Electrostatic Energy Difference Research Articles

Pd/Xu-Phos-catalyzed asymmetric elimination of fully substituted enol triflates into axially chiral trisubstituted allenes.

The β-H elimination, as one of the most important elementary reactions in transition metal chemistry, is a key step in quenching the carbon-palladium bond for the Heck reaction. However, the β-H elimination of the alkenyl palladium species leading to allene is an energetically unfavored process, and therefore, it has been a long-standing challenge in control of this process via enantioselective manner. We developed a concise and efficient methodology to construct trisubstituted chiral allenes from stereodefined fully substituted enol triflates by the enantioselective β-H elimination of the alkenyl palladium species under mild conditions. The identified Xu-Phos play a crucial role in the chemoselectivity and enantioselectivity. Multiple linear regression analysis shows the important steric effect on enantioselectivity. DFT computation results allow us to propose an intramolecular base (-OAc)-assisted deprotonation mechanism for this progress. Distortion-interaction and energy decomposition analysis indicate that the difference in electrostatic energy (Eelec) of the two intramolecular base-assisted deprotonation transition states dominates the stereoselectivity.

Cation Size Mismatch and Charge Interactions Drive Dopant Segregation at the Surfaces of Manganite Perovskites

Cation segregation on perovskite oxide surfaces affects vastly the oxygen reduction activity and stability of solid oxide fuel cell (SOFC) cathodes. A unified theory that explains the physical origins of this phenomenon is therefore needed for designing cathode materials with optimal surface chemistry. We quantitatively assessed the elastic and electrostatic interactions of the dopant with the surrounding lattice as the key driving forces for segregation on model perovskite compounds, LnMnO3 (host cation Ln = La, Sm). Our approach combines surface chemical analysis with X-ray photoelectron and Auger electron spectroscopy on model dense thin films and computational analysis with density functional theory (DFT) calculations and analytical models. Elastic energy differences were systematically induced in the system by varying the radius of the selected dopants (Ca, Sr, Ba) with respect to the host cations (La, Sm) while retaining the same charge state. Electrostatic energy differences were introduced by varying the distribution of charged oxygen and cation vacancies in our models. Varying the oxygen chemical potential in our experiments induced changes in both the elastic energy and electrostatic interactions. Our results quantitatively demonstrate that the mechanism of dopant segregation on perovskite oxides includes both the elastic and electrostatic energy contributions. A smaller size mismatch between the host and dopant cations and a chemically expanded lattice were found to reduce the segregation level of the dopant and to enable more stable cathode surfaces. Ca-doped LaMnO3 was found to have the most stable surface composition with the least cation segregation among the compositions surveyed. The diffusion kinetics of the larger dopants, Ba and Sr, was found to be slower and can kinetically trap the segregation at reduced temperatures despite the larger elastic energy driving force. Lastly, scanning probe image contrast showed that the surface chemical heterogeneities made of dopant oxides upon segregation were electronically insulating. The consistency between the results obtained from experiments, DFT calculations, and analytical theory in this work provides a predictive capability to tailor the cathode surface compositions for high-performance SOFCs.

Novel Design for Quantum Dots Cellular Automata to Obtain Fault-Tolerant Majority Gate

Quantum-dot Cellular Automata (QCA) is one of the most attractive technologies for computing at nanoscale. The principle element in QCA is majority gate. In this paper, fault-tolerance properties of the majority gate is analyzed. This component is suitable for designing fault-tolerant QCA circuits. We analyze fault-tolerance properties of three-input majority gate in terms of misalignment, missing, and dislocation cells. In order to verify the functionality of the proposed component some physical proofs using kink energy (the difference in electrostatic energy between the two polarization states) and computer simulations using QCA Designer tool are provided. Our results clearly demonstrate that the redundant version of the majority gate is more robust than the standard style for this gate.

New version of the theoretical databank of transferable aspherical pseudoatoms, UBDB2011 – towards nucleic acid modelling

The theoretical databank of aspherical pseudoatoms (UBDB) was recently extended with over 100 new atom types present in RNA, DNA and in some other molecules of great importance in biology and pharmacy. The atom-type definitions were modified and new atom keys added to provide a more precise description of the atomic charge-density distribution. X-H bond lengths were updated according to recent neutron diffraction studies and implemented in the LSDB program as well as used for modelling the appropriate atom types. The UBDB2011 databank was extensively tested. Electrostatic interaction energies calculated on the basis of the databank of aspherical atom models were compared with the corresponding results obtained directly from wavefunctions at the same level of theory (SPDFG/B3LYP/6-31G** and SPDFG/B3LYP/aug-cc-pVDZ). Various small complexes were analysed to cover most of the different interaction types, i.e. adenine-thymine and guanine-cytosine with hydrogen bonding, guanine-adenine with stacking contacts, and a group of neutral and charged species of nucleic acid bases interacting with amino acid side chains. The energy trends are well preserved (R(2) > 0.9); however the energy values differ between the two methods by about 4 kcal mol(-1) (1 kcal mol(-1) = 4.184 kJ mol(-1)) on average. What is noticeable is that the replacement of one basis set by another in a purely quantum chemical approach leads to the same electrostatic energy difference, i.e. of about 4 kcal mol(-1) in magnitude. The present work opens up the possibility of applying the UBDB2011 for macromolecules that contain DNA/RNA fragments. This study shows that on the basis of the UBDB2011 databank electrostatic interaction energies can be estimated and structure refinements carried out. However, some method limitations are apparent.

Developing hybrid approaches to predict pKavalues of ionizable groups

Accurate predictions of pKa values of titratable groups require taking into account all relevant processes associated with the ionization/deionization. Frequently, however, the ionization does not involve significant structural changes and the dominating effects are purely electrostatic in origin allowing accurate predictions to be made based on the electrostatic energy difference between ionized and neutral forms alone using a static structure and the subtle structural changes be accounted by using dielectric constant larger than two. On another hand, if the change of the charge state is accompanied by a large structural reorganization of the target protein, then the relevant conformational changes have to be explicitly taken into account in the pKa calculations. Here we report a hybrid approach that first predicts the titratable groups whose ionization is expected to cause large conformational changes, termed "problematic" residues, and then applies a special protocol on them, while the rest of the pK(a)s are predicted with rigid backbone approach as implemented in multi-conformation continuum electrostatics (MCCE) method. The backbone representative conformations for "problematic" groups are generated with either molecular dynamics simulations with charged and uncharged amino acid or with ab-initio local segment modeling. The corresponding ensembles are then used to calculate the titration curves of the "problematic" residues and then the results are averaged to obtain the corresponding pKa.

Light-induced Hydrogen Bonding Pattern and Driving Force of Electron Transfer in AppA BLUF Domain Photoreceptor

The AppA BLUF (blue light sensing using FAD) domain from Rhodobacter sphaeroides serves as a blue light-sensing photoreceptor. The charge separation process between Tyr-21 and flavin plays an important role in the light signaling state by transforming the dark state conformation to the light state one. By solving the linearized Poisson-Boltzmann equation, I calculated E(m) for Tyr-21, flavin, and redox-active Trp-104 and revealed the electron transfer (ET) driving energy. Rotation of the Gln-63 side chain that converts protein conformation from the dark state to the light state is responsible for the decrease of 150 mV in E(m) for Tyr-21, leading to the significantly larger ET driving energy in the light state conformation. The pK(a) values of protonation for flavin anions are essentially the same in both dark and light state crystal structures. In contrast to the ET via Tyr-21, formation of the W state results in generation of only the dark state conformation (even if the initial conformation is in the light state); this could explain why Trp-104-mediated ET deactivates the light-sensing yield and why the activity of W104A mutant is similar to that of the light-adapted native BLUF.

Exploring the origin of the internal rotational barrier for molecules with one rotatable dihedral angle

Continuing our recent endeavor, we systematically investigate in this work the origin of internal rotational barriers for small molecules using the new energy partition scheme proposed recently by one of the authors [S. B. Liu, J. Chem. Phys. 126, 244103 (2007)], where the total electronic energy is decomposed into three independent components, steric, electrostatic, and fermionic quantum. Specifically, we focus in this work on six carbon, nitrogen, and oxygen containing hydrides, CH(3)CH(3), CH(3)NH(2), CH(3)OH, NH(2)NH(2), NH(2)OH, and H(2)O(2), with only one rotatable dihedral angle [angle]H-X-Y-H (X,Y=C,N,O). The relative contributions of the different energy components to the total energy difference as a function of the internal dihedral rotation will be considered. Both optimized-geometry (adiabatic) and fixed-geometry (vertical) differences are examined, as are the results from the conventional energy partition and natural bond orbital analysis. A wealth of strong linear relationships among the total energy difference and energy component differences for different systems have been observed but no universal relationship applicable to all systems for both cases has been discovered, indicating that even for simple systems such as these, there exists no omnipresent, unique interpretation on the nature and origin of the internal rotation barrier. Different energy components can be employed for different systems in the rationalization of the barrier height. Confirming that the two differences, adiabatic and vertical, are disparate in nature, we find that for the vertical case there is a unique linear relationship applicable to all the six molecules between the total energy difference and the sum of the kinetic and electrostatic energy differences. For the adiabatic case, it is the total potential energy difference that has been found to correlate well with the total energy difference except for ethane whose rotation barrier is dominated by the quantum effect.

Influence of the Protein Environment on the Redox Potentials of Flavodoxins from Clostridium beijerinckii

The flavin mononucleotide (FMN) quinones in flavodoxin have two characteristic redox potentials, namely, Em(FMNH./FMNH-) for the one-electron reduction of the protonated FMN (E1) and Em(FMN/FMNH.) for the proton-coupled one-electron reduction (E2). These redox potentials in native and mutant flavodoxins obtained from Clostridium beijerinckii were calculated by considering the protonation states of all titratable sites as well as the energy contributed at the pKa value of FMN during protonation at the N5 nitrogen (pKa(N5)). E1 is sensitive to the subtle differences in the protein environments in the proximity of FMN. The protein dielectric volume that prevents the solvation of charged FMN quinones is responsible for the downshift of 130-160 mV of the E1 values with respect to that in an aqueous solution. The influence of the negatively charged 5'-phosphate group of FMN quinone on E1 could result in a maximum shift of 90 mV. A dramatic difference of 130 mV in the calculated E2 values of FMN quinone of the native and G57T mutant flavodoxins is due to the difference in the pKa(N5) values. This is due to the difference in the influence exerted by the carbonyl group of the protein backbone at residue 57.

Effect of electrostatic energy on partitioning of proteins in aqueous two-phase systems

An attempt has been made to adopt a different approach to evaluate the effect of a protein’s charge on its partitioning behaviour in PEG/salt aqueous two-phase systems (ATPS). This has been done using a computer methodology (DelPhi) that allows the calculation of the electrostatic solvation energy that charged proteins present in a particular media such as aqueous polymer–salt systems. This calculation was done for the protein in each of the phases and a correlation was investigated that related the electrostatic energy difference of the protein in each of the phases and its partition coefficient in ATPS. Such correlation resulted in a statistical model that also included the effect of molecular weight and a shape factor at each particular pH. A global correlation which included the effect of pH was also found. All the correlations were statistically evaluated and gave good results.

Effect of electrostatic energy on partitioning of proteins in aqueous two-phase systems

An attempt has been made to adopt a different approach to evaluate the effect of a protein’s charge on its partitioning behaviour in PEG/salt aqueous two-phase systems (ATPS). This has been done using a computer methodology (DelPhi) that allows the calculation of the electrostatic solvation energy that charged proteins present in a particular media such as aqueous polymer–salt systems. This calculation was done for the protein in each of the phases and a correlation was investigated that related the electrostatic energy difference of the protein in each of the phases and its partition coefficient in ATPS. Such correlation resulted in a statistical model that also included the effect of molecular weight and a shape factor at each particular pH. A global correlation which included the effect of pH was also found. All the correlations were statistically evaluated and gave good results.

A model of VDAC structural rearrangement in the presence of a salt activity gradient

We have considered the structural transformations of a voltage dependent anion-selective channel (VDAC) known as `gating'. We analysed the redistribution of VDAC among its states. The difference in electrostatic energy between the trans-closed and cis-closed states of VDAC is shown to be the cause of changes in the voltage dependence of the gating in the presence of a salt activity gradient. The asymmetry in the voltage dependence of the open probability about zero millivolts was connected with the apparent location of the voltage sensor. The theory describes the experimental data satisfactorily and explains the nature of the shift of the probability curve as well as the differences found in the asymmetry of the curve for different salts.

Coupling of charge and proton movement in cytochrome c oxidase

In order to understand the protonmotive chemistry of terminal oxidases, we have explored the question of the degree to which the net charge of the reaction cycle intermediates is counterbalanced by the uptake of protons. This possibility for charge compensation by protonation originates in free energy considerations and the factors that control redox potentials (for a review see Ref. [1]). One of these is the difference in electrostatic energy between a reduced (with one net charge) and oxidised (with zero net charge) species, which can be expressed by the equation:

Accurate modeling of the intramolecular electrostatic energy of proteins

AbstractThe (ϕ, ψ) energy surface of blocked alanine (N‐acetyl–N′‐methyl alanineamide) was calculated at the Hartree‐Fock (HF)/6‐31G* level using ab initio molecular orbital theory. A collection of six electrostatic models was constructed, and the term electrostatic model was used to refer to (1) a set of atomic charge densities, each unable to deform with conformation; and (2) a rule for estimating the electrostatic interaction energy between a pair of atomic charge densities. In addition to two partial charge and three multipole electrostatic models, this collection includes one extremely detailed model, which we refer to as nonspherical CPK. For each of these six electrostatic models, parameters—in the form of partial charges, atomic multipoles, or generalized atomic densities—were calculated from the HF/6‐31G* wave functions whose energies define the ab initio energy surface. This calculation of parameters was complicated by a problem that was found to originate from the locking in of a set of atomic charge densities, each of which contains a small polarization‐induced deformation from its idealized unpolarized state. It was observed that the collective contribution of these small polarization‐induced deformations to electrostatic energy differences between conformations can become large relative to ab initio energy differences between conformations. For each of the six electrostatic models, this contribution was reduced by an averaging of atomic charge densities (or electrostatic energy surfaces) over a large collection of conformations. The ab initio energy surface was used as a target with respect to which relative accuracies were determined for the six electrostatic models. A collection of 42 more complete molecular mechanics models was created by combining each of our six electrostatic models with a collection of seven models of repulsion + dispersion + intrinsic torsional energy, chosen to provide a representative sample of functional forms and parameter sets. A measure of distance was defined between model and ab initio energy surfaces; and distances were calculated for each of our 42 molecular mechanics models. For most of our 12 standard molecular mechanics models, the average error between model and ab initio energy surfaces is greater than 1.5 kcal/mol. This error is decreased by (1) careful treatment of the nonspherical nature of atomic charge densities, and (2) accurate representation of electrostatic interaction energies of types 1—2 and 1—3. This result suggests an electrostatic origin for at least part of the error between standard model and ab initio energy surfaces. Given the range of functional forms that is used by the current generation of protein potential functions, these errors cannot be corrected by compensating for errors in other energy components. © 1995 by John Wiley & Sons, Inc.

Active transport of ions across membranes: energetic role of electrostatics and binding site asymmetry

The active transport of ions across a membrane by an ATP-driven electrogenic ion pump is often described by an ‘alternate access’ model. The position of the binding site is assumed to be unchanged as the binding cavity opens alternatively to the uptake and discharge sides of the membrane. The ion binding affinity is higher on the uptake side of the membrane than on the discharge side. This difference in affinities is related to the maximum transport rate and to the efficiency with which ATP hydrolysis is coupled to active transport. Here we examine the electrostatic contribution to binding affinities, using a simple geometry for a model membrane-protein system, a continuum dielectric approximation, and a numerical method to calculate binding energy as a function of the binding site location. If the binding site is located asymmetrically, being further from the uptake side of the membrane than from the discharge side, there is a significant difference in binding free energy between the uptake and discharge states. This asymmetry can produce differences in affinities that are consistent with those measured for biological active transport systems. These results may account for the observed asymmetric location of the calcium binding site in the calcium ATPases from sarcoplasmic reticulum and from the plasma membrane. Electrostatic energy differences associated with binding site asymmetry may be a general feature of electrogenic transmembrane ion pumps.

First-principles electronic structure calculations for incommensurately modulated calaverite

Fully relativistic first-principles electronic structure calculations of both the average structure and a supercell approximation of silver-free incommensurately modulated calaverite (AuTe2) are presented. The differences between the results of both calculations are relatively small for the occupation numbers and the density of states, but quite dramatic for the shape of the Fermi surface. From the occupation numbers it is concluded that a previously proposed idea for explaining the modulation, based on mixed valencies for the gold atoms, is probably not applicable. The calculated Fermi surface of the average structure shows that the modulation cannot be understood in terms of Fermi-surface nesting either. The density of states in the supercell approximation compares very favourably with recently obtained X-ray photoelectron spectroscopy data. A rigid-potential calculation shows that the integral of the one-electron valence energies for the supercell is substantially more negative than the corresponding energy for the average structure, while the electrostatic energy difference has the opposite sign but is much smaller. This provides a qualitative indication of the electronic instability of the average structure with respect to the modulation of the supercell. Finally the authors conclude that Te s-like states a (Te p-Au d)-like complex dominate the energetics of the modulation.

Destabilization of an alpha-helix-bundle protein by helix dipoles.

The finite difference Poisson-Boltzmann method is used to calculate the electrostatic work of assembling the four alpha-helices of Themiste dyscritum hemerythrin to form the protein's observed antiparallel helical bundle. The calculations account for the interaction of each helix dipole with the high-dielectric solvent as well as for pairwise interactions of the dipoles with each other. We find that the electrostatic work of assembly is dominated by unfavorable changes in dipole-solvent interactions rather than by favorable interactions between antiparallel helices. Furthermore, the electrostatic energy difference between the observed arrangement of helices in hemerythrin and at least one other possible helical arrangement is less than 1 kT. These results suggest that the helix dipole actually destabilizes the helical bundle and that it plays little or no role in producing the observed bundle geometry.

Wannier-Stark quantization in semiconductor superlattices

We report on some electronic features displayed by semiconductor superlattices subjected to a static electric field applied parallel to the growth axis. When the electrostatic energy difference eFd across one superlattice period d becomes comparable to the subband width, the tunnel coupling between consecutive wells is inhibited. In turn, the superlattice minibands are washed out and replaced by evenly spaced Wannier Stark ladders, while the corresponding eigenfunctions become tightly localized in space. Such changes imply an effective blue shift of the band to band absorption edge as well as the occurence in the intermediate field regime of satellite optical transitions which are oblique in real space and differ by ± eFd, ± 2 eFd,… from the main, vertical, ones. The in-plane dispersions of the valence energy levels are complicated but remain analyzable in terms of an interplay between the field-induced localization and resonances between different subbands belonging to adjacent wells.

ChemInform Abstract: THE ELECTROSTATIC TERM IN MOLECULAR MECHANICS: 1‐CHLORO‐4,4‐DIFLUOROCYCLOHEXANE AND THE CYCLIC ETHYLENE KETAL OF 4‐CHLOROCYCLOHEXANONE

Abstract The performance of the controversial point—dipole formula (“Jeans equation”) is examined through molecular mechanics calculations on two molecules that contain dipolar bonds, 8-chloro-1,4-dioxaspiro [4.5] decane and 1-chloro-4,4-difluorocyclohexane. A general analysis is given of the total point—dipole interaction within a molecule, in terms of the separate dipole—dipole interactions. It is concluded that the set of bond moments in a polar moiety should not be replaced in computations by the overall group moment, as is sometimes considered. It is also stressed that the difference in electrostatic energy between conformations does not account necessarily for the total energy difference: differences in steric strain should not be ignored.

The electrostatic term in molecular mechanics: 1-chloro-4,4-difluorocyclohexane and the cyclic ethylene ketal of 4-chlorocyclohexanone

The performance of the controversial point—dipole formula (“Jeans equation”) is examined through molecular mechanics calculations on two molecules that contain dipolar bonds, 8-chloro-1,4-dioxaspiro [4.5] decane and 1-chloro-4,4-difluorocyclohexane. A general analysis is given of the total point—dipole interaction within a molecule, in terms of the separate dipole—dipole interactions. It is concluded that the set of bond moments in a polar moiety should not be replaced in computations by the overall group moment, as is sometimes considered. It is also stressed that the difference in electrostatic energy between conformations does not account necessarily for the total energy difference: differences in steric strain should not be ignored.

Magnetothermal oscillations, Fermi surface, and band structure of lowest-stage nitric-acid—graphite intercalation compounds

Results on quantum magnetothermal oscillations in graphite acceptor compounds, ${\mathrm{C}}_{8s}$ (HN${\mathrm{O}}_{3}$) $s=2,3,4$ are presented, including de Haas-van Alphen frequencies and effective masses. The frequency spectrum is different for every stage. Combination frequencies are present in every case and are attributed to magnetic breakdown. The interpretation is based on and confirms the independent two-dimensional zone model of the graphite acceptor compounds. A combination of the band-structure calculation of Blinowski and Rigaux and the folding of these bands in the Brillouin zone of the intercalate compound is used. This gives good agreement for the Fermi surfaces and the effective masses. Numerical values are given for the band parameters. Extra parameters are introduced in order to explain the results. For the second stage a charge-transfer ratio of $f=0.6$ and a Fermi-level shift of 1.08 eV are found. For the third stage 99% of the excess charge is localized in the carbon layer adjacent to the intercalate. The electrostatic energy difference between this layer and the inner one is found to be $2\ensuremath{\epsilon}=1.4$ eV.