Nonempirical Modeling Research Articles

Undulating Potentials of Rydberg Σ+-States of Me–Rg Molecules: NonEmpirical Modeling of the Na–He Exciplex

Undulating Potentials of Rydberg Σ+-States of Me–Rg Molecules: NonEmpirical Modeling of the Na–He Exciplex

Frequency-dependent shear wave attenuation across the Central Anatolia region, Türkiye

Abstract. The Central Anatolian Plateau with its volcanic provinces represents a broad transition zone between the compressional deformation in the east and the extensional regime in the west. The Central Anatolian Fault Zone separates the Kırşehir Block in the north and the Anatolide–Tauride Block in the south within the plateau. A proper understanding of physical properties such as seismic attenuation in the crustal volume of this region can provide hints toward the possible source for the geodynamic events in the past and present that likely lead to the observed deformation. In order to model intrinsic and scattering attenuation separately, we perform a nonempirical coda-wave modeling approach in which a fitting process between observed and synthetic coda-wave envelopes is performed for each earthquake in multiple frequency bands. Here, the acoustic radiative transfer theory, assuming multiple isotropic scattering, was utilized for the forward modeling of the synthetic coda-wave envelopes of local earthquakes. Our findings generally highlight the prominent nature of intrinsic attenuation over scattering attenuation, implying the presence of thick volcanic rocks with relatively high attenuation values beneath Central Anatolia. Overall, the spatial distribution of the attenuation at varying frequencies marks the Kırşehir Massif distinctively with its considerable high-attenuating character. Our findings, combined with early seismological and geo-electrical models, suggest a possible partial melt beneath most of the Central Anatolian Volcanic Province, and the resultant zones of elevated fluid-rich content exhibit high and dominant intrinsic attenuation. To the southeast, a gradual decrease in the observed attenuation coincides with the Central Taurus Mountains where high altitude is considered to be evolved following the slab break-off and resulting mantle upwelling.

Nonempirical Modeling of Interactions of Fe2O2 and Fe2O4 Clusters with H2 and O2 Molecules

Quantum-chemical calculations of the geometric and electronic structures of compounds formed by the interaction of Fe2O2 and Fe2O4 clusters with diatomic H2 and O2 molecules in the gas phase have been performed by the density functional theory method in the generalized gradient approximation using the triple-zeta basis set. The trends in changes in the binding energy of H2 and O2 molecules with Fe2O2 and Fe2O4 clusters depending on the number of oxygen atoms have been found. It has been demonstrated that in two of the four reactions considered, the total spins of the initial reagents and final products do not coincide, that is, spin relaxation occurs. It has been concluded that nanoparticles based on Fe2O4 clusters can be used as sensors for detecting H2 and O2 molecules.

Nonempirical Modeling of Interactions of Fe2O2 and Fe2O4 Clusters with H2 and O2 Molecules

Nonempirical Modeling of Interactions of Fe2O2 and Fe2O4 Clusters with H2 and O2 Molecules

Nonempirical modeling of protolytic processes in dimeric molecules of amino acids

Nonempirical modeling of protolytic processes in dimeric molecules of amino acids

Vertical excitation energies from the adiabatic connection.

Vertical single-particle excitations from closed-shell ground states are complicated by the fact that the singlet open-shell states are, even in the first approximation, two-determinantal. Thus two-electron integrals come into play and standard time-independent DFT (density-functional theory) does not apply. In this work, we use the "adiabatic connection" to analyse the role of the two-electron integrals, obtaining a time-independent DFT approach to excitation-energy calculations that is new and simple. A non-empirical modeling of the method works as well as the popular TD-B3LYP time-dependent approach to excited states, and can be made even simpler by introducing one reasonable semi-empirical parameter.

Consistent transfer of protons in molecular rings of water: Origination of H3O+ and OH– ions

For the first time, nonempirical modeling of water clusters composed of several fused molecular rings supplemented with the theoretical analysis of quantum states of the systems provided grounds for clarifying the conditions when consistent shifts of bridge protons within one structural ring promoted by the contraction of the oxygen skeleton can repeatedly cause the formation of H3O+ and OH– ions.

Kinetics and mechanism of inhibition of serine esterases by fluorinated aminophosphonates

This paper reviews previously published data and presents new results to address the hypothesis that fluorinated aminophosphonates (FAPs), (RO) 2P(O)C(CF 3) 2NHS(O) 2C 6H 5, R = alkyl, inhibit serine esterases by scission of the P–C bond. Kinetics studies demonstrated that FAPs are progressive irreversible inhibitors of acetylcholinesterase (AChE, EC 3.1.1.7.), butyrylcholinesterase (BChE, EC 3.1.1.8.), carboxylesterase (CaE, EC 3.1.1.1.), and neuropathy target esterase (NTE, EC 3.1.1.5.), consistent with P–C bond breakage. Chemical reactivity experiments showed that diMe-FAP and diEt-FAP react with water to yield the corresponding dialkylphosphates and (CF 3) 2CHNHS(O) 2C 6H 5, indicating lability of the P–C bond. X-ray crystallography of diEt-FAP revealed an elongated (and therefore weaker) P–C bond (1.8797 (13) Å) compared to P–C bonds in dialkylphosphonates lacking α-CF 3 groups (1.805–1.822 Å). Semi-empirical and non-empirical molecular modeling of diEt-FAP and (EtO) 2P(O)C(CH 3) 2NHS(O) 2C 6H 5 (diEt-AP), which lacks CF 3 groups, indicated lengthening and destabilization of the P–C bond in diEt-FAP compared to diEt-AP. Active site peptide adducts formed by reacting diEt-FAP with BChE and diBu-FAP with NTE catalytic domain (NEST) were identified using peptide mass mapping with mass spectrometry (MS). Mass shifts (mean ± SE, average mass) for peaks corresponding to active site peptides with diethylphosphoryl and monoethylphosphoryl adducts on BChE were 136.1 ± 0.1 and 108.0 ± 0.1 Da, respectively. Corresponding mass shifts for dibutylphosphoryl and monobutylphosphoryl adducts on NEST were 191.8 ± 0.2 and 135.5 ± 0.1 Da, respectively. Each of these values was statistically identical to the theoretical mass shift for each dialkylphosphoryl and monoalkylphosphoryl species. The MS results demonstrate that inhibition of BChE and NEST by FAPs yields dialkylphosphoryl and monoalkylphosphoryl adducts, consistent with phosphorylation via P–C bond cleavage and aging by net dealkylation. Taken together, predictions from enzyme kinetics, chemical reactivity, X-ray crystallography, and molecular modeling were confirmed by MS and support the hypothesis that FAPs inhibit serine esterases via scission of the P–C bond.

Correlation energy of finite two-dimensional systems: Toward nonempirical and universal modeling

The capability of density-functional theory to deal with the ground state of strongly correlated low-dimensional systems, such as semiconductor quantum dots, depends on the accuracy of functionals developed for the exchange and correlation energies. Here we extend a successful approximation for the correlation energy of the three-dimensional inhomogeneous electron gas, originally introduced by Becke [J. Chem. Phys. 88, 1053 (1988)], to the two-dimensional case. The approach is based on nonempirical modeling of the correlation-hole functions satisfying a set of exact properties. Furthermore, the electron current and spin are explicitly taken into account. As a result, good performance is obtained in comparison with numerically exact data for quantum dots with varying external magnetic field, and for the homogeneous two-dimensional electron gas, respectively.

Resonant Capture of Low-Energy Electrons by Gas-Phase Glycine: A Quantum Dynamics Calculation

We present quantum calculations for the low-energy dynamics of electrons interacting with glycine molecules in the gas phase. The scattering equations are formulated within a symmetry-adapted, single-center expansion of both continuum and bound electrons, and the interaction forces are obtained from a combination of ab initio calculations and a nonempirical modeling of exchange plus correlation effects. Several open-channel (shape) resonances are obtained, and the features of the excess electron resonant wave functions are related to the experimental findings about the dissociative electron attachment (DEA) processes that follow the initial formation of those transient negative ions.

Low-energy electron scattering by cubane: resonant states and Ramsauer-Townsend features from quantum calculations in the gas phase.

Calculations are carried out, using a nonempirical modeling of the interaction potential and solving the quantum scattering coupled channel equations, for low energy electron scattering from cubane (C8H8) molecules in the gas phase. Total integral cross sections are obtained and partial contributions are analyzed for the most important irreducible representations that describe the continuum electron in the Oh molecular symmetry. Several trapping resonances are found and analyzed in terms of the molecular-type features of the resonant electron states associated with them. A Ramsauer-Townsend minimum is also found and its possible behavior related to features of the scattering length as k --> 0.

Nonempirical simulations of boron interstitials in tungsten

Formation of W–B solid solutions for different concentrations of boron is studied within nonempirical modeling. We consider ordering tendencies, study electronic structure and provide total energy calculations on the basis of coherent potential approximation. We also study an equilibrium structure of a lattice with Σ 3 〈1 1 1〉 grain boundary in pure tungsten and in tungsten-based solid solution with boron additives. We used simulated annealing methods in atomistic simulations to obtain relaxed configurations of the lattice in the vicinity of grain boundary.

Computational investigation of positron scattering fromC60

The low-energy (0\char21{}6-eV) behavior of positrons scattering from gaseous ${\mathrm{C}}_{60}$ molecules is examined through a computational study which employs a nonempirical modeling of all the relevant interaction forces (static, correlation, and polarization potentials). There is uncertainty concerning the most appropriate correlation-polarization potential to use in the study of positron-molecule scattering. Here we have considered two such potentials which are representative of the potentials which have been proposed for this purpose. The coupled quantum scattering equations are solved in the body-fixed frame of reference, and the fixed-nuclei approximation is used to decouple the nuclear motion during the collision. The elastic integral cross sections without positronium formation exhibit strong one-particle resonances in the very-low-energy region up to $\ensuremath{\sim}4$ eV. The low-angular-momentum scattering components are shown to be the dominant contributions to trapped state wave functions. The existence of resonances in positron scattering from molecules is unusual. In the system studied here there are two types of resonances. First there are angular-momentum barrier resonances with the positron trapped outside of the ${\mathrm{C}}_{60}$ cage. Second, there are resonances of low angular momentum $(ll~2)$ with the positron trapped inside of the ${\mathrm{C}}_{60}$ cage by the repulsive interaction between the positron and the nuclei. The possibility of the experimental observation of these resonances is also discussed.

Cumulative atomic multipole moments for molecular crystals fromab-initio crystal orbital wave functions and for molecules in excited states fromab-initio MRD-CI wave functions

Compact representation of molecular charge distribution in molecular crystals has been derived from ab-initio crystal orbital wavefunction within the framework of cumulative atomic multipole moment (CAMM) expansion. Results for HF, CO2, and cubane C8H8 crystals have been compared with values calculated for corresponding clusters within conventional LCAO MO SCF approach. CAMM technique has also been used to represent molecular charge distribution in electronic excited states using CI wavefunction obtained from multireference configuration interaction (MRD-CI) calculations. This approach supplements previously introduced uncorrelated and correlated CAMM's and allows accurate nonempirical modeling of electrostatic effects involving molecules in excited states or in crystalline environment. Improved point charge model derived from CAMM has been also described.

Nonempirical modeling of the static and dynamic properties of the optimum environment for chemical reactions

The previously proposed approach which allows nonempirical modeling of static properties of the optimal catalyst* has been extended to predict the optimal dynamics of the molecular environment of chemical reactions. This approach was applied here to characterize the optimal static and dynamic environment charge configuration for the reactions: HCN → HNC, HNC → HCN, BCN → BNC, BNC → BCN, F − + CH 3F → FCH 3 + F − and CO 2 + H 2O → H 2CO 3.