Lowest Energy Path Research Articles

Water effect on the excited-state decay paths of singlet excited cytosine

Two low-energy deactivation paths for singlet excited cytosine, one through a S 1/ S 0 conical intersection of the ethylene type, and one through a conical intersection that involves the (n N, π *) state, are calculated in the presence of water. Water is included explicitly for several cytosine monohydrates, and as a bulk solvent, and the calculations are carried out at the complete active space self-consistent field (CASSCF) and complete active space second order perturbation (CASPT2) levels of theory. The effect of water on the lowest-energy path through the ethylenic conical intersection is a lowering of the energy barrier. This is explained by stabilization of the excited state, which has zwitterionic character in the vicinity of the conical intersection due to its similarity with the conical intersection of ethylene. In contrast to this, the path that involves the (n N, π *) state is destabilized by hydrogen bonding, although the bulk solvent effect reduces the destabilization. Overall, this path should remain energetically accessible.

Enthalpies of Formation, Bond Dissociation Energies and Reaction Paths for the Decomposition of Model Biofuels: Ethyl Propanoate and Methyl Butanoate

The complete basis set method CBS-QB3 has been used to study the thermochemistry and kinetics of the esters ethyl propanoate (EP) and methyl butanoate (MB) to evaluate initiation reactions and intermediate products from unimolecular decomposition reactions. Using isodesmic and isogeitonic equations and atomization energies, we have estimated chemically accurate enthalpies of formation and bond dissociation energies for the esters and species derived from them. In addition it is shown that controversial literature values may be resolved by adopting, for the acetate radical, CH3C(O)O(.-), DeltaH(o)(f)298.15K) = -197.8 kJ mol(-1) and for the trans-hydrocarboxyl radical, C(.-)(O)OH, -181.6 +/- 2.9 kJ mol(-1). For EP, the lowest energy decomposition path encounters an energy barrier of approximately 210 kJ mol(-1) (approximately 50 kcal mol(-1)), which proceeds through a six-membered ring transition state (retro-ene reaction) via transfer of the primary methyl H atom from the ethyl group to the carbonyl oxygen, while cleaving the carbon-ether oxygen to form ethene and propanoic acid. On the other hand, the lowest energy path for MB has a barrier of approximately 285 kJ mol(-1), producing ethene. Other routes leading to the formation of aldehydes, alcohols, ketene, and propene are also discussed. Most of these intramolecular hydrogen transfers have energy barriers lower than that needed for homolytic bond fission (the lowest of which is 353 kJ mol(-1) for the C(alpha)-C(beta) bond in MB). Propene formation is a much higher energy demanding process, 402 kJ mol(-1), and it should be competitive with some C-C, C-O, and C-H bond cleavage processes.

From A to B in free energy space

The authors present a new method for searching low free energy paths in complex molecular systems at finite temperature. They introduce two variables that are able to describe the position of a point in configurational space relative to a preassigned path. With the help of these two variables the authors combine features of approaches such as metadynamics or umbrella sampling with those of path based methods. This allows global searches in the space of paths to be performed and a new variational principle for the determination of low free energy paths to be established. Contrary to metadynamics or umbrella sampling the path can be described by an arbitrary large number of variables, still the energy profile along the path can be calculated. The authors exemplify the method numerically by studying the conformational changes of alanine dipeptide.

Interactions in Nb2H and its electronic structure

The total energies and electronic structures of differently configured Nb2H are calculated using pseudopotential plane wave method based on density functional theory and generalized gradient approximation. The results show that hydrogen atom favors tetrahedral (T) sites (T-wells) rather than octahedral (O) ones. There exist lower energy paths along adjacent T-T sites and saddle structures at the midpoint of them. When H is at T-site or along the T-T path, its 1s level is less broadened and the 4d, 5s bands of Nb extend downward from the metallic band area, forming an ionic band (sharp peak) separated by a gap of about 1 eV from the metallic valence bands, showing that the hydrogen atom captures one valence electron to form an anion. This low-lying ionic band loses its T-site hybridization features when H moves from T to O site, where the 1s band of H is widely broadened, extending into the metallic valence bands. The band structure changes only slightly when the hydrogen atom moves from one T site to a neighbor one along the lower energy path, keeping the T-configuration features. The calculated phonon spectra of H are dispersive only near special q-points for the system with H at a T site, showing that the hydrogen atom is probably vibraing locally and weakly interacts with other hydrogen atoms. The behavior of H at a trapping site plays an important role in bonding of the surrounding Nb atoms.

Theoretical study of carbon dioxide-carbon monoxide conversion by La +, Hf + and Ta +

The entire reaction mechanism for the gas-phase CO 2–CO conversion by early transition metal ions, La +, Hf +, and Ta +, are studied using density functional theory (DFT). The results indicate that the lowest energy path corresponds to the η 2-O coordination of CO 2 followed by the insertion of M + into the C–O bond. The reactions are all exothermic due to the participation of the metal ions, to be compared with the strong endothermic process of the unimolecular CO 2 decomposition. Crossing points (CPs) are localized, and possible spin inversion processes are discussed by means of the intrinsic reaction coordinate (IRC) approach.

A finite element model for martensitic thin films

A finite element approximation of the thin film limit for a sharp interface bulk energy for martensitic crystals is given. The energy density models the softening of the elastic modulus controlling the low-energy path from the cubic to the tetragonal lattice, the loss of stability of the tetragonal phase at high temperatures and the loss of stability of the cubic phase at low temperatures, and the effect of compositional fluctuation on the transformation temperature. The finite element approximation is then used to simulate the hysteresis of a martensitic thin film obtained after applying a biaxial loading cycle to the film below the transformation temperature. Keywords: finite element, phase transformation, martensite, austenite, thin film Mathematics Subject Classification (1991): 65C30, 65Z05, 74K35, 74N10, 74N15, 74S05

Theoretical study of the reactivity of 4d transition metal ions with N 2O

The reactions of 4d transition metal ions (except Tc and Cd) with N 2O on two potential energy surfaces, producing the metal oxide ion and N 2, are studied by means of density functional theory. The results indicate that the lowest energy path corresponds to the η O 1 coordination of N 2O followed by the insertion of M + into the N–O bond. The reaction mechanism between 4d transition metal ions and N 2O is an insertion–elimination mechanism. All products are formed in exothermic processes. The potential energy curve crossings, which dramatically affect reaction mechanisms, are discussed in detail.

Atomic-level simulation of epitaxial recrystallization and phase transformation in SiC

A nano-sized amorphous layer embedded in an atomic simulation cell was used to study the amorphous-to-crystalline (a-c) transition and subsequent phase transformation by molecular-dynamics computer simulations in 3C–SiC. The recovery of bond defects at the interfaces is an important process driving the initial epitaxial recrystallization of the amorphous layer, which is hindered by the nucleation of a polycrystalline 2H–SiC phase. The kink sites and triple junctions formed at the interfaces between 2H– and 3C–SiC provide low-energy paths for 2H–SiC atoms to transform to 3C–SiC atoms. The spectrum of activation energies associated with these processes ranges from below 0.8 eV to about 1.9 eV.

The two hydrogen transfer dissociation channels of nicotine molecule in the gas phase

Two possible dissociation channels accompanied with hydrogen transfer between the three functional groups of nicotine are investigated using CBS-4M method based on geometry and ZPE calculation of UB3LYP/6-31+G(d,p). The results indicate that the dissociation of C12–N11 bond contains multiple-step reaction process with three transition states. By comparing different dissociation channels, the lowest energy path of the dissociation between the functional groups of nicotine molecule under the isolated condition is the dissociation path of C5–C7 bond accompanied with intramolecular hydrogen transfer.

Nudged Elastic Band Calculation of Minimal Energy Paths for the Conformational Change of a GG Non-canonical Pair

The nudged elastic band (NEB) technique has been implemented in AMBER to calculate low-energy paths for conformational changes. A novel simulated annealing protocol that does not require an initial hypothesis for the path is used to sample low-energy paths. This was used to study the conformational change of an RNA cis Watson-Crick/Hoogsteen GG non-canonical pair, with one G syn around the glycosidic bond and the other anti. A previous solution structure, determined by NMR-constrained modeling, demonstrated that the GG pairs change from (syn)G-(anti)G to (anti)G-(syn)G in the context of duplex r(GCAGGCGUGC) on the millisecond timescale. The set of low-energy paths found by NEB show that each G flips independently around the glycosidic bond, with the anti G flipping to syn first. Guanine bases flip without opening adjacent base-pairs by protruding into the major groove, accommodated by a transient change by the ribose to C2'-exo sugar pucker. Hydrogen bonds between bases and the backbone, which lower the energetic barrier to flipping, are observed along the path. The results show the plasticity of RNA base-pairs in helices, which is important for biological processes, including mismatch repair, protein recognition, and translation. The modeling of the GG conformational change also demonstrates that NEB can be used to discover non-trivial paths for macromolecules and therefore NEB can be used as an exploratory method for predicting putative conformational change paths.

Influence of the Hydroxylation of γ-Al2O3Surfaces on the Stability and Diffusion of Single Pd Atoms: A DFT Study

Using recent well-defined models of gamma-Al2O3 surfaces, we study the interaction of single Pd atoms with gamma-Al2O3 surfaces corresponding to realistic pretreatment conditions by means of density functional theory periodic calculations. For relevant hydroxylation states of the surface, we determine potential energy surfaces (PES) that depict the relationship between structure and interaction at the metal-oxide interface. This approach enables the determination of the low-energy diffusion paths of the adsorbed Pd species. We applied classical transition-state theory to derive the temperature-dependent hopping rate of Pd on gamma-Al2O3 surfaces. Our work provides new insight into the chemisorption and diffusion process of single Pd atoms on alumina and show that the binding energy and hopping rate of Pd atoms decrease as the surface OH coverage increases. These results offer new highlights on Pd cluster formation at the initial nucleation steps on gamma-Al2O3 surfaces.

Low Energy Pathways and Non-native Interactions: THE INFLUENCE OF ARTIFICIAL DISULFIDE BRIDGES ON THE MECHANISM OF FOLDING

Four versions of a beta-sheet protein (CD2.d1) have been made, each with a single artificial disulfide bond inserted into hairpin structures. Folding kinetics of reduced and oxidized forms shows bridge position strongly influences its effect on the folding reaction. Bridging residues 58 and 62 does not affect the rapidly formed intermediate (I) or rate-limiting transition (t) state, whereas bridging 33 and 38, or 31 and 41, lowers the t-state energy, with the latter having the stronger influence. Bridging residues 79 and 90 stabilizes both I- and t-states. To assess additivity in the energetic effects of these bridges, four double-bridge variants have also been made. All show precise additivity of overall stability, with two showing additivity when ground states and the rate-limiting t-state are assessed, i.e. no measurable change in the folding mechanism occurs. However, combining 31-41 and 79-90 bridges produces a molecule that folds through a different pathway, with a much more stable intermediate than expected and a much higher t-state barrier. This is explained by the artificial introduction of stabilizing, non-native contacts in the I-state. More surprisingly, for another double-bridge version (58-62 and 79-90) both I- and t-states are less stable than expected, showing that conformational constraints introduced by the two bridges prevent formation of non-native contacts that would otherwise stabilize the I- and t-states, thereby lowering the energy of the folding landscape in the wild-type (unbridged) molecule. We conclude that the lowest energy path for folding has I- and t-state structures that are stabilized by non-native interactions.

Facile Ru−H2 Heterolytic Activation and Intramolecular Proton Transfer Assisted by Basic N-Centers in the Ligands

The use of the phosphine PPh2py instead of PPh3 in complexes of the type [Cp*RuH(P)2] enormously alters the kinetic control of the proton-transfer reactions over this compound and its chemical behavior. The reaction at low temperature of [Cp*RuH(PPh2py)2], 2, with HBF4 gives as products the classical dihydride trans-[Cp*RuH2(PPh2py)2](BF4), 3 (1 equiv of HBF4) or the dihydrogen-bonded complex [Cp*RuHH(PPh2pyH)(PPh2py)](BF4)2, 4 (2 equiv of HBF4). These complexes exhibit very accessible intramolecular processes of proton transfer, and finally, a slow release of H2 takes place at room temperature. Derivatives 2 and 3 are active catalysts for the deuterium labeling of H2 using methanol-d4 as an isotopic source. This demonstrates that the release of hydrogen is reversible, that the heterolytic activation of H2 is an easy process, and that acid species participate in the intramolecular proton-transfer processes. These observations are supported by reaction-coordinate calculations at the DFT/B3LYP level that show the existence of a low-energy reaction path that easily transforms the classical trans dihydride complex into the nonclassical cis dihydrogen compound in a reversible way, through the involvement of hydrogen- and dihydrogen-bonded intermediates and the essential participation of the pyridine centers. The different energy minima of this reaction profile are very accessible through low-energy transition states, all of which have been located.

Targeted Cancer Therapy Using Radiolabeled Monoclonal Antibodies

Radioimmunotherapy (RIT) combines the advantages of targeted radiation therapy and specific immunotherapy using monoclonal antibodies. RIT can be used either to target tumor cells or to specifically suppress immunocompetent host cells in the setting of allogeneic transplantation. The choice of radionuclide used for RIT depends on its distinct radiation characteristics and the type of malignancy or cells targeted. Beta-emitters with their lower energy and longer path length are more suitable to target bulky, solid tumors whereas alpha-emitters with their high linear energy transfer and short path length are better suited to target hematopoietic cells (normal or malignant). Different approaches of RIT such as the use of stable radioimmunoconjugates or of pretargeting strategies are available. Encouraging results have been obtained with RIT in patients with hematologic malignancies. The results in solid tumors are somewhat less favorable but new strategies for patients with minimal residual disease using adjuvant and locoregional treatment are evolving. This report outlines basic principles of RIT, gives an overview of available radionuclides and radioimmunoconjugates, and discusses clinical results with special emphasis on their use in hematologic malignancies including use in conditioning regimens for bone marrow transplantation.

Ab initio kinetics of the reaction of HCO with NO: Abstraction versus association/elimination mechanism

The kinetics and mechanism for the reaction of HCO with NO occurring by both singlet and triplet electronic state potential-energy surfaces (PESs) have been studied at the modified Gaussian-2 level of theory based on the geometric parameters optimized by the Becke-3 Lee-Yang-Parr/6-311G(d,p) method. There are two major reaction channels on both singlet and triplet PESs studied: one is direct H abstraction producing CO+HNO and the other is association forming a stable HC(O)NO (nitrosoformaldehyde) molecule. The dominant reaction is predicted to be the direct H abstraction occurring primarily by the lowest-energy path via a loose hydrogen-bonding singlet molecular complex, ON...HCO, with a 2.9-kcal/mol binding energy and a small decomposition barrier (1.9 kcal/mol). The commonly assumed HC(O)NO intermediate, predicted to lie below the reactants by 27.7 kcal/mol, has a high HNO-elimination barrier (34.5 kcal/mol). Bimolecular rate constants for the formation of the singlet products and their branching ratios have been calculated in the temperature range of 200-3000 K. The rate constant for the disproportionation process producing HNO+CO, found to be affected strongly by multiple reflections above the well of the complex at low temperature, is predicted to be k(HNO)=3.08 x 10(-12) T(0.10) exp(242T) for 200-500 K, and 1.72 x 10(-16) T(1.47) exp(888T) for 500-3000 K in units of cm(3) molecule(-1) s(-1). The high- and low-pressure rate constants for the association process forming HC(O)NO can be represented by k(infinity)=4.42 x 10(-11) T(0.25) exp(-28T) cm(3) molecule(-1) s(-1) (200-3000 K) and k(0)=7.30x10(-16) T(-5.75) exp(-719T) (200-1000 K) and 1.82 x 10(2) T(-11.92) exp(1846T) (1000-3000 K) cm(6) molecule(-2) s(-1) for N(2)-buffer gas. The absolute values of total rate constant, predicted to be weakly dependent negatively on temperature but positively on pressure, are in close agreement with most experimental data within their reported errors.

Phase transformation during aging and resulting mechanical properties of two Ti–Nb–Ta–Zr alloys

Phase transformations and mechanical properties of both Ti–29Nb–13Ta–4·6Zr and Ti–39Nb–13Ta–4·6Zr (wt–%) alloys were investigated. The microstructure of the 29Nb alloy is sensitive to solution and aging treatment. Ice water quenching from the solution treatment temperature resulted in (β+α") microstructure but air or furnace cooling led to a mixture of (β+ω). The formation of the orthorhombic α" martensite thus suppresses ω formation in the ice water quenched 29Nb alloy. Cooling rate from the solution treatment temperature also has a significant effect on the formation of α and ω phases during subsequent isothermal aging below the ω start temperature: slow cooling enhances ω but depresses α formation. This cooling rate dependence of aged microstructure was attributed to α" martensite acting as precursor of the α phase, thus providing a low energy path to the precipitation of a at the expense of ω. Phase transformation in the 39Nb alloy is more sluggish than that in the 29Nb alloy, owing to the presence of the higher content of β stabiliser Nb. For the 29Nb alloy, Young's modulus and mechanical properties are sensitive to the fraction of phases, and change significantly during aging, in contrast with the 39Nb alloy.

Stabilization of Cylindrical N12 and N18 by Phosphorus Substitution.

Molecules consisting entirely or predominantly of nitrogen are the subject of much research for their potential as high energy density materials (HEDM). The problem with many such HEDM candidates is their instability with respect to dissociation. For example, a low-energy dissociation path has been shown for a cylindrical cage isomer of N12. The instability is at least partially due to the ease of ring opening at triangles on either end of the molecule. In the current study, nitrogen cage molecules are examined to determine the stabilizing effect of substituting the triangle nitrogens with an element that more naturally forms triangles, namely phosphorus, which is valence isoelectronic with nitrogen. The cylindrical N12, and a larger analogue N18, form the structural basis for cage molecules of N6P6 and N12P6. Theoretical calculations using Hartree-Fock theory and perturbation theory (MP2 and MP4), along with the correlation-consistent basis sets of Dunning, have been carried out to determine dissociation energies along various pathways. The energies are discussed in terms of low-energy dissociation and the ability of the molecules to resist dissociation.

Theoretical study of the reactivity of X( 3P) (X=Ge, Sn, Pb) with N 2O(X 1Σ)

The reactivity of X( 3P) (X=Ge, Sn, Pb) with N 2O(X 1Σ) on both singlet and triplet potential energy surfaces have been investigated at the B3LYP level of theory. To accurately evaluate the activation barrier and reaction energy, the coupled cluster single point calculations using the B3LYP structures is performed. The calculated results are in good agreement with experimental observations. The X ( P 3 ) + N 2 O ( X 1 Σ ) → XO ( X 1 Σ ) + N 2 ( X 1 Σ g + ) (X=Ge, Sn, and Pb) reactions that Arthur Fontijn has been observed are spin-forbidden for formation of ground state products in the experiments. The present paper is discussed with the aid of the direct abstraction (DA) mechanism (also called the surface crossing model), a correlation argument based on separated fragments X+O+N 2 can explain the inefficiency of the X ( P 3 ) + N 2 O ( X 1 Σ ) → XO ( X 1 Σ ) + N 2 ( X 1 Σ g + ) (X=Ge, Sn, and Pb) reactions at 298 K by the need to switch electron configurations along low-energy adiabatic paths from ground-state reactants to energetically accessible XO ( X 1 Σ ) + N 2 ( X 1 Σ g + ) product states.

Ab initio kinetic study on the low-energy paths of the HO + C 2H 4 reaction

The low-energy paths for the reaction of HO with C 2H 4 have been studied at the PMP2/aug-cc-PVQZ//MP2/cc-PVTZ level of theory. The rate constants for the production of C 2H 4OH, CH 2CHOH + H and C 2H 3 + H 2O calculated with variational RRKM theory indicated that below 500 K, the formation of C 2H 4OH ( k 1) via an OH ⋯ π complex with 1.9 kcal/mol binding energy is the major product channel exhibiting a negative-temperature dependence; between 800 and 1000 K, the formation of CH 2CHOH + H ( k 2) and C 2H 3 + H 2O ( k 3) becomes competitive; at T > 1000 K, k 3 becomes dominant. k 1 was found to be strongly affected by multiple reflections above the well of the OH ⋯ π complex. The predicted results are in close agreement with available experimental data.

β-Lactone Synthesis from Epoxide and CO: Reaction Mechanism Revisited

The formation of β-lactone from epoxide and CO catalyzed by CoCO4- has been studied using a novel ab initio molecular dynamics approach. Employing the so-called metadynamics methodology, we show that it is possible to unravel the reaction mechanism of the catalyzed lactone formation in a fairly unbiased way. We were able to reproduce all the elementary steps within relatively short simulation time: the epoxide opening, the CO insertion, the CO addition to the Co site, the lactone ring formation, and the product dissociation, as obtained in previous static calculations. In addition, the simulations revealed that the lowest energy path goes through a stable intermediate featuring a metalla-oxo-furanyl ring. The simulations also indicated a new, higher energy path, in which the lactone ring formation precedes the CO uptake of the Co center. We show that this route becomes competitive when the Lewis acid attached to the lactone oxygen is softer.