Matrix isolation studies of nucleic acid constituents. i. infrared spectra of uracil monomers
01 Sep 1983-Journal of the American Chemical Society (American Chemical Society)-Vol. 105, Iss: 19, pp 5969-5976
TL;DR: In this article, the authors proposed a method to solve the problem of energy minimization in the field of particle physics, using an energy minimisation algorithm based on the concept of energy maximization.
Abstract: Author Institution: Institute of Physics, Polish Academy of Sciences; Department of Chemistry, University of Florida
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TL;DR: An all atom potential energy function for the simulation of proteins and nucleic acids and the first general vibrational analysis of all five nucleic acid bases with a molecular mechanics potential approach is presented.
Abstract: We present an all atom potential energy function for the simulation of proteins and nucleic acids. This work is an extension of the CH united atom function recently presented by S.J. Weiner et al. J. Amer. Chem. Soc., 106, 765 (1984). The parameters of our function are based on calculations on ethane, propane, n−butane, dimethyl ether, methyl ethyl ether, tetrahydrofuran, imidazole, indole, deoxyadenosine, base paired dinucleoside phosphates, adenine, guanine, uracil, cytosine, thymine, insulin, and myoglobin. We have also used these parameters to carry out the first general vibrational analysis of all five nucleic acid bases with a molecular mechanics potential approach.
3,291 citations
TL;DR: Fatty acids have been investigated as boundary structures to construct artificial cells due to their dynamic properties and phase transitions, and the possibility that fatty acid systems also demonstrate movement was explored.
Abstract: Fatty acids have been investigated as boundary structures to construct artificial cells due to their dynamic properties and phase transitions. Here we have explored the possibility that fatty acid systems also demonstrate movement. An oil phase was loaded with a fatty acid anhydride precursor and introduced to an aqueous fatty acid micelle solution. The oil droplets showed autonomous, sustained movement through the aqueous media. Internal convection created a positive feedback loop, and the movement of the oil droplet was sustained as convection drove fresh precursor to the surface to become hydrolyzed. As the system progressed, more surfactant was produced and some of the oil droplets transformed into supramolecular aggregates resembling multilamellar vesicles. The oil droplets also moved directionally within chemical gradients and exhibited a type of chemotaxis.
298 citations
TL;DR: The overall approach proposed in the present work is able to provide the proper accuracy to support experimental investigations even for large molecular systems of biotechnological interest in a fully automated manner, without any ad hoc scaling procedure.
Abstract: A general second-order perturbative approach based on resonance- and threshold-free computations of vibrational properties is introduced and validated. It starts from the evaluation of accurate anharmonic zero-point vibrational energies for semirigid molecular systems, in a way that avoids any singularity. Next, the degeneracy corrected second-order perturbation theory (DCPT2) is extended to a hybrid version (HDCPT2), allowing for reliable computations even in cases where the original formulation faces against severe problems, including also an automatic treatment of internal rotations through the hindered-rotor model. These approaches, in conjunction with the so-called simple perturbation theory (SPT) reformulated to treat consistently both energy minima and transition states, allow one to evaluate degeneracy-corrected partition functions further used to obtain vibrational contributions to properties like enthalpy, entropy, or specific heat. The spectroscopic accuracy of the HDCPT2 model has been also va...
238 citations
TL;DR: In this paper, an improved empirical energy function for energy minimization and dynamics calculations of nucleic acids is developed and evaluated by an examination of its representation of both static and dynamic properties of model systems.
Abstract: An improved empirical energy function for energy minimization and dynamics calculations of nucleic acids is developed and evaluated by an examination of its representation of both static and dynamic properties of model systems. Among the properties studied and used for parameter optimization are base pairing interactions, sugar and phosphate energy surfaces, small crystal heats of sublimation, base, phosphate and sugar analogue vibration spectra, and the overall behavior of a DNA hexamer duplex in vacuum molecular dynamics simulations. The results obtained are compared with those from two other energy functions that have been used recently for nucleic acids. Parameters for two energy functions are given; one includes heavy atoms and only polar hydrogens and the other includes all atoms.
237 citations
TL;DR: The infrared spectra of gas-phase uracil, thymine, and adenine have been recorded from 100 to 3700 cm−1 at a resolution of 1 cm −1 as mentioned in this paper.
186 citations