Semiempirical Quantum Chemistry Research Articles

Combined Theoretical Modeling of Photoexcitation Spectrum of an Isolated Protonated Tyrosine

A photodepletion spectrum of gaseous protonated tyrosine molecules was obtained at 150 K by a UV laser spectroscopic technique in conjunction with mass spectrometry and interpreted by theoretical methods. The spectrum exhibits three distinct bands separated each other by about 800 cm(-1). Stable conformers of the molecular ion were determined by quantum mechanical density functional theory, and their electronic transition energies were obtained by a semiempirical quantum chemistry calculation. The whole pattern of the spectrum was reasonably reproduced by a combination of theoretical methods, the second-order cumulant expansion, a semiempirical quantum chemistry method, molecular dynamics simulation, and a semiclassical time-correlation function approach. The three spectral bands turned out to arise from the vibronic transition of two vibrational modes constituted by the "benzene breathing" mode and a torsional mode of the amino acid backbone. It is suggested that the major factor in spectral broadening is not conformational disorder or lifetime broadening but thermal fluctuation of the stable conformers. The good agreement between experimental and theoretical spectra exemplifies the validity of the theoretical methods applied for the present molecular system.

Photoexcitation Spectrum of Protonated Tyrosine in Vacuum and Theoretical Interpretation

Photodepletion spectrum of gaseous protonated tyrosine molecules was obtained at 150 K by UV laser spectroscopic technique in conjunction with mass spectrometry and interpreted by theoretical methods. The spectrum exhibits distinct three bands separated each other by about 800 . Four stable conformers of the molecular ion were determined by the quantum mechanical density functional theory and their electronic transition energies were obtained by a semi-empirical quantum chemistry calculation. The whole pattern of the spectrum was reproduced very well by a combination of theoretical methods, the second order cumulant expansion, ZINDO/S calculation, molecular dynamics simulation, and a semi-classical time-correlation function approach. The three spectral bands turned out to arise from the vibronic transition of two vibrational modes constituted by the “benzene breathing” mode and a torsional mode of the amino acid backbone. It is suggested that the major factor of the spectral broadening is not conformational disorder but the thermal fluctuation of the most stable conformer. Excellent agreement between the experimental and theoretical spectra exemplifies the validity of the theoretical methods applied for the present molecular system.

The impact of the nucleoside oxidation on the susceptibility to chemical carcinogens studied by first principle and semiempirical quantum chemistry methods

The B3LYP/aug-cc-pvdz and AM1-CI quantum chemistry calculations were used for estimation of adiabatic and vertical ionization potential values of 22 hydroxyl radical modified purine and pyrimidine model nucleosides. Most of studied derivatives are characterized by higher values of IP compared to canonical guanosine, which is known to be the main target for oxidizing agents and chemical carcinogens in cellular DNA. However, three derivatives, namely fapy-guanosine, 8-oxoguanosine and 2-oxoadenosine are characterized by lower IP values than canonical guanosine. Thus, 6,8-diketo- and 6-enol-8-keto-tautomer of 8-oxoguanosine, 6-enol- and 6-keto tautomers of fapy-guanosine as well as 2-keto form of 2-oxoadenosine may be potential hot spot centers for chemical carcinogens. The IEFPCM calculations confirm above conclusion even in the polar environment.

A Gaussian-3X Prediction on the Enthalpies of Formation of Chlorinated Phenols and Dibenzo-p-dioxins

The standard gas-phase enthalpies of formation of chlorinated benzenes, phenols and dibenzo-p-dioxins have been predicted using G3X and/or G3XMP2 model chemistries coupled with isodesmic reactions and compared to the previous theoretical and experimental values. A set of values for chlorinated benzenes are first suggested based on experimental measurements and the closed agreed G3X calculations with different isodesmic reactions. The results on polychlorinated dibenzo-p-dioxins (PCDDs) show a large difference between G3XMP2 and previous experimental measurements and predictions using group additivity methods, semiempirical quantum chemistry, and DFT calculations, especially for highly chlorinated species. Using the well-balanced isodesmic reactions (IR3 and IR5), the discrepancies between G3XMP2 and DFT predictions on PCDDs can be reduced to within 16 kJ/mol. The relative stability of PCDD isomers can be rationalized by the positional interactions, and the overestimation by DFT with less balanced isodesmic reactions is due to the overestimation of the ortho-Cl-Cl repulsive interactions when comparing with G3XMP2. Our calculations suggest further experimental measurements, especially on highly chlorinated phenols and PCDDs.

Synthesis, computational modelling and liquid crystalline properties of some [3]ferrocenophane-containing Schiff’s bases and β-aminovinylketone: Molecular geometry–phase behaviour relationship

Rotationally fixed [3]ferrocenophane extends the variety of possible molecular geometries in its derivatives in comparison with unbridged ferrocenes. In this respect molecular geometry–liquid crystalline properties relationship studies in [3]ferrocenophane mesogens are of considerable interest. Different positional isomers of mono- and di-substituted [3]ferrocenophanes which are obtained by incorporating one or two promesogenic building blocks into the cyclopentadienyl rings are reported in this article. A series of mono-substituted [3]ferrocenophane-containing Schiff’s bases was synthesized by condensing isomeric p-aminophenyl [3]ferrocenophanes with appropriate aldehydes. Isomers of di-substituted [3]ferrocenophane amines gave rise to a series of azomethines with two promesogenic substituents in the cyclopentadienyl rings. Besides, a β-enaminoketone was prepared from 3-( p-aminophenyl)[3]ferrocenophane. Nematic and smectic mesophases were observed in the synthesized compounds under a polarizing optical microscope. The [3]ferrocenophane-containing β-enaminoketone showed complex mesomorphic behaviour connected with occurrence of the keto-enamine and imino-enol tautomeric equilibrium in this compound. On the base of computational models obtained by semi-empirical quantum chemistry calculations the molecular geometry–phase behaviour relationships were examined. It was demonstrated that mesomorphism of [3]ferocenophane azomethines depends on the spatial orientation of the substituents with respect to the propanediyl bridge in a case of mono-, and as well as to each other in a case of di-substituted derivatives.

Structural analysis of dilute-nitride zinc blende InxGa1−xNyAs1−y cluster by a semiempirical quantum chemistry study

We have studied the total energy of a series of dilute-nitride zinc blende InxGa1−xNyAs1−y cluster configurations using a semiempirical quantum chemistry method. It was found that In–N bonding is favorable from an energy point of view when the N atom is substitutional (replacing an As atom at the regular zinc blende lattice site) and the In mole fraction is smaller than 25%. In–N bonding is always favorable when the N atom is interstitial. Furthermore, an analysis of the incorporation of N–N pairs showed that substitutional incorporation is favored over interstitial. In addition, the dissociation of a N–N pair was found to depend on the local environment, being either In rich or In-free, along the dissociation trajectory when the average In mole fraction is high. The theoretical results are in agreement with experimental results.

Measurement of activity coefficients at infinite dilution for hydrocarbons in imidazolium-based ionic liquids and QSPR model

The separations of olefin/paraffin, aromatic/aliphatic hydrocarbons or olefin isomers using ionic liquids instead of volatile solvents have interested many researchers. Activity coefficients γ∞ at infinite dilution of a solute in ionic liquid are generally used in the selection of solvents for extraction or extractive distillation. In fact, the measurement of γ−8 by gas-liquid chromatography is a speedy and cost-saving method. Activity coefficients at infinite dilution of hydrocarbon solutes, such as alkanes, hexenes, alkylbenzenes, styrene, in 1-allyl-3-methylimidazolium tetrafluoroborate ([AMIM][BF4]) and 1-butyl-3-methyl imidazolium hexafluorophosphate ([BMIM][PF6]), 1-isobutenyl-3-methylimidazolium tetrafluoroborate ([MPMIM][BF4]) and [MPMIM][BF4]-AgBF4 have been determined by gas-liquid chromatography using ionic liquids as stationary phase. The measurements were carried out at different temperatures from 298 to 318 K. The separating effects of these ionic liquids for alkanes/hexane, aliphatic hydrocarbons/benzene and hexene isomers have been discussed. The hydrophobic parameter, dipole element, frontier molecular orbital energy gap and hydration energy of these hydrocarbons were calculated with the PM3 semi-empirical quantum chemistry method. The quantitative relations among the computed structure parameters and activity coefficients at infinite dilution were also developed. The experimental activity coefficient data are consistent with the correlated and predicted results using QSPR models.

ADSORPTION OF HYDROGEN ON β-Ga2O3(100): A THEORETICAL STUDY

We have modeled the (100) surface of β- Ga2O3with a clear-cut optimization from ab initio calculations. The adsorption geometry of one hydrogen atom on this surface was determined by a semi-empirical quantum chemistry method. H is found bonded to a tetrahedral Ga atom and no bond with surface oxygen atoms is detected. As a consequence of this Ga – H bond, the Ga – O overlap population decreases. This result is in good agreement with the recent spectroscopic determination of Ga – H IR frequencies on supported catalysts. The orbital composition of the Ga – H bond and density of states of tetrahedral and octahedral gallium ions, Ga ( I ), Ga ( II ), and that of oxygen before and after H adsorption are also addressed.

Computational spectroscopy of ubiquitin: Comparison between theory and experiments

Using the constrained molecular dynamics simulation method in combination with quantum chemistry calculation, Hessian matrix reconstruction, and fragmentation approximation methods, the authors have established computational schemes for numerical simulations of amide I IR absorption, vibrational circular dichroism (VCD), and two-dimensional (2D) IR photon echo spectra of the protein ubiquitin in water. Vibrational characteristic features of these spectra in the amide I vibration region are discussed. From the semiempirical quantum chemistry calculation results on an isolated ubiquitin, amide I local mode frequencies and vibrational coupling constants were fully determined. It turns out that the amide I local mode frequencies of ubiquitin in both gas phase and aqueous solution are highly heterogeneous and site dependent. To directly test the quantitative validity of thus obtained spectroscopic properties, they compared the experimentally measured amide I IR, 2D IR, and electronic circular dichroism spectra with experiments, and found good agreements between theory and experiments. However, the simulated VCD spectrum is just qualitatively similar to the experimentally measured one. This indicates that, due to delicate cancellations between the positive and negative VCD contributions, the prediction of protein VCD spectrum is critically relied on quantitative accuracy of the theoretical model for predicting amide I local mode frequencies. On the basis of the present comparative investigations, they found that the site dependency of amide I local mode frequency, i.e., diagonal heterogeneity of the vibrational Hamiltonian matrix in the amide I local mode basis, is important. It is believed that the present computational methods for simulating various vibrational and electronic spectra of proteins will be of use in further refining classical force fields and in addressing the structure-spectra relationships of proteins in solution.

Analysis of electron interactions in dielectric gases

We present and discuss results concerning electron interactions processes of dielectric gases and their relationship with the macroscopic behavior of these gases, in particular, with their dielectric strength. Such analysis is based on calculating energies of reactions for molecular ionization, dissociative ionization, parent negative ion formation, and dissociative electron attachment processes. We hypothesize that the estimation of the required energy for a reduced number of processes that take place in electrically stressed gases could be related to the gas’ capability to manage the electron flow during an electrical discharge. All calculations were done with semiempirical quantum chemistry methods, including an initial optimization of molecular geometry and heat of formation of the dielectric gases and all of species that appear during electron interaction reactions. The performance of semiempirical methods Austin model 1 and Parametric model 3 (PM3) was compared for several compounds, PM3 being superior in most cases. Calculations performed for a sample of nine dielectric gases show that electron attachment and detachment processes occur in different energy bands that do not overlap for any value of the dielectric strength. We have also analyzed the relationship between dielectric strength and two physical properties: electron affinity and ionization energy. Calculations performed for 43 dielectric gases show no clear correlation between them, although certain guidelines for the qualitative estimation of dielectric strength can still be assessed.

Bond order and valence indices: A personal account

The paper accounts for the author's activity in developing bond order and valence indices since the early 80s. These indices represent an important conceptual link between the physical description of molecules as systems of electrons and nuclei and the chemical picture of molecules consisting of atoms kept together by bonds. They are also useful for a systematization and interpretation of the results obtained in the quantum chemical calculations, by permitting to extract from the wave function different pieces of information that may be assigned chemical significance. In some cases they can have some predictive power, too. Historically, the prototypes of such indices were introduced in the semiempirical quantum chemistry; the most important developments were Coulson's charge-bond order matrix in the simple Hückel theory and the Wiberg index in the CNDO framework. (Valence indices were also introduced in the semiempirical theory.) The definition of the ab initio bond order index emerged from the asymptotic term of the exchange energy component of the partitioning performed in the framework of the author's so-called "chemical Hamiltonian approach" using a "mixed" second quantization formalism for overlapping basis sets. They can also be introduced by studying the exchange part of the two-particle density (or of the second-order density matrix). Some properties of the bond order indices are discussed and the author's (until now unpublished) proof is also presented, showing the sufficient conditions under which the bond order index of a homonuclear diatomics is equal to the "chemist's bond order," i.e., the half of the difference between the number of electrons occupying bonding and antibonding orbitals. The ab initio valence indices are also introduced and discussed, and it is stressed that for correlated wave function the same "exchange only" definition of the bond order and valence indices should be used, which was introduced for the SCF case. The recent concept of the "atomic decomposition of identity" is also discussed and it is utilized for introducing bond orders and valences in the framework of the "3D analysis," when atoms are defined not by their basis orbitals but as regions of the three-dimensional (3D) physical space. Two versions of the 3D analysis are considered--the AIM (atoms in molecules)-type decomposing the space into disjunct atomic domains and the "fuzzy atoms" scheme in which there are no sharp boundaries between the atoms but they exhibit a continuous transition from one to another.

Implementing and evaluating a fictitious electron dynamics method for the calculation of electronic structure: Application to the Si(100) surface

A density matrix based fictitious electron dynamics method for calculating electronic structure has been implemented within a semi-empirical quantum chemistry environment. This method uses an equation of motion that implicitly ensures the idempotency constraint on the density matrix. Test calculations showed that this method has potential of being combined with simultaneous atomic dynamics, in analogy to the popular Car-Parrinello method. In addition, the sparsity of the density matrix and the sophisticated though flexible way of ensuring idempotency conservation while integrating the equation of motion creates the potential of developing a fast linear scaling method.

Reaction of functionalized maleimides with versatile nucleophiles. Synthesis, electronic spectra and molecular orbital study

This article comprehensively describes the condensation reactions of functionalized maleimides (3-methylthio-2,5-dioxo-1 H-pyrroles) with some nucleophilic reagents to afford a series of novel heterocycles, as briefly reported in a previous communication [Tominaga Y, Komiya K, Itonaga S, Yoshioka N, Kataoka S, Sasaki K, et al. Heterocycles 1997;46:41]. The reactions of the functionalized maleimides ( 5a– c) with N, N-dialkylanilines ( 6a– d) smoothly proceeded to give the corresponding 3-(4-dialkylamino)phenyl-1-methyl-1 H-pyrrole-2,5-diones ( 7a– i). Cyclic products, the 2 H,4 H-[1]benzopyrano[3,4- c]pyrrole-1,3,4-triones ( 10a– c, 12, 13) were also obtained within the same reaction framework, using 3-dialkylaminophenols ( 6g– j) and resorcinol ( 6k) as the nucleophilic reagents. Further treatments of ( 7a, b, h) with Lawesson's reagent afforded the brilliant blue mono-thiocarbonyls, 4-(4-dialkylamino)phenyl-3-cyano-1-methyl-5-oxo-pyrrole-2-thiones ( 9a– c). The UV/vis spectral characteristics of the new heterocycles, particularly of the controversial aromatic mono-thiocarbonyl compounds ( 9a– c), were computationally analyzed by means of semi-empirical and Time Dependent Density Functional Theory (TDDFT) quantum chemistry calculations.

Electron–phonon coupling in DNA: a systematic study

The coupling of all twelve possible conformational modes of DNA duplexes and four pair-wise correlations among them to positive charge (hole) motion through these biopolymers has been systematically analysed in regular homogeneous B-DNA trimers and tetramers of adenosine–thymidine (AT) and guanosine–cytidine (GC) Watson–Crick pairs using PM3 semiempirical quantum chemistry. Of these only five modes have been found to be most strongly coupled to the electron motion in DNA, namely stretching of H-bonding both in AT and GC, correlated Buckle–Rise and Stagger–Tilt motions in GC and correlated Shear–Twist motion in AT. The parameters for the corresponding polaronic Hamiltonians have been estimated. The nature of these DNA polarons is discussed taking into account the relevant experimental results currently available.

Polyolefin Macroradical Properties: A Semiempirical Quantum Chemistry Study

AbstractSummary: Semiempirical quantum chemistry simulations have been used to estimate the properties of mid‐chain alkyl radicals of ethylene, propylene and styrene oligomers depending on the chain length. The values of spin density and charge on the radical site proved to be almost unchanged for oligomer radicals having from 2 to 11 repeated units. Bond strength parameters of bonds neighboring the radical site demonstrate stable values starting from pentamers. The reliable inference is that the electron structure of polyethylene, poly(propylene) and polystyrene (PS) macroradicals may be simulated by means of relatively short oligomers. The obtained data indicate clearly that the polystyrene tertiary alkyl radical has noticeably decreased values of both spin and charge onto the radical site as well as very decreased strength of β‐bonds. For that reason the PS tert‐alkyl radical is estimated as that having decreased activity and increased susceptibility to chain scission. The most probable cause is delocalization of the free electron onto the neighboring aromatic ring.Spin density distribution in tertiary radical of polystyrene.magnified imageSpin density distribution in tertiary radical of polystyrene.

Simulation Studies of Amide I IR Absorption and Two-Dimensional IR Spectra of β Hairpins in Liquid Water

Amide I IR absorption and two-dimensional (2D) IR photon echo spectra of a model beta hairpin in aqueous solution are theoretically studied and simulated by combining semiempirical quantum chemistry calculations and molecular dynamics simulation methods. The instantaneous normal-mode analysis of the beta hairpin in solution is performed to obtain the density of states and the inverse participation ratios of the one-exciton states. The motional and exchange narrowing processes are taken into account by employing the time-correlation function theory for the linear and nonlinear response functions. Numerically simulated IR absorption and 2D spectra are then found to be determined largely by the amide I normal modes delocalized on the peptides in the two strands. The site-specific isotope-labeling effects on the IR and 2D IR spectra are discussed. The simulation results for the ideal (A17) beta hairpin are directly compared with those of the realistic 16-residue (GB1) beta hairpin from an immunoglobulin G-binding protein. It was found that the characteristic features in IR and 2D spectra of both the ideal (A17) beta hairpin and the GB1 beta hairpin are the same. The simulated IR spectrum of the GB1 beta hairpin is found to be in good agreement with experiment, which demonstrates that the present computational method is quantitatively reliable.

Amide I IR, VCD, and 2d IR spectra of isotope‐labeled α‐helix in liquid water: Numerical simulation studies

AbstractAmide I infrared (IR), vibrational circular dichroism (VCD), and two‐dimensional IR (2D IR) spectra of various isotope‐labeled α‐helical polyalanines in liquid water were theoretically calculated by combining semiempirical quantum chemistry calculation, Hessian matrix reconstruction, fragmentation approximation, and molecular dynamics simulation methods. The solvation‐induced amide I frequency shift was found to be about −20 cm−1. Properly taking into account the motional narrowing effect in the ensemble averaging, we show that the simulated IR, VCD, and 2D IR spectra are quantitatively in good agreement with experimental results. Depending on the relative positions of the 13C and/or 13C18O labeled peptides in a given α‐helix, the IR absorption line shape, IR intensity distribution, positive‐negative VCD pattern, and diagonal/off‐diagonal 2D IR echo spectral features were found to change dramatically. It is shown that these different spectroscopic observations can be described in a consistent manner by using the present simulation method. We will show that the properly designed isotopomers and their IR, VCD, and 2D IR spectrum analyses can provide incisive information on the three‐dimensional polypeptide structure and dynamics. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005

ProPose: a docking engine based on a fully configurable protein–ligand interaction model

Virtual high-throughput screening of molecular databases and in particular high-throughput protein-ligand docking are both common methodologies that identify and enrich hits in the early stages of the drug design process. Current protein-ligand docking algorithms often implement a program-specific model for protein-ligand interaction geometries. However, in order to create a platform for arbitrary queries in molecular databases, a new program is desirable that allows more manual control of the modeling of molecular interactions. For that reason, ProPose, an advanced incremental construction docking engine, is presented here that implements a fast and fully configurable molecular interaction and scoring model. This program uses user-defined, discrete, pharmacophore-like representations of molecular interactions that are transformed on-the-fly into a continuous potential energy surface, allowing for the incorporation of target specific interaction mechanisms into docking protocols in a straightforward manner. A torsion angle library, based on semi-empirical quantum chemistry calculations, is used to provide minimum energy torsion angles for the incremental construction algorithm. Docking results of a diverse set of protein-ligand complexes from the Protein Data Bank demonstrate the feasibility of this new approach. As a result, the seamless integration of pharmacophore-like interaction types into the docking and scoring scheme implemented in ProPose opens new opportunities for efficient, receptor-specific screening protocols. [figure: see text]. ProPose--a fully configurable protein-ligand docking program--transforms pharmacophores into a smooth potential energy surface.

Theoretical investigation of the linear and second-order nonlinear susceptibilities of the 3-methyl-4-nitropyridine-1-oxyde (POM) crystal.

The linear and nonlinear optical properties of the 3-methyl-4-nitropyridine-1-oxyde (POM) crystal have been evaluated using semiempirical quantum chemistry techniques. The scheme includes (i) the evaluation of the polarizability and first hyperpolarizability of increasingly large one-dimensional, two-dimensional, and three-dimensional clusters of POM, (ii) the use of the time-dependent Hartree-Fock approach to determine the static and dynamic responses in combination with semiempirical Austin model 1 Hamiltonian, (iii) the assessment, for the POM monomer and dimer, of the electron correlation effects using second-order Moller-Plesset perturbation theory with several basis sets containing polarization and diffuse functions, (iv) the assessment of the validity of the multiplicative scheme and its application to get effective polarizability and first hyperpolarizability of the POM unit cell in the crystal, (v) the use of a sum-over-states approach to attribute the first hyperpolarizability to a dominant charge-transfer excited state, and (vi) comparison with experimental data as well as with calculated values obtained using the oriented gas approximation.

Thermodynamics of the growth of carbon nanotubes of various structures from droplets of supersaturated melt

A thermodynamic model is developed to describe the growth of carbon nanotubes from a droplet of supersaturated carbon melt in a metal catalyst. The model employs molecular mechanics and semiempirical quantum chemistry methods. The results of calculations enable construction of a phase diagram showing the type of nanotube depending on the melt supersaturation with carbon and the droplet radius.