Concerning the deprotonation of the trimethylsulfonium ion by the dimethylsulfinyl anion

As shown by deuterium labelling experiments, the deprotonation of the trimethylsulfonium ion (1) by the dimsyl anion (8) is accompanied by extensive hydrogen exchange. This cannot be explained by an acid-base equilibrium between the trimethylsulfonium ion (1) and the dimsyl anion (8) on one side and dimethylsulfonium methylide (2) and DMSO on the other side, because for thermodynamic reasons this process is irreversible due to the limited life-time of 2. Therefore, the isotopic exchange that accompanies the deprotonation is an indicator of a more complex deprotonation process. It is suggested that in a kinetically controlled reaction, a proton of 1 is transferred to the O-atom of 8 rather than to the carbanionic centre. This means that instead of DMSO, its tautomer, hydroxy-methylsulfonium methylide (10), is obtained in the deprotonation process. Similarly, in the acid-base interaction between DMSO and its conjugate base 8, the formation of the DMSO tautomer 10 is kinetically favoured. The intermediate 10 produced in this way transfers a DMSO-derived proton to 1 when it intervenes in the back reaction 10 + 2→8 + 1. An alternative mechanism based on methyl group exchange between 1 and 8 could be excluded by a (13)C-labelling experiment. The hydrogen exchange according to the suggested scenario is taking place in competition with the reaction of dimethylsulfonium methylide (2) with electrophilic substrates. This explains the different degrees of isotopic exchange when compounds of different electrophilicities are used to scavenge 2 from the deprotonation-hydrogen distribution equilibria.     

The energy pump and the origin of the non-equilibrium flux of the dynamical systems and the networks

The global stability of dynamical systems and networks is still challenging to study. We developed a landscape and flux framework to explore the global stability. The potential landscape is directly linked to the steady state probability distribution of the non-equilibrium dynamical systems which can be used to study the global stability. The steady state probability flux together with the landscape gradient determines the dynamics of the system. The non-zero probability flux implies the breaking down of the detailed balance which is a quantitative signature of the systems being in non-equilibrium states. We investigated the dynamics of several systems from monostability to limit cycle and explored the microscopic origin of the probability flux. We discovered that the origin of the probability flux is due to the non-equilibrium conditions on the concentrations resulting energy input acting like non-equilibrium pump or battery to the system. Another interesting behavior we uncovered is that the probabilistic flux is closely related to the steady state deterministic chemical flux. For the monostable model of the kinetic cycle, the analytical expression of the probabilistic flux is directly related to the deterministic flux, and the later is directly generated by the chemical potential difference from the adenosine triphosphate (ATP) hydrolysis. For the limit cycle of the reversible Schnakenberg model, we also show that the probabilistic flux is correlated to the chemical driving force, as well as the deterministic effective flux. Furthermore, we study the phase coherence of the stochastic oscillation against the energy pump, and argue that larger non-equilibrium pump results faster flux and higher coherence. This leads to higher robustness of the biological oscillations. We also uncovered how fluctuations influence the coherence of the oscillations in two steps: (1) The mild fluctuations influence the coherence of the system mainly through the probability flux while maintaining the regular landscape topography. (2) The larger fluctuations lead to flat landscape and the complete loss of the stability of the whole system.     

Modeling the stability and the motion of DNA nucleobases on the gold surface

We simulate the structure and dynamics of the four DNA bases on the most stable gold surface. The experimental adsorption energies are reproduced to about 1 kcal mol(-1), and the existence of anchor points in the molecules is evidenced. The simulations also show that the bases drift on the gold surface with a degree of mobility that is not inversely proportional to the experimental (and calculated) desorption energies. When the same type of calculations is applied to pairs of bases it is seen that for at least two of them, namely GG and TT, there is a cooperative effect that increases their adsorption energy with respect to those of the single molecules. The molecular mobility on the surface is still present when a pair of interacting bases is considered.     

On the Nature of the Temperature-Induced Transition From the Molten Globule to the Unfolded State of Globular Proteins

In this paper we try to perform a thermodynamic analysis of the temperature-induced transition from the molten globule to the unfolded state of globular proteins. A series of calorimetric investigations showed that this process is not associated with an excess heat capacity absorption peak, and cannot be regarded as a first-order phase transition. This result contrasts with the well-established conclusion that the thermal unfolding of the native tertiary structure of globular proteins is a first-order phase transition. First, the theoretical approach developed by Ikegami is outlined to emphasize that a second-order or gradual transition induced by temperature is expected for globular proteins when the various secondary structure elements do not interact cooperatively. Secondly, a simple thermodynamic model is presented which, taking into account the independence of the secondary structure elements among each other, is able to rationalize the shape of the experimental DSC profiles.This revised version was published online in November 2005 with corrections to the Cover Date.     

On the application of the geometric approximation to the calculation of ring-current properties

Burrows' formula giving an upper bound for the error in the geometric approximation is applied to the calculation of the ring-current contribution to the diamagnetic anisotropies of conjugated molecules. It is also emphasized that this approximation is easily applied in practice.     

On the validity of the elastic model for the nematic surface anchoring energy

Abstract

The intrinsic uniform and non-uniform contributions to the anisotropic part of the surface energy are considered. Our analysis shows that the uniform part can be separated into an intrinsic and an extrinsic term. The first one is due to the nematic-nematic interaction only, whereas the second one is due to the nematic-substrate interaction. They are found to be of the same order of magnitude (≈1 erg cm²). The non-uniform part takes its origin from the spatial variation of the elastic constants. By means of a semi-microscopic model it is shown that, in the framework of perfect nematic order, the extrapolation length of the elastic origin is microscopic. On the contrary, if the spatial variation of the scalar order parameter is taken into account, simple calculations indicate that the extrapolation length is of the order of the coherence length in the nematic phase.     

Characterizing the mechanism of the double proton transfer in the formamide dimer

The double proton transfer in the formamide dimer is characterized computationally by combining density functional theory and ab initio methods. The intrinsic reaction coordinate (IRC) is obtained at the B3LYP level of theory. Energies of several points along the IRC are treated by the more rigorous focal point method to test the validity of the B3LYP functional. The reaction mechanism is examined in terms of the energy profile, the reaction force, the chemical potential, and the reaction electronic flux. The energy profile for the activation process of the formamide dimer to the imino ether product obtained with the B3LYP functional is in agreement with the results of the focal point method. Together with the reaction force analysis and the reaction electronic flux a precise assignment of the structural and electronic contributions to the activation barrier becomes possible. The results show that the reaction starts with a structural rearrangement, where the two dimers approach each other, and is followed by electronic changes before the system reaches the transition state. This electronic contribution to the activation barrier steers the activation process. After the transition state is reached, deviations of the B3LYP functional from the more accurate focal point energies become apparent, where the errors may be rationalized in terms of the treatment of exchange. The inconsistency could be assigned to the incapacity of the functional to describe delocalization effects over the whole system.     

On the validity of the elastic model for the nematic surface anchoring energy

The intrinsic uniform and non-uniform contributions to the anisotropic part of the surface energy are considered. Our analysis shows that the uniform part can be separated into an intrinsic and an extrinsic term. The first one is due to the nematic-nematic interaction only, whereas the second one is due to the nematic-substrate interaction. They are found to be of the same order of magnitude (≈1 erg cm²). The non-uniform part takes its origin from the spatial variation of the elastic constants. By means of a semi-microscopic model it is shown that, in the framework of perfect nematic order, the extrapolation length of the elastic origin is microscopic. On the contrary, if the spatial variation of the scalar order parameter is taken into account, simple calculations indicate that the extrapolation length is of the order of the coherence length in the nematic phase.     

On the theory underlying the Car-Parrinello method and the role of the fictitious mass parameter

The theory underlying the Car-Parrinello extended-Lagrangian approach to ab initio molecular dynamics (CPMD) is reviewed and reexamined using "heavy" ice as a test system. It is emphasized that the adiabatic decoupling in CPMD is not a decoupling of electronic orbitals from the ions but only a decoupling of a subset of the orbital vibrational modes from the rest of the necessarily coupled system of orbitals and ions. Recent work [J. Chem. Phys. 116, 14 (2002)] has pointed out that, due to the orbital-ion coupling that remains once adiabatic decoupling has been achieved, a large value of the fictitious mass mu can lead to systematic errors in the computed forces in CPMD. These errors are further investigated in the present work with a focus on those parts of these errors that are not corrected simply by rescaling the masses of the ions. It is suggested that any comparison of the efficiencies of Born-Oppenheimer molecular dynamics (BOMD) and CPMD should be performed at a similar level of accuracy. If accuracy is judged according to the average magnitude of the systematic errors in the computed forces, the efficiency of BOMD compares more favorably to that of CPMD than previous comparisons have suggested.     

Importance of the diamine reactant in the production of polyphosphonamides by the interfacial technique

The stirred interfacial polycondensation of phenylphosphonic dichloride and 1,6-hexanediamine has been studied as a function of several reaction variables. The reaction is rapid, being completed in less than 1 min. When organic solvent is varied and reactant molar ratio is varied with an excess of the acid chloride, yield is constant. When reactant molar ratio is varied polymer yield increases with increase in amine concentration. When reactant concentration is increased yield increases. With the addition of a soluble salt in the aqueous phase yield is increased. The above indicates that the diffusion of the amine to the reaction zone is of primary importance in determining polymerization rate and that the diffusion of the acid chloride is relatively unimportant. Polymer yield was found to be dependent on the pH of the amine in the aqueous phase. The observed trend is related to the apparent solubility of the amine in the aqueous phase such that the greater the apparent solubility of the amine, the less the polymer yield. Polymer molecular weight is found to be independent of reaction variables tested. Polymer was also formed from the condensation of phenylphosphonic dichloride with p-phenylenediamine, H₂N-D-NH₂ (where D is a 36-carbon hydrocarbon chain), 1,3-di-4-piperidylpropane, and 4-aminomethylpiperidine; phenyl phosphorodichloridate with 1,6-hexanediamine; chloromethyl phosphonic dichloride with 1,6-hexanediamine.     

All-trans-retinal is the chromophore bound to the photoreceptor of the alga Chlamydomonas reinhardtii.

Rhodopsin is the general name for a family of visual pigments that receive light and transmit this signal to the rest of an organism. Chlamydomonas reinhardtii is a unicellular eukaryote whose light-tracking system consists of a single eye. Through spectral studies of Chlamydomonas' reaction to light of different wavelengths (action spectroscopy), it has been shown in vivo that the photoreceptor of Chlamydomonas is functionally similar to vertebrate rhodopsin. We seek to characterize the photoreceptor further by identifying the molecule that is incorporated into the rhodopsin of Chlamydomonas forming the chromophore. High performance liquid chromatography analysis of organic extracts of retinaloximes from membrane fractions enriched in eye-spots and in cells virtually free of interfering carotenoids identified syn-all-trans as the existing retinaloxime isomer. We conclude that all-trans-retinal is the native molecule that is available to be incorporated into the rhodopsin of Chlamydomonas and therefore forms the functioning chromophore on binding.     

On the nature of the anhydride of the lactam of guanidinoglutaric acid

When glutamic acid is amidinated, guanidinoglutaric acid is formed. This is readily converted by boiling in water to its lactam [2-imino-4-oxo-5-(3′-propane acid) imidazolidine; GGAL]. In the present study GGAL is dehydrated to form a second lactam, anhydro-GGAL (AGGAL), with trifluoroacetic anhydride. The molecular weight of this compound was ascertained gravimetrically by precipitation with flavianic acid and by mass spectrography to be 153.14. UV and infrared spectra and hydrogen and ¹³C NMR studies determined its structure as an imidazolidine ring fused to a pyrrol ring, 2-imino-4-oxo-imidazolidine-1,5-pyrrolidone-8. On paper electrophoresis, GGAL traveled to the anode, while AGGAL traveled to the cathode. On TLC plates (butanol 60, H₂O 25, acetic 15), the R_f value of GGAL was 0.42 and that of AGGAL was 0.38, confirming that AGGAL was more basic than GGAL. The preparation of 1,3-di-(phenylcarbamoyl)-GGAL is also described.     

On the Neglect of the Philosophy of Chemistry

In this paper I present a historiography of the recent emergence of philosophy of chemistry. Special attention is given to the interest in this domain in Eastern Europe before the collapse of the USSR. It is shown that the initial neglect of the philosophy of chemistry is due to the unanimous view in philosophy and philosophy of science that only physics is a proper science (to put in Kant's words). More recently, due to the common though incorrect assumption that chemistry can in principle be reduced to physics, the neglect continued, even when interest in sciences such as biology and psychology entered more strongly in philosophy of science. It is concluded that chemistry is an autonomous science and is perhaps a more typical science than physics.     

Effect of the Hydration Shell on the Carbonyl Vibration in the Ala-Leu-Ala-Leu Peptide

The vibrational spectrum of the Ala-Leu-Ala-Leu peptide in solution, computed from first-principles simulations, shows a prominent band in the amide I region that is assigned to stretching of carbonyl groups. Close inspection reveals combined but slightly different contributions by the three carbonyl groups of the peptide. The shift in their exact vibrational signature is in agreement with the different probabilities of these groups to form hydrogen bonds with the solvent. The central carbonyl group has a hydrogen bond probability intermediate to the other two groups due to interchanges between different hydrogen-bonded states. Analysis of the interaction energies of individual water molecules with that group shows that shifts in its frequency are directly related to the interactions with the water molecules in the first hydration shell. The interaction strength is well correlated with the hydrogen bond distance and hydrogen bond angle, though there is no perfect match, allowing geometrical criteria for hydrogen bonds to be used as long as the sampling is sufficient to consider averages. The hydrogen bond state of a carbonyl group can therefore serve as an indicator of the solvent’s effect on the vibrational frequency.     

The computation of the representation matrices of the generators of the unitary group

A method is presented for the efficient computation of the representation matrices of the unitary group, U(n) in the Gelfand—Tsetlin basis (corresponding to the usual spin-symmetry adapted basis for an N electron CI). The present scheme is conceptually and computationally attractive in that it is formulated directly in terms of Weyl tableaux and also that it permits simultaneous basis vector generation and matrix element evaluation. In addition the basis vectors are ordered so that subsequent restriction to the three dimensional rotation group is facilitated. An illustrative example is also presented.Taken in part from a thesis submitted to the University of London in partial fulfilment of the requirements for the degree of PhD.     

Features of the ESI mechanism that affect the observation of multiply charged noncovalent protein complexes and the determination of the association constant by the titration method

Several factors, attributable to the ESIMS mechanism, that can affect the assumptions of the titration method are examined: (1) The assumption that the concentrations in solution of the protein P, the ligand L, and the complex PL are proportional to the respective ion intensities observed with ESIMS, is examined with experiments in which ion intensities of two non-interacting proteins are compared with the respective concentrations. The intensities are found to be approximately proportional to the concentrations. The proportionality factors are found to increase as the mass of the protein is decreased. Very small proteins have much higher intensities. The results suggest that it is preferable to use only the intensity ratio of PL and P, whose masses are very close to each other when L is small, to determine the association constant KA in solution. (2) From the charge residue model (CRM) one expects that the solution will experience a very large increase of concentration due to evaporation of the precursor droplets, before the proteins P and PL are produced in the gas phase. This can shift the equilibrium in the droplets: P + L = PL, towards PL. Analysis of the droplet evaporation history shows that such a shift is not likely, because the time of droplet evolution is very short, only several micros, and the equilibrium relaxation time is much longer. (3) The droplet history shows that unreacted P and L can be often present together in the same droplet. On complete evaporation of such droplets L will land on P leading to PL and this effect will lead to values of KA that are too high. However, it is argued that mostly accidental, weakly bonded, complexes will form and these will dissociate in the clean up stages (heated transfer capillary and CAD region). Thus only very small errors are expected due to this cause. (4) Some PL complexes may have bonding that is too weak in the gas phase even though they have KA values in solution that predict high solution PL yields. In this case the PL complexes may decompose in the clean up stages and not be observed with sufficient intensity in the mass spectrum. This will lead to KA values that are too low. The effect is expected for complexes that involve significant hydrophobic interaction that leads to high stability of the complex in solution but low stability in the gas phase. The titration method is not suited for such systems.     

An improvement of the resolution of the identity approximation for the formation of the Coulomb matrix

A straightforward modification of the resolution of the identity (RI) approximation to the Coulomb interaction is described. In the limit of basis sets that are dominated by high angular momentum functions the observed speedups in realistic test systems reach a factor of 2 compared to the standard RI algorithm, and a factor of up to 300 compared to the standard algorithm to form the Coulomb matrix. More moderate savings on the order of 0-20% are obtained for the more commonly used smaller basis sets. A series of test calculations is reported to illustrate the efficiency of the algorithm.     

On the origin of the redshift of the OH stretch in Ice Ih: evidence from the momentum distribution of the protons and the infrared spectral density

Recent measurements of the momentum distribution in water and ice have shown that the proton is in a considerably softer potential in ice Ih than in water or the free monomer. This is broadly consistent with the large red shift observed in the vibrational spectrum. We show that existing water models, which treat the intramolecular potential as unchanged by the hydrogen bonding are unable to reproduce the momentum distribution. In addition, even if they can substantially explain the red shift they are unable to explain the large increase in intensity observed in the infrared spectrum in going from the monomer to ice Ih. We show that the inclusion of a bond dipole derivative term is essential to explain the observed intensities in the infrared spectrum. Though this term is partially responsible for the softening of the effective potential of the proton we show that best agreement with the observed momentum distribution requires a further softening of the harmonic component of the intramolecular potential. We introduce an efficient normal-mode molecular dynamics algorithm for calculating the momentum distribution with path-integrals.     

On the Nature of the Positronic Bond

Recently it has been proposed that the positron, the anti-particle analog of the electron, is capable of forming an anti-matter bond in a composite system consists of two hydride anions and a positron [Angew. Chem. Int. Ed. 57 , 8859–8864 (2018)]. In order to dig into the nature of this novel bond the newly developed multi-component quantum theory of atoms in molecules (MC-QTAIM) is applied to this positronic system. The topological analysis reveals that this species is composed of two atoms in molecules, each containing a proton and half of the electronic and the positronic populations. Further analysis elucidates that the electron exchange phenomenon is virtually non-existent between the two atoms and no electronic covalent bond is conceivable in between. On the other hand, it is demonstrated that the positron density enclosed in each atom is capable of stabilizing interactions with the electron density of the neighboring atom. This electrostatic interaction suffices to make the whole system bonded against all dissociation channels. Thus, the positron indeed acts like an anti-matter glue between the two atoms.     

Cluster expansion for the energy of the many-electron atom in the nth order of the perturbation theory

A cluster expansion for the nth order correction to the energy of a many-electron atom is derived. A possible application to the calculation of the third order correction to the energy is considered.