation of the first elemental components 201. In a cyclic five-water complex, those components simulating oxygen (first elemental components 201) lie approximately in the same plane forming a pentagonal shape when viewed from above or below.
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 FIG. 10, a schematic view of an embodiment of the invention modeling a hydrogen-bonded cyclic six-water complex (primitive unit cell of hexagonal ice) is shown. Six first elemental components 301, simulating oxygen atoms, are in a complex held together by six second elemental components 303, simulating hydrogen atoms, that are each attached to one first elemental component in a manner to simulate covalent bonding and attached to one first elemental component in a manner to simulate hydrogen bonding. In a cyclic six-water complex, those components simulating oxygen (first elemental components 301) do not lie flat in the same plane, but rather take on a “puckered” configuration in the plane.
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 FIG. 11, an offset view of an embodiment of the invention modeling a complete unit cell of hexagonal ice is shown.
In an embodiment, the invention can be used to model ion-dipole bonding. Referring now to FIG. 12A, a model of a hydroxyl ion 403 is shown along with a model of a water molecule 401. The hydroxyl ion 403 includes a first elemental component 413 with three secondary structural magnets 419 disposed thereon having tetrahedral symmetry (only two of the three are shown). A second elemental component 415 is attached to the first elemental component 413 through a primary structural bond (not shown). A separate secondary structural magnet 417 is disposed on the second elemental component 415. Referring now to FIG. 12B, the hydroxyl ion 403 and the water molecule 401 can move together in the direction of arrow 421 (shown in FIG. 12A) to form the structure of H₃O₂ ⁻, a hydrated hydroxyl molecule 430.
One of skill in the art will appreciate that ion dipole bonding can take on more complex forms. Referring now to FIG. 13A, the formation of a model hydronium ion (H₃O⁺) 440 and 450 is shown along with models of three water molecules that can hydrate the hydronium ion. A first elemental component 441 has two magnets 449 (only one shown) disposed on its surface. The first elemental component 441 is attached through primary structural bonds to a pair of second elemental components 445. Magnets 447 are disposed on the surface of the second elemental components 445. The first elemental component 441 and the pair of second elemental components 445 together, in this example, represent a water molecule 440. A third elemental component 453, in this case representing a hydrogen atom 450, has two magnets 455 disposed on its surface. One of the magnets 455 can be attracted to and attach to magnet 449 as indicated by arrow 457. Together, the hydrogen atom 450 and the water molecule 440 form a hydronium ion that has a net positive charge, shared equally among the three hydrogen atoms following the theory of resonance. Three molecular modeling components 401, in this case representing other water molecules, having magnets 409 disposed on their surfaces can attach to the exposed magnets 447 and 455 of the newly formed hydronium ion as indicated by arrows 449, 451, and 452, to form a hydrated hydronium ion (H₉O₄ ⁺) as shown in FIG. 13B. One of skill in the art will appreciate that many other types of ion-dipole bonds can be modeled in a like manner using embodiments of the invention.
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)₂₀forming 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 FIG. 9 and then arranging fifteen additional water models into a dodecahedron having a total of twelve pentagon water structures attached to one another through the magnets contained on their surface, modeling further hydrogen bonding, in order to create the cage compound. There are many examples of water clathrates reported in the literature containing different guest molecules and having a variety of host structures, and we expect the present invention to be applicable to modeling for all.
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.