BIOVIA MATERIALS STUDIO VAMPDATASHEETBIOVIA Materials Studio VAMP is a semi-empirical molecularorbital package for molecular organic and inorganic systems.
BIOVIA Materials Studio VAMP is an ideal intermediate module
between force-field and first principles methods and is capableof rapidly calculating many physical and chemical molecularproperties. BIOVIA Materials Studio VAMP is optimized to be
numerically stable and fast, enabling most calculations to be
run interactively on a PC.

For example, BIOVIA Materials Studio VAMP contains threemethods designed explicitly to handle transition elements,
an area very challenging for semiempirical methods MNDO/
d1 , AM1*2 and PM63. The AM1* method predicts accurate
geometries and energies for metals such as Ti, Zr, and Mo. The
method, in addition, increases the accuracy of results for nontransition elements such as Al, Si, and P. The new PM6 method
provides parameters for 70 elements include transition metals.

OVERVIEWBIOVIA Materials Studio VAMP provides fast and reliablepredictions of structural and electronic properties of molecules.
BIOVIA Materials Studio VAMP is an ideal choice when making
trade-offs between the speed of force-field methods and theaccuracy of first-principles methods. BIOVIA Materials Studio
VAMP is optimized to be numerically stable and fast, enablingusers to perform high throughput calculations using even a PC.
Semiempirical molecular orbital (MO) theory was developed as
an everyday tool for answering questions related to standard
problems in the laboratory. BIOVIA Materials Studio VAMP
provides an efficient way of obtaining these results, including
a simple graphical interface to make these powerful methods
easily accessible. The tasks that can be performed by BIOVIA
Materials Studio VAMP include geometry optimization,transition state search and optimization, and the evaluation ofmany chemical and physical properties.
The breadth of BIOVIA Materials Studio VAMP encompasses
organic, inorganic, and organometallic molecules, polymers,
oligomers, and peptides. Because of its speed, BIOVIA Materials
Studio VAMP can be used to perform scans over wide areas ofa potential energy surface or reaction pathway; or it can beused to perform high-throughput calculations on hundreds
or even thousands of molecules. Such results can be used inconjunction with Quantitative Structure-Activity Relationships(QSAR) to create a formidable predictive tool for areas such as
drug design.
BIOVIA Materials Studio VAMP contains other truly uniquefeatures that make it a powerful tool for any researcher in thechemical, pharmaceutical, or materials industry who needs topredict properties of new compounds.

The dye indigo showing a section of isosurface with theelectrostatic potential mapped onto the electron density.
Molecular electrostatic potential and total electronic density
calculated using BIOVIA Materials Studio VAMP. Image generatedusing BIOVIA Materials Studios volumetric analysis tools.

BIOVIA Materials Studio VAMP is the only program that
calculates both ESR hydrogen hyperfine coupling constants
and 13C chemical shifts. Current accuracy (standard deviations
from experiment) is about 0.5 Gauss for ESR coupling constantsand 6-8 ppm for 13C chemical shifts4.
Solvent effects must be considered when determining theproperties of molecules in almost all real situations, yet theseare often ignored by calculations. Solvent effects are simulated
in integrals via a multipole approximation, rather than an exact
calculation.
BIOVIA Materials Studio VAMP uses two different models forsolvation: numerical Self-Consistent Reaction Field (SCRF)5
calculations, and COnductor-like Screening MOdel (COSMO)5.
Such models are essential for understanding the propertiesof molecules in solution and are easily included in BIOVIA
Materials Studio VAMP calculations.

BIOVIA Materials Studio VAMP computes optical excitation
spectra (UV/vis) using the ZINDO Hamiltonians which wereparameterized for this very purpose. ZINDO provides a numberof different model Hamiltonians7,8 that can be selectedaccording to the desired property, accuracy, and available
elements. The parameterization includes a wide number oftransition metals, allowing the prediction of UV spectra fororganometallic compounds as well as for organic molecules.
Electrostatic potential maps are often essential for understanding
the activity of a molecule. BIOVIA Materials Studio VAMP
includes routines for a rapid an accurate evaluation of thepotential. The Natural Atomic Orbital-Point Charge (NAO-PC)9
model is used for molecular electrostatic properties. The typeof analysis obtained using NAO-PC provides a more exact
picture of the molecular electronics than the normal population
analysis—a picture that rivals the accuracy of ab initio methods
hundreds of times slower.
Finally, BIOVIA Materials Studio VAMP provides a number ofmolecular properties such as ionization potential, multipole
moments, accurate molecular polarizabilities, atomic
polarizabilites, and optical spectra.

By default, BIOVIA Materials Studio VAMP performs a MNDO
Hamiltonian calculation. However, you can use controls on
the BIOVIA Materials Studio VAMP setup dialog to select AM1,
PM3, MNDO/C or MINDO/3 Hamiltonians. The elements forwhich each of these methods is parameterized are given in the‘Features and Capabilities’ section of this document.
Geometry may be optimized in BIOVIA Materials Studio VAMPby several different schemes. The default optimizer is Jon Baker’s
Eigenvector Following (EF) routine14 which was chosen for its
reliability and excellent general performance. A typical geometry
optimization starts either by calculating all or part of the Hessian
matrix, or by estimating its diagonal values. BIOVIA Materials
Studio VAMP also offers two different and very effective transition
state optimizers: EF and Powell’s transition state optimizer.
You can access BIOVIA Materials Studio VAMP through theMaterialsScript API. Scripting allows you to automate repetitive
task and customize workflows.

FEATURES AND CAPABILITIESFeatures marked with an asterisk (*) can not be accessed via
the user interface, but are available by modifying the input file.

THE BIOVIA MATERIALS STUDIO ADVANTAGE

Calculation Tasks

BIOVIA Materials Studio VAMP is operated from within the
BIOVIA Materials Studio® software environment that provides
a user-friendly interface, complying with Windows® standards.
BIOVIA Materials Studio Visualizer offers a wide range ofmodel building and visualization tools that allow you to rapidly
construct models of the system of interest, select the BIOVIA
Materials Studio VAMP module with two mouse clicks, and run
a semi-empirical calculation. BIOVIA Materials Studio VAMP
can, of course, be used to compute molecular properties as
described above; or it can be used in conjunction with othermodules in the BIOVIA Materials Studio suite of programs.
BIOVIA Materials Studio VAMP predictions provide goodstarting points for refinement with more accurate calculations
such as density functional theory (DFT). Alternatively, BIOVIA
Materials Studio VAMP can compute optical & IR spectra, 13C
NMR shifts, or optical polarizability on molecular structures
predicted by other modules of BIOVIA Materials Studio.

• Open- and closed-shell Hartee-Fock methods: Restricted(RHF), Unrestricted (UHF) and spin-Annihilated Unrestricted
Hartee-Fock, (A-UHF)• Geometry optimization• Transition state optimization• Vibrational frequency calculation• Solvent effects: Self-Consistent Reaction Field (SCRF) and• COnductor-like Screening MOdel (COSMO) (available solvents
are acetone, acetonitrile, benzene, carbon tetrachloride,
chloroform, diethyl ether, dimethyl sulfoxide, ethanol,
methanol, methylene chloride, n-hexane, n-hexadecane,
nitrobenzene, pyridine, water)• CI calculations : Full, CIS, CISD and PECIHOW DOES BIOVIA MATERIALS STUDIO
VAMP WORK?
BIOVIA Materials Studio VAMP uses semi-empirical techniques
in which many of the more complex terms are ignoredor replaced using approximations. Empirical parameters andfunctions are used to compensate for the errors introduced bythese approximations. These empirical parameters are fitted
to reproduce experimental data. Suitable methods for theevaluation of energetic data are MINDO/310, MNDO11, AM112,
and PM313. Accurate optical spectra can be obtained using the
INDO7 and CNDO8 methods.
BIOVIA Materials Studio VAMP uses semi-empirical calculations
to determine a molecular wavefunction which can then be
used to derive molecular properties such as energy and dipole
moments. The molecular wavefunction is constructed according
to the LCAO method in which molecular orbitals are obtained as alinear combination of Slater-type atomic orbitals. Semi-empiricalmethods can use Slater functions by evaluating the two-electron
integrals via a multipole approximation, rather than an exact
calculation.

Hamiltonians• PM6 [H through Bi, with the exception of trans-Lanthanides]• MNDO [H, He, Li, Be, B, C, N, O, F, Mg, Al, Si, P, S, Cl, K, Ca,
Zn, Ge, Br, Sn, I, Hg, Pb]• MNDO/C is an MNDO method designed to be used with aperturbational theory correction for electron correlation. It isonly parameterized for C, H, N and O• AM1 [H, B, C, N, O, F, Mg, Al, Si, P, S, Cl, Zn, Ge, Br, Sn, I, Hg]• PM3 [H, Li, Be, B, C, N, O, F, Na, Mg, Al, Si, P, S, Cl, Ca, Zn,
Ga, Ge, As, Se, Br, Cd, In, Sn, Sb, Te, I, Hg, Tl, Pb, Bi]• MNDO/d : standard MNDO parameters for : H, He, Li, Be, B,
C, N, O, F, and MNDO/d parameters for: Na, Mg, Al, Si, P, S,
Cl, Zn, Br, Cd, I, Hg• AM1*: Standard AM1 parameters for H, C, N, O, F, andparameter sets with d-orbitals for elements Al-Cl, Ti-Zn, Br,
Zr Mo, I, and Au.
• CNDO/1 [H, Li, Be, B, C, N, O, F, Na, Mg, Al, Si, P S, Cl, K, Ca,
Sc, Ti, V, Cr, Mn, Fe, Co, Ni, Cu, Zn, As Se, Br, Y, Zr, Nb, Mo,
Tc, Ru, Rh, Pd, Ag, I, Lu, La, Ce Pr, Nd, Pm, Sm, Eu, Gd, Tb,
Dy, Ho, Er, Tm, Yb]• CNDO/2 [H, Li, Be, B, C, N, O, F, Na, Mg, Al, Si, P, S, Cl, K, Ca,
Sc , Ti, V, Cr, Mn, Fe, Co, Ni, Cu, Zn, As Se, Br, Y, Zr, Nb, Mo,
Tc, Ru, Rh, Pd, Ag]• INDO/1 [H, Li, Be, B, C, N, O, F, Na, Mg, Al, Si, P, S Cl, K, Ca,
Sc, Ti, V, Cr, Mn, Fe, Co, Ni, Cu, Zn, As, Se Br, Y, Zr, Nb, Mo,
Tc, Ru, Rh, Pd, Ag, I]• INDO/2 [H, Li, Be, B, C, N, O, F, Na, Mg, Al, Si, P, S Cl, K, Ca,
Sc, Ti, V, Cr, Mn, Fe, Co, Ni, Cu, Zn, As, Se, Br]• BIOVIA Materials Studio VAMP jobs can be run as backgroundprocesses on a server or as synchronous (interactive) jobs on
your PC.

Properties• Electron density• Molecular orbitals (canonical), or localized orbitals• Electrostatic potentials• Atomic charges : NAO-PC, Coulson, and Mulliken• Molecular and atomic multipoles• Static first-order polarizabilities(*)• ESR hyperfine coupling constants to hydrogen(*)• 13C chemical shifts• Optical spectra• Heat of formation, entropy, and heat capacity.

Analysis of BIOVIA Materials Studio VAMP results

REFERENCES:
1. Thiel, W; Voityuk, A. A., J. Phys. Chem. 1996, 100(2), 616-626; Thiel, W.; Voityuk, A. A., THEOCHEM
1994, 119(1), 141-154; Thiel, .; Voityuk, A. A.,Theoretica Chimica Acta 1992, 81(6), 391-404(with an erratum in Theoretica Chimica Acta 1996, 93(5), 315).
2. Voityuk, A. A.; Roesch, N., J. Phys. Chem. A 2000, 104(17), 4089-4094.
3. J.J.P. Stewart, J. Mol. Model. 2007, 13, 1173-1213.
4. Clark, T.; Breindl, A.; Rauhut, G., J. Mol. Model. 1995, 1, 22.
5. Rauhut, G.; Clark, T.; Steinke, T., J. Am. Chem. Soc. 1993, 115, 9174.
6. Klamt, A.; Schüürmann, G., J. Chem. Soc., Perkin Trans. 2, 1993, 799.
7. Ridley, J.; Zerner, M., Theor. Chim. Acta (Berlin) 1972, 32, 111.
8. Pople, J. A.; Santry, D. F.; Segal,G. A., J. Chem. Phys. 1965, 43, S129.7.
9. Rauhut,G.; Clark, T., J. Comput. Chem. 1993, 14, 503.
10. Bingham, R.C.; Dewar, M.J.S.; Lo, D.H., J. Am. Chem. Soc. 1975, 97, 285; 1294; 1302; 1307; Dewar,
M.J.S.; Lo, D.H.; Ramsden, C.A., J. Am. Chem. Soc. 1975, 97, 1311.
11. Dewar, M.J.S.; Thiel, W., J. Am. Chem. Soc. 1977, 99, 4899.
12. Dewar, M.J.S.; Zoebisch, E.G.; Healy, E.F.; Stewart, J.J.P., J. Am. Chem. Soc. 1985, 107, 3902.
13. Stewart, J.J.P ., J. Am. Chem. Soc. 1989, 103, 1413.

• Volumetric display of: total electronic density, spin density,
electrostatic potential, molecular orbitals, and localized
orbitals• Thermodynamic properties (enthalpy, entropy, and heat
capacity)• Atomic charges and bond orders.

14. Baker, J., J. Comput. Chem. 1986, 7, 385.

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