Molecular Geometry & Bonding
what the shape decides
Concept

Polarity — where it appears

Whether a molecule has a permanent dipole moment, which its point group settles outright. A polar molecule must have all its symmetry operations preserving one direction, which excludes every group with a centre or with crossed axes.

Named by 22 essays across 5 fields — each of them below, with the objects they name alongside it.

What the group settles. For each molecule, the point group found from its coordinates and the two properties that follow from the group alone. Neither column required knowing anything about the bonds.

Symmetry forbids a dipole

Whether a molecule can have a dipole moment follows from its point group alone. The usual argument — adding up bond vectors — gets the right answer for easy cases by a route that does not generalise.

symmetry · Point group What the group settles. For each molecule, the point group found from its coordinates and the two properties that follow from the group alone. Neither column required knowing anything about the bonds.

The dipole is not a sum of bonds

Adding bond dipoles as vectors gets the easy cases right and rests on a quantity with several incompatible definitions. The symmetry argument is exact, needs no electronegativities, and says when the answer must be zero.

wrong · Dipole Four scales, four orderings. Each column ranks the elements by one electronegativity scale, most electronegative at the top, with a line joining each element across the columns. Every crossing is a pair of elements that two scales order differently.

Electronegativity is not one quantity

Four scales, four definitions, four sets of units, and a defence — "they correlate well" — that answers a question nobody asked. Two scales can correlate at 0.99 and still put hydrogen on the wrong side of carbon.

wrong · Electronegativity One dihedral, three point groups. Hydrogen peroxide built at 13 values of its dihedral angle, with the point group searched for from the coordinates at each. The group is C2v when the hydrogens eclipse, C2h when they are anti, and C2 at every angle strictly between. The rails below are what the group settles on its own: the molecule may be polar except at the anti arrangement, and it is chiral except at the two ends. No energy is computed anywhere, and the marked angle is the measured one rather than a minimum found here.

One coordinate, three point groups

Hydrogen peroxide has four atoms and one soft internal coordinate. Turning it from nought to a hundred and eighty degrees takes the molecule through C2v, C2 and C2h — so it is chiral at every angle but two, and forbidden a dipole at exactly one of them.

shape · Dipole The moment that does not depend on where the origin is. For each molecule, the dipole and the largest quadrupole component about the centre, and the same two about an origin moved 1.6 bohr away. The lowest non-vanishing moment is unchanged in every row and the one above it moves in every row. The 4 non-polar molecules here have a quadrupole that is a property of the molecule; the polar ones have one that is a property of a choice.

What a dipole cannot tell apart

A dipole moment is three numbers extracted from a whole charge distribution, and enormously many distributions give the same three. The moment above it is not even a property of the molecule unless the one below it vanishes — which is why a quadrupole is quoted with an origin and a dipole is not.

shape · Dipole How many groups a molecule can fall to. For each molecule, every subgroup of its point group, found by closing subsets of the operations recovered from its atom positions — beside the number the corresponding abstract group is known to have. The two agree in all 4 cases. The last column is how many of those subgroups this site holds a character table for, which is a minority in every row but the first.

Every group a molecule can fall to

A distortion takes a molecule's symmetry away, and what is left is not a free choice — it has to be a group. Closing subsets of methane's twenty-four operations returns thirty of them, which is exactly the number the symmetric group on four letters has.

symmetry · Point group The bond sum, the measurement, and what is left over. For each pyramid: the vector sum of three bond moments estimated from the electronegativity difference and the measured geometry, the measured dipole, and the difference between them. Positive is towards the lone pair. Ammonia's bonds point that way and nitrogen trifluoride's point the other, which is why the trifluoride's far more polar bonds give it a dipole six times smaller. The leftover is 0.58 D for ammonia and at least 1.48 D for the trifluoride, so it is not one lone pair's property.

The lone pair is not the missing term

Ammonia's dipole is 1.47 debye and nitrogen trifluoride's is 0.235, although the N–F bonds are far more polar than the N–H ones. The bond sums explain the reversal exactly and point in opposite directions — and the lone pair that is supposed to make up the difference has to be worth 0.58 debye in one molecule and at least 1.48 in the other.

shape · Dipole Bonds the scales disagree about. For each bond, which atom each scale calls the more electronegative. Every row is a bond whose polarity would be drawn in opposite directions depending on which of these four tables in common use was consulted: Pauling, Mulliken, Allred–Rochow, Allen.

A ranking is not a difference

Four electronegativity scales agree about order to a Spearman coefficient of 0.99 and disagree about size by a factor of sixty-two. Put each on its own range and the O–H bond is 39 per cent of the way across on three scales and 4.5 on the fourth.

wrong · Electronegativity Every set of point groups here that shares a table. Found by comparing character matrices rather than named: five sets among the tabulated groups, at orders 2, 4, 6, 8, 20. The smallest is the most startling — a mirror plane, a centre of inversion and a twofold axis all have the two-row table with entries 1, 1 and 1, −1, and one of the three describes a chiral molecule. The largest is the eclipsed and staggered conformers of ferrocene, which are one molecule at two temperatures.

One table, three groups

A mirror plane, a centre of inversion and a twofold axis have the same character table — two rows, entries 1, 1 and 1, −1 — and one of the three describes a chiral molecule. A character table is a property of an abstract group; a point group is that plus an action on space, and the action is what a molecule has.

symmetry · Representation Face to face repels, edge to face attracts. Two benzene molecules 5 Å apart, one turned against the other, with only the quadrupole interaction between them. Stacked, the two negative faces meet and the energy is +8.8 kJ/mol; perpendicular, one molecule's positive rim meets the other's negative face and it is -4.6. The sign changes on the way, so the preference is not that one arrangement is weaker — it is that they are opposite. This is a molecule with no dipole moment at all.

Zero dipole is not no interaction

Benzene's dipole moment is exactly zero at every origin, and its quadrupole moment is large enough to decide a crystal structure. Two benzenes face to face repel by nine kilojoules a mole; edge to face they attract, and the sign changes on the way between.

shape · Dipole The same difference, at five repulsions. The charge transferred to the more electronegative of two atoms against the difference in their orbital energies, at five strengths of the repulsion between the two electrons. Only the topmost curve is the two-level result; every other one moves far less charge at the same difference.

A difference does not make a transfer

Every electronegativity scale reports one thing: how far apart two atoms are in their appetite for electrons. Put that difference into a model with repulsion in it and the charge it actually moves is not determined at all — the same difference of one moves 0.447 of an electron with no repulsion and 0.0019 with a strong one, a factor of two hundred and forty-two, and nothing on any scale distinguishes the two cases.

bonding · Electronegativity The dipole moment, and how many bands there are. For each of five molecules: the dipole moment of the point-charge model, the number of modes whose dipole derivative does not vanish, and the largest derivative. The molecules with no dipole at all have the most active bands, which is the whole of the argument.

A dipole is not what an infrared spectrum sees

Carbon dioxide has no dipole moment at all and three of its four modes are infrared active. Methane has none and six of nine; boron trifluoride none and five of six. Water, which has the largest dipole of the five, has three modes and three bands — and its dipole predicted neither number.

shape · Dipole Two derivatives of the same energy, and only one is tabulated. The 18 elements of the electronegativity tables, placed by their chemical potential — half the sum of the ionisation energy and the electron affinity, which is the Mulliken electronegativity — against their hardness, half the difference of the same two numbers. Hardness runs from 1.92 to 7.3 electronvolts, a factor of 3.8, and does not follow the horizontal axis. Ringed points are the three elements whose anion is not bound, so whose affinity is not a measurement.

The quantity no scale prints

Every electronegativity table is half of a calculation. The other half is the hardness — half the difference of the same two measurements the Mulliken scale is half the sum of — and it varies by a factor of 3.8 across eighteen elements. Put both halves in and B–F, with an electronegativity difference of 6.12 electronvolts, moves less charge than lithium iodide, whose difference is 3.75.

bonding · Electronegativity Three quarters, exactly, for every mode that is not totally symmetric. The depolarisation ratio of every Raman-active mode of five molecules, computed from a bond-polarisability model. 18 of the 26 sit on three quarters to better than a millionth, and they are exactly the modes that are not totally symmetric: the mean polarisability derivative is a trace, a trace is invariant, and an invariant has no derivative along any other species. The polarised ones below the line are the totally symmetric modes, and where they sit is a property of the model rather than of the group.

The one intensity symmetry does fix

Symmetry says which bands exist and declines to say how strong they are. It makes exactly one exception, and it is a ratio: every Raman band that is not totally symmetric is depolarised by exactly three quarters, whatever the molecule and whatever the model — and methane's symmetric stretch is polarised by exactly zero, because its group is cubic.

symmetry · Spectrum Carbon is not one number. The charge equalisation puts on carbon in the four fluoromethanes, and on hydrogen in the three that have one. Carbon's runs from 0.07 to 0.31, and hydrogen's changes sign between methane and fluoromethane, so the same C–H bond is polarised one way in one molecule and the other way in the next. A table with one number for carbon is printing the value an iteration starts from.

The value that only exists in the bond

A difference in electronegativity moves charge, and moving charge closes the difference — until every atom in the molecule has the same chemical potential. Solving that gives one number per molecule and a charge per atom, and carbon's runs from +0.0692 in methane to +0.3074 in tetrafluoromethane. Hydrogen's changes sign between the first and the second, so the same C–H bond is polarised one way in one compound and the other way in the next.

bonding · Electronegativity Twelve hydrogen bonds, four tables. The bond dipole of hydrogen against each partner, in debye, on each of the four tables after all four are anchored to the same hydrogen–fluorine separation. Positive is hydrogen at the positive end. A bond whose marks straddle the axis is one the tables disagree about the direction of, and there are 3 of them.

Four tables and one molecule to disagree about

A molecule of two elements is provably safe from the choice of electronegativity table, and a series down a group should land where the tables do disagree. It does. All four agree that hydrogen iodide is the exception — and they disagree about what its dipole is by 1.245 debye, which is two and a half times the 0.448 that was measured.

shape · Dipole Correlated tables stop cancelling each other's luck. The number of the 19 flagged pairs expected to show all tables agreeing by chance, against the number of tables, for four correlations between them. Independent tables halve it with every table added, and it falls below the 0.0513 at which one agreement would be significant at ten tables. Correlated tables share part of their luck, and the expectation falls only as a power of the panel size: at a correlation of a half it is still 0.095 with four hundred.

No panel of this kind can find an exception

Four electronegativity tables leave three exceptions to a rule for which bond polarities they dispute, and four independent coins would produce two and a half. How many tables before one exception would mean something? Ten, if tables were coins. Near the boundary they are not: they correlate at 0.32, two of the four are nearly one table, and the requirement becomes seventy-three — with a plausible range running past any panel that could exist.

wrong · Dipole Letting disputed pairs through narrows the rule and barely moves the panel. Over 61,353 straight boundaries in the plane of difference and dispute, the fewest pairs any boundary flags for each number of disputed pairs it lets through (bars), and the number of tables that flagged count needs at the measured correlation of 0.325 (dots). Missing none, nineteen is the least — the published rule. Each miss saves one or two flags and two to five tables; at eight misses, half the disputed pairs, the rule flags 8 and still needs 46 tables.

The rule is not the lever

One exception among nineteen flagged bond pairs would need seventy-three electronegativity tables to mean anything, and a rule that flagged fewer pairs looked like the way to need fewer. Searched over sixty-one thousand boundaries, nineteen is already the fewest that misses no disputed pair; each missed pair buys a table or five; and a rule flagging a single pair would still need fourteen. The requirement lives in the correlation between the tables, which moves it nine times as far as any rule can.

wrong · Dipole The minimum fills in, and it fills in before any charge moves. The σ profile along the bond for three pairs of atoms, each with equal coefficients on the two atoms — no charge transfer at all. The homonuclear pair has an exact zero at π/R because its two atomic contributions are identical and cancel. The other two do not, because their radial functions differ: the cancellation at π/R needs cₐ gₐ = cᵇ gᵇ everywhere, and two Slater functions of different exponents are nowhere proportional.

A floor no charge transfer explains

A σ bond between two identical atoms has a momentum profile that is exactly zero at π/R, because the two atomic contributions are identical and cancel. Two different atoms cannot cancel there at any coefficients, so the depth of the minimum becomes a measure of polarity — and it is one, monotone in the charge imbalance in the direction chemistry moves charge. What it is not is a measure with a zero: it has a floor set by how far the two radial functions are from proportional, and B–N's floor is deeper than C–O's although C–O is the more polar bond.

orbitals · Orbital A p function fills the polar bond's minimum, and a pair of them fills it nine times over. Carbon monoxide's σ profile along the bond at equal coefficients, for three bases: one s function on each atom, a quarter p mixed into carbon's, and a quarter p on both atoms in the sense that maximises their overlap. The minimum at π/R is 1.35% of the peak with s alone, 3.63% with p on carbon and 12.53% with p on both. The p function proposed to reduce the floor raises it, and the pair raises it most.

The third function fills the floor

A polar σ bond built from one s function per atom has a momentum profile whose minimum at π/R never reaches zero — for carbon monoxide, 1.35 per cent of the peak. The natural hope was that a p function mixed into the diffuse atom would reshape it towards the compact one and lower that floor. It cannot. At π/R an s function on one atom and a p function on the other are exactly out of phase, so a p function on one atom cancels nothing and only adds itself. With p on both atoms in the sense that makes the bond, the pair adds fifteen times as strongly as the s pair cancels: a quarter p takes the minimum to 12.5 per cent. That is eight times the whole range through which polarity moves the s-only bond.

orbitals · Orbital Carbon monoxide's three σ orbitals, and what each does at π/R. The momentum profile along the bond of each occupied σ orbital of carbon monoxide, with weights from an extended Hückel calculation over carbon and oxygen 2s and 2pσ, each scaled to its own peak, against momentum in units of π/R. At π/R the lowest, 3σ, reads 2.52% of its peak; the middle, 4σ, 8.40%; and the highest, 5σ, 85.3% — its profile peaks at 0.82 π/R and has no minimum near π/R at all.

The lone pair sits where the floor was

A polar σ bond's momentum profile has a minimum at π/R whose floor was proposed as a measure of polarity, and the essay that swept the p weight could not say whether carbon monoxide's own σ bond sat near the s-only floor of 1.35 per cent or the quarter-p value of 12.5. With the weights computed — carbon and oxygen 2s and 2pσ, extended Hückel — the answer is that carbon monoxide has no such bond. Its lowest σ orbital reads 2.5 per cent, its middle one 8.4 per cent of its own peak, and its highest, the orbital with the lone pair's sense, has no minimum at π/R at all: it peaks there. The six σ electrons together have no minimum anywhere, and the polar molecule reads lower at π/R than nitrogen does.

orbitals · Orbital Lithium hydride's one σ bond, and the minimum it would need to be covalent to have. The momentum profile along the bond of lithium hydride's occupied σ orbital, from an extended Hückel calculation over lithium 2s and 2pσ and hydrogen 1s, each curve scaled to its own peak, against momentum in units of π/R. As computed the orbital is 91% hydrogen and its profile falls monotonically, reading 10% of its peak at π/R. The same lithium 2s and hydrogen 1s with a quarter of the orbital on hydrogen do have a minimum — at 0.525 π/R, not at π/R, just below lithium's 2s node in momentum at 0.624 π/R.

The minimum belongs to the heavy atom's node

Carbon monoxide had no single σ bond for the momentum-space polarity reading to read, so the next place to look was a hydride, where there is one. Lithium hydride's computed σ orbital is ninety-one per cent hydrogen and its profile falls straight through π/R without a minimum. Across all seven first-row hydrides one occupied orbital of thirteen has a minimum at all, and where a lithium-to-boron hydride could have one, it would not be the bond's fringe: it would be the heavy atom's 2s node in momentum, a flat point that a little hydrogen tips over.

orbitals · Orbital

Named alongside it

The objects these essays reach for when they reach for this one.

ElectronegativityModel limitConventionDipole momentPartial chargeBond dipolePoint groupMulliken scalePauling scaleSymmetry operationRank correlationChirality

All concepts