Modern Quantum Chemistry Research Articles

Density Functional Calculations on Class III Ribonucleotide Reductase: Substrate Reaction Mechanism with Two Formates

Hybrid density functional theory (DFT) B3LYP method is applied to study the four diverse enzyme systems: zinc-containing peptidases (thermolysin and stromelysin), methyl-coenzyme M reductase, ribonucleotide reductases (classes I and III), and superoxide dismutases (Cu,Zn- and Ni-dependent enzymes). Powerfull tools of modern quantum chemistry are used to address the questions of biological pathways at their molecular level, proposing a novel mechanism for methane production by methyl-coenzyme M reductase and providing additional insights into hydrolysis by zinc peptidases, substrate conversion by ribonucleotide reductases, and biological superoxide dismutation. Catalysis by these enzymes, with the exception of zinc peptidases, involves radical chemistry.

Fukui Function in Chemistry

AbstractFor Abstract see ChemInform Abstract in Full Text.

Excited states of transition metal compounds: Quantum chemistry of relaxation effects

AbstractThe electronic excitation of coordination compounds is followed by a number of relaxation effects (geometry changes, emission, nonradiative transitions, electron transfer). This article concerns the possible ways to use the standard methods of modern quantum chemistry in conjunction with the time‐dependent formalism (wave packets dynamics) to study these effects in the metal‐to‐ligand charge transfer (MLCT) excited states. The first example concerns the estimation of the geometry changes in organic ligands due to the electronic excitation. The second example concerns the prediction of the trends in the constants of nonradiative transitions. The results of the calculations for several sets of Ru(II) and Os(II) complexes with 2,2′‐bipyridine and its derivatives are in good agreement with experiment. © 2003 Wiley Periodicals, Inc. Int J Quantum Chem, 2004

Non‐Classical Structures of Organic Compounds: Unusual Stereochemistry and Hypercoordination

AbstractFor Abstract see ChemInform Abstract in Full Text.

Ab initio study of three- and five-electron bond molecules, and introducing a new chemical representation

The purpose of this research is to present two subjects. The study of the electronic structure of some chemical species, such as, FO ( 2Π), O 2 − ( 2Π g), NO ( 2Π), O 2 + ( 2Π g) and N 2O, which they have three or five electrons in their bonds is the first subject. We have found that it is difficult to represent the electronic structure of these molecules by current theories such as Lewis's, Pauling's and Linnett's. Hence, the second subject, as a first step, is to introduce a new representation (notation) for electronic structure of chemical species based on modern quantum chemistry, which represents the nature of electronic density of chemical compounds correctly. The importance of this new representation is leading the chemists to make appropriate decision for reactions mechanisms.

Numerical Study of Quantum Resonances in Chaotic Scattering

This paper presents numerical evidence that in quantum systems with chaotic classical dynamics, the number of scattering resonances near an energy E scales like ħ−(D(KE)+1)/2 as ħ→0. Here, KE denotes the subset of the energy surface {H=E} which stays bounded for all time under the flow generated by the classical Hamiltonian H and D(KE) denotes its fractal dimension. Since the number of bound states in a quantum system with n degrees of freedom scales like ħ−n, this suggests that the quantity (D(KE)+1)/2 represents the effective number of degrees of freedom in chaotic scattering problems. The calculations were performed using a recursive refinement technique for estimating the dimension of fractal repellors in classical Hamiltonian scattering, in conjunction with tools from modern quantum chemistry and numerical linear algebra.

Per‐Olov Löwdin curriculum vitae

Per‐Olov Löwdin curriculum vitae

Improving protein circular dichroism calculations in the far-ultraviolet through reparametrizing the amide chromophore

The two most prominent peaks in the far-ultraviolet (UV) circular dichroism (CD) spectra of proteins occur at 190 nm (associated with the ππ* transition) and 220 nm (associated with the nπ* transition). The mean residue ellipticity at 220 nm, [θ]220, is commonly used to estimate the helix content of a protein. We have assessed first principles CD calculations in the far-UV using 23 different proteins, whose x-ray crystal structures and CD spectra are known. Using the standard parameters, derived from semiempirical calculations, for the ground state, nπ* and ππ* electronic states of models of the peptide group to describe the relevant charge distributions of the backbone chromophore, we find weak correlation between the computed and measured mean residue ellipticity at 220 nm (Spearman rank correlation coefficient, r=0.41) and no correlation at 190 nm. Replacing the standard parameters with ones derived from modern quantum chemistry methods (multireference configuration interaction calculations) gives a significant correlation (r=0.62) between the computed and measured [θ]220, but still no correlation at 190 nm. We suggest that further improvements might be expected from a parametrization of the higher energy states of the backbone chromophore, and from a more modern parametrization of side-chain chromophoric groups.

Unique determination of the cavity radius in Onsager reaction field theory

A method based on the combined use of classical Maxwell field theory and modern quantum chemistry reaction field theory is outlined for determining the spherical cavity radius of pure liquids in the Onsager reaction field model. For each electronic structure model the method provides a unique value for the radius of the spherical cavity.

On fundamentals, logic, and the connection between the natural sciences

AbstractThe importance of deductive theories in the modern natural sciences built essentially on experiments is briefly discussed. The logical structure of the deductive theories, their axioms, undefined quantities, and realizations is treated in some detail. In all the natural sciences, there is a striving to explain all the various phenomena in nature in terms of a few basic principles, and this “reductionism” leads to a certain amount of unification of these sciences. The chain that goes from biology, over molecular biology, biochemistry, chemistry, and physics to the description of nature in terms of the elementary particles obeying the laws of modern quantum chemistry is reviewed. Since all the measurements of microcosmos involve an observer, who according to the Copenhagen school experiences the outside universe as a projection on his or her mind through his or her senses, some theoreticians may be inclined to reduce the natural sciences to the human mind as the fundamental (undefined) quantity. However, since the observer is a biological structure, one is also back where one started, and it is evident that one can start the reduction or unification of the natural sciences in any point on this circle (or spiral). Hence, there are many descriptions of the natural sciences and their connections that are possible—as illustrated at this symposium. © 1995 John Wiley & Sons, Inc.

Formycin triphosphate-terbium complex: a novel spectroscopic probe for phosphoryl transfer enzymes

The conditions under which the fluorescent pyrazolopyrimidine nucleotide formycin A triphosphate (7-amino-3-(β- d-(5′-tripolyphosphate)ribofuranosyl)pyrazolo [4,3-d] pyrimidine , FTP) forms a 1:1 complex in solution with Tb 3+ have been characterized. The complex has a dissociation constant of approx. 10 −7 M. Within the complex, the luminescence of Tb 3+ is dramatically sensitized by energy transfer from formycin. The value for 50% transfer efficiency, Förster's R o (Förster, T. (1964) in Modern Quantum Chemistry (Sinanoglu, O., ed.), pp 93–137, Academic Press, New York) was determined to be 3.34 ± 0.4 A ̊ , and the effective distance between the donor and acceptor transition dipoles, R, in the complex was estimated to be 6.6 ± 1.0 A ̊ . The quantum yield of Tb 3+ in the complex is sensitive to the number of O-H oscillators bound to the Tb 3+, which allows determination of the number of waters bound to it (approx. 4). Preliminary results show that the complex binds to the phosphoryl transfer enzyme hexokinase in the presence of the glucose analogs N-acetylglucosamine, frucose and xylose, which are not phosphorylated by the enzyme. The binding occurs with a loss of energy efficiency consistent with a new distance from the effective transition dipole of formycin to that of terbium of approx. 9.6 Å. The FTP-terbium complex can be used as both a spectroscopic and an X-ray diffraction probe. Studies with this compound should be most valuable for correlating solution and crystallographic data.

Fluorine peroxide (FOOF): A continuing problem for normally reliable theoretical methods

AbstractThe greatest single success of modern computational quantum chemistry has been its ability to correctly predict the geometrical structures of molecules. The FOOF molecule stands in contrast to the overwhelming mass of comparisons between theory and experiment. This research shows that configuration interaction (CI) methods including all single and double excitations (SD) fail to predict the correct FOOF structure, even when high‐quality basis sets are employed.

Die organischen Verbindungen und Komplexe von Germanium, Zinn und Blei

This field is of special interest within the organometallic chemistry, which was and still is one of the most developing areas of chemistry for twenty years. The electronic structure around the atoms of germanium, tin, and lead favors both polar and radical reactions, and a plentiful coordination chemistry, too. Modern quantum chemistry arrived at these heavy atoms and allows better understanding also of low valent species, R2M. Chiral compounds with asymmetric Sn atoms, an object aimed at since 1905, have been prepared now, and dynamic stereochemistry has been studied. Industrial use of organotins has grown quickly and includes stabilization of plastics and plant and material protection as well. Biomethylation and environmental problems open this field both to biochemists and ecologists.

Modern state of molecular orbital calculations for coordination compounds

The modern state of electronic structure calculations for coordination compounds of non-transition, transition and heavy elements is reviewed. The application of calculations for quantum chemical studies of bonding problems and for the interpretation of molecular properties [e g charge distnbutions dipole moments, ionization potentials (validity of Koopmans' theorem)], is discussed. Modern quantum chemistry methods, and among them various schemes of the MO LCAO SCF theory (exact non empirical and approximate non empirical methods including neglect of atomic orbitals overlap as well as semi-empirical methods), are considered. Along with this traditional treatment of problems m quantum chemistry the possibilities and the perspectives of alternative approaches to molecular electronic structure studies, such as the scattered wave method, are described briefly. The consideration of modern quantum chemistry calculations is illustrated with examples taken from the literature and with the authors' own results. SOME REMARKS ON MOLECULAR ORBITAL THEORY The molecular orbital method has now become a generally accepted basis for dealing with the electronic structure of coordination compounds It is not only the most common calculation method used in quantum chemistry but also the language for discussing the results of experimental studies of the physical properties, structure and bonding of molecules The starting point of the MO method is the one-electron approximation based on the concept of 'molecular orbitals which describe the behaviour of each electron in the effective field determined by the atomic nuclei and other electrons of the molecule There are several calculation schemes using the MO method1.