Bond Force Constants Research Articles

Atomistic insight into orthoborate-based ionic liquids: force field development and evaluation.

We have developed an all-atomistic force field for a new class of halogen-free chelated orthoborate-phosphonium ionic liquids. The force field is based on an AMBER framework with determination of force field parameters for phosphorus and boron atoms, as well as refinement of several available parameters. The bond and angle force constants were adjusted to fit vibration frequency data derived from both experimental measurements and ab initio calculations. The force field parameters for several dihedral angles were obtained by fitting torsion energy profiles deduced from ab initio calculations. To validate the proposed force field parameters, atomistic simulations were performed for 12 ionic liquids consisting of tetraalkylphosphonium cations and chelated orthoborate anions. The predicted densities for neat ionic liquids and the [P6,6,6,14][BOB] sample, with a water content of approximately 2.3-2.5 wt %, are in excellent agreement with available experimental data. The potential energy components of 12 ionic liquids were discussed in detail. The radial distribution functions and spatial distribution functions were analyzed and visualized to probe the microscopic ionic structures of these ionic liquids. There are mainly four high-probability regions of chelated orthoborate anions distributed around tetraalkylphosphonium cations in the first solvation shell, and such probability distribution functions are strongly influenced by the size of anions.

Understanding the Polar Character Trend in a Series of Diels-Alder Reactions Using Molecular Quantum Similarity and Chemical Reactivity Descriptors

In molecular similarity there is a premise “similar molecules tend to behave similarly”; however in the actual quantum similarity field there is no clear methodology to describe the similarity in chemical reactivity, and with this end an analysis of charge-transfer (CT) processes in a series of Diels-Alder (DA) reactions between cyclopentadiene (Cp) and cyano substitutions on ethylene has been studied. The CT analysis is performed in the reagent assuming a grand canonical ensemble and the considerations for an electrophilic system using B3LYP/6-31G(d)and M06-2X/6-311 +G(d,p)methods. An analysis for CT was performed in agreement with the experimental results with a good statistical correlation(R2=0.9118)relating the polar character to the bond force constants in DA reactions. The quantum distortion analysis on the transition states (TS) was performed using molecular quantum similarity indexes of overlap and coulomb showing good correlation(R2=0.8330)between the rate constants and quantum similarity indexes. In this sense, an electronic reorganization based on molecular polarization in terms of CT is proposed; therefore, new interpretations on the electronic systematization of the DA reactions are presented, taking into account that today such electronic systematization is an open problem in organic physical chemistry. Additionally, one way to quantify the similarity in chemical reactivity was shown, taking into account the dependence of the molecular alignment on properties when their position changes; in this sense a possible way to quantify the similarity of the CT in systematic form on these DA cycloadditions was shown.

A bond-order theory on the phonon scattering by vacancies in two-dimensional materials.

We theoretically investigate the phonon scattering by vacancies, including the impacts of missing mass and linkages () and the variation of the force constant of bonds associated with vacancies () by the bond-order-length-strength correlation mechanism. We find that in bulk crystals, the phonon scattering rate due to change of force constant is about three orders of magnitude lower than that due to missing mass and linkages . In contrast to the negligible in bulk materials, in two-dimensional materials can be 3–10 folds larger than . Incorporating this phonon scattering mechanism to the Boltzmann transport equation derives that the thermal conductivity of vacancy defective graphene is severely reduced even for very low vacancy density. High-frequency phonon contribution to thermal conductivity reduces substantially. Our findings are helpful not only to understand the severe suppression of thermal conductivity by vacancies, but also to manipulate thermal conductivity in two-dimensional materials by phononic engineering.

Chemical composition, crystal structure, and their relationships with the intrinsic properties of spinel-type crystals based on bond valences.

Spinel-type crystals may possess complex and versatile chemical composition and crystal structure, which leads to difficulty in constructing relationships among the chemical composition, crystal structure, and intrinsic properties. In this work, we develop new empirical methods based on bond valences to estimate the intrinsic properties, namely, compressibility and thermal expansion of complex spinel-type crystals. The composition-weighted average of bond force constants in tetrahedral and octahedral coordination polyhedra is derived as a function of the composition-weighted average of bond valences, which can be calculated according to the experimental chemical composition and crystal structural parameters. We discuss the coupled effects of tetrahedral and octahedral frameworks on the aforementioned intrinsic properties. The bulk modulus could be quantitatively calculated from the composition-weighted average of bond force constants in tetrahedral and octahedral coordination polyhedra. In contrast, a quantitative estimation of the thermal expansion coefficient could be obtained from the composition-weighted average of bond force constants in octahedral coordination polyhedra. These empirical methods have been validated by the results obtained for a new complex quaternary spinel-type oxynitride Mg0.268Al2.577O3.733N0.267 as well as MgAl2O4 and Al2.85O3.45N0.55 from the literature. Further, these empirical methods have the potential to be extensively applied in other types of complex crystals.

Magma redox and structural controls on iron isotope variations in Earth's mantle and crust

The heavy iron isotopic composition of Earth's crust relative to chondrites has been explained by vaporization during the Moon-forming impact, equilibrium partitioning between metal and silicate at core–mantle-boundary conditions, or partial melting and magma differentiation. The latter view is supported by the observed difference in the iron isotopic compositions of MORBS and peridotites. However, the precise controls on iron isotope variations in igneous rocks remain unknown. Here, we show that equilibrium iron isotope fractionation is mainly controlled by redox (Fe3+/Fetot ratio) and structural (e.g., polymerization) conditions in magmas. We measured, for the first time, the mean force constants of iron bonds in silicate glasses by synchrotron Nuclear Resonant Inelastic X-ray Scattering (NRIXS, also known as Nuclear Resonance Vibrational Spectroscopy – NRVS, or Nuclear Inelastic Scattering – NIS). The same samples were studied by conventional Mössbauer and X-ray Absorption Near Edge Structure (XANES) spectroscopy. The NRIXS results reveal a +0.2 to +0.4‰ equilibrium fractionation on 56Fe/54Fe ratio between Fe2+ and Fe3+ end-members in basalt, andesite, and dacite glasses at magmatic temperatures. These first measurements can already explain ∼1/3 of the iron isotopic shift measured in MORBs relative to their source. Further work will be required to investigate how pressure, temperature, and structural differences between melts and glasses affect equilibrium fractionation factors. In addition, large fractionation is also found between rhyolitic glass and commonly occurring oxide and silicate minerals. This fractionation reflects mainly changes in the coordination environment of Fe2+ in rhyolites relative to less silicic magmas and mantle minerals, as also seen by XANES. We provide a new calibration of XANES features vs. Fe3+/Fetot ratio determinations by Mössbauer to estimate Fe3+/Fetot ratio in situ in glasses of basaltic, andesitic, dacitic, and rhyolitic compositions. Modeling of magma differentiation using rhyolite-MELTS shows that iron structural changes in silicic magmas can explain the heavy iron isotopic compositions of granitoids and rhyolites. This study demonstrates that iron stable isotopes can help reveal planetary redox conditions and igneous processes. Other heterovalent elements such as Ti, V, Eu, Cr, Ce, or U may show similar isotopic variations in bulk rocks and individual minerals, which could be used to establish past and present redox condition in the mantles of Earth and other planets.

The bond force constant and bulk modulus of C60

Computations of the bulk modulus (B) of the C60 molecule have been conducted by using density functional theory (DFT) and finite element analysis (FEA). The accuracy of an FEA approach to calculate the bulk modulus of the C60 molecule is evaluated by considering ab initio computations based on DFT as a reference. DFT predicts a value of the bond force constant of kr=691N/m and a strong influence of this parameter on the FEA predictions of B is found. DFT predicts the numerical value of B as 874 and 759GPa, depending if the molecule is considered as a solid truncated icosahedron or a solid sphere; the corresponding values of B calculated by FEA are within 5.3% difference with respect to DFT. The relevance of considering a shell model as well as of using the detailed equilibrium coordinates of C60 in FEA calculations is assessed. The atomistic FEA is reliable for the calculation of bulk modulus of the C60 molecule, as long as the bond force constant is accurately known.

Fe–As Bond-Dynamics Revealed from the Arsenic K-Edge EXAFS Studies of NdFeAsO1−x F x Iron-Pnictide Superconductors

Arsenic K-edge extended x-ray absorption fine structure (EXAFS) spectroscopy results of the NdFeAsO1−xFx (x=0 and 0.12) system at room temperature and 12 K are presented. The Fe–As bond seems to be hardly affected by doping and temperature. However, a careful analysis of the temperature dependence of the Fe–As bond mean-square relative displacements reveals a hardening of the Fe–As bond force constant in the superconductor compared to the NdFeAsO, revealing the distinct local lattice dynamics in the active iron-arsenic layer in governing the superconducting properties.

An assessment of finite element analysis to predict the elastic modulus and Poisson’s ratio of singlewall carbon nanotubes

Molecular mechanics implemented in finite element codes is becoming a popular method to predict elastic properties of carbon nanotubes. However, the limits of application of this approach have not yet been systematically assessed. Therefore, this work investigates the accuracy and range of application of finite element analysis (FEA) to predict the elastic modulus and Poisson’s ratio of singlewall carbon nanotubes (SWCNTs), by comparing predictions of FEA to ab initio computations based on density functional theory (DFT). FEA predicts an elastic modulus which agrees well with DFT for SWCNTs with diameters larger than 0.8nm. FEA underpredicts the Poisson’s ratio with respect to DFT, unless the FEA bond force constants previously computed for benzene are adjusted. The use of adequate values of bond force constants and the equilibrium configuration of atomic coordinates predicted by DFT as the input geometry for FEA improves its predictions. The significance of the numerical values chosen for the bond force constants in FEA is also discussed.

Solvation properties and behaviour of lutetium(III) in aqueous solution—A quantum mechanical charge field (QMCF) study

This work presents the first ab initio molecular dynamics study of trivalent lutetium in aqueous solution. The hybrid quantum and molecular mechanics simulation has been carried out on Hartree-Fock level and the results were compared to extended X-ray absorption fine structure and X-ray diffraction data. In addition to the structural characterisation via radial and angular distribution functions, the influence of the ion on the surrounding solvent was further investigated by local-density-corrected three-body distribution functions and frequency calculations. The obtained results for the mean Lu-O bond distance and force constant were in very good agreement with the literature. Furthermore, deeper insight into the dynamics and geometry of the solvation shell and the number of involved solvent molecules was obtained.

Parameters for Molecular Dynamics Simulations of Manganese-Containing Metalloproteins.

A set of geometrical parameters has been determined for single manganese metalloproteins for the AMBER force field, and ultimately to other force fields with a similar philosophy. Twelve (12) models from 9 different single-cluster manganese proteins were optimized and parametrized, using a bonded model approach. Mn-ligand bonds, Mn-ligand angles, and Restrained Electrostatic Potential charges for all the 74 residues in the first metal coordination sphere of each Mn metalloprotein were parametrized. The determined parameters were validated with molecular dynamics simulations and several statistics strategies were used to analyze the results. In addition, to validate the parametrized models, frequency and normal mode calculations were performed and comparisons were obtained for the overall structures both with quantum mechanics and molecular mechanics calculations. Linear and polynomial fittings were performed to estimate Mn-ligand bond force constants for generic manganese centers. Furthermore, averages are proposed for the main Mn-ligand angle interactions of typical manganese coordination centers: axial, square and triangular equatorial planes, and tetrahedral positions, for the different combinations of donor atoms from waters and hard ligands.

Spectroscopic, thermal analyses, structural and antibacterial studies on the interaction of some metals with ofloxacin

Reaction between the fluoroquinolone antibacterial agent ofloxacin and V(IV), Zr(IV) and U(VI) in methanol and acetone was studied. The ability of ofloxacin to form metal complexes is high. The isolated solid complexes were characterized by elemental analysis, magnetic moment, conductance measurements, infrared, electronic, 1H NMR spectra and thermal investigation. In all complexes the ofloxacin ligand is coordinated through the pyridone and carboxylate oxygen forming 1:2M:HOfl complexes. The calculated bond length and force constant, F(UO), in the uranyl complex are 1.73Å and 640.83Nm−1, respectively. The metal–ligand binding of the V(IV) and Zr(IV) complexes was predicted by using the density functional theory (DFT) at the B3LYP-CEP-31G level of theory and total energy, dipole moment estimation of different V(IV) and Zr(IV) ofloxacin structures. All the synthesized complexes exhibited higher biocidal activity against S. aureus K1, Bacillus subtilis K22, Br. otitidis K76, Escherichia coli K32, Pseudomonas aeruginosa SW1 and Klebsiella oxytoca K42. compared to parent compounds and standard drugs.

Force correcting atom centred potentials for generalised gradient approximated density functional theory: Approaching hybrid functional accuracy for geometries and harmonic frequencies in small chlorofluorocarbons

Generalised gradient approximated (GGA) density functional theory (DFT) typically overestimates polarisability and bond-lengths, and underestimates force constants of covalent bonds. To overcome this problem we show that one can use empirical force correcting atom centred potentials (FCACPs), parametrised for every nuclear species. Parameters are obtained through minimisation of a penalty functional that explicitly encodes hybrid DFT forces and static polarisabilities of reference molecules. For hydrogen, fluorine, chlorine and carbon the respective reference molecules consist of H2, F2, Cl2 and CH4. The transferability of this approach is assessed for harmonic frequencies in a small set of chlorofluorocarbon molecules. Numerical evidence, gathered for CF4, CCl4, CCl3F, CCl2F2, CClF3, ClF, HF, HCl, CFH3, CF2H2, CF3H, CHCl3, CH2Cl2 and CH3Cl indicates that the GGA+FCACP level of theory yields harmonic frequencies that are significantly more consistent with hybrid DFT values, as well as slightly reduced molecular polarisability.

Theoretical Modeling of Large Molecular Systems. Advances in the Local Self Consistent Field Method for Mixed Quantum Mechanics/Molecular Mechanics Calculations

Molecular mechanics methods can efficiently compute the macroscopic properties of a large molecular system but cannot represent the electronic changes that occur during a chemical reaction or an electronic transition. Quantum mechanical methods can accurately simulate these processes, but they require considerably greater computational resources. Because electronic changes typically occur in a limited part of the system, such as the solute in a molecular solution or the substrate within the active site of enzymatic reactions, researchers can limit the quantum computation to this part of the system. Researchers take into account the influence of the surroundings by embedding this quantum computation into a calculation of the whole system described at the molecular mechanical level, a strategy known as the mixed quantum mechanics/molecular mechanics (QM/MM) approach. The accuracy of this embedding varies according to the types of interactions included, whether they are purely mechanical or classically electrostatic. This embedding can also introduce the induced polarization of the surroundings. The difficulty in QM/MM calculations comes from the splitting of the system into two parts, which requires severing the chemical bonds that link the quantum mechanical subsystem to the classical subsystem. Typically, researchers replace the quantoclassical atoms, those at the boundary between the subsystems, with a monovalent link atom. For example, researchers might add a hydrogen atom when a C-C bond is cut. This Account describes another approach, the Local Self Consistent Field (LSCF), which was developed in our laboratory. LSCF links the quantum mechanical portion of the molecule to the classical portion using a strictly localized bond orbital extracted from a small model molecule for each bond. In this scenario, the quantoclassical atom has an apparent nuclear charge of +1. To achieve correct bond lengths and force constants, we must take into account the inner shell of the atom: for an sp(3) carbon atom, we consider the two core 1s electrons and treat that carbon as an atom with three electrons. This results in an LSCF+3 model. Similarly, a nitrogen atom with a lone pair of electrons available for conjugation is treated as an atom with five electrons (LSCF+5). This approach is particularly well suited to splitting peptide bonds and other bonds that include carbon or nitrogen atoms. To embed the induced polarization within the calculation, researchers must use a polarizable force field. However, because the parameters of the usual force fields include an average of the induction effects, researchers typically can obtain satisfactory results without explicitly introducing the polarization. When considering electronic transitions, researchers must take into account the changes in the electronic polarization. One approach is to simulate the electronic cloud of the surroundings by a continuum whose dielectric constant is equal to the square of the refractive index. This Electronic Response of the Surroundings (ERS) methodology allows researchers to model the changes in induced polarization easily. We illustrate this approach by modeling the electronic absorption of tryptophan in human serum albumin (HSA).

A general moment NRIXS approach to the determination of equilibrium Fe isotopic fractionation factors: Application to goethite and jarosite

The equilibrium Fe isotopic fractionation factors of goethite and jarosite have considerable importance for interpreting Fe isotope variations in low temperature aqueous systems on Earth and possibly Mars in the context of future sample return missions. We measured the β-factors of goethite FeO(OH), potassium-jarosite KFe3(SO4)2(OH)6, and hydronium-jarosite (H3O)Fe3(SO4)2(OH)6, by Nuclear Resonant Inelastic X-ray Scattering (NRIXS, also known as Nuclear Resonance Vibrational Spectroscopy – NRVS or Nuclear Inelastic Scattering – NIS) at the Advanced Photon Source. These measurements were made on synthetic minerals enriched in 57Fe. A new method (i.e., the general moment approach) is presented to calculate β-factors from the moments of the NRIXS spectrum S(E). The first term in the moment expansion controls iron isotopic fractionation at high temperature and corresponds to the mean force constant of the iron bonds, a quantity that is readily measured and often reported in NRIXS studies. The mean force constants of goethite, potassium-jarosite, and hydronium-jarosite are 314±14, 264±12, and 310±14N/m, respectively (uncertainties include statistical and systematic errors). The general moment approach gives 56Fe/54Fe β-factors of 9.7, 8.3, and 9.5‰ at 22°C for these minerals. The β-factor of goethite measured by NRIXS is larger than that estimated by combining results from laboratory exchange experiments and calculations based on electronic structure theory. Similar issues have been identified previously for other pairs of mineral–aqueous species, which could reflect inadequacies of approaches based on electronic structure theory to calculate absolute β-factors (differences in β-factors between aqueous species may be more accurate) or failure of laboratory experiments to measure mineral–fluid equilibrium isotopic fractionation at low temperature. We apply the force constant approach to published NRIXS data and report 1000×lnβ for important Fe-bearing phases of geological and biochemical relevance such as myoglobin, cytochrome f, pyroxene, metal, troilite, chalcopyrite, hematite, and magnetite.

Periodic tables of diatomic and triatomic molecules

The Mendeleev periodic table of atoms is one of the most important principles in natural science. However, there is shortage of analog for molecules. Here we propose two periodic tables, one for diatomic molecules and one for triatomic molecules. The form of the molecular periodic tables is analogous to that of Mendeleev periodic table of atoms. In the table, molecules are classified and arranged by their group number G, which is the number of valence electrons, and the periodic number P, which represents the size of the molecules. The basic molecular properties, including bond length, binding energy, force constant, ionization potential, spin multiplicity, chemical reactivity, and bond angle, change periodically within the tables. The periodicities of diatomic and triatomic molecules are thus revealed. We also demonstrate that the periodicity originates from the shell-like electronic configurations of the molecules. The periodic tables not only contain free molecules, but also the “virtual” molecules present in polyatomic molecules. The periodic tables can be used to classify molecules, to predict unknown molecular properties, to understand the role of virtual molecules in polyatomic molecules, and to initiate new research fields, such as the periodicities of aromatic species, clusters, or nanoparticles. The tables should be of interest not only to scientists in a variety of disciplines, but also to undergraduates studying natural sciences.

Structure, analysis and some magnetic properties for low temperature fired Ni–Cu ferrite

Cu2+ ions substituted Ni-ferrite having the general formula Ni1-xCuxFe2O4 (where x=0.0, 0.2, 0.4 and 0.6) were prepared by the sintering ceramic method. X-ray diffraction, infrared spectra and magnetization of the above ferrite were carried out to investigate structural and magnetic characterization of this ferrite. Crystallite size, lattice parameters, positional oxygen parameter and ionic radii for both tetrahedral and octahedral sites were calculated. The experimental lattice parameter was found to vary between 8.3856 and 8.3865Å. The infrared spectra were measured in the frequency range 650–150cm−1. Two prominent bands were observed, high frequency band ν1 and low frequency band ν2 were assigned to tetrahedral and octahedral sites. Bond length and force constant were also calculated for both tetrahedral and octahedral sites. The effect of Cu concentration on, saturation magnetization, coercivity ratio and magnetic moment were investigated using vibrating sample magnetometer (VSM). It was found that both saturation magnetization (MS) and coercivity (Hc) decreases with increasing in Cu content.

Spectroscopic, thermal analysis, and antimicrobial evaluation of new Y(III), Zr(IV), and U(VI) ibuprofen complexes

New complexes of Y(III), Zr(IV), and U(VI) with the anti-inflammatory drug ibuprofen (IBU) have been synthesized and characterized by elemental analysis, spectroscopic techniques (UV-Visible, IR, and 1H NMR), magnetic moment determination, conductance measurements, and thermal analyses (thermogravimetric and differential thermogravimetric). The anti-inflammatory drug acts as bidentate chelate bound to metal ions through the deprotonated carboxylate. The calculated bond length and force constant, F(U=O), in the uranyl complex are 1.815 Å and 671.69 Nm−1, respectively. The metal–ligand binding of the Zr(IV) and Y(III) complexes is predicted using density functional theory at the B3LYP-CEP-31G level of theory and total energy, dipole moment estimation of different Zr(IV) and Y(III) ibuprofen structures. The antibacterial activity of the ligand, metal salts, and metal complexes have been tested, showing that the complexes are significant against all six bacterial species compared with IBU and metal salts.

A study of Sn addition on bonding arrangement of Se-Te alloys using far infrared transmission spectroscopy

Far infrared transmission spectra of Se92Te8−xSnx (x = 0, 1, 2, 3, 4, 5) glassy alloys are obtained in the spectral range 50–600 cm−1 at room temperature. The results are interpreted in terms of the vibrations of the isolated molecular units in such a way so as to preserve fourfold and twofold coordination for Sn and chalcogen atoms (Se,Te), respectively. With the addition of Sn, Far-IR spectra shift toward high frequency side and some new bands start appearing. Sn atoms appear to substitute for the selenium atoms in the outrigger sites due to large bond formation probability. Theoretical calculations of bond energy, relative probability of bond formation, force constant, and wave number were also made to justify the result.

Hydroxide Hydrogen Bonding: Probing the Solvation Structure through Ultrafast Time Domain Raman Spectroscopy.

The mechanism of charge transport in aqueous media is critical in molecular, materials, and life sciences. The structure of the solvated hydroxide ion has been an area of some controversy. Polarization-resolved ultrafast time domain polarizability relaxation is used here to resolve the terahertz frequency Raman spectrum of hydroxide solutions. The measurements reveal the totally symmetric hydrogen-bond stretching (HO(-)···HOH) mode of the solvated hydroxide, permitting an experimental measurement of the bond force constant. The observed polarized Raman spectra are compared with those obtained from DFT calculations performed on HO(-)(H2O)n clusters. Good agreement between the observed frequency and the polarization dependence is found for the n = 3 or 4 clusters, particularly for those in which the solvating water molecules adopt a planar structure. The frequency of the symmetric stretch increases with concentration, consistent with an effect of ionic strength on either the H-bond or the structure of the cluster.

Multiscale Simulation of Intra-Protein Communication

We develop a new computational framework to model intra-protein communication. The configurations sampled in atomic molecular dynamics trajectories are used to compute bond lengths and force constants in an elastic network approximation of the distribution of protein structures. To go beyond the harmonic approximation, a key novelty is to compute model parameters in consecutive time windows with a user-specified size to follow the time evolution of the mechanical coupling network of protein conformation. In analogy to spectrogram of sound waves, sequential elastic network models calculated from atomic trajectories are termed the fluctuogram of protein dynamics. By analyzing and comparing the fluctuograms of Ca2+-bound and apo subtilisin, we illustrate that intermittent conformational changes and mechanical coupling variation are important mechanisms of intra-protein communication. We also show that the fluctuogram can be used to predict residues with high tendency to co-evolve by comparing with the results of statistical coupling analysis of a multiple sequence alignment. In addition to the strength of mechanical coupling, we found that the fluctuation of inter-residue force constants is also an important descriptor for co-evolution. Together, the results of this work (a) reveal the intermittent nature of conformational changes and the mechanical coupling variation, (b) show that intra-protein communication can proceed without a drastic change of protein structure and the pathways of which can be identified by the fluctuogram, and (c) support the theory that mechanically coupled residues tend to co-evolve.