Alumni Dissertations

 

Alumni Dissertations

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  • Nanoelectrochemical sensors for kinetic measurements and electroanalytical chemistry

    Author:
    Yixian Wang
    Year of Dissertation:
    2013
    Program:
    Chemistry
    Advisor:
    Michael Mirkin
    Abstract:

    My PhD research is in the field of nanoelectrochemistry. It includes both fundamental kinetics studies of charge transfer processes and chemical reactions at nanoscopic liquid/liquid and solid/liquid interfaces and applications of the nanometer-sized probes and scanning electrochemical microscopy (SECM) as analytical tools. Nanopipettes can be used to study kinetics of heterogeneous ion transfer (IT) reactions. Common ion voltammetry was developed for determining the kinetic parameters of the rapid tetraethylammonium transfer at the dichloroethane/water interface. This new type of voltammetry provides two limiting currents corresponding to the ingress of the common ion into the pipette and its egress to the external solution, from which one can evaluate the related geometric and transport parameters. Then, the kinetics of IT processes of tetrabutylammonium and similarly sized but asymmetric 1-methyl-3-octylimidazolium at the water/ionic liquid nanointerface was determined for the first time by employing this new approach. Nanopipettes were also used as SECM tips to carry out feedback-mode imaging of various substrates with the nanoscale resolution. Quantitative SECM measurements performed with the polished pipettes as small as 8 nm radius at extremely short tip/substrate distances (~1 nm). A new mode of the SECM operation--electron transfer/ion transfer mode--was developed for simultaneous mapping of surface reactivity and topography. We developed the methodology for resistive-pulse sensing with nanopipettes and used it to detect Au nanoparticles, nanoparticles coated with an allergen epitope peptide layer, and gold particles with bound antipeanut antibodies on the peptide layer. The current pulses produced by antibody-conjugated particles and either bare gold or Au-peptide nanoparticles occurred at different translocation voltages and exhibited opposite signs of the current change, which is essential for selective resistive-pulse sensing of antibodies with nanopipettes. I modified Pt nanoelectrodes with platinum black and then used them to detect reactive oxygen and nitrogen species (ROS and RNS) inside macrophages. Our results supported the hypothesis of the ROS/RNS leakage from phagolysosomes. The data also showed that a macrophage can avoid oxidative damage by rapidly reducing ROS/RNS concentration levels in its cytoplasm.

  • Organic pi-stacking Semiconducting Material: Design, Synthesis and the Analysis of Structure and Properties

    Author:
    Bin Wang
    Year of Dissertation:
    2014
    Program:
    Chemistry
    Advisor:
    Shi Jin
    Abstract:

    Organic semiconducting materials have been under intensive investigation in the recent decades for potential applications in various electronic or optoelectronic devices such as light emitting diodes, photovoltaic cells and field effect transistors. Compared to inorganic counterparts, organic charge transport materials are attractive for their abilities of forming thin-films, large area manufacturing, compatibility with flexible substrate, light weight and potential low fabrication cost. The charge transport property of the organic active layer is one of the key factors to the electronic or optoelectronic performance of devices. Research projects presented in this thesis focused on improving charge carrier mobility of organic charge transport materials as it is a property determined by the hierarchical structure of the material. Strong effort has been made to the design of advanced molecular structures and controlling self-assembly behaviors. Chapter 1 introduces the general background of charge transport materials, including: the nature of charge transport in organic semiconducting materials, three widely used methods for charge carrier mobility measurements and the current development of organic charge transport materials. Advantages and drawbacks in applications were analyzed with ordered and disordered organic systems. A more thorough review was given to the engineering and the application of the discotic columnar liquid crystalline (DCLC) phase. Chapter 2 describes a DCLC phase with a novel hierarchical structure in which each supra-molecular column features a bundled-stack structure. The molecular design rationale was explained and the thermal behavior and phase structure were characterized. Charge carrier mobility of compound 1 was measured to be 0.05 cm2V-1s-1 with pulse radiolysis time-resolved microwave conductivity. The incorporation of the bundled stack structure may potentially be a fundamental solution towards enhancing the organic semiconductor's electronic performance. Chapter 3 introduces three chain functionalized perylene tetracarboxylic monoimide diester derivatives (PEIs) with monotropic DCLC phases. The intra-column rotation angle was determined to be 60 o between neighboring PEI molecules, which is a substantial improvement of the transfer integral compared to the perylene tetracarboxylic diimides with a 90 o rotation angle. The rotation angle was further tuned by incorporating branched aliphatic substitution to the PEI core as described in chapter 4. By reducing the length of the alkyl swallow tail, the rotation angle changes from 60 o to 72 o which is even more favorable to the electronic coupling between neighboring PEI units. Through those studies, we have shown that the engineering of DCLC phase may lead to substantial improvements on charge transport properties of organic semiconducting materials. 

  • SYNTHESIS AND INVESTIGATION OF BIPHENYLENE PLANARIZED AROMATIC AND ANTI-AROMATIC SYSTEMS

    Author:
    YOUCHUN WU
    Year of Dissertation:
    2012
    Program:
    Chemistry
    Advisor:
    Klaus Grohmann
    Abstract:

    The aim of the dissertation was to develop synthetic routes to biphenylene planarized aromatic and anti-aromatic systems such as bis(diacetylene)biphenylene 109, and 4,5,6,7-dibenzocyclobutathionin(biphenylenothionin) 110. Bis(diacetylene)anthracene 209 was prepared by Nakagawa by dimerization of 1,8-diethynylanthracene 208. In the first part of this dissertation, biphenylene systems were synthesized by different methods: by aryne generation, coupling a biphenyl and by extrusion of gas. Key intermediate 1, 8-diacetylene biphenylene 114 was synthesized successfully by coupling dihalo substituted biphenylene and alkyne. Nucleophilic addition of sulfide ion to 1, 8-diacetylene biphenylene 114, instead of an expected nine-membered ring compound 4,5,6,7-dibenzocyclobutathionin 110, gave an unexpected eight-membered ring compound (Z)-1-methylene-1H-biphenyleno[1,8-cde]thiocine 189, with structure confirmed by DEPT 13C NMR, IR , X-ray and GC-MS. Two comparisons of 4,5,6,7-dibenzocyclobutathionin 110, (Z)-5, 6-dihydrodibenzo[d,f]thionine 111 and dibenzo[d,f]thionine 112, were synthesized and NMR data were analyzed and compared.

  • SYNTHESIS, CHARACTERIZATION AND OPTICAL APPLICATIONS OF NANOMATERIALS

    Author:
    Fen Xu
    Year of Dissertation:
    2010
    Program:
    Chemistry
    Advisor:
    Hiroshi Matsui
    Abstract:

    Nanomaterials have been studied extensively due to their potential application in electronics, photonics and nanodevices. There are a wide variety of methods developed to create the nano-scale materials. Chemical colloidal synthesis is the way most used since it is reproducible and high efficiency. Nanoparticles lie at the heart of nanoscience for their novel electronic, magnetic and optical properties. In this dissertation, there are two parts where researches have been performed based on the synthesis of metal and semiconductor nanoparticles. In part I, Semiconductor type-II core-shell quantum dots (QDs) ZnO-CdS have been synthesized by chemical colloidal method which was carried out in a two-step process. We initially synthesized ZnO core nanoparticles and overcoat them with CdS shell. UV-Visible spectra, photoluminescence spectra (PL), high resolution TEM images and X-ray microanalysis for composition studies of the core-shell nanoparticles were characterized. PL lifetime measurements showed this type-II ZnO-CdS core-shell QDs presented extended exciton lifetime due to the spatial separation of electrons and holes between the core and the shell, which opens various useful applications in biosensors and photovoltaic devices. In part II, normal Raman (NR) and surface enhanced Raman scattering (SERS) spectra of 3-hydroxyflavone (3-HF) have been measured. The SERS spectra were obtained both on a Ag electrode surface and on Ag colloidal nanoparticles. The experimental results support the DFT geometry calculations, which show that an adatom site at the vertex of Ag20 cluster binding with the 3-HF molecular plane tilted at an angle of about 53ºto the surface is a low-energy structure. This is consistent with the enhancement of in-plane vibrational modes. Furthermore, the effect of fluence level on the discoloration of marble surfaces after the removal of the encrustation by 355 nm laser pulses was comparatively studied. Considering the thermochemical reaction possibly occurring in the encrustation during laser irradiation, the mechanism responsible for the discoloration of the cleaned marble surface was analyzed. The reduction of iron oxides by graphite plays a key role in determining the final color of the cleaned marble surface. The marble surfaces before and after laser irradiation were characterized in terms of the chemical components through surface enhanced Raman spectroscopy on Ag colloidal nanoparticles. To analyze the working mechanism of the liquid layer covering the marble encrustation, distilled water, ethanol and acetone were used in marble cleaning to compare the cleaning efficiency at different fluence levels. Surface-enhanced Raman spectroscopy (SERS) on silver colloidal nanoparticles was also used to identify the chemical constituents of the cleaned marble with these three different liquids.

  • Pi-Stack Engineering of Semiconducting Perylene Tetracarboxylic Derivatives

    Author:
    Chenming Xue
    Year of Dissertation:
    2011
    Program:
    Chemistry
    Advisor:
    Shi Jin
    Abstract:

    Abstract Pi-Stack Engineering of Semiconducting Perylene Tetracarboxylic Derivatives By Chenming Xue Advisor: Professor Shi Jin In the past decades, there has been intensive research in generating novel perylene tetracarboxylic derivatives because of a vast number of applications based on their semiconducting characteristics. The properties of the new materials rely heavily on not only the single molecular structure, but also the way of molecular packing in condensed states. The formation of effective π-stacking structures is the key issue. In this thesis, I focused in synthesizing novel perylene tetracarboxylic derivatives by attaching various substituents at the imide nitrogens. Consequently different phases appeared and exhibited different way of molecular packing. In Chapter 1, it is the general background of perylene tetracarboxylic derivatives including (a) synthesis routes, (b) optical and electronic properties, (c) the molecular packing in condensed phases or assembling in solutions; and also the introduction of condensed state phases including amorphous, crystalline and liquid crystalline (LC) phases. In Chapter 2, a series of solution processible amorphous glassy perylene tetracarboxylic diimides (PDIs) has been designed, synthesized and characterized. The π-stacking order in the amorphous glass phase was successfully tailored by the steric means and qualitatively evaluated. In Chapter 3, the n-alkyl chain length dependence of a series of two-dimensional (2D) smectic LC PDIs has been explored. When the n-alkyl chain is no shorter than decyl group, the PDI could exhibit a novel 2D crystalline smectic LC phase. In this phase, the PDI cores microphase separate from flexible n-alkyl chains forming 2D crystalline layers. Thermoanalysis data quantitatively reveal that the n-alkyl chains in this phase have the essentially the same order as that in the isotropic liquid state. Such truly disordered n-alkyl chains effectively decouple the inter-layer molecular correlation and make the phase genuine LC. The PDI -stacking order in this LC phase is crystalline because it is a part of the 2D crystalline intra-layer order. Chapter 4, PDI -stacking order has been engineered in the crystalline phase. By introducing two structuring factors, a series of crystalline PDIs with finely tunable PDI -stacking order was obtained. The crystalline PDIs with exceptionally red-shifted max were obtained. Several PDIs possess max values greater than any literature-reported ones. These materials can be excellent candidates in solar cell devices. In Chapter 5, new chiral main-chain PDI containing polymers were synthesized. These polymers can form intramolecular helical π-stacks in diluted solutions. In Chapter 6, a novel synthetic route leading to unsymmetrical perylene tetracarboxylic derivatives has been developed. Based on this synthetic method, more perylene tetracarboxylic derivatives can be generated. In my research in this thesis, not only synthesis is an important part because it provides novel materials, but the characterization is critical as well. Infrared spectroscopy, Ultra-violet, fluorescence, differential scanning calorimetry, circular dichroism, polarized light microscopy, gel permeation chromatography, X-ray diffraction including both small angle and wide angle have been used. Additionally, molecular simulation is also very useful in design and obtaining details in molecular packing. Overall, the achievements in this research contribute a considerable advance in the field of generating semiconducting perylene tetracarboxylic derivatives which have versatile potential applications such as in solar cell devices, organic field effect transistors and light emitting diodes.

  • SYNTHESE OF POLYMER-SUPPORTED AMIDE-TYPE LIGANDS AND COMPLEXATION OF LANTHANIDE IONS

    Author:
    Yijia Yang
    Year of Dissertation:
    2011
    Program:
    Chemistry
    Advisor:
    Spiro Alexandratos
    Abstract:

    The complexation of lanthanide ions from acidic solutions was studied with cross-linked polystyrene modified with amide-type ligands: N,N,N',N'-tetramethylmalonamide (TMMA), monoamidated malonate and urea. The TMMA resin showed preference towards Tb, Dy and Eu from highly acidic solutions. Ionic recognition is achieved through a mechanism in which two opposing processes--electrostatic attraction of M(H2O)xCl4- or M(H2O)x(NO3)your4- by the protonated ligand and (partial) loss of the waters of hydration--dominate at different points along the lanthanide series. The proposed complexation mechanism consists of protonation of one of the carbonyls, which is stabilized by hydrogen bonding to the neighboring carbonyl oxygen, formation of iminium site and ion exchange by exchanging the chloride ion with the lanthanide chloro or nitro complex. The importance of the substituents at amide nitrogen was probed with immobilized malonate ligands monoamidated with diethylenetriamine (DETA-MAm) and immobilized diethylenetriamine ligands with one amine nitrogen converted to urea (Urea-3). The comparison of the lanthanides complexation by the TMMA, DETA-MAm and Urea-3, was carried out under conditions in which each resin has its best performance: 6 M HCl for TMMA and 8 M HCl for DETA-MAm and Urea-3. The protonated TMMA, with two electron-donating methyl groups at the iminium nitrogen to attenuate the (+) charge (=NR2(+)), is the weakest ligand with ionic recognition properties towards the lanthanides in the middle of the series. The reduced ligand strength makes it more responsive towards changes between the electrostatic attraction and the enthalpy of dehydration. The protonated Urea-3 showed much higher lanthanide affinities than the TMMA and DETA-MAm, and its affinity trend paralleled the trend of lanthanides ionization potentials due to the absence of methyl group to attenuate the (+) charge (=NH2(+)). The DETA-Mam is somewhere in between the TMMA and Urea-3 because its iminium has only one −CH2− moiety attenuating the (+) charge (=NHR(+)) and it is also a two-site interaction with the ammonium group probably contributing to the electrostatic stabilization of the chlorocomplex.

  • EUKARYOTIC INITIATION FACTOR 4F (elF4F) ENHANCES HIGH AFFINITY BINDING OF 40S RIBOSOMAL SUBUNIT TO TOBACCO ETCH VIRUS (TEV) INTERNAL RIBOSOME ENTRY SITE (IRES)

    Author:
    Sumeyra Yumak
    Year of Dissertation:
    2010
    Program:
    Chemistry
    Advisor:
    Dixie Goss
    Abstract:

    Many viruses and some eukaryotic mRNAs employ a cap-independent pathway in which an RNA element called the internal ribosome entry site (IRES), drives preinitiation complex formation by positioning the ribosome on the message, either at or just upstream of the start site. We have studied binding of wheat germ 40S subunit of wheat germ ribosome to wild type PK1 RNA, which shows 100 % translation activity. To explore the specificity of the IRES RNA*40S interaction, we also measured the affinity for IRES RNA mutants, S2-3 RNA and to S1-3 RNA that have been previously characterized in terms of in vitro translation initiation activity (1). The level of expression from each mutant is calculated relative to the corresponding wild-type sequence, which is set at 100%.S2-3 RNA shows about 30% translation activity while S1-3 RNA shows about 7% translation activity. While ribosome binding to eukaryotic mRNAs requires the participation of eukaryotic initiation factors eIF4A, eIF4B, and eIF4F and the hydrolysis of ATP, our results suggest that the 40S ribosomal subunit binds directly to the PK1 RNA with dissociation constant (Kd) of 67 nM. While 40S ribosome bound to S2-3 RNA with Kd of 138 nM; significant binding to S1-3 RNA was not observed. Direct binding measurements of both wild type and mutant TEV IRES RNAs suggest that TEV message is driven through a high affinity TEV RNA*40S interaction, involving a novel strategy of ribosome recruitment distinct from eukaryotic cap-dependent mechanisms. Fluorescence anisotropy data showed that eIF4F increased 40S Ribosome binding affinity to PK1 RNA by approximately 2.6 fold. To determine the effects of initiation factor mediated RNA unwinding in cap independent initiation, we determined RNA binding activity of elF4A, elF4B and 40S Ribosome with TEV RNAs. The fluorescence anisotropy data revealed that in the presence of eIF4A, eIF4B, and hydrolysis of ATP, binding affinity of 40S ribosome to PK1 RNA increased 4 fold; giving Kd of 17 nM. Under the same conditions, while binding affinity of 40S ribosome to S2-3 RNA increased 2 fold, there was no significant change in S1-3 RNA binding to 40S.These data correlate well with the observed translational data and provide more detailed information on the translational strategy of tobacco etch virus.

  • Arylboronic Acid-Catalyzed Hydrolyses of Salicylaldehyde Imines

    Author:
    Sheuli Zakia
    Year of Dissertation:
    2011
    Program:
    Chemistry
    Advisor:
    Manfred Philipp
    Abstract:

    ABSTRACT Arylboronic Acid-Catalyzed Hydrolyses of Salicylaldehyde Imines By Sheuli Zakia Adviser: Prof. Manfred Philipp Boronic acids accelerate hydrolyses of the Schiff's bases derived from salicylaldehyde and primary amines. The accelerations of Schiff's base hydrolyses are due to the formation of a complex between the boronic acid and the imine followed by the break-down of the complex to products. The formation of a reversible complex between arylboronic acids and imines allows the rate of hydrolysis to display typical Michaelis-Menten enzyme-substrate kinetics, including situations where the imine is completely saturated with the boronic acid. This thesis focuses on the ability of different arylboronic/benzeneboronic acids(BBAs) to catalyze the hydrolysis of different imines, most of them being salicylaldehyde imines made using primary amines or amino acids, an example being salicylidene-threonine. In order to better understand the mechanism involved in the imine hydrolysis by arylboronic acids, I studied structure-activity relationships(SAR) for different substituted BBAs and of different imine substrates undergoing hydrolyses. Herein, I present the most important aspects of these SAR studies on both the catalysts(BBAs) and on their imine substrates. I hypothesized that electron withdrawing groups would enable BBAs to be more easily ionized, thus becoming better hydrogen bond donors and making it easier to have higher affinities for the imine substrates. SAR experiments conducted with different fluoro-substituted benzeneboronic acids showed that all fluoro-BBAs have higher catalytic efficiencies of imine hydrolysis than the un-substituted boronic acid except for the catalysts with two fluorine atoms substituted in the ortho- position with respect to the boron atom. The latter presumably induced steric hindrance. SAR on BBAs enabled me to discover novel catalysts for the hydrolysis of salicylidene-3-hydroxyaniline imine. The best ones are with 2,3,5-trifluoroBBA and 2,3,4,5-tetrafluoroBBA and their kcat/KM values go over 1000 fold higher than with the unsubstituted BBA. Furthermore, SAR of different imine substrates highlights the most important structural determinants of the enhanced catalytic efficiency. The most important contribution to the efficiency of imine hydrolysis are shown to be the hydrogen bonding donors or acceptors (hydroxy or amino groups) in the imine substrates which are demonstrated to activate the catalytic turn-over (kcat) of the arylboronic acid catalyst. The pH dependencies for BBA catalyzed hydrolysis of salicylaldehyde-3-hydroxyaniline shows that rate constants are maximal at lower pH values and decrease with increasing pH. The kinetics shows single proton ionizations, demonstrating that there is no other ionization event related to the imine itself which could affect catalytic efficiency. Moreover, the kcat, KM and kcat/ KM dependencies with pH shows that kcat is independent of pH. This indicates the absence of hydroxide or hydronium ion involvement in the hydrolysis. The plots of Log10 (KM), Log10 (kcat), Log10 (kcat/KM), vs. Hammett sigma substituent constants indicate that kcat, KM and kcat/KM all dependent on electron withdrawing substituent groups present in the benzeneboronic acids. The hydrogen bonding network provided by the hydroxyl or amino groups in the imine substrates during the hydrolysis could assist the BBA catalysts in binding tighter to the substrate, which in turn, are reflected in higher catalytic efficiencies. The presence of hydroxyl and amino groups in imine substrates of 2,3,4,5-tetrafluoroBBA resulted in 5- to over 100-fold increases in kcat/KM values. Thus the 2,3,4,5-tetrafluoroBBA-catalyzed kcat/KM value for salicylidene-threonine is 33 M-1sec-1 and for salicylidene-lysine is 17 M-1sec-1 whereas for salicylidene-valine, without an amino acid side chain hydroxyl or amino group, it is only 8 M-1sec-1. The relative stabilities of the complexes between BBAs and imines are predicted through docking experiments with the software SCULPT provided by MDL. NMR spectroscopy experiments are performed to confirm the structures. This thesis highlights the importance of the hydroxyl group substituted to the benzene ring in aniline or benzylamine based imines in inducing better catalytic efficiencies for their hydrolyses by fluoro-substituted BBAs. Examples are shown in the kcat/KM values for the hydrolysis of salicylidene-3-hydroxyaniline with 2,3,5-trifluoroBBA (232 M-1sec-1), and 2,3,4,5-tetrafluoroBBA (175 M-1sec-1).

  • Hybrid Fiber-Optic Device For Spatiotemporal Control of Photosensitizer Release and Singlet Oxygen Delivery

    Author:
    Matibur Zamadar
    Year of Dissertation:
    2011
    Program:
    Chemistry
    Advisor:
    Alexander Greer
    Abstract:

    Abstract: This thesis outlined the gradual progress towards the development of the first fiber-optic singlet-oxygen generator designed for releasing singlet oxygen locally, which can surmount the challenges associated with current photodynamic therapy and water disinfection. We developed a photochemical approach to clean generation of singlet oxygen in aqueous solution with a sensitizer (meso-tetra(N-methyl-4 pyridyl)porphine) adsorbed onto solid porous Vycor glass (PVG)]. Photophysical analysis revealed that oxygen collision onto the sensitizer adsorbed porous Vycor glass matrix converts ground-state oxygen into singlet oxygen (1O2) which diffuses into bulk aqueous solution. Singlet oxygen was detected in water by time-resolved methods and by chemical trapping with alkene, N-benzoyl methionine, and anthracene derivative to give hydroperoxide, N-benzoyl sulfoxide, and anthracene endoperoxide derivative. Based on this study, we developed a device that channels light and oxygen through a hollow core fiber optic into the sensitizer adsorbed Vycor glass which acts as a cap. Singlet oxygen was generated on a microscale at the fiber cap site selectively which then diffused out into the surrounding aqueous solution. A complete Escherichia coli inactivation was observed in 2 h when the fiber cap was immersed in 0.1 mL aqueous samples of 0.1-4.4 × 107 cells. The prototype device was further modified to enhance singlet oxygen diffusion in aqueous solution as singlet oxygen has lifetime's ranges from microseconds to milliseconds and the corresponding diffusion distances of singlet oxygen ranges from nanometers to millimeters. Our efforts included 1O2 generation by cleaving off sensitizer molecules away from the fiber optic probe to increase 1O2 formation at a distance from the probe tip. Synthetic methodology was developed to modify the glass probe to release photosensitizer molecules into the surrounding medium by an oxidative self-cleaving mechanism where 1O2 was used as a sole reagent. We successfully attached pyropheophorbide photosensitizer containing a photosensitive electron rich alkene covalently to porous Vycor glass which is triggered for release on-site by visible light irradiation, via dioxetane decomposition to give two carbonyl fragments. The cleaved photosensitizer diffuses into solution to produce singlet oxygen at a distance from the glass surface which also improves the photooxidation efficiency of the heterogenous photosensitizer. Finally, a review of the literature on `singlet oxygen as a reagent in organic synthesis' was accomplished, which represent the last chapter of the thesis.

  • ENHANCEMENT TO IMPLICIT SOLVENT MODELING OF PEPTIDES IN WATER AND IN LIPID BILAYERS

    Author:
    Huan Zhan
    Year of Dissertation:
    2013
    Program:
    Chemistry
    Advisor:
    Themis Lazaridis
    Abstract:

    In recent years implicit solvation models have been increasingly used in molecular dynamics (MD) simulations of proteins/peptides due to their computational efficiency. While these models can account for electrostatic interactions and hydrophobic effect of proteins/peptides in both water and lipid membranes, other properties of the solvent, such as the local dielectric screening effect at the binding sites of metalloproteins, the membrane dipole potential, and the membrane lateral pressure, have not yet been included. In this work, first the effective energy function (EEF1) is extended to simulate metalloproteins by neutralizing ligand carboxylates based on their exposure to solvent water. The new model is then applied to MD simulation of calcium-binding proteins calbindin d9k, calmodulin, troponin C, and parvalbumin. Although structures consistent with experiments are obtained, the model is limited by the fact that the selection of charges for carboxylates is arbitrary, and that the charges cannot be modified as the protein structure changes during the simulation. Second the implicit membrane mode (IMM1) is extended to include the membrane dipole potential, and the new model is applied to MD simulation of the helical peptides alamethicin, WALP23, influenza hemagglutinin fusion peptide, HIV fusion peptide, magainin, and the pre-sequence of cytochrome c oxidase subunit IV (p25). The results show that the orientation of the peptides in the membrane can be influenced by the dipole potential. In general peptides that tend to insert the N-terminus in the membrane and/or have positively charged side chains will lose binding affinity upon increase of the dipole potential. Finally, IMM1 is extended to include lateral pressure effects and tested by MD simulation of the peptides alamethicin, melittin, cyclotide kalata B1, 18A, and KKpL15. The simulations of alamethicin binding to pure DOPC bilayer show that increase in the peptide/lipid molar ratio favors the transmembrane orientation, which is explained by the difference in the cross-sectional area of the two orientations. The simulations of all peptides binding to mixed DOPC/DOPE bilayers show that the binding energy can increase, decrease, or not change as the molar fraction of DOPE increases, which is explained by the difference in the binding location of the peptides.