HyperChem

The HyperChem programs of Hypercube, Inc webpage http //www.hvper.com... 

Using semi-einpirical methods, which are also based on approximate solutions of the Schrodingcr equation but use parameterized equations, the computation times can be reduced by twu orders of magnitude. HyperChem from Hypercubc,... 

Figure 10.2-2. Calculatiorr of H NMR chemical shifts and coupling constants arrd simulation of the spectrum with HyperChem 7.

It gives an overview of th e com pu tation al ch ern istry m ethods that you ll find in HyperChem. I he overview acquaints yon with the program and the powerof methods. 

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... 

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. 

HyperChem contains a database of amino and nucleic acid residues so you can quickly build polymers con laining these subunits. You can also read in structures in files from standard databases, such as the Brookhaven Protein Data Bank (see the HyperChem Reference Manual). 

Yon can use HyperChem to investigate the reactivity ofmoleciiles and their fiinciional groups. One method is to use Frontier Molec-... 

Th is discussion focuses on th e individual compon en ts of a typical molecular mechanics force field. It illustrates the mathematical functions used, wdi y those functions are chosen, and the circiim -Stan ces u n der wh ich the fun ction s become poor approxirn atiori s. Part 2 of th is book, Theory and Melhadx, includes details on the implementation of the MM+,. AM BHR, RlO-g and OPl.S force fields in HyperChem. 

HyperChem UNCN ti irmoniL fuiiclioriN U) calcuhUi potentials foi hmuls and bond angles (equation 9). 

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. 

Once HyperChem calciilates potential energy, it can obtain all of th c forces on the n uclei at negligible addition a I expen se, I h is allows for rapid optimi/ation of equilibrium and tran sitiori-state geometries and th e possibility of com put in g force con stan ts, vibra-tiorial modes, and molecular dynamics trajectories. 

HyperChem tjuantum tn ech an ics calcu lation s tn ust start with the number of electrons (N) and how many of them have alpha spins (th e remain in g electron s have beta spin s ). HyperCh em obtain s th is in form ation from the charge an d spin m u Itiplicity th at you specify in th e Sem i-em pirical Op lion s dialog box or. Ab Initio Option s dialog box. is th en computed by coun ting the electron s (valence electrons in sem i-em pirical methods and all electrons in a/ irti/io m ethod) associated with each (assumed neutral) atom and... 

Some systems converge poorly, particularly those with multiple bonds or weak interactions between open-shell systems. HyperChem includes two convergence accelerators. One is the default con verge rice accelerator, effective in speed in g up ri orm ally... 

HyperChem provides two versions of the conjugate gradient method, Fletcher-Reeves and Bolak-Rihiere. Polak-Ribiere is more refined and is the default eh oiee in HyperChem,... 

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. 

I he eigenvector-following (or Hessian mode) method implemented in HyperChem is based on an effieien t quasi-Newton like algorithm for loca tin g tran sitiori states, wh ieh can locate tran si-tion states for alternative rearran gern eri t/dissoeiation reactions, even when startin g from th e wron g regio n on th e poten tial en ergy surface. 

HyperChem employs the leap frog algorith m to integrate the et uaLioMs of motion. Th is algoritlim updates the positions of atom s and the velocities for the n e.x 1 time step by tli is ca leu la lion (equation 26). 

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. 

Often yon need to add solvent molecules to a solute before running a molecular dynamics simiilatmn (see also Solvation and Periodic Boundary Conditions" on page 62). In HyperChem, choose Periodic Box on the Setup m en ii to enclose a soln te in a periodic box filled appropriately with TIP3P models of water inole-cii les. 

I o sorn c ex ten t you can rn on itor eon stan t tern peratii re sim ula-tion s by th e tern perature (I KMP) an cl its deviation (D TKM P) or by kinetic en ergy (KKIN) an d its deviation (D HKIN). Plot th ese values using the HyperChem Molecular Averages dialog box. 

HyperChem supplements the standard MM2 force field (see References on page 106) by providing additional parameters (force eon slants) using two alternative schemes (see the second part of th is book. Theory and Melhod.s). I h is exten ds th e ran ge of chem ical compounds that MM-t-can accommodate. MM-t-also providescut-offs for calcu latin g nonbonded in teraction s an d periodic bou n d-arv condition s. 

Note MM-i- is derived from the public domain code developed by Dr. Norm an Allinger, referred to as M.M2( 1977), and distributed by the Quantum Chemistry Program Exchange (QCPE). The code for MM-t is not derived from Dr. Allin ger s present version of code, which IS trademarked MM2 . Specifically. QCMPOlO was used as a starting point Ibr HyperChem MM-t code. The code was extensively modified and extended over several years to include molecular dynamics, switching functuins for cubic stretch terms, periodic boundary conditions, superimposed restraints, a default (additional) parameter scheme, and so on. 

Many con ven tio n al and com m on I y-used ah initiohiisis setsare supported in HyperChem. fhese basis sets include ... 

You can use multiple basis sets in a single inoleeular system. I ti e Apply Basis E3et m HyperChem applies the currently selected basis set to the selected atom s or to all the atom s in IlypcrChem if th ere is no current selection. For example, some heavy atoms might have a b-1 IG basis set (s and p only) while other heavy atoms m igh t use a 6-151 CE basis set (with d-orbitals). Th is is an iiii usual but flexible option for ah miiro calculalioiis. 

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). 

I h c Hiickel eon stari t (k) scales Ih e in teraetiou energy between two atomic orbitals (see Kxtended Hiickel Method on page 125). HyperChem uses the defatill value of 1.75 (see the second part of th is book. Theory and Methods). You shoti Id tise th is value for m ost eases, A suggested ran ge for experimcri tal adjiistmen L of th is eon -stant is 1,6 2,0.- ... 

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. 

HyperChem residue templates. HyperChem uses these templates wh en it reads a Protein Data Ban k file or when you con struct a molecule from residues. 

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