com.actelion.research.chem.conf.VDWRadii Maven / Gradle / Ivy
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package com.actelion.research.chem.conf;
public interface VDWRadii {
/**
* VDW Radii indexed by atomic numbers, taken from DOI: 10.1039/c3dt50599e
* Santiago Alvarez: A cartography of the van der Waals territories
* Published on 01 May 2013 on http://pubs.rsc.org | doi:10.1039/C3DT50599E
*
* (in a few cases no value was given (marked ??), where we use estimated values)
*/
public static final float[] VDW_RADIUS = new float[]{
1.00f, 1.20f, 1.43f, 2.12f, // ??,H,He,Li
1.98f, 1.91f, 1.77f, 1.66f, // Be,B,C,N
1.50f, 1.46f, 1.58f, 2.50f, // O,F,Ne,Na
2.51f, 2.25f, 2.19f, 1.90f, // Mg,Al,Si,P
1.89f, 1.82f, 1.83f, 2.73f, // S,Cl,Ar,K
2.62f, 2.58f, 2.46f, 2.42f, // Ca,Sc,Ti,V
2.45f, 2.45f, 2.44f, 2.40f, // Cr,Mn,Fe,Co
2.40f, 2.38f, 2.39f, 2.32f, // Ni,Cu,Zn,Ga
2.29f, 1.88f, 1.82f, 1.86f, // Ge,As,Se,Br
2.25f, 3.21f, 2.84f, 2.75f, // Kr,Rb,Sr,Y
2.52f, 2.56f, 2.45f, 2.44f, // Zr,Nb,Mo,Tc
2.46f, 2.44f, 2.15f, 2.53f, // Ru,Rh,Pd,Ag
2.49f, 2.43f, 2.42f, 2.47f, // Cd,In,Sn,Sb
1.99f, 2.04f, 2.06f, 3.48f, // Te,I,Xe,Cs
3.03f, 2.98f, 2.88f, 2.92f, // Ba,La,Ce,Pr
2.95f, 2.92f, 2.90f, 2.87f, // Nd,??,Sm,Eu
2.83f, 2.79f, 2.87f, 2.81f, // Gd,Tb,Dy,Ho
2.83f, 2.79f, 2.80f, 2.74f, // Er,Tm,Yb,Lu
2.63f, 2.53f, 2.57f, 2.49f, // Hf,Ta,W,Re
2.48f, 2.41f, 2.29f, 2.32f, // Os,Ir,Pt,Au
2.45f, 2.47f, 2.60f, 2.54f, // Hg,Tl,Pb,Bi
2.5f, 2.5f, 2.5f, 2.5f, // ??,??,??,??
2.5f, 2.80f, 2.93f, 2.88f, // ??,Ac,Th,Pa
2.71f, 2.82f, 2.81f, 2.83f, // U,Np,Pu,Am
3.05f, 3.40f, 3.05f, 2.70f // Cm,Bk,Cf,Es
};
/**
* These covalent single bond radii values were taken from the
* following source:
* 'Molecular Double-Bond Covalent Radii for Elements Li–E112', 2009,
* Pyykkö and Atsumi, doi: 10.1002/chem.200901472
*/
public static final float[] COVALENT_RADIUS = new float[] {
0.25f, 0.32f, 0.46f, 1.33f, // ?,H,He,Li
1.02f, 0.85f, 0.75f, 0.71f, // Be,B,C,N
0.63f, 0.64f, 0.96f, 1.60f, // O,F,Ne,Na
1.39f, 1.26f, 1.16f, 1.11f, // Mg,Al,Si,P
1.03f, 0.99f, 1.07f, 1.96f, // S,Cl,Ar,K
1.71f, 1.48f, 1.36f, 1.34f, // Ca,Sc,Ti,V
1.22f, 1.19f, 1.16f, 1.11f, // Cr,Mn,Fe,Co
1.10f, 1.20f, 1.20f, 1.24f, // Ni,Cu,Zn,Ga
1.21f, 1.21f, 1.16f, 1.14f, // Ge,As,Se,Br
1.21f, 2.10f, 1.85f, 1.63f, // Kr,Rb,Sr,Y
1.54f, 1.47f, 1.38f, 1.28f, // Zr,Nb,Mo,Tc
1.25f, 1.25f, 1.20f, 1.39f, // Ru,Rh,Pd,Ag
1.44f, 1.46f, 1.40f, 1.40f, // Cd,In,Sn,Sb
1.36f, 1.33f, 1.35f, 2.32f, // Te,I,Xe,Cs
1.96f, 1.80f, 1.63f, 1.76f, // Ba,La,Ce,Pr
1.74f, 1.73f, 1.72f, 1.68f, // Nd,Pm,Sm,Eu
1.69f, 1.68f, 1.67f, 1.66f, // Gd,Tb,Dy,Ho
1.65f, 1.64f, 1.70f, 1.62f, // Er,Tm,Yb,Lu
1.52f, 1.46f, 1.37f, 1.31f, // Hf,Ta,W,Re
1.29f, 1.22f, 1.23f, 1.24f, // Os,Ir,Pt,Au
1.42f, 1.50f, 1.44f, 1.51f, // Hg,Tl,Pb,Bi
1.45f, 1.47f, 1.45f, 2.23f, // Po,At,Rn,Fr
2.01f, 1.86f, 1.75f, 1.69f, // Ra,Ac,Th,Pa
1.70f, 1.71f, 1.72f, 1.66f, // U,Np,Pu,Am
1.66f, 1.68f, 1.68f, 1.65f, // Cm,Bk,Cf,Es
1.67f, 1.73f, 1.76f, 1.61f, // Fm,Md,No,Lr
1.57f, 1.49f, 1.43f, 1.41f, // Rf,Db,Sg,Bh
1.34f, 1.29f, 1.28f, 1.21f, // Hs,Mt,Ds,Rg
1.37f, 1.36f, 1.43f, 1.62f, // Cn,Uut,Fl,Uup
1.75f, 1.65f, 1.57f // Lv, Uus, Uuo
};
public static float getVDWRadius(int atomicNo) {
return VDW_RADIUS[atomicNo < VDW_RADIUS.length ? atomicNo : 6]; // we assume some kind of carbon from the MDL special types
}
public static float getCovalentRadius(int atomicNo) {
return COVALENT_RADIUS[atomicNo < COVALENT_RADIUS.length ? atomicNo : 6]; // we assume some kind of carbon from the MDL special types
}
}