The role of vibrational spectroscopy in the testing of force fields of biological molecules and in the determination of improved force fields is discussed. Analysis shows that quantitative testing of potential energy surfaces by comparison with spectroscopic data generally requires calculations that include anharmonic couplings between different vibrational modes. Applications of the vibrational self-consistent field (VSCF) method to calculations of spectroscopy of biological molecules are presented, and comparison with experiment is used to determine the merits and flaws of various types of force fields. The main conclusions include the following: (1) Potential surfaces from ab initio methods at the level of MP2 yield very satisfactory agreement with spectroscopic experimental data. (2) By the test of spectroscopy, ab initio force fields are considerably superior to the standard versions of force fields such as AMBER or OPLS. (3) Much of the spectroscopic weakness of AMBER and OPLS is due to incorrect description of anharmonic coupling, between different vibrational modes. (4) Potential surfaces of the QM/MM (Quantum Mechanics/Molecular Mechanics) type, and potentials based on improved versions of semi-empirical electronic structure theory, which are feasible for large biological molecules, yield encouraging results by the test of vibrational spectroscopy. (C) 2003 Wiley Periodicals, Inc.
Computed dc transport in compressed arrays of metallic quantum dots exhibits a voltage-induced phase transition at low temperatures. The transition is seen in the temperature dependence of the conductance at different voltages: from a variable hopping dependence at low voltage to an ohmic, activated behavior at higher voltages. The computations also exhibit the transition as a break in the current versus voltage plots at low temperatures where, at higher voltages, the plot is linear. At higher temperatures, the conductance is ohmic. A many-electron basis is used. The same transition is seen in the surface potential contours. (C) 2003 American Institute of Physics.
Various factors governing the detectability of explosive traces after being soaked in water were studied. The variables are: the type of the surface (surfaces liable to be found in aircraft were chosen), the type of explosive, the type of water (tap or seawater), and movement of the immersed surface in the water. The maximal immersion times (tmax) after which explosive detection was possible were evaluated. This datum was found to depend on the type of explosive (one of the important factors is soly. in water), the surface material and the environmental conditions (tap or seawater movement). Detection of PETN on high-d. polyethylene, linoleum, glass and aluminum, by the chem. Explosive Testing Kit (ETK), was possible even after a month of soaking in seawater. In addn., it was found that movement of bulk water around the samples with deposited explosives considerably decreases tmax values. It is, therefore, recommended to retrieve samples for explosive anal. as soon as possible and in areas where the currents of water is minimal. [on SciFinder(R)]
Publisher Summary This chapter reviews the evidence for endocrine influences on division of labor in insect societies. Juvenile hormone (JH) has been studied most extensively. The influence of JH is widespread. It is involved in the control of four major forms of division of labor: division of labor for reproduction among adults, division of labor for reproduction via caste differentiation, division of labor for colony growth and development among adults, and division of labor for colony growth and development via adult physical castes. These controls involve both pre-adult developmental processes of caste determination, and processes of physiological and behavioral maturation in adults. Studies on ecdysteroids and biogenic amines in these contexts have been started. Ecdysteroids are implicated in the control of caste determination and reproductive maturation in bees. The biogenic amine, octopamine, influences the division of labor among workers; octopamine and serotonin exert neurohormonal influences on the production of JH by the corpora allata in both larval and adult honey bees; and octopamine and dopamine are correlated suggestively with aspects of reproductive development in both bumble bees and honey bees.
The second-order Moller-Plesset ab initio electronic structure method is used to compute points for the anharmonic mode-coupled potential energy surface of N-methylacetamide (NMA) in the trans,, configuration, including all degrees of freedom. The anharmonic vibrational states and the spectroscopy are directly computed from this potential surface using the correlation corrected vibrational self-consistent field (CC-VSCF) method. The results are compared with CC-VSCF calculations using both the standard and improved empirical Amber-like force fields and available low-temperature experimental matrix data. Analysis of our calculated spectroscopic results show that (1) the excellent agreement between the ab initio CC-VSCF calculated frequencies and the experimental data suggest that the computed anharmonic potentials for N-methylacetamide are of a very high quality. (2) For most transitions, the vibrational frequencies obtained from the ab initio CC-VSCF method are superior to those obtained using the empirical CC-VSCF methods, when compared with experimental data. However, the improved empirical force field yields better agreement with the experimental frequencies as compared with a standard AMBER-type force field. (3) The improved empirical force field in particular overestimates anharmonic couplings for the amide 11 mode, the methyl asymmetric bending modes, the out-of-plane methyl bending modes, and the methyl distortions. (4) Disagreement between the ab initio and empirical anharmonic couplings is greater than the disagreement between the frequencies, and thus the anharmonic part of the empirical potential seems to be less accurate than the harmonic contribution. (5) Both the empirical and ab initio CC-VSCF calculations predict a negligible anharmonic coupling between the amide I and other internal modes. The implication of this is that the intramolecular energy flow between the amide I and the other internal modes may be smaller than anticipated. These results may have important implications for the anharmonic force fields of peptides, for which N-methylacetamide is a model.
Anharmonic vibrational frequencies and intensities are computed for hydrogen fluoride clusters (HF)(n) with n = 3, 4 and mixed clusters of hydrogen fluoride with water (HF)(n)(H(2)O)(n) where n = 1, 2. For the (HF)(4)(H(2)O)(4) complex, the vibrational spectra are calculated at the harmonic level, and anharmonic effects are estimated. Potential energy surfaces for these systems are obtained at the MP2/TZP level of electronic structure theory. Vibrational states are calculated from the potential surface points using the correlation-corrected vibrational self-consistent field method. The method accounts for the anharmonicities and couplings between all vibrational modes and provides fairly accurate anharmonic vibrational spectra that can be directly compared with experimental results without a need for empirical scaling. For (HF)(n), good agreement is found with experimental data. This agreement shows that the Moller-Plesset (MP2) potential surfaces for these systems are reasonably reliable. The accuracy is best for the stiff intramolecular modes, which indicates the validity of MP2 in describing coupling between intramolecular and intermolecular degrees of freedom. For (HF)(n)(H(2)O)(n) experimental results are unavailable. The computed intramolecular frequencies show a strong dependence on cluster size. Intensity features are predicted for future experiments. Published by Elsevier Science B.V.
The article discusses the results of the analysis of the assemblage that came from a test excavation conducted by Jean Perrot in 1962 at the site of Abu Zureiq, located in the vicinity of Kibbutz Hazorea on the western boundary of the Jezreel Valley in Israel. The site is attributed to the Wadi Rabah culture of the seventh millenium BP, which was coined by J. Kaplan in 1958 in his published articles on his excavations. Results show that the Abu Zureiq assemblage represents all known aspects of material culture of the Wadi Rabah. Despite the limited excavation area, the assemblage represents a wide range of tasks concentrated in a single locality. These include storage and processing of plant and animal food, lithic tool production and use and other economic and symbolic activities.
The adsorption of charge rigid macromolecules, such as proteins from solution, on mixed (charged and neutral) lipid membranes is affected by several important factors. First, the mobile lipids in the membrane may rearrange, and demix locally to match the charge density of the apposed macromolecule, thus lowering the adsorption free energy. On the other hand, the (electrostatic) interaction between adsorbed macromolecules tends to lower the saturation coverage of the membrane. Additional factors, such as non-ideal lipid demixing or an elastic membrane response, enhanced by the presence of the charged macromolecules, may be at the base of the experimentally observed formation of high density protein domains and lateral macro-phase separation in lipid membranes. (C) 2002 Elsevier Science B.V. All rights reserved.
We point out and simulate the possible utility of anti-coherence in molecular electronics. In ballistic transfer through a molecule with a large loop that fulfils a certain phase condition on the loop structure, the transfer would be anti-coherent. By applying one or two control voltages to the molecule, that modify the relative phase through the two parts of the loop, the transfer could be controlled, just like in FET or in XOR gates. The simulations use the absorbing-potential based flux-flux formulae with a Huckel-Hamiltonian in a Landauer formulation, and are numerically equivalent to a weighted time-dependent correlation function. (C) 2002 Elsevier Science B.V. All rights reserved.
The role of anharmonic effects in the vibrational spectroscopy of small biological molecules and their 1:1 complexes with water is discussed. The strengths and limitations of the vibrational self-consistent field (VSCF) method and its extensions as a computational tool for this purpose are examined. Anharmonic coupling between different vibrational modes is found to be very important for these systems, even for fundamental transitions, and incorporation of these effects seems essential for quantitative interpretation of experimental data. Both analytical, empirical force fields, and potential surfaces computed from electronic structure methods are used in VSCF calculations of several benchmark systems and compared with experimental spectroscopic data. Glycine in several conformers, the glycine water complex, and N-methylacetamide are among the systems discussed. The main conclusions are: (1) Electronic structure methods such as MP2/DZP and density functional B97, give very good agreement with experimental data. Thus, MP2 and B97 clearly provide an accurate description of the anharmonic interactions. VSCF calculations, including all modes, with MP2, B97 and other successful methods are presently feasible for molecules with up to 15-20 atoms. (2) The electronic structure methods seem to give spectroscopic predictions in much better accord with experiment than standard empirical force fields such as AMBER or OPLS. The anharmonic couplings provided by these methods differ greatly, in the cases tested to date, from the ab initio ones. The implications of these results for future modeling of small biomolecules are discussed. Comments are provided on future directions in this subject, including extensions to large biomolecules.
