E-raamat: Annual Reports in Computational Chemistry

Contributors		ix
Preface		xiii
Section 1: Simulation Methodologies (Section Editor: Carlos Simmerling)
Molecular Simulations of pH-Mediated Biological Processes		3	(12)
Jana Khandogin
Charles L. Brooks
Introduction		3	(1)
Static Structure Based pKa Prediction Methods		4	(1)
Molecular Dynamics Coupled with Acid-Base Titration		5	(2)
Applications of CPHMD		7	(3)
Summary and Outlook		10	(5)
Acknowledgement		11	(1)
References		11	(4)
Extending Atomistic Time Scale Simulations by Optimization of the Action		15	(16)
A.S. Clarke
S.M. Hamm
A.E. Cardenas
Introduction		15	(7)
Applications		22	(3)
Conclusions		25	(6)
Acknowledgements		26	(1)
References		27	(4)
Fishing for Functional Motions with Elastic Network Models		31	(10)
A.J. Rader
Introduction		31	(1)
Background		32	(1)
Identification of Functional Motions		33	(1)
Detailed EN Models		34	(2)
Merging EN Models and MD Simulations		36	(1)
Summary & Future Prospects		36	(5)
References		37	(4)
Alchemical Free Energy Calculations: Ready for Prime Time?		41	(22)
Michael R. Shirts
David L. Mobley
John D. Chodera
Introduction		41	(1)
Background		42	(1)
Equilibrium Methods		43	(2)
Nonequilibrium Methods		45	(1)
Intermediate States		46	(2)
Sampling		48	(3)
Applications		50	(1)
Conclusion		51	(12)
Acknowledgements		53	(1)
References		53	(10)
Section 2: Biological and Biophysical Applications (Section Editor: Heather Carlson)
Linear Quantitative Structure--Activity Relationships for the Interaction of Small Molecules with Human Cytochrome P450 Isoenzymes		63	(22)
Thomas Fox
Jan M. Kriegl
Introduction		63	(1)
The Cytochrome P450 Superfamily		64	(2)
Methodological Overview		66	(2)
Applications		68	(5)
Discussion and Outlook		73	(12)
References		75	(10)
Section 3: Chemical Education (Section Editor: Theresa Zielinski)
Observations on Crystallographic Education		85	(14)
Phillip E. Fanwick
Introduction		85	(1)
Objectives for Teaching Crystallography		86	(3)
Bragg's Law		89	(1)
Relating Crystallography to Chemistry		90	(6)
Creativity		96	(2)
Conclusions		98	(1)
References		98	(1)
Achieving a Holistic Web in the Chemistry Curriculum		99	(38)
Henry S. Rzepa
Introduction: The Impact of the Web on the Chemistry Curriculum		99	(2)
Background: The Trend Towards an Accumulation of Acrobat		101	(2)
The Properties of a PDF Collection		103	(3)
Formal Metadata Based Approaches		106	(5)
The Concept of Document Re-Use		111	(2)
Data as the Intel Inside		113	(5)
Towards the Holistic Approach: The Podcast		118	(3)
The Wiki		121	(16)
Conclusion		131	(1)
References		132	(5)
Section 4: Materials and Polymers (Section Editor: Jeffry Madura)
The Role of Long-Time Correlation in Dissipative Adsorbate Dynamics on Metal Surfaces		137	(18)
Jeremy M. Moix
Rigoberto Hernandez
Introduction		137	(3)
Classical Surface Diffusion		140	(3)
Molecular Dynamics Simulations and Projective Models		143	(3)
Summary and Conclusions		146	(9)
Acknowledgements		147	(1)
References		147	(8)
Section 5: Quantum Chemistry (Section Editor: T. Daniel Crawford)
An Active Database Approach to Complete Rotational--Vibrational Spectra of Small Molecules		155	(22)
Attila G. Csaszar
Gabor Czako
Tibor Furtenbacher
Edit Matyus
Introduction		155	(3)
Nonadiabatic Computations---Where Theory Delivers		158	(1)
MARVEL---An Active Database Approach		158	(2)
Electronic structure computations		160	(5)
Variational Nuclear Motion Computations		165	(4)
Outlook		169	(8)
Acknowledgement		169	(1)
References		169	(8)
The Effective Fragment Potential: A General Method for Predicting Intermolecular Interactions		177	(18)
Mark S. Gordon
Lyudmilla Slipchenko
Hui Li
Jan H. Jensen
Introduction		177	(1)
EFP2 Theory		178	(5)
Example Applications		183	(7)
Summary and Future Developments		190	(5)
Acknowledgements		191	(1)
References		191	(4)
Gaussian Basis Sets Exhibiting Systematic Convergence to the Complete Basis Set Limit		195	(14)
Kirk A. Peterson
Introduction		195	(1)
Correlation Consistent Basis Sets: A Review		196	(4)
Recent Advances in Correlation Consistent Basis Sets		200	(3)
Conclusions		203	(6)
Acknowledgements		203	(1)
References		203	(6)
Section 6: Emerging Technologies (Section Editor: Wendy Cornell)
Principles of G-Protein Coupled Receptor Modeling for Drug Discovery		209	(20)
Irache Visiers
Introduction		209	(2)
Homology Models of Rhodopsin-Like GPCRs		211	(8)
Ab Initio Methods		219	(1)
Modeling the Activated State		220	(2)
Conclusions		222	(7)
Acknowledgement		222	(1)
References		222	(7)
Index		229	(4)
Cumulative Index Vols 1--2		233

David Spellmeyer is a Biotechnology Executive and Entrepreneur with over 30 years of broad experience in the life sciences industry. He is Principal at Interlaken Associates where he works closely with both early-stage companies and venture capital firms to build and lead strong pre-clinical R&D scientific teams focused on establishing scientific proof-of-concept for novel innovations. David is also an adjunct Associate Professor of Pharmaceutical Chemistry at the University of California San Francisco (UCSF). He has been actively involved in the entrepreneurship and innovation ecosystem supporting founders, students, post-docs, and faculty, serving as a mentor in programs at UCSF, California Life Sciences Institutes FAST programs, California State Universitys CSUPERB, UC Davis MentorNet, and as a reviewer for NIH SBIR/STTR Study Sections. David has recently served as CSO at Circle Pharma, an Executive-in-Residence at Pandect Biosciences, head of Quality for a diagnostics company, and an executive advisor for several startups. Prior to building Interlaken Associates, he held positions at DuPont Pharma (BMS), Chiron (Novartis), Signature BioScience, Nodality, and IBM Research. David works very closely with business development teams and has completed over 20 non-dilutive strategic corporate partnerships, several mergers, acquisitions, and joint ventures and participated in several rounds of venture financing. He received his BS in computer science and chemistry from Purdue University and his PhD in theoretical organic chemistry from UCLA and completed his post-doctoral training in pharmaceutical chemistry at UCSF.