Initio Quantum Chemical Calculations Research Articles

Characterizing the E⊗e Jahn–Teller Potential Energy Surfaces by Differential Geometry Tools

The term ‘mathematical chemistry’ is mostly associated with applications of graph theory in topological issues of 3D chemical structures, thought of as a collection of atoms as dots and bonds as lines. We propose here new directions in this field, coming from the side of theoretical chemistry approached with modern computational tools. Possible challenges are proposed in using ancillary tools of differential geometry for examining the potential energy surfaces of certain specific structural prototypes. Concretely, we describe here the geodesics on the surfaces related to the potential energy functions of the so-called E⊗e Jahn–Teller effect, a spontaneous symmetry-breaking phenomenon also known as a case of conical intersection. To illustrate the case, first-principles (ab initio) quantum chemical calculations are performed on the cyclo-propenyl molecular radical C3H3.

Optical Spectra of Oligofurans: A Theoretical Approach to the Transition Energies, Reorganization Energies, and the Vibronic Activity.

There is experimental evidence of high vibronic activity that accompanies the allowed transition between the ground state and the lowest electronic singlet excited state of oligofurans that contain two, three, and four furan rings. The absorption and emission spectra of the three lowest oligofurans measured at liquid nitrogen temperature show distinct fine structures that are reproduced using the projection-based model of vibronic coupling (with Dushinsky rotation included) parameterized utilizing either Density Functional Theory (DFT, with several different exchange-correlation functionals) or ab initio (CC2) quantum chemistry calculations. Using as a reference the experimental data concerning the electronic absorption and fluorescence for the eight lowest oligofurans, we first analyzed the performance of the exchange-correlation functionals for the electronic transition energies and the reorganization energies. Subsequently, we used the best functionals alongside with the CC2 method to explore how the reorganization energies are distributed among the totally symmetric vibrations, identify the normal modes that dominate in the fine structures present in the absorption and emission bands, and trace their evolution with the increasing number of rings in the oligofuran series. Confrontation of the simulated spectra with the experiment allows for the verification of the performance of the selected DFT functionals and the CC2 method.

Calibration of the dianionic phosphate group: Validation on the recognition site of the homodimeric enzyme phosphoglucose isomerase.

We calibrate and validate the parameters necessary to represent the dianionic phosphate group (DPG) in molecular mechanics. DPG is an essential fragment of signaling biological molecules and protein-binding ligands. It is a constitutive fragment of biosensors, which bind to the dimer interface of phosphoglucose isomerase (PGI), an intracellular enzyme involved in sugar metabolism, as well as an extracellular protein known as autocrine motility factor (AMF) closely related to metastasis formation. Our long-term objective is to design DPG-based biosensors with enhanced affinities for AMF/PGI cancer biomarker in blood. Molecular dynamics with polarizable potentials could be used toward this aim. This requires to first evaluate the accuracy of such potentials upon representing the interactions of DPG with its PGI ligands and tightly bound water molecules. Such evaluations are done by comparisons with high-level ab initio quantum chemistry (QC) calculations. We focus on the Sum of Interactions Between Fragments Ab initio computed (SIBFA) polarizable molecular mechanics procedure. We present first the results of the DPG calibration. This is followed by comparisons between ΔE(SIBFA) and ΔE(QC) regarding bi-molecular complexes of DPG with the main-chain and side-chain PGI residues, which bind to it in the recognition site. We then consider DPG complexes with an increasing number of PGI residues. The largest QC complexes encompass the entirety of the recognition site, with six structural water molecules totaling up to 211 atoms. A persistent and satisfactory agreement could be shown between ΔE(SIBFA) and ΔE(QC). These validations constitute an essential first step toward large-scale molecular dynamics simulations of DPG-based biosensors bound at the PGI dimer interface. © 2020 Wiley Periodicals, Inc.

RHF and DFT study of the molecular properties of the malaria drug proguanil in different environments

The molecular geometries of the common malaria drug Proguanil in gas phase, water and Ethanol have been studied using ab- initio Quantum Chemical calculations at the Restricted Hartree-Fock (RHF) level of theory by employing 6-31+G basis set. Density functional calculation at the Becke3LYP (B3LYP) have been carried out by employing 6-31+G basis set for inclusion of electron correlation. The molecular structure, dipole moment, charge transfer, polarizability and energy were calculated. The shortest bonds were found to be H10-N20, H11-N17, H12-N16, N18-H22 with bond lengths less than 1 A . The dipole moments, thermal energies and polarizabilities were found to be higher in water compared to gas phase and ethanol at both levels of theory. Keywords : Proguanil, Molecular Dynamics, ab initio, DFT Calculations.

On the protonation of water

Dissociative photoionization onsets of water and water dimer, measured by Imaging Photoelectron Photoion Coincidence (iPEPICO) Spectroscopy, are used in a floating thermochemical cycle to determine the proton affinity of water with unprecedented accuracy, as confirmed by state-of-the-artab initioquantum-chemical calculations.

Rate Constant Computation on Some Chlorination Reactions of Hg in Combustion Flue Gas

The geometry optimizations of reactants, products and transition states were made by the quantum chemistry MP2 method at the SDD basis function level for Hg, and 6-311++G(3df, 3pd) for others. The properties of stable minimums were validated by vibration frequencies analysis. Furthermore, the microcosmic chemical reaction mechanisms of reactions were investigated by ab initio calculations of quantum chemistry. Among these chlorination reactions involving mercury, the processes of reaction Hg+Cl2 → HgCl+Cl and reaction Hg+HOCl→HgCl+OH are Hg+Cl2 →M(HgClCl) →TS(HgClCl) → HgCl+Cl and Hg+HOCl→M(HgClOH)→TS(HgClOH)→HgCl+OH, which include intermediates (M) that others do not have. On the basis of the geometry optimization, reaction rate constants within 200- 2000K are calculated neither from experimental data nor by estimated, but directly from Quantum Chemistry software–Khimera.

Matrix isolation ESR spectroscopy and quantum chemical calculations on 5-methylhexa-1,2,4-triene-1,3-diyl, a highly delocalized triplet “hybrid” carbene

The ESR spectrum of 5-methylhexa-1,2,4-triene-1,3-diyl (1) was recorded in an argon matrix at 15 K. The derived zero-field splitting (ZFS) parameters (D = 0.5054 ± 0.0006 cm(-1) and E = 0.0045 ± 0.0002 cm(-1)) fall between those determined previously for propargylene (2) and vinylcarbene (3). DFT and ab initio (CAS and MRCI) quantum-chemical calculations of the ZFS parameters of 1, 2, and 3 were performed. These calculations indicate that multireference methods are needed to successfully predict ZFS parameters of delocalized carbenes/biradicals such as 1-3. The calculated singly occupied MOs and spin density distributions show that the spin is more delocalized in 1 than in 2 and 3, indicating that 1 is a "hybrid" of the constituent ethynyl- and vinylcarbenes, 2 and 3, respectively. The dominant contribution to the D-value in 1 and 2 is found to result from spin-spin interactions on the C atoms of the propylidene moiety, which is strongly affected by spin polarization. Accurate values for the D-parameter are also predicted for other types of delocalized triplet carbenes such as HC(5)H and HCCN.

ChemInform Abstract: N-2 Radical Anion Reversibly Formed at the Surface of “Electron-Rich” Alkaline-Earth Oxides.

Physisorption of N2 gas onto the surface of a metal oxide (MgO or CaO), containing paramagnetic trapped electron centers (FS + color centers), leads to the formation of a paramagnetic species that, on the basis of its EPR spectrum and of the related spin-Hamiltonian parameters, is identified as a N2 - radical anion. The species in fact contains two nitrogen atoms and its g and A tensors are in agreement with what observed for the N2 - radical trapped in irradiated crystal of various azides. The surface N2 - species is formed by surface-tomolecule one-electron transfer, and its stability strictly parallels the stability of the physisorbed layer, the species formation being completely reversible and pressure dependent. When the N2 adlayer is desorbed, in fact, the N2 - spectrum vanishes and the original Fs + spectrum is restored. Ab initio quantum chemical calculations on an embedded MgO cluster fully confirm the observed phenomenon indicating, in agreement with EPR analysis, the electron transfer of a large fraction of electron density into the ð orbitals of the admolecule.

Ab initio energy calculations and macroscopic rate modeling of hydroformylation of higher alkenes by Rh‐based catalyst

AbstractAb initio quantum chemical computations have been done to determine the energetics and reaction pathways of hydroformylation of higher alkenes using a rhodium complex homogeneous catalyst. Calculation of fragments of the potential energy surfaces of the HRh(CO)(PPh3)3‐catalyzed hydroformylation of 1‐decene, 1‐dodecene, and styrene were performed by the restricted Hartree‐Fock method at the second‐order MØller‐Plesset (MP2) level of perturbation theory and basis set of 6‐31++G(d,p). Geometrically optimized structures of the intermediates and transition states were identified. Three generalized rate models were developed on the basis of above reaction path analysis as well as experimental findings reported in the literature. The kinetic and equilibrium parameters of the models were estimated by nonlinear least square regression of available literature data. The model based on H2‐oxidative addition fitted the data best; it predicts the conversion of all the alkenes quite satisfactorily with an average deviation of 7.6% and a maximum deviation of 13%. © 2009 American Institute of Chemical Engineers AIChE J, 2009

Kinetic calculation and modeling of trace element reactions during combustion

Homogeneous mercury speciation in combustion-generated flue gases was modeled by a detailed kinetic model. This kinetic model includes the oxidation and chlorination of key flue-gas components, as well as six mercury reactions involving HgO with new reaction rate constants calculated neither from experimental data nor by estimated, which was commonly used by other investigators before, but directly from transition state theory (TST). The microcosmic kinetic mechanisms of reactions between mercury and oxidizing species were investigated by ab initio calculations of quantum chemistry. The geometry optimizations of reactants, transition states, intermediates and products were made by the quantum chemistry MP2 method at SDD basis function level. Among those reactions involving HgO, the progress of reaction HgO + HCl → HgCl + OH is HgO + HCl → TS1(HgClOH) → M(HgClOH) → TS2(HgClOH) → HgCl + OH, in which the controlling step is HgO + HCl → TS1(HgClOH) → M(HgClOH). The progress of reaction HgO + HOCl → HgCl + HO 2 is HgO + HOCl → M(HgClOOH) → TS(HgClOOH) → HgCl + HO 2, in which the controlling step is M(HgClOOH) → TS(HgClOOH) → HgCl + HO 2. Four other reactions are one-step, with no intermediates formed. The performance of the model was assessed through comparisons with experimental data conducted by three different groups. The comparison shows that model calculations were in agreement with only one set of all the three groups experimental data. The deviation occurs due to the absence of accurate rate constants of existing mechanism, the adding of reactions involving HgO, as well as the exclusion of heterogeneous Hg oxidation mechanism. Analyses by quantum chemistry and sensitivity simulations illustrated that the pathway Hg + ClO = HgO + Cl is more significant than some of the key reactions in the kinetic mechanism proposed in the literature, which indicates the necessity of including reactions involving HgO in the mercury kinetic mechanism. Studies on the effects of oxygen show that O 2 weakly promotes homogeneous Hg oxidation, especially under the condition of low Cl 2 concentration.

Conformational mobility of the O=C−N−H fragments in isolated dipeptides of L-amino acids

Ab initio MP2 and semiempirical PM3 quantum-chemical calculations are used to discuss the bistability of the nonplanar O=C−N−H fragment in simple amides and dipeptides. The side group is shown to influence the structural polymorphism of the peptide group.

Kinetics of reaction with water vapor and ab initio study of titanium beryllide

Beryllium is one of the candidate materials of the neutron multiplier in the tritium-breeding blanket. Titanium beryllides such as Be 12Ti are known to have advantages over beryllium from the perspectives of higher melting point, lower chemical reactivity, lower swelling and so forth. The reaction of titanium beryllides with water vapor was investigated. The sample disks of Be 12Ti were exposed to an argon gas with 10 000 ppm of water vapor, and the sample temperature was raised to 1000 °C. However, the chaotic breakaway reaction was not observed. The kinetics of oxidation on the surface of Be 12Ti by water vapor was investigated using a model differential equation, and the reaction constant was quantified. Furthermore, to know the electron state in Be 12Ti, ab initio calculations of quantum chemistry were performed using CRYSTAL 98. The structure optimization of Be 12Ti crystal was attempted, and an electron density map was generated.

Geometries, vibrational frequencies, and electron affinities of X2Cl (X=C,Si,Ge) clusters

AbstractAb initio quantum chemical calculations have been performed on X2Cl− and X2Cl (X = C, Si, Ge) clusters. The geometrical structures, vibrational frequencies, electronic properties and dissociation energies are investigated at the Hartree–Fock (HF), Møller–Plesset second‐ and fourth‐order (MP2, MP4), CCSD(T) level with the 6‐311+G(d) basis set. The X2Cl (X = C, Si, Ge) and X2Cl− (X = Si, Ge) take a bent shape obtained at the ground state, while C2Cl− has a linear structure. The impact on internal electron transfer between the X2Cl and the corresponding anional clusters is studied. The three different types of electron affinities (EAs) at the CCSD(T) are reported. The most reliable adiabatic electronic affinities, obtained at the CCSD(T)/cc‐pvqz level of theory, are predicted to be 3.30, 2.62, and 1.98 eV for C2Cl, Si2Cl, and Ge2Cl, respectively. The calculated EAs of C2Cl and Ge2Cl are in good agreement with theoretical results reported. The correlation effects and basis sets effects on the geometrical structures and dissociation energies are discussed. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007

Mechanism of H2S molecule adsorption on the GaAs(100) surface: Ab initio quantum-chemical analysis

Ab initio quantum-chemical cluster calculations within the density-functional theory were carried out to study the mechanism of H2S molecule adsorption on the gallium-rich surface of GaAs(100). It was shown that adsorption can occur in four stages: molecular adsorption; dissociative adsorption, during which an HS radical is adsorbed on a gallium atom comprising a dimer while the detached hydrogen atom is adsorbed on another surface atom of the semiconductor; hydrogen adatom migration between neighboring surface atoms of the semiconductor; and the formation of a Ga-S-Ga bridge bond and of a hydrogen molecule. The stationary-state energies and energy barriers to transitions between these states were determined. The conclusions drawn based on an analysis of calculated diagrams of the potential energy of the processes that occur are in good agreement with the experimental data available in the literature.

Proton affinity of five‐membered heterocyclic amines: Assessment of computational procedures

AbstractAb initio quantum chemical calculations, G3B3, second‐order Møller–Plesset (MP2), and the hybrid density functional method B3LYP were employed to compute the proton affinities of 24 heterocyclic amines. A range of basis sets are employed, starting from double‐ζ polarization quality to triple‐ζ quality basis set with augmented diffuse and polarization function. Experimental values were used to calibrate the performance of various theoretical models. The regioselectivity for the protonation has been unambiguously established by performing B3LYP/6‐31G* calculations on the possible putative sites of attack. For the given series of compounds the performance of B3LYP/6‐31++G** and G3B3 levels of theory have been in excellent agreement with the experimental results with the deviations are of the order comparable with the experimental error. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2006

X-ray photoelectron and voltammetry studies of the charged state of the metal atom in nickel(II) chelate complexes with ligands containing CS 2 − and PS 2 − groups and in their mixed-ligand complexes

X-ray photoelectron and voltammetry studies of the charged state of the metal atom in nickel(II) chelate complexes with ligands containing CS 2 − and PS 2 − groups and in heteroligand complexes on their basis were carried out. It is shown that the degree of formal oxidation of the nickel atom in the complexes corresponds to Ni(II). In the case of heteroligand complexes, addition of nitrogen heterocycles causes an increase in the electron density on the atoms of the coordination center. Theoretical data obtained in ab initio quantum chemical model calculations correlate with the experimental results.

Kinetic mechanism studies on reactions of mercury and oxidizing species in coal combustion

The emission of mercury by coal-fired power plants has become a recent concern on the part of the electric utility industry. Knowledge of mercury kinetic mechanisms is imperative for the research of predicting mercury transformation and finding its effective control methods in coal combustion flue gas. Near the end of the flue gas path, mercury exists as a combination of elemental vapor and HgCl 2 vapor. HgCl 2 is more likely to be removed from the flue gas. Thus, the degree of oxidation is considered to be a critical factor that tends to reduce emission. In the present work, the microcosmic kinetic mechanisms of reactions between mercury and oxidizing species were investigated by ab initio calculations of quantum chemistry. The geometry optimizations of reactants, transition states, intermediates and products were made by the quantum chemistry MP2 method at SDD basis function level. All molecule energies were calculated at QCISD(T)/SDD level and corrected with zero point energy. The activation energies and heat of reactions were calculated. The reaction rate constants were calculated from transition state theory (TST). The performance of the ab initio calculations of quantum chemistry was assessed through comparisons with the literature data. The comparisons showed that the ab initio calculations of quantum chemistry were in agreement with the literature data. The results showed that quantum chemistry was an effective means for investigating kinetic mechanism of mercury interaction with combustion-generated flue gas.

04/00937 Reaction mechanism of mercury and gases during coal combustion: Liu, J. et al. Gongcheng Rewuli Xuebao, 2003, 24, (1), 161–164. (In Chinese)

Predicting emissions of mercury and the speciation of mercury in combustion emissions cannot be done without a fundamental understanding of the chemical reaction mechanism of mercury in flue gas. The microcosmic mechanism of reaction between mercury and gases was studied by ab initio calculations of quantum chemistry. The geometry optimizations of reactant, transition state, intermediate and product were made at MP2/SDD level. The reaction potential barriers and enthalpy were calculated. The rate constant was derived by application of transition state theory and compared with the data of reference. The results show that quantum chemistry is an effective method to study the reaction mechanism of trace elements and gas during coal combustion.

Valence Structural Analysis of the Metal-Ligand Bond in the {RuNO}6 Group

The electronic structure of complexes [Ru(XY)L5]q (L = NH3, Cl-, CN-; XY = NO, CO, N2) was represented as a combination of valence schemes based on ab initio and semiempirical quantum-chemical calculations. It was found that schemes corresponding to a covalent π bond between Ru(III) and NO contribute most in the case of the complexes containing a {RuNO}3 + group, which makes possible the nitroso ligands in these compounds to be considered as uncharged NO molecules. The necessity of inclusion of electron correlation in the description of π interactions between the metal and ligands was shown.

The role of intra- and intermolecular hydrogen bonds in the formation of β-cyclodextrin head-to-head and head-to-tail dimers. The results of ab initio and semiempirical quantum-chemical calculations

The conformation of a free β-cyclodextrin molecule optimized by the MNDO/PM3 quantum-chemical calculations has C7 symmetry. The “right” orientation of the interglucose hydrogen bonds in β-cyclodextrin, in which the 2-OH groups act as the proton donors and the O atoms of the nearby 3"-OH groups function as the proton acceptors, is advantageous for thermodynamic reasons. The ring of seven H bonds thus formed stabilizes the symmetrical form of β-cyclodextrin. The β-cyclodextrin head-to-head dimer has D7 symmetry and consists of molecules whose 2-OH groups partcipate as proton donors in the formation of fourteen complementary intermolecular hydrogen bonds. The energy of H bonds in the β-cyclodextrin monomer and dimer was estimated to be 1.0--1.4 kcal mol–1. Of the two possible β-cyclodextrin dimers, the “head-to-tail” dimer is more thermodynamically stable. The thermodynamic preference of the right orientation of the inter-glucose H bonds in β-cyclodextrin was confirmed by the MP2/6-31G(d,p)//6-31G(d,p) abinitio calculations for maltose (α-glucodioside). The maltose molecule with inter-glucose H bonds of the type 2-OH→O(3")-H is more stable than the structure with the H-(2)O←H-O(3") orientation of H bonds with a difference of ∼2.7 kcal mol–1. According to the MNDO/PM3 method, the maltose structure with the right H bond orientation is more stable by ∼3.1 kcal mol–1.