Molecular geometry Molecular geometry or molecular structure is the three-dimensional arrangement of the atoms that constitute a molecule

. It determines several properties of a substance including its reactivity, polarity, phase of matter, color, magnetism, and biological activity.[1][2] Molecular geometry determination The molecular geometry can be determined by various spectroscopic methods and diffraction methods. IR, microwave and Raman spectroscopy can give information about the molecule geometry from the details of the vibrational and rotational absorbances detected by these techniques. X-ray crystallography, neutron diffraction and electron diffraction can give molecular structure for crystalline solids based on the distance between nuclei and concentration of electron density. Gas electron diffraction can be used for small molecules in the gas phase. NMR and FRET methods can be used to determine complementary information including relative distances, [3][4][5] dihedral angles, [6] [7] angles, and connectivity. Molecular geometries are best determined at low temperature because at higher temperatures the molecular structure is averaged over more accessible geometries (see next section). Larger molecules often exist in multiple stable geometries (conformational isomerism) that are close in energy on the potential energy surface. Geometries can also be computed by ab initio quantum chemistry methods to high accuracy. The molecular geometry can be different as a solid, in solution, and as a gas. The position of each atom is determined by the nature of the chemical bonds by which it is connected to its neighboring atoms. The molecular geometry can be described by the positions of these atoms in space, evoking bond lengths of two joined atoms, bond angles of three connected atoms, and torsion angles (dihedral angles) of three consecutive bonds. The influence of thermal excitation Since the motions of the atoms in a molecule are determined by quantum mechanics, one must define ´motionµ in a quantum mechanical way. The overall (external) quantum mechanical motions translation and rotation hardly change the geometry of the molecule. (To some extent rotation influences the geometry via Coriolis forces and centrifugal distortion, but this is negligible for the present discussion.) A third type of motion is vibration, which is the internal motion of the atoms in a molecule. The molecular vibrations are harmonic (at least to good approximation), which means that the atoms oscillate about their equilibrium, even at the absolute zero of temperature. At absolute zero all atoms are in their vibrational ground state and show zero point quantum mechanical motion, that is, the wavefunction of a single vibrational mode is not a sharp peak, but an exponential of finite width. At higher temperatures the vibrational modes may be thermally excited (in a classical interpretation one expresses this by stating that ´the molecules will vibrate fasterµ), but they oscillate still around the recognizable geometry of the molecule. To get a feeling for the probability that the vibration of molecule may be thermally excited, we inspect the Boltzmann factor

, where ¨E is the excitation energy of the vibrational mode, k the Boltzmann constant and T the absolute temperature. At 298K (25 °C), typical values for the Boltzmann factor are: 0.089 for ¨E = 500 cmí1 ; ¨E = 0.008 for 1000 cmí1 ; 7 10í4 for ¨E = 1500 cmí1. That is, if the excitation energy is 500 cmí1, then about 9 percent of the molecules are thermally excited at room temperature. The lowest excitation vibrational energy in water is the bending mode (about 1600 cmí1). Thus, at room temperature less than 0.07 percent of all the molecules of a given amount of water will vibrate faster than at absolute zero. As stated above, rotation hardly influences the molecular geometry. But, as a quantum mechanical motion, it is thermally excited at relatively (as compared to vibration) low temperatures. From a classical point of view it can be stated that more molecules rotate faster at higher temperatures, i.e., they have larger angular velocity and angular momentum. In quantum mechanically language: more eigenstates of higher angular momentum become thermally populated with rising temperatures. Typical rotational excitation energies are on the order of a few cmí1. The results of many spectroscopic experiments are broadened because they involve an averaging over rotational states. It is often difficult to extract geometries from spectra at high temperatures, because the number of rotational states probed in the experimental averaging increases with increasing temperature. Thus, many spectroscopic observations can only be expected to yield reliable molecular geometries at temperatures close to absolute zero, because at higher temperatures too many higher rotational states are thermally populated. Bonding Molecules, by definition, are most often held together with covalent bonds involving single, double, and/or triple bonds, where a "bond" is a shared pair of electrons (the other method of bonding between atoms is called ionic bonding and involves a positive cation and a negative anion). Molecular geometries can be specified in terms of bond lengths, bond angles and torsional angles. The bond length is defined to be the average distance between the centers of two atoms bonded together in any given molecule. A bond angle is the angle formed between three atoms across at least two bonds. For four atoms bonded together in a chain, the torsional angle is the angle between the plane formed by the first three atoms and the plane formed by the last three atoms.

A water molecule has a non-linear shape because it has two pairs of bonded electrons and two unshared lone pairs. A bond angle is very simply the geometric angle between two adjacent bonds. In accordance with the VSEPR (valence-shell electron pair repulsion theory). Lone pair . electrons must be spaced as far as pair repulsions change the angle from the tetrahedral angle to a slightly lower value. followed by the actual angle for the example given in the following column where this differs. o Functional isomers are special kinds of structural isomers. Lone pair . such as trigonal pyramidal and bent. the atomic orbitals are said to mix in a process called orbital hybridisation. Protein folding concerns the complex geometries and different isomers that proteins can take. boiling point) and at the same time very different biochemical activities. often forming alternate molecular geometries with very different properties. Bent: The final basic shape of a molecule is the non-linear shape. or H2O. An example of this is boron trifluoride.5°) does. Stereoisomers may have many similar physicochemical properties (melting point. leaving one unshared lone pair. An example of a tetrahedral molecule is methane (CH4). An example of an octahedral molecule is sulfur hexafluoride (SF6). the bond angles between the electron bonds are arccos(í1/3) = 109. The bond angles are set at 180°. with no extra unshared electron pairs. Octahedral: pair repulsions push the angle from the tetrahedral angle down to around 106°. For example. Tetrahedral: Tetra. where certain groups of atoms exhibit a special kind of behavior. it can easily be said that molecules with the trigonal planar shape are somewhat triangular and in one plane (meaning a flat surface). but all examples differ by different amounts. resulting in very different properties: y y A pure substance is composed of only one type of isomer of a molecule (all have the same geometrical structure).signifies eight. Pyramidal: Pyramidal-shaped molecules have pyramid-like shapes.Molecular geometry is determined by the quantum mechanical behavior of the electrons. For example. the angle in H2S (92°) differs from the tetrahedral angle by much more than the angle for H2O (104. Consequently. Unlike the linear and trigonal planar shapes but similar to the tetrahedral orientation. The two most common types of bonds are Sigma bonds and Pi bonds. The atoms are not bonded (connected) together in the same orders.signifies four. y y Types of molecular structure Main article: VSEPR Theory There are six basic shape types for molecules y y y Linear: In a linear model. Trigonal planar: Just from its name. Here. so octahedral almost literally means "eight surfaces." The bond angle is 90 degrees. Using the valence bond approximation this can be understood by the type of bonds between the atoms that make up the molecule." This is when there are four bonds all on one central atom. such as an ether or an alcohol. so tetrahedral almost literally means "four surfaces. the actual angle for the example differs from the ideal angle. and -hedral relates to a surface. Structural isomers have the same chemical formula but different physical arrangements. For many cases. Isomers Isomers are types of molecules that share a chemical formula but have different geometries. An understanding of the wavelike behavior of electrons in atoms and molecules is the subject of quantum chemistry. One of the most unquestionably important molecules any chemist studies is water. Like in the other arrangements. This is because they exhibit a handedness that is commonly found in living systems. When atoms interact to form a chemical bond. The geometry can also be understood by molecular orbital theory where the electrons are delocalised. and -hedral relates to a surface. the bond angles are set at 120°. An example is NH3 (ammonia). pyramidal shapes requires three dimensions in order to fully separate the electrons.5°. y y y VSEPR Table The bond angles in the table below are ideal angles from the simple VSEPR theory. there are only three pairs of bonded electrons. . One manifestation of this chirality or handedness is that they have the ability to rotate polarized light in different directions. also known as bent or angular. atoms are connected in a straight line. carbon dioxide has a linear molecular shape.

5° (107. < 180°) ClF3 2 3 5 linear 180° XeF2 6 0 6 octahedral 90° SF6 5 1 6 square pyramidal 90° (84.5°.8°) BrF5 4 2 6 square planar 90° XeF4 7 0 7 pentagonal bipyramidal 90°.5°) NH3 2 2 4 bent 109. 72° IF7 . 180° (87.6°) SF4 3 2 5 T-shaped 90°.5°) H2O 5 0 5 trigonal bipyramidal 90°.Bonding Electron Pairs Lone Pairs Electron Domains Shape linear trigonal planar Ideal Bond Angle (example's bond angle) 180° 120° Example Image 2 3 0 0 2 3 CO2 BF3 2 1 3 bent 120° (119°) SO2 4 0 4 tetrahedral 109. 120° PCl5 4 1 5 seesaw 180°. 120° (173. 101.5° (104.5° CH4 3 1 4 trigonal pyramidal 109.1°.

The molecular geometry is the shape of the molecule. We already have a concept of bonding pair of electrons and nonbonding pairs of electrons. Bonding pairs of electrons are those electrons shared by the central atom and any atom to which it is bonded. If asked for the electron-pair geometry on the central atom we must respond with the electron-pair geometry. Group is used when a central atom has two terminal atoms bonded by single bonds and a terminal atom bonded with two pairs of electrons (a double bond). In the table below the term bonding groups (second from the left column) is used in the column for the bonding pair of electrons.5 2 2 tetrahedral . Molecular geometry is the name of the geometry used to describe the shape of a molecule. but different molecular geometries.5 less than 109. then use the associated name for that shape. The table below summarizes the molecular and electron-pair geometries for different combinations of bonding groups and nonbonding pairs of electrons on the central atom. Notice that there are several examples with the same electron-pair geometry.5 less than 109. We will use a model called the Valence Shell Electron-Pair Repulsion (VSEPR) model that is based on the repulsive behavior of electron-pairs. In this case there are three groups of electrons around the central atom and the molecualr geometry of the molecule is defined accordingly. The table below contains several columns. The electron-pair geometry provides a guide to the bond angles of between a terminal-central-terminal atom in a compound. Groups is a more generic term.Molecular Geometry VSEPR At this point we are ready to explore the three dimensional structure of simple molecular (covalent) compounds and polyatomic ions. # of lone pair electrons on 'central' atom 0 0 1 0 1 # of bonding groups (pair electrons) on 'central' atom 2 3 2 4 3 Electron-pair Geometry linear trigonal planar trigonal planar tetrahedral tetrahedral Molecular Geometry linear trigonal planar bent tetrahedral trigonal pyramidal bent Bond Angle 180 120 less than 120 109. Non-bonding pairs of electrons are those pairs of electrons on an individual atom that are not shared with another atom. You should note that to determine the shape (molecular geometry) of a molecule you must write the Lewis structure and determine the number of bonding groups of electrons and the number of non-bonding pairs of electrons on the central atom. This model is fairly powerful in its predictive capacity. So when asked to describe the shape of a molecule we must respond with a molecular geometry. To use the model we will have to memorize a collection of information. The term electron-pair geometry is the name of the geometry of the electron-pairs on the central atom. whether they are bonding or non-bonding.

For bent molecular geometry when the electron-pair geometry is tetrahedral the bond angle is around 105 degrees. For trigonal pyramidal geometry the bond angle is slightly less than 109. 120 and 180 90. . 120 and 180 90 and 180 180 90 and 180 90 and 180 90 and 180 1 4 2 3 T-shaped 3 2 linear 0 6 octrahedral square pyramidal square planar 1 5 octahedral 2 4 octahedral Note: for bent molecular geometry when the electron-pair geometry is trigonal planar the bond angle is slightly less than 120 degrees.0 5 trigonal bipyramidal trigonal bipyramidal trigonal bipyramidal trigonal bipyramidal octahedral trigonal bipyramidal seesaw 90. around 107 degrees. around 118 degrees. Lets consider the Lewis structure for CCl4.5 degrees. The most convenient way is shown here. We can draw the Lewis structure on a sheet of paper.

This geometry is a direct result of the repulsion experienced by the four groups of bonding electrons. the actual bond angles in this molecule are 109. The shape we see is the only possible shape for a central carbon atom with four bonds. The arrangement of the atoms is correct in my structure.Notice that there are two kinds of electron groups in this structure. Lets look at what I mean. which belong to a particular atom but do not participate in bonding. Here we have a ball and stick model of CCl4. However. Each chlorine atom has three nonbonding pairs of electrons. In CCl4 the central carbon atom has four bonding groups of electrons. but is tetrahedral. The Cl-C-Cl bond angles appear to be 90 degrees. which are shared by a pair of atoms and nonbonding electrons. . But this drawing does not tell us about the shape of the molecule.5 degrees. Bonding electrons. What does this do to our geometry? Lets rotate this molecule to see what has happened. That is the carbon is the central atom and the four chlorine atoms are terminal. This is a nice representation of a two dimensional. This ball and stick model does not adequately represent why the molecule has to have this 3dimensional arrangement. We see the actual molecular geometry is not flat. flat structure.

the correct geometry based on the numbers of bonding and nonbonnding groups of electrons. Arriving at the geometry of a molecules requires writing a correct Lewis structure. whether they are bonding pairs of electrons (single bonds). Two Electron Pairs (Linear) The basic geometry for a molecule containing a central atom with two pairs of electrons is linear. We need to recognize that multiple bonds should be treated as a group of electron pairs when arriving at the molecular geometry. If we replace a bonding pair with a lone pair.The shape of this molecule is a result of the electrons in the four bonds positioning themselves so as to minimize the repulsive effects. Lone pairs of electrons are assumed to have a greater repulsive effect than bonding pairs. However. When four balloons of the same size are tied together the natural arrangement is as a tetrahedron. any compound containing a central atom with four bonding groups (pairs) of electrons around it will exhibit this particular geometry. determining the number of bonding groups and nonbonding groups on the central atom of the molecule and then recalling. This was seen in the 'balloon' example we used in class. Four Electron Pairs (Tetrahedral) . nonbonding pairs or groups of electrons (multiple bonds) move as far apart as possible. for nonbonding pairs of electrons to be as far away as possible from each other in space. its Lewis structure contains two double bonds. The positions can be predicted by imagining that all groups of electrons. So it is more favorable. BeF2 is an example. These ideas have been explored and have resulted in a theory for molecular geometry known as Valence Shell Electron-Pair Repulsion Theory. energetically. As indicated in Table I. Because of the nonbonding pairs of electrons are spread over a larger volume of space compared to bonding electrons. the geometry is described as bent or angular. So LP-LP repulsions are > LP-BP repulsions > BP-BP repulsions. Three Electron Pairs (Trigonal Planar) The basic geometry for a molecule containing a central atom with three pairs of electrons is trigonal planar. Another example of a linear compound is CO2. By recognizing that electrons repel each other it is possible to arrive at geometries which result from valence electrons taking up positions as far as possible from each other. This can be used to explain the change in bond angles observed in going from methane to ammonia to water. VSEPR focuses on the positions taken by the groups of electrons on the central atom of a simple molecule. as in SO2. from memory. BF3 is an example. through the five basic electron-pair geometries and detail the variations in molecular geometries that can occur. systematically. Let's progress. To predict the geometry of a molecule a reasonable Lewis structure must be written for the molecule. The number of bonding and nonbonding pairs of electrons on the central atom are then determined. Because nonbonding electrons are spread over more space they repel other electrons from a greater region of space. With bond angles of 109. The position of the atoms is dictated by the position of the bonding groups of electrons.5 degrees.

That insoluble compound is called a precipitate. As we replace bonding pairs with nonbonding pairs the molecular geometry changes to square pyramidal(five bonding and one nonbonding) to square planar (four bonding and two nonbonding). do not necessarily have the same geometry. The axial atoms are those above and below the trigonal plane. axial and equitorial. As we replace bonding pairs with nonbonding pairs the molecular geometry become trigonal pyramidal (three bonding and one nonbonding). . An example of this geometry is PCl5. about 118 degrees. Six Electron Pairs (Octahedral) The basic geometry for a molecule containing a central atom with six pairs of electrons is octahedral. BF3 and NF3. bent or angular (two bonding and two nonbonding) and linear (one bonding and three nonbonding). An example of this geometry is CH4. Here are some examples of the 3-dimensional structure in simple compounds.) Here is the Purdue site we used in class. Notice that compounds with the same number of terminal atoms. while NF3 has three bonding pairs and one nonbonding pair with a geometry of trigonal pyramidal. not the axial positions. For SO2 the O-S-O angle is near 120 degrees. If the lone pair replaced an axial atom the repulsions would be greater. However the seond bonding group replaced is always opposite the first producing the square planar molecular geometry. The equitorial terminal atoms are those in the trigonal plane.The basic geometry for a molecule containing a central atom with four pairs of electrons is tetrahedral. Precipitation Reactions A precipitation reaction is a reaction in which soluble ions in separate solutions are mixed together to form an insoluble compound that settles out of solution as a solid.) Here are some examples of the 3-dimensional structure for more complex compounds. (Note: you will need the MDL ChemScape Chime Plugin to view these files. Also note that SO2 and H2O have a similar descriptor for their respective geometry. There are no other combinations of bonding groups and nonbonding pairs of electrons when the electron-pair geometry is octahedral. (Note: you will need the MDL ChemScape Chime Plugin to view these files. An example of this geometry is SF6. Five Electron Pairs (Trigonal Bipyramidal) The basic geometry for a molecule containing a central atom with five pairs of electrons is trigonal bipyramidal. The replacement of the first bonding group can occur in any position and always produces a square pyramidal molecular geometry. This is an interesting system because of the two different types of terminal atoms in the structure. So as the bonding pairs of electrons are replaced with nonbonding pairs the equitorial atoms are replaced. the reason for this is due to the smaller replusions between the lone pair and the bonding pairs of electrons. As we replace bonding pairs with nonbonding pairs the molecular geometry changes to seesaw (four bonding and one nonbonding). In this case BF3 has three bonding pairs and no nonbonding pairs with a geometry of trigonal planar. When the first bonding pair of electrons is replaced with a nonbonding pair that occurs in the trigonal plane. So as we move from trigonal bipyramidal to linear the nonbonding pairs of electrons occupy the equitorial plane. for H2O the H-O-H angle is near 105 degrees. actually slightly less than 120. Although each molecule can be described as having a bent geometry the respective bond angles are different. T-shaped (three bonding and two nonbonding) and linear (two bonding and three nonbonding). Here are some VSEPR animations that do not require a plug-in to view.

partly because it is plentiful and partly because of its unique properties. Since ionic compounds and polar covalent compounds constitute the main classes which are appreciably soluble in water. each at a concentration of 1. if so. and in the outside environment a tremendous number of reactions take place in aqueous solutions. and.Solubility Rules for Ionic Compounds Solubility rules are useful summaries of information about which ionic compounds (or combinations of ions) are soluble in water and which are not. of what type. acidbase reactions. In addition. in other living systems. Measurement of the electrical current conducted by a solution of known concentration enables us to determine whether a solute is an electrolyte. Reactions in aqueous solutions usually involve ionic or polar covalent compounds. especially the hydration of ions.1 M . There are three important classes of reactions which occur in aqueous solution: precipitation reactions.00 × 10±7 mol dm±3 at 25°C. In this section you will use solubility rules to predict precipitation reactions and then write equations to represent them. Water itself is an extremely weak electrolyte. Reactions in Aqueous Solutions In other sections we emphasized the importance of liquid solutions as a medium for chemical reactions. Water is by far the most important liquid solvent. reactions in aqueous solutions usually involve these types of substances. will be devoted to developing an understanding of reactions which occur in water. You will be responsible for being able to use the solubility rules to achieve the tasks listed above. producing hydronium ions and hydroxide ions. In your body. and redox reactions. as well as significant portions of many subsequent sections. although you will not be responsible for memorizing the solubility rules. Consequently this section. They are also important tools for making predictions about whether certain ions will react with one another to form a precipitate. they are useful for figuring out what ions might be involved when a precipitation reaction has been observed. The solubilities of such compounds are enhanced because of their interactions with water molecules. Whether or not a precipitate will form when solutions of about 0.

because proton transfers and other bond-making and bondbreaking processes occur at the same time as electron transfer. Example 3: K3PO4(aq) + 3HNO3(aq) p ? Molecular Equation: K3PO4(aq) + 3HNO3(aq) p H3PO4(aq) + 3KNO3(aq) . In doing so. oxidizing power and reducing power. Example 1: CaCO3(s) + HCl p ? Molecular Equation: CaCO3(s) + 2HCl(aq) p CaCl2(aq) + H2O(l) + CO2(g) Total Ionic Equation: CaCO3(s) + 2H+(aq) + 2Cl-(aq) p Ca2+(aq) + 2Cl-(aq) + H2O(l) + CO2(g) Net Ionic Equation: CaCO3(s) + 2H+(aq) p Ca2+(aq) + H2O(l) + CO2(g) The driving force was the formation of water and gas! Example 2: Fe(s) + AgNO3(aq) p ? Molecular Equation: Fe(s) + 2AgNO3(aq) p 2Ag(s) + Fe(NO3)2(aq) Total Ionic Equation: Fe(s) + 2Ag+(aq) + 2NO3-(aq) p 2Ag(s) + Fe2+(aq) + 2NO3-(aq) Net Ionic Equation: Fe(s) + 2Ag+(aq) p 2Ag(s) + Fe2+(aq) The driving force was the transfer of electrons from iron (the reducing agent) to the silver ion (the oxidizing agent). then the compound is separated into the appropriate aqueous ions. Both conjugate acid-base pairs and redox couples may be tabulated in order of acidic strength. while redox reactions involve electron transfers. each half-equation involves a redox couple. Redox reactions are somewhat more complicated. The oxidizing agent in the reactant that receives the electrons from the reactant that is oxidized. Remember: The reducing agent is the reactant that donates the electrons to the reactant that is reduced.base reactions and redox reactions are similar in that something is being transferred from one species to another. though. Such behavior is also quantified in terms of acid constants.concentration are mixed can be predicted using the solubility rules. Acid-base reactions involve proton transfers. Otherwise it is left in an undisassociated (ionic compounds) state or unionized state (weak acids. The total and net ionic equations show the real physical state of every component of the reaction. the oxidizer is reduced.reduction reactions. basic strength. Precipitation reactions are useful for detecting the presence of various ions and for determining the concentrations of solutions. bases and water). and one to describe acceptance of a proton (or electrons). it is oxidized. For acid-base reactions. The compound is a strong electrolyte (a soluble ionic compound or a strong acid). Both proton transfer and electron transfer can be broken into half-equations: one to describe donation of a proton (or electrons). base constants and reduction potentials. For oxidation. Acid. When the reducing agent loses electrons. each half-equation involves a conjugate acid-base pair. In each case such tabulations may be used to determine whether a given reaction will go to com Total Ionic and Net Ionic Equations The presence (or lack) of a driving force for reactions done in water can be evaluated using a net ionic equation.

Total Ionic Equation: 3K+(aq) + PO43-(aq) + 3H+(aq) + 3NO3-(aq) p H3PO4(aq) + 3K+(aq) + 3NO3-(aq) Net Ionic Equation: PO43-(aq) + 3H+(aq) p H3PO4(aq) The driving force was the formation of the weakly ionized acid. occur only to a limited extent. or not occur at all. pletion. Example 4: KNO3(aq) + HCl(aq) p ? Molecular Equation: KNO3(aq) + HCl(aq) p KCl(aq) + HNO3(aq) Total Ionic Equation: K+(aq) + NO3-(aq) + H+(aq)+ Cl-(aq) p K+(aq) + Cl-(aq) + H+(aq) + NO3-(aq) Net Ionic Equation: There is no net because all species remained as aqueous ions before and after my hypothesized double replacement reaction. The lack of a driving force leads me t0o conclude that the correct hypothesis is No Reaction. .

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