Extended treatment of charge response kernel comprising the density functional theory and charge regulation procedures

We propose an extended treatment of the charge response kernel (CRK), (partial differential Q(a)/partial differential V(b)), which describes the response of partial charges on atomic sites to external electrostatic potential, on the basis of the density functional theory (DFT) via the coupled perturbed Kohn-Sham equations. The present CRK theory incorporates regulation procedures in the definition of partial charges to avoid unphysical large fluctuation of the CRK on "buried" sites. The CRKs of some alcohol and organic molecules, methanol, ethanol, propanol, butanol, dimethylsulfoxide (DMSO), and tetrahydrofuran (THF) were calculated, demonstrating that the new CRK model at the DFT level has greatly improved the performance of accuracy in comparison with that at the Hartree-Fock level previously proposed. The CRK model was also applied to investigate spatial nonlocality of the charge response through alkyl chain sequences. The CRK model at the DFT level enables us to construct a nonempirical strategy for polarizable molecular modeling, with practical reliability and robustness.     

Electrode independent chemoresistive response for cobalt phthalocyanine in the space charge limited conductivity regime

The electrical properties of 50 nm thick metallophthalocyanine films, prepared by organic molecular beam epitaxy (OMBE) on interdigitated electrodes, were studied with DC current-voltage measurements and impedance spectroscopy. The transition from Ohmic behavior at low voltages to space-charge-limited conductivity (SCLC) at higher voltages depends on the metal electrode (Pt, Pd, and Au), but does not correlate with the work function of the electrode. Impedance spectroscopy studies show the coexistence of low- and high-frequency traps in the thin film devices, and the contribution of low-frequency traps associated with Ohmic behavior diminishes at higher bias. Although device resistances are strongly influenced by the electrode material, and vary by a factor of over 300, the relative chemical sensor responses on exposure to dimethyl methylphosphonate (DMMP), methanol, water, or toluene vapors are similar for CoPc on Pt, Pd, and Au electrodes when these devices are operated in the SCLC regime at room temperature. When the devices are operated at voltages where the low-frequency interfacial traps are filled, the sensor response to analyte becomes uniform and reliable regardless of the specific interfacial electrode contact.     

Atomic-scale determination of DNA conformational response to strained furanose: a static mode approach

An original approach of macromolecular ‘induced-fit’ flexibility, namely the static modes, is applied to shed light on some fundamental mechanisms impacting DNA conformations. We first investigate a constrained nucleic acid of the D-CNA family, in which some backbone torsional angles are conformationally restricted by a dioxaphosphorinane ring structure. We take a special interest in α,β-D-CNA, in which α and β angles are restricted to the canonical conformation. We used the static mode method to evaluate the impact of the insertion of modified nucleotides on the stability of DNA/DNA and DNA/RNA duplexes. Although our approach authorizes the design of complex excitation modes on a specific molecule, we here establish with an atomic precision how a DNA south to north transition can be optimally operated through C5′ and O5′ single excitations.     

On searching in, sampling of, and dynamically moving through conformational space of biomolecular systems: A review

Methods to search for low-energy conformations, to generate a Boltzmann-weighted ensemble of configurations, or to generate classical-dynamical trajectories for molecular systems in the condensed liquid phase are briefly reviewed with an eye to application to biomolecular systems. After having chosen the degrees of freedom and method to generate molecular configurations, the efficiency of the search or sampling can be enhanced in various ways: (i) efficient calculation of the energy function and forces, (ii) application of a plethora of search enhancement techniques, (iii) use of a biasing potential energy term, and (iv) guiding the sampling using a reaction or transition pathway. The overview of the available methods should help the reader to choose the combination that is most suitable for the biomolecular system, degrees of freedom, interaction function, and molecular or thermodynamic properties of interest.     

Systematic stepsize variation: Efficient method for searching conformational space of polypeptides

A new and efficient method for overcoming the multiple minima problem of polypeptides, the systematic stepsize variation (SSV) method, is presented. The SSV is based on the assumption that energy barriers can be passed over by sufficiently large rotations about rotatable bonds: randomly chosen dihedral angles are updated starting with a small stepsize (i.e., magnitude of rotation). A new structure is accepted only if it possesses a lower energy than the precedent one. Local minima are passed over by increasing the stepsize systematically. When no new structures are found any longer, the simulation is continued with the starting structure, but other trajectories will be followed due to the random order in updating the torsional angles. First, the method is tested with Met-enkephalin, a peptide with a known global minimum structure; in all runs the latter is found at least once. The global minimum conformations obtained in the simulations show deviations of ±0.0004 kcal/mol from the reference structure and, consequently, are perfectly superposable. For comparison, Metropolis Monte Carlo simulated annealing (MMC-SA) is performed. To estimate the efficiency of the algorithm depending on the complexity of the optimization problem, homopolymers of Ala and Gly of different lengths are simulated, with both the SSV and the MMC-SA method. The comparative simulations clearly reveal the higher efficiency of SSV compared with MMC-SA. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 1470–1481, 1998     

Quantifying polypeptide conformational space: sensitivity to conformation and ensemble definition

Quantifying the density of conformations over phase space (the conformational distribution) is needed to model important macromolecular processes such as protein folding. In this work, we quantify the conformational distribution for a simple polypeptide (N-mer polyalanine) using the cumulative distribution function (CDF), which gives the probability that two randomly selected conformations are separated by less than a "conformational" distance and whose inverse gives conformation counts as a function of conformational radius. An important finding is that the conformation counts obtained by the CDF inverse depend critically on the assignment of a conformation's distance span and the ensemble (e.g., unfolded state model): varying ensemble and conformation definition (1 --> 2 A) varies the CDF-based conformation counts for Ala(50) from 10(11) to 10(69). In particular, relatively short molecular dynamics (MD) relaxation of Ala(50)'s random-walk ensemble reduces the number of conformers from 10(55) to 10(14) (using a 1 A root-mean-square-deviation radius conformation definition) pointing to potential disconnections in comparing the results from simplified models of unfolded proteins with those from all-atom MD simulations. Explicit waters are found to roughen the landscape considerably. Under some common conformation definitions, the results herein provide (i) an upper limit to the number of accessible conformations that compose unfolded states of proteins, (ii) the optimal clustering radius/conformation radius for counting conformations for a given energy and solvent model, (iii) a means of comparing various studies, and (iv) an assessment of the applicability of random search in protein folding.     

New optimization method for conformational energy calculations on polypeptides: Conformational space annealing

A new optimization method is presented to search for the global minimum-energy conformations of polypeptides. The method combines essential aspects of the build-up procedure and the genetic algorithm, and it introduces the important concept of “conformational space annealing.” Instead of considering a single conformation, attention is focused on a population of conformations while new conformations are obtained by modifying a “seed conformation.” The annealing is carried out by introducing a distance cutoff, D_cut, which is defined in the conformational space; D_cut effectively divides the whole conformational space of local minima into subdivisions. The value of D_cut is set to a large number at the beginning of the algorithm to cover the whole conformational space, and annealing is achieved by slowly reducing it. Many distinct local minima designed to be distributed as far apart as possible in conformational space are investigated simultaneously. Therefore, the new method finds not only the global minimum-energy conformation but also many other distinct local minima as by-products. The method is tested on Met-enkephalin, a 24-dihedral angle problem. For all 100 independent runs, the accepted global minimum-energy conformation was obtained after about 2600 minimizations on average. © 1997 John Wiley & Sons, Inc. J Comput Chem 18: 1222–1232     

Genetic algorithms: A robust scheme for geometry optimizations and global minimum structure problems

A Genetic Algorithm for Geometry Optimizations (GALGO) program has been developed to study the efficiency of this method of finding global minimum structures. Using a semiempirical tight-binding potential, the behavior of different genetic algorithm (GA) operators has been tested for the linear chain isomer of a C₈ cluster. An optimum set of parameters for the GA operators is proposed for this problem and afterward is used to obtain the global minimum structure of rare-gas atomic clusters of up to 13 atoms using the 12–6 Lennard-Jones interatomic pair potential. © 1995 by John Wiley & Sons, Inc.     

Electronegativity equalization method: parameterization and validation for organic molecules using the Merz-Kollman-Singh charge distribution scheme

The electronegativity equalization method (EEM) was developed by Mortier et al. as a semiempirical method based on the density-functional theory. After parameterization, in which EEM parameters A(i), B(i), and adjusting factor kappa are obtained, this approach can be used for calculation of average electronegativity and charge distribution in a molecule. The aim of this work is to perform the EEM parameterization using the Merz-Kollman-Singh (MK) charge distribution scheme obtained from B3LYP/6-31G* and HF/6-31G* calculations. To achieve this goal, we selected a set of 380 organic molecules from the Cambridge Structural Database (CSD) and used the methodology, which was recently successfully applied to EEM parameterization to calculate the HF/STO-3G Mulliken charges on large sets of molecules. In the case of B3LYP/6-31G* MK charges, we have improved the EEM parameters for already parameterized elements, specifically C, H, N, O, and F. Moreover, EEM parameters for S, Br, Cl, and Zn, which have not as yet been parameterized for this level of theory and basis set, we also developed. In the case of HF/6-31G* MK charges, we have developed the EEM parameters for C, H, N, O, S, Br, Cl, F, and Zn that have not been parameterized for this level of theory and basis set so far. The obtained EEM parameters were verified by a previously developed validation procedure and used for the charge calculation on a different set of 116 organic molecules from the CSD. The calculated EEM charges are in a very good agreement with the quantum mechanically obtained ab initio charges.     

Optimal N-caps for N-terminal helical templates: effects of changes in H-bonding efficiency and charge

A family of efficient helix-initiating N-terminal caps X-Hel is introduced that expand the scope and versatility of the previously reported reporting conformational template Ac-Hel, (Kemp, D. S.; Allen, T. J.; Oslick, S. J. Am. Chem. Soc. 1995, 117, 6641-6657) and a working principle for predicting cap performance is described, based on structurally specific intramolecular hydrogen bond formation. Replacement of the N-acetyl by urethane, urea, or sulfonamide generated less efficient polypeptide helix inducers. The N-formyl cap is found to be equivalent to the N-acetyl and may provide more convenient quantitative helix reporting properties. Anionic N-caps derived from the series X = (-)O(2)C-(CH(2))(n)-CO, 0 < or = n < or = 3, are superior to N-acetyl, as are N-acylglycyl and N-acyl-beta-aspartyl. The latter pair of caps permit introduction of the X-Hel functionality within a polypeptide chain, allowing control of helicity of a peptide sub-sequence. Applications of these capping functions are discussed. This work has been focused primarily on immediate practical goals directed toward enhancing the maximum helicity of isolated short to medium-sized peptides in aqueous solution, but its developing concepts and working hypotheses are likely to significantly enhance our understanding at a chemical level of the protein folding problem.     

Photoinduced charge shift and charge recombination through an alkynyl spacer for an expanded acridinium-based dyad

The photophysical and electrochemical properties of a dyad comprising an expanded acridinium light-harvester, coupled via a triple bond to a trialkyloxybenzene donor, are described. Laser excitation of the dyad in 1,2-dichloroethane (DCE) results in rapid charge shift (5 ps) followed by slower charge recombination (81 ps) to completely restore the ground state. Discrimination between forward and return electron transfer (k(ret)/k(for) ~ 16) is rather poor. There is no indication of triplet formation on the expanded acridinium-based group following charge recombination.     

Spectrophotometric determination of rifampicin through chelate formation and charge transfer complexation in pharmaceutical preparation and biological fluids

Two simple and accurate spectrophotometric methods for determination of Rifampicin (RIF) are described. The first method is based on charge transfer (CT) complex formation of the drug with three pi-electron acceptors either 2,3-dichloro-5,6-dicyano-1,4-benzoquinone (DDQ), 7,7,7,8-Tetracyanoquinodimethane (TCNQ) or 2,3,5,6-Tetrachloro-1,4-benzoquinone (p-chloranil) in acetonitrile. The method is followed spectrophotometrically by measuring the maximum absorbance at 584 nm, 761 nm (680 nm) or 560 nm for DDQ, TCNQ and p-chloranil, respectively. Under the optimized experimental conditions, the calibration curves showed a linear relationship over the concentration ranges of 5-140 microg/ml, 2-45 microg/ml (5-120 microg/ml) and 15-200 microg/ml, respectively. The second method is based on the reaction of RIF with iron(III) forming a water insoluble violet complex which is extracted into chloroform. The method determines RIF in concentration range of 10-240 microg/ml at 540 nm. The proposed methods applied to determination of RIF in capsule, human serum and urine samples with good accuracy and precision. The results were compared statistically with the official method and showed no significant different between the methods compared in terms of accuracy and precision.     

Energy partitioning scheme based on self-consistent method for subsystems: populational space approach

The refinement of the previously proposed energy partitioning scheme, self-consistent charge and configuration method for subsystems (Korchowiec and Uchimaru, J Chem Phys 2000, 112, 1623), is proposed. Our new realization takes rigorously into account all the interactions between subsystems and guarantees proper symmetry of the intermediate wavefunctions. In addition, the scheme is supplemented with natural orbitals for chemical valence to trace the charge reorganization during polarization and charge transfer steps. The water dimer and ammonia borane are used to illustrate the proposed formalism.     

Q-fit: a probabilistic method for docking molecular fragments by sampling low energy conformational space

A new method is presented that docks molecular fragments to a rigid protein receptor. It uses a probabilistic procedure based on statistical thermodynamic principles to place ligand atom triplets at the lowest energy sites. The probabilistic method ranks receptor binding modes so that the lowest energy ones are sampled first. This allows constraints to be introduced to limit the depth of the search leading to a computationally efficient method of sampling low energy conformational space. This is combined with energy minimization of the initial fragment placement to arrive at a low energy conformation for the molecular fragment. Two different search methods are tested involving (i) geometric hashing and (ii) pose clustering methods. Ten molecular fragments were docked that have commonly been used to test docking methods. The success rate was 8/10 and 10/10 for generating a close solution ranked first using the two different sampling procedures. In general, all five of the top ranked solutions reproduce the observed binding mode, which increases confidence in the predictions. A set of ten molecular fragments that have previously been identified as problematic were docked. Success was achieved in 3/10 and 4/10 using the two different methods. Again there is a high level of agreement between the two methods and again in the successful cases the top ranked solutions are correct whilst in the case of the failures none are. The geometric hashing and pose clustering methods are fast averaging 13 and 11 s per placement respectively using conservative parameters. The results are very encouraging and will facilitate the process of finding novel small molecule lead compounds by virtual screening of chemical databases.     

Antifungal diastereomeric furanones from Mutisia friesiana: structural determination and conformational analysis

Two diastereomeric furanones, (4S,5S)-5-(4′-methyl-3′-pentenyl)-4-hydroxy-5-methyldihydrofuran-2-one 1 and (4S,5R)-5-(4′-methyl-3′-pentenyl)-4-hydroxy-5-methyldihydrofuran-2-one 2 were isolated for the first time from the shrub Mutisia friesiana. The relative stereochemistries of 1 and 2 were ascertained from NOESY NMR data and confirmed by a combination of molecular modeling (molecular mechanics and ab initio molecular orbital calculations) and NMR data. Comparison between experimental and calculated ¹H–¹H vicinal coupling constants revealed that both furanones exist in an equilibrium of two stable conformers of the five-membered ring. Application of Mosher's method suggests that both diastereomeric furanones have the same (S)-configuration at C-(4) and are epimers at C-(5). Furanones 1 and 2 showed antifungal activity against the pathogenic fungus Cladosporium cucumerinum.     

Dynamics and conformational properties of polyampholytes in external electrical fields: Influence of the charge distribution

In the present work we study the dynamics and conformational properties of polyampholytes (PAs, polymers containing positive and negative charges) in the presence of external electrical fields. In terms of the Rouse Model of polymer dynamics we obtain for PAs in the so-called weak coupling limit explicitly the mean square displacement both of the center of mass and of individual beads, and the PAs' end-to-end distance. We study both ordered and also random charge distributions along the chains; in the latter case we also consider the role of different correlation lengths.     

Ion diffusion coefficients through polyelectrolyte multilayers: temperature and charge dependence

The diffusion coefficient is a fundamental parameter for devices exploiting the ion transport properties of polyelectrolyte multilayers (PEMUs) and complexes. Here, the transport of ferricyanide through a multilayer made from poly(diallyldimethylammonium chloride) (PDADMA) and polystyrene sulfonate (PSS) was studied as a function of temperature or salt concentration. Accurate and precise measurements of ion diffusion coefficients were obtained using steady-state electrochemistry to determine the flux and Fourier transform infrared (FTIR) spectroscopy to measure the PEMU concentration. It was found that the concentration of ferricyanide inside the film decreased with temperature. Membrane transport is strongly thermally activated with activation energy 98 kJ mol(-1). A potential shift with decreasing salt concentration in cyclic voltammograms was translated into a differential flux caused by significantly higher diffusion coefficients for ferricyanide as compared to ferrocyanide.     

Direct space decomposition of ELI-D: interplay of charge density and pair-volume function for different bonding situations

The topological features, i.e., gradients and curvatures of the same-spin electron pair restricted electron localizability indicator (ELI-D) in position space are analyzed in terms of those of the electron density and the pair-volume function. The analysis of the topology of these constituent functions and their interplay on ELI-D attractor formation for a number of molecules representing chemically different bonding situations allows distinguishing between different chemical bonding scenarios on a quantum mechanical basis without the recourse to orbitals. The occurrence of the Laplacian of the electron density in the expression for the Laplacian of ELI-D allows us to establish a physical link between electron localizability and electron pairing as displayed by ELI-D and the role of Laplacian of the density in this context.