High-level Theoretical Calculations Research Articles

Substituent Effects on Dynamics at Conical Intersections: α,β-Enones

Femtosecond time-resolved photoelectron spectroscopy and high-level theoretical calculations were used to study the effects of methyl substitution on the electronic dynamics of the alpha,beta-enones acrolein (2-propenal), crotonaldehyde (2-butenal), methylvinylketone (3-buten-2-one), and methacrolein (2-methyl-2-propenal) following excitation to the S2(pipi*) state at 209 and 200 nm. We determine that following excitation the molecules move rapidly away from the Franck-Condon region, reaching a conical intersection promoting relaxation to the S1(npi*) state. Once on the S1 surface, the trajectories access another conical intersection, leading them to the ground state. Only small variations between molecules are seen in their S2 decay times. However, the position of methyl group substitution greatly affects the relaxation rate from the S1 surface and the branching ratios to the products. Ab initio calculations used to compare the geometries, energies, and topographies of the S1/S0 conical intersections of the molecules are not able to satisfactorily explain the variations in relaxation behavior. We propose that the S1 lifetime differences are caused by specific dynamical factors that affect the efficiency of passage through the S1/S0 conical intersection.

Structures and Properties of Stable Al4, Al4+, and Al4- Comparatively Studied by ab Initio Theories

Previous high-level theoretical calculations of aluminum clusters mostly relied on density functional theory (DFT) or theories less sophisticated than it. Here, we point out that a second-order Møller-Plesset perturbation (MP2) method is more appropriate and is the minimum level of theory in the predictions of property such as geometries, electronic structures, and IR and Raman spectra of Al4, Al4+, and Al4- clusters. The theoretical electron affinities and ionization potentials predicted with MP2 geometries are closer to experimental ones than those by DFT. The p-electron characters and single valence state of aluminum atoms and IR and Raman spectra of the aluminum clusters were also reliably predicted by MP2 and could be based on for further experimental and theoretical studies.

Molecular Structure of Chloro-dodecafluorosubphthalocyanato Boron(III) by Gas-Phase Electron Diffraction and Quantum Chemical Calculations

The molecular structure of the chloro-dodecafluorosubphthalocyaninato boron(III) (F-SubPc) was determined with use of Gas Electron Diffraction (GED) and high-level quantum chemical calculations. The present results show that the F-SubPc molecule has a cone-shaped configuration, isoindole units are not planar, and the pyrrole ring has an envelope conformation. The structure parameters in the gas phase are determined. Some structural details can be observed such as the dihedral angle about the bond connecting the pyrrole ring and the benzene ring being ca. 174 degrees . High-level theoretical calculations with several extended basis sets for this molecule have been carried out. The calculations are in very good agreement with experimental methods: X-ray and GED. Nevertheless, some disagreements particularly related to the B-Cl bond distance found in GED are discussed. Vibrational frequencies were computed obtaining eight values below 100 cm-1 and three bending potentials were examined. They suggest that this molecule is very flexible.

Theoretical studies on farnesyl transferase: Evidence for thioether product coordination to the active‐site zinc sphere

Farnesyltransferase (FTase), an interesting zinc metaloenzyme, has been the subject of great attention in anticancer research over the last decade. However, despite the major accomplishments in the field, some very pungent questions on the farnesylation mechanism still persist. In this study, the authors have analyzed a mechanistic paradox that arises from the existence of several contradicting and inconclusive experimental evidence regarding the existence of direct coordination between the active-site zinc cation and the thioether from the farnesylated peptide product, which include UV-vis spectroscopy data on a Co(2+)-substituted FTase, two X-ray crystallographic structures of the FTase-product complex, and extended X-ray absorption fine structure results. Using high-level theoretical calculations on two models of different sizes, and QM/MM calculations on the full enzyme, the authors have shown that the farnesylated product is Zn coordinated, and that a subsequent step where this Zn bond is broken is coherent with the available kinetic results. Furthermore, an explanation for the contradicting experimental evidence is suggested.

Probing Actinide Electronic Structure Using Fluorescence and Multi‐photon Ionization Spectroscopy

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Acidoswitchable NLO-phores: Benzimidazolo[2,3-b]oxazolidines

This paper presents a series of acidoswitchable NLO-phores combining the 9-methylbenzimidazolo[2,3-b]oxazolidine core with various pi systems such as phenylethenyl, phenylethynyl, and naphthylethenyl. All the prepared derivatives are shown to display acidochromic behavior at ambient temperature. The remarkable contrast in the NLO response along the reversible transformations observed in HRS experiments is rationalized by high level theoretical calculations.

Ion chemistry of NOO+

The kinetics for the reactions of NOO+ ions with neutral molecules having ionization potentials (IPs) from 9.27 to 15.58 eV was measured in a selected ion flow tube at 298 K. The NOO+ ions are produced from the reaction of N3+ + O2 and have been reacted with the following: NO, C6F6, CS2, CF3I, C3F6, OCS, C2H6, Xe, SO2, O3, N2O, CO2, Kr, CO, D2, and N2. Numerous types of reactions were observed with the various neutral reagents, including production of NO+ (which may involve loss of an O from the ion or addition of O to the neutral reactant, although the two channels could not be distinguished here), charge transfer, isomerization of NOO+ to ONO+, and hydride abstraction. High level theoretical calculations of the structures and energetics of the various isomers, electronic states, and transition states of NOO and NOO+ were performed to better understand the observed reactivity. All neutral species with an IP< or =11.18 eV were observed to react with NOO+ in part by charge transfer. Detailed calculations showed that the recommended adiabatic and vertical IPs of NOO are 10.4 and 11.7 eV, respectively, at the MRCISDQ/AVQZ level of theory. The observed experimental limit for charge transfer of 11.18 eV agreed well with the energetics of the final products obtained from theory if dissociation of the neutral metastable product occurred, i.e., the products were X+ +[O(3P) + NO(2Pi)], where [O(3P)+NO(2Pi)] formed via dissociation of metastable NOO. Charge exchange with neutral reagent X would, therefore, be exothermic if IP(X)<[IPad(NOO)-DeltaE(O+NO)-NOO]= approximately 11.1 eV, where IPad(NOO) is the adiabatic IP. The potential energy surface for the reaction of NOO+ with C2H6 was also calculated, indicating that two pathways for formation of HNO2 + C2H5 (+) exist.

Density Functional Investigation of High-Spin XY (X = Cr, Mo, W and Y = C, N, O) Molecules

The performance of a density functional theory approach in calculating the equilibrium bond length, dipole moment, and harmonic vibrational frequency in a series of group 6 (Cr, Mo, W) transition metal-containing diatomic molecules is evaluated. Using flexible basis sets comprised of Slater type functions, a wide range of exchange-correlation functionals is investigated. Comparing with known experimental values and published results from high-level theoretical calculations, the most suitable functional form is selected. The importance of relativistic effects is checked, and predictions are made for several unknown dipole moments. The best agreement with experimental parameters is obtained when using a general gradient approximation, while special and hybrid functional forms give less accurate results.

Conformational Analysis of 2,2′-bifuran: Correlated High-level Ab initio and DFT Results

The torsional potential for inter-ring rotation in 2,2′-bifuran has been systematically tackled using highly accurate ab initio calculations as well as cost-effective DFT methods. The successful convergence of the ab initio results allowed to confirm the presence of a shallow gauche minimum in the torsional potential curve. The standard DFT methods failed to capture such a tiny energy barrier but, interestingly, the results could be remarkably improved by a mixture of wavefunction and DFT energies in a multi-coefficient fashion; thus, accurate DFT-based and ab initio reference data also become available. Since the experimental evaluation of torsional potentials faces quantitative problems, the outcome of high-level theoretical calculations is expected to be reliably used in further investigation on structure and conformational distribution of this system.

Probing actinide electronic structure using fluorescence and multi-photon ionization spectroscopy

The role of the 5f orbitals in actinide bond formation is one of the central issues of actinide chemistry. This question can be explored using relativistic quantum chemistry calculations, but the theoretical methods must be validated using definitive experimental data. For simple ionic compounds such as actinide oxides and halides, the electronic structure can be examined using electronic and photoelectron spectroscopy of gas phase molecules. The present article surveys recent spectroscopic and theoretical studies of the oxides of thorium and uranium. The results show that the 5f-like states are spectators and that the complex patterns of low-lying electronic states for these molecules can be understood in terms of a semi-empirical ligand field model. Comparisons with recent high-level theoretical calculations are presented and discussed.

Matrix Isolation Study of the Reactions of CrO2Cl2 with a Series of Silanes

The reactions between CrO2Cl2 and a series of silanes have been investigated using matrix isolation infrared spectroscopy. Twin-jet codeposition of the two reagents into argon matrices at 14 K followed by irradiation with light of lambda > 300 nm led to the growth of a number of new bands. These have been assigned to the appropriate silanol species formed by oxygen insertion into the Si-H bond, strongly complexed to CrCl2O. The structures and vibrational frequencies of these complexes have been characterized by high-level theoretical calculations. These calculations also support the relative preference for the insertion reaction compared to other possible pathways. Merged-jet codeposition of SiH2Cl2 with CrO2Cl2 at 200 degrees C also led to the formation of the free silanol, HSiCl2OH.

A matrix isolation study of the reactions of OVCl 3 with a series of silanes

The reactions between OVCl 3 and a series of silanes have been investigated using matrix isolation infrared spectroscopy. Twin-jet co-deposition of the two reagents into argon matrices at 14 K followed by irradiation with light of λ>300 nm led to the growth of a number of new bands. These have been assigned to the appropriate silanol species formed by oxygen insertion into the Si–H bond, complexed to VCl 3. The structures and vibrational frequencies of these complexes have been characterized by high-level theoretical calculations. These calculations also support the relative preference for the insertion reaction compared to other possible pathways.

Conformational Analysis of 2,2‘-Bithiophene: A 1H Liquid Crystal NMR Study Using the 13C Satellite Spectra

We have obtained a very large data set of spectral parameters from the analysis of (1)H NMR and (13)C satellite spectra of 2,2'-bithiophene dissolved in anisotropic, partially orienting mesophases. In particular, this parameter set includes 33 dipolar couplings, which are directly related to the interatomic distances, the dihedral angle phi between the two thiophenic rings, and the anisotropic solute-solvent interaction potential. This allows an exhaustive investigation of the conformational equilibrium of 2,2'-bithiophene in a liquidlike phase. Comparison with the predictions of high-level theoretical calculations for the isolated molecule provides evidence of a strong flattening as well as the sharpening effect of the medium on the conformer population. The approximations needed to apply vibrational corrections to flexible molecules are discussed in detail and some general conclusions concerning their effect on structure and conformational equilibria are proposed.

Cu, Zn Superoxide dismutase: distorted active site binds substrate without significant energetic cost

Copper, Zinc superoxide dismutase (CuZnSOD) catalyzes the dismutation of the toxic superoxide radical into molecular oxygen and hydrogen peroxide. Dismutation is achieved by reduction and re-oxidation of the active site copper ion, where the superoxide substrate binds. This enzyme is considered to be a perfect enzyme, as the catalytic rate is very high and diffusion controlled. The redox active copper ion is coordinated by four histidine residues in a distorted square planar geometry. Much has been written about the biological significance of the geometry distortion. It is sometimes considered that it should help to tune the redox potential of the copper ion in order to efficiently reduce the first superoxide molecule and oxidize the second one. In this work we present a series of high level theoretical calculations using realistic models, which demonstrate that the distorted geometry is fundamental for the catalytic efficiency of the enzyme by allowing substrate binding without extensive geometric reorganization of the copper complex, upon changing from four to five ligands. A lower limit for the reorganization energy is calculated here in 22 kcal/mol, which would slow down the reaction kinetics by more than 13 orders of magnitude, transforming a perfect enzyme into an inefficient one.

Evaluation of weak intermolecular interactions in molecular crystals via experimental and theoretical charge densities

Analysis of charge density distributions in molecular crystals has received considerable attention in the last decade both from high-resolution X-ray diffraction studies and from high-level theoretical calculations. An overview of the progress made in deriving one-electron properties, intermolecular interactions in terms of the Atoms in Molecule (AIM) approach (R.F.W. Bader. Atoms in Molecules-A Quantum Theory, Clarendon, Oxford (1990), R.F.W. Bader. J. Phys. Chem., A102, 7314 (1998)) is given with special emphasis on improvements in charge density models and development of both experimental and theoretical techniques to interpret and analyse the nature of weak intermolecular interactions. The significance of the derived results from the charge density of coumarin and its derivatives have been analysed to obtain insights into the nature of intermolecular C–H ··· O, C–H ··· π, π ··· π, C–H ··· S, and S ··· S contacts. The appearance of a ‘region of overlap’ to segregate hydrogen bonds from van der Waals interactions based on the criteria proposed by Koch and Popelier (U. Koch, P.L.A. Popelier. J. Phys. Chem., 99, 9747 (1995), P.L.A. Popelier. Atoms in Molecules. An Introduction, pp. 150–153, Prentice Hall, UK (2000)) and the identification of differences in energy surfaces in concomitant polymorphs of 3-acetylcoumarin are described.

Theoretical insights into the mechanism of acetylcholinesterase‐catalyzed acylation of acetylcholine

Acylation of acetylcholine (ACh) catalyzed by acetylcholinesterase (AChE) has been studied using high-level theoretical calculations on a model system that mimics the reaction center of the enzyme, and compared with uncatalyzed acylation reaction. The geometries of all the intermediates and transition states, activation energies, and solvent effects have been calculated. The calculations predict simultaneous formation of two short-strong hydrogen bonds (SSHB) in the rate-determining transition state structures [the first SSHB involves the hydrogen atom of Ser-200 (H(s)) and another involves the hydrogen atom of His-440 (H(h))]. In the intermediate states, the H-bond corresponding to H(h) involves SSHB, whereas the one corresponding to H(s) does not.

Farnesyltransferase—New Insights into the Zinc-Coordination Sphere Paradigm: Evidence for a Carboxylate-Shift Mechanism

Despite the enormous interest that has been devoted to the study of farnesyltransferase, many questions concerning its catalytic mechanism remain unanswered. In particular, several doubts exist on the structure of the active-site zinc coordination sphere, more precisely on the nature of the fourth ligand, which is displaced during the catalytic reaction by a peptide thiolate. From available crystallographic structures, and mainly from x-ray absorption fine structure data, two possible alternatives emerge: a tightly zinc-bound water molecule or an almost symmetrical bidentate aspartate residue (Asp-297 β). In this study, high-level theoretical calculations, with different-sized active site models, were used to elucidate this aspect. Our results demonstrate that both coordination alternatives lie in a notably close energetic proximity, even though the bidentate hypothesis has a somewhat lower energy. The Gibbs reaction and activation energies for the mono-bidentate conversion, as well as the structure for the corresponding transition state, were also determined. Globally, these results indicate that at room temperature the mono-bidentate conversion is reversible and very fast, and that probably both states exist in equilibrium, which suggests that a carboxylate-shift mechanism may have a key role in the farnesylation process by assisting the coordination/displacement of ligands to the zinc ion, thereby controlling the enzyme activity. Based on this equilibrium hypothesis, an explanation for the existing contradictions between the crystallographic and x-ray absorption fine structure results is proposed.

Ion-molecule rate constants and branching ratios for the reaction of N3++O2 from 120 to 1400 K

The kinetics of the reaction of N(3) (+) with O(2) has been studied from 120 to 1400 K using both a selected ion flow tube and high-temperature flowing afterglow. The rate constant decreases from 120 K to approximately 1200 K and then increases slightly up to the maximum temperature studied, 1400 K. The rate constant compares well to most of the previous measurements in the overlapping temperature range. Comparing the results to drift tube data shows that there is not a large difference between increasing the translational energy available for reaction and increasing the internal energy of the reactants over much of the range, i.e., all types of energies drive the reactivity equally. The reaction produces both NO(+) and NO(2) (+), the latter of which is shown to be the higher energy NOO(+) linear isomer. The ratio of NOO(+) to NO(+) decreases from a value of over 2 at 120 K to less than 0.01 at 1400 K because of dissociation of NOO(+) at the higher temperatures. This ratio decreases exponentially with increasing temperature. High-level theoretical calculations have also been performed to compliment the data. Calculations using multi-reference configuration interaction theory at the MRCISD(Q)/cc-pVTZ level of theory show that singlet NOO(+) is linear and is 4.5 eV higher in energy than ONO(+). A barrier of 0.9 eV prevents dissociation into NO(+) and O((1)D); however, a crossing to a triplet surface connects to NO(+) and O((3)P) products. A singlet and a triplet potential energy surface leading to products have been determined using coupled cluster theory at the CCSD(T)/aug-cc-pVQZ level on structures optimized at the Becke3-Lee, Yang, and Parr (B3LYP)/aug-cc-pVTZ level of theory. The experimental results and reaction mechanism are evaluated using these surfaces.

Bound state spectroscopy of NH-He.

The NH-He van der Waals complex was characterized via laser excitation of bands associated with the NH A (3)Pi-X (3)Sigma(-) transition. It was demonstrated that the ground state supports a bound level with a rotational constant of B"=0.334(2) cm(-1). These results are in agreement with the predictions of recent high-level theoretical calculations. Spin-orbit predissociation of the excited complex was observed, and the spectra yield insights regarding the NH(A)+He potential energy surfaces.

Gas phase analysis of laser ablated biomolecules and their clusters with metals

Fundamental aspects concerning the inter and intramolecular properties of association complexes of metals and molecules of biological interest are not yet fully understood. The study of their structures and dynamics is an important research field for applications in chemistry and pharmacology. Information on their intrinsic properties can be gathered by studying isolated molecules and their complexes in a solvent-free environment, which permits a comparison with high-level theoretical calculations. Most of the biological molecules have, however, extremely low vapor pressure and are thermally labile. Many efforts have been made to find new vaporization methods. Pulsed laser ablation (PLA) technique proved to be suitable to desorbe solid amino acids and nucleic bases and their complexes with metals, in neutral and ionized states, and to perform mass spectrometry in gas-phase. Here we report mass spectra of biomolecules complexed with metals, generated by laser ablation PLA-mass spectrometry, or ablation followed by supersonic expansion (REMPI).