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Register a new userQM/MM Lineshape Simulation of the Hydrogen-bonded Uracil NH Stretching Vibration of the Adenine:Uracil Base Pair in CDCl$_3$
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A hybrid Car-Parrinello QM/MM molecular dynamics simulation has been carried out for the Watson-Crick base pair of 9-ethyl-8-phenyladenine and 1-cyclohexyluracil in deuterochloroform solution at room temperature. The resulting trajectory is analyzed putting emphasis on the N-H$...$N Hydrogen bond geometry. Using an empirical correlation between the $NN$-distance and the fundamental NH-stretching frequency, the time-dependence of this energy gap along the trajectory is obtained. From the gap-correlation function we determine the infrared absorption spectrum using lineshape theory in combination with a multimode oscillator model. The obtained average transition frequency and the width of the spectrum is in reasonable agreement with recent experimental data.
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Computational prediction of enzyme mechanism and protein function requires accurate physics-based models and suitable sampling. We discuss recent advances in large-scale quantum mechanical (QM) modeling of biochemical systems that have reduced the cost of high-accuracy models. Trade-offs between sampling and accuracy have motivated modeling with molecular mechanics (MM) in a multi-scale QM/MM or iterative approach. Limitations to both conventional density functional theory (DFT) and classical MM force fields remain for describing non-covalent interactions in comparison to experiment or wavefunction theory. Because predictions of enzyme action (i.e., electrostatics), free energy barriers, and mechanisms are sensitive to the protocol and embedding method in QM/MM, convergence tests and systematic methods for quantifying QM-level interactions are a needed, active area of development.
Analysis of the electron density distribution in clusters composed of hydrogen fluoride, water, and ammonia molecules, especially within the hydrogen-bond domains, reveals the existence of both sigma- and pi-binding between molecules. The sigma-kind density distribution determines the mutual orientation of molecules. A pi-system may be delocalized conjugated, which provides additional stabilization of molecular clusters. In those clusters where the sequence of hydrogen bonds is not planar, a peculiar kind of pi-conjugation exists. HF anion and H5O2 cation are characterized by quasi-triple bonds between the electronegative atoms. The most long-lived species stabilized by delocalized pi-binding are rings and open or closed hoops composed of fused rings. It is conjugated pi-system that determines cooperativity phenomenon.
Numerous molecular systems, including solutions, proteins, and composite materials, can be modeled using mixed-resolution representations, of which the quantum mechanics/molecular mechanics (QM/MM) approach has become the most widely used. However, the QM/MM approach often faces a number of challenges, including the slow sampling of the large configuration space for the MM part, the high cost of repetitive QM computations for changing coordinates of atoms in the MM surroundings, and a difficulty in providing a simple, qualitative interpretation of numerical results in terms of the influence of the molecular environment upon the active QM region. In this paper, we address these issues by combining QM/MM modeling with the methodology of bottom-up coarse-graining (CG) to provide the theoretical basis for a systematic quantum-mechanical/coarse-grained molecular mechanics (QM/CG-MM) mixed resolution approach. A derivation of the method is presented based on a combination of statistical mechanics and quantum mechanics, leading to an equation for the effective Hamiltonian of the QM part, a central concept in the QM/CG-MM theory. A detailed analysis of different contributions to the effective Hamiltonian from electrostatic, induction, dispersion and exchange interactions between the QM part and the surroundings is provided, serving as a foundation for a potential hierarchy of QM/CG-MM methods varying in their accuracy and computational cost. A relationship of the QM/CG-MM methodology to other mixed resolution approaches is also discussed.
Hydrogen-bonded mixtures with varying concentration are a complicated networked system that demands a detection technique with both time and frequency resolutions. Hydrogen-bonded pyridine-water mixtures are studied by a time-frequency resolved coherent Raman spectroscopic technique. Femtosecond broadband dual-pulse excitation and delayed picosecond probing provide sub-picosecond time resolution in the mixtures temporal evolution. For different pyridine concentrations in water, asymmetric blue versus red shifts (relative to pure pyridine spectral peaks) were observed by simultaneously recording both the coherent anti-Stokes and Stokes Raman spectra. Macroscopic coherence dephasing times for the perturbed pyridine ring modes were observed in ranges of 0.9 - 2.6 picoseconds for both 18 and 10 cm-1 broad probe pulses. For high pyridine concentrations in water, an additional spectral broadening (or escalated dephasing) for a triangular ring vibrational mode was observed. This can be understood as a result of ultrafast collective emissions from coherently excited ensemble of pairs of pyridine molecules bound to water molecules.
We present state-selective measurements on the NH$_2^{+}$ + H$^{+}$ and NH$^{+}$ + H$^{+}$ + H dissociation channels following single-photon double ionization at 61.5 eV of neutral NH$_{3}$, where the two photoelectrons and two cations are measured in coincidence using 3-D momentum imaging. Three dication electronic states are identified to contribute to the NH$_2^{+}$ + H$^{+}$ dissociation channel, where the excitation in one of the three states undergoes intersystem crossing prior to dissociation, producing a cold NH$_2^+$ fragment. In contrast, the other two states directly dissociate, producing a ro-vibrationally excited NH$_2^+$ fragment with roughly 1 eV of internal energy. The NH$^{+}$ + H$^{+}$ + H channel is fed by direct dissociation from three intermediate dication states, one of which is shared with the NH$_2^{+}$ + H$^{+}$ channel. We find evidence of autoionization contributing to each of the double ionization channels. The distributions of the relative emission angle between the two photoelectrons, as well as the relative angle between the recoil axis of the molecular breakup and the polarization vector of the ionizing field, are also presented to provide insight on both the photoionization and photodissociation mechanisms for the different dication states.
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