Ab Initio Quantum Calculations Research Articles

Carbon cations and silicon atoms in the ISM: modelling their charge exchange reaction

The time-dependent rate coefficients for the charge exchange reaction C+ + Si -> C + Si+ for doublet and quartet states have been determined with ab initio quantum calculations coupled with a non-adiabatic transition model based on a simple Landau-Zener picture. This reaction plays a key role in determining the abundances of C, Si, and their ions, in the ISM since these abundances affect the fine structure cooling and hence the star formation rates. We also provide additional calculations to evaluate the differences between the gas evolution as obtained by using the empirical rate estimates found in the current literature and the calculations presented in this work which are based on our more realistic evaluation of such rates from ab initio transition probabilities . We shall thus show here that the new rates yield important differences for metal-rich environments where $T<10^4$ K and the UV flux is almost negligible, while becoming less important at higher T values and higher photon fluxes.

Excited state properties of formamide in water solution: An ab initio study

We present ab initio quantum calculation of the optical properties of formamide in vapor phase and in water solution. We employ time dependent density functional theory for the isolated molecule and many-body perturbation theory methods for the system in solution. An average over several molecular dynamics snapshots is performed to take into account the disorder of the liquid. We find that the excited state properties of the gas-phase formamide are strongly modified by the presence of the water solvent: the geometry of the molecule is distorted and the electronic and optical properties are severely modified. The important interaction among the formamide and the water molecules forces us to use fully quantum methods for the calculation of the excited state properties of this system. The excitonic wave function is localized both on the solute and on part of the solvent.

Communication: A vibrational study of propargyl cation using the vacuum ultraviolet laser velocity-map imaging photoelectron method

By employing the vacuum ultraviolet (VUV) laser velocity-map imaging photoelectron (VUV-VMI-PE) method, we have obtained a vibrationally resolved photoelectron spectrum of gaseous propargyl radical [C(3)H(3)(X(2)B(1))] in the energy range of 0-4600 cm(-1) above its ionization energy. The cold C(3)H(3) radicals were produced from a supersonically cooled radical beam source based on 193 nm ArF photodissociation of C(3)H(3)Cl. The VUV-VMI-PE spectrum of C(3)H(3) thus obtained reveals a Franck-Condon factor (FCF) pattern with a highly dominant origin band along with weak vibrational progressions associated with excitations of the C-C ν(5)(+)(a(1)) and C≡C ν(3)(+)(a(1)) symmetric stretching modes and the CCH ν(7)(+)(b(1)) out-of-plane bending mode of C(3)H(3)(+)(X(1)A(1)). The ν(5)(+)(a(1)) vibrational frequency of 1120 cm(-1) determined in the present study is lower than the value deduced from the recent Ar-tagged infrared photodissociation study by 102 cm(-1), confirming the highly accurate vibrational frequency predictions obtained by the most recent state-of-the-art ab initio quantum calculations. The observation of the FCF disallowed ν(7)(+)(b(1)) mode is indicative of vibronic interactions. The discrepancy observed between the FCF pattern determined in the present study and that predicted by a recent high-level quantum theoretical investigation can be taken as evidence that the potential energy surfaces used in the latter theoretical study are in need of improvement in order to provide a reliable FCF prediction for the C(3)H(3)/C(3)H(3)(+) photoionization system.

Experimental and computational thermochemistry of 6,7-dihydro-4(5H)-benzofuranone

The standard (p=0.1MPa) molar enthalpy of formation of 6,7-dihydro-4(5H)-benzofuranone was measured, at T=298.15K, by static bomb calorimetry and the standard molar enthalpy of vaporization, at T=298.15K, was obtained using Calvet microcalorimetry. These values were combined together to derive the standard molar enthalpy of formation of the title compound in gaseous phase, at T=298.15K, −(226.0±2.8)kJ·mol−1. [Display omitted] Additionally, density functional theoretical calculations using the B3LYP hybrid exchange-correlation energy functional with extended basis sets and also other higher-level ab initio quantum calculations have been performed.

Hydration structure and dynamics of a hydroxide ion in water clusters of varying size and temperature: Quantum chemical and ab initio molecular dynamics studies

We have investigated the hydration structure and dynamics of OH−(H2O)n clusters (n=4, 8, 16 and 20) by means of quantum chemical and ab initio molecular dynamics calculations. Quantum chemical calculations reveal that the solvation structure of the hydroxide ion transforms from three and four-coordinated surface states to five-coordinated interior state with increase in cluster size. Several other isomeric structures with energies not very different from the most stable isomer are also found. Ab initio simulations show that the most probable configurations at higher temperatures need not be the lowest energy isomeric structure. The rates of proton transfer in these clusters are found to be slower than that in bulk water. The vibrational spectral calculations reveal distinct features for free OH (deuterated) stretch modes of water in different hydrogen bonding states. Effects of temperature on the structural and dynamical properties are also investigated for the largest cluster considered here.

Is cocaine a social drug? Exploration of the stereo-structure of cocaine’s pharmacophore

Based on a line of evidence (logP, pKa, 1H-, and 13C-NMR, and molecular modeling studies), it appears that cocaine undergoes a hydrophobic collapse which may account for its unprecedented ADME properties, in particular, its exceptional capacity to cross biological membranes. Using molecular simulation techniques, the hypothesis of hydrophobic collapse undergone by the protonated form of cocaine was substantiated using semi-empirical quantum calculations (mainly AM1 and PM3) performed as well as ab initio quantum calculations (6–31 G**). A molecular electrostatic potential map of the internally hydrogen-bonded structure was acquired under AM1 and showed a continuum of high electron density in the central part of the molecule around the methyl ammonium and the two ester moieties. This picture is consistent with the picture of the ammonium being locked between the two C=O and forming a strong “canonical” primary H bond with the methyl ester and a weaker secondary H bond (“non-canonical”) with the benzoate ester. Cocaine represents the prototypical example of molecular concision because the pharmacophore and the vector are embedded in the same molecular scaffold.

High-Resolution Rotational Spectroscopy of a Cyclic Ether.

The conformational landscape of crown ethers has constituted a central topic in the development of host-guest supramolecular chemistry. We report a high-resolution rotational study of a crown ether, 1,4,7,10,13-pentaoxacyclopentadecane (15-crown-5), by means of molecular beam Fourier transform microwave spectroscopy. The considerable size and the broad range of conformations allowed by the flexibility of the cyclic backbone of this ether pose important challenges to spectroscopy approaches. In this investigation, three stable rotamers of the 15-crown-5 ether have been identified and characterized through their rotational constants and centrifugal distortion coefficients. Ab initio quantum calculations at the MP2 level predict these conformers as the most stable ones for the title system and reproduce accurately their distinct structural features. The results pave the ground for an extensive survey of the conformational landscape of the 15-crown-5 and related cyclic ethers in the near term.

Quenching vibrations by collisions in cold traps: A quantum study for MgH + (X 1Σ + ) with 4He(1S) #

Quantum dynamics of superelastic collisions involving vibrational levels of MgH + (X1Σ + ) ions in cold traps, interacting with 4He(1S) as a buffer gas at relative temperatures down to millikelvins, is discussed using an ab initio computed potential energy surface. The relative efficiency of collisional cooling with respect to collisional quenching of the internal vibrations is examined from the results of the relative sizes of the relevant cross sections in relation to predicting actual behaviour in cold traps. The present study indicates the feasibility of cooling vibrationally ‘hot’, trapped ions with the buffer gas. The quenching process of the MgH+ vibrational energy induced by collisions with He has been characterized by extensive ab initio quantum calculations.

Quantum-mechanical equilibrium isotopic fractionation correction to radiocarbon dating: a theory study.

This paper relates the quantum–mechanical equilibrium isotopic fractionation correction to the radiocarbon dating method by Eq. 9, and also shows the significant influence of temperature on the method. It is suggested that the correction is a function of the frequencies and temperature of a specific sample and these two variables can be evaluated theoretically by the ab initio quantum calculations and experimentally by analyzing the clumped-isotope ratios in it, respectively. This paper also suggests that the 14C/12C ratio in the atmosphere in geological time can be calculated by Eq. 10.

Origin of the Pseudogap in High-Temperature Cuprate Superconductors

Cuprate high-temperature superconductors exhibit a pseudogap in the normal state that decreases monotonically with increasing hole doping and closes at x ≈ 0.19 holes per planar CuO2 while the superconducting doping range is 0.05 < x < 0.27 with optimal Tc at x ≈ 0.16. Using ab initio quantum calculations at the level that leads to accurate band gaps, we found that four-Cu-site plaquettes are created in the vicinity of dopants. At x ≈ 0.05, the plaquettes percolate, so that the Cu dx2y2/O pσ orbitals inside the plaquettes now form a band of states along the percolating swath. This leads to metallic conductivity and, below Tc, to superconductivity. Plaquettes disconnected from the percolating swath are found to have degenerate states at the Fermi level that split and lead to the pseudogap. The pseudogap can be calculated by simply counting the spatial distribution of isolated plaquettes, leading to an excellent fit to experiment. This provides strong evidence in favor of inhomogeneous plaquettes in cuprates.

Charge Resonance Enhanced Ionization ofCO2Probed by Laser Coulomb Explosion Imaging

The process by which a molecule in an intense laser field ionizes more efficiently as its bond length increases towards a critical distance R(c) is known as charge resonance enhanced ionization (CREI). We make a series of measurements of this process for CO(2), by varying pulse duration from 7 to 200 fs, in order to identify the charge states and time scales involved. We find that for the 4+ and higher charge states, 100 fs is the time scale required to reach the critical geometry <R(CO)> ≈ 2.1 Å and <θ(OCO)> ≈ 163° (equilibrium CO(2) geometry is <R(CO)> ≈ 1.16 Å and <θ(OCO)> ≈ 172°). The CO(2)(3+) molecule, however, appears always to begin dissociation from closer than 1.7 Å indicating that dynamics on charge states lower than 3+ is not sufficient to initiate CREI. Finally, we make quantum ab initio calculations of ionization rates for CO(2) and identify the electronic states responsible for CREI.

Ab Initio Study of Hydroxyl Torsional Barriers and Molecular Properties of Mono- and Di-iodotyrosine

Phenol rings with one or two iodine atoms bonded to ortho carbons are the essential organic source of iodine for living organisms. The salvage of this halogen fundamental for a variety of biological functions is accomplished through enzymatic processes that rely on recognition of mono- and di-iodotyrosine (MIT and DIT, respectively). Ab initio quantum calculations are used to investigate molecular properties of MIT and DIT associated with their recognition by cognate proteins. Energies, electron density properties, atomic charges, and electrostatic potentials are analyzed in relation with the presence of one or two iodine atoms and internal rotation of hydroxyl hydrogen. The formation of an intramolecular hydrogen bond at some conformations has little effect on the properties that might affect the recognition and further deiodination of MIT and DIT. Polarizability of iodine and the reactive nature of iodinated tyrosines as nucleophilic targets are the essential features revealed in this work.

Theoretical study of the neutral hydrolysis of methyl formate via a concerted and stepwise water-assisted mechanism using free-energy curves and molecular dynamics simulation

A procedure previously described by us is used for the theoretical study of chemical reactions in solution by means of molecular dynamics simulation, with solute–solvent interaction potentials LJ (12-6-1) derived from ab initio quantum calculations. We apply the procedure to the case of the neutral hydrolysis of methyl formate, HCOOCH3 + 3H2O → HCOOH + CH3OH + 2H2O in aqueous solution, via concerted and stepwise water-assisted mechanisms. We use the solvent as reaction coordinate, and the free-energy curves for the calculation of the activation energies. The theoretical calculation for the thermodynamics of this hydrolysis reaction in aqueous solution, assisted by three water molecules, is in agreement with the available experimental information. In particular our study gives values of ΔG ≠ = 28.88 and 28.17 kcal/mol for the concerted and stepwise mechanisms, close to the experimental activation barrier of 28.8 kcal/mol, and a significant improvement over the values of 48.05 and 45.66 kcal/mol found in another similar study using the PCM model.

HERG channel blockade by externally applied quaternary ammonium derivatives

The human ether-à-go-go related gene potassium channel is a key player in cardiac rhythm regulation, thus being an important subject for a cardiac toxicity test. Ever since human ether-à-go-go related gene channel inhibition-related cardiac arrest was proven to be fatal, numerous numbers of data on human ether-à-go-go related gene channel inhibition have been piled up. However, there has been no quantitative study on human ether-à-go-go related gene channel inhibition by quaternary ammonium derivatives, well-known potassium channel blockers. Here, we present human ether-à-go-go related gene channel blockade by externally applied quaternary ammonium derivatives using automated whole-cell patch-clamp recordings as well as ab initio quantum calculations. The inhibitory constants and the relative binding energies for human ether-à-go-go related gene channel inhibition were obtained from quaternary ammoniums with systematically varied head and tail groups, indicating that more hydrophobic quaternary ammoniums have higher affinity blockade while cation-π interactions or size effects are not a deterministic factor for human ether-à-go-go related gene channel inhibition by quaternary ammoniums. Further studies on the effect of quaternary ammoniums on human ether-à-go-go related gene channel inactivation implied that hydrophobic quaternary ammoniums either with a longer tail group or with a bigger head group than tetraethylammonium permeate the cell membrane to easily access the high-affinity internal binding site in human ether-à-go-go related gene channel and exert stronger blockade. These results may be informative for the rational drug design to avoid cardiac toxicity.

FFopt: An Automated Molecular Dynamics Force Field Parameter Optimization

An empirical Molecular Dynamics (MD) force-field's usefulness is limited by the accuracy of the parameter set. FFOpt is a general approach for optimization of these parameters. The method explores a vector field in parameter space, searching for minima. The field is determined by the error in the comparison of MD observables with external data. These data can consist of experimentaly determined quantities as well as the results of ab initio quantum calculations. Different geometries are used to generate comparable MD data. The method has been applied to Purdue Reactive Molecular Dynamics (PuReMD). A training set of quantum mechanical data is used to tune a force-field for the simulation of water systems. We present the results of the parameter fitting procedure, as well as comparison of PuReMD data with experimental and quantum data.

The Kernel energy method: Application to graphene and extended aromatics

AbstractThe quantum chemistry of finite aperiodic graphene flakes is a matter of considerable interest because of the anticipated technological importance of such objects. Since real aperiodic graphene flakes will in general be composed of many thousands of carbon atoms, theoretical methods appropriate to such large molecules would need to be used for the ab initio quantum calculation of their properties. The Kernel energy method is discussed here, and it is shown to be accurately applicable to graphenes and analogous extended aromatic molecules. It is necessary to define the kernels of a graphene molecule in a new way because of the extensive aromaticity, which defines its electronic structure. The kernels used in the reconstruction of the full graphene sheet preserve the total number of π‐electrons, Clar sextets, and the approximate overall aromaticity. Sivaramakrishnan et al. [J Phys Chem A, 2005, 109, 1621] define similar “ring conserved isodesmic reactions (RCIR).” The principal innovation of this article is the suggestion that kernels may be mathematically extracted from an extended aromatic molecule such as graphene by a fissioning of aromatic bonds. Hartree Fock (HF) and Møller‐Plesset (MP2) chemical models using a Gaussian basis of 3‐21G orbitals are used to calculate the total energy of a graphene flake. This demonstration calculation is performed on a graphene flake in which dangling bonds are saturated with hydrogens (C78H26) composed of a total of 104 atoms arranged in 27 benzenoid rings. The KEM with both types of chemical model are shown to be accurate to nearly 1 kcal/mol, of a total energy, which is nearly 3000 atomic units, that is, with an absolute error within “chemical accuracy” and a relative error of the order of 5 × 105% of the total energy. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2011

Synthesis and evaluation of sesquiterpene lactone inhibitors of phospholipase A2 from Bothrops jararacussu

Several sesquiterpene lactone were synthesized and their inhibitive activities on phospholipase A2 (PLA2) from Bothrops jararacussu venom were evaluated. Compounds Lac01 and Lac02 were efficient against PLA2 edema-inducing, enzymatic and myotoxic activities and it reduces around 85% of myotoxicity and around 70% of edema-inducing activity. Lac05–Lac08 presented lower efficiency in inhibiting the biological activities studied and reduce the myotoxic and edema-inducing activities around only 15%. The enzymatic activity was significantly reduced. The values of inhibition constants (KI) for Lac01 and Lac02 were approximately 740 μM, and for compounds Lac05–Lac08 the inhibition constants were approximately 7.622–9.240 μM. The enzymatic kinetic studies show that the sesquiterpene lactones inhibit PLA2 in a non-competitive manner. Some aspects of the structure–activity relationships (topologic, molecular and electronic parameters) were obtained using ab initio quantum calculations and analyzed by chemometric methods (HCA and PCA). The quantum chemistry calculations show that compounds with a higher capacity of inhibiting PLA2 (Lac01–Lac04) present lower values of highest occupied molecular orbital (HOMO) energy and molecular volume (VOL) and bigger values of hydrophobicity (LogP). These results indicate some topologic aspects of the binding site of sesquiterpene lactone derivatives and PLA2.

Fragment molecular orbital (FMO) study on stabilization mechanism of neuro-oncological ventral antigen (NOVA)–RNA complex system

We report the molecular mechanism of protein–RNA complex stabilization based on the electronic state calculation. Fragment molecular orbital (FMO) method based quantum mechanical calculations were performed for neuro-oncological ventral antigen (NOVA)–RNA complex system. The inter-molecular interactions and their effects on the electronic state of NOVA were examined in the framework of ab initio quantum calculation. The strength of inter-molecular interactions was evaluated using inter-fragment interaction energies (IFIEs) associated with residue–RNA base and residue–RNA backbone interactions. Under the influence of inter-molecular interactions, the change of electronic state of NOVA upon the complex formation was examined based on IFIE values associated with intra-NOVA residue–residue interactions and the change of atomic charges by each residue. The results indicated that non-specifically recognized bases contributed to the stability of the complex as well as specifically recognized bases and that the secondary structure of NOVA was remarkably associated with the change of electronic state upon the complex formation.

Molecular dynamics study of formamidine decomposition in gas and solution phases via free energy curves from ab initio interaction potentials

A procedure is described for the theoretical study of chemical reactions in solution by means of molecular dynamics simulation, with solute–solvent interaction potentials derived from ab initio quantum calculations. We apply the procedure to the case of the decomposition of formamidine, HCNHNH2 → NH3 + HCN, in both gas and solution phases, via the non-assisted and assisted mechanisms. We used the solvent as reaction coordinate and the free energy curves for the calculation of the activation energies. The results showed that the decomposition assisted with one or two water molecules in aqueous solution is preferred over the non-assisted mechanism, reducing significantly the activation barrier.

Vibrational spectra of conformers of V and V x gases

Based on ab initio quantum calculations of the electronic structure for different conformers of V and V x gases, we propose an assignment of the fundamental vibrational states of the compounds.