Computer-Assisted Solution of Chemical Problems—The Historical Development and the Present State of the Art of a New Discipline of Chemistry

The topic of this article is the development and the present state of the art of computer chemistry, the computer-assisted solution of chemical problems. Initially the problems in computer chemistry were confined to structure elucidation on the basis of spectroscopic data, then programs for synthesis design based on libraries of reaction data for relatively narrow classes of target compounds were developed, and now computer programs for the solution of a great variety of chemical problems are available or are under development. Previously it was an achievement when any solution of a chemical problem could be generated by computer assistance. Today, the main task is the efficient, transparent, and non-arbitrary selection of meaningful results from the immense set of potential solutions—that also may contain innovative proposals. Chemistry has two aspects, constitutional chemistry and stereochemistry, which are interrelated, but still require different approaches. As a result, about twenty years ago, an algebraic model of the logical structure of chemistry was presented that consisted of two parts: the constitution-oriented algebra of be- and r-matrices, and the theory of the stereochemistry of the chemical identity group. New chemical definitions, concepts, and perspectives are characteristic of this logic-oriented model, as well as the direct mathematical representation of chemical processes. This model enables the implementation of formal reaction generators that can produce conceivable solutions to chemical problems—including unprecedented solutions—without detailed empirical chemical information. New formal selection procedures for computer-generated chemical information are also possible through the above model. It is expedient to combine these with interactive methods of selection. In this review, the Munich project is presented and discussed in detail. It encompasses the further development and implementation of the mathematical model of the logical structure of chemistry as well as the experimental verification of the computer-generated results. The article concludes with a review of new reactions, reagents, and reaction mechanisms that have been found with the PC-programs IGOR and RAIN.     

Experimental and theoretical study of the V → T,R relaxation of CD4 between 300 and 100 K

Rate constants for the vibrational deactivation of CD₄ by the collision partners CD₄, He, Ne, Ar, Kr, D₂ and O₂ have been measured using a laser-fluorescence technique. The results are compared with those for the deactivation of CH₄ by the same collision partners and with a modified SSH type theoretical treatment.     

Ferromagnetic resonance investigation of dispersed Ni catalysts: epitaxial and textural effects from the support

Catalysts consisting of dispersed Ni particles supported on silica and alumina, with sizes ranging from 6 to 20 nm, have been studied by ferromagnetic resonance. For the Ni on Al₂O₃ catalyst, a textural promotion effect is shown to be present and it is attributed to the possible presence of NiAl₂O₄. The FMR data confirm the epitaxial growth of Ni on SiO₂ when Ni antigorite is reduced and show that some anisotropy is still present after sintering of the catalyst at about 1200K.     

Structural basis for recognition of bacterial cell wall teichoic acid by pseudo-symmetric SH3b-like repeats of a viral peptidoglycan hydrolase

Endolysins are bacteriophage-encoded peptidoglycan hydrolases targeting the cell wall of host bacteria via their cell wall-binding domains (CBDs). The molecular basis for selective recognition of surface carbohydrate ligands by CBDs remains elusive. Here, we describe, in atomic detail, the interaction between the Listeria phage endolysin domain CBD500 and its cell wall teichoic acid (WTA) ligands. We show that 3′O-acetylated GlcNAc residues integrated into the WTA polymer chain are the key epitope recognized by a CBD binding cavity located at the interface of tandem copies of beta-barrel, pseudo-symmetric SH3b-like repeats. This cavity consists of multiple aromatic residues making extensive interactions with two GlcNAc acetyl groups via hydrogen bonds and van der Waals contacts, while permitting the docking of the diastereomorphic ligands. Our multidisciplinary approach tackled an extremely challenging protein–glycopolymer complex and delineated a previously unknown recognition mechanism by which a phage endolysin specifically recognizes and targets WTA, suggesting an adaptable model for regulation of endolysin specificity.

Combining genetic, biochemical and computational approaches, we elucidated the molecular mechanisms underlying the recognition of Listeria wall teichoic acid by bacteriophage-encoded SH3b repeats.     

Tuning cell adhesion on gradient poly(2-hydroxyethyl methacrylate)-grafted surfaces

A simple yet versatile method was developed to prepare a low-density polymerization initiator gradient, which was combined with surface-initiated atom transfer radical polymerization (ATRP) to produce a well-defined poly(2-hydroxyethyl methacrylate) (HEMA) gradient substrate. A smooth variation in film thickness was measured across the gradient, ranging from 20 A to over 80 A, but we observed a nonmonotonic variation in water contact angle. Fits of X-ray reflectivity profiles suggested that at the low graft density end, the polymer chain structure was in a "mushroom" regime, while the polymer chains at high graft density were in a "brush" regime. It was found that the "mushroom" region of the gradient could be made adhesive to cells by adsorbing adhesion proteins, and cell adhesion could be tuned by controlling the density of the polymer grafts. Fibroblasts were seeded on gradients precoated with fibronectin to test cellular responses to this novel substrate, but it was found that cell adhesion did not follow the expected trend; instead, saturated cell adhesion and spreading was found at the low grafting density region.     

Solution conformation by NMR and molecular modeling of three sulfide-free somatostatin octapeptide analogs compared to angiopeptin

Summary The conformation in dimethylsulfoxide of the somatostatin derivative angiopeptin and of three disulfide-free analogs was estimated by two-dimensional nuclear magnetic resonance spectroscopy at room temperature. The resulting 3D molecular graphics were compared and shown to reflect the observed differences in the inhibition of restenosis after rat aorta balloon injury by these octapeptide inhibitors. Angiopeptin and its active analog 2 displayed a relatively rigid conformation of the cyclic hexapeptide backbone due to the presence of two well-defined hydrogen bonds, further stabilized by a third hydrogen bond outside the ring. No such constraints were detected for the two biologically inactive analogs, which, compared to 2, had a two-atom longer or shorter hexapeptide ring. The well-defined structure of compound 2 may serve as an improved pharmacophore for this new class of drugs.     

Relaxation dynamics of 2,7- and 3,6-distyrylcarbazoles in solutions and in solid films: mechanism for efficient nonradiative deactivation in the 3,6-linked carbazole

We performed time-resolved spectral investigations of two distyrylcarbazole derivatives, 2,7- and 3,6-distyrylcarbazole (2,7-DPVTCz and 3,6-DPVTCz, respectively), in dilute toluene solution and in solid films mixed with poly(methyl methacrylate) (PMMA). The lifetime of 2,7-DPVTCz in its excited state in solution is approximately 100 times as great as that of 3,6-DPVTCz, consistent with their photophysical nature. The former shows intense emission, but the latter is nearly nonfluorescent in a free environment. Moreover, the lifetime of 3,6-DPVTCz in its excited state increased also approximately 100 times when the molecule was encapsulated in a 3,6-DPVTCz/PMMA solid film, indicating that intramolecular motion of the molecule significantly affects the observed relaxation dynamics in a confined environment. Calculations on the excited states indicate that an efficient intersystem crossing is activated upon twisting of the bridged C-C single bond in a free 3,6-linked carbazole; such efficient deactivation is impractical in 2,7-linked carbazole or for 3,6-linked carbazole in a PMMA matrix. Information obtained from experiments on femtosecond fluorescence enables us to distinguish crucial relaxation processes in the excited state for a profound understanding of the details of vibrational and electronic relaxations of 3,6-DPVTCz in solution.     

Phase sensitive demodulation in multiphoton microscopy.

Multiphoton laser scanning microscopy offers advantages in depth of penetration into intact samples over other optical sectioning techniques. To achieve these advantages it is necessary to detect the emitted light without spatial filtering. In this nondescanned (nonconfocal) approach, ambient room light can easily contaminate the signal, forcing experiments to be performed in absolute darkness. For multiphoton microscope systems employing mode-locked lasers, signal processing can be used to reduce such problems by taking advantage of the pulsed characteristics of such lasers. Specifically, by recovering fluorescence generated at the mode-locked frequency, interference from stray light and other ambient noise sources can be significantly reduced. This technology can be adapted to existing microscopes by inserting demodulation circuitry between the detector and data collection system. The improvement in signal-to-noise ratio afforded by this approach yields a more robust microscope system and opens the possibility of moving multiphoton microscopy from the research lab to more demanding settings, such as the clinic.     

Homoclinic orbits on compact hypersufaces in 293-1293-1293-1, of restricted contact type

Consider a smooth Hamiltonian system in ^2N , , the energy surface ={x/H(x)=H(0)} being compact, and 0 being a hyperbolic equilibrium. We assume, moreover, that {0} is of restricted contact type. These conditions are symplectically invariant. By a variational method, we prove the existence of an orbit homoclinic, i.e. non-constant and doubly asymptotic, to 0.     

Logarithmic correction to the probability of capture for dissipatively perturbed Hamiltonian systems

Hamiltonian systems are analyzed with a double homoclinic orbit connecting a saddle to itself. Competing centers exist. A small dissipative perturbation causes the stable and unstable manifolds of the saddle point to break apart. The stable manifolds of the saddle point are the boundaries of the basin of attraction for the competing attractors. With small dissipation, the boundaries of the basins of attraction are known to be tightly wound and spiral-like. Small changes in the initial condition can alter the equilibrium to which the solution is attracted. Near the unperturbed homoclinic orbit, the boundary of the basin of attraction consists of a large sequence of nearly homoclinic orbits surrounded by close approaches to the saddle point. The slow passage through an unperturbed homoclinic orbit (separatrix) is determined by the change in the value of the Hamiltonian from one saddle approach to the next. The probability of capture can be asymptotically approximated using this change in the Hamiltonian. The well-known leading-order change of the Hamiltonian from one saddle approach to the next is due to the effect of the perturbation on the homoclinic orbit. A logarithmic correction to this change of the Hamiltonian is shown to be due to the effect of the perturbation on the saddle point itself. It is shown that the probability of capture can be significantly altered from the well-known leading-order probability for Hamiltonian systems with double homoclinic orbits of the twisted type, an example of which is the Hamiltonian system corresponding to primary resonance. Numerical integration of the perturbed Hamiltonian system is used to verify the accuracy of the analytic formulas for the change in the Hamiltonian from one saddle approach to the next. (c) 1995 American Institute of Physics.