The ground state of TiC revisited

The ground state of TiC is ³⁺, as predicted by previous configuration interaction calculations. It is shown that there are two low-lying ¹⁺ states and that the density functional theory solution corresponds to the higher of the two ¹⁺ states.Contribution to the Björn Roos Honorary Issue     

A theoretical study of radical-only and combined radical/carbocationic mechanisms of arachidonic acid cyclooxygenation by prostaglandin H synthase

Prostaglandin H synthase catalyzes the oxygenation of arachidonic acid into the cyclic endoperoxide, prostaglandin G₂ (PGG₂), and the subsequent reduction of PGG₂ to the corresponding alcohol, prostaglandin H₂ (PGH₂), the precursor of all prostaglandins and thromboxanes. Both radical abstraction by a neighboring tyrosyl radical and combined radical/carbocationic models have been proposed to explain the cyclooxygenase part of this reaction. We have used density functional theory calculations to study the mechanism of the formation of the cyclooxygenated product PGG₂. We found an activation free energy for the initial hydrogen abstraction by the tyrosine radical of 15.6 kcal/mol, and of 14.5 kcal/mol for peroxo bridge formation, in remarkable agreement with the experimental value of 15.0 kcal/mol. Subsequent steps of the radical-based mechanism were found to happen with smaller barriers. A combined radical/carbocation mechanism proceeding through a sigmatropic hydrogen shift was ruled out, owing to its much larger activation free energy of 36.5 kcal/mol. Supplementary material is available in the online version of this article at http://dx.doi.org/10.1007/s00214-003-0476-9. Electronic Supplementary MaterialSupplementary material is available in the online version of this article at Electronic Supplementary Material: Supplementary material is available in the online version of this article at     

Ab initio and density functional studies on the structure and vibrational spectra of 2-hydroxy-1,4-naphthoquinone-1-oxime derivatives

Structure and vibrational frequencies of lawsoneoxime and its C₃-substituted (R=CH₃, NH₂, Cl, NO₂) derivatives in keto and nitrosophenol forms have been obtained employing the Hartree–Fock and density functional methods. Charge distributions in different conformers have been studied using the molecular electrostatic potential topography as a tool. For all these derivatives except for nitrolawsoneoxime the amphi conformer in the keto form is predicted to be of lowest energy, which can partly be attributed to hydrogen bonding through the oximino nitrogen. In the nitro derivative, however, the preference to form a six membered ring owing to O–H–O hydrogen-bonded interactions makes the anti conformer (keto) the stablest. Further one of the nitrosophenol conformers of nitrolawsoneoxime turns out to be very close in energy (0.21 kJ mol^–1 higher) to this anti conformer. The consequences of hydrogen bonding on charge distribution and vibrational spectra are discussed.     

Bond length alternation in ground and HOMO→LUMO excited states in polyenes. Dynamic Stokes shift?

Complete-active-space self-consistent-field calculation of the reorganisation energy, , corresponding to the strongly allowed HOMOLUMO transition in planar polyenes in the trans form (C _{2 h} symmetry), gives >0.5 eV. This large depends on the fact that the short and long bond lengths of the excited ¹B _u (or ³B _u ) state compared to the ¹A _g ground state are almost cancelled. The emission redshift (Stokes shift) in molecules with the same type of system is quite small, however, which suggests that the Stokes shift may be dynamic, owing to the presence of another excited state at lower or about the same energy. Acknowledgement.We congratulate Björn on his birthday and at the same time thank him for the CASSCF method and for many years of collaboration and help from him and his collaborators to make this wonderful method work in our laboratory.Contribution to the Björn Roos Honorary Issue     

The performance of density functional theory for LnF (Ln=Nd,Eu, Gd,Yb) and YbH

Different density functional theory (DFT) functionals have been evaluated by studying geometries and bond strengths of YbH, YbF, EuF, GdF, and NdF and compared with accurate CCSD(T) results and, when available, experiment. The agreement between the CCSD(T) results and experiment, when available, is good. The agreement is also good between bond strengths calculated at the DFT level using relativistic effective core potentials and the CCSD(T) results. However, the all-electron ADF calculations systematically overestimate binding energies. The geometries obtained by both the all-electron and the effective-core-potential-based DFT calculations are generally in good agreement with the CCSD(T) results.Contribution to the Björn Roos Honorary Issue     

New structural parameters of fullerenes for principal component analysis

The Kekulé structure count and the permanent of the adjacency matrix of fullerenes are related to structural parameters involving the presence of contiguous pentagons p, q, r, q/p and r/p, where p is the number of edges common to two pentagons, q is the number of vertices common to three pentagons and r is the number of pairs of nonadjacent pentagons adjacent to another common pentagon. The cluster analysis of the structural parameters allows classification these parameters. Principal component analysis (PCA) of the structural parameters and the cluster analyses of the fullerenes permit their classification. PCA clearly distinguishes five classes of fullerenes. The cluster analysis of fullerenes is in agreement with PCA classification. Cluster analysis shows greatest similarity for the q–q/p and r–r/p pairs. PCA provides five orthogonal factors F ₁–F ₅. The use of F ₁ gives an error of 28%. The inclusion of F ₂ decreases the error to 2%.From the Proceedings of the 28th Congreso de Químicos Teóricos de Expresión Latina (QUITEL 2002)     

Systematic convergence of energies with respect to basis set and treatment of electron correlation: focal-point conformational analysis of methanol

A practical means of overcoming the limitation in accuracy of conformational analysis due to incompleteness of basis sets used in ab initio calculations involves calculating the energy with a series of systematically improving basis sets and extrapolating to the basis set limit. We report here a focal-point conformational analysis for methanol. The Hartree–Fock energy converges exponentially to the basis set limit, while the convergence of second-order correlation energy is well described by the formula . This formula also describes well the convergence of fourth-order correlation energy. The height of the rotational barrier at the Hartree–Fock level can be obtained reliably by taking the difference of the extrapolated energies of the two conformations and correcting the difference for correlation effects. Electron correlation has only a small decreasing effect on the height of the rotational barrier in methanol. The focal-point value for the torsional barrier in methanol is 0.999±0.007 kcal/mol. Acknowledgement.This project was supported by Provost Funds at University of California, Santa Barbara (UCSB). The computational resources were provided partially by the National Computational Science Alliance and UCSBs Supercomputer Facility. We also acknowledge the Horgan Award (University of Missouri-Columbia) to K. K., which made possible the purchase of additional computational resources. We thank Robert Gdanitz and Bernie Kirtman for valuable discussions and Jozef Noga for providing us with a copy of the DIRCCR12-OS program.     

Modeling water exchange on monomeric and dimeric Mn centers

Water exchange on Mn centers in proteins has been modeled with density functional theory using the B3LYP functional. The reaction barrier for dissociative water exchange on [Mn^IV(H₂O)₂(OH)₄] is only 9.6 kcal mol^–1, corresponding to a rate of 6×10⁵ s^–1. It has also been investigated how modifications of the model complex change the exchange rate. Three cases of water exchange on Mn dimers have been modeled. The reaction barrier for dissociative exchange of a terminal water ligand on [(H₂O)₂(OH)₂Mn^IV(-O)₂Mn^IV(H₂O)₂(OH)₂] is 8.6 kcal mol^–1, while the bridging oxo group exchange with a ring-opening mechanism has a barrier of 19.2 kcal mol^–1. These results are intended for interpretations of measurements of water exchange for the oxygen evolving complex of photosystem II. Finally, a tautomerization mechanism for exchange of a terminal oxyl radical has been modeled for the synthetic O₂ catalyst [(terpy)(H₂O)Mn^IV(-O)₂Mn^IV(O)(terpy)]³⁺ (terpy=2,2:6,2-terpyridine). The calculated reaction barrier is 14.7 kcal mol^–1.Contribution to the Björn Roos Honorary Issue     

Semidirect parallel self-consistent field: the load balancing problem in the input/output intensive self-consistent field iterations

The full capacity of contemporary parallel computers can, in the context of iterative ab initio procedures like, for example, self-consistent field (SCF) and multiconfigurational SCF, only be utilized if the disk and input/output (I/O) capacity are fully exploited before the implementation turns to an integral direct strategy. In a recent report on parallel semidirect SCF http://www.tc.cornell.edu/er/media/1996/collabrate.html, http://www.fp.mcs.anl.gd/grand-challenges/chem/nondirect/index.html it was demonstrated that super-linear speedups are achievable for algorithms that exploit scalable parallel I/O. In the I/O-intensive SCF iterations of this implementation a static load balancing, however, was employed, dictated by the initial iteration in which integral evaluation dominates the central processing unit activity and thus determines the load balancing. In the present paper we present the first implementation in which load balancing is achieved throughout the whole SCF procedure, i.e. also in subsequent iterations. The improved scalability of our new algorithm is demonstrated in some test calculations, for example, for 63-node calculation a speedup of 104 was observed in the computation of the two-electron integral contribution to the Fock matrix.Contribution to the Björn Roos Honorary Issue Acknowledgement.We thank J. Nieplocha for valuable help and making the toolkit (including ChemIO) available to us. R.L. acknowledges the Intelligent Modeling Laboratory and the University of Tokyo for financial support during his stay in Japan.     

Ab initio and density functional theory based studies on collagen triplets

An understanding of the amino acid sequence dependent stability of polypeptides is of renowned interest to biophysicists and biochemists, in order to identify the nature of forces that stabilize the three-dimensional structure of proteins. In this study, the role of various collagen triplets influencing the stability of collagen has been addressed. It is found from this study that proline can stabilize the collagen triplet only when other residues are also in the polyproline II conformation. Solvation studies of various triplets indicate that the presence of polar residues increases the free energy of solvation. Especially the triplets containing arginine residues displays a higher solvation free energy. The chemical hardness of all the triplets in collagen-like conformation has been found to be higher than that in the extended conformation. Studies on Gly–X–Y, Gly–X–Hyp, and Gly–Pro–Y triplets confirm that there will be local variations in the stability of collagen along the entire sequence.     

Correlation factor approach to the correlation energy functional

A global survey of the correlation factor energy functionals and its application to atomic and molecular properties is made. Its performances are compared with those of the density functional theory (DFT) correlation energy functionals, and some interesting conclusions from previous publications are reinforced here; namely, after removing the one-Slater-determinant hypothesis from the Kohn–Sham method, all DFT correlation functionals are able to provide reasonable results in any circumstance, with an additional restriction, for systems having a quasi-degenerate wave function, the DFT correlation functionals must depend explicitly on the on-top density. Acknowledgement.This work has been done under the support of the Spain DGICYT, project n⁰ BQU2001-0883.     

Valence ab initio calculation of the potential-energy curves for the Ca<Subscript>2</Subscript> dimer

The electronic structure of the Ca₂ molecule has been investigated by use of a two-valence-electron semiempirical pseudopotential and applying the internally contracted multireference configuration interaction method with complete-active-space self-consistent-field reference wave functions. Core–valence correlation effects have been accounted for by adding a core-polarization potential to the Hamiltonian. The ground-state properties of the Ca₂ and Ca₂⁺ dimers have also been studied at the single-reference coupled-cluster level with single and double excitations including a perturbative treatment of triple excitations. Good agreement with experiment has been obtained for the ground-state potential curve and the only experimentally known A¹_u⁺ excited state of Ca₂. The spectroscopic parameters D_e and R_e deduced from the calculated potential curves for other states are also reported. In addition, spin–orbit coupling between the singlet and triplet molecular states correlating, respectively, with the (4p)¹P and (4p)³P Ca terms has been investigated using a semi-empirical two-electron spin–orbit pseudopotential. Acknowledgement.This work was supported by grant 5 P03B 082 21 from the Polish State Committee for Scientific Research (KBN).     

The curvature of the Arrhenius plots predicted by conventional canonical transition-state theory in the absence of tunneling

The reasons for the nonlinearity of the Arrhenius plots of gas-phase reactions are analyzed in detail within the frame of conventional canonical transition-state theory and in the absence of tunneling effects. The purpose is to show how the vibrational normal mode frequencies of reactants and the transition state determine the curvature of an Arrhenius plot. Conventional canonical transition-state theory without tunneling corrections predicts curved Arrhenius plots with an inflexion point that separates the concave (high-temperature range) and convex region (at low temperatures). The frequencies of the transitional modes at the transition-state structure determine the temperature at which an Arrhenius plot presents upward curvature. AcknowledgementsWe are grateful for financial support from the Spanish Ministerio de Ciencia y Tecnología and the Fondo Europeo de Desarrollo Regional through project no. BQU2002–00301, and the use of the computational facilities of the CESCA.     

Electric properties of hydrogen iodide: Reexamination of correlation and relativistic effects

The electric dipole moment and the static dipole polarizability of the hydrogen iodide molecule were studied using sophisticated correlated and relativistic methods. Both scalar and spin–orbit relativistic effects were carefully accounted for. We conclude that the large differences between the theoretical and experimental dipole moment, the dipole moment derivative and the polarizability cannot be reconciled by improved account of electron correlation and relativistic effects. The most striking difference between theory and experiment is observed for the polarizability anisotropy. We believe that experimental data, namely the experimental dipole moment (the most recent value is 0.176 au as compared to our best theoretical estimate, 0.154±0.003 au), the parallel polarizability (44.4 and 38.47±0.05 au) and the anisotropy (11.4 and 2.33±0.05 au) must be inaccurate. Experimental and theoretical perpendicular polarizability components (33.0 and 36.14±0.05 au,) and the mean polarizability (36.8 and 36.92±0.05 au) agree better. Our vibrationally corrected relativistic CCSD(T) results represent the most sophisticated predictions of electric properties of HI obtained so far.Contribution to the Björn Roos Honorary Issue     

Electronic coupling in electron transfer and the influence of nuclear modes: theoretical and computational probes

Long-range electronic coupling of local donor and acceptor sites is formulated in the context of thermal and optical electron transfer and then illustrated with examples based on electronic structure calculations. The relationship of the calculated results to available experimental kinetic and optical data is discussed in detail. The influence of nuclear modes on the magnitude of the coupling (i.e., departures from the Condon approximation) is investigated in terms of both discrete molecular modes and solvent modes, and a general expression is presented for the modulation of the superexchange tunneling gap by motion along the electron transfer reaction coordinate. AcknowledgementsThe author is grateful to R.J. Cave and M. Rust for making available molecular coordinates for acridinium derivatives, and to R.J. Cave for several valuable discussions. This work was supported by the Division of Chemical Sciences, US Department of Energy, under grant DE-AC02-98CH10886.     

Nonlinear electric response of polyampholytes

The behavior of polyampholytes (PAs) in electric fields is investigated by Monte Carlo simulations. In bulk it is found that the response of the PA depends on the charge sequence. For small repeating units of positive and negative charges the response is linear, while bigger units results in a nonlinear response in both the induced dipole moment and the resulting polymer conformation. This is reflected in how PAs modify colloidal suspensions, and while PAs always decrease the repulsion between charged colloidal particles, some net-neutral PAs can even induce an effective attraction between the colloidal particles.Contribution to the Björn Roos Honorary Issue     

Long-distance electron tunneling in proteins

Long-distance tunneling is the major mechanism of electron transfer (ET) in proteins. For a number of years, a major question has been whether specific electron tunneling pathways exist. This question is still debated in the literature, because the pathways are not observed directly, and interpretation of experimental results on ET rates involves ambiguities. The extremely small tunneling interactions are difficult to calculate accurately. Recently, there has been remarkable progress in the area; however, some problems still remain unresolved. The accurate prediction of the absolute rates of long-distance ET reactions and other biological charge-transfer reactions is a particularly pressing issue. The current theoretical calculations indicate that the specific paths do exist in static protein structures. However, the protein motions can result in significant averaging of the spatial tunneling patterns, and it is not clear how accurately subtle quantum interference effects are described by the present theories. The key to resolving these issues is to perform accurate, first-principles calculations of electron tunneling that include the dynamics of the protein. This paper reviews some of theoretical issues of electron tunneling dynamics in inhomogeneous organic media.     

First Total Synthesis of Mappain with a Prenylated and Geranylated Stilbene

The first total synthesis of naturally occurring mappain has been achieved by a convergent sequence. The key strategy involved in the synthesis of mappain was a (E)‐stilbene formation by Horner–Wadsworth–Emmons reaction of the corresponding prenylated benzaldehyde with a geranylated benzyl phosphonate.     

Use of TLC-Densitometric Method for Determination of Valproic Acid in Capsules

Determination of valproic acid in the drug was carried out on the aluminum silica gel 60F₂₅₄ plates and using acetone–water–chloroform–ethanol–ammonia at a volume ratio of 30:1:8:5:11 as the mobile phase, respectively. Two methods of detection of valproic acid were used. The first was a 2% aqueous CuSO₄×5H₂O solution, and the second was a 2′,7′-dichlorofluorescein-aluminum chloride-iron (III) chloride system. The applied TLC-densitometric method is selective, linear, accurate, precise, and robust, regardless of the visualizing reagent used for the determination of valproic acid in Convulex capsules. It has low limits of detection (LOD) and limits of quantification (LOQ), which are equal to 5.8 μg/spot and 17.4 μg/spot using a 2% aqueous CuSO₄×5H₂O solution as visualizing agent and also 0.32 μg/spot and 0.97 μg/spot using a 2′,7′-dichlorofluorescein-aluminum chloride-iron (III) chloride system as visualizing reagent, respectively. The described analytical method can additionally be used to study the identity of valproic acid in a pharmaceutical preparation. The linearity range was found to be 20.00–80.00 μg/spot and 1.00–2.00 μg/spot for valproic acid detected on chromatographic plates using a 2% aqueous CuSO₄×5H₂O solution and the 2′,7′-dichlorofluorescein-aluminum chloride-iron (III) chloride system, respectively. A coefficient of variation that was less than 3% confirms the satisfactory accuracy and precision of the proposed method. The results of the assay of valproic acid equal 96.2% and 97.0% in relation to the label claim that valproic acid fulfill pharmacopoeial requirements. The developed TLC-densitometric method can be suitable for the routine analysis of valproic acid in pharmaceutical formulations. The proposed TLC-densitometry may be an alternative method to the modern high-performance liquid chromatography and square wave voltammetry in the control of above-mentioned substances, and it can be applied when other analytical techniques is not affordable in the laboratory.     

Accuracy of geometries: influence of basis set,exchange–correlation potential,inclusion of core electrons,and relativistic corrections

The geometries of a set of small molecules were optimized using eight different exchange–correlation (xc) potentials in a few different basis sets of Slater-type orbitals, ranging from a minimal basis (I) to a triple-zeta valence basis plus double polarization functions (VII). This enables a comparison of the accuracy of the xc potentials in a certain basis set, which can be related to the accuracies of wavefunction-based methods such as Hartree–Fock and coupled cluster. Four different checks are done on the accuracy by looking at the mean error, standard deviation, mean absolute error and maximum error. It is shown that the mean absolute error decreases with increasing basis set size, and reaches a basis set limit at basis VI. With this basis set, the mean absolute errors of the xc potentials are of the order of 0.7–1.3 pm. This is comparable to the accuracy obtained with CCSD and MP2/MP3 methods, but is still larger than the accuracy of the CCSD(T) method (0.2 pm). The best performing xc potentials are found to be Becke–Perdew, PBE and PW91, which perform as well as the hybrid B3LYP potential. In the second part of this paper, we report the optimization of the geometries of five metallocenes with the same potentials and basis sets, either in a nonrelativistic or a scalar relativistic calculation using the zeroth-order regular approximation approach. For the first-row transition-metal complexes, the relativistic corrections have a negligible effect on the optimized structures, but for ruthenocene they improve the optimized Ru–ring distance by some 1.4–2.2 pm. In the largest basis set used, the absolute mean error is again of the order of 1.0 pm. As the wavefunction-based methods either give a poor performance for metallocenes (Hartree–Fock, MP2), or the size of the system makes a treatment with accurate methods such as CCSD(T) in a reasonable basis set cumbersome, the good performance of density functional theory calculations for these molecules is very promising; even more so as density functional theory is an efficient method that can be used without problems on systems of this size, or larger.