Transferability of some properties of localized molecular orbitals

The localized molecular orbitals of some related ten- and eighteen-electron systems have been studied. The transferability of the kinetic, self-interaction, Coulomb and exchange interaction energies on localized orbitals have been shown. The standard deviation of the kinetic and of the interaction energies (including exchange) are less than 2.5% except for lone pair orbitals of the oxygen atoms where the standard deviation is close to 4%.     

Organic polymers with indirect magnetic interaction caused by the symmetry of the elementary units

The magnetic properties of a class of 1-D π-systems having a frontier half-filled band of degenerate MOs localized within the elementary units (EU) were studied theoretically. The localization of the MOs is caused by the symmetry of the π-fragments which form the EUs. The localization and non-overlapping of the MOs results in vanishing of the direct (Hund) and the kinetic exchange interaction between the unpaired electrons. The indirect exchange of the unpaired electrons (spin-polarization exchange) occurs via the delocalized π-electrons in the filled energy bands. An approach allowing the calculation of the indirect exchange interaction is applied for a class of polymers having pyrene, azulene, and s-indacene as fragments of the EUs. © 1998 John Wiley & Sons, Inc. Int J Quant Chem 66 : 425–434, 1998     

Isotropic magnetic exchange between anisotropic Yb(III) ions. Study of Cs3Yb2Cl9 and Cs3Yb2Br9 crystals

Despite the prevalent belief about a strong anisotropy of the magnetic exchange in rare-earth compounds, Cs3Yb2Cl9 and Cs3Yb2Br9 crystals are found to exhibit fully isotropic exchange coupling between Yb3+ ions. In this article, we attempt to reveal the physical origin of this surprising feature. Our theoretical consideration is based on a model of the kinetic exchange between two octahedrally coordinated Yb3+ ions in their ground Kramers doublet states. It is shown that a mechanism of kinetic exchange involving intercenter electron hopping between 4f orbitals of two Yb3+ ions in a face-shared binuclear unit results in fully isotropic antiferromagnetic exchange coupling, while a mechanism in which the electron jumps from the 4f to the 5d orbital gives rise to a highly anisotropic interaction. Comparison of these results with the experimental data along with qualitative arguments regarding the relative significance of these two contributions to the overall exchange indicate that, in face-shared Yb3+ binuclear units, the 4f <--> 4f mechanism plays a dominant role.     

Atom-atom partitioning of total (super)molecular energy: the hidden terms of classical force fields

Classical force fields describe the interaction between atoms that are bonded or nonbonded via simple potential energy expressions. Their parameters are often determined by fitting to ab initio energies and electrostatic potentials. A direct quantum chemical guide to constructing a force field would be the atom-atom partitioning of the energy of molecules and van der Waals complexes relevant to the force field. The authors used the theory of quantum chemical topology to partition the energy of five systems [H2, CO, H2O, (H2O)2, and (HF)2] in terms of kinetic, Coulomb, and exchange intra-atomic and interatomic contributions. The authors monitored the variation of these contributions with changing bond length or angle. Current force fields focus only on interatomic interaction energies and assume that these purely potential energy terms are the only ones that govern structure and dynamics in atomistic simulations. Here the authors highlight the importance of self-energy terms (kinetic and intra-atomic Coulomb and exchange).     

Solid state catalytic tritiation: Isotopic exchange and tritium addition in high specific activity synthesis

Solid state catalytic saturation of double bond with hydrogen, deuterium and tritium is a valid route to incorporate selectively isotopes in specific positions. We studied the best fitting of all parameters that rule the radioactive yield of tritiation of an unsatured substrate, to guarantee the maximum incorporation of labeled atom in the product at room temperature. The wise choice of experimental parameters allowed very high radiochemical yields. The number of tritium exceeded the statistical presence of two atoms. Relative magnitudes for addition and exchange kinetic constants are provided.     

Deuterium exchange in the systems of H2O+/H2O and H3O+/H2O

The reactions of H₂O⁺, H₃O⁺, D₂O⁺, and D₃O⁺ with neutral H₂O and D₂O were studied by tandem mass spectrometry. The H₂O⁺ and D₂O⁺ ion reactions exhibited multiple channels, including charge transfer, proton transfer (or hydrogen atom abstraction), and isotopic exchange. The H₃O⁺ and D₃O⁺ ion reactions exhibited only isotope exchange. The variation in the abundances of all ions involved in the reactions was measured over a neutral pressure range from 0 to 2 × 10⁻⁵ Torr. A reaction scheme was chosen, which consisted of a sequence of charge transfer, proton transfer, and isotopic exchange reactions. Exact solutions to two groups of simultaneous differential equations were determined; one group started with the reaction of ionized water, and the other group started with the reactions of protonated water. A nonlinear least-squares regression technique was used to determine the rate coefficients of the individual reactions in the schemes from the ion abundance data. Branching ratios and relative rate coefficients were also determined in this manner.A delta chi-squared analysis of the results of the model fitted to the experimental data indicated that the kinetic information about the primary isotopic exchange processes is statistically the most significant. The errors in the derived values of the kinetic information of subsequent channels increased rapidly. Data from previously published selected ion flow tube (SIFT) study were analyzed in the same manner. Rigorous statistical analysis showed that the statistical isotope scrambling model was unable to explain either the SIFT or the tandem mass spectrometry data. This study shows that statistical analysis can be utilized to assess the validity of possible models in explaining experimentally observed kinetic behaviors.     

Synthetic analogs of active centers of iron-sulfur proteins: Reactions with phosphates

The interaction of synthetic analogs of active centers of iron-sulfur proteins with phosphates of different structures was studied. It was shown that the process involves ligand exchange and obeys the first-order reaction kinetic equation. The most rapid exchange occurred with the most acidic compound diphenyl phosphate.A. E. Arbuzov Institute of Organic and Physical Chemistry, Kazan' Scientific Center, Russian Academy of Sciences, 420083 Kazan'. Translated from Izvestiya Akademii Nauk, Seriya Khimicheskaya, No. 10, pp. 2301–2305, October, 1992.     

Statistical rate theory and kinetic energy-resolved ion chemistry: theory and applications

Ion chemistry, first discovered 100 years ago, has profitably been coupled with statistical rate theories, developed about 80 years ago and refined since. In this overview, the application of statistical rate theory to the analysis of kinetic-energy-dependent collision-induced dissociation (CID) reactions is reviewed. This procedure accounts for and quantifies the kinetic shifts that are observed as systems increase in size. The statistical approach developed allows straightforward extension to systems undergoing competitive or sequential dissociations. Such methods can also be applied to the reverse of the CID process, association reactions, as well as to quantitative analysis of ligand exchange processes. Examples of each of these types of reactions are provided and the literature surveyed for successful applications of this statistical approach to provide quantitative thermochemical information. Such applications include metal-ligand complexes, metal clusters, proton-bound complexes, organic intermediates, biological systems, saturated organometallic complexes, and hydrated and solvated species.     

Modulation of the thermodynamic, kinetic, and magnetic properties of the hydrogen monomer on graphene by charge doping

The thermodynamic, kinetic, and magnetic properties of the hydrogen monomer on doped graphene layers were studied by ab initio simulations. Electron doping heightens the diffusion potential barrier, while hole doping lowers it. However, both kinds of dopings heighten the desorption potential barrier. The underlying mechanism was revealed by investigating the effect of charge doping on the bond strength of graphene and on the electron transfer and the coulomb interaction between the hydrogen monomer and graphene. The kinetic properties of H and D monomers on doped graphene layers during both the annealing process (annealing time t(0) = 300 s) and the constant-rate heating process (heating rate α = 1.0 K/s) were simulated. Macroscopic diffusion of hydrogen monomers on graphene can be achieved when the doping-hole density reaches 5.0 × 10(13) cm(-2). Both electron and hole dopings linearly reduce the total magnetic moment and exchange splitting, which was explained by a simple exchange model. The laws found in this work had been generalized to explain many phenomena reported in literature. This study can further enhance the understanding of the interaction between hydrogen and graphene and was expected to be helpful in the design of hydrogenated-graphene-based devices.     

Kinetics and Mechanism of Bilirubin Oxidation by Benzoyl Peroxide in Dimethyl Sulfoxide

The kinetics of the redox reaction of bilirubin by the action of benzoyl peroxide in dimethyl sulfoxide was analyzed. It is shown that the first reaction product is biliverdin, which oxidizes to purpurin and further to choletelin. The kinetic and activation parameters of the oxidation reactions were obtained. A kinetic model of the process was proposed. An assumed route of the reaction is related to the exchange interaction of CH protons of methylene and methine spacers with free radicals in the rate‐limiting step with the further destruction of the “ridge‐tile” pigment conformation. The mechanism steps are confirmed by quantum‐chemical calculations and HPLC. It is found that in organic solvents the end products of bilirubin oxidation are not monopyrrolic derivatives. The data obtained will be useful in constructing antioxidant action models of the pigment.     

General theory of photochemical reaction kinetics. I. Quantum-statistical description

By methods of statistical mechanics a consistent derivation of photochemical kinetic equations has been carried out. The method of density matrix and projection operator formalism was used. A self-consistent set of kinetic equations describing the combined behaviour of field and medium under the conditions (1) interaction of field with optically active scribing the combined behavior of field and medium under the conditions of (I) interaction of field with optically active molecule transition, (2) chemical reaction in the medium, and (3) effects of relaxation processes caused by collisions has been obtained. These equations, unlike the balance equations widely used in photochemistry, correctly take into account the role of medium polarization in a photochemical process.     

Behavior of human serum albumin on strong cation exchange resins: I. Experimental analysis

Experiments with human serum albumin on the strong cation exchange resin Fractogel EMD SE Hicap (M) were carried out. Even though human serum albumin was used at high purity, two peaks in gradient elution experiments occurred. The obtained data can be explained by considering that human serum albumin binds to Fractogel EMD SE Hicap (M) in two different binding conformations: the protein adsorbs instantaneously in the first conformation and then changes into the second one with a kinetic limitation. The two-peak behavior of human serum albumin was analyzed in detail, especially at various gradient lengths, concentrations and temperatures. Breakthrough curves were performed at four modifier concentrations and three velocities. The characteristic adsorption behavior, found for gradient experiments, was confirmed by the breakthrough curves. The two-peak elution pattern of human serum albumin was also found for other strong cation exchange resins, but not for weak cation exchange resins. It is concluded that the described behavior is peculiar for the interaction of human serum albumin with the strong cation exchange ligand of the resin.     

Bimolecular reactions of vibrationally excited molecules. Roaming atom mechanism at low kinetic energies

Quasiclassical trajectory calculations have been performed for the H + H'X(v) → X + HH' abstraction and H + H'X(v) → XH + H' (X = Cl, F) exchange reactions of the vibrationally excited diatomic reactant at a wide collision energy range extending to ultracold temperatures. Vibrational excitation of the reactant increases the abstraction cross sections significantly. If the vibrational excitation is larger than the height of the potential barrier for reaction, the reactive cross sections diverge at very low collision energies, similarly to capture reactions. The divergence is quenched by rotational excitation but returns if the reactant rotates fast. The thermal rate coefficients for vibrationally excited reactants are very large, approach or exceed the gas kinetic limit because of the capture-type divergence at low collision energies. The Arrhenius activation energies assume small negative values at and below room temperature, if the vibrational quantum number is larger than 1 for HCl and larger than 3 for HF. The exchange reaction also exhibits capture-type divergence, but the rate coefficients are larger. Comparisons are presented between classical and quantum mechanical results at low collision energies. At low collision energies the importance of the exchange reaction is enhanced by a roaming atom mechanism, namely, collisions leading to H atom exchange but bypassing the exchange barrier. Such collisions probably have a large role under ultracold conditions. The calculations indicate that for roaming to occur, long-range attractive interaction and small relative kinetic energy in the chemical reaction at the first encounter are necessary, which ensures that the partners can not leave the attractive well. Large orbital angular momentum of the primary products (equivalent to large rotational excitation in a unimolecular reaction) is favorable for roaming.     

Numerical Methods for a Quantum Drift–diffusion Equation in Semiconductor Physics

We present the numerical methods and simulations used to solve a charge transport problem in semiconductor physics. The problem is described by a Wigner–Poisson kinetic system we have recently proposed and whose results are in good agreement with known experiments. In this model, we consider doped semiconductor superlattices in which electrons are supposed to occupy the lowest miniband, exchange of lateral momentum is ignored, the electron–electron interaction is treated in the Hartree approximation and elastic and inelastic collisions are taken into account. Nonlocal drift-diffusion equations derived systematically elsewhere from the hyperbolic limit of a kinetic Wigner–Poisson model are solved. The nonlocality of the original quantum kinetic model equations implies that the derived drift-diffusion equations contain spatial averages over one or more superlattice periods. Numerical methods are based upon prior knowledge on physical properties of the phenomenon and have shown to be effective in validating our formulation. Numerical solutions of the equations show self-sustained oscillations of the current through a voltage biased superlattice, in good agreement with known experiments.     

Features of EPR spectra of complexes of ortho-benzoquinones with Tl(I) and Tl(III) diethyldithiocarbamates

A study has been made of the EPR spectra of Tl(l) and Tl(III) o-semiquinolates, obtained by the interaction of o-benzoquinones with thallium amalgam and thallium(III) diethyldithiocarbamate, respectively. A strong temperature dependence has been found for the constant of hyperfine coupling (HFC) with the metal nucleus in thallium(III) 3,5-di-tert-butyl-o-semiquinolate; this is explained by the presence of competing mechanisms of spin transfer from the o-semiquinone ligand to the metal. Cation exchange and effective complexation of the Tl(I) o-semiquinolate with thallium diethyldithiocarbamate have been observed. The kinetic parameters of exchange have been determined.Translated from Izvestiya Akademii Nauk SSSR, Seriya Khimicheskaya, No. 4, pp. 786–790, April, 1990.     

Coupling of replica exchange simulations to a non-Boltzmann structure reservoir

Computing converged ensemble properties remains challenging for large biomolecules. Replica exchange molecular dynamics (REMD) can significantly increase the efficiency of conformational sampling by using high temperatures to escape kinetic traps. Several groups, including ours, introduced the idea of coupling replica exchange to a pre-converged, Boltzmann-populated reservoir, usually at a temperature higher than that of the highest temperature replica. This procedure reduces computational cost because the long simulation times needed for extensive sampling are only carried out for a single temperature. However, a weakness of the approach is that the Boltzmann-weighted reservoir can still be difficult to generate. We now present the idea of employing a non-Boltzmann reservoir, whose structures can be generated through more efficient conformational sampling methods. We demonstrate that the approach is rigorous and derive a correct statistical mechanical exchange criterion between the reservoir and the replicas that drives Boltzmann-weighted probabilities for the replicas. We test this approach on the trpzip2 peptide and demonstrate that the resulting thermal stability profile is essentially indistinguishable from that obtained using very long (>100 ns) standard REMD simulations. The convergence of this reservoir-aided REMD is significantly faster than for regular REMD. Furthermore, we demonstrate that modification of the exchange criterion is essential; REMD simulations using a standard exchange function with the non-Boltzmann reservoir produced incorrect results.     

Theoretical insights into the magnetostructural correlations in Mn3-based single-molecule magnets

Density functional theory (DFT) and the valence bond configuration interaction (VBCI) model have been applied to the oximato-based Mn(III)(3)O single-molecule magnets (SMMs), allowing one to correlate the Mn(III)-Mn(III) exchange coupling energy (J) with the bridging geometry in terms of two structural angles: the Mn-O-N-Mn torsion angle (γ) and the Mn(3) out-of-plane shift of O (angle δθ). Using DFT, a two-dimensional (γ, δθ) energy surface of J is derived and shown to yield essentially good agreement with the reported J values deduced from magnetic susceptibility data on trigonal oximato-bridged Mn(3) SMMs. VBCI is used to understand and analyze the DFT results. It is shown that the exchange coupling in these systems is governed by a spin-polarization mechanism inducing a pronounced and dominating ferromagnetic exchange via the oximato bridge as opposed to kinetic exchange, which favors a weaker and antiferromagnetic exchange via the bridging oxide. In the light of these results, a discussion of the exchange coupling in the Mn(6) family of the SMM with a record demagnetization barrier is given.     

Statistical evaporation of rotating clusters. III. Molecular clusters

Unimolecular evaporation of weakly bound clusters made of rigid molecules is considered from the points of view of statistical theories and molecular dynamics simulations. We explicitly work out expressions for the kinetic energy released and product angular momentum distributions within the sphere+sphere and sphere+linear rigid body assumptions of phase space theory (PST). Various approximations are investigated, including the shape of the interaction potential between the two fragments and the anharmonicity of the vibrational density of states. The comparison between phase space theory and simulation for nitrogen and methane clusters shows a quantitative agreement, thereby suggesting that PST is accurate in predicting statistical observables in a wide range of systems under various physical conditions.     

Computer simulations of solute exchange using micelles by a collision-driven fusion process

In this work, the kinetic process of collision-driven solute exchange in an aqueous phase in which micelles are used as solute carriers is investigated by dissipative particle dynamics simulations. Here, we try to answer two questions about the exchange process of hydrophobic solute molecules: How the solute molecules are exchanged and what factors affect the process. For the first question, the simulation results indicate that, after a stage of intermittent collision between two neighboring aggregates, there are roughly three sequential events in a coalescence stage: (1) molecular contact, (2) neck formation, and (3) neck growth. The coalescence stage is followed by a stage of solute transfer and diffusion. It is found that there are two rate-limiting steps in the whole process of solute exchange, i.e., the break of the water film between two neighboring aggregates and the nucleation of a pore between two surfactant films. For the second question, the effects of the collision velocity, the surface tension, the repulsive interaction between the surfactant films of the colliding aggregates, as well as the steric repulsion are examined. For example, the simulation results show that the depletion force plays an important role during the coalescence stage, while the initial collision velocity basically does not change the fusion ratio. The results also demonstrate that the surface tension and interaction show different effects on the different stages of a solute exchange process.