JP3668070B2 - Molecular structure model - Google Patents

Description

[0001]
BACKGROUND OF THE INVENTION
The present invention relates to a molecular structure model.
[0002]
[Prior art]
In general, in a compound composed of a plurality of types of atoms and ions, even if the types of atoms, ions or atomic groups constituting the compound are the same, the arrangement and bonding modes of atoms, ions or various atomic groups are different. Some have different properties. For example, optical isomers are typical examples, and a plurality of types of compounds having different arrangements of atoms, ions or atomic groups are known even though they have exactly the same chemical formula.
[0003]
On the other hand, as a conventional molecular model, there is an atomic position model configured such that the positions of atoms and ions are indicated by spheres, and the bonds between atoms and ions are indicated by shafts. There is also a polyhedron model configured in a polyhedron shape to show a geometrical arrangement such as crystal plane orientation in which atoms and ions are arranged. However, since these conventional models show only one of the position of atoms and ions and the geometrical plane arrangement, the relationship between the position of atoms and ions and the geometric structure is recognized. However, it is difficult to intuitively grasp the material structure. Therefore, the inventor of the present application has previously devised a crystal model of a skeleton structure, and has received Patent No. 2790247 as being able to intuitively grasp both the position of atoms and ions and the geometric structure of the crystal.
[0004]
[Problems to be solved by the invention]
Some molecules have a (chiral) structure that does not have mirror symmetry. For example, optical isomers are typical examples. In order to understand chiral molecular structures such as optical isomers, it is necessary to make it easy to grasp the asymmetry, but the conventional atomic position model can construct the structure itself, but the asymmetry is clear. There is a problem that it cannot be expressed.
In addition, although the crystal model of the skeleton structure can show the geometric structure of the crystal along with the arrangement of individual atoms and ions, the position of the atoms and ions is indicated by the center position and the vertex position of the skeleton structure. Therefore, since atoms and ions cannot be represented by substantial shapes, the types of atoms and ions cannot be indicated only by their shapes. For this reason, if only a macroscopic understanding of the crystal structure is required, even such a model can be expected to have a sufficient effect, but the molecular structure that does not have mirror symmetry, for example, the structural difference of optical isomers. There is a problem that it is difficult to grasp.
[0005]
Therefore, the present invention solves the above-mentioned problems, the problem is that in the molecular structure model of the skeleton structure, the molecular structure that does not have mirror symmetry by indirectly indicating the type of atom, molecule or atomic group The purpose is to provide a model that can clearly grasp the structural features of the model.
[0006]
[Means for Solving the Problems]
In order to solve the above problems, the molecular structure model of the present invention is commonly connected at a central point, and a plurality of plate-like portions arranged around the central point are connected to each other by crossing lines, The outer edge of the plate-shaped part forms a ridge line and the ridge lines are connected to each other to form a vertex, the ridge line corresponds to a ridge line between each face of the polyhedron, and the vertex is a vertex of the polyhedron A molecular structure model having a skeleton structure configured to correspond to: at least a part of the central point and the apex represents a position of an atom, an ion, or an atomic group, and at least the intersection line and the edge line some represents a bond between atoms or ions or atomic group, the plurality of the plate-shaped portion, indicated by the type or the ridge of the atomic or ionic or atomic group represented by the vertex Said include the plate-like portion having a different color tone from each other depending on the type of binding, the sequence of the plurality of plate-like portions of the color tone in the skeleton structure as shown mirror symmetry having no chiral conformation Of the atoms, ions, or atomic groups indicated by the vertices so that combinations of color tones of the plurality of plate-like portions constituting the vertices corresponding to different types of atoms, ions, or atomic groups are different from each other. The skeleton structure represents a chiral molecular structure having no mirror symmetry when the type and the combination of color tones of the plurality of plate-like portions constituting the vertex are associated with each other .
[0007]
According to the present invention, a plurality of plate-like portions having different colors according to the types of atoms or ions or atomic groups indicated by the apexes show a plurality of molecular structures having no mirror symmetry. Differences in the arrangement mode of atoms or ions or atomic groups between models can be distinguished from each other by the arrangement mode of the color tone of the plate-like portion. Further, since the to be shown by combination of color tone between a plurality of plate-like portions constituting the vertices sequence differences embodiment of atomic or ionic or atomic group corresponding thereto, atom or ion indicated some vertices Alternatively, it is possible to specify the type of atomic group relatively easily, and it is only necessary to change the color tone for each plate-like portion, and the model production is not unnecessarily complicated.
[0008]
In the present invention, the skeleton structure is a tetrahedral skeleton structure, and the plurality of vertices are constituted by the three plate-like portions, and the types of atoms or ions or atomic groups indicated by the vertices constitute the vertices. It is preferable that the three color combinations of the plate-like portions correspond to each other. According to this means, various kinds of molecular structures such as amino acids can be obtained by the type of atom or ion or atomic group indicated by the vertex corresponding to the combination of the color tones of the three plate-like portions constituting the vertex. Can be expressed easily.
[0009]
In the present invention, in the skeleton structure, the vertex formed at the outer edge of the surface region in the surface region composed of the surfaces of the plurality of plate-like portions surrounded by three or more ridgelines with the center point as the center It is preferable that the kind of atom or ion or atomic group indicated by the above corresponds to the color tone combination of the two plate-like portions in the surface region constituting the vertex. According to this means, the type of atom or ion or atomic group indicated by the vertex formed at the outer edge of the surface region surrounded by three or more ridgelines surrounding the center point is the surface constituting the vertex. An atom or ion or atom indicated by each vertex formed at the outer edge of the surface region in a state where the surface region can be seen from a certain orientation by corresponding to a combination of color tones of two plate-like portions in the region Since the kind of group can be specified, the arrangement | sequence aspect of molecular structure can be understood more easily.
[0010]
In this invention, it is preferable that the said skeleton structure is connected with another structure part in at least any one of the said center point, the said vertex, and the said ridgeline. Here, the other structural portion may have a structure corresponding to the above skeleton structure, or may have a structure not corresponding to the above skeleton structure.
[0012]
DETAILED DESCRIPTION OF THE INVENTION
[First Embodiment] Next, an embodiment of a molecular structure model according to the present invention will be described in detail with reference to the accompanying drawings. FIG. 1 illustrates a molecular structure model for representing an amino acid according to the present embodiment. FIG. 1 (a) is a chemical structural formula showing the basic structure of an amino acid, with respect to a central carbon atom ( _Cα ) 11, a hydrogen atom (H) 12, an amino group (NH ₂ ) 13, a carboxyl group (COOH). 14 and side chain (R) 15 are bonded. 20 types of amino acids that can exist in the body (hydrophobic amino acids alanine, valine, phenylalanine, isoleucine, leucine, proline, methionine, charged amino acids aspartic acid, glutamic acid, lysine, polar amino acids serine, threonine, Tyrosine, cysteine, asparagine, glutamine, arginine, glycine having the simplest structure), and these amino acids differ only in the structure of the side chain R and have the same basic structure. For amino acids, a chiral molecular structure without mirror symmetry is important.
[0013]
The molecular structure model of this embodiment is shown in FIGS. FIGS. 1B to 1D show states in which the same molecular structure model is viewed from different directions. This embodiment has a regular tetrahedral skeleton structure. The regular tetrahedron skeleton structure includes six isosceles triangular plate-like portions B _{1 to} B ₆ sharing the center point CT. The four vertices P _{1 to} P ₄ of this structure are each constituted by three plate-like portions. In this model, 12 intersecting lines extending from the center point CT to the vertices P _{1 to} P ₄ are formed, and 6 ridge lines are formed between the vertices P _{1 to} P ₄ .
[0014]
In this model, the front and back surfaces of the plate-like portions B ₁ , B ₂ and B ₃ are both in a first color tone (for example, purple), and the front and back surfaces of the plate-like portion B ₄ are in a second color tone (for example, yellow). front and back surfaces of the Jo portion B ₅ to the third color (e.g. red), the front and back surfaces of the plate-like portion B ₆ in the fourth color (e.g. blue), are colored respectively.
[0015]
The center point CT indicates the central carbon atom 11. Further, the vertex P ₁ to which the plate-like parts B ₁ , B ₂ and B ₃ are connected indicates a side chain 15, and the vertex P ₂ to which the plate-like parts B ₁ , B ₄ and B ₆ are connected is hydrogen. The vertex P ₃ indicating the atom 12 and connected to the plate-like parts B ₁ , B ₄ and B ₅ denotes the amino group 13, and the vertex P ₄ connected to the plate-like parts B ₁ , B ₅ and B _6. Represents a carboxyl group 14.
[0016]
Thus, in this model, all vertices P ₁ plate portion is a first color indicates a side chain 15, the color of the plate-like portion to be connected first color connected, the second color and fourth vertex P ₂ is a combination of color tone represents a hydrogen atom 12, the color of the plate-like portion to be connected first color, the apex P ₃ is a combination of the second tone and the third tone amino An apex P ₄ indicating the base 13 and the connected plate-like portions having the first color tone, the third color tone, and the fourth color tone indicates the carboxyl group 14. Therefore, it is possible to know the difference between the types of atoms (or ions), groups, and other atomic groups indicated at each vertex by the combination of the color tones of the plate-like portions connected to each vertex. In addition, the combination of the appearances (color tones) of a plurality of plate-like portions connected to the vertices indicating different atoms, ions, or atomic groups is different from each other, so that the atoms, ions, or atomic groups in the overall structure of the molecular structure. Arrangement and symmetry can be grasped intuitively. For example, in two types of molecular structures with similar bond structures, it is easy to see how the arrangement modes taking into account the types of atoms, ions or atomic groups are different. I can know.
[0017]
In the present embodiment, the model indicates amino acids, and in particular, since the structure of the side chain 15 is different for each type of amino acid, the plate connected to the vertex P ₁ indicating the noted side chain 15 The color portions B ₁ , B ₂ and B ₃ have the same color tone so that the position of the side chain 15 can be grasped immediately from any orientation. In particular, when each of a plurality of different types of amino acids is represented by a model, the second color tone, the third color tone, and the fourth color tone are all common to each model, and for the first color tone, different amino acids are used. It is preferable that the groups have different colors.
[0018]
FIGS. 2A and 2B show models representing optical isomers in specific amino acids. Amino acids have two optical isomers, L-type and D-type. FIG. 2A shows a clock around the central carbon atom 11 when the central carbon atom 11 is viewed from the bonding direction of the hydrogen atom 12. FIG. 2 (b) shows an L shape arranged around a carboxyl group 14, a side chain 15, and an amino group 13 around the central carbon atom 11 when viewed from the same direction. The D-type is arranged around the carboxylic acid, the amino group 13 and the side chain 15 in this order. In addition, all the amino acids which comprise the protein synthesize | combined in the living body are L type.
[0019]
In the model of this embodiment, when explaining the structural difference between the L-type amino acid and the D-type amino acid, the L-type model shown in FIG. a D-type model shown in both the plate portion B _4, B ₅ and the surface area of the B ₆ (the area surrounded by the three ridge lines connecting the three vertices P ₂ to P ₄ each other) It may be shown side by side in a visually recognizable posture. By doing so, it can be seen at a glance that the L-type model and the D-type model are arranged in different orders around the central point CT indicating the central carbon atom in the color of the three plate-like portions. .
[0020]
Second Embodiment Next, a protein molecular structure model constructed on the basis of the above-described amino acid molecular structure model will be described. As is well known, a protein is formed by binding a plurality of amino acids through the peptide bond S shown in FIG. Although it is extremely difficult to explain the protein with the conventional model, as shown in FIG. 3B, the apex of the tetrahedral skeleton structure portion 20 having the same structure as the above-mentioned amino acid model, and a quadrangular plate shape A protein molecular structure model can be constructed by linking the apexes of the quadrilateral structure portion 30 representing the peptide bond formed in (1). In this model, each plate-like portion is colored in the same manner as in the first embodiment. In FIG. 3B, instead of representing the coloring, atoms (atomic groups in the case of atomic groups) are shown. Indicates the atom involved in the bond. In proteins, all atoms from one central carbon atom (C _α ) to the next central carbon atom (C _α ) in the polypeptide chain are all located on the same plane, and the bond distance and bond angle are substantially constant. However, it has two degrees of freedom that can rotate around the bond axis between the central carbon atom (C _α ) and the N atom and the bond axis between the central carbon atom (C _α ) and the C atom.
[0021]
In order to realize the above structure, for example, a flexible body such as a string or a wire is introduced into the plate-shaped portions of the tetrahedral skeleton structure portion 20 and the quadrilateral structure portion 30 to form a tetrahedral skeleton structure. The vertex indicating the carboxyl group 14 (carbon atom thereof) in the portion 20 and the vertex indicating the carbon atom in the quadrilateral structure portion 30 are butted so that the above-mentioned strip passes through this butting portion. That's fine. In this structure, the apex of the tetrahedral skeleton structure portion 20 and the apex of the quadrilateral structure portion 30 are maintained in contact with each other, but both structure portions can freely rotate about the butted portion, Can rotate around the axis. Moreover, it becomes a structure which has the same freedom degree by comprising a universal joint as this butt | matching part. Of course, it is also possible to configure such that only rotation around the bond axis between the central carbon atom 11 and the carboxyl group 14 and rotation around the bond axis between the central carbon atom 11 and the amino group 13 are possible. it can.
[0022]
According to this model, it is also possible to represent a secondary structure of a protein generated by hydrogen bonding (a three-dimensional structure connected to a chain), such as an α-helix or β sheet.
[0023]
[Third Embodiment] Next, a molecular structure model of tartaric acid will be described. Tartaric acid also has a chiral molecular structure with no mirror symmetry. The structure shown in FIG. 4A is called D (−)-tartaric acid, and the structure shown in FIG. 4B is called L (+)-tartaric acid. In addition, what is shown in FIG. 4 (c) is called meso-tartaric acid, and the achiral type molecular structure with mirror symmetry is formed as a whole by making a pair of chiral type structural parts. is there. Among these, D type and L type are optical isomers. The connecting arm shown in each figure represents that the narrower side protrudes below the page.
[0024]
This model is as shown in FIG. 4 (d), and a slightly vertically long (long in the vertical direction in the figure) same-shaped tetrahedral skeleton structure is turned upside down and rotated 60 degrees around the vertical axis. It has a structure that is combined in a posture. The upper tetrahedral skeleton structure portion 40 has vertices P _{1 to} P ₃ arranged at the upper end, and the remaining one vertex coincides with the center point CT ₂ of the lower tetrahedral skeleton structure portion 50. The lower tetrahedral skeleton structure 50 is configured such that vertices Q _{1 to} Q ₃ are arranged at the lower end, and the remaining one vertex coincides with the center point CT ₁ of the upper skeleton structure 40. Further, the plate-like portions B _{4 to} B ₆ and D _{4 to} D ₆ are alternately connected so as to share a ridge line connecting the center points CT ₁ and CT ₂ .
[0025]
Also in this model, the plate-like parts B ₁ , B ₂ and B ₃ are colored in mutually different colors, and the plate-like parts D ₁ , D ₂ and D ₃ are also colored in mutually different colors. Yes. Therefore, the hydrogen atom, hydroxyl group, and carboxyl group bonded to the central carbon atom indicated by the center point CT ₁ are distinguished by combinations of different color tones in two different plate-like portions of the plate-like portions B ₁ , B _2, and B _3. It is possible to show by vertices P _{1 to} P ₃ where the two plate-like parts are connected. Further, the hydrogen atom, hydroxyl group and carboxyl group bonded to the central carbon atom indicated by the center point CT2 can be distinguished by combinations of different color tones in two different plate-like portions among the plate-like portions D ₁ , D ₂ and D _3. Are indicated by vertices Q _{1 to} Q ₃ to which the two plate-like portions are connected.
[0026]
Therefore, the three types of tartaric acid shown in FIGS. 4A to 4C have the color tones of the plate-like portions B _{1 to} B ₃ and D _{1 to} D ₃ , respectively, according to the structural model shown in FIG. 4D. Anything can be expressed simply by changing the arrangement, and can be clearly distinguished from each other. By using this model, the structures of the above three kinds of tartaric acid can be explained very easily, and the explained side can be intuitively understood. In particular, by explaining the three types of models so as to show the surface region of the upper end surface where the _three plate-like portions B _{1 to} B ₃ are arranged and the surface region of the lower end surface where the plate-like portions D _{1 to} D ₃ are arranged. Can easily show the differences between the three models.
[0027]
【The invention's effect】
As described above, according to the present invention, the plate-like portions having different color tones according to the types of atoms or ions or atomic groups indicated by the vertices are included , thereby providing mirror symmetry. Differences in the arrangement of atoms, ions, or atomic groups among models showing a plurality of molecular structures that are not allowed to be distinguished from each other can be distinguished from each other by a combination of color tones of the plate-like portion. Also, since the as atomic or ionic or atomic group is shown by the different color tones among a plurality of plate-like portions constituting the vertices corresponding thereto, it is only changing the color tone for each plate-like portion, model production Is not complicated.
[Brief description of the drawings]
FIG. 1 shows a chemical structural formula (a) showing the structure of an amino acid expressed in the first embodiment of the molecular structure model according to the present invention, and the appearance of the first embodiment viewed from three directions. It is a perspective view (b)-(d).
FIG. 2 is a perspective view (a) and (b) showing two optical isomers of amino acids according to the first embodiment.
FIG. 3 is a chemical structural formula (a) showing the structure of a protein expressed in the second embodiment of the molecular structure model according to the present invention and a perspective view (b) showing the appearance of the second embodiment.
FIG. 4 is a perspective view showing chemical structural formulas (a) to (c) showing the structures of three kinds of tartaric acid expressed in the third embodiment of the molecular structure model according to the present invention and the appearance of the third embodiment. (D).
[Explanation of symbols]
10 amino acid 11 central carbon atom 12 hydrogen atom 13 amino group 14 carboxyl group 15 side chain 20 tetrahedral skeleton structure 30 tetragonal structure 40 upper tetrahedral skeleton structure 50 lower tetrahedral skeleton structure

Claims (4)

A plurality of plate-like portions connected in common at the center point and connected around each other by cross lines, and the outer edges of the plate-like portions form ridge lines and the ridge lines are mutually connected Are connected to each other to form vertices, the ridge line corresponds to the ridge line between each face of the polyhedron, and the molecular structure model has a skeleton structure configured to correspond to the vertex of the polyhedron Because
At least a part of the center point and the apex represents a position of an atom or ion or an atomic group, and at least a part of the intersecting line and the ridge line represents a bond between the atom, the ion or the atomic group;
The plurality of plate-like portions include the plate-like portions having different colors depending on the type of atom or ion or atomic group indicated by the vertex or the type of bond indicated by the ridgeline ,
In the skeleton structure, the arrangement of color tones of the plurality of plate-like parts is configured to show a chiral three-dimensional structure having no mirror symmetry,
The types of atoms, ions, or atomic groups indicated by the vertices so that combinations of color tones of the plurality of plate-like portions constituting the vertices corresponding to different types of the atoms, ions, or atomic groups are different from each other; A molecular structure model in which the skeleton structure represents a chiral molecular structure having no mirror symmetry when a plurality of combinations of color tones of the plate-like portions constituting the vertex are associated with each other . The skeleton structure according to claim 1, wherein the skeleton structure is a tetrahedral skeleton structure, and the plurality of vertices are configured by the three plate-like portions, and the types of atoms or ions or atomic groups indicated by the vertices are configured. A molecular structure model in which the three color combinations of the plate-like parts correspond to each other. 3. The outer edge of the surface region according to claim 1 , wherein, in the skeleton structure, in a surface region composed of the surfaces of the plurality of plate-like portions surrounded by the three or more vertices and the ridge lines with the central point as a center. The types of atoms or ions or atomic groups indicated by the three or more vertices formed on the surface correspond to combinations of the color tones of the two plate-like portions in the surface region constituting the vertex. Characteristic molecular structure model.   4. The molecular structure according to claim 1, wherein the skeleton structure is connected to another structure portion at least one of the center point, the apex, and the ridge line. 5. model.

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