Electron capture dissociation of weakly bound polypeptide polycationic complexes

We have previously reported that, in electron capture dissociation (ECD), rupture of strong intramolecular bonds in weakly bound supramolecular aggregates can proceed without dissociation of weak intermolecular bonds. This is now illustrated on a series of non-specific peptide-peptide dimers as well as specific complexes of modified glycopeptide antibiotics with their target peptide. The weak nature of bonding is substantiated by blackbody infrared dissociation, low-energy collisional excitation and force-field simulations. The results are consistent with a non-ergodic ECD cleavage mechanism.     

Anharmonicity of weakly bound M(+)-H2 complexes

The anharmonicity of weakly bound complexes is studied using the vibrational self-consistent field (VSCF) approach for a series of metal cation dihydrogen (M(+)-H(2)) complexes. The H-H stretching frequency shifts of M(+)-H(2) (M(+) = Li(+), Na(+), B(+), and Al(+)) complexes are calculated with the coupled-cluster method including all single and double excitations with perturbative triples (CCSD(T)) level of theory with the cc-pVTZ basis set. The calculated H-H stretching frequency of Li(+)-H(2), B(+)-H(2), Na(+)-H(2), and Al(+)-H(2) is red-shifted by 121, 202, 74, and 62 cm(-1), respectively, relative to that of unbound H(2). The calculated red shifts and their trends are in good agreement with the available experimental and previously calculated data. Insight into the observed trends is provided by symmetry adapted perturbation theory (SAPT).     

On the spectroscopic manifestations of weakly bound complexes in rarefied gases

A considerable fraction of weakly bound complexes is shown to occupy states metastable with respect to spontaneous decay, even at normal temperature in an equilibrium gas of moderate density. Collisionless decay of molecules results in anomalous broadening of spectral lines of hydrogen-bonded or van der Waals complexes.     

Some observations on the stereospecificity of weakly bound complexes of organic molecules

Vinyl bromide-benzene/p-xylene and acrylonitrile-benzene/p-xylene complexes have been studied by measuring the ¹H chemical shifts induced in the vinyl protons by the aromatic molecules. Evidence is presented that indicates that the complexes are 1:1, and values for the equilibrium quotient, K_x, and the full induced shift Δ_c, are deduced for each proton; similar values of K_x are obtained for each of the three viny] protons. It is shown that the molecular interactions are specific. However, the complexes cannot be considered to have fixed geometry, but molecules involved take up a variety of relative orientations.     

Rotational predissociation of extremely weakly bound atom-molecule complexes produced by Feshbach resonance association

We study the rotational predissociation of atom-molecule complexes with very small binding energy. Such complexes can be produced by Feshbach resonance association of ultracold molecules with ultracold atoms. Numerical calculations of the predissociation lifetimes based on the computation of the energy dependence of the scattering matrix elements become inaccurate when the binding energy is smaller than the energy width of the predissociating state. We derive expressions that represent accurately the predissociation lifetimes in terms of the real and imaginary parts of the scattering length and effective range for molecules in an excited rotational state. Our results show that the predissociation lifetimes are the longest when the binding energy is positive, i.e., when the predissociating state is just above the excited state threshold.     

Molecular dynamics with quantum statistics: time correlation functions and weakly bound nano-clusters

An account of recent developments in the study of molecular dynamics with the inclusion of quantum exchange effects is presented. Approaches for quantum dynamical calculations are reviewed and the determination of time correlation functions is a special point of focus. It is shown that the exact basis set techniques can be used to perform highly accurate calculations but are restricted to relatively small systems since computational cost scales exponentially with system size. Alternate formulations can be introduced to circumvent this problem, and semi-classical initial value representation and Feynman path centroid approaches are considered. It is then showed that from a practical point of view, for complex bosonic systems such as doped helium clusters, Quantum Monte Carlo techniques can currently be used for the calculation of quantities of experimental interest. A perspective on future prospects for the calculation of real time correlation functions of bosonic nano-scale systems is presented     

Fusion of weakly bound nuclei

We discuss the effect of the break-up of weakly bound nuclei on the fusion cross section of these projectiles with light, medium and heavy mass targets, at energies close to the Coulomb barrier. The discussion is based mostly on data obtained by our group in collaborative experiments. We also show that the break-up process at near and sub-barrier energies is responsible for the vanishing of the usual threshold anomaly of the optical potential.     

Excited States of weakly bound bosonic clusters: discrete variable representation and quantum Monte Carlo

We compare two approaches for the accurate calculation of the energy levels of weakly bound boson trimers. The first approach is based on correlation function Monte Carlo employing optimized trial functions, while the second approach is based on the discrete variable representation. A trimer with atoms of half the mass of neon is used as a test problem for benchmark calculations. The two approaches yield identical results, within error bars, for all the J = 0 energy levels below the dissociation threshold. The relative merits of the two techniques are discussed, and a perspective is given for extension to larger clusters.     

Classical and quantum mechanical infrared echoes from resonantly coupled molecular vibrations

The nonlinear response function associated with the infrared vibrational echo is calculated for a quantum mechanical model of resonantly coupled, anharmonic oscillators at zero temperature. The classical mechanical response function is determined from the quantum response function by setting variant Planck's over 2pi-->0, permitting the comparison of the effects of resonant vibrational coupling among an arbitrary number of anharmonic oscillators on quantum and classical vibrational echoes. The quantum response function displays a time dependence that reflects both anharmonicity and resonant coupling, while the classical response function depends on anharmonicity only through a time-independent amplitude, and shows a time dependence controlled only by the resonant coupling. In addition, the classical response function grows without bound in time, a phenomenon associated with the nonlinearity of classical mechanics, and absent in quantum mechanics. This unbounded growth was previously identified in the response function for a system without resonant vibrational energy transfer, and is observed to persist in the presence of resonant coupling among vibrations. Quantitative agreement between classical and quantum response functions is limited to a time scale of duration inversely proportional to the anharmonicity.     

Accurate prediction of the energetics of weakly bound complexes using the machine learning method kriging

Structural Chemistry - Here, we extend the system energy prediction approach used in the force field FFLUX (Maxwell et al. Theor Chem Acc 135:195, 2016) to complexes bound by weak intermolecular...     

Water induced weakly bound electrons in DNA

We have studied the effect of humidity on the electronic properties of DNA base pairs. We found that the hydrogen links of the nucleobases with water molecules lead to a shift of the pi electron density from carbon atoms to nitrogen atoms and can change the symmetry of the wave function for some nucleobases. As a result, the orbital energies are shifted which leads to a decrease in the potential barrier for the hole transfer between the G-C and A-T pairs from 0.7 eV for the dehydrated case to 0.123 eV for the hydrated. More importantly, the pi electron density redistribution activated by hydration is enhanced by the intrastrand interactions. This leads to a modification of the nucleobase chemical structures from the covalent type to a resonance structure with separated charges, where some pi electrons are not locked up into the covalent bonds. Within the (G-C)(2) sequences, there is overlapping of the electronic clouds of such unlocked electrons belonging to the stacked guanines, that significantly increases the electron coupling between them to V(DA)=0.095 eV against the V(DA)=0.025 eV for the dehydrated case. Consequently, the charge transfer between two guanines within the (G-C)(2) sequences is increased by 250 times due to hydration. The presence of nonbonded electrons suppress the band gap up to approximately 3.0 eV, that allows us to consider DNA as a narrow band gap semiconductor.     

Lewis acid-base interactions in weakly bound formaldehyde complexes with CO2, HCN, and FCN: considerations on the cooperative H-bonding effects

Ab initio quantum chemistry calculations reveal that HCN and mainly FCN can form Lewis acid-base complexes with formaldehyde associated with cooperative H bonds, as first noticed by Wallen et al. (Blatchford, M. A.; Raveendran, P.; Wallen, S. L. J. Am. Chem. Soc. 2002, 124, 14818-14819) for CO2-philic materials under supercritical conditions. The present results, obtained with MP2(Full)/aug-cc-pVDZ calculations, show that the degeneracy of the nu(2) mode in free HCN or FCN is removed upon complexation in the same fashion as that of CO2. The splitting of these bands along with the electron structure analysis provides substantial evidence of the interaction of electron lone pairs of the carbonyl oxygen with the electron-deficient carbon atom of the cyanides. Also, this work investigates the role of H bonds acting as additional stabilizing interactions in the complexes by performing the energetic and geometric characterization.     

Dynamics and counterion-dependence of the structures of weakly bound Ag+-P4S3 complexes

In an earlier publication (J. Am. Chem. Soc. 2002 , 124, 7111) we showed that polymeric cationic [Ag(P₄S₃)_n]⁺ complexes (n=1, 2) are accessible if partnered with a suitable weakly coordinating counterion of the type [Al(OR^F)₄]^? (OR^F: poly‐ or perfluorinated alkoxide). The present work addresses the following questions that could not be answered in the initial report: How many P₄S₃ cages can be bound to a Ag⁺ ion? Why are these complexes completely dynamic in solution in the ³¹P NMR experiments? Can these dynamics be frozen out in a low‐temperature ³¹P MAS NMR experiment? What are the principal binding sites of the P₄S₃ cage towards the Ag⁺ ion? What are likely other isomers on the [Ag(P₄S₃)_n]⁺ potential energy surface? Counterion influence: Reactions of P₄S₃ with Ag[Al{OC(CH₃)(CF₃)₂}₄] (Ag[hftb]) and Ag[{(CF₃)₃CO}₃Al‐F‐Al{OC(CF₃)₃)}₃] (Ag[al‐f‐al]) gave [(P₄S₃)Ag[hftb]]_∞ ( 7 ) as a molecular species, whereas [Ag₂(P₄S₃)₆]²⁺[al‐f‐al]^?₂ ( 8 ) is an isolated 2:1 salt. We suggest that a maximum of three P₄S₃ cages may be bound on average to an Ag⁺ ion. Only isolated dimeric dications are formed with the largest cation, but polymeric species are obtained with all other smaller aluminates. Thermodynamic Born–Haber cycles, DFT calculations, as well as solution NMR and ESI mass spectrometry indicate that 8 exhibits an equilibrium between the dication [Ag₂(P₄S₃)₆]²⁺ (in the solid state) and two [Ag(P₄S₃)₃]⁺ monocations (in the gas phase and in solution). Dynamics: ³¹P MAS NMR spectroscopy showed these solid adducts to be highly dynamic, to an extent that the ²J_P,P coupling within the cages could be resolved (J‐res experiment). This is supported by DFT calculations, which show that the extended PES of [Ag(P₄S₃)_n]⁺ (n=1–3) and [Ag₂(P₄S₃)₂]⁺ is very flat. The structures of α‐ and γ‐P₄S₃ were redetermined. Their variable‐temperature ³¹P MAS NMR spectra are discussed jointly with those of all four currently known [Ag(P₄S₃)_n]⁺ adducts with n=1, 2, and 3.     

Classical and quantum dynamical regimes in the bound space projected dynamics of strongly driven H Rydberg atoms

The bound space projected dynamics of the one dimensional model of H Rydberg atoms subjected to strong microwave radiation exhibits three dynamical regimes:(i) perturbatively localized,(ii) chaotic,(iii) external field dominated. This classification holds classically as well as quantum mechanically. The spectral properties of the bound space projected dipole operator dominating regime(iii) are studied analytically. A semiclassical analysis shows that its eigenfunctions, projected on the unperturbed basis states |n〉 of the one dimensional model, decay liken ^?7/3.     

Classical and quantum mechanical calculations of conformational probability density distributions. Two-rotor molecules

In order to study the dynamical structure of a two-rotor molecule, such as acetone, as a function of temperature, conformational probability density distributions are computed by using three different approaches: the so-called current approach, the classical approach, and the quantum mechanical oscillator approach. It is found that the three procedures yield comparable results, at least at normal temperature (25°C), although the current and, especially, the classical approaches give rise to too sharp distributions when compared with the quantum mechanical results. Owing to its simplicity, the current approach may be used advantageously, and it is easily extendible to many-rotor systems. Finally, it is verified that deuteration does not affect appreciably the conformation.     

Classical theory of vibration energy transfer in collinear collisions

Classical theory of collisions is cast in a form which also includes the uncertainty principle. This theory is used for analyzing the vibration energy transfer in the collinear collision which approximates the He-H₂ system. The results are compared with the quantum calculations and several classical and semiclassical approaches. Very good agreement with quantum theory is found, for all the parameters investigated.