Set Of Point Charges Research Articles

Modeling the Absorption Spectrum of Tryptophan in Proteins

We have applied time-dependent density functional theory (TDDFT) to study the valence pi-pi* excited states of the tryptophan chromophore in the environment of the proteins barnase and human serum albumin. The chromophore is represented by indole. Due to the approximate nature of TDDFT, in the gas phase the calculated vertical transition energies to the 1L valence states are reordered with respect to experiment. The 1L(a) state responds more than the 1L(b) state to the local environment, described fully at the TDDFT level, and to bulk environment, described by a set of point charges. Nevertheless, the vertical transitions are readily identified. For human serum albumin, our calculations predict distinct spectral characteristics between structures with different tryptophan side chain torsion angles. The computational tractability of TDDFT relative to more accurate ab initio methods allows a large part of the surrounding protein environment (up to 100 atoms) to be explicitly included in the TDDFT calculations.

A comparison of the electronic structure and NO adsorption on the (0 0 1)-V 2O 5 surfaces and (0 0 1)-V 2O 5 surfaces with Mo defects—DFT cluster studies

DFT calculations were performed for models of the (0 0 1) surfaces of non-reduced and reduced vanadia, represented by V 12O 30 and V 12O 29 clusters, as well as for models of (0 0 1) V 2O 5 surfaces with Mo defects, represented by V 11MoO 30 and V 11MoO 29 clusters. The clusters were embedded in a set of point charges in order to consider electrostatic bulk influence. Surface reduction was modeled by the removal of vanadyl/molybdenyl oxygen. Analysis of the electronic structure in all the clusters was conducted in terms of the Mulliken population analysis, Mayer bond-orders, atomic Fukui function values, and molecular electrostatic potential (MEP) distribution. The results show that substituting a V atom with Mo leads to a reduction of the adjacent metal atom, practically without changing the electronic properties of the oxygen atoms. Furthermore, the NO adsorption on the reduced surfaces of V 2O 5 and V 2O 5 with Mo defects has been studied. In all cases, adsorption is exothermic; the energetic stabilization is the largest for the V 11MoO 29 from which the molybdenyl atom was removed. However, the calculated adsorption energies are similar, within ca. 3 kcal/mol (12 kJ/mol). Thus, the effect of the molybdenum presence for energetic stabilization of adsorbed NO is not very distinct.

Charge optimization of the interface between protein kinases and their ligands.

Examining the potential for electrostatic complementarity between a ligand and a receptor is a useful technique for rational drug design, and can demonstrate how a system prioritizes interactions when allowed to optimize its charge distribution. In this computational study, we implemented the previously developed, continuum solvent-based charge optimization theory with a simple, quadratic programming algorithm and the UHBD Poisson-Boltzmann solver. This method allows one to compute the best set of point charges for a ligand or ligand region based on the ligand and receptor shape, and the receptor partial charges, by optimizing the binding free energy obtained from a continuum-solvent model. We applied charge optimization to a fragment of the heat-stable protein kinase inhibitor (PKI) of protein kinase A (PKA), to three flavopiridol inhibitors of CDK2, and to cyclin A which interacts with CDK2 to regulate the cell cycle. We found that a combination of global (involving every charge) and local (involving only charges in a local region) optimization can give useful hints for designing better inhibitors. Although some parts of an inhibitor may already contribute significantly to binding, we found that they could still be the most important targets for modifications to obtain stronger binders. In studying the binding of flavopiridol inhibitors to CDK2, comparable binding affinity could be obtained regardless of whether the net charges of the inhibitors were constrained to -2, -1, 0, 1, or 2 during the optimization. This provides flexibility in inhibitor design when a certain net charge of the inhibitor is desired in addition to strong binding affinity. For the study of the PKA-PKI and CDK2-cyclin A interfaces, we identified residues whose charge distributions are already close to optimal and those whose charge distributions could be refined to further improve binding.

Charge Distribution in La2-xSrxCuO4

The electronic structure of La 2 CuO 4 has been studied by first-principles cluster calculations before and after doping. Clusters containing up to five planar copper atoms were investigated using the density functional method. At variance with band-structure calculations, we have been able to determine the charge and spin distributions from molecular orbitals expressed as linear combinations of atomic orbitals localised at the nuclear sites. Doping is achieved by subtracting an electron from the cluster which, although there is a change of spin state, produces a charge distribution which is remarkably similar to the charge distribution of the peripheral charge method which does not involve changes in spin state. The peripheral charge method is designed to simulate doping by placing a carefully chosen set of point charges beyond the periphery of the cluster and relies on the supposition that the hole distribution is closely related to the charge distribution. More importantly the peripheral charge method enables charge distribution changes to be obtained for fractional changes in doping. The results show that with fixed nuclear positions, doping not only depopulates the 2pσ orbitals but also affects other orbitals. This redistribution of charges influences the electric field gradients and hyperfine coupling parameters. The theoretical values for the field gradients are compared to values derived from experiments.

Oxygen vacancies in tetragonal ZrO 2: ab initio embedded cluster calculations

Formation of oxygen vacancies in bulk tetragonal ZrO 2 and at its (101) and (001) surfaces was studied using ab initio embedded cluster calculations. A new technique was proposed for generating a set of point charges that represents the Coulomb field of the crystal environment both for bulk and surface cluster structures. This technique provides the rapid convergence of the calculated Madelung potential to the unique true value. The estimated bulk vacancy formation energy in tetragonal ZrO 2 is 8.8 eV, while surface vacancy energy formation depends on the type of the surface and position of removed oxygen atom and varies from 8.3 to 9.3 eV. The calculated activation energy of oxygen vacancy migration in bulk ZrO 2 is 1.95 eV.

Energy decomposition in molecular complexes: implications for the treatment of polarization in molecular simulations.

This study examines the contribution of electrostatic and polarization to the interaction energy in a variety of molecular complexes. The results obtained from the Kitaura-Morokuma (KM) energy decomposition analysis at the HF/6-31G(d) level indicate that, for intermolecular distances around the equilibrium geometries, the polarization energy can be determined as the addition of the polarization energies of interacting blocks, as the mixed polarization term is typically negligible. Comparison of KM and QM/MM results shows that the electrostatic energy determined in the KM method is underestimated (in absolute value) by QM/MM methods. The reason of such underestimation can be attributed to the simplified representation of treating the interaction between overlapping charge distribution by the interaction of a QM molecule with a set of point charges. Nevertheless, the polarization energies calculated by KM and QM/MM methods are in close agreement. Finally, a consistent, automated strategy to derive charge distributions that include implicitly polarization effects in pairwise, additive force fields is presented. The strategy relies in the simultaneous fitting of electrostatic and polarization energies computed by placing a suitable perturbing particle at selected points around the molecule. The suitability of these charges to describe molecular interactions is discussed.

Ab initioembedded cluster study of optical second-harmonic generation below the gap of a NiO(001) surface

An embedded cluster approach was applied to study the electronic excitations on the NiO(001) surface. Using a quantum chemical calculation, a small $({\mathrm{NiO}}_{5}{)}^{8\ensuremath{-}}$ cluster was embedded in a set of point charges to model the NiO(001) surface. Starting from the unrestricted Hartree-Fock level of theory, we calculate the ground-state properties to provide some insight into electronic structure and excitation. We estimate the excitation energies and oscillator strengths using the single excitation configuration-interaction (CIS) technique. Our results show that the CIS method is reasonably accurate for estimating the low-lying $d\ensuremath{-}d$ excitations below the gap. We then demonstrate the electron correlation effects on the $d\ensuremath{-}d$ transitions at several levels of ab initio correlated theory [CID (with all double substitutions), CISD (with all single and double substitutions), (quadratic) QCISD, and (with all single, double, and triple substitutions) QCISD $(T)].$ The electron correlation tends to decrease the magnitude of d-electron excitation energies. Using the many-body wave functions and energies resulting from CID and $\mathrm{QCISD}(T)$ calculations, we compute the second harmonic generation (SHG) tensor for the NiO(001) surface. In contrast to bulk NiO, where the SHG response is forbidden within the electric-dipole approximation because of the inversion symmetry, the ${C}_{4v}$ symmetry of the surface leads to five nonzero tensor elements. From that, the intensity of the nonlinear optical response as a function of photon energy at different polarizations of the incident and outgoing photons is obtained. This quantity can be directly measured in experiment, and we suggest possible conditions in order to detect it.

A parametrical embedding method for catalytic modeling

In this work, an embedding procedure is proposed for parametric methods. An application to modeling a nickel catalyst supported on γ-alumina was carried out by considering a set of point charges and parametric functionals to simulate short- and long-range interactions. Several clusters were calculated Al n O m and Al n O m Ni o ( n=4, 8, 14, 18, 20; m=6, 12, 21, 27, 30; o=1–5). An analysis of calculated properties for different cluster sizes indicates that, in order to model chemical properties in an adequate way, a minimum cluster size is required. Results show that the long-range effects in the modeling of Ni cluster formation on alumina have to be considered, because they produce changes in bond energies and charges.

Tuning the two-photon absorption response of quadrupolar organic molecules

We apply correlated quantum-chemical techniques to study the origin of the large two-photon absorption (TPA) cross sections, δ, in stilbene derivatives in which electron-donating and electron-withdrawing substituents provide a quadrupolar charge-transfer arrangement. An additional field created by a set of point charges is used to systematically modify the ground-state polarization to determine its consequences for the TPA response. The effect on the molecular structure can be quantified by the evolution of the π-bond-order alternation (π-BOA) of the conjugated backbone. For moderate ground-state polarizations, a marked increase of the TPA response occurs; for large polarizations, δ peaks and then drops dramatically. Insight into the origin of this evolution is gained by comparing the values of δ obtained via the converged sum-over-states approach to the results of a simple three-state model.

A density functional model for tuning the charge transfer between a transition metal electrode and a chemisorbed molecule via the electrode potential

A simple approach is proposed to predict the magnitude of charge transfer between a polarized transition metal electrode and a chemisorbed molecule in an electrolytic solution. The approach is based on the equalization of the chemical potentials, as defined in density-functional theory (DFT). The system is modeled by a metal cluster, a molecule, and a set of point charges (counter ions) and the properties evaluated using methods derived from DFT; specifically, we study here the chemisorption of acrylonitrile on nickel. This approach allows us to point out the various factors determining the charge transfer. The results show a linear increase in the amount of charge transferred to the chemisorbed molecule with the polarization of the metal electrode.

The hydration of the uranyl dication: Incorporation of solvent effects in parallel density functional calculations with the program PARAGAUSS

AbstractThe parallel density functional program PARAGAUSS has been extended by a tool for computing solvent effects based on the conductor‐like screening model (COSMO). The molecular cavity in the solvent is constructed as a set of overlapping spheres according to the GEPOL algorithm. The cavity tessellation scheme and the resulting set of point charges on the cavity surface comply with the point group symmetry of the solute. Symmetry is exploited to reduce the computational effort of the solvent model. To allow an automatic geometry optimization including solvent effects, care has been taken to avoid discontinuities due to the discretization (weights of tesserae, number of spheres created by GEPOL). In this context, an alternative definition for the grid points representing the tesserae is introduced. In addition to the COSMO model, short‐range solvent effects are taken into account via a force field. We apply the solvent module to all‐electron scalar‐relativistic density functional calculations on uranyl, UO22+, and its aquo complexes in aqueous solution. Solvent effects on the geometry are very small. Based on the model [UO2(H2O)5]2+, the solvation energy of uranyl is estimated to be about −400 kcal/mol, in agreement with the range of experimental data. The major part of the solvation energy, about −250 kcal/mol, is due to a donor–acceptor interaction associated with a coordination shell of five water ligands. One can interpret this large solvation energy also as a compounded effect of an effective reduction of the uranyl moiety plus a solvent polarization. The energetic effect of the structure relaxation in the solution is only about 8 kcal/mol. © 2001 John Wiley & Sons, Inc. Int J Quantum Chem, 2001

Electrostatic models of inhibitory activity

AbstractVarious models of electrostatic interactions have been applied and tested for several leucine aminopeptidase (LAP) inhibitors interacting with the enzyme active site. Our results indicate that atomic multipoles up to quadrupole moment as well as potential derived Merz–Kollman and RESP charges reproduce reasonably the ab initio electrostatic interaction energies and the expectation values of the molecular electrostatic potential. These electrostatic models together with CHELP atomic point charges, yield the satisfactory correlation of the electrostatic interaction energy with the experimental activities of the inhibitors, in contrast to the results obtained from atomic monopoles (Mulliken charges) and atomic dipoles. Reasonable correlation has been also obtained for the simple electrostatic “key‐lock” model proposed by Náray‐Szabó, in which the LAP active site is represented by set of point charges (“lock”) interacting with the molecular electrostatic potential of each inhibitor (“key”). © 2001 John Wiley & Sons, Inc. Int J Quant Chem 83: 180–192, 2001

Spectral Analysis of Cytochrome c: Effect of Heme Conformation, Axial Ligand, Peripheral Substituents, and Local Electric Fields

We present in this work low-temperature visible absorption spectra for recombinant Thermus thermophilus cytochrome c552. The Q-band presents a remarkable splitting at low temperature. We performed quantum chemical calculations to evaluate quantitatively the effect of heme conformation, axial ligand, peripheral substituents and local electric fields on the electronic spectra. In an attempt to find correlation between protein structure and spectral splitting, we carried out the same calculations on three other cytochrome c's: horse heart, tuna heart, and yeast. The quantum chemical calculations were performed at the INDO level with extensive configuration interaction. The electric field at the heme pocket was included in the calculations through a set of point charges fitting the actual electric field. The results obtained show clearly that all mentioned effects contribute to the observed spectral splitting in a complex nonadditive way.

Modeling of the adsorption on Cr2O3 clusters of small molecules and ions present in seawater. A preliminary non-empirical study

Non-empirical calculations of a Cr2O3 unit, taken as an initial model of chromium oxide clusters, interacting with ions and (small models of) molecules present in natural seawater have been carried out. The results obtained for the isolated oxide unit show that the coupling between the unpaired 3d electrons of the two chromium atoms has a negligible influence on the charge distribution. The results concerning the adsorption show that: (i) water, methanol and formic acid are dissociated; (ii) the chlorine anion, which is not strongly adsorbed, can easily be removed from the cluster; (iii) the Mg2+ adsorption energy is considerably larger than that of Na+ and Ca2+; (i) the interaction energy of these cations is enhanced by Cr2O3 hydroxylation; () dissociated methanol and formic acid are, of all the molecules considered in this study, those having the strongest interaction energy with Cr2O3. In a very limited number of cases the computations were repeated for a larger cluster (Cr4O6), for a Cr2O3 cluster embedded in a set of point charges, or for a hydroxylated Cr2O3 unit, to study the influence of the environment on the binding energy and geometrical arrangements of the complexes.

Correction of cavity-induced errors in polarization charges of continuum solvation models

We present a formal and numerical analysis of the errors related to the use of molecular cavities in the continuum description of solute–solvent electrostatic interactions. In this approximation the solvent response is fully described by an apparent charge distribution induced on the cavity surface. The latter is then discretized into a set of point charges that are generally affected by errors of different origin but all depending on the definition of the cavity boundaries, and the way its surface is partitioned. The numerical analysis is based on results obtained for a set of couples of neutral/anionic solutes obtained with various versions of PCM methods, exploiting different correction procedures, as well as with two recently developed continuum methods, complementing PCM. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 833–846, 1998

Base stacking in cytosine dimer. A comparison of correlatedab initio calculations with three empirical potential models and density functional theory calculations

Ab initio MP2/6-31G* interaction energies were calculated for more than 80 geometries of stacked cytosine dimer. Diffuse polarization functions were used to properly cover the dispersion energy. The results of ab initio calculations were compared with those obtained from three electrostatic empirical potential models, constructed as the sum of a Lennard-Jones potential (covering dispersion and repulsion contributions) and the electrostatic term. Point charges and point multipoles of the electrostatic term were also obtained at the MP2/6-31G* level of theory. The point charge MEP model (atomic charges derived from molecular electrostatic potential) satisfactorily reproduced the ab initio data. Addition of π-charges localized below and above the cytosine plane did not affect the calculated energies. The model employing the distributed multipole analysis gave worse agreement with the ab initio data than the MEP approach. The MP2 MEP charges were also derived using larger sets of atomic orbitals: cc-pVDZ, 6-311 + G(2d, p), and aug-cc-pVDZ. Differences between interaction energies calculated using these three sets of point charges and the MP2/6-31G* charges were smaller than 0.8 kcal/mol. The correlated ab initio calculations were also compared with the density functional theory (DFT) method. DFT calculations well reproduced the electrostatic part of interaction energy. They also covered some nonelectrostatic short-range effects which were not reproduced by the empirical potentials. The DFT method does not include the dispersion energy. This energy, approximated by an empirical term, was therefore added to the DFT interaction energy. The resulting interaction energy exhibited an artifact secondary minimum for a 3.9-4.0 vertical separation of bases. This defect is inherent in the DFT functionals, because it is not observed for the Hartree-Fock + dispersion interaction energy.© 1996 John Wiley & Sons, Inc.

Image solution for Poisson's equation in wedge geometry

The Poisson's equation for a dielectric wedge is solved by deriving a static image that corresponds to the potential contribution of the wedge. The problem is studied mainly in three dimensions but the solution for the analog two-dimensional problem is also provided. It appears that the use of image sources provides numerically a simple and efficient method to compute the potential inside and outside the wedge. Image sources for the exterior and interior regions consist of a line charge that decays exponentially as a function of complex angle and a set of point charges that can be interpreted as reflection or transmission images of a dielectric plane. All known closed-form solutions in terms of elementary functions are derived for an electrically and magnetically conducting half plane. >

Success and pitfalls of the dielectric continuum model in quantum chemical calculations

Recently we presented an extension of the direct reaction field (DRF) method, in which a quantum system and a set of point charges and interacting polarizabilities are embedded in a continuum that is characterized by a dielectric constant epsilon and a finite ionic strength. The reaction field of the continuum is found by solving the (linearized) Poisson-Boltzmann equation by a boundary element method for the complete charge distribution in a cavity of arbitrary size and form. Like many other authors, we found that the results depend critically on the choice of the size of the cavity, in the sense that the continuum contribution to the solvation energy decreases rapidly with the relative cavity size. The literature gives no clues for the definition of the cavity size beyond ''physical intuition'' or implicit fitting to experimental or otherwise desired results. From theoretical considerations, a number of limitations on the position of the boundary are derived. With a boundary defined within these limitations, the experimental hydration energies cannot be reproduced, mainly because of the neglected specific interactions. In addition, we found that the description of the solute's electronic states also depends on the solvation model. We suggest that one or more explicit solvent layers are needed to obtain reliable solvation and excitation energies. (C) 1993 John Wiley & Sons, Inc.

Transverse laser patterns. I. Phase singularity crystals.

We analyze the interaction and the competition of a set of transverse cavity modes, which belong to a frequency-degenerate family. The laser turns out to be able to realize several different stationary spatial patterns, which differ in the transverse configuration of the intensity or of the field and are met by varying the values of the control parameters. A striking feature that emerges in almost all steady-state patterns is the presence of dark points, in which both the real and the imaginary part of the electric field vanish and such that, if one covers a closed loop around one of these points, the field phase changes by a multiple of 2\ensuremath{\pi}, which corresponds to the topological charge of the point. We show in detail the analogy of these phase singularities to the vortex structures well known in such fields as, for example, hydrodynamics, superconductivity, and superfluidity. In our case, at steady state, these singularities are arranged in the form of regular crystals, nd the equiphase lines of the field exhibit a notable similarity to the field lines of the electrostatic field generated by a corresponding set of point charges. We analyze in detail the patterns that emerge in the cases 2p+l=2 and 2p+l=3, where p and l are the radial and angular modal indices, respectively, and we compare the results with the experimental observations obtained from a ${\mathrm{Na}}_{2}$ laser. The observed patterns agree in detail with those found by theory; in particular, they exhibit the predicted phase singularities in each pattern. The transitions from one pattern to another, that one observes under variation of the control parameters, basically agree with those predicted by theory.

Cumulative atomic multipole moments and point charge models describing molecular charge distribution

The program for decomposition of a molecular charge distributions into the sets of cumulative atomic multipole moments (CAMM) up to hexadecapole moment is presented. Additionally decomposition of all atomic multipole moments into sets of point charges can be done reproducing simultaneously all atomic and molecular multipole moments up to quadrupole. The program follows the convention used in GAUSSIAN-82/GAUSSIAN-86 ab initio programs and can be used for further analysis of results obtained with these programs.