1 MOLDEN Molden - is a package for displaying MOLecular DENsity 2 DESCRIPTION MOLDEN is a package for displaying molecular density. It is tuned to the Ab Initio packages GAMESS* and GAUSSIAN. It can read all the information it needs from a GAMESS or GAUSSIAN outputfile. In this form it has been running on a CONVEX C-120, an APOLLO DN10000, an IRIS 4D/70GT, a DECSTATION 5000 and a SUN, and in slightly adapted versions on a VAX and a CRAY-YMP. It should run smoothly on most Unix machines. See section INSTALLATION GUIDE on how to install MOLDEN. (* The GAMESS version referred to here is the european version maintaned by M.F. Guest et al not to be confused with the american version maintained by M.W. Schmidt et al) MOLDEN was written by: G. Schaftenaar CAOS/CAMM Center Nijmegen Toernooiveld, Nijmegen The Netherlands (1991) e-mail adress : schaft@caos.kun.nl 2 FILES MOLDEN reads two files, these are: Inputfile File holding the title and keyword lines ( FORTRAN unit 5 ) GAMESS/GAUSSIAN Outputfile A file produced by running GAMESS/GAUSSIAN. The name of this file must be defined with the keyword FILE . This must be the output of a single GAMESS/GAUSSIAN run. Care must be taken not to turn off printing of vectors and/or basis set in the case of GAMESS. In the case of GAUSSIAN printing of basis set information has to be turned on by the use of the keyword GFINPUT. Printing of MO coefficients has to be turned on by use of the keyword IOP(6/7=1). ( FORTRAN unit 30 ) MOLDEN writes two files, these are: Outputfile Results file. ( FORTRAN unit 6 ) plotfile The Plotter/Screen File called plot ( FORTRAN unit 15 ). At the end of the MOLDEN run, a Screen file can be displayed by : - simply typing 'CAT PLOT' on Unix machines 'TYPE PLOT.DAT' on VAX machines Depending on the configuration of the Plotter, the Plot file can be displayed in the same way or has to be sent to a queue ( usually by a SUBMIT command or an lpr command ). INPUTFILE The layout of Inputfile for a MOLDEN job is as follows; ( 80 columns maximum ) <First line of key words> ( 80 columns maximum ) <Second line of key words> ( 80 columns maximum ) Both capitals and lowercase can be used. The keywords taking no parameters usually can be abbreviated to four characters. 2 SPECIFICATION_OF_TERMINAL/PLOTTER_TYPE The following commands specify which terminal or plotter driver is to be used. TEK4014 Syntax: TEK4014 The Tektronix4014 graphics language is considered to be something of a standard. A lot of graphical terminals can emulate tek4014 although you probably need to tell your terminal it is to do so. Some PC's having a VT100 terminal emulation can also emulate tek4014 (it runs at least on an ATARI and in an impaired way on a Macintosh) (some HP terminals with a tek4014 emulation run tek4014 faster than the HP language) XWINDOWS has an application xterm in which you can turn on a tek window. (Under Unix this command is usually located in the directory /usr/bin/X11) HPGL Syntax: HPGL HPGL stands for Hewlett Packard Graphics Language. The HP plotters all speak this language. Also HP laserwriters understand HPGL. HP2392A Syntax: HP2392A Most HP terminals with graphics capability probably will be able to understand these escape codes. POSTSCRIPT Syntax: POSTSCRIPT Most Laserwriters understand POSTSCRIPT. Although sometimes you have to tell them it is not getting plain text but POSTSCRIPT. XWINDOWS Syntax: XWINDOWS Most workstations have XWINDOWS capability (See section INSTALLATION GUIDE how to install MOLDEN with an XWINDOWS driver). Before running MOLDEN you have to define the display you will be working on. On Unix machines just type; SETENV DISPLAY :0 when you want to use the display of the machine MOLDEN is executing on, and for instance SETENV DISPLAY CAMMS3.CAOS.KUN.NL:0 when you want to use the display of the remote machine with internet address CAMMS3.CAOS.KUN.NL. On VAX machine, the same is accomplished by typing SET DISPLAY/CREATE /NODE=CAMMS3.CAOS.KUN.NL/TRANS=TCPIP. A window will be created at run time, holding the picture. A rectangular part of this picture can be magnified by pressing the left mouse button and holding it down while dragging it untill the rectangle has the required size. Pressing the middle mouse button subsequently will undo the magnification. Pressing the right mouse button will end the MOLDEN session. When the cursor is in the MOLDEN window, the arrow keys can be used to rotate the 3-d picture and I and D keys will respectively Increase and Decrease the vertical scale op the 3-d plot. The letter M is a toggle, which turns on/off the displaying of the molecule in the 3-d picture. FIGURE Syntax: FIGURE Figure is a Graphics language developed by the Genetics Computer Group. With it goes a package that can convert Figure to a variety of graphics/plotter languages. SILLY Syntax: SILLY The Silicon Graphics 3D version is requested through the use of the keyword SILLY. This is an experimental version. (See section INSTALLATION GUIDE on how to install this version.) 2 DEFINITION_OF_DENSITY The following keys define ; whether the total electron density has to be plotted or the sum of the density owing to some specified molecular orbitals. (OCCU, VALENCE) whether the electron density or the value of an molecular orbital itself has to be plotted (HOMO, LUMO, PSI, PHASE) whether the molecular density minus spherically averaged atomic density has to be plotted (BONDS) or whether for O,F,S and Cl oriented ground state atomic densities have to be substracted. (BONDS in combination with ORIENT) whether the interatomic overlap density has to be plotted (OVERLAP) or the atomic part of difference density (ATOMIC). These are the two components that make up the density matrix used by BONDS (possibly in combination with ORIENT) ATOMIC Syntax: ATOMIC Specifies that the electron density of the free atoms is to be subtracted from the molecular electron density as with the use of the keyword BONDS, only now the contribution from the interatomic overlap is set to zero. In fact the density matrices used by ATOMIC and OVERLAP together make up the density matrix used by BONDS. The density map predominantly will have a negative value, since some of the atomic density has been transferred to interatomic overlap density. However lone pairs usually show up as positive contributions in the density map. (As with BONDS it can be used in combination with the keyword ORIENT) See also BONDS, ORIENT and OVERLAP !! BONDS Syntax: BONDS Not to be used in conjunction with HOMO, LUMO, PSI or OCCU. BONDS subtracts the spherically averaged atomic density from the molecular density . The result is a plot whose average value is zero, and shows where the electrons have come from and gone to when the bonds are formed. However a problem can arise. Most atomic ground states are not spherically symmetric. Oxygen for example has a 3P ground state f.i. Px2Py1Pz1. The electron density now is maximal along the x-axis, so that in fact when an atom in the molecular environment has retained a lot of its ground state character it will have a preferable orientation. Subtracting a spherically symmetric atom Px4/3Py4/3Pz4/3 in this case can result in subtracting too much in the y and z directions and too little in the x direction. As a result the density difference plot may show a misleading decrease in electron density along for example a C-O axis. In this case the keyword ORIENT must be used.(See also ORIENT, OVERLAP and ATOMIC) This effect is usually most pronounced for the atoms O,F,S, and Cl, whereas for example Carbon in the molecular environment usually has a lot of spherically symmetric character. BONDS can only be used when one of the following basissets have been employed; STO3G, 3-21G, 4-31G, 6-31G, optionally with polarisation functions ( *, or ** ). They may differ per atom however and the atoms must be in the range Hydrogen up to Chlorine. HINT : for contour plots CUT=0.1 is recommended for 3d plots MULT=20 is recommended HOMO Syntax: HOMO For closed-shell systems with non-degenerate Highest Occupied Molecular Orbitals, the keyword HOMO can be used to produce an intensity map of the highest occupied molecular orbital. For other systems, the keyword PSI should be used. LUMO Syntax: LUMO For closed-shell systems with non-degenerate Lowest Unoccupied Molecular orbitals, the keyword LUMO can be used to produce an intensity map of the lowest unoccupied molecular orbital. For other systems, the keyword PSI should be used. OCCU Syntax: for example; OCCU = (1-22/0,9/1.0,10/2 ) When the user wants to explicitly define an electronic configuration for a system, overriding the occupancies read in from the GAMESS/ GAUSSIAN output file, the keyword OCCU has to be used. Taking the occupancies read in from the outputfile as a starting point, the orbital occupancies in the example are modified in the following way, in sequential order; ORBITAL OCCUPANCY 1-22 0 9 1 10 2 For the use with Unrestricted Hartree Fock wavefunctions the keywords OCCA (for the alpha electrons) and OCCB (for the beta electrons) have to be used. ORIENT Syntax: ORIENT or ORIENT = (n1,n2/n.nn/n.nn,...) To be used in conjunction with the keyword BONDS and not to be used in conjunction with HOMO, LUMO, PSI or OCCU. BONDS subtracts the the spherically averaged atomic density from the molecular density . The result is a plot whose average value is zero, and shows where the electrons have come from and gone to when the bonds are formed. However a problem can arise. Most atomic ground states are NOT spherically symmetric. Oxygen for example has a 3P ground state f.i. Px2Py1Pz1 the electron density now is maximal along the x-axis ,so that in fact when an atom in the molecular environment has retained a lot of its ground state character it will have a preferable orientation. Subtracting a spherically symmetric atom Px4/3Py4/3Pz4/3 in this case can result in subtracting too much in the y and z directions and too little in the x direction. As a result the density difference plot may show a misleading decrease in electron density along for example a C-O axis. This effect is usually most pronounced for the atoms O,F,S, and Cl, wheras for example Carbon in the molecular environment usually has a lot of spherically symmetric character. When using ORIENT without parameters, the atomic density (DATOM) of O,F,S and Cl atoms will be oriented in such a way that the sum of (DMOL(i,j)-DATOM(i,j))2 (delta squared on the output file) is at a minimum. (DMOL being the atomic part of the molecular density matrix and i and j run over the Px,Py,Pz Atomic orbitals). This is done per atom. When using ORIENT = (N1,N2,..) only the specified atoms are oriented. For all others the spherically averaged atomic density is used. Checked is whether atom number N1,N2 etc are O,F,S or Cl atoms. When using ORIENT = (N1,N2/N.NN/N.NN,...) the automatic orientation mechanism is overridden for atom N2. Instead it is oriented using the two angles supplied on the keyword after the slashes (alfa and beta on the output file). For example the atomic ground state density of Oxygen has an oval symmetry, having one direction in which 2 electrons participate and two perpendicular directions in which 1 electron each participates. The supplied angles define the direction of the unique axis. If the atom in the molecular environment has lost a lot of its ground state character the automatic orientation mechanism can give physically meaningless orientations. In the ultimate case when the oxygen has a pure spherical O2- character, the use of oriented ground state densities is clearly erroneous. When the atomic part of the molecular density matrix shows one direction in which 1 electron participates and two directions in which 1.5 electrons each participate, the automatic orientation mechanism may provide a direction which results in a decrease in electron density at the middle of a bond axis. Here orientation by hand can result in a density-difference plot with the expected increase in electron density at the middle of a bond axis. ORIENT can only be used when one of the following basissets have been employed ; STO3G, 3-21G, 4-31G, 6-31G optionally with polarisation functions (*, or **). They may differ per atom however and the atoms must be in the range Hydrogen up to Chlorine. HINT : for contour plots CUT = 0.1 is recommended for 3d plots MULT = 20 is recommended (see also Chemical Deformation Densities, W.H.E. Schwarz, K. Ruedenberg and L. Mensching, J. Am. Chem. Soc. 1989,111,6926-6933, where the orientation used here is termed 'naive' ) OVERLAP Syntax: OVERLAP The interatomic overlap density will be plotted. This is done by setting the atomic part of the Molecular density matrix to zero. The density map will predominantly have positive values with maxima roughly at midway the bond axes. PHASE Syntax: PHASE PHASE is used to to reverse the sign of a Molecular Orbital. Used in conjuction with PSI. PSI Syntax: PSI = NN A specified molecular orbital is to be plotted (see also PHASE). VALENCE Syntax: VALENCE Since the inclusion of non-valence electrons in ab initio calculations results in the predominance of the inner shell electron density on the total electron density, the interpretation of the chemically more interesting valence electron density is clouded. The use of VALENCE results in non occupying those molecular orbitals which predominantly contain inner-shell electron density. It only works when your molecule exclusively consists of atoms from H to Ar. Otherwise you should use the keyword OCCU. 2 DEFINITION_OF_THE_PLOTPLANE The plane of the plot is essentially defined by : The center of the plot ((PX,PY,PZ) on the MOLDEN outputfile ) The vector perpendicular to the plane of the plot ((CX,CY,CZ) on the MOLDEN outputfile ) The EDGE keyword specifying the size of the square plot The center and vector perpendicular to the plane of the plot can either be specified ; directly in cartesian coordinates by using the absolute form of the keywords CENTER and LINE. indirectly, by using the coordinates of the atoms on the PLANE and ROT keywords ( or the atomic form of the keywords CENTER and LINE). The use of CENTER/LINE and PLANE(/ROT) are mutually exclusive. Of these, the PLANE(/ROT) keywords are the most flexible and easy to use. PLANE defines the plane of the plot by specifing three atoms and optionally this plane can then be rotated round the axis formed by two of these three atoms by use of the keyword ROT. The remaining atom will then no longer lie in the plane of the plot. Finally, when having defined the plane of the plot by either CENTER/LINE or PLANE(/ROT) the plane can be translated along the vector perpendicular to the plane by use of the keyword LIFT. PLANE Syntax: PLANE = (N,N,N) This keyword is essential, it defines the plane of the plot. For example PLANE=(1,2,3) means the first three atoms in the coordinate list define the plane of the plot. The center of the triangle will be taken as center of the plot. The keywords CENTER/LINE and PLANE are mutually exclusive. ROT Syntax: ROT = (N,N,NNN.NN) This keyword is optional, it can only be use in conjunction with the keyword PLANE. For example, when previously having defined the plane of the plot by the first three atoms (PLANE=(1,2,3) ), this plane can be rotated round the axis formed by atoms 2 and 3 by 45 degrees, by using ROT=(2,3,45.0), atom 1 will now no longer be part of the plane of the plot . The center of the plot has been shifted to the point midway the line connecting atoms 2 and 3. CENTER Syntax: CENTER = NN or CENTER = (N.NN,N.NN,N.NN) This keyword is essential, it defines the center of the plot Two formats are provided to define the center: (A) an atom number can be used, and (B) an absolute cartesian coordinate can be specified. Irrespective of which option is used, the center of the plot will be converted internally into absolute cartesian coordinates. Atomic Syntax: CENTER = N. The location of atom N is defined as the center of the plot. Thus if atom n has cartesian coordinates (x=0.5, y=1.4, z=-0.8) then the center of the plot is (x=0.5, y=1.4, z=-0.8). Dummy atoms are not counted, so if any dummy atoms were used in the definition of the geometry, the atoms will have been renumbered (see the MOLDEN output file; coordinates section for the new numbering ) Absolute Syntax: CENTER = (N.NN,N.NN,N.NN) .The location of the center of the plot is defined as being (n.nn,n.nn,n.nn). Of course, before such a center can be defined, the user must know the cartesian coordinates of the atoms in the molecule. LINE Syntax: LINE = NN or LINE = (N.NN,N.NN,N.NN) This keyword is essential, it defines a vector perpendicular to the plane of the plot. Two formats are provided to define the axis perpendicular to the plane of the plot. These formats use radically different concepts, so users are cautioned to verify that they understand both definitions, and the distinction between them. (A) an atom number can be used, and (B) an absolute cartesian coordinate can be specified. Irrespective of which option is used, the axis of the plot will be converted internally into a unit vector in cartesian coordinates. Atomic Syntax: LINE = N The axis of the plot is defined by the vector drawn from atom N to the defined center of the plot. Thus if atom n has cartesian coordinates (x=0.5, y=1.4, z=0.2) and the center of the plot is at point (x=0.5, y=1.4, z=-0.8) then the axis of the plot is (0.0, 0.0, 1.0). Dummy atoms are not counted, so if any dummy atoms were used in the definition of the geometry, the atoms will have been renumbered (see the MOLDEN output file, coordinates section for the new numbering ) Absolute Syntax: LINE = (N.NN,N.NN,N.NN) The axis of a line perpendicular to the plane of the plot is (n.nn,n.nn,n.nn). This axis need not be normalized, but must be finite, that is the only axis not allowed is (0,0,0). LIFT Syntax: LIFT = N.NN This keyword is optional. When having defined the plane of the plot by either CENTER/LINE or PLANE(/ROT) the plane can be translated along the vector perpendicular to the plane by use of the keyword LIFT. The length of this vector is specified as N.NN Atomic Units. EDGE Syntax: EDGE = N.NN The length of the sides of the graph-plot is defined as being n.nn Atomic Units (1 AU = 0.529177 Angstrom). 2 DEFINITION_OF_THE_PLOTTYPE Two kinds of plots are possible; a contour plot ( See CONTOUR ) a three dimensional plot ( See 3D ) CONTOUR Syntax: CONTOUR The use of CONTOUR requests a contour plot. This is the default, so that its specification is not required, except when the combination of a 3-D grid plot with a contour plot is desired. (See also CUT, FINE and STEP .) CUT Syntax: CUT = N.NNN This keyword sets the maximum contour value at n.nnn times the maximum encountered density/intensity. CUT should be within the range 0.0 - 1.0. This keyword was specially devised for use with gaussians since the inclusion of non-valence electrons in ab initio calculations results in the predominance of the inner shell electron density on the total electron density, which clouds the interpretation of the chemically more interesting valence electron density. FINE Syntax: FINE Normally between 10 and 25 contours are plotted. In order to increase this number FINE can be used, in which case 40 to 100 contours will be generated. STEP Syntax: STEP = N.NN Normally between 10 and 25 contours are plotted. The program itself figures out which contour interval should be used. Sometimes the program comes up with different contour intervals for plots one would like to compare. In this case STEP should be used to force a contour interval used by previous runs. 3D Syntax: 3D 3D can be used to create a 3-D mesh of lines plot. 3D can be used in conjuction with the keyword AXIS specifying the view direction. When AXIS is omitted a value of 0.5 is used. 3D can also be used in combination with CONTOUR. (See also AXIS and MULT) AXIS Syntax: AXIS = N.NNN AXIS determines the view direction when a three dimensional plot is requested by the use of the keyword 3D. The range of n.nn in AXIS = N.NN is 1.0 to 0.0. Where 1.0 would give a square plot, as if the user was viewing the plot from directly overhead looking straight down, 0.0 gives a view of the plot as if the user was looking at it from the horizon, looking horizontally. Clearly, AXIS=1.0 would not show the relief. If 3D was used only a perfectly square grid would be seen. A better choice would be AXIS = 0.6. Conversely, AXIS = 0.0 would show the contours as straight lines (as they would be being viewed edge-on). MULT Syntax: MULT = N.NN There is a default scale for the relief of a plot, when viewed as a 3-D structure. If this default is not suitable, say the plot is too flat, then MULT = N.NN can be used to change the vertical scale. MULT=1.0 will do nothing, MULT = 2.0 will increase the vertical relief. Use in conjunction with the keyword 3D. (See also 3D and AXIS) 2 MISCELLANEOUS_COMMANDS BEFORE Syntax: BEFORE In case GAMESS/GAUSSIAN has performed a geometry optimise/saddle run, two sets of vectors are available from the outputfile, those before optimisation and those after. Specifying BEFORE results in using the vectors and geometry before optimisation. DEBUG Syntax: DEBUG This keyword is in fact a way of getting a lot more output, such as: basis set information, vectors, density matrices and so on. FILE Syntax: FILE = filename This keyword must be used to specify the GAMESS/GAUSSIAN outputfile from which is read. This must be the output of a single run and care must be taken not to turn off printing of vectors. (When using the keyword MOLPOT the output of a DMA analysis by GAMESS is expected, without the output of the corresponding startup job.) GENERATE Syntax: GENERATE This keyword results in the writing of the density matrix in FORTRAN data statements. It is used to generate atomic data for use by the program internally. (of course a preceding atomic run by GAMESS has to be performed, do not use with a GAUSSIAN outputfile ) MOLPOT Syntax: MOLPOT This keyword can only be used when the output of a DMA analysis by GAMESS is supplied. In a Distributed Multipole Analysis the molecular electron density and atomic charges are fitted by an expansion of multipoles. With these multipoles the electrostatic potential of a point charge in the field of the molecule can be calculated and plotted. The DEFINITION DENSITY keywords are nolonger active when using MOLPOT. (see A.J. Stone and M. Alderton, Molecular Physics, 1985, 56, 1047-1064) 2 EXAMPLES BASIS SET EFFECTS When using the minimal basis set STO3G together with the BONDS option and comparing the electron density of the free atoms with that of the molecule, one usually finds an increase of electron density at the middle of the bonds axes and a decrease of electron density at the atoms themselves. Doing the same for the split-valence basis sets, such as 3-21G, 4-31G and 6-31G, one also finds an increase of electron density at the middle of the bond axes, but also an increase of electron density close to the atom centres themselves is observed. A decrease of electron density is found in the outer regions of the molecule. This reflects the capability of the split-valence to yield a more contracted atom on going from the free atoms to the molecule. The minimal STO3G basis set clearly does not have this flexibility. This effect is illustrated for the Hydrogen molecule with STO3G and 4-31G basis sets. (See FIGURES 1 and 2 respectively) FIGURE 1 Inputfile: 1: H2 sto3g Molecular Density minus atoms 2: CENTER=(0.0,0.0,0.0) LINE=(1.0,0.0,0.0) CUT=0.1 EDGE=10.0 3: BONDS FILE=h2stoout POSTSCRIPT DEBUG FIGURE 2 Inputfile: 1: H2 4-31g molecule minus atoms 2: CENTER=(0.0,0.0,0.0) LINE=(1.0,0.0,0.0) CUT=0.1 3: EDGE=10.0 POST DEBUG BONDS FILE=h2gam431out RING STRAIN FIGURE 3 shows the electron density of the benzene molecule minus that of the free atoms. An increase of electron density at the middle of the C-C bond axes is observed. FIGURE 4 shows the result of the same procedure followed for the cyclopropane molecule. Here the increase of electron density is clearly positioned outside the C-C bond axes. The overlap of atomic orbitals of the different C atoms is not optimal because of ring-strain. This effect is also known as the formation of banana bonds in cyclopropane. FIGURE 3 Inputfile: 1: benzene sto3g molecular minus atomic density 2: PLANE=(1,3,5) EDGE=13.22 BONDS CUT=0.08 3: FILE=benzene.out POSTSCRIPT FIGURE 4 Inputfile: 1: cyclopropane sto3g molecular density minus atomic 2: PLANE=(1,2,3) EDGE=10.0 BONDS CUT=0.08 3: FILE=cyclopropaan.out POSTSCRIPT THE USE OF KEYWORD ORIENT When using the keyword BONDS, default the spherically averaged electron density of the atoms is subtracted form the molecular density. However some atoms have a groundstate that strongly deviates from the spherical symmetry. Oxygen for example has a 3P ground state, characterised by one direction in which 2 electrons participate and two perpendicular directions in which 1 electron each participates, this might be termed as an oval symmetry. If the atoms within the molecule have retained a lot of this oval symmetry, then subtracting spherically averaged atoms would result in subtracting too little (4/3 electrons) in the direction in which 2 electrons participate and too much(4/3 electrons) in the directions in which 1 electron each participate. The latter are the directions in which oxygen will form bonds and the overall result would be a seemingly decrease of electron density along the bond axes (See FIGURE 5, the planar conformation of Hydrogen Peroxide). By using the keyword ORIENT, the true atomic ground state density, after optimising its orientation within the molecule, is subtracted from the molecular density. This leads to the expected increase in electron density along the O-O axis in Hydrogen Peroxide (see FIGURE 6 and 7) FIGURE 5 Inputfile: 1: H2O2 sto3g Molecular Density minus Spherical atoms 2: PLANE=(2,3,4) EDGE=7.0 BONDS CUT=0.1 3: FILE=h2o2out POSTSCRIPT DEBUG FIGURE 6 Inputfile: 1: H2O2 sto3g Molecular Density minus Oriented Oxygens 2: PLANE=(2,3,4) EDGE=7.0 BONDS ORIENT CUT=0.1 3: FILE=h2o2out POSTSCRIPT DEBUG FIGURE 7 Inputfile: 1: H2O2 sto3g Molecular Density minus Oriented Oxygens 2: PLANE=(2,3,4) EDGE=7.0 POST DEBUG 3D 3: FILE=h2o2out BONDS ORIENT MULT=20 MORE ON THE USE OF THE KEYWORDS BONDS, ORIENT, ATOMIC AND OVERLAP The use of the keywords BONDS,ORIENT,ATOMIC and OVERLAP is illustrated for the NH2COOCH3+.. molecule. Removing an electron from the neutral species results in an extra distortion of the atomic contribution to the molecular density. Before the geometry optimisation of this molecule, the automatic orientation mechanism of ORIENT provides a chemically sensible orientation for both oxygens (See FIGURE 8). After the geometry optimisation however, the automatic orientation mechanism fails for the second oxygen, resulting in a decrease in electron density along the C-O-C axes (See FIGURE 10). Looking at the part of the density matrix involving Px,Py and Pz orbitals of the oxygens, it is clear to see why. For the first oxygen the p-part of the density matrix resembles that of the oxygen ground state. For the second oxygen we see a heavily distorted oxygen ground state (this is reflected in a larger value of delta squared). Where the oxygen ground state has one direction in which 2 electrons participate and two perpendicular directions where 1 electron each participate. The second oxygen has one direction in which roughly 1 electron participates (the y direction) and 2 perpendicular directions in which roughly 1.5 electrons each participate (the x and z directions). The automatic orientation mechanism now will try to align the unique atomic ground state axis with one of the 1.5 electrons axes in the molecule, after the geometry optimisation the balance topples over in favour of the x-direction. By forcing the unique axis to lie in the z-direction, a chemically sensible picture re-emerges in which an increase of electron density midway the C-O-C bond axes can be seen (See FIGURE 11). FIGURE 8: MOLECULAR DENSITY MINUS ORIENTED GROUNDSTATE ATOMIC DENSITY - Before geometry optimisation Inputfile: 1: NH2COOCH3+. sto3g Mol. Density - Oriented Atoms before Optimisation 2: PLANE=(1,2,3) EDGE=12.0 BONDS ORIENT CUT=0.1 3: BEFORE FILE=carbso POSTSCRIPT Excerpt from the MOLDEN outputfile: ---- O sto3g ----------------------------------------- p-part atomic density matrix before orientation 2.0000 0.0000 0.0000 0.0000 1.0000 0.0000 0.0000 0.0000 1.0000 delta squared = 8.092850549116692E-002 alfa optimised = 0. beta optimised = 90.0000000000000 p-part molecular density matrix 0.9728 0.0184 0.0000 0.0184 0.9900 0.0000 0.0000 0.0000 1.7182 p-part oriented atomic density matrix 1.0000 0.0000 0.0000 0.0000 1.0000 0.0000 0.0000 0.0000 2.0000 ---- O sto3g The C-O-C Oxygen -------------------------- p-part atomic density matrix before orientation 2.0000 0.0000 0.0000 0.0000 1.0000 0.0000 0.0000 0.0000 1.0000 delta squared = 0.486484885670038 alfa optimised = 0. beta optimised = 90.0000000000000 p-part molecular density matrix 1.4122 -0.1816 0.0000 -0.1816 0.8539 0.0000 0.0000 0.0000 1.5212 p-part oriented atomic density matrix 1.0000 0.0000 0.0000 0.0000 1.0000 0.0000 0.0000 0.0000 2.0000 FIGURE 9: MOLECULAR DENSITY MINUS SPHERICALLY AVERAGED ATOMIC DENSITY - After geometry optimisation Inputfile: 1: NH2COOCH3+. sto3g Mol.Density - Spherical Atoms after Optimisation 2: PLANE=(1,2,3) EDGE=12.0 BONDS CUT=0.1 3: FILE=carbso POSTSCRIPT FIGURE 10: MOLECULAR DENSITY MINUS ORIENTED GROUNDSTATE ATOMIC DENSITY - After geometry optimisation Inputfile: 1: NH2COOCH3+. sto3g Mol. Density - Oriented Atoms after Optimisation 2: PLANE=(1,2,3) EDGE=12.0 BONDS ORIENT CUT=0.1 3: FILE=carbso POSTSCRIPT Excerpt from the MOLDEN outputfile: ---- O sto3g --------------------------------------------- p-part atomic density matrix before orientation 2.0000 0.0000 0.0000 0.0000 1.0000 0.0000 0.0000 0.0000 1.0000 delta squared = 7.890606938493698E-002 alfa optimised = 0. beta optimised = 90.0000000000000 p-part molecular density matrix 0.9712 0.0198 0.0000 0.0198 0.9809 0.0000 0.0000 0.0000 1.7226 p-part oriented atomic density matrix 1.0000 0.0000 0.0000 0.0000 1.0000 0.0000 0.0000 0.0000 2.0000 ---- O sto3g The C-O-C Oxygen --------------------------- p-part atomic density matrix before orientation 2.0000 0.0000 0.0000 0.0000 1.0000 0.0000 0.0000 0.0000 1.0000 delta squared = 0.517238577646048 alfa optimised = 18.3000000000000 beta optimised = 180.000000000000 p-part molecular density matrix 1.4285 -0.2000 0.0000 -0.2000 0.8900 0.0000 0.0000 0.0000 1.4804 p-part oriented atomic density matrix 1.9014 -0.2981 0.0000 -0.2981 1.0986 0.0000 0.0000 0.0000 1.0000 FIGURE 11: FORCED ORIENTATION OF THE SECOND OXYGEN - AFTER GEOMETRY OPTIMISATION Inputfile: 1: NH2COOCH3+. sto3g Mol. - Atoms forced orientation C-O-C oxygen 2: PLANE=(1,2,3) EDGE=12.0 ORIENT=(2,3/0/90) BONDS CUT=0.1 3: FILE=carbso POSTSCRIPT DEBUG Excerpt from the MOLDEN outputfile: ---- O sto3g The C-O-C Oxygen -------------------------- p-part atomic density matrix before orientation 2.0000 0.0000 0.0000 0.0000 1.0000 0.0000 0.0000 0.0000 1.0000 delta squared = 0.545626478874887 alfa optimised = 0. beta optimised = 90.0000000000000 p-part molecular density matrix 1.4285 -0.2000 0.0000 -0.2000 0.8900 0.0000 0.0000 0.0000 1.4804 p-part oriented atomic density matrix 1.0000 0.0000 0.0000 0.0000 1.0000 0.0000 0.0000 0.0000 2.0000 INTERATOMIC OVERLAP PLOTS FIGURE 12: INTERATOMIC OVERLAP CONTOUR PLOT Inputfile: 1: sto3g NH2COOCH3+. Interatomic Overlap Density 2: PLANE=(1,2,3) EDGE=12.0 OVERLAP 3: FILE=carbso POSTSCRIPT DEBUG FIGURE 13: INTERATOMIC OVERLAP 3-D PLOT Inputfile: 1: sto3g NH2COOCH3+. 2: PLANE=(1,2,3) EDGE=12.0 3D POSTSCRIPT DEBUG 3: FILE=carbso OVERLAP ATOMIC DEFORMATION FIGURE 14: - Molecular density minus oriented groundstate Atomic density - ATOMIC deformation only - Forced Orientation of second Oxygen - After Geometry Optimisation Inputfile: 1: NH2COOCH3+. sto3g Mol.- Atoms forced orientation C-O-C Oxygen Atomic 2: PLANE=(1,2,3) EDGE=12.0 BONDS CUT=0.1 3: FILE=carbso POSTSCRIPT ORIENT=(3,3/0/90) ATOMIC specification of BONDS is not necessary when using keyword ATOMIC. INSTALLATION GUIDE For some machines MOLDEN contains some machine specific code (Particulary for the VAX and in lesser extent for the CRAY and the 3-D version for the SILICON GRAPHICS). Before compiling MOLDEN these lines have to be made active, by removing the comment in front of these lines, like cvax, ccray or csg. For the VAX and the SILICON GRAPHICS, these lines are exclusively located at the back of the program source. Depending on the local situation a compiler can run out of space, in this case you should chop MOLDEN up in two pieces and try again. When you want to use the XWINDOWS driver of MOLDEN, the last subroutine of MOLDEN,xwin has to be deleted or commented out. In addition the file xwin.c has to be compiled with a C compiler. On Unix machines it is assumed that the following files are present: FILE DIRECTORY libX11.a /usr/lib Xlib.h /usr/include/X11 Xutil.h /usr/include/X11 Xos.h /usr/include/X11 keysym.h /usr/include/X11 If you do have these files, but they are not in the directories listed above, you can use the -Idirectory option on the CC command to tell the C compiler where the include files are. And you can specify the -Ldirectory option in front of the -lX11 option to tell the loader where the X library file is to be found. Following are the specific instructions per machine (If your machine is not one of the below and it is a Unix machine, try the DEC/ULTRIX instructions). VAX/VMS Type: RENAME MOLDEN.F MOLDEN.FOR .Remove the comment cvax from lines starting with it. Installation of MOLDEN without the XWINDOWS driver. $ fortran/contin=90 molden $ link molden Installation of MOLDEN with the XWINDOWS driver; Create the file MAKE.COM containing the following lines. $ fortran/contin=90 molden.for $ cc/define="VMS" xwin.c $ define lnk$library sys$library:vaxcrtl $ link molden,xwin,sys$input/opt sys$share:decw$xlibshr/share Execute it by typing @MAKE. To run MOLDEN, create the file MOLDEN.COM containing the following lines; $ assign 'p1' for005 $ assign 'p2' for006 $ run cc:[schaft.molden]molden.exe $ deassign for005 $ deassign for006 Adapt the reference to the directory where MOLDEN is located. Execute it by typing @MOLDEN INPUTFILE OUTPUTFILE. DEC/ULTRIX Installation of MOLDEN without the XWINDOWS driver. f77 -o molden molden.f Installation of MOLDEN with the XWINDOWS driver. f77 -c molden.f cc -c xwin.c f77 -o molden molden.o xwin.o -lX11 To run MOLDEN: molden <inputfile >outputfile& SUN Installation of MOLDEN without the XWINDOWS driver. f77 -Nl90 -o molden molden.f Installation of MOLDEN with the XWINDOWS driver. f77 -Nl90 -c molden.f cc -c xwin.c f77 -o molden molden.o xwin.o -lX11 To run MOLDEN: molden <inputfile >outputfile& APOLLO Installation of MOLDEN without the XWINDOWS driver. f77 -c molden.f ld -o molden -A stacksize,FFFFF molden.o Installation of MOLDEN with the XWINDOWS driver. f77 -c molden.f cc -c xwin.c ld -o molden -A stacksize,FFFFF molden.o xwin.o -lX11 To run MOLDEN: molden <inputfile >outputfile& CONVEX Installation of MOLDEN without the XWINDOWS driver. fc -o molden molden.f Installation of MOLDEN with the XWINDOWS driver. fc -c molden.f cc -c xwin.c fc -o molden molden.o xwin.o -lX11 To run MOLDEN: molden <inputfile >outputfile& CRAY UNDER UNICOS The source lines specific for the CRAY version can be made active by typing: vi molden.f : 1,$s/^ccray// : x Installation of MOLDEN without the XWINDOWS driver. cft77 molden.f segldr -o molden molden.o Installation of MOLDEN with the XWINDOWS driver. cft77 molden.f cc -c xwin.c segldr -o molden molden.o xwin.o -lX11 To run MOLDEN: molden <inputfile >outputfile& SILICON GRAPHICS The source lines for the 3-D real time rotation version can be made active by typing: vi molden.f : 1,$s/^csg// : x Installation of MOLDEN without the XWINDOWS driver, and with the 3-D real time rotation capability, activated by the use of the keyword SILLY; f77 -o molden molden.f -lfgl -lgls Installation of MOLDEN with the XWINDOWS driver; and with the 3-D real time rotation capability; f77 -c molden.f cc -c xwin.c f77 -o molden molden.o xwin.o -lfgl -lgls -lX11 To run MOLDEN: molden <inputfile >outputfile&