Potential functions for hydrogen bond interactions - IV. Minimum Energy Conformation of the α-Helical Structure of PoIy-L-Alanine

Making use of the empirical potential functions for peptide NH .. O bonds, developed in this laboratory, the relative stabilities of the rightand left-handed α-helical structures of poly-L-alanine have been investigated, by calculating their conformational energies (V). The value of Vmin of the right-handed helix (αP) is about - 10.4 kcal/mole, and that of the left-handed helix (αM) is about - 9.6 kcal/mole, showing that the former is lower in energy by 0.8 kcal/mole. The helical parameters of the stable conformation of αP are n ∼ 3.6 and h ∼ 1.5 Å. The hydrogen bond of length 2.85 Å and nonlinearity of about 10° adds about 4.0 kcal/ mole to the stabilising energy of the helix in the minimum enregy region. The energy minimum is not sharply defined, but occurs over a long valley, suggesting that a distribution of conformations (φ{symbol}, ψ) of nearly the same energy may occur for the individual residues in a helix. The experimental data of a-helical fibres of poly-L-alanine are in good agreement with the theoretical results for αP. In the case of proteins, the mean values of (φ{symbol}, ψ) for different helices are distributed, but they invariably occur within the contour for V = Vmin + 2 kcal/mole for αP.

Levitation effect and its relationship with the underlying potential energy landscape

Positions of potential energy minima for spherical monatomic sorbates in zeolite NaY have been identified for different sizes of the sorbate. It is found that for small sorbates (sigma less than or equal to 4.96 Angstrom) there are only six adsorption sites per alpha-cage, which are located close to the inner surface of the alpha-cage. For larger sorbates, additional sites of comparable energies appear close to the 12-ring window which forms the bottleneck for intercage diffusion. Minimum energy paths between these sites have been computed. These suggest that the barriers for both intracage and intercage site-to-site migrations are comparable and decrease with increase in sorbate size. Earlier simulation studies on the diffusion of monatomic sorbates in zeolites indicated that there is a dramatic change in the nature of dependence of D on sorbate size around 4.96 Angstrom, for zeolite NaY. Therefore, the present results suggest that the dependence of D on sorbate size and the changes in the potential energy landscape are correlated. The sorbate-zeolite system is characterized by a flatter potential energy landscape when the sorbate size is large. (C) 1999 American Institute of Physics. [S0021-9606(99)51110-0].

All Digital Energy Sensing for Minimum Energy Tracking

Minimizing energy consumption is of utmost importance in an energy starved system with relaxed performance requirements. This brief presents a digital energy sensing method that requires neither a constant voltage reference nor a time reference. An energy minimizing loop uses this to find the minimum energy point and sets the supply voltage between 0.2 and 0.5 V. Energy savings up to 1275% over existing minimum energy tracking techniques in the literature is achieved.

Global Search for Minimum Energy (H2O)n Clusters, n = 3−5

The Gaussian-3 (G3) model chemistry method has been used to calculate the relative ΔG° values for all possible conformers of neutral clusters of water, (H2O)n, where n = 3−5. A complete 12-fold conformational search around each hydrogen bond produced 144, 1728, and 20 736 initial starting structures of the water trimer, tetramer, and pentamer. These structures were optimized with PM3, followed by HF/6-31G* optimization, and then with the G3 model chemistry. Only two trimers are present on the G3 potential energy hypersurface. We identified 5 tetramers and 10 pentamers on the potential energy and free-energy hypersurfaces at 298 K. None of these 17 structures were linear; all linear starting models folded into cyclic or three-dimensional structures. The cyclic pentamer is the most stable isomer at 298 K. On the basis of this and previous studies, we expect the cyclic tetramers and pentamers to be the most significant cyclic water clusters in the atmosphere.

Selection of optimal operating conditions based on minimum energy consumption for an acrylonitrile recovery unit

The selection of the optimal operating conditions for an industrial acrylonitrile recovery unit was conducted by the systematic application of the response surface methodology, based on the minimum energy consumption and products specifications as process constraints. Unit models and plant simulation were validated against operating data and information. A sensitivity analysis was carried out in order to identify the set of parameters that strongly affect the trajectories of the system while keeping products specifications. The results suggest that energy savings of up to 10% are possible by systematically adjusting operating conditions.

AD-HOC principles of minimum energy expenditure as corollaries of the constructal law the cases of river basins and human vascular systems

In a recent paper [1] Reis showed that both the principles of extremum of entropy production rate, which are often used in the study of complex systems, are corollaries of the Constructal Law. In fact, both follow from the maximization of overall system conductivities, under appropriate constraints. In this way, the maximum rate of entropy production (MEP) occurs when all the forces in the system are kept constant. On the other hand, the minimum rate of entropy production (mEP) occurs when all the currents that cross the system are kept constant. In this paper it is shown how the so-called principle of "minimum energy expenditure" which is often used as the basis for explaining many morphologic features in biologic systems, and also in inanimate systems, is also a corollary of Bejan's Constructal Law [2]. Following the general proof some cases namely, the scaling laws of human vascular systems and river basins are discussed as illustrations from the side of life, and inanimate systems, respectively.

Hydrogen spillover mechanism on a pd-doped mg surface as revealed by ab initio density functional calculation

The hydrogenation kinetics of Mg is slow, impeding its application for mobile hydrogen storage. We demonstrate by ab initio density functional theory (DFT) calculations that the reaction path can be greatly modified by adding transition metal catalysts. Contrasting with Ti doping, a Pd dopant will result in a very small activation barrier for both dissociation of molecular hydrogen and diffusion of atomic H on the Mg surface. This new computational finding supports for the first time by ab initio simulationthe proposed hydrogen spillover mechanism for rationalizing experimentally observed fast hydrogenation kinetics for Pd-capped Mg materials.

On the Relaxation Mechanisms of 6-Azauracil

The nonadiabatic photochemistry of 6-azauracil has been studied by means of the CASPT2//CASSCF protocol and double-zeta plus polarization ANO basis sets. Minimum energy states, transition states, minimum energy paths, and surface intersections have been computed in order to obtain an accurate description of several potential energy hypersurfaces. It is concluded that, after absorption of ultraviolet radiation (248 nm), two main relaxation mechanisms may occur, via which the lowest (3)(pi pi*) state can be populated. The first one takes place via a conical intersection involving the bright (1)(pi pi*) and the lowest (1)(n pi*) states, ((1)pi pi*/(1)n pi*)(CI), from which a low energy singlet-triplet crossing, ((1)n pi*/(3)pi pi*)(STC), connecting the (1)(n pi*) state to the lowest (3)(pi pi*) triplet state is accessible. The second mechanism arises via a singlet-triplet crossing, ((1)pi pi*/(3)n pi*)(STC), leading to a conical intersection in the triplet manifold, ((3)n pi*/(3)pi pi*)(CI), evolving to the lowest (3)(pi pi*) state. Further radiationless decay to the ground state is possible through a (gs/(3)pi pi*)(STC).

On the Mechanisms of Triplet Excited State Population in 8-Azaadenine

The photophysics of 8-azaadenine (8-AA) has been studied with the CASPT2//CASSCF protocol and ANO-L double-zeta basis sets. Stationary equilibrium structures, surface crossings, minimum energy paths, and linear interpolations have been used to study possible mechanisms to populate the lowest triplet state, T-1 (3)(pi pi*), capable of sensitizing molecular oxygen. Our results show that two main mechanisms can occur after photoexcitation to the S-2 (1)(pi pi*) state. The first one is through the S-2/S-1 conical intersection (((1)pi pi*/(1)n pi*)(Cl)), leading to the S-1 ((1)n pi*) state minimum, (S-1 ((1)n pi*))(min), where a singlet-triplet crossing, ((1)n pi*/(3)pi pi*)(STC), is accessible. The second one starts with the ((1)pi pi*/(3)n pi*)(STC) at the (S-2((1)pi pi*))(min), from which the system can evolve to the (T-2 ((3)n pi*))(min), with subsequent population of the T-1 excited electronic state, due to the ((3)n pi*/(3)pi pi*)(Cl) conical intersection.

Kinetics and coverage dependent reaction mechanisms of the copper atomic layer deposition from copper dimethylamino-2-propoxide and diethylzinc

Atomic layer deposition (ALD) has been recognized as a promising method to deposit conformal and uniform thin film of copper for future electronic devices. However, many aspects of the reaction mechanism and the surface chemistry of copper ALD remain unclear. In this paper, we employ plane wave density functional theory (DFT) to study the transmetalation ALD reaction of copper dimethylamino-2-propoxide [Cu(dmap)2] and diethylzinc [Et2Zn] that was realized experimentally by Lee et al. [ Angew. Chem., Int. Ed. 2009, 48, 4536−4539]. We find that the Cu(dmap)2 molecule adsorbs and dissociates through the scission of one or two Cu–O bonds into surface-bound dmap and Cu(dmap) fragments during the copper pulse. As Et2Zn adsorbs on the surface covered with Cu(dmap) and dmap fragments, butane formation and desorption was found to be facilitated by the surrounding ligands, which leads to one reaction mechanism, while the migration of ethyl groups to the surface leads to another reaction mechanism. During both reaction mechanisms, ligand diffusion and reordering are generally endothermic processes, which may result in residual ligands blocking the surface sites at the end of the Et2Zn pulse, and in residual Zn being reduced and incorporated as an impurity. We also find that the nearby ligands play a cooperative role in lowering the activation energy for formation and desorption of byproducts, which explains the advantage of using organometallic precursors and reducing agents in Cu ALD. The ALD growth rate estimated for the mechanism is consistent with the experimental value of 0.2 Å/cycle. The proposed reaction mechanisms provide insight into ALD processes for copper and other transition metals.

Long-term exploration and tours for energy constrained robots with online proprioceptive traversability estimation

This paper is concerned with how a localised and energy-constrained robot can maximise its time in the field by taking paths and tours that minimise its energy expenditure. A significant component of a robot's energy is expended on mobility and is a function of terrain traversability. We estimate traversability online from data sensed by the robot as it moves, and use this to generate maps, explore and ultimately converge on minimum energy tours of the environment. We provide results of detailed simulations and parameter studies that show the efficacy of this approach for a robot moving over terrain with unknown traversability as well as a number of a priori unknown hard obstacles.

Stereochemical studies on cyclic peptides: Detailed energy minimization studies on hydrogen bonded all-trans cyclic pentapeptide backbones

Conformational studies have been carried out on hydrogenbonded all-trans cyclic pentapeptide backbone. Application of a combination of grid search and energy minimization on this system has resulted in obtaining 23 minimum energy conformations, which are characterized by unique patterns of hydrogen bonding comprising of β- and γ-turns. A study of the minimum energy conformationsvis-a-vis non-planar deviation of the peptide units reveals that non-planarity is an inherent feature in many cases. A study on conformational clustering of minimum energy conformations shows that the minimum energy conformations fall into 6 distinct conformational families. Preliminary comparison with available X-ray structures of cyclic pentapeptide indicates that only some of the minimum energy conformations have formed crystal structures. The set of minimum energy conformations worked out in the present study can form a consolidated database of prototypes for hydrogen bonded backbone and be useful for modelling cyclic pentapeptides both synthetic and bioactive in nature.

A Search for Energy Minimized Sequences of Proteins

In this paper, we present numerical evidence that supports the notion of minimization in the sequence space of proteins for a target conformation. We use the conformations of the real proteins in the Protein Data Bank (PDB) and present computationally efficient methods to identify the sequences with minimum energy. We use edge-weighted connectivity graph for ranking the residue sites with reduced amino acid alphabet and then use continuous optimization to obtain the energy-minimizing sequences. Our methods enable the computation of a lower bound as well as a tight upper bound for the energy of a given conformation. We validate our results by using three different inter-residue energy matrices for five proteins from protein data bank (PDB), and by comparing our energy-minimizing sequences with 80 million diverse sequences that are generated based on different considerations in each case. When we submitted some of our chosen energy-minimizing sequences to Basic Local Alignment Search Tool (BLAST), we obtained some sequences from non-redundant protein sequence database that are similar to ours with an E-value of the order of 10(-7). In summary, we conclude that proteins show a trend towards minimizing energy in the sequence space but do not seem to adopt the global energy-minimizing sequence. The reason for this could be either that the existing energy matrices are not able to accurately represent the inter-residue interactions in the context of the protein environment or that Nature does not push the optimization in the sequence space, once it is able to perform the function.