Constituent Fragments Research Articles

Electronic Structure and Chemical Reactivity: Density Functional and Information‐Theoretic Perspectives

AbstractFor Abstract see ChemInform Abstract in Full Text.

Theoretical study of indole: protonation, indolyl radical, tautomers of indole, and its interaction with water

Abstract The electronic and structural properties of indole and indole–(H 2 O) n =1, 2 are studied using the density functional formalism. Specific attention is paid to the relation between indole and its constituent fragments for properties such as proton affinity, hydrogenation, and tautomerization. The hydrogenation study is extended to include the hydroxy-indole isomers. The IR spectra and the stabilities of the indole–(H 2 O) 1 complexes are determined. Indole–(H 2 O) 2 geometries are calculated and classified into five groups, based on both geometry and IR considerations.

Simulation of the molecular recombination yield for swiftH2+ions through thin carbon foils

We have calculated the recombination yield for swift H 2 + molecular ions at the exit of thin amorphous carbon foils, as a function of the dwell time and incident energy. Our results are based on a detailed simulation of the motion through the target of the H 2 + molecular ion (before dissociation takes place) and its constituent fragments (after dissociation), including the following effects: Coulomb repulsion, nuclear scattering, electron capture and loss, as well as self-retarding and wake forces, which provide the relative distance and velocity of the dissociated fragments at the foil exit. The recombination of an H 2 + ion at the exit of the foil depends on the interproton separation and internal energy of the dissociated fragments, and on their probability to capture an electron. Comparison of our results with the available experimental data shows a good agreement.

Electrostatic interactions in the reconstitution of an SH2 domain from constituent peptide fragments.

Fragment complementation has been used to delineate the essential recognition elements for stable folding in Src homology 2 (SH2) domains by using NMR spectroscopy, alanine scanning, and surface plasmon resonance. The unfolded 9-kD and 5-kD peptide fragments formed by limited proteolytic digestion of the N-terminal SH2 domain from the p85alpha subunit of phosphatidylinositol 3'-kinase fold into an active native-like structure on interaction with one another. The corresponding 5-kD fragment of the homologous Src protein, however, was not capable of structurally complementing the p85 9-kD fragment, indicating that fragment complementation among these SH2 domains is sensitive to the sequence differences between the Src and p85 domains. Partial complementation and folding activity could be recovered with hybrid sequences of these SH2 domains. Complete alanine scanning of the 5-kD p85 fragment was used to identify the sequence recognition elements required for complex formation. The alanine substitutions in the p85 5-kD fragment that abolished binding affinity with the cognate 9-kD fragment correlate well with highly conserved residues among SH2 domains that are either integrally involved in core packing or found at the interface between fragments. Surprisingly, however, mutation of a nonconserved surface-exposed aspartic acid to alanine was found to have a significant effect on complementation. A single additional mutation of arginine to aspartic acid allowed for recovery of native structure and increased the thermal stability of the designed Src-p85 chimera by 18 degrees C. This modification appears to relieve an unfavorable surface electrostatic interaction, demonstrating the importance of surface charge interactions in protein stability.

True polar wander and supercontinents

I present a general model for true polar wander (TPW), in the context of supercontinents and simple modes of mantle convection. Old, mantle-stationary supercontinents shield their underlying mesosphere from the cooling effects of subduction, and an axis of mantle upwelling is established that is complementary to the downwelling girdle of subduction zones encircling the old supercontinent. The upwelling axis is driven to the equator by TPW, and the old supercontinent fragments at the equator. The prolate axis of upwelling persists as the continental fragments disperse; it is rotationally unstable and can lead to TPW of a different flavor, involving extremely rapid (≤m/year) rotations or changes in paleolatitude for the continental fragments as they reassemble into a new supercontinent. Only after several hundred million years, when the new supercontinent has aged sufficiently, will the downwelling zone over which it amalgamated be transformed into a new upwelling zone, through the mesospheric shielding process described above. The cycle is then repeated. The model explains broad features of the paleomagnetic database for the interval 1200–200 Ma. Rodinia assembled around Laurentia as that continent experienced occasionally rapid, oscillatory shifts in paleolatitude about a persistent axis on the paleo-equator, an axis that may have been inherited from the predecessor supercontinent Nuna. By 800 Ma, long-lived Rodinia stabilized its equatorial position and disaggregated immediately thereafter. Gondwanaland assembled as its constituent fragments documented rapid, oscillatory shifts of apparent polar wander, here interpreted as TPW. The Gondwanaland–Pangea centroid migrated to the equator immediately prior to Jurassic–Cretaceous breakup. Lack of substantial TPW since 200 Ma may indicate the stabilizing effects of specific plate boundary conditions (i.e., persistent convection patterns in the Tethys–Indian Ocean region), possibly superimposed on a secular geodynamic shift governed by increased lower-mantle viscosity associated with long-term planetary cooling. TPW is a significant geodynamic process that, in terms of continental motions, may even dominate plate tectonics for certain intervals of Earth history. The effects of such rapid TPW may be found among regional tectonics and sea-level changes, and possibly global climate change and biological evolution.

Trinuclear pyrazine-bridged ruthenium complexes: syntheses, electrochemistry, NIR-Vis spectra, and their interpretation in terms of a 5-orbital-3-parameter model.

A study of absorption spectra in the near-infrared (NIR) and visible (vis) regions of trinuclear Ru complexes containing pyrazine (pyz) as bridging ligand, trans-[(Ru(NH(3))(5)pyz)(2)Ru(NH(3))(4)](m+)(m = 6-9), is reported. The spectra were recorded on aqueous solutions containing the described species formed in situ by stoichiometric additions of a standard solution of Ce(SO(4))(2). They were interpreted in terms of a simple 5-orbital-3-parameter model which includes the effects of d-pi interaction and electronic correlation. The model is shown to account for the observed NIR-vis spectra of the complex ions. The 6+ parent species was synthesized by an improved literature method and fully characterized. The novel 8+ complex was also prepared and characterized. The 9+ ion was established to be slowly reduced by water, with dioxygen formation. Electrochemical (CV and DPV) studies were performed on the trinuclear 6+ complex, as well as on its constituent fragments [Ru(NH(3))(5)(pyz)](2+) and trans-[Ru(NH(3))(4)(pyz)(2)](2+).

Computational Aspects of Combinatorial Quantum Chemistry

The Additive Fuzzy Density Fragmentation (AFDF) principle and the Adjustable Density Matrix Assembler (ADMA) methods are proposed for a combinatorial construction of electron density representations of a series of macromolecules, related to one another by combinatorial reassignments of constituent fragments. Some of the fundamental computational aspects of the ADMA-based Combinatorial Quantum Chemistry (ADMA-CQC) approach are discussed, with special emphasis on the constraints provided by the recently proven holographic properties of molecular electron densities.

Fragment mode analysis and its application to the vibrational normal modes of boron trichloride–ammonia and boron trichloride–pyridine complexes

A method for expressing quantitatively the vibrational normal modes of a molecule in a basis set consisting of the normal vibrations (plus translations and rotations) of its constituent fragments is presented. The method is illustrated by describing the vibrational modes of BCl 3–NH 3 and BCl 3–pyridine electron donor–acceptor complexes in terms of motions of BCl 3 and either NH 3 or pyridine. These complexes show examples of mixing between modes located on different fragments, mixing between modes of one fragment due to symmetry lowering, and the transformation of six fragment translations/rotations into vibrations of the complex. Although perturbation theory has been proposed to explain such examples of mode mixing, calculations imply that interactions between fragments of both complexes are too strong for perturbation theory to be generally applicable. In addition, the transformation of fragment rotations and/or translations into vibrations of the composite molecule will always occur and cannot be understood in detail by using perturbation theory. For the BCl 3–pyridine complex, a band observed at 1107 cm −1 is re-assigned as a combination of CH in-plane bending and a ring-breathing mode of the pyridine fragment.

Theoretical Study of the Double Proton Transfer in the CHX−XH···CHX−XH (X = O, S) Complexes

A theoretical study of double-proton-transfer processes in bimolecular complexes formed by combinations of molecules of the type CHX−XH (X = O, S) is reported. The reactions are rationalized in terms of the energy, chemical potential, and hardness of hydrogen-bonded and isolated species. Sanderson's rule to determine molecular chemical potential and hardness from the values of the constituent fragments is used to characterize the relaxation effects due to hydrogen bonding. In ten formation and seven double-proton transfer processes studied here, the principles of maximum hardness and minimum polarizability are verified. The mechanism for double proton transfer has been analyzed through the force acting on the system to bring reactants into products and the corresponding energy barriers have been qualitatively classified according to its through bond or through space nature.

Computation of pattern invariance in brain-like structures

A fundamental capacity of the perceptual systems and the brain in general is to deal with the novel and the unexpected. In vision, we can effortlessly recognize a familiar object under novel viewing conditions, or recognize a new object as a member of a familiar class, such as a house, a face, or a car. This ability to generalize and deal efficiently with novel stimuli has long been considered a challenging example of brain-like computation that proved extremely difficult to replicate in artificial systems. In this paper we present an approach to generalization and invariant recognition. We focus our discussion on the problem of invariance to position in the visual field, but also sketch how similar principles could apply to other domains. The approach is based on the use of a large repertoire of partial generalizations that are built upon past experience. In the case of shift invariance, visual patterns are described as the conjunction of multiple overlapping image fragments. The invariance to the more primitive fragments is built into the system by past experience. Shift invariance of complex shapes is obtained from the invariance of their constituent fragments. We study by simulations aspects of this shift invariance method and then consider its extensions to invariant perception and classification by brain-like structures.

Crystal and molecular structures of [(2-amino-5-methyl-1,3-thiazole)(1,4,7-triazaheptane)copper(II)] dinitrate

The reaction of (1,4,7-triazaheptane)Cu(NO 3) 2 with 2-amino-5-methyl-1,3-thiazole (amtz) yields the compound [(amtz)(dien)Cu](NO 3) 2 (dien=1,4,7-triazaheptane). The compound has been characterised by elemental analyses, molar conductance and magnetic measurements, as well as by its electronic and IR spectra and X-ray diffraction. There are two crystallographically discernible cations [(amtz)(dien)Cu] 2+ and four NO 3 − in the asymmetric unit of the structure. Dien is tridentate with mean Cu–N=1.997(5) and 2.021(5) Å in the two Cu-ions, respectively. Amtz is coordinated through its endocyclic N with Cu–N=2.063(7) and 1.945(6) Å in the two ions, respectively. The CuN 4 unit is approximately square planar and almost perpendicular to the tz plane. Both the cations make two long (trans-Cu…O=2.6–2.7 Å) contacts. Ab initio calculations on the constituent fragments [(dien)Cu] 2+, [(amtz)Cu] 2+ and [(dien)(amtz)Cu] 2+ reproduced the average molecular structure parameters of the two Cu-ions in the unit cell and also helped interpret the details of the molecular structure as well as the assignment of the vibrational and electronic spectra.

Early completion of occluded objects.

We show that early vision can use monocular cues to rapidly complete partially-occluded objects. Visual search for easily-detected fragments becomes difficult when the completed shape is similar to others in the display; conversely, search for fragments that are difficult to detect becomes easy when the completed shape is distinctive. Results indicate that completion occurs via the occlusion-triggered removal of occlusion edges and linking of associated regions. We fail to find evidence for a visible filling-in of contours or surfaces, but do find evidence for a 'functional' filling-in that prevents the constituent fragments from being rapidly accessed. As such, it is only the completed structures--and not the fragments themselves--that serve as the basis for rapid recognition.

Conformational analysis of a 12‐membered crown dithioether in the solid state and in solution

The solid-state molecular structure and the conformational behaviour in solution of the 12-membered crown dithioether 8- methyl-1,4-dioxa-7,10-dithiacyclododecane-5,12-dione were studied by x-ray crystallography, H-1 and C-13 NMR spectroscopy and molecular mechanics. The conformational rigidity of some constituent structural fragments allowed a detailed analysis of the structure and distribution of the conformers. A protocol for studies of multiconformational equilibrium was developed by means of the combined use of structure calculations and dynamic NMR measurements. (C) 1998 John Wiley & Sons, Ltd.

Ab initio solution of a complex crystal structure from powder-diffraction data using simulated-annealing method and a high degree of molecular flexibility

The previously unknown crystal structure of the polymer/salt complex poly(ethylene oxide):${\mathrm{NaSO}}_{3}$${\mathrm{CF}}_{3}$ was solved from a powder-diffraction pattern collected on a laboratory x-ray diffractometer. The solution was performed starting from a random arrangement of constituent molecular fragments in the unit cell using a full-profile-fitting technique and a simulated-annealing method for finding the global minimum of the figure-of-merit function. Unlike the only other structure solution using this approach, the procedure was successful only when the highest degree of flexibility was applied to stereochemically constrained species.

Structural determinants associated with risk of human developmental toxicity

OBJECTIVES: Identifying drugs or chemicals that represent hazards to human development is a continuous challenge. Of the approximately 60,000 chemicals in commercial use only 5% have been evaluated for developmental toxicity. Identification of inexpensive, rapid, validated techniques to demonstrate chemical hazards for the human embryo or fetus is the objective of this research. STUDY DESIGN: This research explored identification of structure activity predictors associated with human developmental toxicity by means of MULTICASE (multiple computer-automated structure evaluation), an algorithm that evaluates associations between chemicals and their constituent fragments and a biologic response. This algorithm allows identification of chemicals (and specific substructures) that may be human developmental toxicants. Developmental toxicity data were compiled from two sources (the Teratogen Information System and Food and Drug Administration guidelines) and analyzed to identify structural determinants (biophores) associated with human developmental toxicity. RESULTS: This analysis identified 17 biophores associated with human developmental toxicity. Testing the biophores against the learning set demonstrated 99% concordance, 100% sensitivity, and 98% specificity. Cross-validation studies were conducted, in which the original database was randomly separated into five learning and test sets; these demonstrated a mean concordance of 73%, with a mean sensitivity of 63% and a mean specificity of 79%. CONCLUSIONS: The MULTICASE structure-activity model is useful for identifying potential human developmental toxicants, as well as serving as a starting point for mechanistic investigations. (Am J Obstet Gynecol 1997;176:799-806.)

Fragment chemistry of the hydrogen thioperoxide molecule; energy, chemical potential and hardness

In this paper we present a complete theoretical study of the hydrogen thioperoxide molecule (HSOH). We characterize the internal rotation by studying the evolution of the energy, chemical potential and hardness along the torsional angle. We have found that hydrogen thioperoxide in its electronic singlet state is a gauche molecule. Barrier heights, activation chemical potential and activation hardness have been obtained, and it has been found that the trans barrier is lower than the cis one. Good agreement of rotation barriers is obtained on the basis of comparisons with the available literature experimental data for the HOOH and HSSH parent molecules. Another important result is that the maximum hardness principle is verified for the torsional motion. On the other hand, we characterize the thermochemistry of chemical reactions leading to formation of HSOH from the electronic properties associated with the free constituent fragments. The procedure, which involves the use of Sanderson's rule to estimate chemical potentials and hardnesses, is shown to be promising and opens the possibility of rationalizing the behavior of other series of reactions.

Characterization of underivatized tetrapeptides by negative-ion fast-atom bombardment mass spectrometry.

The [M-H]- ions derived from tetrapeptides generally show two different collision-induced backbone cleavages which allow the determination of the amino acid sequence of the peptide. The first of these involves the formation of the carboxylate anions of either constituent amino acids or fragment peptides. In the second, amino acids or fragment peptides are eliminated as neutrals. There are a number of residues which undergo characteristic side-chain fragmentations irrespective of their position in the tetrapeptide, e.g. Ser, Thr, Cys, Met, Phe, and Tyr. However, there are also some residues which, when situated at the C-terminal end of the peptide, promote pronounced fragmentation at the C-terminal position which occurs to the exclusion of the normal backbone cleavages. We conclude that the data obtained from these negative-ion cleavages are analytically useful, and complement those provided by the cognate positive-ion technique.

The magnetism of meteorites and early Solar System magnetic fields

The characteristics of the remanent magnetization of chondrite, achondrite and shergottite, nakhlite and chassignite (SNC) meteorites are described, and interpretation in terms of magnetizing fields in the ancient Solar System discussed. The magnetism of ordinary chondrites is commonly scattered in direction within samples, implying magnetization of constituent fragments before accumulation. The magnetic history of these meteorites is uncertain because of lack of knowledge of the origin and properties of tetrataenite, an ordered FeNi alloy often carrying the bulk of the magnetization. Achondrites also often possess scattered magnetization, the primary component probably being acquired during cooling after differentiation of the parent body. A magnetizing field of internal origin is possible. Estimates of magnetizing field strength are in the approximate range 5-100 μ T, with carbonaceous chondrites showing the highest values. The SNC meteorites, probably originating on Mars, provide evidence for a weak, ancient Martian magnetic field of the order 1 μ T.

Magnetic properties of howardite, eucrite and diogenite (HED) meteorites: Ancient magnetizing fields and meteorite evolution

The remanent magnetism and other magnetic properties of four howardites (Kapoeta, Petersburg, Le Teilleul and EET 87503), two eucrites (Sioux County and PCA 82502) and three diogenites (Shalka, Johnstown and EET 79002) have been investigated. The dominant carrier of magnetic properties is low-nickel kamacite, present to the extent of 3–5% by weight in Petersburg and 0.1–1% in the others. A wide range of remanent magnetization (NRM) intensities, characteristics and behaviour during alternating field and thermal demagnetization is observed. Two common features are scattered directions of NRM between meteorite subsamples and anomalous behaviour of NRM direction and intensity during demagnetization. All the meteorites show evidence of a primary NRM acquired during an early evolutionary and some acquired secondary NRM. The heterogeneous NRM, with which anomalous demagnetization appears to be associated, implies magnetization of constituent fragments of the meteorite prior to, and no remagnetization after final meteorite assembly. It is tentatively proposed that the primary magnetizing field was of internal origin in the parent body, and that thermoremanent magnetization occurred when the body cooled after differentiation. The coherent magnetic fabric observed in all but two of the HEDs was most probably imparted at the time of final assembly of the meteorites.

Ab initio valence bond study of the origin of barriers to hydrogen exchange reactions: application of the valence bond self-consistent-field method to the fluorine atom + hydrogen fluoride .fwdarw. FH + F reaction

A combination of ab initio methods, in particular the valence bond self-consistent field (VB-SCF) and the valence bond configuration interaction (VB-CI) methods, are used to examine the origins of barriers to chemical reactions in a quantitative manner. Valence bond methods are well suited to this type of study as their underlying philosophy relies on constructing the molecular (or supermolecular) electronic wave functions from those of the constituent atoms or fragments.