Quantum mechanics HyperChem

Containsnine reviews in computational chemistry by various experts. This book is particularly useful for beginning computational chemists. Six chapters address issues relevant to HyperChem. including semi-empirical quantum mechanics... 

Apractical introduction to molecular mechanics and semi-empirical quantum mechanics calculations, with extensive examples from the MMP2 (not in HyperChem), MINDO/3, and MNDO methods. One of the more accessible books for new computational chemists. 

HyperChem is a versatile molecular modeler and editor and a powerful computational package. It offers many types of molecular and quantum mechanics calculations. 

HyperChem can plot orbital wave functions resulting from semi-empirical and ab initio quantum mechanical calculations. It is interesting to view both the nodal properties and the relative sizes of the wave functions. Orbital wave functions can provide chemical insights. 

HyperChem uses two types of methods in calculations molecular mechanics and quantum mechanics. The quantum mechanics methods implemented in HyperChem include semi-empirical quantum mechanics method and ab initio quantum mechanics method. The molecular mechanics and semi-empirical quantum mechanics methods have several advantages over ab initio methods. Most importantly, these methods are fast. While this may not be important for small molecules, it is certainly important for biomolecules. Another advantage is that for specific and well-parameterized molecular systems, these methods can calculate values that are closer to experiment than lower level ab initio techniques. 

This section provides an overview and review of quantum mechanics calculations. The information can help you use Hyper-Chem to solve practical problems. For quantitative details of quantum mechanics calculations and how HyperChem implements them, see the second part of this book. Theory and Methods. 

HyperChem can perform quantum mechanics MO calculations on molecules containing 100 or more atoms. There is no restriction on the number of atoms, but larger structures may require excessive computing times and computer main memory. 

The quantum mechanics methods in HyperChem differ in how they approximate the Schrodinger equation and how they compute potential energy. The ab initio method expands molecular orbitals into a linear combination of atomic orbitals (LCAO) and does not introduce any further approximation. 

HyperChem quantum mechanics calculations must start with the number of electrons (N) and how many of them have alpha spins (the remaining electrons have beta spins). HyperChem obtains this information from the charge and spin multiplicity that you specify in the Semi-empirical Options dialog box or Ab Initio Options dialog box. N is then computed by counting the electrons (valence electrons in semi-empirical methods and all electrons in fll) mitio method) associated with each (assumed neutral) atom and... 

In addition to total energy and gradient, HyperChem can use quantum mechanical methods to calculate several other properties. The properties include the dipole moment, total electron density, total spin density, electrostatic potential, heats of formation, orbital energy levels, vibrational normal modes and frequencies, infrared spectrum intensities, and ultraviolet-visible spectrum frequencies and intensities. The HyperChem log file includes energy, gradient, and dipole values, while HIN files store atomic charge values. 

HyperChem can calculate geometry optimizations (minimizations) with either molecular or quantum mechanical methods. Geometry optimizations find the coordinates of a molecular structure that represent a potential energy minimum. 

HyperChem can calculate transition structures with either semi-empirical quantum mechanics methods or the ab initio quantum mechanics method. A transition state search finds the maximum energy along a reaction coordinate on a potential energy surface. It locates the first-order saddle point that is, the structure with only one imaginary frequency, having one negative eigenvalue. 

There are three steps in carrying out any quantum mechanical calculation in HyperChem. First, prepare a molecule with an appropriate starting geometry. Second, choose a calculation method and its associated (Setup menu) options. Third, choose the type of calculation (single point, geometry optimization, molecular dynamics, Langevin dynamics, Monte Carlo, or vibrational analysis) with the relevant (Compute menu) options. 

Use the HyperChem Model Builder to construct an approximate geometry. If you want to look at the relative energies of a set of molecules, you may want to carry out the calculations using fully optimized molecular geometries. These geometry optimization calculations can use either molecular mechanics or quantum mechanics to further refine the molecular geometry beyond that given by the Model Builder. 

You can perform quantum mechanical calculations on a part of a molecular system, such as a solute, while using molecular mechanics for the rest of the system, such as the solvent surrounding the solute. This boundary technique is available in HyperChem for all quantum mechanical methods. It is somewhat less complete with ab initio calculations than with semi-empirical calculations, however. With ab initio calculations the boundary must occur between molecules rather than inside a molecule. 

The algorithms of the mixed classical-quantum model used in HyperChem are different for semi-empirical and ab mi/io methods. The semi-empirical methods in HyperChem treat boundary atoms (atoms that are used to terminate a subset quantum mechanical region inside a single molecule) as specially parameterized pseudofluorine atoms. However, HyperChem will not carry on mixed model calculations, using ab initio quantum mechanical methods, if there are any boundary atoms in the molecular system. Thus, if you would like to compute a wavefunction for only a portion of a molecular system using ab initio methods, you must select single or multiple isolated molecules as your selected quantum mechanical region, without any boundary atoms. 

Semi-empirical methods could thus treat the receptor portion of a single protein molecule as a quantum mechanical region but ab mdio methods cannot. However, both semi-empirical and ab initio methods could treat solvents as a perturbation on a quantum mechanical solute. In the future, HyperChem may have an algorithm for correctly treating the boundary between a classical region and an ab mdio quantum mechanical region in the same molecule. For the time being it does not. 

Certain options are needed to setup for running quantum mechanics calculations in HyperChem via the corresponding option dialog boxes on the Setup menu. 

The HyperChem log file includes calculated dipole moments of molecules. To set the amount of information collected in the log file, change the value of the QuantumPrintLevel setting in the chem.ini file. Note that the sign convention used in the quantum mechanical calculation of dipoles is opposite to that used in molecular mechanics dipole calculations this reflects the differing sign conventions of physics and chemistry. 

The theory and methods discussed in this book are HyperChem s two fundamental force-energy-generator modules one for molecular mechanics and one for quantum mechanics. Molecular mechanics and quantum mechanics are described in subsequent chapters as modules capable of delivering an energy, or derivatives of the energy. Other chapters describe the uses for these energies and their derivatives in more generic parts of HyperChem. 

The back end is the component of HyperChem that performs the more time-consuming scientific calculations. This is where molecular mechanical and quantum mechanical calculations are performed. The back end can be thought of as the computational chemistry component of HyperChem. 

The semi-empirical methods of HyperChem are quantum mechanical methods that can describe the breaking and formation of chemical bonds, as well as provide information about the distribution of electrons in the system. HyperChem s molecular mechanics techniques, on the other hand, do not explicitly treat the electrons, but instead describe the energetics only as interactions among the nuclei. Since these approximations result in substantial computational savings, the molecular mechanics methods can be applied to much larger systems than the quantum mechanical methods. There are many molecular properties, however, which are not accurately described by these methods. For instance, molecular bonds are neither formed nor broken during HyperChem s molecular mechanics computations the set of fixed bonds is provided as input to the computation. 

In addition to molecular mechanics calculations, HyperChem can perform various quantum mechanical calculations. These calculations are more universal than molecular mechanics, but are also more time consuming and less empirical. 

HyperChem quantum mechanical calculations are ab initio and semi-empirical. Ab initio calculations use parameters (contracted basis functions) associated with shells, such as an s shell, sp shell, etc., or atomic numbers (atoms). Semi-empirical calculations use parameters associated with specific atomic numbers. The concept of atom types is not used in the conventional quantum mechanics methods. Semi-empirical quantum mechanics methods use a rigorous quantum mechanical formulation combined with the use of empirical parameters obtained from comparison with experiment. If parameters are available for the atoms of a given molecule, the ab initio and semi-empirical calculations have an a priori aspect when compared with a molecular mechanics calculation, letting... 

For small molecules, the accuracy of solutions to the Schrodinger equation competes with the accuracy of experimental results. However, these accurate ab initio calculations require enormous computation and are only suitable for the molecular systems with small or medium size. Ab initio calculations for very large molecules are beyond the realm of current computers, so HyperChem also supports semi-empirical quantum mechanics methods. Semi-empirical approximate solutions are appropriate and allow extensive chemical exploration. The inaccuracy of the approximations made in semi-empirical methods is offset to a degree by recourse to experimental data in defining the parameters of the method. Indeed, semi-empirical methods can sometimes be more accurate than some poorer ab initio methods, which require much longer computation times. 

Thus, HyperChem occasionally uses a three-point interpolation of the density matrix to accelerate the convergence of quantum mechanics calculations when the number of iterations is exactly divisible by three and certain criteria are met by the density matrices. The interpolated density matrix is then used to form the Fock matrix used by the next iteration. This method usually accelerates convergent calculations. However, interpolation with the MINDO/3, MNDO, AMI, and PM3 methods can fail on systems that have a significant charge buildup. 

HyperChem assumes that it is easiest for you to just use subset selection to select that portion of the molecular system that is to be treated quantum mechanically. You can then extend the initial selection to form a convenient and universally acceptable boundary. Thus, you make a simple selection of atoms for the first pass at selecting the quantum mechanical portion. The selected atoms are quantum atoms and the unselected atoms are classical atoms. 

If you request a semi-empirical quantum mechanical calculation now, HyperChem carries on as well as possible (as described below) in choosing how the atoms for quantum mechanical calculation is capped. If, however, an aromatic benzene ring (with delo-... 

Note The capping atoms are only supported in the semi-empirical quantum mechanics methods in HyperChem. If you want to use the mixed model in the ab mi/io method in HyperChem, you must select an entire molecule or molecules without any boundary atom between the selected and unselected regions and then carry out the calculation. 

HyperChem does not use constrained optimization but it is possible to restrain molecular mechanics and quantum mechanics calculations by adding extra restraining forces. 

The theory of chemical reactions has many facets including elaborate quantum mechanical scattering approaches that treat the kinetic energy of atoms by proper wave mechanical methods. These approaches to chemical reaction theory go far beyond the capabilities of a product like HyperChem as many of the ideas are yet to have wide-spread practical implementations. 

Notice that although the energies and forces are evaluated quantum mechanically in HyperChem, the vibrational analysis has been purely classical. 

HyperChem Release 7 , available in 2002, is a full 32-bit application, developed for the Windows 95, 98, NT, ME, 2000 and XP operating systems. Density Functional Theory (DFT) has been added to complement Molecular Mechanics, Semi-Empirical Quantum Mechanics and Ab Initio Quantum Mechanics already available. The HyperNMR package has been integrated into the core of HyperChem, allowing for the simulation of NMR spectra. A full database capability is integrated into HyperChem 7. Many other features are updated and improved. 

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