Molecular potential semiempirical calculation

Tel. 800-424-9737, fax 415-491-8311 (U.S.A.), tel. 41-38-337633 (U.K.) Model building, display, charge density, electrostatic potential, and molecular orbital plots. Stick, sphere, and dot surface display. 2D to 3D conversion. Protein and DNA fragment libraries. MM+, BIO+ (implementations of MM2 and CHARMM, respectively), OPLS, and AMBER molecular mechanics and dynamics. Solvent box. Semiempirical calculations by Extended Hiickel, CNDO, INDO, MINDO/3, MNDO, AMI, and PM3. Originated at Hypercube, Inc. (Dr. N. Ostlund et al.), of Ontario, Canada. Runs under Windows on a 386 or 486 PC and under Motif on a Silicon Graphics workstation. 

G. P. Ford and B. Wang, J. Comput. Chem., 14, 1101 (1993). New Approach to the Rapid Semiempirical Calculation of Molecular Electrostatic Potential Based on the AMI Wave Function Comparison with Ab Initio HF/6-31G Results. 

Any spatial dependence of the coupling between two molecular potentials derives from the spatial dependence of the transition matrix element. Quantum chemical calculations of the transition dipole moment tend to be rather difficult and require considerable effort in order to be reliable. Different approaches to calculate the transition dipole moments lead to contradictory results [Hessel 1974 Akopyan 1999 Magnier 2000], and no general trend seems to emerge. We found only few attempts to determine the generic behavior that governs such effect from semiempirical considerations [Woerdman 1981 Akopyan 1999 Johnston 2003]. 

By H-NMR spectroscopy and dipole measurements, the 3,7-dimethyl-3,7-diazabicyclo[3.3.1]nonane (dimethylbispidine) 88 was shown to adopt a cc conformation with flattened wings (108). This was later confirmed by C-NMR spectroscopy and semiempirical molecular orbital (MO) calculations (EH, CNDO/2 the double-chair form was found to be more stable than the cb isomer by --83.8kJmoP and the bb form is even more destablized (133). This preference for cc is not due to solvent or packing effects since 88 has the same conformational preference in the gas phase, as shown by a computational study, which involved a scan of the potential energy surface (PES) and the calculated... 

Once the functional form of the potential energy function has been written down, the next step in molecular mechanics is to assign values to the parameters. Some parameters, e.g., Kj, Tq, K , Oq, V, and can be obtained from a variety of experimental methods, such as X-ray, IR, NMR, and micro-wave techniques. Some of the nonbonded parameters, such as and molecular beam experiments on small molecules. To obtain the rest of the parameters, theoretical methods must be used. For example, charges can be calculated using ab initio and semiempirical calculations. In recent years, attempts have been made to produce all of the parameters by fitting the potential function to ab initio and semiempirical calculations. ... 

Lattice dynamics studies of the disordered j -phase are more scarce because, obviously, the standard harmonic method and the SCP method cannot be applied to this phase (although in some studies the harmonic method has still been used for the translational phonons, while neglecting the anisotropy of the potential.) Most calculations on have been made by classical Monte Carlo or Molecular Dynamics methods, using semiempirical atom-atom or quadrupole-quadrupole potentials. In our group [50, 52] we have investigated the motions in and the a — jS order/ disorder phase transition by means of the MF, RPA and TDH methods, using the same spherically expanded anisotropic ab initio potential which yields accurate properties for a-N2. 

Molecular dynamics methods based on quantum chemical calculations to compute the energy of a cluster as a function of the nuclei positions avoid the difficult task of building an intermolecular potential. Tight-binding molecular dynamics, semiempirical and Hartree-Fock ab initio Born-Oppenheimer dynamics, Car-Parrinello DFT molecular dynamics, and ADMP molecular dynamics are becoming more and more popular. The more sophisticated techniques are still Hmited to the study of clusters over short simulation times (ps time scale). The tight-binding approach SCC-DFTB is cheap and appears to be quite accurate. 

The hydroxyl acidities of sucrose, assessed through semiempirical calculations of the deprotonation enthalpies, followed the order OH-2g OH-3g > OH-3f > OH-lf = OH-4g > OH-4f OH-6g > OH-6f. The molecular electrostatic potential profile of sucrose in polar, aprotic solvents indicated likewise that in the main conformation OH-2g is the most electropositive hydroxyl group the preparations of selectively benzylated and acetylated sucrose derivatives on the basis of these findings are referred to in Chapters 5 and 7, respectively. ... 

Combined Quantum Mechanical and Molecular Mechanical Potentials Combined Quantum Mechanics and Molecular Mechanics Approaches to Chemical and Biochemical Reactivity Configuration Interaction Configuration Interaction Semiempirical Calculations Density Functional Theory (DFT), Hartree-Fock (HF), and the Self-consistent Field Force Fields A General Discussion Hybrid Methods MNDO Quantum Mechanical/Molecular Mechanical (QM/MM) Coupled Potentials Quantum Mecha-nics/Molecular Mechanics (QM/MM). 

For symmetric carbocyanines the experimental and theoretical data of the ground-state potential energy surface are in agreement. In laser-induced optoacoustic spectroscopy studies, Braslavsky and her group found that the molecular volume change due to photoisomerization of T2 in ethanol-water is 52 ml mok and that of 02 (iodide) is zero. A combination with semiempirical calculations indicates mainly rearrangement of solvent molecules. ... 

The use of RECP s is often the method of choice for computations on heavy atoms. There are several reasons for this The core potential replaces a large number of electrons, thus making the calculation run faster. It is the least computation-intensive way to include relativistic effects in ah initio calculations. Furthermore, there are few semiempirical or molecular mechanics methods that are reliable for heavy atoms. Core potentials were discussed further in Chapter 10. 

PLS (partial least-squares) algorithm used for 3D QSAR calculations PM3 (parameterization method three) a semiempirical method PMF (potential of mean force) a solvation method for molecular dynamics calculations... 

A common application of the direct calculation of molecular energy is the study of organic reaction mechanisms. You can investigate the energies of different potential intermediates, species not easily studied by experiment. A review by Thiel lists many such 39. Thiel, W. Semiempirical Methods Current Status and Perspectives Tetrahedron, 44 7393, 1988. 

The molecular and liquid properties of water have been subjects of intensive research in the field of molecular science. Most theoretical approaches, including molecular simulation and integral equation methods, have relied on the effective potential, which was determined empirically or semiempirically with the aid of ab initio MO calculations for isolated molecules. The potential parameters so determined from the ab initio MO in vacuum should have been readjusted so as to reproduce experimental observables in solutions. An obvious problem in such a way of determining molecular parameters is that it requires the reevaluation of the parameters whenever the thermodynamic conditions such as temperature and pressure are changed, because the effective potentials are state properties. 

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