Molecular modeling of solvation. Cl−(D2O)

Structural and electronic properties of guanine and guanosine

We present putative global minimum energy structures for nanoscopic transition metal clusters, with sizes ranging from N = 3 to 100 atoms, described by the original embedded atom potential of Finnis and Sinclair (FS), using their parameter sets for molybdenum and iron, and compare selected results with predictions from semi-empirical molecular orbital (SE-MO) theory via further optimization using the AM1* and PM6 Hamiltonians. We find that, for Fe clusters, the global minima found for the FS potential consist mainly of polyicosahedral structures with magic numbers N = 13, 19, 23, 26, 29, 39, 60 and 78, whereas, for Mo clusters with sizes N > 30, they are more likely to be bcc terminated by {110} and {100}-type surface facets. We find that the global minimum energy structures obtained for the FS potential are, in general, very good starting points for further SE-MO optimization, although the relative ordering of the resulting structures by energy compared to those obtained from global minima of other potentials used to model metal clusters does not, in general, agree.

The vapor pressure isotope effect of /sup 13/C//sup 12/C-substitution in CClF/sub 3/ was measured at temperatures between 169/sup 0/ and 206/sup 0/K by means of cryogenic distillation. The /sup 13/C//sup 12/C-vapor pressure isotope effect in CHF/sub 3/ was also studied at temperatures between 161/sup 0/ and 205/sup 0/K by a similar method. The construction of a cryostat has progressed as scheduled. The investigation of carbon isotope exchange equilibria between carbon dioxide and various carbamates dissolved in various organic solvents has continued. The five-stage system of Taylor-Ghate design was improved to shorten the transient time. A single stage apparatus was designed, built, and tested. These systems are used to measure the equilibrium constants and various phase equilibria involved in the carbon dioxide--carbamate system. The investigation of the explicit method of total isotope effect has made progress. A satisfactory approximation was found for the classical partition function of a Morse oscillator. The method gives a reasonable result at rho identical with /sup 1///sub 2/..sqrt..(u/sub e//x/sub e/) greater than 1.5. The medium cluster approach was applied to isotopic methanes to investigate the effects of intermolecular distance and mutual orientations of molecules in the liquid upon vapor pressure isotope effect. It was found that all geometrical effects studied tend to vanish as the size of clusters is increased. Isotope effect in the zero-point energy shifts on condensation was calculated on the basis of London dispersion forces in liquid and a semi-empirical molecular orbital theory, and was favorably compared with experimental results. (auth)

We have developed a unified quantum molecular dynamics method, in which the centroid molecular dynamics including the quantum effect of atomic nuclei is unified with the semiempirical molecular orbital calculation for the atomic configuration generated in the molecular dynamics. This unified method has successfully been applied to a couple of diatomic molecular systems for examining its performance. The method has yielded excellent agreement with exact quantum results and taken sufficiently short CPU time for practical use. © 2003 Wiley Periodicals, Inc. Int J Quantum Chem, 2003

We have attempted to calculate heats of formation (δHf° for aliphatic nitro compounds with the semi-empirical molecular orbital theory, PM3 and the molecular mechanics, MM2'. Both methods can estimate δHf° accurately, though in case of polynitro compounds, differences between observed and calculated values become slightly larger. By combining heats of vaporization and sublimation obtained by the additivity rule with δHf° in gas phase obtained by PM3 and MM2', δHf° in condensed phase can be estimated with accuracy enough to use δHf° for energy hazards prediction.

The difference which is present between the semi- and the nonempirical value of a Slater-Condon parameter (SCP) is discussed. It is pointed out that the nonempirical value which is to be compared with its semiempirical counterpart, must be determined with the same least-squares method as that used in the determination of the semiempirical values, by treating the Hartree-Fock (HF) total energy of each state of a configuration as the term value of the respective state, although it is usually determined for each of the states by a direct integration using the HF AO's appropriate to respective states. The data for the atoms and the ions having the electron configurations of 1s22sm2pn type show that the nonempirical value of an SCP thus determined for a particular configuration is more or less the same as that is obtained as the weighted mean of the values of the parameter determined for various states belonging to the configuration by integrations using HF AO's. The difference between the nonempirical value of an SCP thus obtained from the HF total energies and its semiempirical value obtained from the observed term values is analyzed with reference to the correlation energy of the atom in its various states of the configuration. Through this analysis, the semiempirical evaluation of the valence-state energy of an atom is critically considered and prescriptions for obtaining the most appropriate values of the one-center two-electron repulsion integrals in the semiempirical molecular orbital theory are given.

An additional charge carrier described as its wave function is propagated in imaginary time using stepwise matrix multiplication and a correction to ensure that the simulation is norm-conserving. The propagation Hamilton operator uses the local ionization energy of a rubrene single crystal, calculated with semiempirical molecular orbital theory, as an external potential for holes to model the interaction with the underlying molecular structure. Virtual electrodes are modeled by setting the potentials in the appropriate areas to constant values with the difference corresponding to the source-drain voltage. Although imaginary time cannot be interpreted directly as time, the simulated gate-dependent imaginary transfer rate is in acceptable qualitative agreement with the experimentally measured gate-dependent hole-transfer rate through a rubrene single crystal.

Theoretical studies of the Stevens' rearrangement of alkylammonium ylides

We present an application of the reaction class transition state theory (RC-TST) in predicting thermal rate constants of the hydrogen abstraction reactions H + H−C(sp3) where C(sp3) is a saturated carbon atom. Combining the RC-TST with the linear energy relationship (LER) allows rate constants of any reaction in the class to be estimated from only reaction energy information. We have derived from first-principles all parameters for the RC-TST/LER method so rate constants for any reaction in this class can be predicted from only reaction energy, that can easily be computed from either the density functional theory or semiempirical molecular orbital theory. We have performed error analyses for a large number of reactions in the above class for which some experimental measurements or estimates are available. By comparisons with results from full TST/Eckart calculations we also found the RC-TST/LER method is quite cost-effective and has accuracy comparable to first-principles predictions using more rigorous methodologies.

[sup 31]P and [sup 27]Al NMR spectroscopies have been used to characterize acidic, aqueous solutions of orthophosphoric acid, aluminum chloride, and tetramethylammonium (TMA) hydroxide. The final compositions of the solutions range from 0.1 to 1 mol % P, 0.0 to 20 mol % HCl, P/Al = 0.1 to 20, and P/(TMA)[sub 2]O = 2 to 20. Soluble aluminophosphate cations form reactions of hexaaqua Al monomeric cations, [Al(H[sub 2]O)[sub 6]][sup 3+], with phosphate ligands (i.e., H[sub 3]PO[sub 4], H[sub 2]PO[sub 4][sup [minus]], and acid dimers H[sub 6]P[sub 2]O[sub 8] and H[sub 5]P[sub 2]O[sub 7][sup [minus]]). [sup 31]P NMR spectra of aluminophosphate solutions reveal five distinct chemical shift regions. A correlation between the partial charge on P nuclei (calculated using semiempirical molecular orbital theory, MNDO [modified neglect of differential overlap]) and the [sup 31]P NMR chemical shift confirms the assignments of the [sup 31]P NMR resonances. Regardless of the total charge of the complex or the connectivity of the Al to -O-P units, the MNDO calculations show that P atoms in the same type of phosphate ligand bonded to Al monomers have similar partial charges, and, therefore, exhibit nearly identical [sup 31]P chemical shifts. [sup 27]Al NMR spectra of aluminophosphate solutions displaymore » four resonances. The assignment of the [sup 27]Al NMR resonances is based on the manner in which the [sup 27]Al and [sup 31]P NMR peaks change in intensity with pH, P, and Al concentration. Estimates of the number of Al-O-P bonds are calculated independently from [sup 31]P and [sup 27]Al NMR spectra and agree quite closely for a range of pH's and both Al and P concentrations. 44 refs., 17 figs., 3 tabs.« less

A new tetracationic molecular receptor has been synthesized and studied by semiempirical molecular orbital theory. This novel macrocycle, 1(4+), derived from pentacyclo[5.0.0.0.(2,6)0.(3,10)0(5,9)]undecane-8,11-dione (PCU-8,11-dione), structurally resembles cyclobis(paraquat-p-phenylene), 2(4+), in which a xylyl group has been replaced by a PCU unit. This derivatization effectively increases the size and flexibility of 1(4+) and changes its electronic, dynamical, and binding properties. A conformational search using Osawa's corner flapping technique and the PM3 semiempirical method identifies eight unique and low-energy 1(4+) conformers. The principal regions of structural variation occur in the bipyridinium torsion and in the ethylene bridges between PCU and the tetracationic unit. The inclusion complexes of 1(4+) with 1,4-disubstituted benzenes and 4,4'-disubstituted biphenyls have been studied by PM3. The first shell of solvation is approximated by the explicit inclusion of 12 acetonitriles in the computed supramolecular complexes. Binding of 1,4-disubstituted benzenes and 4,4'-biphenol is shifted from the 1(4+) geometric center. From the computations, host 1(4+) is predicted to have an enhanced binding preference for benzidine over 4,4'-biphenol, as compared to 2(4+). For all guests computed, 1(4+) binds more strongly than 2(4+). These properties can be exploited in the future design of supramolecular systems with potential applications as nanoscale devices.

The interaction of ethylene with the Si(100) 2*1 surface has been studied by a semi-empirical molecular orbital theory using a four-layer silicon cluster model Si29H24-C2H4. Ethylene is shown to create a di- sigma bond with the surface dimer sites, and to rehybridize to a near sp3 state. Its initial C-C double bond is reduced to nearly a single bond, while its C-H bonds are almost not weakened. Both the ethylene pi donation to the surface and the substrate back-donation to the ethylene pi * orbital result in the equilibrium di- sigma bonding geometry. The C2H4 decomposition behaviour is somewhat different from that for C2H2(ads) on Si(100), and C2H4(ads) on transition metals. Ethylene favours C-C bond scission first, and then dehydrogenation. The calculated vibrational properties of the C2H4(ads) and C2H4-induced species confirm the results of a recent HREELS study.

Mean-square amplitudes of vibration and shrinkage effects from mindo/2 calculations

Theoretical investigations of the equol molecule: semi-empirical and density functional theory calculations

Semiempirical molecular orbital (PM3, PM6, and RM1) and density functional theory (DFT) (B3LYP/6‐31G*) studies are carried out for 1‐ and 2‐styrylnaphthalenes and their aza‐derivatives—2‐ and 4‐styrylquinolines. Relative stabilities of three isomeric forms: E‐ and Z‐isomers and the closed‐ring dihydrocyclophotoproduct (derivative of dihydrophenanthrene) are calculated. Compared to PM3, PM6 and especially RM1 understate heats of formation; in some cases, PM6 and RM1 even place Z‐isomer in energy below E‐isomer. PM3 rather close to DFT predicts heats of isomerization reaction, whereas PM6 and especially RM1 underestimate these values. Semiempirical methods in comparison with DFT markedly underestimate heats of cyclization reaction; however, reproduce trends in relative stabilities of different isomers in dependence on the structure of styrylnaphthalenes and styrylquinolines. Qualitative correlation is found between calculated relative stabilities of the closed‐ring forms (heats of cyclization reaction) and experimental data: cyclized products with low heats of cyclization are observed in steady‐state photolysis and those with high heats of cyclization are not. In the latter case, the closed‐ring compounds, if formed in the excited state, due to thermal instability decompose rapidly with ring opening in the ground state that prevents their observation. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011