Comment on “A stationary‐wave model of enzyme catalysis” by Carlo Canepa

Energy barriers for enzyme‐catalyzed reactions calculated with quantum mechanics/molecular mechanics (QM/MM) and empirical valence bond (EVB) methods can be in excellent agreement with activation energies derived from experiments, supporting the applicability of transition state theory for enzymic reactions. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2011     

Conformational analysis of cycloheptane,oxacycloheptane, 1,2‐dioxacycloheptane, 1,3‐dioxacycloheptane,and 1,4‐dioxacycloheptane

The conformational analysis of cycloheptane (1), oxacycloheptane (2), 1,2‐dioxacycloheptane (3), 1,3‐dioxacycloheptane (4), and 1,4‐dioxacycloheptane (5) has been carried out using B3LYP, CCD, CCSD, and QCISD with the 6‐311+G(d,p) and cc‐pVDZ basis sets. The twist chair conformers are predicted to be lower in energy than their corresponding boat and chair conformations. All levels of theory predict (4) to be lower in energy than (3) and (5). CCSD predicts remarkably similar activation barriers for the conformational interconversion of the twist chair conformers to their corresponding boat conformers. Small barriers to pseudorotation are also predicted. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2008     

Comment on “chiral discrimination in spherical tops”

The difference in the interaction energies of two co-rotating, and two counter-rotating, spherical-top molecules is of second order in the rotational constant B, and not first order. Co- and counter-spinning alkali-metal atoms exhibit a similar but numerically much larger “chiral” discrimination.     

Comment on “Realization of Lewis Basic Sodium Anion in the NaBH3− Cluster”

We challenge the interpretation of the chemical bond in NaBH₃^? proposed by Liu et al. We argue that NaBH₃^? has an electron‐sharing Na?BH₃^? covalent bond rather than a dative bond Na^?→BH₃.     

Comment on “The Interplay between Steric and Electronic Effects in SN2 Reactions”

We respond to a paper by Fernández, Frenking, and Uggerud (FFU: Chem. Eur. J. 2009 , 15, 2166) in which they conclude that not steric hindrance but reduced electrostatic attraction and reduced orbital interactions are responsible for the S_N2 barrier, in particular in the case of more highly substituted substrates, for example, F^? + C(CH₃)₃F. We disagree with this conclusion, which we show is the result of neglecting geometry relaxation processes that are induced by increased Pauli repulsion in the sterically congested S_N2 transition state.     

Reply to “Comment on Aromatic‐Backbone Interactions in Model α‐Helical Peptides”

In response to Van Mourik's comments on our paper (J Comput Chem 2007, 28, 1208.) we present an extended version of our rotation method. We also prove that intramolecular interaction energies as well the basis set superposition errors calculated with our rotation method are comparable with those obtained by the counterpoise method of Boys and Bernardi (Mol Phys 1970, 19, 533). In intramolecular interaction energy calculations, if the interacting groups are in proximity, our rotation method is recommended to avoid artificial interactions, which can be induced by fragmentation. © 2007 Wiley Periodicals, Inc.J Comput Chem, 2008     

Free energy calculations,enhanced by a gaussian ansatz,for the “chemical work” distribution

The evaluation of the free energy is essential in molecular simulation because it is intimately related with the existence of multiphase equilibrium. Recently, it was demonstrated that it is possible to evaluate the Helmholtz free energy using a single statistical ensemble along an entire isotherm by accounting for the “chemical work” of transforming each molecule, from an interacting one, to an ideal gas. In this work, we show that it is possible to perform such a free energy perturbation over a liquid vapor phase transition. Furthermore, we investigate the link between a general free energy perturbation scheme and the novel nonequilibrium theories of Crook's and Jarzinsky. We find that for finite systems away from the thermodynamic limit the second law of thermodynamics will always be an inequality for isothermal free energy perturbations, resulting always to a dissipated work that may tend to zero only in the thermodynamic limit. The work, the heat, and the entropy produced during a thermodynamic free energy perturbation can be viewed in the context of the Crooks and Jarzinsky formalism, revealing that for a given value of the ensemble average of the “irreversible” work, the minimum entropy production corresponded to a Gaussian distribution for the histogram of the work. We propose the evaluation of the free energy difference in any free energy perturbation based scheme on the average irreversible “chemical work” minus the dissipated work that can be calculated from the variance of the distribution of the logarithm of the work histogram, within the Gaussian approximation. As a consequence, using the Gaussian ansatz for the distribution of the “chemical work,” accurate estimates for the chemical potential and the free energy of the system can be performed using much shorter simulations and avoiding the necessity of sampling the computational costly tails of the “chemical work.” For a more general free energy perturbation scheme that the Gaussian ansatz may not be valid, the free energy calculation can be expressed in terms of the moment generating function of the “chemical work” distribution. © 2014 Wiley Periodicals, Inc.     

Reply to “Comment on the Comparative Use of the Electron Density and Its Laplacian”

In our reply to the preceding comment by Richard Bader we show that the statements of the author are not justified and that he contradicts his own previous work.     

“Precipitation on Nanoparticles”: Attractive Intermolecular Interactions Stabilize Specific Ligand Ratios on the Surfaces of Nanoparticles

Confining organic molecules to the surfaces of inorganic nanoparticles can induce intermolecular interactions between them, which can affect the composition of the mixed self‐assembled monolayers obtained by co‐adsorption from solution of two different molecules. Two thiolated ligands (a dialkylviologen and a zwitterionic sulfobetaine) that can interact with each other electrostatically were coadsorbed onto gold nanoparticles. The nanoparticles favor a narrow range of ratios of these two molecules that is largely independent of the molar ratio in solution. Changing the solution molar ratio of the two ligands by a factor of 5 000 affects the on‐nanoparticle ratio of these ligands by only threefold. This behavior is reminiscent of the formation of insoluble inorganic salts (such as AgCl), which similarly compensate positive and negative charges upon crystallizing. Our results pave the way towards developing well‐defined hybrid organic–inorganic nanostructures.     

Microfluidics in the “Open Space” for Performing Localized Chemistry on Biological Interfaces

Local interactions between (bio)chemicals and biological interfaces play an important role in fields ranging from surface patterning to cell toxicology. These interactions can be studied using microfluidic systems that operate in the “open space”, that is, without the need for the sealed channels and chambers commonly used in microfluidics. This emerging class of techniques localizes chemical reactions on biological interfaces or specimens without imposing significant “constraints” on samples, such as encapsulation, pre‐processing steps, or the need for scaffolds. They therefore provide new opportunities for handling, analyzing, and interacting with biological samples. The motivation for performing localized chemistry is discussed, as are the requirements imposed on localization techniques. Three classes of microfluidic systems operating in the open space, based on microelectrochemistry, multiphase transport, and hydrodynamic flow confinement of liquids are presented.     

Synthesis,purification, and characterization of “perfect” star polymers via “Click” coupling

The copper (I)‐catalyzed azide‐alkyne cycloaddition “click” reaction was successfully applied to prepare well‐defined 3, 6, and 12‐arms polystyrene and polyethylene glycol stars. This study focused particularly on making “perfect” star polymers with an exact number of arms, as well as developing techniques for their purification. Various methods of characterization confirmed the star polymers high purity, and the structural uniformity of the generated star polymers. In particular, matrix‐assisted laser desorption ionization‐time‐of‐flight mass spectrometry revealed the quantitative transformation of the end groups on the linear polymer precursors and confirmed their quantitative coupling to the dendritic cores to yield star polymers with an exact number of arms. In addition to preparing well‐defined polystyrene and poly(ethylene glycol)homopolymer stars, this technique was also successfully applied to amphiphilic, PCL‐b‐PEG star polymers. © 2011 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2012     

Comment on “Bad Language”: Resolving some Ambiguities about Chirality

In this comment on the Essay entitled “Bad Language” by Dunitz I add new elements which enlighten the discussion. I hope that they contribute to suppress ambiguities and preconceived ideas about chirality.     

Silica Scaffold with Shifted “Plumber's Nightmare” Networks and their Interconversion into Diamond Networks

Bicontinuous structures with hyperbolic surfaces have been found in a variety of natural and synthetic systems. Herein, we present the synthesis and structural study of the shifted double‐primitive networks, which is known as the rare “plumber's nightmare”, and its interconversion into diamond networks. The scaffold was prepared by self‐assembly of an amphiphilic triblock terpolymer and silica precursors. Electron crystallography indicates that the structure consists of two sets of hollow primitive networks shifted along 0.75b and 0.25c axes ( 2pcu (38 63), space group Cmcm ). The “side‐by‐side” epitaxial relationship of the primitive and diamond networks with unit cell ratio of about 1.30 has been directly observed with the intermediate surface related to the rPD family. These results bring new insights to previous theoretical studies.     

Comment “On the quadratic reaction path evaluated in a reduced potential energy surface model and the problem to locate transition states” [by J. M. Anglada,E. Besalú, J. M. Bofill,and R. Crehuet,J Comput Chem 2001, 22, 4, 387–406]

The difference is explained between steepest ascent and following a reduced gradient (distinguished coordinate method) for the location of saddle points. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 537–540, 2001