---------------------------------------------------------------------------------------------------------------------------------
|
New Book (February 2010): C. F. Matta
(Editor) Quantum Biochemistry: Electronic Structure and Biological
Activity (Wiley-VCH, Weinheim,
2010) TABLE OF CONTENTS: BOOK
PRELIMINARIES i.
Acknowledgment ii.
Congratulations to Professor Ada Yonath for Winning the 2009 Nobel Prize in Chemistry iii.
Introductory Reflections on Quantum Biochemistry: From Context to Contents XI Chérif F. Matta iv. List of
Contributors VOLUME I PART I: NOVEL
THEORETICAL, COMPUTATIONAL, AND
EXPERIMENTAL METHODS AND TECHNIQUES 1
Quantum Kernels and Quantum
Crystallography: Applications in Biochemistry Lulu Huang, Lou Massa and Jerome Karle 2
Getting the Most out of ONIOM:
Guidelines and Pitfalls Fernando R. Clemente, Thom Vreven, and
Michael J. Frisch 3
Modeling Enzymatic Reactions in Metalloenzymes and Photobiology by Quantum Mechanics (QM)
and Quantum Mechanics/Molecular Mechanics (QM/MM) Calculations Lung Wa Chung, Xin Li, and
Keiji Morokuma 4
From Molecular Electrostatic Potentials
to Solvation Models and Ending with Biomolecular Photophysical
Processes Jacopo Tomasi, Chiara
Cappelli, Benedetta Mennucci, and Roberto Cammi 5
The Fast Marching Method for Determining
Chemical Reaction Mechanisms in Complex Systems Yuli Liu, Steven K. Burger, Bijoy K. Dey, Utpal Sarkar,
Marek R. Janicki, and
Paul W. Ayers PART TWO:
NUCLEIC ACIDS, AMINO ACIDS, PEPTIDES AND THEIR INTERACTIONS 6
Chemical Origin of Life: How do Five
HCN Molecules Combine to form Adenine under Prebiotic
and Interstellar Conditions Debjani Roy and Paul von Ragué Schleyer 7
Hydrogen Bonding and Proton Transfer in
ionized DNA Base Pairs, Amino Acids and Peptides Luis Rodríguez-Santiago, Marc Noguera, Joan Bertran, and Mariona Sodupe 8
To Nano-Biochemistry:
Picture of the Interactions of DNA with Gold Eugene S. Kryachko 9
Quantum Mechanical Studies of Noncovalent DNA–Protein Interactions Lesley R. Rutledge and Stacey D. Wetmore 10
The Virial
Field and Transferability in DNA Base-Pairing Richard F.W. Bader and Fernando Cortés-Guzmán 11
An Electron Density-Based Approach to
the Origin of Stacking Interactions Ricardo A. Mosquera,
María J. González Moa, Laura Estévez, Marcos Mandado, and Ana M. Graña 12
Polarizabilities of Amino Acids: Additive Models and Ab Initio Calculations Noureddin El-Bakali Kassimi
and Ajit J. Thakkar 13
Methods in Biocomputational
Chemistry: A Lesson from the Amino Acids Hugo J. Bohórquez, Constanza
Cárdenas, Chérif F. Matta,
Russell J. Boyd, and Manuel E. Patarroyo 14
From Atoms in Amino Acids to the
Genetic Code and Protein Stability, and Backwards Chérif F. Matta 15
Energy Richness of ATP in Terms of
Atomic Energies: A First Step Chérif F. Matta and Alya
A. Arabi VOLUME II Part
Three: Reactivity, Enzyme Catalysis, Biochemical Reaction Paths and
Mechanisms 16
Quantum Transition State for Peptide
Bond Formation in the Ribosome Lou Massa, Chérif F. Matta,
17
Hybrid QM/MM Simulations of
Enzyme-Catalyzed DNA Repair Reactions Denis Bucher, Fanny Masson, J. Samuel Arey
and Ursula Röthlisberger 18
Computational Electronic Structure of
Spin-Coupled Diiron-Oxo Proteins Jorge H. Rodriguez 19
Accurate Description of Marcel Swart, Mireia Güell
and Miquel Solà 20
Quantum Mechanical Approaches to
Selenium Biochemistry Jason K. Pearson and Russell J. Boyd 21
Catalytic Mechanism of Metallo b-Lactamases: Insights
from Calculations and Experiments Matteo Dal Peraro,
Alejandro J. Vila and Paolo Carloni 22 Computational Simulation of the Terminal
Biogenesis of Sesquiterpenes: The Case of
8-Epiconfertin José Enrique
Barquera-Lozada and Gabriel Cuevas 23
Mechanistics of Enzyme Catalysis: From Small to Large
Active-Site Models Jorge Llano and James W. Gauld Part
Four: From Quantum Biochemistry to Quantum Pharmacology, Therapeutics,
and Drug Design 24
Developing Quantum Topological
Molecular Similarity (QTMS) Paul L.A. Popelier 25 Quantum-Chemical Descriptors in QSAR/QSPR
Modeling: Achievements, Perspectives and Trends Anna V. Gubskaya 26
Platinum Complexes as Anti-Cancer
Drugs: Modeling of Structure, Activation and Function Konstantinos Gkionis, Mark
Hicks, Arturo Robertazzi and J. Grant Hill, and James
A. Platts 27
Protein Misfolding:
The Quantum Biochemical Search for a Solution to Alzheimer’s Disease Donald F. Weaver 28
Targeting Butyrylcholinesterase
for Alzheimer’s Disease Therapy Katherine V. Darvesh, Ian R. Pottie, Robert S. McDonald, Earl Martin, and Sultan Darvesh 29
Reduction Potentials of Peptide-Bound
Copper (II) – Relevance for Alzheimer’s Disease and Prion
Diseases Arvi Rauk 30
Theoretical Investigation of NSAID Photodegradation Mechanisms Klefah A.K. Musa and Leif
A. Eriksson Part
Five: Biochemical Signature of Quantum Indeterminism 31
Quantum Indeterminism, Mutation, Natural Selection, and the Meaning of
Life David N. Stamos 32
Molecular Orbitals:
Dispositions or Predictive Structures? Jean-Pierre Llored and Michel Bitbol ------------------------------------------------------------------------------------------------------- SOME FAVOURITE QUOTES: "THE
HISTORY of acceptance of new theories frequently shows the following steps:
At first the new idea is treated as pure nonsense, not worth looking at. Then
comes a time when a multitude of contradictory objections are raised, such
as: the new theory is too fancy, or merely a new terminology; it is not
fruitful, or simply wrong. Finally a state is reached when everyone seems to
claim that he had always followed this theory. This usually marks the last
state before general acceptance." Kurt
Lewin
(1966): in "Some Theories of Organization.", A. H. Rubenstein and C. J. Haberstroh
(Eds.), Richard D. Irwin, Inc. and the Dorsey Press, ---------------------------------------------------------------------- "...
it is in virtue of the form that the matter is some
one definite thing, and this is the substance of the thing. What Aristotle
means seems to be plain common sense: a "thing" must be bounded,
and the boundary constitutes its form. ... We should not naturally say
that it is the form that confers substantiality, but that is because the
atomic hypothesis is ingrained in our imagination. Each atom, however, if it
is a "thing", is so in virtue of its being delimited from other
atoms, and so having, in some sense, a "form". Bertrand
Russell (1945)
"A History of Western Philosophy"; Simon and
Schuster: ---------------------------------------------------------------------- "Life
may be defined operationally as an information processing system - a
structural hierarchy of functioning units - that has acquired through
evolution the ability to store and process the information necessary
for its own accurate reproduction. The key word in the definition is information." Lila
Gatlin (1972) "Information
Theory and the Living System", ---------------------------------------------------------------------- "There
is no such thing as a private intellectual, since the moment you set down
words and then publish them you have entered the public world. Nor is there only
a public intellectual, someone who exists just as a figurehead or
spokesperson or symbol of a cause, movement, or position. There is always the
personal inflection and the private sensibility, and those give meaning to
what is being said or written. Least of all should an intellectual be there
to make his/her audiences feel good: the whole point is to be embarrassing,
contrary, even unpleasant." Edward
W. Said (1994),
"Representations of the Intellectual: The 1993 Reith Lectures",
Pantheon Books, ---------------------------------------------------------------------- "En résumé, la seule réalité objective, se sont
les rapports des choses d'où résulte l'harmonie universelle. Sans doute ces
rapports, cette harmonie ne sauraient être conçus en dehors d'un esprit qui
les conçoit ou qui les sents. Mais ils sont
néanmoins objectifs parce qu'ils sont, deviendront, ou resteront communs á
tous les êtres pensants." " Et cependant - étrange contradiction pour ceux qui
croient au temps - l'histoire géologique nous montre que la vie n'est qu'un
court épisode entre deux éternités de mort, et que, dans cet épisode même, la
pensée consciente n'a duré et ne durera qu'un moment. La pensée n'est qu'un
éclair au milieu d'une longue nuit. Mais c'est cet éclair qui est tout" Henri Poincaré (1927), "La
Valeur de la Science"; Ernest Flammarion, Paris. ---------------------------------------------------------------------- "J'entends par Réalité, tout d'abord, ce qui résiste
à nos expériences, représentations, descriptions, images ou formalisations
mathématiques. La physique quantique nous a fait découvrir que l'abstractions n'est pas un simple intermédiaire entre
nous et la Nature, un outil pour décrire la réalité, mais une des parties
constitutives de la Nature. Dans la physique quantique, le formalisme
mathématique est inseparable de l'expérience. Il
résiste, à sa manière, à la fois pas son souci d'autoconsistance
interne et son besoin d'intégrer les données expérimentales sans détruire
cette autoconsistance." Basarab Nicolescu (1996),
"LA TRANSDISCIPLINARITÉ: Manifeste"; Éditions du
Rocher, Paris. ---------------------------------------------------------------------- Since
1 September 2005, you are visitor # ©
Chérif F. Matta,
2002-2009 |
|
|
|
|