Atomic forces for geometry‐dependent point multipole and Gaussian multipole models

In standard treatments of atomic multipole models, interaction energies, total molecular forces, and total molecular torques are given for multipolar interactions between rigid molecules. However, if the molecules are assumed to be flexible, two additional multipolar atomic forces arise because of (1) the transfer of torque between neighboring atoms and (2) the dependence of multipole moment on internal geometry (bond lengths, bond angles, etc.) for geometry‐dependent multipole models. In this study, atomic force expressions for geometry‐dependent multipoles are presented for use in simulations of flexible molecules. The atomic forces are derived by first proposing a new general expression for Wigner function derivatives . The force equations can be applied to electrostatic models based on atomic point multipoles or Gaussian multipole charge density. Hydrogen‐bonded dimers are used to test the intermolecular electrostatic energies and atomic forces calculated by geometry‐dependent multipoles fit to the ab initio electrostatic potential. The electrostatic energies and forces are compared with their reference ab initio values. It is shown that both static and geometry‐dependent multipole models are able to reproduce total molecular forces and torques with respect to ab initio, whereas geometry‐dependent multipoles are needed to reproduce ab initio atomic forces. The expressions for atomic force can be used in simulations of flexible molecules with atomic multipoles. In addition, the results presented in this work should lead to further development of next generation force fields composed of geometry‐dependent multipole models. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010     

Accuracy and tractability of a kriging model of intramolecular polarizable multipolar electrostatics and its application to histidine

We propose a generic method to model polarization in the context of high‐rank multipolar electrostatics. This method involves the machine learning technique kriging, here used to capture the response of an atomic multipole moment of a given atom to a change in the positions of the atoms surrounding this atom. The atoms are malleable boxes with sharp boundaries, they do not overlap and exhaust space. The method is applied to histidine where it is able to predict atomic multipole moments (up to hexadecapole) for unseen configurations, after training on 600 geometries distorted using normal modes of each of its 24 local energy minima at B3LYP/apc‐1 level. The quality of the predictions is assessed by calculating the Coulomb energy between an atom for which the moments have been predicted and the surrounding atoms (having exact moments). Only interactions between atoms separated by three or more bonds (“1, 4 and higher” interactions) are included in this energy error. This energy is compared with that of a central atom with exact multipole moments interacting with the same environment. The resulting energy discrepancies are summed for 328 atom–atom interactions, for each of the 29 atoms of histidine being a central atom in turn. For 80% of the 539 test configurations (outside the training set), this summed energy deviates by less than 1 kcal mol^?1. © 2013 Wiley Periodicals, Inc.     

Improved intermolecular force field for molecules containing H,C, N,and O atoms,with application to nucleoside and peptide crystals

A new intermolecular force field for nitrogen atoms in organic molecules was derived from a training dataset of 76 observed azahydrocarbon crystal structures and 11 observed heats of sublimation. The previously published W99 force field for hydrogen, carbon, and oxygen was thus extended to include nitrogen atoms. Nitrogen atoms were divided into four classes: N(1) for triply bonded nitrogen, N(2) for nitrogen with no bonded hydrogen (except the triple bonded case), N(3) for nitrogen with one bonded hydrogen, and N(4) for nitrogen with two or more bonded hydrogens. H(4) designated hydrogen bonded to nitrogen. Wavefunctions of 6‐31g** quality were calculated for each molecule and the molecular electric potential (MEP) was modeled with net atomic and supplementary site charges. Lone pair electron charge sites were included for nitrogen atoms where appropriate, and methylene bisector charges were used for CH₂ and CH₃ groups when fitting the MEP. X? H bond distances were set to standard values for the wave function calculation and then foreshortened by 0.1 Å for the MEP and force field fitting. Using the force field optimized to the training dataset, each azahydrocarbon crystal structure was relaxed by intermolecular energy minimization. Predicted maximum changes in unit cell edge lengths for each crystal were 3% or less. The complete force field for H, C, N, and O atoms was tested by intermolecular energy relaxation of nucleoside and peptide molecular crystals. Even though these molecules were not included in any of the training datasets for the force field, agreement with their observed crystal structures was very good, with predicted unit cell edge shifts usually less than 2%. These tests included crystal structures of representatives of all eight common nucleosides found in DNA and RNA, 15 dipeptides, four tripeptides, two tetrapeptides, and a pentapeptide with two molecules in the asymmetric unit. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 1154–1166, 2001     

A liquid crystal cell with double-side protrusion electrodes for fast response and low-voltage operation

We propose a homogeneously aligned liquid crystal (LC) cell with double-side protrusion electrodes for fast response and low-voltage operation. In the proposed device, both the bottom and top substrates have pixel electrodes to generate the fringe electric field. Because the penetration depth of the electric field is increased owing to the protrusion electrodes, the operating voltage is very low and the turn-on time is dramatically reduced compared with the conventional in-plane switching (IPS) mode. Moreover, LC molecules anchored strongly to the penetrated protrusion electrodes on both substrates exert a strong restoring force, resulting in a fast turn-off time. We found that the total response time of the LC cell with the proposed structure is three times faster than that of the conventional IPS mode.     

Effect of the cell type and cell density on the binding of living cells to a silica particle: an atomic force microscope study

We used the atomic force microscope to study how the cell type and the density of cells adsorbed at a substrate can affect the adhesion between a living cell and a model drug delivery system (DDS) carrier nano-particle. We used three different anchorage-dependent cells, i.e., a living mouse fibroblast cell (L929), a living human colon cancer cell (Caco2), and a living mouse malignant melanoma cell (B16F10). For the DDS model nano-particle, we used a silica colloid. In order to correlate the adhesion force with the cell types, the growth curve of the cells were determined with a haemocytometer. The shapes of the cells at the different stages were monitored by light microscopy, and the morphology of their surfaces obtained by tapping mode atomic force microscopy.

Force measurements showed that the Caco2 cell bound little to a silica particle, regardless of the cell density. The L929 cell bound well to a silica particle for low and high cell densities. The B16F10 cell bound little to a silica particle for low cell densities, but bound well for high cell densities. AFM images showed that the L929 cell did not contain folds. The B16F10 cells, however, displayed folds in the cell surface for low cell densities, but no folds in the cell for high cell densities. As literature also reported that the Caco2 cell contains folds, these results suggested that cells with folds showed less adhesion to a silica particle than cells without folds. The presence of folds in the cell presumably decreased the number of sites on the cell that could hydrogen bond or undergo van der Waals binding with the silanol groups of the silica particle.     

Modifying the OPLS-AA force field to improve hydration free energies for several amino acid side chains using new atomic charges and an off-plane charge model for aromatic residues

The hydration free energies of amino acid side chains are an important determinant of processes that involve partitioning between different environments, including protein folding, protein complex formation, and protein-membrane interactions. Several recent papers have shown that calculated hydration free energies for polar and aromatic residues (Trp, His, Tyr, Asn, Gln, Asp, Glu) in several common molecular dynamics force fields differ significantly from experimentally measured values. We have attempted to improve the hydration energies for these residues by modifying the partial charges of the OPLS-AA force field based on natural population analysis of density functional theory calculations. The resulting differences between calculated hydration free energies and experimental results for the seven side chain analogs are less than 0.1 kcal/mol. Simulations of the synthetic Trp-rich peptide Trpzip2 show that the new charges lead to significantly improved geometries for interacting Trp-side chains. We also investigated an off-plane charge model for aromatic rings that more closely mimics their electronic configuration. This model results in an improved free energy of hydration for Trp and a somewhat altered benzene-sodium potential of mean force with a more favorable energy for direct benzene-sodium contact.     

CHARMM fluctuating charge force field for proteins: I parameterization and application to bulk organic liquid simulations

A first-generation fluctuating charge (FQ) force field to be ultimately applied for protein simulations is presented. The electrostatic model parameters, the atomic hardnesses, and electronegativities, are parameterized by fitting to DFT-based charge responses of small molecules perturbed by a dipolar probe mimicking a water dipole. The nonbonded parameters for atoms based on the CHARMM atom-typing scheme are determined via simultaneously optimizing vacuum water-solute geometries and energies (for a set of small organic molecules) and condensed phase properties (densities and vaporization enthalpies) for pure bulk liquids. Vacuum solute-water geometries, specifically hydrogen bond distances, are fit to 0.19 A r.m.s. error, while dimerization energies are fit to 0.98 kcal/mol r.m.s. error. Properties of the liquids studied include bulk liquid structure and polarization. The FQ model does indeed show a condensed phase effect in the shifting of molecular dipole moments to higher values relative to the gas phase. The FQ liquids also appear to be more strongly associated, in the case of hydrogen bonding liquids, due to the enhanced dipolar interactions as evidenced by shifts toward lower energies in pair energy distributions. We present results from a short simulation of NMA in bulk TIP4P-FQ water as a step towards simulating solvated peptide/protein systems. As expected, there is a nontrivial dipole moment enhancement of the NMA (although the quantitative accuracy is difficult to assess). Furthermore, the distribution of dipole moments of water molecules in the vicinity of the solutes is shifted towards larger values by 0.1-0.2 Debye in keeping with previously reported work.     

Homohelicity-enriched zinc bilinone dimers with chiral aliphatic spacers. Synthesis and application to chiral induction of a nematic liquid crystal

The zinc bilinone (ZnBL) dimers 4 and 5 bearing chiral aliphatic spacers ((2S,4S)-2,4-pentanedioxy and (3S,5S)-2,6-dimethyl-3,5-heptanedioxy for 4 and 5, respectively) were newly prepared, and their conformational distribution was investigated. The ¹H NMR and circular dichroism spectra revealed that the present dimers predominantly adopted the homohelicity conformation (MM and PP for 4 and 5, respectively), although the reference monomers with the corresponding subunit structures exhibited poor helicity enrichment. The helical twisting powers of these ZnBL dimers for a nematic liquid crystal (N-(4-methoxybenzylidene)-4-butylaniline, MBBA) were also investigated. With the dimers doped into MBBA, highly efficient chiral nematic induction was achieved. Especially, the dimer 5 exhibited the β_M value of +1800 μm⁻¹.     

Desirability-based multiobjective optimization for global QSAR studies: application to the design of novel NSAIDs with improved analgesic, antiinflammatory, and ulcerogenic profiles

Up to now, very few reports have been published concerning the application of multiobjective optimization (MOOP) techniques to quantitative structure-activity relationship (QSAR) studies. However, none reports the optimization of objectives related directly to the desired pharmaceutical profile of the drug. In this work, for the first time, it is proposed a MOOP method based on Derringer's desirability function that allows conducting global QSAR studies considering simultaneously the pharmacological, pharmacokinetic and toxicological profile of a set of molecule candidates. The usefulness of the method is demonstrated by applying it to the simultaneous optimization of the analgesic, antiinflammatory, and ulcerogenic properties of a library of fifteen 3-(3-methylphenyl)-2-substituted amino-3H-quinazolin-4-one compounds. The levels of the predictor variables producing concurrently the best possible compromise between these properties is found and used to design a set of new optimized drug candidates. Our results also suggest the relevant role of the bulkiness of alkyl substituents on the C-2 position of the quinazoline ring over the ulcerogenic properties for this family of compounds. Finally, and most importantly, the desirability-based MOOP method proposed is a valuable tool and shall aid in the future rational design of novel successful drugs.     

Solution of periodic Poisson's equation and the Hartree–Fock approach for solids with extended electron states: Application to linear augmented plane wave method

We formulate a Hartree–Fock‐LAPW method for electronic band structure calculations. The method is based on the Hartree–Fock–Roothaan approach for solids with extended electron states and closed core shells where the basis functions of itinerant electrons are linear augmented plane waves. All interactions within the restricted Hartree–Fock approach are analyzed and in principle can be taken into account. In particular, we obtained the matrix elements for the exchange interactions of extended states and the crystal electric field effects. To calculate the matrix elements of exchange for extended states, we first introduce an auxiliary potential and then integrate it with an effective charge density corresponding to the electron exchange transition under consideration. The problem of finding the auxiliary potential is solved by using the strategy of the full potential LAPW approach, which is based on the general solution of periodic Poisson's equation. Here, we use an original technique for the general solution of periodic Poisson's equation and multipole expansions of electron densities. We apply the technique to obtain periodic potentials of the face‐centered cubic lattice and discuss its accuracy and convergence in comparison with other methods. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2002     

Development of an ultra‐high‐performance liquid chromatography coupled with triple quadrupole mass spectrometry method for comparative pharmacokinetics of six triterpenoids in rat plasma and application to different forms of Phytolacca acinosa

Phytolacca acinosa is an herb for treatment of ascites and tumor. Two forms of P. acinosa, i.e. raw and vinegar‐processed herb, have been used in clinic. However, pharmacokinetic difference between the two forms of P. acinosa has not been fully understood. Herein, a comparative pharmacokinetic method based on liquid chromatography with tandem mass spectrometry was developed for quantification of six bioactive triterpenoids, including esculentoside H, esculentoside T, esculentoside A, esculentoside B, phytolaccagenic acid, and phytolaccagenin in rat plasma after oral administration of different forms of P. acinosa. Separation was performed on an Acquity BEH C₁₈ column (1.7 µm, 2.1 mm × 50 mm). The method was validated over a linear range of 2.0–5000 ng/mL. Intraday and interday bias were within ±5%. Besides, all triterpenoids were stable in plasma during different storage conditions. The described method was successfully applied to a comparative pharmacokinetic study of raw and vinegar‐processed P. acinosa in rats. Notably, double peak phenomenon for six triterpenoids of P. acinosa was observed for the first time. AUC_0→t and C_max values of esculentoside H, esculentoside T, phytolaccagenic acid, and phytolaccagenin were significantly lower in vinegar‐processed group than that of raw group, indicating the oral bioavailability of the four triterpenoids was decreased after vinegar processing.