On the appearance of carboxylates in electrostatic potential maps

Electron microscopy can provide accurate, high‐resolution images of the distribution of electrostatic potential (ESP) in biological macromolecules. Careful examination of ESP maps that have been published for peptides and proteins at resolution ranging from 1.0 Å to 2.9 Å reveals that the negative charges of carboxylate groups have a profound effect on their appearance. It is clear that investigators must take the negative features in their experimental ESP maps into account when modeling the conformations of Asp and Glu side chains and those of the residues that surround them.     

Determination of chemical identity and occupancy from experimental density maps

Three basic electronic properties of molecules, electron density (ED), charge density (CD), and electrostatic potentials (ESP), are dependent on both atomic mobility and occupancy of components in the molecules. Small protein subunits may bind large macromolecular complexes with a reduced occupancy or an increased atomic mobility or both due to affinity‐based functional regulation, and so may substrates, products, cofactors, ions or solvent molecule to the active sites of enzymes. A quantitative theory is presented in this study that describes the dependence of atomic functions on atomic B‐factor in Fourier transforms of the corresponding maps. An application of this theory is described to an experimental ED map at 1.73‐Å resolution, and to an experimental CD map at 2.2‐Å resolution. All the three density functions are linearly proportional to occupancy when the structure factor F(000) term of Fourier transforms of experimental density maps is included. Upon application of this theory to both experimental CD and ESP maps recently reported for photosystem II‐light harvesting complex II supercomplex at 3.2‐Å resolution, the occupancy of two extrinsic protein subunits PsbQ and PsbP is determined to be 20.4 ± 0.2%, and the negative mean ESP value of vitreous ice displaced by the supercomplex on electron scattering path is estimated to be 3% of the mean ESP value of protein α‐helices.     

On contribution of known atomic partial charges of protein backbone in electrostatic potential density maps

Partial charges of atoms in a molecule and electrostatic potential (ESP) density for that molecule are known to bear a strong correlation. In order to generate a set of point‐field force field parameters for molecular dynamics, Kollman and coworkers have extracted atomic partial charges for each of all 20 amino acids using restrained partial charge‐fitting procedures from theoretical ESP density obtained from condensed‐state quantum mechanics. The magnitude of atomic partial charges for neutral peptide backbone they have obtained is similar to that of partial atomic charges for ionized carboxylate side chain atoms. In this study, the effect of these known atomic partial charges on ESP is examined using computer simulations and compared with the experimental ESP density recently obtained for proteins using electron microscopy. It is found that the observed ESP density maps are most consistent with the simulations that include atomic partial charges of protein backbone. Therefore, atomic partial charges are integral part of atomic properties in protein molecules and should be included in model refinement.     

Effects of aligned α‐helix peptide dipoles on experimental electrostatic potentials

Aligned protein α‐helix dipoles have been implicated in protein function and structure. The recent breakthroughs in high‐resolution electron microscopy (EM) of macromolecules makes it possible to explore fundamental aspects of structural biology at the detailed molecular level. The electrostatic potential (ESP) generated by aligned protein α‐helix dipole should be observable in high‐resolution EM maps despite the fact that the effect may be partially screened by induced electric fields. Here, we show that aligned backbone dipoles in protein α‐helices account for long‐range features in the protein ESP functions. Our results are consistent with experimental EM maps and density functional theory calculations, including direct Fourier summation for proper calculation of the ESP due to the nonlocal nature of the ESP function from aligned dipoles and other partial atomic charges.     

Extraordinary Thermal Stability of an Oligodeoxynucleotide Octamer Constructed from Alternating 7‐Deaza‐7‐iodo guanine and 5‐Iodocytosine Base Pairs – DNA Duplex Stabilization by Halogen Bonds?

A reinvestigation of the published X‐ray crystal‐structure analyses of 7‐halogenated (Br, I) 8‐aza‐7‐deaza‐2′‐deoxyguanosines Br⁷c⁷z⁸G_d; 1a and I⁷c⁷z⁸G_d, 1b , as well as of the structurally related 7‐deaza‐7‐iodo‐2′‐deoxy‐β‐D ‐ribofuranosyladenine (β‐I⁷c⁷A_d; 2 = 6e in Table 1) and its α‐D ‐anomer (α‐I⁷c⁷A_d; 3 ) clearly revealed the existence of halogen bonds between corresponding halogen substituents and the adjacent N(3)‐atoms of neighboring nucleoside molecules within the single crystals. These halogen bonds can be rationalized by the presence of a region of positive electrostatic potential, the σ‐hole, on the outermost portion the halogen's surface, while the three unshared pairs of electrons produce a belt of negative electrostatic potential around the central part of the halogen substituent. The N(3) atoms of the halogenated nucleosides carry a partial negative charge. This novel type of bonding between nucleosides was tentatively used to explain the extraordinary high stability of oligodeoxynucleotides constructed from halogenated nucleotide building blocks.     

Spatial electron distribution and population analysis of amides, carboxylic acid, and peptides, and their relation to empirical potential functions.

The properties of the electron distribution in amides, peptides, and carboxylic acids, obtained from ab-initio molecular orbital calculations using both minimal and extended basis sets have been studied. These properties are discussed in terms of some of the common assumptions made in empirical conformational calculations of biomolecules. In particular, population analyses of 15 compounds in these families were carried out with both the minimal and extended basis sets, and compared with results of CNDO/2 calculations. It is suggested that population analysis is a useful tool for recognizing patterns of charge distributions, and investigating the transferability of parameters of different functional groups. However, its use for providing partial charges for conformational analysis is a questionable procedure. A more detailed analysis of the charge distribution was carried out by calculating the spatial electron distribution in the four compounds, N-methylacetamide, acetic acid, diketopiperazine, and N-acetyl-N′-methylalanine. Both total electron-density maps and differencedensity maps are presented. The properties of the overall shape of the molecule and the atoms in the molecule, are discussed in terms of the former along with three-dimensional shape plots of the total density. The distortion accompanying molecular formation, resulting in such features as the lone pair orbital and “bonding deensities” is discussed in terms of the difference maps. Semiquantitative estimates of the bonding and orbital densities resulting from the integration of the densities are also presented. Finally, one of the novel features of the study is the presentation of three-dimensional surfaces of constant difference densities from which the shapes of the orbitals and bonding densities emerge.     

High‐Output Triboelectric Nanogenerator Based on Dual Inductive and Resonance Effects‐Controlled Highly Transparent Polyimide for Self‐Powered Sensor Network Systems

High‐output triboelectric nanogenerators (TENGs) are demonstrated based on polyimide (PI)‐based polymers by introducing functionalities (e.g., electron‐withdrawing and electron‐donating groups) into the backbone. The TENG based on 6FDA‐APS PI, possessing the most negative electrostatic potential and the low‐lying lowest unoccupied molecular orbital level, produces the highest effective charge density of about 860 µC m^?2 in practical working conditions with the ion injection process. This may be ascribed to the excellent charge‐retention characteristics as well as the enhanced charge transfer capability, which increases the output power by 7 times compared to the commercially available Kapton film‐based TENG. Finally, a 6FDA‐APS‐driven sensor network system is demonstrated, providing the identity of three gases (H₂, CO, and NO₂) by illuminating the light‐emitting diodes within several seconds.     

Reduced point charge models of proteins: assessment based on molecular dynamics simulations

A reduced point charge distribution is used to model Ubiquitin and two complexes, Vps27 UIM-1–Ubiquitin and Barnase–Barstar. It is designed from local extrema in charge density distributions obtained from the Poisson equation applied to smoothed molecular electrostatic potentials. A variant distribution is built by locating point charges on atoms. Various charge fitting conditions are selected, i.e. from either electrostatic Amber99 (Assisted Model Building with Energy Refinement) Coulomb potential or forces, considering reference grid points located within various distances from the protein atoms, with or without separate treatment of main and side chain charges. The program GROMACS (Groningen Machine for Chemical Simulations) is used to generate Amber99SB molecular dynamics (MD) trajectories of the solvated proteins modelled using the various reduced point charge models (RPCMs) so obtained. Point charges that are not located on atoms are considered as virtual sites. Some RPCMs lead to stable MD trajectories. They, however, involve a partial loss in the protein secondary structure and lead to a less-structured solute solvation shell. The model built by fitting charges on Coulomb forces calculated at grid points ranging between 1.4 and 2.0 times the van der Waals radius of the atoms, with a separate treatment of main chain and side chain charges, appears to best approximate all-atom MD trajectories.     

X-ray evidence of a native state with increased compactness populated by tryptophan-less B. licheniformis β-lactamase

β‐lactamases confer antibiotic resistance, one of the most serious world‐wide health problems, and are an excellent theoretical and experimental model in the study of protein structure, dynamics and evolution. Bacillus licheniformis exo‐small penicillinase (ESP) is a Class‐A β‐lactamase with three tryptophan residues located in the protein core. Here, we report the 1.7‐Å resolution X‐ray structure, catalytic parameters, and thermodynamic stability of ESP^ΔW, an engineered mutant of ESP in which phenylalanine replaces the wild‐type tryptophan residues. The structure revealed no qualitative conformational changes compared with thirteen previously reported structures of B. licheniformis β‐lactamases (RMSD = 0.4–1.2 Å). However, a closer scrutiny showed that the mutations result in an overall more compact structure, with most atoms shifted toward the geometric center of the molecule. Thus, ESP^ΔW has a significantly smaller radius of gyration (R_g) than the other B. licheniformis β‐lactamases characterized so far. Indeed, ESP^ΔW has the smallest R_g among 126 Class‐A β‐lactamases in the Protein Data Bank (PDB). Other measures of compactness, like the number of atoms in fixed volumes and the number and average of noncovalent distances, confirmed the effect. ESP^ΔW proves that the compactness of the native state can be enhanced by protein engineering and establishes a new lower limit to the compactness of the Class‐A β‐lactamase fold. As the condensation achieved by the native state is a paramount notion in protein folding, this result may contribute to a better understanding of how the sequence determines the conformational variability and thermodynamic stability of a given fold.     

Primary basidiospore charge and taxonomy of Agaricomycetes

This article deals with the polarity of electrostatic charges that are carried on ballistic basidiospores after their liberation from fruiting bodies. The spores were collected by placing a portable device beneath the basidiome and allowing them to fall in a horizontal homogeneous electrostatic field, created by vertical parallel plane electrodes. Thus, the experimental setup enabled to investigate the primary charges, the charges present on spores immediately after the release from spore bearing cells. Spores of 135 basidiomes of 50 species of hymenomycetous fungi were collected in various natural conditions. The non-turgescent (drying up, collapsing or ceasing to sporulate) basidiomes were excluded from the taxonomical analysis; the 128 turgescent basidiomes (223 spore samples) of 47 species were taxonomically analyzed. These species represented eight orders (Agaricomycetes, Basidiomycota), covering 21 families and 36 genera. The analysis showed that the spore charges were distributed according to the polarity similarly in all samples in a species, and in a genus. In most cases also genera of one family had the same type of polarity distribution of spore charges. Possibly all taxa from species to monophyletic families are characterized by specific type of polarity of the primary electrostatic charge of basidiospores. Depending on the taxonomical group, all spore charges were negative, positive, or both negative and positive charges were present. This information could be useful in investing the ballistosporic discharge mechanism and for constructing higher-level phylogeny.     

A Detailed Study of VESPA Electrostatic Potential-Derived Atomic Charges

VESPA, an improved semiempirical method for the calculation of electrostatic potential-derived atomic charges has been tested. It is shown that this approach is even less dependent upon molecular orientation than "high density" CHELPG ab initio ESP-derived charges. The conformational dependence of VESPA charges has been investigated for rotation around the C-N bond in formamide and 11 different conformers of glycerolphosphorylcholine. The results obtained are also compared to the corresponding ab initio values. Finally, VESPA is used to calculate electrostatic potential-derived charges for bioorganic molecules. We discuss the abilities and the limitations of ESP charges in this area.     

Probing the effect of nitro groups in nitramine based energetic molecules: a DFT and charge density study

The structure, electron density distribution, energetic and electrostatic properties of simple nitramine based energetic TMA, DMNA, MDA and TNA molecules were determined using density functional theory (B3LYP) with the 6-311G^** and aug-cc-pVDZ basis sets coupled with Bader's theory of atoms in molecules. In the NO₂ group substituted molecules, the N–N bond distance increases with the increase of NO₂ groups, whereas in C–N bonds, this effect is relatively less, and the distances are almost equal. The topological analysis of electron density reveals that the electron density ρ_bcp(r) of C–N and N–N bonds are significantly decreasing with the increase of NO₂ groups in the nitramine molecules. The Laplacian of electron density ▽²ρ_bcp(r) of N–NO₂ bonds [DMNA: ? 16.7 eÅ^? 5, MDA: ? 12.8 eÅ^? 5 and TNA: ? 7.9 eÅ^? 5] of the molecules are relatively less negative, and the values also decrease with the increase of NO₂ groups; this implies that the charge concentration decreases with the increase of NO₂ groups, which leads to weakening the N–N bonds of the molecules. The isosurface of molecular electrostatic potential displays high electronegative regions around the NO₂ groups. The oxygen balance OB₁₀₀ of the molecules increases as the number of NO₂ group increases in the molecules, in which, the TNA molecule having maximum OB₁₀₀ value [+7.89]. The band gap, heat of detonation, bond dissociation energy and charge imbalance are predominantly depends on the number of NO₂ group present in the molecule. The charge imbalance parameter (ν) has been calculated for all molecules, which reveals that TNA is a highly sensitive molecule, the corresponding ν value is 0.047.     

Importance of polarization effect in the study of metalloproteins: Application of polarized protein specific charge scheme in predicting the reduction potential of azurin

Molecular dynamics (MD) simulation is commonly used in the study of protein dynamics, and in recent years, the extension of MD simulation to the study of metalloproteins is gaining much interest. Choice of force field is crucial in MD studies, and the inclusion of metal centers complicates the process of accurately describing the electrostatic environment that surrounds the redox centre. Herein, we would like to explore the importance of including electrostatic contribution from both protein and solvent in the study of metalloproteins. MD simulations with the implementation of thermodynamic integration will be conducted to model the reduction process of azurin from Pseudomonas aeruginosa. Three charge schemes will be used to derive the partial charges of azurin. These charge schemes differ in terms of the amount of immediate environment, respective to copper, considered during charge fitting, which ranges from the inclusion of copper and residues in the first coordination sphere during density functional theory charge fitting to the comprehensive inclusion of protein and solvent effect surrounding the metal centre using polarized protein‐specific charge scheme. From the simulations conducted, the relative reduction potential of the mutated azurins respective to that of wild‐type azurin (ΔE_cal) were calculated and compared with experimental values. The ΔE_cal approached experimental value with increasing consideration of environmental effect hence substantiating the importance of polarization effect in the study of metalloproteins. This study also attests the practicality of polarized protein‐specific charge as a computational tool capable of incorporating both protein environment and solvent effect into MD simulations. Proteins 2014; 82:2209–2219. © 2014 Wiley Periodicals, Inc.     

New Multicentre Point Charge Models for Molecular Electrostatic Potentials from Semiempirical M0-Calculations

Two quasi-multipole electrostatic models for molecular charge distributions are presented. They assign arrays of point charges to nonhydrogen atoms on the basis of hybrid orbitals or localised molecular orbitals. When used with common semiempirical MO-techniques, they reproduce natural atomic orbital derived point charge (NAO-PC) and ab initio molecular potentials well. The localised orbital technique (LMO-PC) is intuitively more attractive than the hybrid orbital-point charge (HO-PC) method, although the former is more CPU-intensive.Electronic Supplementary Material available.     

Halogen bonding: the σ-hole

Halogen bonding refers to the non-covalent interactions of halogen atoms X in some molecules, RX, with negative sites on others. It can be explained by the presence of a region of positive electrostatic potential, the σ-hole, on the outermost portion of the halogen’s surface, centered on the R–X axis. We have carried out a natural bond order B3LYP analysis of the molecules CF₃X, with X = F, Cl, Br and I. It shows that the Cl, Br and I atoms in these molecules closely approximate the configuration, where the z-axis is along the R–X bond. The three unshared pairs of electrons produce a belt of negative electrostatic potential around the central part of X, leaving the outermost region positive, the σ-hole. This is not found in the case of fluorine, for which the combination of its high electronegativity plus significant sp-hybridization causes an influx of electronic charge that neutralizes the σ-hole. These factors become progressively less important in proceeding to Cl, Br and I, and their effects are also counteracted by the presence of electron-withdrawing substituents in the remainder of the molecule. Thus a σ-hole is observed for the Cl in CF₃Cl, but not in CH₃Cl. Figure Schematic representation of the atomic charge generation. The molecular electrostatic potential (MEP) is calculated using the AM1* Hamiltonian. The semiempirical MEP is then scaled to DFT or ab initio level and atomic charges are generated from it by the restrained electrostatic potential (RESP) fit method.     

Plasmonic Back Reflectors: A Small Molecule Non‐fullerene Electron Acceptor for Organic Solar Cells

Organic bulk heterojunction photovoltaic devices predominantly use the fullerene derivatives [C60]PCBM and [C70]PCBM as the electron accepting component. This report presents a new organic electron accepting small molecule 2‐[{7‐(9,9‐di‐n‐propyl‐9H‐fluoren‐2‐yl)benzo[c][1,2,5]thiadiazol‐4‐yl}methylene]malononitrile (K12) for organic solar cell applications. It can be processed by evaporation under vacuum or by solution processing to give amorphous thin films and can be annealed at a modest temperature to give films with much greater order and enhanced charge transport properties. The molecule can efficiently quench the photoluminescence of the donor polymer poly(3‐n‐hexylthiophene‐2,5‐diyl) (P3HT) and time resolved microwave conductivity measurements show that mobile charges are generated indicating that a truly charge separated state is formed. The power conversion efficiencies of the photovoltaic devices are found to depend strongly on the acceptor packing. Optimized K12:P3HT bulk heterojunction devices have efficiencies of 0.73±0.01% under AM1.5G simulated sunlight. The efficiencies of the devices are limited by the level of crystallinity and nanoscale morphology that was achievable in the blend with P3HT.     

A Small Molecule Non‐fullerene Electron Acceptor for Organic Solar Cells

Organic bulk heterojunction photovoltaic devices predominantly use the fullerene derivatives [C60]PCBM and [C70]PCBM as the electron accepting component. This report presents a new organic electron accepting small molecule 2‐[{7‐(9,9‐di‐n‐propyl‐9H‐fluoren‐2‐yl)benzo[c][1,2,5]thiadiazol‐4‐yl}methylene]malononitrile (K12) for organic solar cell applications. It can be processed by evaporation under vacuum or by solution processing to give amorphous thin films and can be annealed at a modest temperature to give films with much greater order and enhanced charge transport properties. The molecule can efficiently quench the photoluminescence of the donor polymer poly(3‐n‐hexylthiophene‐2,5‐diyl) (P3HT) and time resolved microwave conductivity measurements show that mobile charges are generated indicating that a truly charge separated state is formed. The power conversion efficiencies of the photovoltaic devices are found to depend strongly on the acceptor packing. Optimized K12:P3HT bulk heterojunction devices have efficiencies of 0.73±0.01% under AM1.5G simulated sunlight. The efficiencies of the devices are limited by the level of crystallinity and nanoscale morphology that was achievable in the blend with P3HT.     

Mutational analysis of the active site residues of a <Emphasis Type="SmallCaps">d</Emphasis>-psicose 3-epimerase from <Emphasis Type="Italic">Agrobacterium tumefaciens</Emphasis>

d-Psicose 3-epimerase from Agrobacterium tumefacience catalyzes the conversion of d-fructose to d-psicose. According to mutational analysis, the ring at position 112, the negative charge at position 156, and the positive charge at position 215 were essential components for enzyme activity and for binding fructose and psicose. The surface contact area and distance to the bound substrate by molecular modeling suggest that the positive charge of Arg215 was involved in stabilization of cis-endiol intermediate. The distances between the catalytic residues (Glu150 and Glu244) and Mn²⁺ are critical to the catalysis, and the negative charges of the metal-binding residues are important for interaction with metal ion. The kinetic parameters of the D183E and H209A mutants for metal-binding residues with substrate and the near-UV circular dichroism spectra indicate that the metal ion bound to Asp183 and His209 is involved not only in catalysis but also in substrate binding.     

Electrostatic effects on polynucleotide transitions. I. Behavior at neutral pH

An approximate analytical expression for the electrostatic free energy of a polynucleo-tide in any of its possible ordered or random conformations is derived by integration of the screened-Coulomb potential energy function over all charge pairs in the structure. The electrostatic free energy of any form is found to be a linear function of the logarithm of the monovalent counterion concentration, in the range of low salt concentrations. Hence the electrostatic free energy difference between ordered and disordered forms in a polynucleotide structural transition is a linear function of the logarithm of the monovalent counterion concentration. A free energy balance applied to a two-state model for the transition then yields a linear dependence of the transition temperature T_m upon the logarithm of the counterion concentration. Calculation of the quantity dT_m/d log M, where M is the monovalent counterion concentration, shows it to be a characteristic constant for a given transition, with a magnitude and sign proportional to the charge density difference between the ordered and disordered forms. Use of any one of several alternate, simple assumptions yields predicted dT_m/d log M values in good agreement with experimental data for various polynucleotide transitions.