Covalent Bond Length Research Articles

Role of Chemistry and Crystal Structure on the Electronic Defect States in Cs-Based Halide Perovskites.

The electronic structure of a series perovskites ABX3 (A = Cs; B = Ca, Sr, and Ba; X = F, Cl, Br, and I) in the presence and absence of antisite defect XB were systematically investigated based on density-functional-theory calculations. Both cubic and orthorhombic perovskites were considered. It was observed that for certain perovskite compositions and crystal structure, presence of antisite point defect leads to the formation of electronic defect state(s) within the band gap. We showed that both the type of electronic defect states and their individual energy level location within the bandgap can be predicted based on easily available intrinsic properties of the constituent elements, such as the bond-dissociation energy of the B–X and X–X bond, the X–X covalent bond length, and the atomic size of halide (X) as well as structural characteristic such as B–X–B bond angle. Overall, this work provides a science-based generic principle to design the electronic states within the band structure in Cs-based perovskites in presence of point defects such as antisite defect.

Analysis of chemistry teachers' covalent bond conceptual understanding through diagnostic interview technique

Conceptual understanding of the subject matter is crucial for teachers in conducting instruction. The covalent bond is one of the essential knowledge of chemistry. This knowledge underlies most of the chemistry body knowledge. The purpose of this study is to investigate the chemistry teachers' conceptual understanding of covalent bonds. This study applied a descriptive qualitative research design. The research subjects were eight chemistry teachers from different schools. Data collection was carried out using a diagnostic interview technique guided by the semi-structured interview protocol. Data analysis was performed using phenomenography techniques. The results show that 25.00% of the interviewees well understood the covalent bond concepts, 22.75% do not understand, and 52.25% have misconceptions. Chemistry teachers have misconceptions about the concepts of intents of atom forming bonds, coordination bonds, types of atoms that form covalent bonds, polar and nonpolar covalent bonds, the level of covalent bonds polarity, Lewis structure writing, and covalent bond length.

From Infrared Spectra to Macroscopic Mechanical Properties of sH Gas Hydrates through Atomistic Calculations.

The vibrational characteristics of gas hydrates are key identifying molecular features of their structure and chemical composition. Density functional theory (DFT)-based IR spectra are one of the efficient tools that can be used to distinguish the vibrational signatures of gas hydrates. In this work, ab initio DFT-based IR technique is applied to analyze the vibrational and mechanical features of structure-H (sH) gas hydrate. IR spectra of different sH hydrates are obtained at 0 K at equilibrium and under applied pressure. Information about the main vibrational modes of sH hydrates and the factors that affect them such as guest type and pressure are revealed. The obtained IR spectra of sH gas hydrates agree with experimental/computational literature values. Hydrogen bond’s vibrational frequencies are used to determine the hydrate’s Young’s modulus which confirms the role of these bonds in defining sH hydrate’s elasticity. Vibrational frequencies depend on pressure and hydrate’s O···O interatomic distance. OH vibrational frequency shifts are related to the OH covalent bond length and present an indication of sH hydrate’s hydrogen bond strength. This work presents a new route to determine mechanical properties for sH hydrate based on IR spectra and contributes to the relatively small database of gas hydrates’ physical and vibrational properties.

Crystal structures of tolfenamic acid polymorphic forms I and II with precise hydrogen-atom positions for nuclear magnetic resonance studies.

The structures of tolfenamic acid [TFA; 2-(3-chloro-2-methyl-anilino)benzoic acid, C14H12ClNO2] polymorph forms I and II have been redetermined [compare Andersen et al. (1989 ▸). J. Chem. Soc., Perkin Trans. 2, pp. 1443-1447] with improved precision using high-resolution X-ray diffraction data and Hirshfield atom refinement in order to better define both hydrogen-atom locations and their associated bond lengths. Covalent bond lengths to hydrogen were found to be significantly longer throughout both structures, especially for the anilino H atom, which is involved in an important intra-molecular N-H⋯O hydrogen bond to the carb-oxy-lic acid group. This hydrogen bond is shown to clearly perturb the electron density around both oxygen atoms in the latter group. The extended structures of both polymorphs feature carb-oxy-lic acid inversion dimers. These structures provide an improved foundation for nuclear magnetic resonance studies in both solution and the solid state.

Structure refinement of black phosphorus under high pressure.

The structure refinement of black phosphorus was performed at pressures of up to 3.2 GPa at room temperature by powder neutron diffraction techniques. The bond lengths and bond angles between the phosphorus atoms at pressures were precisely determined and confirmed to be consistent with those of the previous single crystal x-ray analysis [A. Brown and S. Rundqvist, Acta Cryst. 19, 684 (1965)]. Although the lattice parameters exhibited an anisotropic compressibility, the covalent P1-P2 and P1-P3 bond lengths were almost independent of pressure and only the P3-P1-P2 bond angle was reduced significantly. On the basis of our results, the significant discrepancy in the bond length reported by Cartz et al. [J. Chem. Phys. 71, 1718 (1979)] has been resolved. Our structural data will contribute to the elucidation of the Dirac semimetal state of black phosphorus under high pressure.

Surprisingly broad applicability of the cc-pVnZ-F12 basis set for ground and excited states

Excellent convergence properties for the (aug-)cc-pVnZ-F12 basis set family, purpose-made for explicitly correlated calculations, are demonstrated with conventional wave function methods and Kohn-Sham density functional theory for various ground and excited-state calculations. Among the ground-state properties studied are dipole moments, covalent bond lengths, and interaction and reaction energies. For excited states, we looked at vertical excitation energies, UV absorption, and excited-state absorption spectra. Convergence is compared against the basis sets cc-pVnZ, def2-nVD, aug-pcseg-n, and nZaPa-NR. It is established that the cc-pVnZ-F12 family consistently yields results of n + 1 quality and better. Especially, the cc-pVDZ-F12 basis set is found to be a basis set of good cost vs performance trade-off.

The covalent radii derived from the first-principle data

We present a collection of covalent radii for the elements H, B, C, N, O, F, Si, P, S, Cl, Ge, As, Se, Br, derived from the recently introduced systematic non-empirical dataset of the covalent bond lengths built basing on 26,050 molecular geometries and bond graphs obtained from quantum-chemical calculations using automated CLPO analysis with almost no input of empirical data. The obtained ‘non-empirical’ covalent radii, determined separately for single, double and triple bonds, have been found to be in good agreement with their empirical counterparts available in the literature. The distributions of deviations between the sum of proposed radii and the true bond lengths are analysed in details, with emphasis put on the role of the electron delocalisation on the bond lengths. Corrections to the additive covalent radii model due to the difference in the elements electronegativities are derived for Pauling electronegativity scale. We further assess the accuracy of distance-based discrimination between bonded and non-bonded pairs of atoms in which the interatomic threshold distance is parameterised via the found covalent radii.

First-Principles Study of Van Der Waals Interactions between Halogen Molecules (Cl2 and I2)

Density Functional Theory (DFT) based first-principles calculations have been performed to investigate vander Waals (vdW) interactions in between halogen atoms/molecules —Cl-Cl, I-I, Cl2-Cl2, Cl2-I2, I2-I2—via with and without a non-local exchange-correlation (XC) functional (vdW-DF) using Quantum ESPRESSO codes. The non-polar covalent bond length between atomic halogens (Cl-Cl and I-I) is not observed to be affected by vdW interactions and agrees well with experimental values. The binding energy between theatomic halogens, on the other hand, is slightly corrected by vdW interactions. However, the role of vdW interactions is observed to be crucial to bind molecular halogens. The molecules are weakly bound in the presence of vdW interactions and not correlated (bound) in the absence of them.

Characterizing effects of fast melt deformation on entangled polymers in their glassy state.

Fast deformation of entangled melts is known to cause chain stretching due to affinelike straining of the entanglement network. Since the chain deformation may also result in perturbations of covalent bond angles and bond length, there are always possible enthalpic effects. In this study, we first subject polystyrene and PMMA of different molecular weights to either uniaxial melt extension or planar extension and subsequently impose rapid thermal quenching to preserve the chain deformation. Then, such pre-melt-deformed samples are annealed at various temperatures below the glass transition temperature Tg. During annealing, these samples can undergo appreciable contraction on a time scale much shorter than the alpha relaxation time. Significant retractive stress is observed when such contracting samples are held fixed during the annealing. The stress level can be nearly as high as the Cauchy stress produced during melt stretching. These observations not only allowed us to investigate glassy chain dynamics as well as the molecular nature of mechanical stress but may also suggest that pre-melt-stretched polymers can cause segmental mobilization in the glassy state. The available evidence indicates that the retractive stress is enthalpic in origin, associated with the conformational distortion at the bond level produced by melt stretching.

Cis/Trans Energetics in Epoxide, Thiirane, Aziridine and Phosphirane Containing Cyclopentanols: Effects of Intramolecular OH⋯O, S, N and P Contacts.

A recent computational analysis of the stabilizing intramolecular OH⋯O contact in 1,2-dialkyl-2,3-epoxycyclopentanol diastereomers has been extended to thiiriane, aziridine and phosphirane analogues. Density functional theory (DFT), second-order Møller-Plesset perturbation theory (MP2) and CCSD(T) coupled-cluster computations with simple methyl and ethyl substituents indicate that electronic energies of the isomers are lowered by roughly 3 to 4 kcal mol−1 when the OH group of these cyclopentanol systems forms an intramolecular contact with the O, S, N or P atom on the adjacent carbon. The results also suggest that S and P can participate in these stabilizing intramolecular interactions as effectively as O and N in constrained molecular environments. The stabilizing intramolecular OH⋯O, OH⋯S, OH⋯N and OH⋯P contacts also increase the covalent OH bond length and significantly decrease the OH stretching vibrational frequency in every system with shifts typically on the order of −41 cm−1.

Gas sensing properties of silicon nanowires with different cross-sectional shapes toward ammonia: a first-principles study

Nanostructure-based sensors working based on the adsorption-desorption mechanism received much attention in a wide variety of applications as a way to achieve both ultrasensitive sensing and small dimensions. In this paper, the adsorption of ammonia molecule on silicon nanowire surface with square, circular, and triangular cross-sectional shapes, which has almost similar cross-sectional area (1.2 nm2), is studied. The effects of various adsorption configurations are considered on the sensing properties, utilizing first-principles ab initio density functional theory calculations. Structural properties such as bond lengths and bond angles are obtained along with electronic properties such as band structure, charge transfer, and projected density of states for several adsorption configurations. The most stable and most sensitive structure is calculated to be the triangular nanowire considering formation enthalpy as a stability factor. For this nanowire, adsorption energy, covalent bond length, and charge transfer between ammonia and nanowire are calculated to be 1.296 eV, 3.124 A, and 0.227 |e|, respectively. We also consider nanowires with fully hydrogen-passivated surface and nanowires with a dangling bond. It has been shown that nanowires with a dangling bond are more sensitive toward ammonia than fully passivated nanowires.

The dataset of covalent bond lengths resulting from the first-principle calculations

The non-empirical dataset of the covalent bond lengths is created via the automated procedure combining geometries of 26050 small closed-shell molecules optimized by one of three DFT methods (B3LYP/6-31G*, PBEh-3c, B97-3c) with the covalent bond graphs recovered from the MP2 first-order density matrices by recently introduced property-oriented orbital localization procedure (CLPO). The dataset (https://dx.doi.org/10.5281/zenodo.2631844) contains the distances between H, B, C, N, O, F, Si, P, S, Cl, Ge, As, Se, Br atoms linked by 213404 single, 38732 double and 5031 triple bonds. The statistical distributions of lengths of the covalent bonds were analyzed for different pairs of chemical elements and the influence of electron delocalization on the bond lengths was studied. The average lengths of the bonds not affected by electron delocalization, obtained from the proposed dataset, have been found to be in good agreement with the average bond lengths derived from the available experimental data in the gas-phase.

First-principles study of electronic, magnetic and optical properties of N doping topological insulator Bi2Se3

In this paper, the manipulative effect of N doping on topological insulator Bi 2 Se 3 was investigated by using density functional theory (DFT). The computational results reveal that the van der Waals (vdW) correction is necessary when calculating the geometric structure of Bi 2 Se 3 . Taking into account the spin–orbit coupling(SOC), the electronic structure of Bi 2 Se 3 can be accurately described, especially for the energy bands near the Fermi level. The N doping at anion sites can produce an impurity band which appeared at Fermi energy. Comparing with pure Bi 2 Se 3 , the electronic structure of N doping Bi 2 Se 3 changed obviously at Fermi energy. The valence band and conduction band meet when N doped on Se1 sites, the insulating properties of Bi 2 Se 3 system are damaged. The indirect gaps between the valence band and conduction band are 0.135 eV and 0.115 eV with N doping on Se2 sites with the doping levels 6.67% and 1.67%, respectively. On the other hand, the N doping at Se sites of Bi 2 Se 3 can induce magnetic moments. The magnetic moments are related to the covalent bond length between N atom and Bi atom. Furthermore, the real and imaginary parts of dielectric functions have been computed. The static dielectric constant ε 1 (0) becomes significantly larger and the peaks in the imaginary part of dielectric constant ε 2 ( ω ) spectra move toward low energy. The intensity of the peak is gradually enhanced and there is a small bump in Bi 6 Se 8 N2 at 0.38 eV. The N doping paves a prospective way to tune the topological properties and may find change to potential spintronic applications and electronic devices. • The electronic structure of N doping Bi 2 Se 3 are changed obvious at fermi energy. • The insulation properties of Bi 2 Se 3 system are damaged with N doping on Se1 sites. • The N doping at Se sites can induce magnetic moments.

Analytical gradient for the domain-based local pair natural orbital second order Møller-Plesset perturbation theory method (DLPNO-MP2).

Building upon our previously published work [P. Pinski and F. Neese, J. Chem. Phys. 148, 031101 (2018)], we derive the formally complete analytical gradient for the domain-based local pair natural orbital second order Møller-Plesset (MP2) perturbation theory method. Extensive testing of geometry optimizations shows that the deviations from resolution of the identity-based MP2 structures are small. Covalent bond lengths are reproduced to within 0.1 pm, whereas errors in interatomic distances between noncovalently interacting system parts do not exceed 1% with default truncation thresholds and 0.3% with tight thresholds. Moreover, we introduce a procedure to circumvent instabilities of the gradient caused by singular coupled-perturbed localization equations, as they occur for some symmetric systems with continuously degenerate localized orbitals. The largest system for which a geometry optimization was completed is a host-guest complex with over 200 atoms and more than 4000 basis functions (triple-zeta basis). The most demanding single-point gradient calculation was performed for the small protein crambin containing 644 atoms and over 12 000 basis functions.

The structure of near stoichiometric Ge-Ga-Sb-S glasses: A reverse Monte Carlo study

The structure of Ge22Ga3Sb10S65 and Ge15Ga10Sb10S65 glasses was investigated by neutron diffraction (ND), X-ray diffraction (XRD), and extended X-ray absorption fine structure (EXAFS) measurements at the Ge, Ga and Sb K-edges. Experimental data sets were fitted simultaneously in the framework of the reverse Monte Carlo (RMC) simulation technique. Short range order parameters were determined from the obtained large-scale configurations. It was found that the coordination numbers of Ge, Sb and S are around the values predicted by the Mott-rule (4, 3 and 2, respectively). The Ga atoms have on average 4 nearest neighbors. The structure of these stoichiometric glasses can be described by the chemically ordered network model: Ge-S, Ga-S and Sb-S bonds are the most important. Long Sb-S distances (0.3–0.4 Å higher than the usual covalent bond lengths) are observed, suggesting that Sb atoms can be found in various local environments.

Atomic level structure of Ge-Sb-S glasses: Chemical short range order and long Sb-S bonds

The structure of Ge20Sb10S70, Ge23Sb12S65 and Ge26Sb13S61 glasses was investigated by neutron diffraction (ND), X-ray diffraction (XRD), extended X-ray absorption fine structure (EXAFS) measurements at the Ge and Sb K-edges as well as Raman scattering. For each composition, large scale structural models were obtained by fitting simultaneously diffraction and EXAFS data sets in the framework of the reverse Monte Carlo (RMC) simulation technique. Ge and S atoms have 4 and 2 nearest neighbors, respectively. The structure of these glasses can be described by the chemically ordered network model: Ge-S and Sb-S bonds are always preferred. These two bond types adequately describe the structure of the stoichiometric glass while S-S bonds can also be found in the S-rich composition. Raman scattering data show the presence of Ge-Ge, Ge-Sb and Sb-Sb bonds in the S-deficient glass but only Ge-Sb bonds are needed to fit diffraction and EXAFS datasets. A significant part of the Sb-S pairs has 0.3–0.4 Å longer bond distance than the usually accepted covalent bond length (∼2.45 Å). From this observation it was inferred that a part of Sb atoms have more than 3 S neighbors.

Density Functional Theory for Microwave Spectroscopy of Noncovalent Complexes: A Benchmark Study.

In this work, we compare the results obtained with 89 computational methods for predicting noncovalent bond lengths in weakly bound complexes. Evaluations for the performance in noncovalent interaction energies and covalent bond lengths obtained from five other data sets are included. The overall best performing density functional is the ωB97M-V method, achieving balanced results across all three categories. For noncovalent geometries, the best methods include B97M-V, B3LYP-D3(BJ) and DSD-PBEPBE-D3(BJ). The effects of systematic improvement of the density functional approximation and of dispersion corrections are also discussed.

Chemical order in Ge-Ga-Sb-Se glasses

The short range order in Ge30Ga5Sb10Se55 and Ge21Ga5Sb10Se64 glasses was investigated by X-ray (XRD) and neutron diffraction (ND) as well as extended X-ray absorption fine structure (EXAFS) measurements at the Ge, Ga, Sb and Se K-edges. Large scale structural models were obtained by fitting simultaneously the experimental data sets by reverse Monte Carlo (RMC) simulation technique. It was found that Ge, Sb and Se atoms follow the Mott-rule and have 4, 3 and 2 nearest neighbors, respectively. The average coordination number of the Ga atoms was around 4. The structure of these glasses can be described by the chemically ordered network model: the Ge–Se, Ga–Se and Sb–Se bonds are the most prominent while Ge–Ge and Ge–Sb bonds are formed only in Se-poor compositions. Models generated by RMC contained some long distances (0.3–0.4 Å higher than the usual covalent bond lengths) between Ge–Se and/or Ge–Ge pairs. Dedicated simulation runs confirm the existence of these bonds.

Electrophilic-Nucleophilic Dualism of Nickel(II) toward Ni···I Noncovalent Interactions: Semicoordination of Iodine Centers via Electron Belt and Halogen Bonding via σ-Hole.

The nitrosoguanidinate complex [Ni{NH═C(NMe2)NN(O)}2] (1) was cocrystallized with I2 and sym-trifluorotriiodobenzene (FIB) to give associates 1·2I2 and 1·2FIB. Structures of these solid species were studied by XRD followed by topological analysis of the electron density distribution within the framework of Bader's approach (QTAIM) at the M06/DZP-DKH level of theory and Hirshfeld surface analysis. Our results along with inspection of XRD (CCDC) data, accompanied by the theoretical calculations, allowed the identification of three types of Ni···I contacts. The Ni···I semicoordination of the electrophilic nickel(II) center with electron belt of I2 was observed in 1·2I2, the metal-involving halogen bonding between the nucleophilic nickel(II)-dz2 center and σ-hole of iodine center was recognized and confirmed theoretically in the structure of [FeNi(CN)4(IPz)(H2O)]n (IPz = 4-N-coordinated 2-I-pyrazine), whereas the arrangement of FIB in 1·2FIB provides a boundary case between the semicoordination and the halogen Ni···I bondings. In 1·2I2 and 1·2FIB, noncovalent interactions were studied by variable temperature XRD detecting the expansion of noncovalent contacts with preservation of covalent bond lengths upon the temperature increase from 100 to 300 K. The nature and energies of all identified types of the Ni···I noncovalent interactions in the obtained (1·2I2 and 1·2FIB) and in the previously reported ([FeNi(CN)4(IPz)(H2O)]n, [NiL2](I3)2·2I2 (L = o-phenylene-bis(dimethylphosphine), [NiL]I2 (L = 1,4,8,11-tetra-azacyclotetradecane), Ni(en)2]n[AgI2]2n (en = ethylenediamine), and [NiL](ClO4) (L = 4-iodo-2-((2-(2-(2-pyridyl)ethylsulfanyl)ethylimino)methyl)-phenolate)) structures were studied theoretically. The estimated strengths of these Ni···I noncovalent contacts vary from 1.6 to 4.1 kcal/mol and, as expected, become weaker on heating. This work is the first emphasizing electrophilic-nucleophilic dualism of any metal center toward noncovalent interactions.

Crystal, optical, and electrical characteristics of transparent conducting gallium-doped zinc oxide films deposited on flexible polyethylene naphthalate substrates using radio frequency magnetron sputtering

Gallium-doped zinc oxide (GZO) thin films were deposited on flexible polyethylene naphthalate substrates using radio frequency (RF) magnetron sputtering. The resulting GZO thin films were polycrystalline, displaying a hexagonal wurtzite-type crystal structure with a preferred grain orientation in the (002) direction. The covalent bond length of the films decreased as the RF deposition power increased, an inverse trend to that of the residual stress. In the transmission spectra, the absorption edge was about 380nm, and the optical transmittance decreased from 93.2% to 88.6% in the visible range as the RF deposition power increased from 75 to 150W. A minimum resistivity of 2.994×10−3Ω-cm was obtained for the film deposited at 125W, with a Hall mobility of 8.652cm2Vs−1 and a carrier concentration of 6.3417×1019cm−3. The figure of merit results indicated that the film deposited at 125W possessed satisfactory optical and electrical properties for potential applications.