Bond Charge Research Articles

Chemoselective synthesis, X-ray characterization and DFT studies of new organic single crystal: S-(2-aminophenyl) cyclohexylcarbamothioate

Chemoselective manner of 2-aminothiophenol reaction with cyclohexyl isocyanate under the different conditions was investigated. The product, S-(2-aminophenyl) cyclohexylcarbamothioate, was characterized by 1H, 13C NMR, FT-IR, HRMS and single crystal X-ray diffraction analysis. Single crystal of the molecular structure, C13H18N2OS, crystallizes in monoclinic form, space group P 21/n with a = 6.1808(4) Å, b = 24.8308(12) Å, c = 9.7080(8) Å, β = 103.674(6)°, V = 1303.73(13) Å3, F (000) = 36. The structure exhibits disorder over the phenyl ring, with site occupancies of 0.913(4) and 0.087(4) for the major and minor components, respectively. The conformation is stabilized by intra- and intermolecular N–H. O, N–H. N, and C– H. S hydrogen bonds into running along the a-axis. The title compound has been optimized by DFT/B3LYP/6-31 + G (d, p) basis set, and compared with experimental findings. Natural bond orbital charges of probable intramolecular hydrogen bonds have been calculated to compare with experimental data, and frontier orbital analysis and molecular electrostatic potential (MEP) analysis were also carried out.

Synthesis, structure, electrical properties and Na+ migration pathways of Na2CoP1.5As0.5O7

Sodium cobalt di(phosphate/arsenate) Na2CoP1.5As0.5O7 has been synthesized as polycrystalline powder and single crystals by solid state reaction. The structure has been determined by X-ray diffraction at room temperature. The title material crystallizes in the tetragonal system, space group P42/mnm with the unit cell parameters: a = 7.764(3) Å, c = 10.385(3) Å, V = 626.0(4) Å3 and Z = 4. The two tools of crystal structure validation, Bond Valence Sum (BVS) and Charge distribution (CHARDI) methods, have confirmed the crystal structure model. The anionic framework is built of layers of corner sharing (P/As)O4 and CoO6 polyhedra. The sodium atoms are located in the interlayer space. Quantitative analysis using ICP-MS is used to confirm the elemental composition of the polycrystalline powder. Thermal analyzes show a phase transition at 675 °C before the melting point of 700 °C. The electrical properties of the title compound have been characterized by impedance spectroscopy in the 240°C–360 °C temperature range. At 240 °C, the conductivity value of the sample with relative density of 85% is 4 10−6 Scm−1 and the activation energy was Ea = 0.56 eV. The calculated conductivity corrected for porosity is σd (240°C) = 1.88 10−5 Scm−1. The Na+ transport pathways in the interlayer space was simulated using the Band Valence Site Energy (BVSE) model. The BVSE model was also used to explain the effect of the P/As substitution on the electrical properties of the title compound.

Femtosecond bond breaking and charge dynamics in ultracharged amino acids.

Historically, structure determination of nanocrystals, proteins, and macromolecules required the growth of high-quality crystals sufficiently large to diffract X-rays efficiently while withstanding radiation damage. The development of the X-ray free-electron laser has opened the path toward high resolution single particle imaging, and the extreme intensity of the X-rays ensures that enough diffraction statistics are collected before the sample is destroyed by radiation damage. Still, recovery of the structure is a challenge, in part due to the partial fragmentation of the sample during the diffraction event. In this study, we use first-principles based methods to study the impact of radiation induced ionization of six amino acids on the reconstruction process. In particular, we study the fragmentation and charge rearrangement to elucidate the time scales involved and the characteristic fragments occurring.

Ab initio study on physical and chemical interactions at borates and iron oxide interface at high temperature

Ab initio molecular dynamics (AIMD) simulations were carried out to study the interactions of sodium tetraborate (Na2B4O7) and boron oxide (B2O3) on an iron oxide surface Fe2O3(0 0 0 1) at 1073 K. The results demonstrate that high temperature transforms Na2B4O7 structure by activating sodium mobility and decomposing BO4 complexes into BO3 and non-bridging oxygen. These products engage in chemical reactions with the Fe2O3 surface by forming O–Na ionic and Fe–O–B covalent bonds, which make Na2B4O7 adhere extremely well on the surface. Density profile and charge analysis show that sodium cations play a critical role at the interface by forming O–Na–O stacking and acting as a bridge to connect the negatively charged areas of the O-rich surface and the oxygen of the borate. On the contrary, the molten B2O3 remains intact with no chemical reactions which accounts for its poor adhesion on the Fe2O3 surface. Furthermore, the Blue Moon method was applied to predict bond dissociation and charge analysis was used to rationalize the differences in binding mechanisms at the lubricant-steel interfaces. The above simulations provide a theoretical interpretation for the lubricity of sodium borate and boron oxide at elevated temperature.

Spectroscopic Signature of Chemical Bond Dissociation Revealed by Calculated Core-Electron Spectra.

The advent of ultrashort soft X-ray pulse sources permits the use of established gas-phase spectroscopy methods to investigate ultrafast photochemistry in isolated molecules with element and site specificity. In the present study, we simulate excited-state wavepacket dynamics of a prototypical process, the ultrafast photodissociation of methyl iodide. Using the simulation, we calculate time-dependent excited-state carbon edge photoelectron and Auger electron spectra. We observe distinct signatures in both types of spectra and show their direct connection to C-I bond dissociation and charge rearrangement processes in the molecule. We demonstrate at the CH3I molecule that the observed signatures allow us to map the time-dependent dynamics of ultrafast photoinduced bond breaking with unprecedented detail.

LiNiO2 as a high-entropy charge- and bond-disproportionated glass

Understanding microscopic properties of LiNiO$_2$, a Li-ion battery cathode material with extraordinarily high reversible capacity, has remained a challenge for decades. Based on extensive electronic structure calculations, which reveal a large number of nearly degenerate phases involving local Jahn-Teller effect as well as bond and oxygen-based charge disproportionation, we propose that LiNiO$_2$ exists in a high-entropy charge-glass like state at and below ambient temperatures. Recognizing the glassy nature of LiNiO$_2$ does not only explain its key experimental features, but also opens a new path in designing entropy-stabilized battery cathodes with superb capacities.

Effects of PHB and SFC charge models on the side chain-side chain interactions in the simulation of β-hairpins

In view of the recent development of polarizable force fields namely polarizable hydrogen bond (PHB) and semi-fluctuating charge (SFC) developed by Zhang’s group, we would like to explore the effects of these two models on side chain-side chain interactions through the simulation of two β-hairpins. The results show that the PHB model strengthens but the SFC model weakens side chain-side chain interactions in our studies. Through this study, we aim to have a more comprehensive understanding of these two models which only focus on the charge updating of backbone atoms.

Periodic DFT Study of the Effects of Co-Crystallization on a N-Salicylideneaniline Molecular Switch.

This work aims at better understanding the complex effects of co-crystallization on a single salicylideneaniline molecular switch, (E)-2-methoxy-6-(pyridine-3-yliminomethyl)phenol (PYV3), which can tautomerize between an enol and a keto form. A combination of periodic boundary conditions DFT and molecular wavefunction calculations has been adopted for examining a selection of PYV3 co-crystals, presenting hydrogen bonds (H-bonds) or halogen bonds (X-bonds), for which X-ray diffraction data are available. Three aspects are targeted: i) the energy (H-bond strength, enol to keto relative energy, and geometry relaxation energies), ii) the geometrical structure (PYV3 to co-crystal and enol to keto geometrical variations), and iii) the electron distribution (PYV3 to co-crystal and enol to keto Mulliken charge variations). These allow i) explaining the preference for forming H-bonds with the nitrogen of the pyridine of PYV3 with respect to the oxygens and the importance of the crystal field, ii) distinguishing the peculiar behavior of the SulfonylDiPhenol (SDP) coformer, which stabilizes the keto form of PYV3, iii) describing the relative stabilization of the enol form upon co-crystallization (with the exception of SDP) and therefore iv) substantiating the co-crystallization-induced reduction of thermochromism observed for several PYV3 co-crystals.

Interaction of (G4)2 and (X4)2 DNA quadruplexes with Cu+, Ag+ and Au+ metal cations: a quantum chemical calculation on structural, energetic and electronic properties

The present study is focused to cast light on the structural, electronic and energetic properties of isolated (G4)2 and (X4)2 DNA quadruplexes with transition metal cations which are investigated using ab initio and density functional theory (DFT). The geometrical analysis revealed that (G4)2 and (X4)2 with metal cation can adopt the normal tetraplex Hoogsteen hydrogen bond, and no bifurcated hydrogen bonds are occurred. The addition of metal cation in the central cavity of isolated (G4)2 and (X4)2 bases can affect the structural chirality and their charge distribution. Binding energy and metal ion affinity of (G4)2 and (X4)2 metal complexes follow the interaction energy order of (G4)2-Cu+ > (G4)2-Ag+ > (G4)2-Au+ > and (X4)2-Cu+ > (X4)2-Ag+ > (X4)2-Au+. The quantum theory of atoms in molecule (QTAIM) analysis revealed that the electrostatic interaction has occurred between carbonyl group oxygen atom and metal cation (O6⋯M+). The natural bonding orbital (NBO) analysis reveals that the N-H⋯O and N-H⋯N hydrogen bond strength and charge transfer have been calculated for both (G4)2 and (X4)2 metal complexes. The higher wavelength and lower excitation energies are observed for both (G4)2 and (X4)2 metal complexes which exhibit that the hyperchromic shift occurred during metal ion interaction. The obtained results showed that the transition metal cations are strongly interacted with (G4)2 and (X4)2 bases, and it controls the telomerase activity. While comparing (G4)2 and (X4)2 bases, the (X4)2 bases are having similar properties of (G4)2 bases. Thus, the xanthine and its derivatives are very auspicious candidates for artificial quadruplex DNA.

Mechanistic insights into the phosphoryl transfer reaction in cyclin-dependent kinase 2: A QM/MM study.

Cyclin-dependent kinase 2 (CDK2) is an important member of the CDK family exerting its most important function in the regulation of the cell cycle. It catalyzes the transfer of the gamma phosphate group from an ATP (adenosine triphosphate) molecule to a Serine/Threonine residue of a peptide substrate. Due to the importance of this enzyme, and protein kinases in general, a detailed understanding of the reaction mechanism is desired. Thus, in this work the phosphoryl transfer reaction catalyzed by CDK2 was revisited and studied by means of hybrid quantum mechanics/molecular mechanics (QM/MM) calculations. Our results suggest that the base-assisted mechanism is preferred over the substrate-assisted pathway when one Mg2+ is present in the active site, in agreement with a previous theoretical study. The base-assisted mechanism resulted to be dissociative, with a potential energy barrier of 14.3 kcal/mol, very close to the experimental derived value. An interesting feature of the mechanism is the proton transfer from Lys129 to the phosphoryl group at the second transition state, event that could be helping in neutralizing the charge on the phosphoryl group upon the absence of a second Mg2+ ion. Furthermore, important insights into the mechanisms in terms of bond order and charge analysis were provided. These descriptors helped to characterize the synchronicity of bond forming and breaking events, and to characterize charge transfer effects. Local interactions at the active site are key to modulate the charge distribution on the phosphoryl group and therefore alter its reactivity.

The bond charge current in the monolayer graphene superlattice with hopping beyond nearest neighbor

In this paper, we systematically investigate the transportation properties of the zigzag nano-ribbon graphene in a local potential barrier/well with electrons hopping between and beyond nearest neighbor. When the local potential is present, the conductance exhibits novel periodic oscillation plateaus around increasing quantized conductance. The oscillation plateau hops down with the quantized conductance until vanishes with increasing local potential barrier. Furthermore, when a small voltage is applied between the two terminals of the conductor, the local current presents periodic oscillation in the barrier region. In contrast, when a local potential well is applied, the conductance shows irregular oscillation, exhibiting incommensurate oscillations of local current inside and outside the well. Finally, similar phenomena persists when more local potentials are applied to the system. We expect our studies can facilitate the design of relevant electronic devices.

Pivotal Role of Nonmetal Atoms in the Stabilities, Geometries, Electronic Structures, and Isoelectronic Chemistry of Sc3X@C80 (X = C, N, and O)

The thermodynamic and dynamic stabilities of Sc3 X@C80 (X = C, N, and O) are explored via density functional theory combined with statistical thermodynamic analysis and ab initio molecular dynamics. It is the first time to comprehensively consider the effect of nonmetal atoms on trimetallic endohedral clusterfullerenes. Relative to Sc3 X@Ih (31924)-C80 (X = N and O) with general six-electron transfer, an intriguing electronic structure of unexplored Sc3 C@D5h (31923)-C80 with thermodynamic and dynamic stabilities is clearly disclosed. Natural bond orbitals and charge decomposition analysis simultaneously suggest that one unpaired electron appears on the cage for neutral Sc3 C@D5h (31923)-C80 , which could be prospectively stabilized by effective exohedral derivatization and ionization in the future. Moreover, isoelectronic endohedral clusterfullerenes, (Sc3 C@C80 )- , Sc3 N@C80 , and (Sc3 O@C80 )+ , are also uniquely taken into account. The geometries, electronic structures, reactivities, and reactive sites of isoelectronic species are examined, and it turns out that all the three isoelectronic species would rather electrophilic than nucleophilic reactions. © 2019 Wiley Periodicals, Inc.

Solvation Free Energy Calculations: The Combination between the Implicitly Polarized Fixed-charge Model and the Reference Potential Strategy.

The IPolQ-Mod charges, which are the average of two charge sets fitted in vacuum state and condensed phase, take account of polarization effect implicitly in the solvation free energy calculation. However, the performance of the IPolQ-Mod charges sensitively depends on the QM levels used to generate the electrostatic potential from which the charges are fitted. In addition, the forces on atoms are not accurate theoretically in the molecular dynamics (MD) simulation as the solvent only feels the electrostatic potential of a half-polarized density of the solute according to the derivation of the IPolQ-Mod charges. To study these issues in detail, the IPolQ-Mod charges are combined with the reference potential (RP) strategy to predict the solvation free energies in the present study. It is found that the thermodynamic perturbation (TP) corrections utilizing total energy difference and interaction energy difference are almost the same and free of bias. The solvation free energies estimated by the RP method match very well with those obtained by applying IPolQ-Mod charges into MD simulation directly. By means of the RP strategy, the performances of the IPolQ-Mod charges with the change of the strength of the exact HF exchange in several DFT functionals are determined effectively. Although the "optimal" strengths are found in B3LYP and LC-ωPBE, the improvements over the default strength are not too much. In addition to the IPolQ-Mod charges, other charge models like bond charge correction (BCC) charges could also be combined with the RP strategy to study the thermodynamic properties like solvation free energy. © 2019 Wiley Periodicals, Inc.

Synthesis, crystal structure, phonon, magnetic and electrical properties of new molybdate Na2Mn2(MoO4)3

The single crystals of Na2Mn2(MoO4)3 were successfully grown using the solid-state synthesis method. This compound crystallizes in a triclinic system with space group P1‾ (Ci). Its structure can be described as a three-dimensional anionic framework of Mn2O10 double octahedra units sharing edges with the MoO4 tetrahedra. The Na+ ions are disordered and located in the voids forming infinite channels running along the [100], [010] and [001] directions. The structural model was validated by the bond valence sum (BVS) and charge distribution (CHARDI) methods. The polycrystalline powder of Na2Mn2(MoO4)3 was prepared as well using citrate process. The obtained sample was characterized by powder X-ray diffraction, infrared spectroscopy and Raman scattering at room temperature. The vibrational study confirms the existence of the MoO42− functional groups. Thermal stability of the studied material was analyzed using differential scanning calorimetry. The Na2Mn2(MoO4)3 compound is thermally stable up to 500 °C. Magnetic susceptibility measurements reveal that the title compound is antiferromagnetic with Néel temperature TN = 6.5 (5) K. At higher temperatures, its susceptibility follows a Curie–Weiss law. Electrical measurements of this material were studied by means of the impedance spectroscopy technique, in 0.1 Hz–4 MHz frequency and in 443–691 K temperature ranges. The conductivity of Na2Mn2(MoO4)3 is 2.30 μScm−1 at 691 K and it is thermally activated with energy of 0.47 eV. The sodium migration pathways in the crystal structure were investigated using the bond valence sum pathways (BVSP) analysis and the bond valence site energy (BVSE) model.

Current-induced atomic forces in gated graphene nanoconstrictions

Electronic current densities can reach extreme values in highly conducting nanostructures where constrictions limit current. For bias voltages on the 1 V scale, the highly nonequilibrium situation can influence the electronic density between atoms, leading to significant interatomic forces of the order of 1 nN. An easy interpretation of the nonequilibrium forces is currently not available, to our knowledge. In this work, we present an ab initio study based on density functional theory of bias-induced atomic forces in gated graphene nanoconstrictions consisting of junctions between graphene electrodes and graphene nanoribbons in the presence of current. We find that current-induced bond forces and bond charges are correlated, while bond forces are not simply correlated to bond currents. We discuss, in particular, how the forces are related to induced charges and the electrostatic potential profile (voltage drop) across the junctions. For long current-carrying junctions we may separate the junction into a part with a voltage drop, and a part without voltage drop. The latter situation can be compared to a nanoribbon in the presence of current using an ideal ballistic velocity-dependent occupation function. This shows how the combination of voltage drop and current give rise to the strongest current-induced forces in nanostructures.

Study of inhibition effect of Ca2+ on phosphorus-contained active groups in coal

ABSTRACT In order to study the mechanism of delaying coal spontaneous combustion through CaCl2 and improve inhibition effect, the chemical reactions between CaCl2 and coal have been studied. This research includes the study of ligand structure, formed by combination of Ca2+ and phosphorus (P)-contained active structure of coal, molecular frontier orbital, stabilization energy, natural bond orbital, Mulliken population, and charge transfer. All the calculations are performed with the Gaussian03 program. The calculation results indicate that bidentate, tridentate, and quadridentate ligands can be formed through the chemical reaction between Ca2+ and P-contained active groups in coal. During the generation of the complexes, stabilization energy becomes higher and the energy gap of frontier molecular orbital becomes lower, making a stable complex formed. After the formation of those complexes, the contribution of -PH2 group in the P-contained active structure is greatly reduced in the molecular frontier orbital. The orbital energy level increases dramatically, improving the stability of the active structure and retarding oxidation reaction.

Enhanced π-back-donation resulting in the trans labilization of a pyridine ligand in an N-heterocyclic carbene (NHC) PdII precatalyst: a case study.

The molecular structure of the benzimidazol-2-ylidene-PdCl2-pyridine-type PEPPSI (pyridine-enhanced precatalyst, preparation, stabilization and initiation) complex {1,3-bis[2-(diisopropylamino)ethyl]benzimidazol-2-ylidene-κC2}dichlorido(pyridine-κN)palladium(II), [PdCl2(C5H5N)(C23H40N4)], has been characterized by elemental analysis, IR and NMR spectroscopy, and natural bond orbital (NBO) and charge decomposition analysis (CDA). Cambridge Structural Database (CSD) searches were used to understand the structural characteristics of the PEPPSI complexes in comparison with the usual N-heterocyclic carbene (NHC) complexes. The presence of weak C-H...Cl-type hydrogen-bond and π-π stacking interactions between benzene rings were verified using NCI plots and Hirshfeld surface analysis. The preferred method in the CDA of PEPPSI complexes is to separate their geometries into only two fragments, i.e. the bulky NHC ligand and the remaining fragment. In this study, the geometry of the PEPPSI complex is separated into five fragments, namely benzimidazol-2-ylidene (Bimy), two chlorides, pyridine (Py) and the PdII ion. Thus, the individual roles of the Pd atom and the Py ligand in the donation and back-donation mechanisms have been clearly revealed. The NHC ligand in the PEPPSI complex in this study acts as a strong σ-donor with a considerable amount of π-back-donation from Pd to Ccarbene. The electron-poor character of PdII is supported by π-back-donation from the Pd centre and the weakness of the Pd-N(Py) bond. According to CSD searches, Bimy ligands in PEPPSI complexes have a stronger σ-donating ability than imidazol-2-ylidene ligands in PEPPSI complexes.

Mixed Electron–Proton Conductors Enable Spatial Separation of Bond Activation and Charge Transfer in Electrocatalysis

Electrochemical energy conversion requires electrodes that can simultaneously facilitate substrate bond activation and electron-proton charge transfer. Traditional electrodes co-localize both functions to a single solid|liquid interface even though each process is typically favored in a disparate reaction environment. Herein, we establish a strategy for spatially separating bond activation and charge transfer by exploiting mixed electron-proton conduction (MEPC) in an oxide membrane. Specifically, we interpose a MEPC WOx membrane between a Pt catalyst and aqueous electrolyte and show that this composite electrode is active for the hydrogen oxidation reaction (HOR). Consistent with H2 activation occurring at the gas|solid interface, the composite electrode displays HOR current densities over 8-fold larger than the diffusion-limited rate of HOR catalysis at a singular Pt|solution interface. The segregation of bond activation and charge separation steps also confers excellent tolerance to poisons and impurities introduced to the electrolyte. Mechanistic studies establish that H2 activation at the Pt|gas interface is coupled to the electron-proton charge separation at the WOx|solution interface via rapid H-diffusion in the bulk of the WOx. Consequently, the rate of HOR is principally controlled by the rate of H-spillover at the Pt|WOx boundary. Our results establish MEPC membrane electrodes as a platform for spatially separating the critical bond activation and charge transfer steps of electrocatalysis.

Exploring the Structure, Electron Density and HOMO-LUMO Studies of Tetrathiafulvalene (TTF) as Organic Superconductors: A DFT and AIM Analysis

The Structure, Electron density and HOMO-LUMO analysis of TTF molecule was carefully evaluated by ab initio (HF) and density functional theory (B3LYP) calculations. The optimized (HF/6-311G** and B3LYP/6-311G**, B3LYP/auf-cc-PVDZ) geometric parameters are in excellent agreement with the similar type experimental data. For both levels of calculation, the low charge accumulation have C\(-\)S and C\(\equiv\)N bonds, at the bond critical point, which gives that the bond charges are highly depleted compared with all other bonds in the molecule. Further, AIM theory shows the difference of charge distribution in all bonds. The molecular conductivity (HOMO-LUMO gap) properties are solely related to the ESP of the entire system. The ionization potential gives the very good information of conductivity. These observations give an insight on this kind of super conducting material, which are useful to design navel electronic devices.

Theoretical investigations on the structural stability and miscibility in BAlN and BGaN alloys: bond-order interatomic potential calculations

Structural stability and miscibility of BxAl1−xN and BxGa1−xN alloys including 3-fold coordinated hexagonal (Hex), 4-fold coordinated wurtzite (WZ) and zinc blende (ZB) structures are systematically investigated based on empirical bond-order potential (BOP), which incorporates electrostatic energies due to bond and ionic charges. We find that the Hex structure is stabilized for free-standing BxAl1−xN and BxGa1−xN alloys with boron composition while the ZB (WZ) structure is stabilized for () both in BxAl1−xN and BxGa1−xN alloys due to the electrostatic energy. Furthermore, the miscibility of BxAl1−xN and BxGa1−xN alloys with 4-fold coordinated structures are found to be higher than that with Hex structure owing to the chemical energy contribution to the excess energy. These results suggest that our empirical interatomic potentials approach is feasible to clarify structural stability not only for the 3-fold coordinated Hex structure but also 4-fold coordinated WZ and ZB structures in BxAl1−xN and BxGa1−xN alloys.