The accurate prediction of protein-ligand binding free energies is a primary objective in computer-aided drug design. The solvation free energy of a small molecule provides a surrogate to the desolvation of the ligand in the thermodynamic process of protein-ligand binding. Here, we use explicit solvent molecular dynamics free energy perturbation to predict the absolute solvation free energies of a set of 239 small molecules, spanning diverse chemical functional groups commonly found in drugs and drug-like molecules. We also compare the performance of absolute solvation free energies obtained using the OPLS_2005 force field with two other commonly used small molecule force fields-general AMBER force field (GAFF) with AM1-BCC charges and CHARMm-MSI with CHelpG charges. Using the OPLS_2005 force field, we obtain high correlation with experimental solvation free energies (R(2) = 0.94) and low average unsigned errors for a majority of the functional groups compared to AM1-BCC/GAFF or CHelpG/CHARMm-MSI. However, OPLS_2005 has errors of over 1.3 kcal/mol for certain classes of polar compounds. We show that predictions on these compound classes can be improved by using a semiempirical charge assignment method with an implicit bond charge correction.

Although valence electrons are clearly delocalized in molecular bonding frameworks, chemists and physicists have long debated the question of whether the core vacancy created in a homonuclear diatomic molecule by absorption of a single x-ray photon is localized on one atom or delocalized over both. We have been able to clarify this question with an experiment that uses Auger electron angular emission patterns from molecular nitrogen after inner-shell ionization as an ultrafast probe of hole localization. The experiment, along with the accompanying theory, shows that observation of symmetry breaking (localization) or preservation (delocalization) depends on how the quantum entangled Bell state created by Auger decay is detected by the measurement.

Abstract.The photon-ion merged-beams technique has been employed at the new PhotonIon spectrometer at PETRA III (PIPE) for measuring multiple photoionization of Xe Absolute cross sections for 3d photoionization of Xe q+ ions (1 ≤ q ≤ 5) 2

Helium shows fascinating quantum phenomena unseen in any other element. In its liquid phase, it is the only known superfluid. The smallest aggregates of helium, the dimer (He 2 ) and the trimer (He 3 ) are, in their predicted structure, unique natural quantum objects. While one might intuitively expect the structure of 4 He 3 to be an equilateral triangle, a manifold of predictions on its shape have yielded an ongoing dispute for more than 20 years. These predictions range from 4 He 3 being mainly linear to being mainly an equilateral triangle. Here we show experimental images of the wave functions of 4 He 3 and 3 He 4 He 2 obtained by Coulomb explosion imaging of mass-selected clusters. We propose that 4 He 3 is a structureless random cloud and that 3 He 4 He 2 exists as a quantum halo state.

During the last 15 years a novel decay mechanism of excited atoms has been discovered and investigated. This so called "Interatomic Coulombic Decay" (ICD) involves the chemical environment of the electronically excited atom: the excitation energy is transferred (in many cases over long distances) to a neighbor of the initially excited particle usually ionizing that neighbor. It turned out that ICD is a very common decay route in nature as it occurs across van-der-Waals and hydrogen bonds. The time evolution of ICD is predicted to be highly complex, as its efficiency strongly depends on the distance of the atoms involved and this distance typically changes during the decay. Here we present the first direct measurement of the temporal evolution of ICD using a novel experimental approach.In 1997 Cederbaum and coworkers realized that the presence of loosely bound atomic or molecular neighbors opens a new relaxation pathway to an electronically excited atom or molecule. In the decay mechanism they proposed -termed Intermolecular Coulombic Decay (ICD) -the excited particle relaxes efficiently by transferring its excitation energy to a neighboring atom or molecule [1]. As a consequence the atom or molecule receiving the energy emits an electron of low kinetic energy. The occurrence of ICD was proven in experiments in the mid 2000s by means of electron spectroscopy [2] and multi-coincidence techniques [3]. Since that time a wealth of experimental and theoretical studies have shown that ICD is a rather common decay path in nature, as it occurs almost everywhere in loosely bound matter. It has been proven to occur after a manifold of initial excitation schemes such as innervalence shell ionization, after Auger cascades [4,5], resonant excitation [6,7], shakeup ionization [8] and resonant Auger decay. ICD has also been observed in many systems as rare gas clusters [9], even on surfaces [10] and small water droplets [11,12]. The latter suggested that ICD might play a role in radiation damage of living tissue [13], as it creates low energy electrons, which are known to be genotoxic [14,15]. More recently that scenario was reversed as it was suggested to employ ICD in treatment of tagged malignant cells [16]. Apart from these potential applications the elementary process of ICD is under investigation, as the decay is predicted to have a highly complex temporal * Electronic address: jahnke@atom.uni-frankfurt.de behavior. The efficiency and thus the decay times of ICD depend strongly on the size of the system, i.e. the number of neighboring particles and the distance between them and the excited particle. However, even for most simple possible model systems consisting of only two atoms the temporal evolution of the decay is non-trivial and predicted theoretically to exhibit exciting physics [17]: as ICD happens on a timescale that is fast compared to relaxation via photon emission, but comparable to the typical times of nuclear motion in the system, the dynamics of the decay is complicated and so far only theoretically explored...

Quantum tunneling is a ubiquitous phenomenon in nature and crucial for many technological applications. It allows quantum particles to reach regions in space which are energetically not accessible according to classical mechanics. In this "tunneling region," the particle density is known to decay exponentially. This behavior is universal across all energy scales from nuclear physics to chemistry and solid state systems. Although typically only a small fraction of a particle wavefunction extends into the tunneling region, we present here an extreme quantum system: a gigantic molecule consisting of two helium atoms, with an 80% probability that its two nuclei will be found in this classical forbidden region. This circumstance allows us to directly image the exponentially decaying density of a tunneling particle, which we achieved for over two orders of magnitude. Imaging a tunneling particle shows one of the few features of our world that is truly universal: the probability to find one of the constituents of bound matter far away is never zero but decreases exponentially. The results were obtained by Coulomb explosion imaging using a free electron laser and furthermore yielded He 2 's binding energy of 151.9 ± 13.3 neV, which is in agreement with most recent calculations.clusters | helium dimer | wavefunction | tunneling A ttractive forces allow particles to condense into stable bound systems such as molecules or nuclei with a ground state and (in most cases) energetically excited bound states, as shown in Fig. 1. Classical particles situated in such a binding potential oscillate back and forth between two turning points. The regions beyond these points are inaccessible for a classical particle due to a lack of energy. Quantum particles, however, can penetrate into the potential barrier by a phenomenon known as "tunneling." Tunneling is omnipresent in nature and occurs on all energy scales from megaelectron volts in nuclear physics to electron volts in molecules and solids and to nanoelectron volts in optical lattices. For bound matter, the fraction of the probability density distribution in this classically forbidden region is usually small. For shallow short-range potentials, this situation can change dramatically: upon decreasing the potential depth, excited states are expelled one after the other as they become unbound (transition from A to B in Fig. 1). A further decrease of the potential depth effects the ground state as well, as more and more of its wavefunction expands into the tunneling region ( Fig. 1 C and D). Consequently, at the threshold (i.e., in the limit of vanishing binding energy), the size of the quantum system expands to infinity. For short-range potentials, this expansion is accompanied by the fact that the system becomes less "classical" and more quantumlike. Systems existing near that threshold (and therefore being dominated by the tunneling part of their wavefunction) are called "quantum halo states" (1). These states are known, for example, from nuclear physics where 11 Be and 11 Li form ...

In 1997, it was predicted that an electronically excited atom or molecule placed in a loosely bound chemical system (such as a hydrogen-bonded or van-der-Waals-bonded cluster) could efficiently decay by transferring its excess energy to a neighbouring species that would then emit a low-energy electron. This intermolecular Coulombic decay (ICD) process has since been shown to be a common phenomenon, raising questions about its role in DNA damage induced by ionizing radiation, in which low-energy electrons are known to play an important part. It was recently suggested that ICD can be triggered efficiently and site-selectively by resonantly core-exciting a target atom, which then transforms through Auger decay into an ionic species with sufficiently high excitation energy to permit ICD to occur. Here we show experimentally that resonant Auger decay can indeed trigger ICD in dimers of both molecular nitrogen and carbon monoxide. By using ion and electron momentum spectroscopy to measure simultaneously the charged species created in the resonant-Auger-driven ICD cascade, we find that ICD occurs in less time than the 20 femtoseconds it would take for individual molecules to undergo dissociation. Our experimental confirmation of this process and its efficiency may trigger renewed efforts to develop resonant X-ray excitation schemes for more localized and targeted cancer radiation therapy.

We investigate the ionization of HeNe from below the He 1s3p excitation to the He ionization threshold. We observe HeNe+ ions with an enhancement by more than a factor of 60 when the He side couples resonantly to the radiation field. These ions are an experimental proof of a two-center resonant photoionization mechanism predicted by Najjari et al. [Phys. Rev. Lett. 105, 153002 (2010)]. Furthermore, our data provide electronic and vibrational state resolved decay widths of interatomic Coulombic decay in HeNe dimers. We find that the interatomic Coulombic decay lifetime strongly increases with increasing vibrational state.