978-1-4020-5372-6_BookFrontmatter_OnlinePDF.pdf
Contents
Preface
978-1-4020-5372-6_1_OnlinePDF.pdf
Theory of Intermolecular Forces:an Introductory Account
Robert Moszynski
Robert Moszynski
Quantum Chemistry Laboratory Faculty of Chemistry, Warsaw University Pasteura 1, 02--093 Warsaw, Poland
Modern theory of intermolecular forces is reviewed. The concept of the interaction potential is introduced within the Born-Oppenheimer separation of the electronic and nuclear motions. Various supermolecule approaches for the calculation of accurate interaction potentials are discussed. Perturbation theory of intermolecular forces is reviewed in great details. The problem of symmetry-adaptation is explained and a general symmetry-adapted perturbation theory is formulated. Convergence properties of various symmetry-adapted expansions are surveyed, and illustrated on several examples. Physical interpretation of the interaction potential in terms of the four fundamental interaction components: electrostatics, induction, dispersion, and exchange-repulsion is thoroughly exposed. Many-electron formulation of the symmetry-adapted perturbation theory in both the wave function and density functional approaches is introduced. One-center and multicenter multipole expansions neglecting the charge-overlap effects, as well as the bipolar expansion accounting for these effects are discussed. The relation of some supermolecule approaches with the perturbation theory of intermolecular forces is briefly sketched. Approximate models that can be deduced from the rigorous theory of intermolecular forces, and applicable to the interactions of large systems are discussed. Finally, perturbation theory of nonadditive interactions in trimers and of the collision-induced electric properties of binary collisional complexes is also reviewed. The theory part is completed by an exposition of methods needed on the route from intermolecular potentials and collision-induced properties to physically measurable quantities such as the Raman spectra, rovibrational spectra, scattering cross sections, as well as thermodynamic, dielectric, and refractive properties of dilute gases. The present status of symmetry-adapted perturbation theory applied to the calculations of state-of-the-art ab initio potential energy surfaces and collision-induced properties is presented, and illustrated by means of applications to rovibrational spectra of Van der Waals molecules, scattering cross sections and pressure broadening coefficients, collision-induced Raman spectra of atomic gases, solvation processes, and thermodynamic, dielectric, and refractive properties of dilute gases. Theoretical results are compared with high accuracy experimental data
intermolecular forces, Born-Oppenheimer approximation, supermolecular method, polarization approximation, symmetry-adapted perturbation theory, electrostatics, induction, dispersion, exchange-repulsion, multipole expansion, one-center and multicenter expansions, bipolar expansion, charge overlap and damping effects, approximate models, relation between supermolecule approaches and perturbation theory, nonadditive interactions, collision-induced properties, optical spectra of Van der Waals complexes, scattering cross sections, dielectric, refractive, and thermodynamic properties of dilute gases, state-of-the-art ab initio potential energy surfaces, infrared spectra, integral and differential cross sections, pressure broadening coefficients, thermodynamic virial coefficients for binary complexes, high accuracy ab initio nonadditive potentials, radial distribution functions from first principle computer simulations, solvation processes, state-of-the-art ab initio Raman spectra, and dielectric and refractive properties of atomic gases, comparison with high precision experimental data
Introduction
The Born-Oppenheimer approximation
Born-Huang Expansion of the Total Wave Function
Adiabatic and Born-Oppenheimer Approximations
Electronic Schrรถdinger Equation
Schrรถdinger Equation for the Nuclear Motions
Failures of the Born-Oppenheimer Approximation and the Nonadiabatic Approach
Supermolecular approach to intermolecular interactions
Perturbation theory of intermolecular forces
Rayleigh-Schrรถdinger Perturbation Theory
Symmetry Adaptation
Physical interpretation of the low-order polarization and exchange energies
Electrostatic Energy
First-order Exchange (Heitler-London) Energy
Induction Energy
Exchange-induction Energy
Dispersion Energy
Exchange-dispersion Energy
Third-order Polarization and Exchange Contributions
Multipole expansion of the interaction energy
One-center Expansion
Multicenter Expansions
Bipolar Expansion of the Interaction Energy
Importance of the Charge-overlap (Damping) Effects
Many-electron formulation of the SRS theory
Relations between the perturbation theoryof intermolecular forces and supermolecular approaches
Hartree-Fock Theory
M"01Cller-Plesset Theory
Coupled Cluster Theory
Selfconsistent Reaction Field Theory
Approximate models for pair interaction potentials
Morokuma Partitioning of the Hartree-Fock Interaction Energy
Variation-Perturbation Approach
Tang-Toennies Model
Atom-Atom and Site-Site Potentials
Empirical Force Fields
Nonadditive interactions
Supermolecular Approach
Perturbation Theory of Three-Body Interactions
Physical Interpretation of the Polarization Effects
Exchange Effects
Symmetry-adapted perturbation theory of the interaction-induced properties
From intermolecular potentials and collision-induced propertiesto the measured properties of isolated complexesand condensed phases
Collision-induced Raman Light Scattering in Atomic Gas
Dielectric Second Virial Coefficients of Atomic Gases
Refractive (Kerr) Second Virial Coefficients of Atomic Gases
Rovibrational Spectra of Weakly Bound Complexes
Scattering Cross Sections for Rotational Excitation
Thermodynamic Second Virial Coefficients
Simulations of Condensed Phases
Illustrative applications
Pair Potentials and Modelling of Spectroscopic, Collisional,and Thermodynamic Properties of Binary Complexes
Nonadditive Interactions, Spectroscopic Signatures of Molecular Clusters, and Simulations of Condensed Phases
Solvation Processes in Small Water Clusters
Collision-induced Properties and Modellingof Raman Spectra of Atomic Gases
Modelling of Dielectric and Refractive Properties of Atomic Gases
Conclusions and outlook for the future
978-1-4020-5372-6_2_OnlinePDF.pdf
Hohenberg-Kohn-Sham Density Functional Theory
The formal basis for a family of succesful and still evolvingcomputational methods for modelling interactionsin complex chemical systems.
Tomasz A. Wesoowski
Wesoowski
University of Geneva, Switzerland
The emergence of a family of computational methods, known under the label density functional theory' orDFT', revolutionalized the field of computer modelling of complex molecular systems. Many computational schemes belonging to the DFT family are currently in use. Some of them are designed to be universal (nonempirical) whereas other to treat specific systems and/or properties (empirical). This review starts with the introduction of the formal elements underlying all these methods: Hohenberg-Kohn theorems, reference system of noninteracting electrons, exchange-correlation energy functional, and the Kohn-Sham equations. The main roads to approximate the exchange-correlation-energy functional based on: local density approximation (LDA), generalized gradient approximation (GGA), meta-GGA, and adiabatic connection formula (hybrid functionals), are outlined. The performance of these approximations in describing molecular properties of relevance to intermolecular interactions and their interactions with environment in condensed phase (ionization potentials, electron affinities, electric moments, polarizabilities) is reviewed. Developments concerning new methods situated within the general Hohenberg-Kohn-Sham framework or closely related to it are overviewed in the last section
computer modelling, density functional theory, dipole moment, dipole polarizability, electron affinity, empirical methods, exchange-correlation energy functional, hydrogen bonding, intermolecular interactions, ionization potential, Kohn-Sham equations, non-empirical methods, van der Waals complex
Introduction
The Kohn-Sham Equations
Commonly used Approximations to the Exchange-Correlation-Energy Functional
The Starting Point: Local Density Approximation
The First Breakthrough: Generalized Gradient Approximation
Meta-GGA
Hybrid Functionals
Beyond Meta-GGA
Performance of Common Approximations to the Exchange-Correlation Energy
Electric Properties: Electric Moments
Electric Properties: Polarizabilities
Ionization Potentials and Electron Affinities
Intermolecular Interactions
Ongoing Developments
Optimized Effective Potential
Weighted Density Approximation
Exchange-correlation Energy-functional from Adiabatic Connection Fluctuation-dissipation Theorem
Van der Waals Density Functional of Langreth and Lundqvist
Current-dependent Exchange-Correlation Functional
Density Functional Theory without the System of Noninteracting Electrons
Dispersion Interactions from the Analysis of the Dipole Moment of the Exchange Hole
Subsystem Formulation of DFT
Density-matrix Functional Theory
Concluding Remarks
978-1-4020-5372-6_3_OnlinePDF.pdf
Selected Microscopic and Mezoscopic Modelling Tools and Models -- an Overview
Magdalena Gruziel1,2, Piotr Kmiec1,2, Joanna Trylska2 and Bogdan Lesyng1,2
Gruziel et al.
1Faculty of Physics, Warsaw University, Zwirki i Wigury 93, 02-089 Warsaw, Poland 2Interdisciplinary Centre For Mathematical And Computational Modelling, Pawinskiego 5a, 02-106 Warsaw, Poland The authors contributed equally to this work.
In order to model (bio)molecular systems and to simulate their dynamics one requires the potential energy functions at the microscopic, classical and/or quantum levels, as well as fast generators of the free-energy functions at the mezoscopic level. A brief overview of the methods which allow computations of the potential energy functions and the free energies is presented. The ongoing research is focused on designing molecular mezoscopic interaction potentials, applicable to nanoscale (bio)molecular systems, and on utilizing conformationally dependent atomic charges. In particular, the coupling of a fast quantum SCC-DFTB method with the Poisson-Boltzmann (PB) or Generalized Born (GB) models is discussed, and the role of the SCC-DFTB CM3 charges in computations of the mean-field electrostatic energies of molecular systems in real molecular environments is indicated. These charges reproduce very well molecular dipole moments, and are obtained from the Mรผlliken ones by applying a mapping procedure, using a quadratic function of the Mayer's bond orders. The PB and GB models give electrostatic reaction field energies of molecular environments, in particular, provide electrostatic contributions to the solvation energies. It is assumed that the solvation energy consists of the mean-field electrostatic and nonpolar (hydrophobic) energy contributions. Typically, the nonpolar term consists of the cavity formation free energy, and sometimes also of a mean van der Waals interaction energy of the molecular system with its environment. This allows to reproduce experimental solvation/hydration energies assuming different analytical forms of the nonpolar energy terms. Refined GB models, with new formulae for the Born radii are discussed. The nonpolar energies are quite well reproduced using the solvent accessible surface area (SASA), or a polynomial series depending on reciprocal values of the Born radii. Presence of the mean van der Waals energy on the quality of the fits is also discussed. Reliable mezoscopic models and theories play a key role in describing the functioning of nanoscale (bio)molecular systems
microscopic models; density functional; SCC-DFTB; CM3 charges; mezoscopic models; Poisson-Boltzmann; Generalized Born; nonpolar interactions; solvent accessible surface area
Introduction
Microscopic and Mezoscopic Molecular Models
Atomic Resolution of Molecular Models and Microscopic Potential Energy Functions
Coarse-grained Models for Biomolecules
SCC-DFTB Method and CM3 Charges
Solvation Free Energy
Potential of Mean Force and Landau Free Energy
Outline of the Poisson-Boltzmann (PB) Model
Outline of the Generalized Born (GB) Model
Models for Computing the Generalized Born Radii
Nonpolar Contribution to the Free Energy of Solvation
Conclusions
978-1-4020-5372-6_4_OnlinePDF.pdf
Modeling Chemical Reactions with First-Principle Molecular Dynamics
Artur Michalak1 and Tom Ziegler2
Michalak and Ziegler
1Department of Theoretical Chemistry, Faculty of Chemistry, Jagiellonian University, R. Ingardena 3, 30-060 Cracow, Poland2Department of Chemistry, University of Calgary, University Drive 2500, Calgary, Alberta, Canada T2N 1N4
Density functional theory (DFT)-based molecular dynamics (MD) has established itself as a valuable and powerful tool in studies of chemical reactions. Thanks to the rapid increase in power of modern computers, ab initio MD has nowadays become practical. Within the Car-Parinello approach, first-principle MD is already quite popular methodology in molecular modeling. MD reveals the dynamical effects at finite temperatures and is particularly useful in probing the potential energy surfaces. Also, it can be utilized to directly determine the reaction free-energy barriers, as it explicitly includes temperature and thus the entropic effects. The first part of the chapter provides a brief introduction to ab initio MD, within the Born-Oppenheimer and Car-Parinello approaches. Here, we introduce basic concepts of Car-Parinello MD, with focus on the practical aspects of the simulation. The next part of the chapter summarizes the approaches used to overcome high-energy barriers in a simulation, and thus to probe the part of the potential energy surface relevant for chemical reactions (from the reactants to products through transition states). A special emphasis is placed on the MD simulation along the intrinsic reaction path. The last part of the chapter presents examples from CP-MD simulations from the studies on a complex catalytic process: copolymerization of ethylene with polar monomers catalyzed by late transition-metal-complexes
First-Principle Molecular Dynamics, Car-Parinello Molecular Dynamics, Density Functional Theory, Reaction Paths, Olefin Polymerization
Introduction
Basic Concepts and Practical Aspects of Car-Parinello MD
Born-Oppenheimer MD and Car-Parinello MD
Forces in ab initio MD; Plane-wave-based Electronic Structure Methods
Finite Temperature Simulations: Thermostats
Practical Aspects of Car-Parinello MD Simulation
Modeling Chemical Reactions; MD Along Intrinsic Reaction Paths
Towards Overcoming High Energy Barriers
Constrained Dynamics, Thermodynamic Integration, and Free-energy Barriers
MD along Intrinsic Reaction Paths
Illustrative Examples
Molecular Dynamics in the Studies of the Ethylene -- Methyl Acrylate Copolymerization
The Polar Copolymerization Process and its Mechanism
DFT and MD Studies on the Monomer Binding and Insertion
MD Studies on the Chelate Opening by Ethylene
Concluding Remarks
978-1-4020-5372-6_5_OnlinePDF.pdf
Computational Enzymology: Insights into Enzyme Mechanism and Catalysis from Modelling
Adrian J. Mulholland and Ian M. Grant
Mulholland, Grant
Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, UK E-mail: [email protected]
Modern modelling methods can now give a uniquely detailed understanding of enzyme-catalysed reactions, including analysing mechanisms and identifying determinants of specificity and catalytic efficiency. A new field of computational enzymology has emerged, which has the potential to contribute significantly to structure-based design, and in developing predictive models of drug metabolism; for example, in predicting the effects of genetic polymorphisms. This review outlines important techniques in this area, including quantum chemical model studies, and combined quantum mechanics/molecular mechanics (QM/MM) methods. Some recent applications to enzymes of pharmacological interest are also covered, showing the types of problems that can be tackled, and the insight they can give
QM/MM, molecular dynamics, transition state, drug metabolism, polymorphism, cytochrome P450, pharmacogenomics
Introduction
Aims in Modelling Enzyme Reactions
Methods for Modelling Enzyme-catalysed Reaction Mechanisms
Quantum Chemical Approaches to Modelling Enzyme Reactions: Cluster (or Supermolecule) Approaches
Empirical Valence Bond Methods
Combined Quantum Mechanics/Molecular Mechanics (QM/MM) Methods
Examples of Recent Modelling Studies of Enzymic Reactions
Chorismate Mutase: Analysing Fundamental Principles of Enzyme Catalysis
Cytochrome P450: Mechanism and Structure--Reactivity Relationships
Other Recent Modelling Studies of Enzyme-Catalysed Reactions
Conclusions
978-1-4020-5372-6_6_OnlinePDF.pdf
Computational Determination of the Relative Free Energy of Binding -- Application to Alanine Scanning Mutagenesis
Irina S. Moreira, Pedro A. Fernandes and Maria J. Ramos
Moreira, Fernandes and Ramos
REQUIMTE/Departamento de Quรญmica, Faculdade de Ciรชncias da Universidade do Porto, Rua do Campo Alegre 687, 4169-007 Porto- Portugal
Protein-protein recognition and complex formation are key issues in understanding cellular functions. Therefore, having in mind that it is of extreme importance to detect the functional sites in proteins interfaces, the present review focuses on computational approaches used to calculate the binding free energy contributions of each of the interface residues. Usually these methods do not allow the calculation of the contribution of each residue for binding in the wild type complex, but instead the difference in binding free energy between the wild type and a given residue. Although the first would be more meaningful from a phenomenological point of view, the second is the only one that is possible to measure experimentally. A number of quantitative models with different levels of rigor and speed are available for determination of the relative binding energy upon alanine mutation of residues in protein-protein interfaces. These algorithms can be divided essentially in two types: (a) empirical functions or simple physical methods and (b) fully atomistic methods Computer simulations complement experimental analysis, and add molecular insight to the macroscopic properties, by allowing the decomposing of the binding free energy into contributions of the various energetic factors. The capacity of predicting protein-protein associations is essential in computational chemistry because it establishes the connecting bridge between structure and function of biomolecular systems, and it allows the characterization of the energetics of molecular complexes
binding free energy; computational mutagenesis; empirical functions; fully atomistic methods; protein-protein association; MM-PBSA
Introduction
Computational Calculation of the Relative Binding Energy
Empirical Approaches and Simple Physical Models
Wallqvist Model
Molecular Statics (MS) Method
Partitioning Approach
Kortemme- Simple Physical Model
Linear Interaction Energy (LIE)
MM-PBSA
Force Fields for Bimolecular Simulations
Solvation
The MM-PBSA approach fundamental theory
Free Energy Perturbation (FEP) and Thermodynamic Integration (TI)
PROFEC and OWFEG
- Dynamics and Chemical Monte Carlo/Molecular Dynamics (CMC/MD)
Conclusion
978-1-4020-5372-6_7_OnlinePDF.pdf
Substrate-Enzyme Interactions from Modeling and Isotope Effects
Renata A. Kwiecien1, Andrzej Lewandowicz2,and Piotr Paneth1
Kwiecien, Lewandowicz and Paneth
1Institute of Applied Radiation Chemistry, Department of Chemistry, Technical University, Zeromskiego 116, 90-924 Lodz, Poland2International Institute of Molecular and Cell Biology, 02-109 Warsaw, Trojdena 4 Street, Poland
Isotope effects provide a powerful tool for learning structures of transition states, species that are not amenable for direct observation. In the case of enzymatic processes, however, their application for the purpose of transition state structure elucidation is often obscured by reaction complexity. However, experimental measurements of isotope effects, enhanced by theoretical QM/MM modeling of the chemical step of enzymatic catalysis, allows study of the changes that occur upon conversion of substrates to transition states. Information obtained about the nature of specific interactions within the active site of an enzyme may be used for practical purposes. In this communication we will summarize studies of haloacid dehalogenases, ornithine decarboxylase, and methylmalonyl-CoA mutase to exemplify these studies. Studies of transition state structure will also be presented for purine nucleoside phosphorylases (PNP). Experimental measurements of kinetic IEs for this enzyme together with theoretical analysis of their values led to rational synthesis of new inhibitors of this enzyme. The application of transition state theory to PNP has led to the most potent and specific inhibitors known for this important enzyme
QM/MM calculations, isotope effects, rational drug design, PNP, purine nucleoside phosphorylase, DADMe, Immucillin, nucleosidase, transition state analogue
Introduction
Binding can be reflected in isotope effects
Isotope effects and hydrogen bonding
Purine nucleoside phosphorylase -- multiple KIEs study and TS analogues design
What do KIEs Tell us about the TS Properties and its Interactions with Enzymes?
978-1-4020-5372-6_8_OnlinePDF.pdf
From Inhibitors of Lap to Inhibitors of Pal
Lessons from Molecular Modeling and Experiment Interface
ukasz Berlicki, Jolanta Grembecka, Edyta Dyguda-Kazimierowicz, Pawe Kafarski, W. Andrzej Sokalski
Berlicki et al.
Department of Chemistry, Wrocaw University of Technology, Wybrzee Wyspiaskiego 27, 50-370 Wrocaw, Poland
Computer-aided techniques of rational design of enzyme inhibitors were reviewed. In silico lead generation and optimization protocols were outlined and several methods of inhibitor potency estimation by both empirical scoring functions as well as ab initio based calculations were described. Two representative examples of successful computer-aided analysis and design of novel, highly potent inhibitors of leucine aminopeptidase and glutamine synthetase were demonstrated. In addition fully nonempirical and systematic analysis of the physical nature of enzyme active site interactions has been performed for series of leucine aminopeptidase (LAP) and phenylalanine ammonia lyase (PAL) inhibitors. Results derived from ab initio calculations indicate that inhibitory activity is controlled by interactions with limited number of active site residues. Examination of entire hierarchy of theoretical models indicates that the inhibitory activity could be well represented by electrostatic interactions, leading to so called ``electrostatic key-lock'' principle
Drug design, molecular modeling, agrochemicals, enzyme inhibitors, ab initio, intermolecular interactions, leucine aminopeptidase, glutamine synthetase, phenylalanine ammonia lyase
Introduction
Computer Aided Inhibitor Design
Lead Generation
Lead Optimization
The Physical Nature of Ligand Binding
Leucine Aminopeptidase Inhibitors
Glutamine Synthetase Inhibitors
L-Phenylalanine Ammonia Lyase Inhibitors
Conclusions
978-1-4020-5372-6_9_OnlinePDF.pdf
Theoretical Studies of the Transition States Along the Reaction Coordinates of [NIFE] Hydrogenase
Hiroshi Nakano, Pawe Szarek, Kentaro Doi,Akitomo Tachibana
Nakano et al.
Department of Micro Engineering, Kyoto University, Kyoto 606--8501, Japan
[NiFe] hydrogenase has recently received attention as an enzyme for catalyzing hydrogen production. We review the theoretical investigations of the catalysis mechanism. The hydrogen production reaction occurs at the active site of the hydrogenase and the active site has several paramagnetic and several EPR-silent states, the structures of which are still controversial. Moreover, different catalysis mechanisms have been proposed. We review the proposed mechanisms focusing on the reaction paths
[NiFe] hydrogenase, hydrogen, fuel cell, Desulfovibrio gigas, Desulfovibrio vulgaris Miyazaki F, density functional theory
Introduction
Theoretical Investigations of [Nife] Hydrogenase
Active Site of Dg
Active Site of DvMF
Conclusion
978-1-4020-5372-6_10_OnlinePDF.pdf
Bacteriorhodopsin Energy Landscape: Current Status
V. Renugopalakrishnan
Renugopalakrishnan
Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
The folding and stability of bacteriorhodopsin remains of great interest in view of its technological importance. Single molecules of bacteriorhodopsin are unfolded by attaching them to the tip of an AFM probe and then applying force <50 pico Newtons can be pulled one or more at a time. These experiments provide force profiles of individual chains which exhibit dependence and independence on rest of the helices until all of them are unfolded. Unlike differential scanning calorimetric studies which provide the global thermodynamic profile of proteins, AFM dynamic force probe methods provide a wealth of force profiles of the individual chains at a single molecule level which can then be reconstituted to map the energy landscape of bacteriorhodopsin. Energy landscape of bacteriorhodopsin from dynamic force probe method using atomic force spectroscopy is reviewed in this chapter
Atomic Force Microscopy (AFM), Dynamic Force Spectroscopy (DFS), Unfolding Pathway, Bacteriorhodopsin, Protein Energy Landscape
Unfolding Pathway of wild type bR
How does pH influence the unfolding Pathway of w-bR
Unfolding helices G and F
Unfolding helices E and D
Unfolding helices C and B
Unfolding helix A
Stability of the loops
Temperature Dependence of Unfolding Profiles of w- bR
978-1-4020-5372-6_11_OnlinePDF.pdf
Dimerization and Oligomerizationof Rhodopsin and Other G Protein-Coupled Receptors
Sawomir Filipek, Anna Modzelewskaand Krystiana A. Krzysko
Filipek et al.
International Institute of Molecular and Cell Biology, 4Ks. Trojdena St, 02--109 Warsaw, Poland
Dimerization, and more generally oligomerization, of G protein-coupled receptors (GPCRs) is experimentally proven and possibly all GPCRs act in oligomeric form. The coupling with G protein, phosphorylation by kinase and binding to arrestin what starts internalization process have also been shown to be influenced by the oligomeric state of the receptors. Cooperative interactions within homo- and heterodimers of GPCRs may be critical for the propagation of an external signal across the cell membrane, activation of a G protein and passing the signal down to effector proteins
Rhodopsin; GPCR; membrane proteins; dimerization; oligomerization; G protein; arrestin; signal transduction
Introduction
G Protein-Coupled Receptors
Importance of GPCRs
Rhodopsin as a Template
Dimerization and Oligomerization
Experimental evidence
Modeling the Complexes of Oligomeric Rhodopsin
Conclusions and Challenges
978-1-4020-5372-6_12_OnlinePDF.pdf
Molecular Dynamics Simulations of Hydrogen Adsorption in Finite and Infinite Bundles of Single Walled Carbon Nanotubes
Hansong Cheng1, Alan C. Cooper1, Guido P. Pez1,Milen K. Kostov2, M. Todd Knippenberg1,3,Pamela Piotrowski3 and Steven J. Stuart3
Cheng et al.
1Air Products and Chemicals, Inc. 7201 Hamilton Boulevard, Allentown, PA 18195-15012 Department of Physics, Pennsylvania State University, University Park, PA 16802-63003Department of Chemistry, Clemson University, Clemson, SC 29634
Molecular dynamics simulations have been used to systematically study hydrogen storage in single walled carbon nanotubes of various diameters and chiralities using a recently developed curvature-dependent force field. Several fundamental issues related to the effects of nanotube size, chirality and the thickness of nanotube bundles have been examined. A novel methodology for the analysis of effective average adsorption energy and storage capacity was developed. Our simulation results suggest strong dependence of H2 adsorption energies on the nanotube diameter but less dependence on the chirality. Substantial lattice expansion upon H2 adsorption was found. The average adsorption energy increases with the lowering of nanotube diameter (higher curvature) and decreases with higher H2 loading. The calculated H2 vibrational power spectra and radial distribution functions indicate a strong attractive interaction between H2 and nanotube walls. The calculated diffusion coefficients are much higher than what has been reported for H2 in microporous materials such as zeolites, indicating that diffusivity does not present a problem for adsorption energy and effective capacity hydrogen storage in carbon nanotubes. We show that adsorption energy and effective storage capacity can be defined in a distance-dependent manner, providing a more comprehensive understanding of adsorption behavior
carbon nanotubes; hydrogen adsorption, molecular dynamics
Introduction
Computational Methods
H2 Adsorption in an Infinite Bundle of Swnt
H2 Distribution
Heat of Adsorption
Radial Distribution Functions
H2 Vibrational Spectrum
H2 Diffusion Coefficients in SWNT
H2 Adsorption in Finite Swnt Bundles
Conclusions
978-1-4020-5372-6_13_OnlinePDF.pdf
The Remarkable Capacities of (6,0) Carbon and Carbon/Boron/Nitrogen Model Nanotubes for Transmission of Electronic Effects
Peter Politzer, Jane S. Murray, Pat Lane and Monica C. Concha
Politzer et al.
Department of Chemistry, University of New Orleans, New Orleans, LA 70148, USA
We have found that at least some (6,0) carbon and carbon/boron/nitrogen model nanotubes possess a remarkable capability for transmitting electronic effects along their full lengths. This can be triggered by even a rather minor asymmetric perturbation at one or both ends of the system. We have analyzed these quite striking effects as they are manifested in the computed electrostatic potentials and local ionization energies on the tube surfaces and, in one instance, in a reorganization of the framework structure. These observations, and some implications, are presented and discussed
(6,0) carbon nanotubes, (6,0) C/B/N nanotubes, electrostatic potentials, local ionization energies, charge delocalization
Introduction
Procedures
Electrostatic Potential
Average Local Ionization Energy
Computational Approach
Results and Discussion
General
Functionalized Open Carbon Model Nanotubes
Closed Model Nanotubes
Applications in Area of Nonlinear Optics
Summary and Future Work
978-1-4020-5372-6_14_OnlinePDF.pdf
Electronic Properties and Fragmentation Dynamics of Organic Species Deposited on Silicon Surfaces
Jian-Ge Zhou and Frank Hagelberg
Zhou and Hagelberg
Department of Physics, Atmospheric Sciences, and Geoscience, Jackson State University, USA
This contribution summarizes recent progress in the computational treatment of organic species deposited on silicon surfaces, with emphasis on the Si(100) surface. Representative theoretical studies of various organic species in contact with Si surfaces are surveyed, involving unsaturated hydrocarbons, amines, phosphines, and alcohols as adsorbates. The connection of the presented computational results to spectroscopic measurement is outlined in each individual case. The strengths and the limitations of a finite cluster model for simulating the Si substrate are discussed. Further, a comprehensive investigation of one specific system is presented, namely 1-propanol adsorbed on Si(001)-(21). It is shown by density functional theory within periodic boundary conditions that 1-propanol in contact with Si(001)-(21) initially occupies a metastable physisorbed state which turns into a stable chemisorbed ground state by dissociative hydrogen transfer. This fragmentation effect is confirmed by ab initio molecular dynamics at room temperature. The adsorbed organic layer induces further surface reconstruction. For the first time, the band structure of the 1-propanole/Si(001) film is determined. The tendency of the energy gap as a function of 1-propanole coverage indicates that the surface becomes increasingly insulating as the areal density of the organic adsorbate is enhanced
Silicon surface; CVD; Chemisorption; Proton transfer
Introduction
Recent Progress in the Computational Treatment of Organic Species Deposited on Silicon Surfaces
The Si Surface
Unsaturated Hydrocarbons
Amines
Phosphines
Alcohols
Case Study: Adsorption of 1-Propanol on the Si(001)-(2bold0mu mumu Rect1) Surface
Motivation and Methodology
The Physisorbed and Chemisorbed Configurations
Energy Barriers
Band Structure
Dependence on the Level of Coverage
Room Temperature Molecular Dynamics Calculations
Summary
978-1-4020-5372-6_15_OnlinePDF.pdf
Recent Advances in Fullerene Deposition on Semiconductor Surfaces
C. G. Zhou1, L. C. Ning1, J. P. Wu1, S. J. Yao1, Z. B. Pi1, Y. S. Jiang2, H. Cheng1,
Zhou et al.
1Institute of Theoretical Chemistry and Computational Materials Science,China University of Geosciences, Wuhan, China 2Institute of Computational Chemistry, Nanjing University, Nanjing, China
Development of novel chemistry on semiconductor surfaces is an area of increasing research interests due to its technological importance. The possibility of depositing fullerenes on semiconductor surfaces via the formation of stable chemical bonds provides an opportunity to design and develop novel materials that meet the increasing stringent technology challenge. In this chapter, we review recent advances in the theoretical modeling of fullerene chemisorption on GaAs and Si surfaces. We show that strong covalent chemical bonds can be formed upon deposition of fullerenes of various sizes on these surfaces, forming well-ordered thin films. The chemical/physical properties of such thin films can be tailored by using different sizes of fullerenes
Fullerenes; Semiconductor surfaces; GaAs(001)-c(44); Si(001)-(21); Density of States
Introduction
Computational Details
Fullerene Adsorption on the C(44) Reconstructed Gaas(001) Surface
Structure and Energetics of Fullerenes
C28 Adsorption on the GaAs(001) c(44) Surface
Cn(n=32, 36, 40, 44, 48, 60) Adsorption on the GaAs(001)-c(44) Surface
Bonding Analyses
C60 Adsorption on Si(001)-C(2 1) Surface
Summary
978-1-4020-5372-6_16_OnlinePDF.pdf
A Quest for Efficient Methods of Disintegration of Organophosphorus Compounds: Modeling Adsorption and Decomposition Processes
Andrea Michalkova1, Leonid Gorb2 and Jerzy Leszczynski1,
Michalkova, Gorb and Leszczynski
1Computational Center of Molecular Structure and Interactions, Department of Chemistry, Jackson State University, 1400 J. R. Lynch Street, P. O. Box 17910, Jackson, MS 39217, USA 2U.S. Army Engineer Research and Development Center (ERDC, SpecPro), Vicksburg, MS 39180
The problem with a contamination of soil and groundwater by organophosphorus compounds is a widespread environmental concern with environmental deterioration. However, the high cost of remediation becomes evident. Organophosphorus compounds have several applications (agricultural, industrial, and military). Nevertheless, assessments of the hazards from these applications quite often do not take into account chemical processes. The management of contaminants requires considerable knowledge and understanding of contaminant behavior. Unique properties of transition metals and metal oxides such as having high adsorption and catalytic ability have resulted in their applications as natural adsorbents and catalysts in the development of clean-up technologies. An understanding of the physical characteristics of the adsorption sites of selected parts of soil (metal oxides) and transition metals, the physical and chemical characteristics of the contaminant, details of sorption of contaminants on soil, on soil in water solution, and on transition metals, and its distribution within the system is of practical interest. Quantum-chemical calculations provide more insight into the aforementioned characteristics of organophosphorus compounds. This review summarizes experimental studies and the computational techniques and applications which are used to develop theoretical models that explain and predict how transition metals and metal oxides can affect the adsorption and decomposition of selected organophosphorus compounds. The results can contribute to a better knowledge of impact of such processes in existing remedial technologies and in a development of new removal and decompositiontechniques
organophosphorus compound; nerve agent; adsorption; decomposition; soil; metal oxide; transition metal; cluster approach; surface reactivity; solvent; supermolecular approximation; continuum model; reaction kinetics
Introduction
Computational Methods and Models
Applications of Transition Metals and Metal Oxides as Catalysts for Adsorption and Decomposition of Organophosphorus Compounds
Summary and Future Research Area
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