Abstract
Atomic radii are not precisely defined but are nevertheless widely used parameters in modeling and understanding molecular structure and interactions. The van der Waals radii determined by Bondi from molecular crystals and noble gas crystals are the most widely used values, but Bondi recommended radius values for only 28 of the 44 main-group elements in the periodic table. In the present article we present atomic radii for the other 16; these new radii were determined in a way designed to be compatible with Bondi’s scale. The method chosen is a set of two-parameter correlations of Bondi’s radii with repulsive-wall distances calculated by relativistic coupled-cluster electronic structure calculations. The newly determined radii (in Å) are Be, 1.53; B, 1.92; Al, 1.84; Ca, 2.31; Ge, 2.11; Rb, 3.03; Sr, 2.50; Sb, 2.06; Cs, 3.43; Ba, 2.68; Bi, 2.07; Po, 1.97; At, 2.02; Rn, 2.20; Fr, 3.48; and Ra, 2.83.
1. Introduction
Van der Waals radii, as tabulated by Bondi,1 have been used for a wide range of applications.2-10 Bondi radii result from a refinement of the work of Pauling,11 who determined standard values of atomic radii from contact distances between nonbonded atoms in molecular crystals. Although one may question the choices of data used by Bondi12 and although he did not have the same kind of data available for all elements that he considered, the accuracy of Bondi’s radii was later confirmed by Gavezotti13 and Rowland and Taylor,14 who compared Bondi radii to contact distances for small organic molecules from the Cambridge Structural Database.15
The concept of a van der Waals radius is intrinsically approximate because atoms in molecules are not spherical, whereas assigning them a single radius implies a spherical model. Bondi radii are based on molecular crystals, and Allinger16 pointed out that Bondi radii are “distances of closest approach” that are shorter than gas-phase equilibrium distances. Bondi’s van der Waals radii represent average or typical values and they cannot be equated precisely to a distance that can be uniquely defined in terms of potential energy surfaces for any specific system. Numerous authors17-19 have since observed that the contact distance between atoms Z and Y varies as a function of the angles between the Z•••Y axis and the bonds at Z and Y. Those authors17-19 also observed that Z•••Y contacts that are off of the bond axes are typically longer than those along the bond axes, and Nyburg19 further observed that some of Bondi’s radii are much closer to the off-bond-axis contact distances.
In spite of the various caveats that may be made, Bondi’s values for the van der Waals radii are certainly very reasonable, the best argument for which is that they have been found useful for an inordinately large number of applications by later workers. The value for hydrogen atom has, however, been found to problematic. Rowland and Taylor,14 taking advantage of the large amount of additional crystal data that has been accumulated since Bondi’s study, made a systematic analyses of intermolecular contact distances in organic crystals and redetermined the values of the van der Waals radii. They found that Bondi’s values were consistent with the new data with the single exception of hydrogen, for which they suggested lowering the van der Waals radius from 1.2 Å to 1.1 Å. Bondi’s value of 1.2 Å describes well the size of H in H•••H contacts, but for interactions with other elements, the smaller value is more appropriate. Bondi had drawn similar conclusions, but he favored using the higher value as a standard. We accept the Rowland-Taylor recommendation for H.
Given the importance of van der Waals radii, their prediction has been the subject of many different approaches. These approaches include radii based on: the minimum in potential energy curves,20,21 Slater-type orbitals,22-24 isodensity surfaces of the atomic wavefunction,25-27 deBroglie wavelengths,1 other computed properties,28 and periodic trends.29 In this article, another approach is presented. The new method is based on gas-phase complexes of the elements with a probe, and it is designed such that, for main-group elements for which Bondi proposed a radius, the new method yields a value in good agreement with that radius.
Some considerations, including the level of theory and basis set, involved in choosing the method to reproduce Bondi’s radii are given in Section 2. Section 3 then presents the calculations that lead to the final correlations along with the 16 newly determined radii. Combining these with Rowland and Taylor’s recommendation for H and Bondi’s recommendations for the other 27 main-group elements leads to a consistent set of van der Waals radii for all main-group elements. Since the present article is solely concerned with main-group elements, neither the transition metals (Ni, Cu, Zn, Pd, Ag, Cd, Pt, Au, Hg) nor the actinide (U) discussed by Bondi are addressed; however if we combine his radii for these elements with the 44 main-group radii we have a consistent set of radii for 54 elements.
2. Methodology
Our calculations of van der Waals radii begin with the calculation of ground-state potential energy curves for the interaction of an atom with a probe. Since the van der Waals radius is a characteristic of nonbonding interactions the probe is required to be a closed-shell singlet, such as Ne or a closed-shell molecule. We found that molecules give van der Waals radii that correlate better with Bondi’s values so our final method is based on molecules, in particular HF approaching the atom collinearly with H towards the atom, HF approaching the atom collinearly with F towards the atom, and CH4 approaching the atom along the bisector of an H-C-H bond (thus the vector from C to the atom is normal to a line connecting two of the hydrogens). However, our calculations of probe radii and our decisions about the treatment of core electrons and basis sets are based on Ne probes, and so we will consider Ne probes as well.
As mentioned in the introduction, Bondi’s van der Waals radii are more closely associated with the distance of closest approach than with the equilibrium distance in the gas-phase, and so we will define them in the present paper based on the classical distance of closest approach. The distance to which two systems will approach depends on their kinetic energy and impact parameter, and we assume zero kinetic energy and zero impact parameter, as explained next. In the ground state, as the probe approaches the atom, the potential energy, relative to the probe infinitely separated from the atom, becomes negative and then it becomes positive as the subsystems approach more closely. The distance at which the potential energy passes through zero is the distance of closest approach in a head-on collision in the limit where the kinetic energy tends to zero. It is called the repulsive wall distance and is, by the definition used here, equal to the sum of the van der Waals radius of the probe and the van der Waals radius of the atom. The van der Waals radius of an atom of element Z is called σZ.
The van der Waals radius of neon was determined first, by considering the neon dimer, for which σNe is one half of the repulsive wall distance. Next we considered the interaction of the other probes with Ne. Since the Ne radius has been determined, it can be subtracted from the sum of the van der Waals radii, and that yields the van der Waals radius of the probe.
In the case of atoms in the boron group, carbon group, chalcogens, and halogens, the outer p subshell is partially occupied. There are two possible directions of approach of a probe to the same atomic configuration of the atom, the state where the probe approaches the least filled p-orbital and the state where it approaches the most filled p-orbital. We found that the former is the ground state for approach by Ne or the F atom of HF, whereas the latter is the ground state for approach by the H atom of HF.
The interatomic potential for each complex was initially mapped using single-point energies spaced at ~0.2 Å intervals, and then the region around the repulsive wall distance was refined until the location of the repulsive wall (i.e., the zero of the potential) was determined to a sufficient precision.
The prediction of accurate nonbonding potentials in the gas phase is sensitive to the choice of theory; the effect of this level upon predicted dimer properties has been the subject of extensive research. (See Ruette et al.30 for a bibliography of theoretical papers on computing gas-phase dimer properties.) It has been consistently found that use of a large enough basis set and coupled cluster theory with single and double excitations and a quasi-perturbative treatment of connected triple excitations, called CCSD(T), reproduces experimental dimer properties quite well.31-35 The calculations presented in this article were all carried out at the CCSD(T) level using the MOLPRO36 computer program.
The choice of basis set37-48 can have a significant effect upon the accuracy of calculated nonbonding interactions. Table 1 shows results obtained with three different basis sets. Our final choice was the atomic natural orbital–relativistic correlation consistent (ANO-RCC)46-48 all-electron basis set. The ANO-RCC basis set was obtained from the MOLCAS basis-set library49 and converted into a format that can be used by MOLPRO.36 Table 1 shows that the ANO-RCC basis set gives results that are within 0.01 Å of the experimental repulsive wall distances50-54 when they are available.
TABLE 1.
H | He | |||||||
|
||||||||
SDD (MWB)b | 1.75 | 1.43 | ||||||
MG3c | 1.81 | 1.32 | ||||||
ANO-RCCd | 1.66 | 1.33 | ||||||
Experiment | – | 1.33e | ||||||
|
||||||||
Li | Be | B | C | N | O | F | Ne | |
|
||||||||
SDD (MWB)b | 3.68 | 2.66 | 1.52 | 1.31 | 1.55 | – | 1.10 | 1.40 |
MG3c | 2.97 | 2.19 | 1.64 | 1.31 | 1.61 | 1.10 | 1.20 | 1.34 |
ANO-RCCd | 3.20 | 2.41 | 1.70 | 1.30 | 1.62 | 1.37 | 1.18 | 1.40 |
Experiment | – | – | – | – | – | – | 1.19f | 1.39g |
|
||||||||
Na | Mg | Al | Si | P | S | Cl | Ar | |
|
||||||||
SDD (MWB)b | 3.95 | 3.18 | 2.31 | 1.61 | 2.63 | 2.21 | 1.81 | 1.79 |
MG3c | 2.56 | 2.37 | 1.86 | 1.54 | 2.05 | 2.18 | 1.57 | – |
ANO-RCCd | 3.27 | 2.71 | 2.03 | 1.61 | 2.14 | 1.83 | 1.59 | 1.74 |
Experiment | – | – | – | – | – | 1.83h | 1.60i | – |
The calculations in this table do not include relativistic effects or counterpoise corrections. For this table the choice of which orbitals to correlate follows the top scheme in Table 3 except for Si, for which the 2p orbitals were correlated for this table.
The MG3 basis set41-45 is equivalent to a 6-311++G(3d2f,2df,2p) basis for H–Si, and it corresponds to an improved 6-311+G(3d2f) basis for P–Ar.
Ne-Ne data from Farrar et al.51
Generally it is not necessary to correlate all electrons. If one arranges the electrons into shells with a given principal quantum number n, and if the outermost occupied orbitals have n = v, then it is usually sufficient to correlate only electrons with n = v (valence electrons) and v – 1 (the outermost shell of the core), and sometimes it is not necessary to correlate all electrons with n = v – 1. (Correlating a large number of electrons increases the computer time and storage needed for the calculations, and eventually, if too many electrons are correlated, one needs more basis functions for core orbitals, and the calculations become too expensive.) Electrons that are not correlated are called frozen. The effect of correlating the outer core electrons can be quite large; this is shown in Table 2. Hence the use of a basis set such as ANO-RCC that is designed to correlate some of the core electrons is essential. ANO-RCC was designed46-48 to include the correlation of a certain subset of electrons, as indicated in the upper part of Table 3. In our work, though, that scheme was modified to correlate more electrons, as indicated in the lower half of the table. The scheme in the lower half of Table 3 is used for all calculations after Table 2.
TABLE 2.
Basis set | Ga | Ge | As | Br | Kr |
---|---|---|---|---|---|
|
|||||
frozen 3d | 1.95 | 1.54 | 2.01 | 1.50 | 1.78 |
correlated 3d | 1.85 | 1.49 | 1.95 | 1.47 | 1.76 |
CCSD(T)/ANO-RCC with Ne probe without relativistic effects and counterpoise correction. For this table, the choice of which orbitals to correlate follows the top scheme in Table 3 unless specified (e.g. correlated 3d).
The Ne probe radius used for this table is 1.399 Å, from CCSD(T)/ANO-RCC without relativistic effects and also without counterpoise correction.
TABLE 3.
uncorrelated orbitals | correlated orbitals | |
---|---|---|
in the scheme used to develop ANO-RCC | ||
H-He | – | 1s |
Li-Be | – | 1s2s |
B | – | 1s2s2p |
C-Ne | [He] | 2s2p |
Na | [He] | 2s2p3s |
Mg | [He]2s | 2p3s |
Al | [He]2s | 2p3s3p |
Si-Ar | [Ne] | 3s3p |
K | [Ne] | 3s3p4s |
Ca | [Ne]3s | 3p4s |
Ga-Ge | [Ar] | 3d4s4p |
As-Kr | [Ar]3d | 4s4p |
Rb-Sr | [Ar]3d4s | 4p5s |
In-Xe | [Kr] | 4d5s5p |
Cs-Ba | [Kr]4d5s | 5p6s |
Tl-Rn | [Xe] | 5d6s6p |
Fr-Ra | [Xe]5d6s | 6p7s |
in the scheme used in tables 4–11 | ||
H-He | – | 1s |
Li-Be | – | 1s2s |
B-Ne | [He] | 2s2p |
Na-Mg | [He] | 2s2p3s |
Al-Ar | [Ne] | 3s3p |
K-Ca | [Ne] | 3s3p4s |
Ga-Kr | [Ar] | 3d4s4p |
Rb-Sr | [Ar]3d | 4s4p5s |
In-Xe | [Kr] | 4d5s5p |
Cs-Ba | [Kr]4d | 5s5p6s |
Tl-Rn | [Xe] | 5d6s6p |
Fr-Ra | [Xe]5d | 6s6p7s |
In Tables 1 and 2 the calculations are non-relativistic, although the ANO-RCC basis set was explicitly designed to be used with the Douglas-Kroll55,56 (DK) relativistic Hamiltonian. However, relativistic effects become significant as early as the 3d transition metals57,58 and certainly have significant effects in the post-3d elements, as illustrated in Table 4. In all subsequent calculations (after Table 4) the calculations were performed entirely using the relativistic DK Hamiltonian.
TABLE 4.
Ga | Ge | As | Br | Kr | |
---|---|---|---|---|---|
|
|||||
Non-relativistic | 1.85 | 1.49 | 1.95 | 1.47 | 1.76 |
Relativistic (DK) | 1.84 | 1.52 | 2.19 | 1.70 | 1.87 |
CCSD(T)/ANO-RCC with Ne probe without counterpoise corrections; 3d orbitals are correlated and [Ar] core is frozen following the bottom scheme in Table 3.
The Ne probe radius used for this table 1s 1.399 Å for non-relativistic calculations and 1.401 Å for relativistic calculations, from CCSD(T)/ANO-RCC calculations without counterpoise corrections.
An additional consideration is the effect of basis set superposition error (BSSE) on the predicted energies. This is significant for an all-electron basis set such as ANO-RCC. To account for the effect of BSSE, a counterpoise correction59 (CpC) can be included. It has been observed that the value at the infinite-basis-set limit sometimes tends to converge to a value roughly halfway between the fully counterpoise corrected and the uncorrected energies.60,61 Table 5 shows atomic radii computed using ½ of the CpC correction. The counterpoise corrections computed this way generally vary between 0.01 and 0.04 Å and consistently make the radii larger, which is a consequence of the fact that BSSE overstabilizes the complex.
TABLE 5.
K | Ca | Ga | Ge | As | Se | Br | Kr | |
---|---|---|---|---|---|---|---|---|
|
||||||||
without CpC | 4.32 | 3.30 | 1.84 | 1.52 | 2.19 | 1.90 | 1.70 | 1.87 |
including ½CpC | 4.34 | 3.33 | 1.85 | 1.53 | 2.21 | 1.93 | 1.72 | 1.89 |
CCSD(T)/ANO-RCC+DK with Ne probe
The Ne probe radius used for this table is of 1.401 Å without CpC and 1.408Å with ½CpC, from CCSD(T)/ANO-RCC calculations with relativistic effects.
In the rest of this article we use the CCSD(T)/ANO-RCC method with the DK method for relativistic effects, one half the counterpoise correction, and the correlation scheme in the lower half of Table 3. This illustrates an important advantage of having chosen the ANO-RCC basis set, namely that this basis set is available over a very large portion of the periodic table, which allows one to compute atomic radii using a consistent approach rather than a patchwork of radii calculated with different basis sets.
Table 6 shows that the radii computed using Ne as a probe are very roughly the same size as Bondi radii, but they do not exhibit the same periodic trends as Bondi radii. For instance, Bondi radii for the pnictogens are consistently smaller than those of the carbon group or chalcogen atoms in the same row, whereas the gas-phase dimer radii based on Ne complexes have the reverse trend. The Bondi radii were computed from a collection of Z•••Y contact distances where Z and Y were any number of different atoms. This means that the attractive interactions are not purely dispersion-like, but include electrostatic and inductive effects (the latter, such as dipole-induced dipole interactions, are sometimes called polarization effects) that are probably better simulated using molecular probes (for example, HF probes interact with the atom by dipole-induced dipole interactions in addition to dispersion-like interactions, and open-shell atoms often have non-zero permanent quadrupole moments that can also interact with permanent and induced moments on the probe).
TABLE 6.
H |
He |
|||||
σ Ζ | 1.67 | 1.33 | ||||
Standard radiusa | 1.10 | 1.40 | ||||
|
||||||
C | N | O | F | Ne | ||
|
||||||
σ Ζ | 1.30 | 1.63 | 1.37 | 1.18 | 1.41 | |
Bondi radius | 1.70 | 1.55 | 1.52 | 1.47 | 1.54 | |
|
||||||
Si | P | S | Cl | Ar | ||
|
||||||
σ Ζ | 1.62 | 2.16 | 1.85 | 1.61 | 1.76 | |
Bondi radius | 2.10 | 1.80 | 1.80 | 1.75 | 1.88 | |
|
||||||
As | Se | Br | Kr | |||
|
||||||
σ Ζ | 2.21 | 1.93 | 1.72 | 1.89 | ||
Bondi radius | 1.85 | 1.90 | 1.83 | 2.02 |
Rowland-Taylor for H; Bondi for He
We next considered hydrogen fluoride as a probe. HF is isoelectronic with Ne. Since the two atoms of the probe have distinct properties, we used both ends of the probe. In all cases the atom approached HF along the molecular axis of HF. The geometry of the probe was held frozen throughout these calculations at an internuclear H-F distance of 0.917720 Å which was optimized at the CCSD(T)/ANO-RCC level of theory.
We also considered CH4 as a probe. CH4 is also isoelectronic with Ne, but it is more polarizable. Unlike HF, it is nonpolar.
The approach we adopted is to seek to write a multilinear regression with no intercept
(1) |
and to try to find values of the constants b, c, and d such that the left hand side of eq. (1) agrees with the standard values for the main-group elements for which Bondi determined the van der Waals radii, except substituting the Rowland-Taylor value for H. Then this formula can be used to predict the van der Waals radii for the other elements. The coefficients in eq. (1) are obtained by minimizing the root-mean-square error using the generalized reduced gradient code of Lasdon et al.62 as implemented in Microsoft Excel™.
3. Results
The radii for the nonmetals with the three molecular probes are given in Table 7 for all the main group atoms for which Bondi present radii. In a few cases (e.g., Li, Na, and K) when the probe is the F atom of HF, the radii are very much smaller than those obtained with other probes; this indicates that this kind of probe can lead to a significant covalent interaction. Therefore, the values based on the F atom of the HF probe will be used only for fitting noble gases.
TABLE 7.
Group | 1 | 2 | 13 | 14 | 15 | 16 | 17 | 18 |
---|---|---|---|---|---|---|---|---|
|
|
|||||||
H |
He |
|||||||
σZ from H of HF | 1.25 | 1.35 | ||||||
σZ from F of HF | 1.45 | 1.32 | ||||||
σZ from CH4 | 1.39 | 1.43 | ||||||
Standard radiusa | 1.10 | 1.40 | ||||||
|
|
|||||||
Li | C | N | O | F | Ne | |||
|
|
|||||||
σZ from H of HF | 2.03 | 1.19 | 1.42 | 0.96 | 1.14 | 1.41 | ||
σZ from F of HF | 0.30 | 0.94 | 1.53 | 1.20 | 1.01 | 1.41 | ||
σZ from CH4 | 2.30 | 1.72 | 1.46 | 1.75 | 1.51 | 1.41 | ||
Bondi radius | 1.81 | 1.70 | 1.55 | 1.52 | 1.47 | 1.54 | ||
|
|
|||||||
Na | Mg | Si | P | S | Cl | Ar | ||
|
|
|||||||
σZ from H of HF | 2.27 | 2.03 | 1.59 | 1.77 | 1.30 | 1.40 | 1.60 | |
σZ from F of HF | 0.79 | 1.89 | b | 1.88 | 1.51 | 1.29 | 1.69 | |
σZ from CH4 | 2.37 | 2.18 | 2.25 | 1.81 | 2.04 | 1.83 | 1.64 | |
Bondi radius | 2.27 | 1.73 | 2.10 | 1.80 | 1.80 | 1.75 | 1.88 | |
|
|
|
||||||
K | Ga | As | Se | Br | Kr | |||
|
|
|
||||||
σZ from H of HF | 2.70 | 1.47 | 1.84 | 1.39 | 1.50 | 1.69 | ||
σZ from F of HF | 1.04 | 1.20 | 1.92 | 1.56 | 1.36 | 1.78 | ||
σZ from CH4 | 2.68 | 1.29 | 1.85 | 2.08 | 1.90 | 1.72 | ||
Bondi radius | 2.75 | 1.87 | 1.85 | 1.90 | 1.83 | 2.02 | ||
|
|
|||||||
In | Sn | Te | I | Xe | ||||
|
|
|||||||
σZ from H of HF | 1.61 | 1.76 | 1.58 | 1.68 | 1.85 | |||
σZ from F of HF | 1.27 | 1.08 | 1.70 | 2.33 | 1.93 | |||
σZ from CH4 | 2.75 | 2.27 | 2.25 | 2.05 | 1.88 | |||
Bondi radius | 1.93 | 2.17 | 2.06 | 1.98 | 2.16 | |||
|
||||||||
Tl | Pb | |||||||
|
||||||||
σZ from H of HF | 1.61 | 1.78 | ||||||
σZ from F of HF | 1.24 | 1.10 | ||||||
σZ from CH4 | 2.75 | 2.36 | ||||||
Bondi radius | 1.96 | 2.02 |
Rowland-Taylor for H; Bondi for He
not available
We attempted to fit the Bondi radii using these data and eq. (1). We found that we could not fit all the standard values well with a single b, c, and d, even if we treated noble gases separately and even if we set c equal zero to eliminate radii with significant covalent interaction. Including Ne-probe radii in the fit also did not lead to a good global fit. Therefore, we investigated using different sets of parameters for different chemical classes of elements. We eventually adopted the goal of having a mean unsigned error no larger than 0.06 Å for any of the classes while using the minimum number of classes and using no more than two of the three possible parameters for a given class (i.e., we restrict the correlations to linear or bilinear with no intercept). We examined various ways to group the elements into classes and found that a very reasonable fit could be made to the standard radii by recognizing four classes of elements: noble gases, open-shell p-block nonmetals, p-block metals, and s-block elements. The coefficients of the resulting correlations are given in Table 8, a comparison of the fitted radii to the standard ones is in Table 9, and the mean errors as compared to the Bondi-Rowland-Taylor standard values are in Table 10. This approach produced reasonable results, which can then be used to obtain radii for all main-group elements for which Bondi did not report radii. The additional data needed for these elements was calculated, and it is given in Table 11. In these calculations we treated the open-shell p-block elements Al and Po as metals and B, Ge, Sb, Bi and At as nonmetals.
TABLE 8.
Noble gases | Open-shell p-block nonmetals |
p-block metals |
s-block elements |
|
---|---|---|---|---|
b | 0.000 | 0.318 | 1.206 | 2.121 |
c | 1.743 | 0.000 | 0.000 | 0.000 |
d | −0.639 | 0.708 | 0.000 | −1.108 |
TABLE 9.
Model ↓ Group → | 1 | 2 | 13 | 14 | 15 | 16 | 17 | 18 |
---|---|---|---|---|---|---|---|---|
|
|
|||||||
H |
He |
|||||||
Final model | 1.10 | 1.39 | ||||||
Standard radiusa | 1.10 | 1.40 | ||||||
|
|
|||||||
Li | C | N | O | F | Ne | |||
|
|
|||||||
Final model | 1.75 | 1.60 | 1.49 | 1.54 | 1.40 | 1.55 | ||
Bondi radius | 1.81 | 1.70 | 1.55 | 1.52 | 1.47 | 1.54 | ||
|
|
|||||||
Na | Mg | Si | P | S | Cl | Ar | ||
|
|
|||||||
Final model | 2.19 | 1.88 | 2.09 | 1.84 | 1.85 | 1.74 | 1.89 | |
Bondi radius | 2.27 | 1.73 | 2.10 | 1.80 | 1.80 | 1.75 | 1.88 | |
|
|
|
||||||
K | Ga | As | Se | Br | Kr | |||
|
|
|
||||||
Final model | 2.74 | 1.77 | 1.90 | 1.91 | 1.82 | 2.00 | ||
Bondi radius | 2.75 | 1.87 | 1.85 | 1.90 | 1.83 | 2.02 | ||
|
|
|||||||
In | Sn | Te | I | Xe | ||||
|
|
|||||||
Final model | 1.95 | 2.12 | 2.09 | 1.99 | 2.16 | |||
Bondi radius | 1.93 | 2.17 | 2.06 | 1.98 | 2.16 | |||
|
||||||||
Tl | Pb | |||||||
|
||||||||
Final model | 1.94 | 2.15 | ||||||
Bondi radius | 1.96 | 2.02 |
Rowland-Taylor for H; Bondi for He
TABLE 10.
Class | MSE (Å) | MUE (Å) | RMSE (Å) |
---|---|---|---|
Noble gases (He, Ne, Ar, Kr, Xe) | 0.00 | 0.01 | 0.01 |
p-block open-shell nonmetals (C, N, O,M F, Si, P, S, Cl, As, Se, Br, Te, I) |
0.00 | 0.04 | 0.05 |
p-block open-shell metals (Ga, In, Sn, Tl, Pb) |
0.00 | 0.06 | 0.08 |
s-block elements (H, Li, Na, K, Mg) | 0.00 | 0.06 | 0.08 |
TABLE 11.
1 | 2 | 13 | 14 | 15 | 16 | 17 | 18 | |
---|---|---|---|---|---|---|---|---|
|
||||||||
Be | B | |||||||
|
||||||||
σZfrom H of HF | 1.741 | 1.124 | ||||||
σZfrom CH4 | 1.953 | 2.205 | ||||||
|
||||||||
Al |
||||||||
σZfrom H of HF | 1.528 | |||||||
|
|
|||||||
Ca |
Ge |
|||||||
σZfrom H of HF | 2.423 | 1.599 | ||||||
σZfrom CH4 | 2.549 | 2.263 | ||||||
|
|
|||||||
Rb | Sr | Sb | ||||||
|
|
|||||||
σZfrom H of HF | 2.834 | 2.586 | 2.012 | |||||
σZfrom CH4 | 2.694 | 2.696 | 2.014 | |||||
|
|
|||||||
Cs | Ba | Bi | Po | At | Rn | |||
|
|
|||||||
σZfrom H of HF | 3.026 | 2.768 | 2.050 | 1.634 | 1.738 | |||
σZfrom F of HF | 1.967 | |||||||
σZfrom CH4 | 2.696 | 2.877 | 2.009 | 2.080 | 1.914 | |||
|
||||||||
Fr | Ra | |||||||
|
||||||||
σZfrom H of HF | 3.026 | 2.813 | ||||||
σZfrom CH4 | 2.652 | 2.833 |
Table 12 gives the prescribed van der Waals radii for all main group elements, including the new values obtained as described in the previous paragraph. Unlike atomic radii determined from internuclear distances in bonds (covalent radii, metallic radii),63-65,66a van der Waals radii do not follow a generally monotonic trend as one moves across or down in the periodic table. One possible way to explain some of the trends is by classifying the elements as metal, nonmetal, and semimetal. We note though that classifications of some nonmetals as semimetals or metalloids are not unique because they depend on the properties that are chosen for the classification.66b,67-69 Nevertheless, even without using a strict classification, Table 12 shows that the van der Waals radii of incompletely-filled-p-block elements increase with decreasing metallic nature as we move to the right along a period and then decrease with increasing nonmetallic nature. The trends in the table are seen to result from (i) the shape (s or p) of the highest occupied atomic orbital, (ii) the classification of the element as a metal or nonmetal, and (iii) the subclassification of p-block elements into non-inert nonmetals (incomplete p subshell) and inert gases (complete p subshell). These factors are evident in Table 12 in the higher van der Waals radii of s-block elements relative to those for p-block elements, in the relatively large sizes of some elements near the metallic-nonmetallic border as compared to other partially filled p-block elements in their respective periods (B, Si, Ge, Sn, and Bi are larger than either their left-side neighbor or their right-side neighbor in the periodic table), and the larger size of the noble-gas elements with completely filled p orbitals.
TABLE 12.
H 1.10 |
He 1.40 |
||||||
Li 1.81 |
Be 1.53 |
B 1.92 |
C 1.70 |
N 1.55 |
O 1.52 |
F 1.47 |
Ne 1.54 |
Na 2.27 |
Mg 1.73 |
Al 1.84 |
Si 2.10 |
P 1.80 |
S 1.80 |
Cl 1.75 |
Ar 1.88 |
K 2.75 |
Ca 2.31 |
Ga 1.87 |
Ge 2.11 |
As 1.85 |
Se 1.90 |
Br 1.83 |
Kr 2.02 |
Rb 3.03 |
Sr 2.49 |
In 1.93 |
Sn 2.17 |
Sb 2.06 |
Te 2.06 |
I 1.98 |
Xe 2.16 |
Cs 3.43 |
Ba 2.68 |
Tl 1.96 |
Pb 2.02 |
Bi 2.07 |
Po 1.97 |
At 2.02 |
Rn 2.20 |
Fr 3.48 |
Ra 2.83 |
Bold values are from the present work, value for H is from Rowland and Taylor, and other values are from Bondi
4. Summary
We determined van der Waals radii for the main-group elements by calculating the locations of the repulsive wall in the potential energy curve for the interactions of the elements with various probes, and then determining linear and bilinear correlations with the standard radii of Bondi and Rowland and Taylor. The correlations, based on a maximum of two parameters per class of elements, reproduce the standard van der Waals radii mean unsigned deviations of 0.01, 0.04, 0.06, and 0.06 Å for the four classes of main-group elements. These correlations are useful because they provide us with a straightforward approach to determining consistent van der Waals radii for the rest of the main-group elements, and we have produced such radii.
5. Acknowledgments
This work was supported in part by the National Science Foundation under grants nos. CHE07-04974 and CHE06-10183, by the National Institutes of Health training grant for Neuro-physical-computational Sciences, and by the Office of Naval Research under grant no. 00014-05-01-0538.
References
- (1).Bondi A. J. Phys. Chem. 1964;68:441. [Google Scholar]
- (2).Weiner PK, Kollman PA. J. Comp. Chem. 1981;2:287. [Google Scholar]; Weiner SJ, Kollman PA, Case DA, Singh UC, Ghio C, Alagona G, Profeta SJ, Weiner PK. J. Am. Chem. Soc. 1984;106:765. [Google Scholar]
- (3).Orozco M, Luque FJ. J. Comp. Chem. 1982;14:587. [Google Scholar]
- (4).Brooks BR, Bruccoleri RE, Olafson BD, States DJ, Swaminathan S, Karplus M. J. Comp. Chem. 1983;4:187. [Google Scholar]
- (5).Hanai T, Hatano H, Minura N, Kinoshita K. J. Liq. Chromatogr. 1993;16:1453. [Google Scholar]
- (6).Beckman EJ, Hoefling TA, Vanopstal L, Koningsveld R, Porter RS. Fluid Phase Equil. 1994;99:121. [Google Scholar]
- (7).Simha R, Carri G. J. Polymer Sci. Part B. 1994;32:2645. [Google Scholar]
- (8).Marenich AV, Olson RM, Kelly CP, Cramer CJ, Truhlar DG. J. Chem. Theory Comput. 2007;3:2011. doi: 10.1021/ct7001418. [DOI] [PubMed] [Google Scholar]
- (9).Marenich AV, Olson RM, Chamberlin AC, Cramer CJ, Truhlar DG. J. Chem. Theory Comput. 2007;3:2055. doi: 10.1021/ct7001539. [DOI] [PubMed] [Google Scholar]
- (10).Olson RM, Marenich AV, Cramer CJ, Truhlar DG. J. Chem. Theory Comput. 2007;3:2046. doi: 10.1021/ct7001607. [DOI] [PubMed] [Google Scholar]
- (11).Pauling L. The nature of the chemical bond and the structure of molecules and crystals: An introduction to modern structural chemistry. 3rd ed Cornell University Press; Ithaka, NY: 1960. [Google Scholar]
- (12).Zefirov YV. Russian J. Coord. Chem. 1997;23:311. [Google Scholar]
- (13).Gavezzotti A. J. Am. Chem. Soc. 1983;105:1983. [Google Scholar]
- (14).Rowland RS, Taylor R. J. Phys. Chem. 1996;100:7384. [Google Scholar]
- (15).Allen FH, Davies JE, Gallo JJ, Johnson O, Kennard O, Macrae CF, Mitchell EM, Mitchell GF, Smith JM, Watson D. J. Chem. Inf. Computer Sci. 1991;31:187. [Google Scholar]
- (16).Allinger NA. Adv. Phys, Org. Chem. 1976;13:13. [Google Scholar]
- (17).Zefirov YV, Porai-Koshits MA. J. Struct. Chem. 1980;21:526. [Google Scholar]
- (18).Row TNG, Parthasarathy R. J. Am. Chem. Soc. 1981;103:477. [Google Scholar]
- (19).Nyburg SC, Faerman CH. Acta Crystallographica. Section B. 1985;41:274. [Google Scholar]
- (20).Sen KD, Politzer P. J. Chem. Phys. 1989;90:4370. [Google Scholar]
- (21).Contreras RR, Aizman AJ. J. Mol. Struct. (THEOCHEM) 1993;282:143. [Google Scholar]
- (22).Slater JC. Phys. Rev. 1930;36:57. [Google Scholar]
- (23).Slater JC. J. Chem. Phys. 1964;41:3199. [Google Scholar]
- (24).Ghosh DC, Biswas R. Int. J. Mol. Sci. 2002;3:87. [online computer file] [Google Scholar]
- (25).Deb BM, Singh R, Sukumar N. THEOCHEM. 1992;259:121. [Google Scholar]
- (26).Foresman JB, Keith TA, Wiberg KB, Snoonian J, Frisch MJ. J. Phys. Chem. 1996;100:16098. [Google Scholar]
- (27).Chipman D. Theor. Chem. Acc. 2004;111:61. [Google Scholar]; Zhou B, Agarwal M, Wong CF. J. Chem. Phys. 2008;129:014509. doi: 10.1063/1.2949821. [DOI] [PMC free article] [PubMed] [Google Scholar]
- (28).Badenhoop JK, Weinhold F. J. Chem. Phys. 1997;107:5422. [Google Scholar]; Putz MV, Russo N, Sicilia E. J. Phys. Chem. 2003;107:5461. [Google Scholar]; Hollett JW, Kelly A, Poirier RA. J. Phys. Chem. A. 2006;110:13884. doi: 10.1021/jp066011h. [DOI] [PubMed] [Google Scholar]
- (29).Chauvin R. J. Phys. Chem. 1992;96:9194. [Google Scholar]
- (30).Ruette F, Sánchez M, Añez R, Bermúdez A, Sierraalta A. THEOCHEM. 2005;729:19. [Google Scholar]
- (31).Haley TP, Cybulski SM. J. Chem. Phys. 2003;119:5487. [Google Scholar]
- (32).Kurita N, Sekino H. Int. J. Quantum Chem. 2003;91:355. [Google Scholar]
- (33).Czuchaj E, Kros’nicki M, Stoll H. Chem. Phys. 2003;292:101. [Google Scholar]
- (34).Watts JD, Gauss J, Bartlett RJ. J. Chem. Phys. 1993;98:8718. [Google Scholar]
- (35).Knowles PJ, Hampel C, Werner H-J. J. Chem. Phys. 1993;99:5219. [Google Scholar]
- (36).Werner H-J, Knowles PJ, Lindh R, Manby FR, Schütz M, Celani P, Korona T, Rauhut G, Amos RD, Bernhardsson A, Berning A, Cooper DL, Deegan MJO, Dobbyn AJ, Eckert F, Hampel C, Hetzer G, Lloyd AW, McNicholas SJ, Meyer W, Mura ME, Nicklaß A, Palmieri P, Pitzer R, Schumann U, Stoll H, Stone AJ, Tarroni R, Thorsteinsson T. MOLPRO. 2006 May 1; version of. [Google Scholar]
- (37).Fuentealba P, Preuss H, Stoll H, Szentpaly L. v. Chem. Phys. Lett. 1982;89:418. [Google Scholar]
- (38).Fuentealba P, Szentpaly L. v., Preuss H, Stoll H. J. Phys. B. 1985;18:1287. [Google Scholar]
- (39).Kuechle W, Dolg M, Stoll H, Preuss H. Mol. Phys. 1991;74:1245. [Google Scholar]
- (40).Bergner A, Dolg M, Kuchle W, Stoll H, Preuss H. Mol. Phys. 1993;80:1431. [Google Scholar]
- (41).Krishnan R, Binkly JS, Seeger R, Pople JA. J. Chem. Phys. 1980;72:650. [Google Scholar]
- (42).Clark T, Chandrasekhar J, Spitznagel GW, Schleyer P. v. R. J. Comp. Chem. 1983;4:294. [Google Scholar]
- (43).Curtiss LA, Redfern C, Raghavachari R,V, Pople JA. J. Chem. Phys. 1999;110:4703. [Google Scholar]
- (44).Fast PL, Sanchez ML, Truhlar DG. Chem. Phys. Lett. 1999;306:407. [Google Scholar]
- (45).Tratz C, Fast PL, Truhlar DG. PhysChemComm. 1999;2:14. [Google Scholar]
- (46).Widmark P-O, Malmqvist P-A, Roos BO. Theor. Chim. Acta. 1990;77:291. [Google Scholar]
- (47).Roos BO, Veryazov V, Widmark P-O. Theor. Chem. Acc. 2003;111:345. [Google Scholar]
- (48).Roos BO, Lindh R, Malmqvist P-A, Veryazov V, Widmark P-O. J. Phys. Chem. A. 2004;108:2851. [Google Scholar]
- (49).Karlström G, Lindh R, Malmqvist P-Å, Roos BO, Ryde U, Veryazov V, Widmark P-O, Cossi M, Schimmelpfennig B, Neogrady P, Seijo L. Comput. Mat. Sci. 2003;28:222. [Google Scholar]
- (50).Das G, Wagner AF, Wahl AC. J. Chem. Phys. 1978;68:4917. [Google Scholar]
- (51).Farrar JM, Lee YT, Goldman VV, Klein ML. Chem. Phys. Lett. 1973;19:359. [Google Scholar]
- (52).Becker CH, Casavecchia P, Lee YT. J. Chem. Phys. 1979;70:2986. [Google Scholar]
- (53).Aquilanti V, Ascenzi D, Braca E, Cappelletti D, Pirani F. Phys. Chem. Chem. Phys. 2000;2:4081. [Google Scholar]
- (54).Aquilanti V, Cappelletti D, Lorenti V, Luzzatti E, Pirani F. J. Phys. Chem. 1993;97:2063. [Google Scholar]
- (55).Douglas M, Kroll NM. Ann. Phys. (N.Y.) 1974;82:89. [Google Scholar]
- (56).Hess BA. Phys. Rev. A. 1986;33:3742. doi: 10.1103/physreva.33.3742. [DOI] [PubMed] [Google Scholar]
- (57).Balabanov NB, Peterson KA. J. Chem. Phys. 2005;123:064107. doi: 10.1063/1.1998907. [DOI] [PubMed] [Google Scholar]
- (58).Schultz N, Zhao Y, Truhlar DG. J. Comp. Chem. 2008;29:185. doi: 10.1002/jcc.20717. N. [DOI] [PubMed] [Google Scholar]
- (59).Boys SF, Bernardi F. Mol. Phys. 1970;19:553. [Google Scholar]
- (60).Woon DE. Chem. Phys. Lett. 1993;204:29. [Google Scholar]
- (61).Woon DE. J. Chem. Phys. 1994;100:2838. [Google Scholar]
- (62).Lasdon L, Waren AD, Jain A, Ratner M. ACM Transactions on Mathematical Software. 1978;4:34. [Google Scholar]
- (63).Pauling L. J. Am. Chem. Soc. 1947;69:542. [Google Scholar]
- (64).Slater JC. J. Chem. Phys. 1964;41:3199. [Google Scholar]
- (65).Cordero B, Gómez V, Platero-Plats AE, Revés M, Echeverría J, Cremades E, Barragán F, Alvarez S. Dalton Trans. 2008:2832. doi: 10.1039/b801115j. [DOI] [PubMed] [Google Scholar]
- (66).Maciel GE, Traficante DD, Lavallee D. Chemistry. D. C. Heath; Lexington, MA: 1978. [Google Scholar]; (a) p. 276.; (b) p. 414.
- (67).Hawkes SJ. J. Chem. Educ. 2001;78:1686. [Google Scholar]
- (68). [accessed Feb. 7, 2009]; http://www.webelements.com.
- (69). [accessed Feb. 7, 2009]; http://en.wikipedia.org/wiki/Semimetal.