The application of the genetic algorithm to the minimization of potential energy functions

We adapted the genetic algorithm to minimize the AMBER potential energy function. We describe specific recombination and mutation operators for this task. Next we use our algorithm to locate low energy conformation of three polypeptides (AGAGAGAGA, A9, and [Met]-enkephalin) which are probably the global minimum conformations. Our potential energy minima are –94.71, –98.50, and –48.94 kcal/mol respectively. Next, we applied our algorithm to the 46 amino acid protein crambin and located a non-native conformation which had an AMBER potential energy 150 kcal/mol lower than the native conformation. This is not necessarily the global minimum conformation, but it does illustrate problems with the AMBER potential energy function. We believe this occurred because the AMBER potential energy function does not account for hydration.     

Substituent effects in the fragmentation reactions of acetanilides and phenyl acetates

The mass spectra of a group of m- and p-substituted acetanilides were measured to determine the effect of the substituents, if any, on the rate of C₂H₂O expulsion (rearrangement) vs. the rate of [CH₃CO]⁺ formation (simple cleavage). Our results agree with observations of others in that substituents which raise the ionization potential of the aromatic ring appear to localize, on the average, less charge density on this locus, and conversely. The atomic composition of the substituent, however, irrespective of its position, seems to determine the relative rates of the competing reaction. Although in several cases Z_m/Z_p values were close to unity, rearrangement of isomeric molecular ions to a common species is shown not to occur.     

Encapsulation of cationic ruthenium complexes into a chiral self-assembled cage

A chiral supramolecular assembly encapsulates the two cationic ruthenium sandwich complexes [CpRu(eta(6)-C(6)H(6))](+) and [CpRu(p-cymene)](+). The host-guest complexes K(11)[CpRu(eta(6)-C(6)H(6)) subset Ga(4)L(6)] (2) and K(11)[CpRu(p-cymene) subset Ga(4)L(6)] (3) were characterized by one- and two-dimensional NMR techniques as well as by electrospray mass spectrometry. Encapsulation of the prochiral complex [CpRu(p-cymene)](+) by the chiral host renders enantiotopic protons diastereotopic as evidenced by (1)H NMR spectroscopy.     

Solid-state supramolecular organization, established directly from powder diffraction data, and photoluminescence efficiency of rigid-core oligothiophene-S,S-dioxides

The "rigid-core" material 3,5-dimethyl-2,3'-bis(3-methylthiophene)-dithieno[3,2-b:',3'-d]thiophene-4,4-dioxide (DTTOMe4) has the highest photoluminescence ever reported for thiophene-based molecules in the solid state. We report the structure of this material, determined directly from powder X-ray diffraction data using the Genetic Algorithm method for structure solution, followed by Rietveld refinement, and the structural properties are discussed in relation to the structures of the corresponding subsystems DTTO and DTTOMe. While the crystal structures of the latter compounds contain cofacial dimers, the crystal structure of DTTOMe4 comprises layers of molecules aligned in an antiparallel fashion. Intermediate neglect of differential overlap with single configuration interaction (INDO/SCI) calculations on the intermolecular interactions in the three crystal structures show that the different solid-state photoluminescence efficiencies of DTTOMe4, DTTOMe, and DTTO cannot be correlated with the different types of dipole-dipole alignment in the solid state. Instead, photoluminescence efficiencies correlate well with the rate of formation of nonradiatively decaying charge-transfer pairs upon photoexcitation. Because of larger intermolecular distances in DTTOMe4, the photoluminescence is less effectively quenched by charge-transfer processes than in DTTOMe and DTTO.     

Thermal rearrangements of spiro[2.4]hepta-1,4,6-trienes

Thermolysis of spiro[2.4]hepta-1,4,6-triene (1a) at 50 degrees C yielded bicyclo[3.2.0]hepta-1,3,6-triene (5), which dimerized in two different fashions to form cyclobutanes. The 1,2-dimethyl and 1-propyl derivatives of 1a also rearranged at 50 degrees C, but at a faster rate, each yielding a pair of cyclobutane dimers. The structures of these symmetrical dimers were investigated by 1D and 2D NMR and NOE difference spectroscopy. Ab initio calculations indicated that the two strained olefins 1a and 5 had comparable energies about 50 kcal/mol lower than norborna-1(7),2,5-triene, which was thus excluded as a reaction intermediate.     

LAMMA mass spectra of β-diketone,bis(benzoylacetone)ethylenediimine and bis(salicylidene)ethylenediimine complexes of some transition metals

Complexes of 2,4-pentanedione (acetylacetone, acac), [Cu(acac)₂], [VO(acac)₂] and [CO(acac)₃], and the chromium(III) derivative of 3-methyl-2,4-pentanedione (methylacetylacetone, meac), [Cr(meac)₃], the ligands bis(benzoylacetone)ethylenediimine and bis(salicylidene)ethylenediimine, and their cobalt(II), nickel(II) and copper(II) chelates were analysed by laser desorption mass spectrometry (LAMMA) and compared to electron impact (EI) results. The positive ion LAMMA spectra generally reveal mostly small fragments, although metal cationization peaks are seen for most complexes. Negative ion LAMMA produce carbon clusters and some structurally important fragments.     

Pose scoring by NMR

Recently, we have developed a fast approach to calculate NMR chemical shifts using the divide and conquer method at the semiempirical level. To demonstrate the utility of this approach for characterizing protein-ligand interactions, we used the deviation of calculated chemical shift perturbations from experiment to determine the orientation of a ligand (GPI-1046) in the binding pocket of the FK506 binding protein (FKBP12). Moreover, we were able to select the native state of the ligand from a collection of decoy poses. A key hydrogen bond between O1 and HN in Ile56 was also identified. Our results suggest that ligand-induced chemical shift perturbations can be used to refine protein/ligand structures.     

A systematic sequence of relativistic approximations

An approach to the development of a systematic sequence of relativistic approximations is reviewed. The approach depends on the atomically localized nature of relativistic effects, and is based on the normalized elimination of the small component in the matrix modified Dirac equation. Errors in the approximations are assessed relative to four-component Dirac-Hartree-Fock calculations or other reference points. Projection onto the positive energy states of the isolated atoms provides an approximation in which the energy-dependent parts of the matrices can be evaluated in separate atomic calculations and implemented in terms of two sets of contraction coefficients. The errors in this approximation are extremely small, of the order of 0.001 pm in bond lengths and tens of microhartrees in absolute energies. From this approximation it is possible to partition the atoms into relativistic and nonrelativistic groups and to treat the latter with the standard operators of nonrelativistic quantum mechanics. This partitioning is shared with the relativistic effective core potential approximation. For atoms in the second period, errors in the approximation are of the order of a few hundredths of a picometer in bond lengths and less than 1 kJ mol(-1) in dissociation energies; for atoms in the third period, errors are a few tenths of a picometer and a few kilojoule/mole, respectively. A third approximation for scalar relativistic effects replaces the relativistic two-electron integrals with the nonrelativistic integrals evaluated with the atomic Foldy-Wouthuysen coefficients as contraction coefficients. It is similar to the Douglas-Kroll-Hess approximation, and is accurate to about 0.1 pm and a few tenths of a kilojoule/mole. The integrals in all the approximations are no more complicated than the integrals in the full relativistic methods, and their derivatives are correspondingly easy to formulate and evaluate.     

Triplet-triplet energy transfer in the tryptophyl-tyrosinate dipeptide

Direct evidence for intermolecular triplet-triplet energy transfer in the dipeptide tryptophyl-tyrosine is presented. The methods of steady state ODMR and transient ODMR yield rates for the triplet-triplet energy transfer process of order 10 s^?1.