HyperChem Calculations

Both inoleciilar and qiiantnin mechanics in ethods rely on the Born-Oppenheimer approximation. In qnantiinn mechanics, the Schrddmger equation (1) gives the wave function s and energies of a inolecii le. 

Nuclei have many times more mass than electrons. Diiringa very small period of tim e wh en th e mo vein en t of heavy nuclei is n egli-gible, electrons are moving so fast that their distribution is smooth. Th is leads to the approximation that the elec iron distri-biition IS dependent only on the fixed positions of nuclei and not on their velocities. This approximaiion allows two simplifications 

Sin ce th e n uclear-n iiclear repulsion is constant for a fixed conlig-11 ration of atom s, this term also drops on t. The Ilam il Ionian is now purely electronic. 

Generating the potential energy surface (PCS) using this equation requires solutions for many configurations ofnnclei. In molecular mechanics, the electronic energy is not evaluated explicitly. 

In stead, these m eth od s solve the poten tial energy surface by using a force field equation (see Molecular Mechanics on page2] i.The force field equation represen ts electron ic energy implicitly th roil gh param eteri/ation. 

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Theory and Methods includes the equations, analytical descriptions, and data you need to understand the calculations. It deals with the science behind HyperChem calculations. Information on parameters and settings lets you modify and customize calculations. 

Once HyperChem calculates potential energy, it can obtain all of the forces on the nuclei at negligible additional expense. This allows for rapid optimization of equilibrium and transition-state geometries and the possibility of computing force constants, vibrational modes, and molecular dynamics trajectories. 

During a molecular dynamics simulation, HyperChem stores the current positions, Tj (t), and the mid-step velocities, Vj (t - 1/2 At). Since the algorithm provides mid-step velocities, but not velocities, Vj (t), for the positions at time t, HyperChem calculates approximate values of Ej-qt (O- This results in slightly larger fluctuations in Ej-ot (t) than an algorithm that calculates exact values of... 

The second summation of the above is over the orbitals of atom A. HyperChem calculates the electrostatic potential using this last expression for the semi-empirical methods. 

A textbook describing the theory associated with calculation s of Ih e electronic structure of molecti lar system s. While the book focuses on ab ini/rci calculation s, much of the in formation is also relevant to semi-empirical methods. The sections on the Hartree-fock an d Con figuration ItUeracTion s tn elh ods, in particular, apply to HyperChem. fhe self-paced exercisesare useful for the beginning computational chemist. 

Siibmiinng a sinicture to a calculation can be expensive in terms ol hnmati time and elTort. HyperChem lets you build and display inolecn les easily. Since IlyperCh em con tains a graph ical in lerface. you can monitor the con sirnction ofmoleciiles. 

Using the coordinates of special geometries, minima, and saddle points, together with the nearby values of potential energy, you can calculate spectroscopic properties and macroscopic therm ody-riatriic and kinetic parameters, sncfi as enthalpies, entropies, and thermal rate constants. HyperChem can provide the geometries and energy values for many of these ealeulatiori s. 

HyperChem uses th e ril 31 water m odel for solvation. You can place th e solute in a box of T1P3P water m oleeules an d impose periodic boun dary eon dition s. You may then turn off the boundary conditions for specific geometry optimi/.aiion or molecular dynamics calculations. However, th is produces undesirable edge effects at the solvent-vacuum interface. 

Tor all restraints, HyperChem uses named selections that contain two, three, or four atoms each. You use Name Selection on the Selectmenn to assign nam es to groups of selected atom s. Th en you can apply named selections as restraints for a calculation in the Restraint Forces dialog box from Restraints on the Setup menu. 

Choose LHH(spin Unrestricted Hartree-Fock) or RHF (spin Restricted Ilartree-Fock) calculations according to your molecular system. HyperChem supports UHF for both open-sh el I and closed-shell calcii lation s an d RHF for cUised-shell calculation s on ly, Th e closed-shell LHFcalculation may be useful for studyin g dissociation of m olectilar system s. ROHF(spin Restricted Open-shell Hartree-Fock) is not supported in the current version of HyperChem (for ah initio calculations). 

HyperChem always com putes the electron ic properties for the molecule as the last step of a geometry optimization or molecular dyn am ics calcu lation. However, if you would like to perform a configuration interaction calculation at the optimized geometry, an additional sin gle poin t calcu lation is requ ired with theCI option being turned on. 

The back end is the conipoiicii 1 oT IlypcrChcm LhaL performs the more Lime-ccm siiming sclen Lific calculation s. This is where molecular mechanical and quail Lit m mechanical calculations are performed. The back end can be thought of as the compii laLion al chemistry component of HyperChem. ... 

The HyperChem philosophy associated with back end computations is one which is in tended to in still eon fiden ce. as far as is possible. in the scientific results emanating from HyperChem. This ph ilosoph y is on e of open n ess — open n ess aboii t the prod net. the calculations being performed, the science embodied in the product, etc. Apart from protecting the proprietary code associated with a commercial product. Hypercube wushes to document and describe as fully as is possible tb e calculation s th at HypcrCb cm performs. There should be no mystery about the scientific results obtained with HyperChem. 

HyperChem should not he viewed as a black box that computes on ly wb at its design ers th ougb L correct, tthasan open architecture that makes it possible to customize it many ways. As far as is possible, the parameters of molecular mechanics and semi-empir-ieal calculations are in the user s baruis. As the tech n ic ues of software engineering advance and onr expertise in building new... 

I lle HIO+force field option in HyperChem hasno hydrogen bond-in g term, Th is is con sisten I with evolution andcommon useofthe CH.ARMM force field (even the 1983 paper did n ot usc a liydrogen boruiin g term in its exam pic calculation s an d men lion ed that the functional form used then was u n satisfactory and under review). 

HyperChem supports MP2 (second order Mdllcr-l Icsset) correlation energy calcu latiou s u sin g any available basis set. lu order to save main memory and disk space, the HyperChem MP2 electron correlation calculation normally uses a so called frozen-core approximation, i.e. th e in n er sh el I (core) orbitals are omitted. A sett in g in CHHM.IX I allows excitation s from th e core orbitals to be include if necessary (melted core). Only the single poin t calcula-tion is available for this option. 

The dipole moment for a calculation is reported and is contained in the log file if logging is turn ed on. It is also reported on the status line if you Display DipoleMoment on iheDisplay menu. Other expectation values besides the dipole moment (for example, qna-dnipole moment ) could he reported with a wave function but the set reported with this release of HyperChem is limited to on ly a few. Below we discuss the properties or oth er ch aracteri/ation s of the calculated wave function that can he interactively visnali/ed. 

HyperChem performs an empirical Hiickel calculation to produce th e MO coefficien ts for a minimal basis set and th en projects th ese coefficien ts to the real basis set used in an cife calculation. Th e projected Htickel guess can be applied to rn olecular system s with an atom ic n um ber less th an or equal to 54 (Xe). 

Some of these software packages also have semiempirical or molecular mechanics functionality. However, the primary strength of each is ah initio calculation. There are also ah initio programs bundled with the Unichem, Spartan, and Hyperchem products discussed previously in this appendix. 

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