Editorial
Quantum Nanobiology and Biophysical Chemistry
The fields of quantum nanobiology and biophysical chemistry are the natural evolution of the
fields of biology, chemistry and physics as applied to biological problems and systems.
Starting from atoms, to molecules, to molecular complexes, aggregates, organelles, cells and
tissues, the complexity of life processes have developed. In these systems one must bridge
the gap between various length, energy and time scales. To do so has required one to do socalled frontier science and develop new and exciting methods, both experimental and
theoretical. The use of multi-method and multidisciplinary approaches has forced researchers
in these multidisciplinary fields to integrate and understand both theoretical and experimental
data in areas outside their former comfort zones and areas of expertise. The manuscripts in
this two issue special volume of Current Physical Chemistry give a snapshot of the various
problems, approaches and methods, both experimental and theoretical, which are currently
used and define the fields of quantum nanobiology and biophysical chemistry.
There were two primary motivations for the creation of this special volume of Current
Physical Chemistry. The first was a sense among some commentators [1] on science that the
last century was the “Age of Physics” and that we are now in the “Age of Biology”.
Meaning, the tremendous excitement of discovery in physics especially in the first half of the
last century is now much more evident in the various sub-disciplines of biology. This may be
true, but key to any success in biology is the depth of understanding of biological systems
that can only come from the application of physical principles, and the connecting centrality
of the field of chemistry. This special volume is replete with examples that straddle the fields
of biology, physics, and chemistry.
The second motivation was the occasion of the 60 th Birthday of a key figure in this multidisciplinary adventure – Dr. Henrik Georg Bohr, the Director of the Quantum Protein Center
at the Technical University of Denmark. It was Professor Bohr and his Center – which
recently celebrated a 10th anniversary - that inspired the particular sub-topics – Quantum
Nanobiology and Biophysical Chemistry – that fill out the two issues of this special volume
[2].
With the recent development of advanced experimental and theoretical tools to study
chemical and biological systems at the atomic and molecular levels, quantum- molecular- and
nano-biology have become important topics of biophysical chemistry and chemical
biophysics. With biotechnology providing ever increasing amounts of native and mutated
proteins, and onward to highly genetically or expression modified systems, one is now able to
ever more rapidly perform experiments in vivo and use this knowledge to generate and refine
functionally bio-mimetic systems in vitro, often at nanometer scales. Critical in this
analytical interplay is the use of modern chemistry and physics, both classical and quantum
mechanical. As an example, several articles in the issue illustrate the need for the
development of ab initio and novel semi-empirical methods which allow a better
understanding of recent experiments involving electronic, vibrational/vibronic and
absorption/emission phenomena as they related to the spectroscopic interrogation of
biomolecule structure and function.
A general theme of the issue is on recent advances in both experimental and theoretical
quantum nanobiology/ biophysical chemistry and on the marriage between theory and
experiment, as well as the marriage between the multi-method approaches and multidisciplinary approaches in the spirit advocated by Zaccai, Zaccai, and Serdyuk [3].
The Guest Editors offer best personal wishes to Professor H.G. Bohr, thank all the
contributors and referees who have helped create a series of papers worthy of the lofty
subject matter, and earnestly hope the work may inspire a continued re-joining of what have
at times become perhaps somewhat myopic approaches as science went from a philosophia
naturalis to today’s focus on sub-disciplines (and further, the bifurcation of ‘applied’ and
‘basic’ research), especially in the education of young scientists.
THE CONTENTS
For issue 1 of the two part volume, we naturally start with a review by Professor Bohr, which in part is
concerned with problems and perspectives of Molecular Biophysics of today and especially with
respect to quantum aspects. Zaccai gives discussion of the ecology of protein dynamics – especially
focusing on the time scale elements often missed in thinking about these systems. Mouritsen, drawing
on what he and others have learned in many years working on the epitome of nanosytems – liposomes
- provides a biophysical analysis of the consequences of biomembrane curvature. Wade and
Berynskyy explore docking of dynamically active and flexible protein systems – that to go beyond
older treatments where two rigid pairs connect. Otero et al. provide an update from the renewed field
of in situ spectroscopy; in this case, vibrational spectroscopic analysis of cancer cells. Jensen reviews
combined multi-disciplinary theoretical and experimental studies on simple ferredoxins - the paradigm
metalloproteins – which studies can form the foundation for methods and basic physical principles
relevant to the most complex metalloenzyme systems. Koch provides a review of Locked Nucleic
Acids (LNA); both fundamental properties of LNA and a review of the most advanced preclinical/clinical LNA data. Dal Molin and Caliri apply statistical mechanics to early time scale protein
folding events. De Providência et al. take a journey through analysis of color superconductivity of
matter at high density to the issue of nuclear chirality in biomolecular systems. Ponomareva et al.
provide an extensive conformational analysis of a medically important nucleoside reverse
transcriptase inhibitor. Malik and Bohr provide an analysis of a bio-Auger process as it relates to
photosynthesis. Zhu and Aoki provide a novel theoretical approach for the qualitative prediction of
ferromagnetism in alternant conjugated hydrocarbon radical polymers. Rahim et al. provide
molecular dynamics simulations of the behavior of various sugars and the role they can play in the
structure of lysozyme solutions.
Moving on to Issue 2, Boulos et al. look at the biological interactions of gold nanorods. Kneipp and
Kneipp look at silver nanoparticle interactions with biomolecules using Raman optical activity.
Johannessen and Blanch review recent developments in Raman optical activity calculations of
biomolecules. Masuda et al. explore Raman markers in the xenopus laevis oocyte expression system.
Lobo et al. explore the biocompatibility of carbon nanotubes across the hydrophiliciy/hydropathy
spectrum. Ahmed and Wang explore detailed structural aspects of didehydrodeoxycitidine drugs with
a focus on intramolecular hydrogen bonds. Wu et al. use density functional theory to explore the use
of Ni/Fe bimetallic nanoparticles in the bioremediation of deca-bromodiphenyl esters. Araújo-Chaves
et al. explore the binding and reactivity of Mn(III) porphyrins in model liposomal systems. Claussen
et al. demonstrate extremely low detection performance of acyl-homoserine lactone in biologically
relevant systems using surface enhanced Raman spectroscopy. Jalkanen et al. provide a theoretical
analysis of a model histine bearing peptide, including integrated structure, solvation, and vibrational
absorption and vibrational circular dichroism treatments. Jalkanen et al. provide a theoretical and
experimental investigation of the infrared and Raman spectra of Leu-Enkephalin in dimethylsulfoxide.
Bondar and Milenovich explore electrostatic interactions in the active site of the Sec A motor. Lastly,
Sugihara and Bondar provide an investigation of the influence of methyl-groups and the protein
environment on the retinal geometry in rhodopsin and bacteriorhodopsin, two protypical photo-active
proteins.
The contributions in these two special issues are examples of multidisciplinary research in the areas of
biology, chemistry, physics, both experimental and theoretical at the molecular, molecular complex
and systems biology levels. All major advances in biology and medicine have followed major
advances in the related fields of chemistry and physics, and the fields of quantum nanobiology and
biophysical chemistry are no different. But what has added greatly to the speed and depth of the
breakthroughs are the recent advances in computational and theoretical molecular biophysics, which
has allowed the complexity and level of detail in molecular level simulations to be unsurpassed in the
history of science. We hope that these works will serve as the basis for further works and for the next
generations of students and academics to work in these multidisciplinary fields of endeavor where it is
mandatory that they be well versed not only in their own disciplines and subdisciplines, but also in the
many related and interconnected ones: biology, physics, medicine, pharmacy, environmental,
biomedical, electrical and chemical engineering, and of course mathematics and chemistry (atomic
and molecular structure of matter), the languages of science and engineering.
ACKNOWLEDGEMENTS
We would like to thank the Editors in Chief of Current Physical Chemistry, Dr. Ernesto Paparazzo and
subsequently Ruhong Zhou; Narmeen Khurram, Madiha Zahoor, Sarwat Azis Abbasi, and Qasit Malik
at Benthan Science Publishers; and all of the contributing authors for their scientific and editorial
contributions and work. Finally, we would like to thank the many anonymous referees who were
willing to take some of their valuable time to review the contributions to these two consecutive special
issues of CPC. Without their efforts and contributions, these special issues of CPC would not have
been possible.
REFERENCES
[1] Derbyshire, John. Will Obama Kill Science? National Review Online, 2008, October 7.
http://www.nationalreview.com/articles/225903/will-obama-kill-science/john-derbyshire
(Accessed October 1, 2012).
[2] Quantum Nanobiology and Biophysical Chemistry, special issues of Current Physical
Chemistry, Volume 3, issue 1, January 2013, and issue 2, April 2013.
[3] Serdyuk, I.N.; Zaccai, N.R.; Zaccai, J. Methods in Molecular Biophysics. Cambridge
University Press: Cambridge, 2007.
Karl J. Jalkanena,b and Gerard M. Jensenb
Guest Editors
Karl J. Jalkanen, FRSC
a
DTU Nanotech
Department of Micro- and Nanotechnology
Technical University of Denmark
Ørsteds Plads, Building 345E
DK-2800 Kgs. Lyngby, Denmark
Email1: karja@nanotech.dtu.dk
Email2: karljalkanen@gmail.com
Phone: +1 909-394-2654; Fax: +1 909-592-8530
URL: http://www.researcherid.com/rid/A-2456-2008
Gerard M. Jensen, PhD
b
Gilead Sciences Inc.
650 Cliffside Drive
San Dimas, CA, 91773
Email: Karl.Jalkanen@gilead.com
Email: Gerard.Jensen@gilead.com
Phone: +1 909-394-4000; Fax: +1 909-592-8530