Annual Reports in Computational Chemistry

Volume 1 - Table of Contents



Section 1: Quantum Mechanical Methods
Section Editor: T. Daniel Crawford

1.   An Introduction to the State of the Art in Quantum Chemistry
      Frank Jensen

1. Introduction

2. Hartree-Fock

3. Electron Correlation Methods

3.1 Contiguration Interaction and multi-configurational self-consistent field methods
3.2 Many-body perturbation methods
3.3 Coupled cluster methods

4. Density functional theory

5. Semiempirical methods

6. Basis sets

7. Summary


2.   Time-Dependent Density Functional Theory in Quantum Chemistry
      Filipp Furche and Kieron Burke

1. Background

2. Electronic excitations

3. Computational aspects

4. Performance

4.1 Vertical excitation and CD spectra
4.2 Excited state structure and dynamics

5. Qualitative limitations of present functionals

5.1 Inaccurate ground state KS potentials
5.2 Adiabatic approximation
5.3 Multiple excitations
5.4 Extended systems
5.5 Charge transfer problems

6. Promising developments

6.1 Exact exchange
6.2 Beyond the adiabatic approximation
6.3 TD and current DFT

7. Outlook



3.   Computational Thermochemistry: A Brief Overview of Quantum Mechanical Approaches
      Jan M. L. Martin

1. Introduction

2. Semiempirical methods

3. Density functional methods

4. Ab initio thermochemistry: preliminaries

5. Use of isodesmic and isogyric reactions

6. Empirically corrected methods: G1, G2, G3 theory

7. Hybrid extrapolation/correction methods: CBS-n

8. Nonempirical extropolation approaches: Wn theory

9. Explicitly correlated methods

10. Conclusions


4.   Bond Breaking in Quantum Chemistry
      C. David Sherrill

1. Introduction

2. The challenge of breaking bonds

2.1 Difficulties for Hartree-Fock molecular orbital theory
2.2 The multiconfigurational self-consistent-field method
2.3 The generalized valance bond method

3. Failure of standard single-reference methods

3.1 Methods based on a single, restricted Hartree-Fock reference
3.2 Methods based on a single, unrestricted Hartree-Fock reference

4. Methods improving upon MCSCF/CASSCF

4.1 Multireference configuration interaction
4.2 Multireference perturbation theory
4.3 Multireference coupled-cluster theory

5. New prespectives

5.1 Approximations to CASSCF
5.2 Spin-flip methods
5.3 Improved coupled-cluster methods
5.4 Methods discarding the potential energy surface

6. Conclusions



Section 2: Molecular Modeling Methods
Section Editor: Carlos Simmerling

5.   A Review of the TIP4P, TIP4P-Ew, TIP5P, and TIP5P-E Water Models
      Thomas J. Dick and Jeffry D. Madura

1. Introduction

2. Methods

3. 4-Site water models

3.1 TIP4P
3.2 TIP4P-Ew

4. 5-Site water models

4.1 TIP5P
4.2 TIP5P-E

5. Conclusions



6.   Molecular Modeling and Atomistic Simulation of Nucleic Acids
      Thomas E. Cheatham

1. Introduction

2. Successes

2.1 Agreement with experiment
2.2 Insight beyond experiment?
2.3 Methodological and force field advances

3. Limitations

3.1 Artifacts from the boundary conditions
3.2 Force field issues and sampling limitations

4. Conclusions



7.   Empirical Force Fields for Proteins: Current Status and Future Directions
      Alexamder D. MacKerell Jr.

1. Introduction

2. Protein force fields

2.1 Gas-phase versus condensed-phase target data
2.2 Free energies of aqueous solvation
2.3 Comments on enhancements to protein force fields
2.4 United-atom protein force fields
2.5 Future directions

3. Summary



8.   Nonequilibrium Approaches to Free Energy Calculations
      Adrian E. Roitberg

1. Introduction

2. The original Jarzynski method

3. Experimental applications

4. heoretical developments

5. Computational uses

6. Conclusions



9.   Calculating Binding Free Energy in Protein-Ligand Interaction
      Kaushik Raha and Kenneth M. Merz Jr.

1. Introduction

2. Calculating binding free energy

3. Scoring functions

3.1 Physical chemical
3.2 Empirical scoring functions
3.3 Knowledge-based scoring functions

4. Conclusions



Section 3: Advances in QSAR/QSPR
Section Editor: Yvonne Martin

10.   Computational Prediction of ADMET Properties: Recent
        Developments and Future Challenges
        David E. Clark

1. Introduction

2. Intestinal permeability

3. Aqueous solubility

4. Human intestinal absorption

5. Human oral bioavilability

6. Active transport

7. Efflux by P-glycoprotein

8. Blood-brain barrier permeation

9. Plasma protein binding

10. Metabolic stability

11. Interaction with cytochrome P450s

12. Toxicity

13. Conclusions


Section 4: Applications of Computational Methods
Section Editor: Heather Carlson

11.   Filtering in Drug Discovery
        Christopher A. Lipinski

1. Drug-likeness

2. Drug-likeness and chemistry quality

3. Positive desirable chemistry filters

4. Lead-likeness

5. Oral drug activity

6. CNS drugs

7. Intestinal permeability

8. Aqueous solubility

9. Drug metabolism

10. Promiscous compounds

11. Agrochemicals


12.   Structure-Based Lead Optimization
        Diane Joseph-McCarthy

1. Introduction

2. Lead Discovery

2.1 Compound equity
2.2 High-Throughput Screening
2.3 Virtual Screening

3. Lead Modification

3.1 Structure visualization
3.2 Fragment positioning
3.3 Molecular simulation
3.4 Library enumeration and docking
3.5 Ligand-target complex evaluation

4. Application to a specific target

4.1 Acyl carrier protein synthase

5. Conclusions


13.   Targeting The Kinome With Computational Chemistry
        Michelle L. Lamb

1. Introduction

2. The kinome

2.1 Background
2.2 ATP site recognition elements

3. Methodology for kinase targets

3.1 Homology models
3.2 Docking and scoring
3.3 Selectivity
3.4 Structure-based hybridization

4. Applications across the kinome

4.1 CMGC group
4.2 TK group
4.3 CAMK group
4.4 AGC group
4.5 Other kinase groups

5. Conclusions


Section 5: Chemical Education
Section Editor: Theresa Zielinski

14.   Status of Research-Based Experiences for First- and Second-Year Undergraduate Students
        Jeffrey D. Evanseck and Steven M. Firestine

1. Introduction

2. Current status

3. Council on undergraduate research

4. National Science Foundation

5. Undergraduate research program

6. Conclusions



15.   Crossing the Line: Stochastic Models in the Chemistry Classroom
        Michelle M. Francl

1. Introduction

2. Molecular dynamics

3. Stochastic methods

4. Conclusions


16.   Simulation of Chemical Concepts, Systems and Processes Using
        Symbolic Computation Engines: From Computer-Assisted Problem-Solving
        Approach to Advanced Tools for Research
        Jonathan Rittenhouse and Mihai Scarlete

1. Introduction

2. Creation of self-extracting databases

3. Storage capacity in symbolic/computational form

3.1 Relationships between thermodynamic functions of state
3.2 Storage of the data in functional form
3.3 Storage of quatified versions of chemical principles

4. Use of the graphing power of SCE for enhanced and accurate visualization of chemical concepts

4.1 Visualization of wave functions, orbitals' phase and probability

5. Design of specialized procedures based on the rapidity and numerical computation power of the SCE

5.1 Automatic procedure for the kinetic analysis of van't Hoff reactions

6. Emulation of professional software and advanced application-specific procedures

6.1 Phase of molecular orbitals
6.2 Modeling of molecules with high symmetry (maximum three parameters)

7. Development of tools for research activities requiring quantification of
                the description of the chemical system under scrutiny

7.1 Process design using SCE
7.2 Description of the oscillating systems involving transamination of
                    poly(organo)silanes during polymer-source chemical vapor deposition (PS-CVD)

8. Conclusions


Section 6: Emerging Science
Section Editor: Ralph Wheeler

17.  The Challenges in Developing Molecular Simulations
        of Fluid Properties for Industrial Applications
        Raymond D. Mountain and Anne C. Chaka

1. Introduction

2. The intermolecular potential function barrier

3. The sampling barrier

4. Challenges/opportunities


18.   Computationally Assisted Protein Design
        Sheldon Park and Jeffrey G. Saven

1. Introduction

2. Computational protein design

2.1 Target structure
2.2 Degrees of freedom
2.3 Energy function
2.4 Solvation and patterning
2.5 Search methods

3. Computationally designed proteins

4. Conclusion



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