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Contents list for Physical Chemistry Chemical Physics, issue 19, 2008
Front cover
Phys. Chem. Chem. Phys., 2008, 10, 2561
DOI: 10.1039/b806487n
Inside front cover
Phys. Chem. Chem. Phys., 2008, 10, 2562
DOI: 10.1039/b806488c
Contents
Phys. Chem. Chem. Phys., 2008, 10, 2563
DOI: 10.1039/b806489j
Editorial
Stacking interactions
Phys. Chem. Chem. Phys., 2008, 10, 2581
DOI: 10.1039/b805489b
Stacking interactions between systems with delocalized 
-electrons contribute significantly to the stability of biomacromolecules and complex molecular systems.
Perspectives
Nature and physical origin of CH/ interaction: significant difference from conventional hydrogen bonds
Seiji Tsuzuki and Asuka Fujii,
Phys. Chem. Chem. Phys., 2008, 10, 2584
DOI: 10.1039/b718656h
Although the structures are similar, the nature of CH/ interactions is completely different from that of the hydrogen bonds.
Nature and magnitude of aromatic stacking of nucleic acid bases
Ji
í 
poner, Kevin E. Riley and Pavel Hobza,
Phys. Chem. Chem. Phys., 2008, 10, 2595
DOI: 10.1039/b719370j
We explain details of the complex relationship between the gas-phase base-stacking energies and the highly variable roles of these interactions in nucleic acids, which is rarely discussed in quantum chemical and physical chemistry literature.
Papers
Intermolecular – interactions in solids
Miroslav Rube
and Ota Bludský,
Phys. Chem. Chem. Phys., 2008, 10, 2611
DOI: 10.1039/b718701g
The ZPE-corrected planewave DFT calculation, together with the CCSD(T)/CBS estimate of two-body contributions, provides a reliable framework for predicting properties of aromatic systems.
Induction effects in metal cation–benzene complexes
Ignacio Soteras, Modesto Orozco and F. Javier Luque,
Phys. Chem. Chem. Phys., 2008, 10, 2616
DOI: 10.1039/b719461g
Analysis of the contributions to the interaction energy illustrates the important role of the induction component in the geometrical and energetic properties of the pathway leading to the formation of cation– complexes.
Crystal packing of TCNQ anion 
-radicals governed by intermolecular covalent – bonding: DFT calculations and statistical analysis of crystal structures
Jingsong Huang, Stephanie Kingsbury and Miklos Kertesz,
Phys. Chem. Chem. Phys., 2008, 10, 2625
DOI: 10.1039/b717752f
CSD scatterplot showing the distribution of TCNQ fragments (wireframe) with respect to the central group (ball and stick).
A post-SCF complete basis set study on the recognition patterns of uracil and cytosine by aromatic and –aromatic stacking interactions with amino acid residues
Piotr Cysewski,
Phys. Chem. Chem. Phys., 2008, 10, 2636
DOI: 10.1039/b718394a
From among all aromatic amino acid residues, tryptophan forms the most stable stacked complexes with cytosine and uracil.
Substituent effects in parallel-displaced – interactions
Stephen A. Arnstein and C. David Sherrill,
Phys. Chem. Chem. Phys., 2008, 10, 2646
DOI: 10.1039/b718742d
Substituents tune – interactions through perturbed ring–ring and direct substituent–ring effects.
The excited states of -stacked 9-methyladenine oligomers: a TD-DFT study in aqueous solution
Roberto Improta,
Phys. Chem. Chem. Phys., 2008, 10, 2656
DOI: 10.1039/b718562f
The coexistence and the relative stability of delocalized, localized, and charge transfer excited states in DNA-like 9-methyladenine stacked oligomers is discussed.
The post-SCF quantum chemistry characteristics of the guanine–guanine stacking B-DNA
Piotr Cysewski, 
aneta Czy
nikowska, Robert Zale
ny and Przemys
aw Czele
,
Phys. Chem. Chem. Phys., 2008, 10, 2665
DOI: 10.1039/b718635e
The dependence of G–G stacked pair intermolecular interaction energies on the step B-DNA parameters was determined at the DF-MP2/aug-cc-pVDZ level of theory.
Thermodynamics of stacking interactions in proteins
Simone Marsili, Riccardo Chelli, Vincenzo Schettino and Piero Procacci,
Phys. Chem. Chem. Phys., 2008, 10, 2673
DOI: 10.1039/b718519g
The mutual arrangements of planar residue pairs in proteins have been investigated using the PDB database. The analysis reveals the thermodynamic importance of stacking in proteins.
Through-space interactions between parallel-offset arenes at the van der Waals distance: 1,8-diarylbiphenylene syntheses, structure and QM computations
Franco Cozzi, Rita Annunziata, Maurizio Benaglia, Kim K. Baldridge, Gerardo Aguirre, Jesús Estrada, Yongsak Sritana-Anant and Jay S. Siegel,
Phys. Chem. Chem. Phys., 2008, 10, 2686
DOI: 10.1039/b800031j
A combined NMR, X-ray and computational study of the interactions between parallel-offset arenes spaced at the van der Waals distance in two series of 1,8-diarylbiphenylenes featuring reference rings of opposite polarity is reported.
Ab initio study of substituent effects in the interactions of dimethyl ether with aromatic rings
Jay C. Amicangelo, Benjamin W. Gung, Daniel G. Irwin and Natalie C. Romano,
Phys. Chem. Chem. Phys., 2008, 10, 2695
DOI: 10.1039/b718722j
Substituent effects in the interaction energies of (CH3)2O–arene dimers in different conformations are investigated using ab initio methods.
A QM/MM study of fluoroaromatic interactions at the binding site of carbonic anhydrase II, using a DFT method corrected for dispersive interactions
Claudio A. Morgado, Ian H. Hillier, Neil A. Burton and Joseph J. W. McDouall,
Phys. Chem. Chem. Phys., 2008, 10, 2706
DOI: 10.1039/b715514j
Aromatic–fluoroaromatic interactions at the binding site of carbonic anhydrase II are studied by QM(DFT-D)/MM calculations.
Searching of potential energy curves for the benzene dimer using dispersion-corrected density functional theory
Prakash Chandra Jha, Zilvinas Rinkevicius, Hans Ågren, Prasenjit Seal and Swapan Chakrabarti,
Phys. Chem. Chem. Phys., 2008, 10, 2715
DOI: 10.1039/b717983a
We implemented the dispersion-corrected DFT method to produce potential energy curves of benzene dimers which are comparable to CCSD(T) results.
Structures and interaction energies of stacked graphene–nucleobase complexes
Jens Antony and Stefan Grimme,
Phys. Chem. Chem. Phys., 2008, 10, 2722
DOI: 10.1039/b718788b
A theoretical study of the intermolecular interactions between DNA nucleobases and their pairs with some polycyclic aromatic hydrocarbons of different sizes simulating a graphene sheet is presented. In addition to the given detailed energetic and structural information about adsorption properties, the question of cooperativity of -stacking and H-bonding on graphene is addressed.
Describing weak interactions of biomolecules with dispersion-corrected density functional theory
I-Chun Lin and Ursula Rothlisberger,
Phys. Chem. Chem. Phys., 2008, 10, 2730
DOI: 10.1039/b718594d
The DCACP approach is shown to reach an accuracy comparable with high-level ab initio methods for noncovalent interaction energies of biomolecules.
Physical origins of interactions in dimers of polycyclic aromatic hydrocarbons
Rafa Podeszwa and Krzysztof Szalewicz,
Phys. Chem. Chem. Phys., 2008, 10, 2735
DOI: 10.1039/b719725j
Dimers of several polycyclic aromatic hydrocarbons: naphthalene, anthracene and pyrene have been investigated by symmetry-adapted perturbation theory based on the density functional description of the monomers.
Benchmark database on isolated small peptides containing an aromatic side chain: comparison between wave function and density functional theory methods and empirical force field
Haydee Valdes, Kristýna Pluhá
ková, Michal Pitonák, Jan 
ezá and Pavel Hobza,
Phys. Chem. Chem. Phys., 2008, 10, 2747
DOI: 10.1039/b719294k
Non convalent interactions play a relevant role in isolated small peptides: assessment of different methodologies in comparison with CCSD(T) benchmark data.
Scope and limitations of the SCS-MP2 method for stacking and hydrogen bonding interactions
Rafa A. Bachorz, Florian A. Bischoff, Sebastian Höfener, Wim Klopper, Philipp Ottiger, Roman Leist, Jann A. Frey and Samuel Leutwyler,
Phys. Chem. Chem. Phys., 2008, 10, 2758
DOI: 10.1039/b718494h
The SCS-MP2 method cannot provide sufficient accuracy to replace CCSD(T) for intermolecular interactions where H-bonding and pi-stacking are competitive.
The interaction of carbohydrates and amino acids with aromatic systems studied by density functional and semi-empirical molecular orbital calculations with dispersion corrections
Raman Sharma, Jonathan P. McNamara, Rajesh K. Raju, Mark A. Vincent, Ian H. Hillier and Claudio A. Morgado,
Phys. Chem. Chem. Phys., 2008, 10, 2767
DOI: 10.1039/b719764k
Density functional theory (DFT-D) and semi-empirical (PM3-D) methods having an added dispersion correction have been used to study stabilising carbohydrate–aromatic and amino-acid pyrene interactions.
Probing the effects of heterogeneity on delocalized 
interaction energies
Desiree M. Bates, Julie A. Anderson, Ponmile Oloyede and Gregory S. Tschumper,
Phys. Chem. Chem. Phys., 2008, 10, 2775
DOI: 10.1039/b718720c
Dimers composed of benzene (Bz), 1,3,5-triazine (Tz), cyanogen (Cy) and diacetylene (Di) are used to examine the effects of heterogeneity at the molecular level and at the cluster level on stacking energies.
Competition between stacking and hydrogen bonding: theoretical study of the phenolAr cation and neutral complex and comparison to experiment
Jií 
erný, Xin Tong, Pavel Hobza and Klaus Müller-Dethlefs,
Phys. Chem. Chem. Phys., 2008, 10, 2780
DOI: 10.1039/b801460b
A 
complete
description of the geometry, relative energies, interaction energies and enthalpies of PhOHAr complexes.
Calculating stacking interactions in nucleic acid base-pair steps using spin-component scaling and local second order Møller–Plesset perturbation theory
J. Grant Hill and James A. Platts,
Phys. Chem. Chem. Phys., 2008, 10, 2785
DOI: 10.1039/b718691f
The stacking interaction energies for ten B-DNA base pair steps are computed with density fitting, local MP2 methods that avoid many-body terms, leading to new reference values for these complexes.
Controlled aggregation of adenine by sugars: physicochemical studies, molecular modelling simulations of sugar–aromatic CH– stacking interactions, and biological significance
Marc Maresca, Adel Derghal, Céline Carravagna, Séverine Dudin and Jacques Fantini,
Phys. Chem. Chem. Phys., 2008, 10, 2792
DOI: 10.1039/b802594k
Physicochemical and molecular modelling studies of adenine–sugar interactions reveal the higher stacking propensity of galactose compared with other sugars.
Computational comparison of the stacking interactions between the aromatic amino acids and the natural or (cationic) methylated nucleobases
Lesley R. Rutledge, Holly F. Durst and Stacey D. Wetmore,
Phys. Chem. Chem. Phys., 2008, 10, 2801
DOI: 10.1039/b718621e
The MP2/6-31G*(0.25) stacking interactions were investigated between the aromatic amino acids and ten common methylated nucleobases.
Computational characterization and modeling of buckyball tweezers: density functional study of concave–convex interactions
Yan Zhao and Donald G. Truhlar,
Phys. Chem. Chem. Phys., 2008, 10, 2813
DOI: 10.1039/b717744e
Two buckyball tweezers and their supramolecular complexes are investigated using recently developed density functionals (M06-L and M06-2X).
Non-standard base pairing and stacked structures in methyl xanthine clusters
Michael P. Callahan, Zsolt Gengeliczki, Nathan Svadlenak, Haydee Valdes, Pavel Hobza and Mattanjah S. de Vries,
Phys. Chem. Chem. Phys., 2008, 10, 2819
DOI: 10.1039/b719874d
We observed base pairing and stacking in isolated methylxanthine dimers by IR–UV double resonance spectroscopy and theoretical calculations.
N–H interactions in pyrroles: systematic trends from the vibrational spectroscopy of clusters
Ingo Dauster, Corey A. Rice, Philipp Zielke and Martin A. Suhm,
Phys. Chem. Chem. Phys., 2008, 10, 2827
DOI: 10.1039/b717823a
Raman and IR spectra complement each other in pyrrole dimers and trimers.
Experimental and theoretical determination of the accurate interaction energies in benzene–halomethane: the unique nature of the activated CH/ interaction of haloalkanes
Asuka Fujii, Kenta Shibasaki, Takaki Kazama, Ryousuke Itaya, Naohiko Mikami and Seiji Tsuzuki,
Phys. Chem. Chem. Phys., 2008, 10, 2836
DOI: 10.1039/b717053j
The activated CH/ interaction energies in benzene–halomethanes are precisely determined by the collaboration between laser spectroscopy and high-level ab initio calculations.
IR/UV spectra and quantum chemical calculations of Trp–Ser: Stacking interactions between backbone and indole side-chain
Thomas Häber, Kai Seefeld, Gernot Engler, Stefan Grimme and Karl Kleinermanns,
Phys. Chem. Chem. Phys., 2008, 10, 2844
DOI: 10.1039/b718710f
TrpSer has a compact folded structure with the serine residue stacked above the indole ring.
Fluorine substitution and nonconventional OH intramolecular bond: high-resolution UV spectroscopy and ab initio calculations of 2-(p-fluorophenyl)ethanol
Rosen Karaminkov, Sotir Chervenkov and Hans J. Neusser,
Phys. Chem. Chem. Phys., 2008, 10, 2852
DOI: 10.1039/b718974e
The lowest-energy conformer of a p-fluorinated neurotransmitter analogue, stabilised by an intramolecular hydrogen bond, is not noticeably affected when p-substituted by a strongly electronegative atom.
CH/ interactions in methane clusters with polycyclic aromatic hydrocarbons
Seiji Tsuzuki, Kazumasa Honda, Asuka Fujii, Tadafumi Uchimaru and Masuhiro Mikami,
Phys. Chem. Chem. Phys., 2008, 10, 2860
DOI: 10.1039/b718550b
Dispersion interaction controls the orientation of methane in the pryene–methane and naphthalene–methane clusters.
Back matter
Phys. Chem. Chem. Phys., 2008, 10, 2866
DOI: 10.1039/b806490n
Back cover
Phys. Chem. Chem. Phys., 2008, 10, 2867
DOI: 10.1039/b806491c
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