Ab Initio Quantum Chemical Calculations Research Articles

Unraveling the Orbital Physics in a Canonical Orbital System KCuF_{3}.

We explore the existence of the collective orbital excitations, orbitons, in the canonical orbital system KCuF_{3} using the Cu L_{3}-edge resonant inelastic x-ray scattering. We show that the nondispersive high-energy peaks result from the Cu^{2+} dd orbital excitations. These high-energy modes display good agreement with the abinitio quantum chemistry calculation, indicating that the dd excitations are highly localized. At the same time, the low-energy excitations present clear dispersion. They match extremely well with the two-spinon continuum following the comparison with Müller ansatz calculations. The localized dd excitations and the observation of the strongly dispersive magnetic excitations suggest that the orbiton dispersion is below the resolution detection limit. Our results can reconcile with the strong local Jahn-Teller effect in KCuF_{3}, which predominantly drives orbital ordering.

Vibronic coupling in the first six electronic states of pentafluorobenzene radical cation: Radiative emission and nonradiative decay

Nuclear dynamics in the first six vibronically coupled electronic states of pentafluorobenzene radical cation is studied with the aid of the standard vibronic coupling theory and quantum dynamical methods. A model 6 × 6 vibronic Hamiltonian is constructed in a diabatic electronic basis using symmetry selection rules and a Taylor expansion of the elements of the electronic Hamiltonian in terms of the normal coordinate of vibrational modes. Extensive ab initio quantum chemistry calculations are carried out for the adiabatic electronic energies to establish the diabatic potential energy surfaces and their coupling surfaces. Both time-independent and time-dependent quantum mechanical methods are employed to perform nuclear dynamics calculations. The vibronic spectrum of the electronic states is calculated, assigned, and compared with the available experimental results. Internal conversion dynamics of electronic states is examined to assess the impact of various couplings on the nuclear dynamics. The impact of increasing fluorination of the parent benzene radical cation on its radiative emission is examined and discussed.

Solvent molecules form surface redox mediators in situ and cocatalyze O2 reduction on Pd.

Solvent molecules influence the reactions of molecular hydrogen and oxygen on palladium nanoparticles. Organic solvents activate to form reactive surface intermediates that mediate oxygen reduction through pathways distinct from reactions in pure water. Kinetic measurements and ab initio quantum chemical calculations indicate that methanol and water cocatalyze oxygen reduction by facilitating proton-electron transfer reactions. Methanol generates hydroxymethyl intermediates on palladium surfaces that efficiently transfer protons and electrons to oxygen to form hydrogen peroxide and formaldehyde. Formaldehyde subsequently oxidizes hydrogen to regenerate hydroxymethyl. Water, on the other hand, heterolytically oxidizes hydrogen to produce hydronium ions and electrons that reduce oxygen. These findings suggest that reactions of solvent molecules at solid-liquid interfaces can generate redox mediators in situ and provide opportunities to substantially increase rates and selectivities for catalytic reactions.

Quantitative analysis of weak current rectification in molecular tunnel junctions subject to mechanical deformation reveals two different rectification mechanisms for oligophenylene thiols versus alkane thiols.

Metal-molecule-metal junctions based on alkane thiol (CnT) and oligophenylene thiol (OPTn) self-assembled monolayers (SAMs) and Au electrodes are expected to exhibit similar electrical asymmetry, as both junctions have one chemisorbed Au-S contact and one physisorbed, van der Waals contact. Asymmetry is quantified by the current rectification ratio RR apparent in the current-voltage (I-V) characteristics. Here we show that RR < 1 for CnT and RR > 1 for OPTn junctions, in contrast to expectation, and further, that RR behaves very differently for CnT and OPTn junctions under mechanical extension using the conducting probe atomic force microscopy (CP-AFM) testbed. The analysis presented in this paper, which leverages results from the previously validated single level model and ab initio quantum chemical calculations, allows us to explain the puzzling experimental findings for CnT and OPTn in terms of different current rectification mechanisms. Specifically, in CnT-based junctions the Stark effect creates the HOMO level shifting necessary for rectification, while for OPTn junctions the level shift arises from position-dependent coupling of the HOMO wavefunction with the junction electrostatic potential profile. On the basis of these mechanisms, our quantum chemical calculations allow quantitative description of the impact of mechanical deformation on the measured current rectification. Additionally, our analysis, matched to experiment, facilitates direct estimation of the impact of intramolecular electrostatic screening on the junction potential profile. Overall, our examination of current rectification in benchmark molecular tunnel junctions illuminates key physical mechanisms at play in single step tunneling through molecules, and demonstrates the quantitative agreement that can be obtained between experiment and theory in these systems.

Theoretical analysis of means of preventing Si–C bond cleavage during polycondensation of organosilanes to organosilicas

Practical strategies for suppressing Si–C cleavage during the polycondensation of organosilanes were presented based on ab initio quantum chemical calculations of model compounds.

Sulfur valence-to-core X-ray emission spectroscopy study of lithium sulfur batteries.

In this work, valence-to-core (VtC) Kβ sulfur X-ray emission spectroscopy (XES) was used to perform quantitative analysis of different sulfur compounds produced in a lithium sulfur (Li-S) battery during discharge. The analysis is based on the theoretical sulfur Kβ XES spectra obtained from ab initio quantum chemical calculations based on density functional theory. The emphasis is given to the Kβ sulfur XES spectra of the polysulfide molecules (Li2Sx, x = 2,,8) produced electrochemically within the Li-S battery. Ab initio molecular dynamics calculations are used further to calculate also the Kβ spectra of Li2Sx dissolved in a model solvent. Calculated spectra were directly compared with the experimental ones collected with a Johansson type tender XES spectrometer on laboratory synthesized Li2Sx reference standards and pre-cycled battery cathodes. These results demonstrate that sulfur VtC XES can be used effectively to quantitatively analyze electrochemical sulfur conversion, also in a smaller laboratory without the need for large scale synchrotron facilities.

Assigning XPS features in B,N-doped graphene: input from ab initio quantum chemical calculations

Ab initio quantum chemical calculations using large enough cluster models have been used to predict the core level binding energies of B(1s) and N(1s), including initial and final state effects, in several possible atomic arrangements in B,N-codoped graphene, such as isolated atoms, different types of B,N pairs and BN domains. To a large extent, the observed trends are dominated by initial state effects that support assigning the experimental features to the neutral samples. For the BN domains the present theoretical results are in full agreement with the experimental assignment thus providing support to the rest of the assignments. In particular, the present results strongly suggest that some of the features observed in the experiments are likely to correspond to isolated B or N atoms in graphene and, others fit well to the prediction corresponding to different types of B,N pairs. The importance of having an unambiguous, rigorous way to assign experimental features is emphasized.

Laser-induced electron diffraction of the ultrafast umbrella motion in ammonia.

Visualizing molecular transformations in real-time requires a structural retrieval method with Ångström spatial and femtosecond temporal atomic resolution. Imaging of hydrogen-containing molecules additionally requires an imaging method sensitive to the atomic positions of hydrogen nuclei, with most methods possessing relatively low sensitivity to hydrogen scattering. Laser-induced electron diffraction (LIED) is a table-top technique that can image ultrafast structural changes of gas-phase polyatomic molecules with sub-Ångström and femtosecond spatiotemporal resolution together with relatively high sensitivity to hydrogen scattering. Here, we image the umbrella motion of an isolated ammonia molecule (NH3) following its strong-field ionization. Upon ionization of a neutral ammonia molecule, the ammonia cation (NH3+) undergoes an ultrafast geometrical transformation from a pyramidal () to planar () structure in approximately 8 femtoseconds. Using LIED, we retrieve a near-planar () field-dressed NH3+ molecular structure femtoseconds after ionization. Our measured field-dressed NH3+ structure is in excellent agreement with our calculated equilibrium field-dressed structure using quantum chemical ab initio calculations.

Dipole-dipole polarizability of the cadmium -=SUP=-1-=/SUP=-S-=SUB=-0-=/SUB=- state revisited -=SUP=-*-=/SUP=-

Experimental results and high-level quantum chemical ab initio calculations of the static polarizability &amp;alpha;=&amp;alpha;(&amp;omega;=0)) of the cadmium 1S0 state are still in marked disagreement. Here we analyze this discrepancy by using experimentally determined dipole oscillator strength distributions (DOSD). It will be shown that within this procedure the experimentally determined static polarizability &amp;alpha;0 will shift from 49.7&amp;#177; 1.6 au to considerably lower values. We now conclude an experimentally determined polarizability of &amp;alpha;0 = 47.5 &amp;#177; 2.0 au in much better agreement with the latest calculations of &amp;alpha;0&amp;#126; 46 au. Keywords: cadmium, polarizability, DOSD

Природа тонкой структуры вращательных уровней основного X-=SUP=-2-=/SUP=-Sigma-=SUP=-+-=/SUP=--состояния радикала CN

By means of ab initio high-level quantum-chemical calculations of non-diagonal matrix elements of spin-orbital and electron-rotational coupling between the ground X2Σ+ and excited (1--4)2Π states the observed regular effect of γ-doubling of the rotational levels of the X2Σ+ state was shown to be mainly determined by intramolecular interactions of the mentioned state with remote states (2--4)2Π. In terms of the nonadiabatic model of the effective radial Hamiltonian of the isolated electronic state, it was possible to create the analytical potential of the X2Σ+ state and the corresponding function γ (R) reproducing the frequencies of rotational and vibrational-rotational transitions (for the lowest vibrational levels ν≤3) of the CN molecule at the experimental (spectroscopic) level of accuracy.

Progress towards nanoengineered energetic materials

Given the constraints on typical bond energies and the commonality of final products produced from combustion of CHNO based energetic materials, the possibilities for further increases in stored potential energy and thermodynamic performance from these classes of materials are limited. Thus, modulating the energy release to achieve efficiency and effectiveness for desired applications is of great value. Investigation of nanomaterials as energetic materials began more than twenty years ago with much of the interest to increase reaction rates and reduce sensitivity. During this period, research on energetic nanoparticles was devoted to reducing the loss of energy density with metallic materials due to the naturally occurring oxide passivating layer, managing their high surface area preventing high loadings in solids, minimizing particle-particle interactions making dispersion in the gas-phase difficult, and understanding combustion mechanisms. As an outcome, novel synthesis methods of producing nanocomposites, and new fields of applications, such as micro-pyrotechnics, have developed. Yet, the research community is only beginning to understand how to manipulate and build energetic materials at the nanoscale, and what designs are optimal for desired functions. Furthermore, recognizing the difficulties for increased energy density and reduced sensitivity, the development of multifunctional and smart nanoenergetic materials is currently being researched to enable control of energy release rates and material sensitivity on demand. This research is being advanced by assembly of nanoengineered energetic materials to bulk scales by additive manufacturing, the development and application of combustion diagnostics that resolve nanometer and micron scales, and ab initio quantum chemistry and molecular dynamics calculations. The challenges that have been confronted and the directions of continuing research on nanoenergetics are presented and discussed.

Temperature-Dependent Raman Spectroscopic Study of the Double Molybdate KBi(MoO4)2.

In situ high-temperature Raman spectra of polycrystalline KBi(MoO4)2 were recorded from room temperature to 1073 K. Thermal stability of the monoclinic KBi(MoO4)2 was examined by temperature-dependent XRD. The monoclinic phase transformed into the scheelite tetragonal structure at 833 K, and then to the monoclinic phase at 773 K. Quantum chemistry ab initio calculation was performed to simulate the Raman spectra of the structure of KBi(MoO4)2 high-temperature melt. The experimental Raman band at 1023 K was deconvoluted into seven Gaussian peaks, and the calculated results were in good agreement with the experimental data. Therefore, the vibrational modes of Raman peaks of molten KBi(MoO4)2 were assigned. It was confirmed that the isolated structure of [Bi(MoO4)2]− monomer, consisting of Mo6+ centers and Bi3+ sub-centers connected by edge-sharing, mainly exists in the melt of KBi(MoO4)2.

Real-space quantum-based refinement for cryo-EM: Q|R#3.

Electron cryo-microscopy (cryo-EM) is rapidly becoming a major competitor toX-ray crystallography, especially for large structures that are difficult or impossible to crystallize. While recent spectacular technological improvements have led to significantly higher resolution three-dimensional reconstructions, the average quality of cryo-EM maps is still at the low-resolution end of the range compared with crystallography. A long-standing challenge for atomic model refinement has been the production of stereochemically meaningful models for this resolution regime. Here, it is demonstrated that including accurate model geometry restraints derived from ab initio quantum-chemical calculations (HF-D3/6-31G) can improve the refinement of an example structure (chain A of PDB entry 3j63). The robustness of the procedure is tested for additional structures with up to 7000 atoms (PDB entry 3a5x and chain C of PDB entry 5fn5) using the less expensive semi-empirical (GFN1-xTB) model. The necessary algorithms enabling real-space quantum refinement have been implemented in the latest version of qr.refine and are described here.

Experimental and theoretical evidence for the temperature-determined evolution of PAH functional groups

Elucidating the chemical evolution of various functional groups in polycyclic aromatic hydrocarbons (PAH) and soot aids in understanding soot formation chemistry. In this work, the chemical evolution of various functional groups, including aromatic CH, aliphatic CH, C=O, COH and COC bonds, was experimentally investigated online, rather than with offline diagnostics. Oxidation was performed in a jet-stirred reactor (JSR), fueled with benzene/C2H2/air/N2 and benzene/phenol/C2H2/N2 for a temperature range of 600-1400 K. Kinetic modelling, including ab initio quantum chemistry calculations, reaction rate coefficient calculations and JSR simulations, were conducted to interpret the experimental data and the evolutionary chemistry of the various functional groups. Results show that the formation of functional groups on PAH and oxygenated PAH (OPAH) are highly sensitive to temperature. Aliphatic CH bonds survive mainly in the form of CCH2C, CCH2CH2C or CCH functional groups above 1200 K, and exist in the CHCH2 functional group below 1000 K. For the OPAH, the COC functional group presents stronger thermal stability than COH and C=O functional groups. Simulation results indicate that HACA-like pathway (hydrogen abstraction carbon addition), in which C2H2 attacks the O atom, followed by cyclization and H-atom elimination reactions, qualitatively describe the formation of OPAH with the CO-C functional group at different temperatures. The addition reaction involving PAH radical and C2H4 / C2H3 captures the evolution of PAH with the CHCH2 functional group, but fails to explain the formation of CCH2C and CCH2CH2C functional groups.

Масс-спектрометрическое исследование и теоретическое моделирование комплексов флуконазола с аланином, лизином и треонином

Investigation of the triazole-derived drugs action mechanisms and understanding of their affinity and specificity molecular basis may contribute to the new drugs development. The study was aimed to investigate the triazoles class representative (fluconazole) complexes with amino acids using mass spectrometry, molecular dynamics and ab initio quantum chemistry calculations. During the experimental study, the fluconazole, alanine, lysine and threonine solutions were analyzed by electrospray ionization mass spectrometry and tandem mass spectrometry. The molecular dynamics modeling of the fluconazole–amino acid complexes was performed using the CHARMM force field. The quantum chemistry calculations of the complexes structure and energy parameters were carried out using the density-functional theory by B3LYP calculations (3-21G and 6-311++G** basis sets). Mass spectra indicated that fluconazole formed stable complexes with amino acids in the 1 : 1 stoichiometric ratio. In accordance with the tandem mass spectrometry with varying fluconazole–amino acid associates ion fragmentation energy, the following sequence was obtained: [Fluc + Ala + H]+ &lt; [Fluc + Lys + H]+ &lt; [Fluc + Thr + H]+. The fluconazole–amino acid interaction energy values resulting from the quantum chemistry calculations formed the sequence similar to that obtained by experiment. Thus, as seen in the case of fluconazole–amino acid complexes, it is possible to combine the experimental mass spectrometry studies with quantum chemical modeling for the complexes properties assessment.

Investigation of solvated calcium dication structure in pure water, methanol, and ethanol solutions by means of K and L2,3-edges X-ray absorption spectroscopy

The interaction of an ion with surrounding solvent molecules is revealed by X-ray absorption spectroscopy in transmission mode for the case of calcium dication dissolved in pure water, methanol and ethanol at the Ca K and L2,3-edges. The near-threshold K-shell excitation leads to two distinct solvent-dependent features, the Ca 1s to 3d and 4p electronic transitions, clearly indicating the ligand field decreases as water is changed to methanol and methanol to ethanol. On the other hand, the Ca L2,3-edge excitation leads to small changes in the absorption spectra and the peak assignment – mostly in terms of Ca 2p to eg and t2g transitions for each of the two spin orbit components – is strongly depending on the geometry of the first solvation shell around the dication and on the magnitude of the ligand-field multiplet effects. Our interpretation is supported by ab-initio quantum chemical calculations of the solvent dependence of chemical shifts for the Ca 3d and 4p unoccupied levels of the 1s and 2p excited states, performed on a small cluster including the nearest neighbor solvent molecules surrounding the Ca dication assuming a cubic (8-fold) solvent coordination.

Quantum chemical modeling of spontaneous reactions of N2O4 with hydrazines in CCl4 solution at low temperature

The spontaneous reactions of N2O4 (NTO) with hydrazines (XNH2, X = NH2, CH3NH and (CH3)2N, denoted as HZs) have been studied by ab initio quantum chemical calculations at the PCM-CCSD(T)/6-311+G(3df,2p) level in CCl4 solution at low temperature to elucidate the mechanisms and predict the kinetics of these well-known hypergolic processes experimentally studied by Saad et al. [AIAA J. 10 (1972) 1073; Ref. 1]. The key initiation reactions in these systems, similar to those unraveled recently by us for the gas-phase reactions, occur by the isomerization process of N2O4 → ONONO2 via very loose transition states within the pre-reaction complexes (N2O4:XNH2) with barriers from 7.2 to 8.7 kcal/mol, followed by concurrent ONONO2 attack on XNH2 through abstraction of one of H atoms by the NO3 group to form HNO3 + XN(H)NO. The predicted rate constants for these bimolecular reactions in CCl4 at 253 K were primarily controlled by transformation of N2O4:XNH2 to ONONO2:XNH2 within 4.7–278 ms. This result can satisfactorily account for the occurrence of the hypergolic reactions of NTO and HZs in CCl4 solution at 253 K reported by Saad et al.

Rigorous analysis of non-ideal solubility of sodium and copper chlorides in water vapor using Pitzer-Pabalan model

Gaseous mixtures of water vapor and neutral molecules of salt (e.g., NaCl, CuCl etc.) can be highly non-ideal due to a strong attractive interaction between salt and water molecules. In particular, this can result in high solubility of salts in water vapor and a strong dependence of solubility on vapor pressure. The analysis of salt solubility in water vapor can be done using the Pitzer-Pabalan model, which is based on the thermodynamic theory of imperfect gases. The original Pitzer-Pabalan work demonstrated that one can reproduce experimental data for NaCl solubility in vapor. No analysis was performed on the reliability of their original fits, which we believe has contributed to the lack of applications of the Pitzer-Pabalan model despite the apparent success of the original paper. In this work, we report our recent progress in developing a rigorous fitting procedure to parameterize the Pitzer-Pabalan model using experimental data. Specifically, we performed fitting of the experimental results obtained elsewhere for NaCl and CuCl. We investigate the degree of underfitting/overfitting and the sensitivity of the fitting quality to variations in the resulting fitting parameters. The results, as represented by the thermodynamic parameters describing the energetics of formation of salt-bearing water clusters, were successfully benchmarked against Gaussian 16 ab initio quantum chemistry calculations. The resulting rigorous fitting procedure presented here can now be applied to other systems.

Synthesis, characterization, ab initio quantum chemical calculations and molecular docking studies of Se bearing phenoxo-bridged bimetallic Ni(II) complexes

In this paper, we report the reactivity of Ni(dppe)Cl2; dppe = bis(diphenylphosphino)ethane, with phenol based selenium bearing macroacyclic Schiff bases, 2,6-bis({N-[2-(phenylselenato)ethyl]} benzimidoyl)-4-methylphenol and 2,6-bis({N-[3-(phenylselenato)propyl]}benzimidoyl)-4-methylphenol. The reaction of Ni(dppe)Cl2 with these Se2N2O ligands in 1:1 M ratio yield [{(PhC = NCH2CH2SePh)(C6H2(O)(4-CH3)(PhCO)}2Ni2Cl2], 1 and [{(PhC = NCH2CH2CH2SePh) (C6H2(O)(4-CH3)(PhCO)}2Ni2Cl2], 2 as suggested by analytical and spectroscopic data of respective complexes and supported by single crystal X-ray crystallography of phenylseleno(ethyl)amine hydrochloride. In both of these bimetallic complexes, one arm of the ligand undergoes hydrolysis at the CN bond and the 1,2-bis(diphenylphosphenoethane) moiety of 1,2-bis(diphenylphosphino)ethanenickel(II) chloride is displaced by stronger chelating donors; nitrogen and oxygen of the ligands. Two molecules of the partially hydrolyzed ligand coordinate to two Ni(II) through azomethine nitrogen, benzoyl oxygen and the phenolic oxygen. The phenolic oxygen bridges the two Ni(II) ions. Each nickel is bonded to one chloride. Nickel adopts square pyramidal coordination geometry with trans-NiNO3Cl core as evaluated by spectroscopic data and ab initio quantum chemical calculations at Hartree-Fock level. The cyclic voltammograms of complex 1 and 2 show metal centered two electron quasi-reversible redox processes. Molecular docking study of the ligands L1H and L2H and complexes 1 and 2 with DNA revealed non-covalent interaction and bind at active sites of B-DNA. The minimum calculated binding energy is −6.44 kcal/mol in complex 2.

Isomers in Interstellar Environments. I. The Case of Z- and E-cyanomethanimine

Abstract In this work, we present the results of our investigation into the chemistry of Z- and E-cyanomethanimine (HNCHCN), both of which are possible precursors to the nucleobase adenine. Ab initio quantum chemical calculations for a number of reactions with atomic hydrogen were carried out. We find that the reaction H + Z/E-HNCHCN leading both to H-addition as well as H2-abstraction proceed via similar short-range barriers with bimolecular rate coefficients on the order of ∼10−17 cm3 s−1. These results were then incorporated into astrochemical models and used in simulations of the giant molecular cloud G+0.693. The calculated abundances obtained from these models were compared with previous observational data and found to be in good agreement, with a predicted [Z/E] ratio of ∼3—somewhat smaller than the previously derived value of 6.1 ± 2.4. We find that the [Z/E] ratio in our simulations is due mostly to ion-molecule destruction rates driven by the different permanent dipoles of the two conformers. Based on these results, we propose a general rule-of-thumb for estimating the abundances of isomers in interstellar environments, which we call the “relative dipole principle.”