Ambiguities in Decomposing Molecular Polarizability into Atomic Charge Flow and Induced Dipole Contributions.

The molecular dipole polarizability can be decomposed into components corresponding to the charge flow between atoms and changes in atomic dipole moments. Such decompositions are recognized to depend on how atoms are defined within a molecule, as, for example, by Hirshfeld, iterative Stockholder, or quantum topology partitioning of the electron density. For some of these, however, there are significant differences between the numerical results obtained by analytical response methods and finite field calculations. We show that this difference is due to analytical response methods accounting for (only) the change in electron density by a perturbation, while finite field methods may also include a component corresponding to a perturbation-dependent change in the definition of an atom within a molecule. For some atom-in-molecule definitions, such as the iterative Hirshfeld, iterative Stockholder, and quantum topology methods, the latter effect significantly increases the charge flow component. The decomposition of molecular polarizability into atomic charge flow and induced dipole components thus depends on whether the atom-in-molecule definition is taken to be perturbation-dependent.

Aqueous pyruvate partly dissociates under deep ultraviolet irradiation but is resilient to near ultraviolet excitation.

The deep ultraviolet photochemistry of aqueous pyruvate is believed to have been essential to the origin of life, and near ultraviolet excitation of pyruvate in aqueous aerosols is assumed to contribute significantly to the photochemistry of the Earth's atmosphere. However, the primary photochemistry of aqueous pyruvate is unknown. Here we study the susceptibility of aqueous pyruvate to photodissociation by deep ultraviolet and near ultraviolet irradiation with femtosecond spectroscopy supported by density functional theory calculations. The primary photo-dynamics of the aqueous pyruvate show that upon deep-UV excitation at 200 nm, about one in five excited pyruvate anions have dissociated by decarboxylation 100 ps after the excitation, while the rest of the pyruvate anions return to the ground state. Upon near-UV photoexcitation at a wavelength of 340 nm, the dissociation yield of aqueous pyruvate 200 ps after the excitation is insignificant and no products are observed. The experimental results are explained by our calculations, which show that aqueous pyruvate anions excited at 200 nm have sufficient excess energy for decarboxylation, whereas excitation at 340 nm provides the aqueous pyruvate anions with insufficient energy to overcome the decarboxylation barrier.

High-harmonic spectroscopy of impulsively aligned 1,3-cyclohexadiene: Signatures of attosecond charge migration.

High-harmonic spectroscopy is an all-optical technique with inherent attosecond temporal resolution that has been successfully employed to reconstruct charge migration, electron-tunneling dynamics, and conical-intersection dynamics. Here, we demonstrate the extension of two key components of high-harmonic spectroscopy, i.e., impulsive alignment and measurements with multiple driving wavelengths to 1,3-cyclohexadiene and benzene. In the case of 1,3-cyclohexadiene, we find that the temporal sequence of maximal and minimal emitted high-harmonic intensities as a function of the delay between the alignment and probe pulses inverts between 25 and 30 eV and again between 35 and 40 eV when an 800-nm driver is used, but no inversions are observed with a 1420-nm driver. This observation is explained by the wavelength-dependent interference of emission from multiple molecular orbitals (HOMO to HOMO-3), as demonstrated by calculations based on the weak-field asymptotic theory and accurate photorecombination matrix elements. These results indicate that attosecond charge migration takes place in the 1,3-cyclohexadiene cation and can potentially be reconstructed with the help of additional measurements. Our experiments also demonstrate a pathway toward studying photochemical reactions in the molecular frame of 1,3-cyclohexadiene.

Cluster perturbation theory IX: Perturbation series for the coupled cluster singles and doubles ground state energy.

In this paper, we develop and analyze a number of perturbation series that target the coupled cluster singles and doubles (CCSD) ground state energy. We show how classical Møller-Plesset perturbation theory series can be restructured to target the CCSD energy based on a reference CCS calculation and how the corresponding cluster perturbation series differs from the classical Møller-Plesset perturbation series. Subsequently, we reformulate these series using the coupled cluster Lagrangian framework to obtain series, where fourth and fifth order energies are determined only using parameters through second order. To test the methods, we perform a series of test calculations on molecular photoswitches of both total energies and reaction energies. We find that the fifth order reaction energies are of CCSD quality and that they are of comparable accuracy to state-of-the-art approximations to the CCSD energy based on local pair natural orbitals. The advantage of the present approach over local correlation methods is the absence of user defined threshold parameters for neglecting or approximating contributions to the correlation energy. Fixed threshold parameters lead to discontinuous energy surfaces, although this effect is often small enough to be ignored, but the present approach has a differentiable energy that will facilitate derivation and implementation of gradients and higher derivatives. A further advantage is that the calculation of the perturbation correction is non-iterative and can, therefore, be calculated in parallel, leading to a short time-to-solution.

Basis Set Superposition Errors Are Partly Basis Set Imbalances.

When calculating fragment interaction energies by electronic structure methods employing medium-sized atom-centered basis sets, it is often observed that the effect is systematically overestimated. The common interpretation is that the systematic error arises because the basis set for the complex is more complete than for the isolated fragments, and this is denoted basis set superposition errors. It has been observed, however, that the interaction energy in some cases is underestimated, which defies the interpretation in terms of basis set completeness, and instead suggests that the effect partly is due to basis set imbalance. The imbalance can be removed by explicit optimization of the basis sets for each structure, and it is shown that this to a significant extent reduces the systematic overestimation attributed to basis set superposition error.

Quantifying Intramolecular Basis Set Superposition Errors.

We show that medium-sized Gaussian basis sets lead to significant intramolecular basis set superposition errors at Hartree-Fock and density functional levels of theory, with artificial stabilization of compact over extended conformations for a 186 atom deca-peptide. Errors of ∼80 and ∼10 kJ/mol are observed, with polarized double zeta and polarized triple zeta quality basis sets, respectively. Two different procedures for taking the basis set superposition error into account are tested. While both reduce the error, it appears that polarized quadruple zeta basis sets are required to reduce the error below a few kJ/mol. Alternatively, the basis set superposition error can be eliminated using multiresolution methods based on Multiwavelets.

Nonadiabatic Laser-Induced Alignment Dynamics of Molecules on a Surface.

We demonstrate that a sodium dimer, Na_{2}(1^{3}Σ_{u}^{+}), residing on the surface of a helium nanodroplet, can be set into rotation by a nonresonant 1.0 ps infrared laser pulse. The time-dependent degree of alignment measured, exhibits a periodic, gradually decreasing structure that deviates qualitatively from that expected for gas-phase dimers. Comparison to alignment dynamics calculated from the time-dependent rotational Schrödinger equation shows that the deviation is due to the alignment dependent interaction between the dimer and the droplet surface. This interaction confines the dimer to the tangential plane of the droplet surface at the point where it resides and is the reason that the observed alignment dynamics is also well described by a 2D quantum rotor model.

Unifying Charge-Flow Polarization Models.

We show that several models where electric polarization in molecular systems is modeled by charge-flow between atoms can all be considered as different manifestations of a general underlying mathematical structure. The models can be classified according to whether they employ atomic or bond parameters and whether they employ atom/bond hardness or softness. We show that an ab initio calculated charge response kernel can be considered as the inverse screened Coulombic matrix projected onto the zero-charge subspace, and this may provide a method for deriving charge screening functions to be used in force fields. The analysis suggests that some models contain redundancies, and we argue that a parameterization of charge-flow models in terms of bond softness is preferable as it depends on local quantities and decay to zero upon bond dissociation, while bond hardness depends on global quantities and increases toward infinity upon bond dissociation.

The primary photolysis of aqueous carbonate di-anions.

We study the primary photolysis dynamics of aqueous carbonate, CO32-(aq), and hydrogen carbonate, HCO3-(aq), when they are excited at λ = 200 nm. The photolysis is recorded with sub-picosecond time resolution using UV pump-Vis probe and UV pump-IR probe transient absorption spectroscopy and interpreted with the aid of density functional theory calculations. When CO32- is excited via single photon absorption at λ = 200 nm, Φ(t = 20 ps) = 82 ± 5% of the excited di-anions either detach an electron or dissociate. The electron detachment takes place from the excited state in t < 1 ps and forms ground state CO3˙- and eaq-. Dissociation occurs from both the electronic ground and excited states of CO32-. Dissociation from the CO32- excited state is assisted by water molecules and forms CO2˙-, OH˙ and OH-. The dissociation occurs both directly from the Franck-Condon region in t < 1 ps and indirectly with a time constant of τ = 13.9 ± 0.5 ps as the excited state relaxes. Dissociation of vibrationally excited CO32- molecules in the electronic ground state is also assisted by water molecules and forms CO2 and two OH- anions. The dissociation and subsequent vibrational relaxation of CO2 occur with a time constant of τ = 10.2 ± 0.5 ps. The residual 1 - Φ(t = 20 ps) = 18 ± 5% of the excited CO32- di-anions return by internal conversion to the equilibrated CO32- ground state with a time constant of τ = 4.0 ± 0.4 ps. The extinction coefficient of aqueous hydrogen carbonate HCO3-(aq) at λ = 200 nm is an order of magnitude smaller than that of carbonate, so even though the hydrogen carbonate anions dominate the carbonate di-anions in the hydrogen carbonate solution, the primary photolysis of hydrogen carbonate is obscured by the photo-products of carbonate. Hence, we are unable to assess the primary photolysis of hydrogen carbonate. However, the weak one-photon absorption facilitates two-photon ionization of water, which forms hydronium, H3O+, cations. The sudden increase in the acidity induced by two-photon ionization protonates the ground state hydrogen carbonate molecules, thus offering a rare spectroscopic glimpse of aqueous carbonic acid.

Peptide Bond of Aqueous Dipeptides Is Resilient to Deep Ultraviolet Irradiation.

The susceptibility of aqueous dipeptides to photodissociation by deep ultraviolet irradiation is studied by femtosecond spectroscopy supported by density functional theory calculations. The primary photodynamics of the aqueous dipeptides of glycyl-glycine (gly-gly), alalyl-alanine (ala-ala), and glycyl-alanine (gly-ala) show that upon photoexcitation at a wavelength of 200 nm, about 10% of the excited dipeptides dissociate by decarboxylation within 100 ps, while the rest of the dipeptides return to their native ground state. Accordingly, the vast majority of the excited dipeptides withstand the deep ultraviolet excitation. In those relatively few cases, where excitation leads to dissociation, the measurements show that deep ultraviolet irradiation breaks the Cα-C bond rather than the peptide bond. The peptide bond is thereby left intact, and the decarboxylated dipeptide moiety is open to subsequent reactions. The experiments indicate that the low photodissociation yield and in particular the resilience of the peptide bond to dissociation are due to rapid internal conversion from the excited state to the ground state, followed by efficient vibrational relaxation facilitated by intramolecular coupling among the carbonate and amide modes. Thus, the entire process of internal conversion and vibrational relaxation to thermal equilibrium on the dipeptide ground state occurs on a time scale of less than 2 ps.

Basis Set Extrapolation of Vibrational Frequencies.

We investigate three different approaches for extrapolating harmonic vibrational frequencies to the complete basis set limit, by direct extrapolation of the frequencies, by calculation of frequencies based on extrapolated Hessians, or based on the Hessian from optimization of the extrapolated energy surface. For regular molecules, the three extrapolation procedures yield essentially identical results, but for loosely bound complexes, the frequencies derived from extrapolated Hessians yield unpredictable behavior. None of the basis set extrapolations, however, provide any significant improvement over the results upon which the extrapolation is based.

Theoretical Sum Frequency Generation Spectra of Protein Amide with Surface-Specific Velocity-Velocity Correlation Functions.

Vibrational sum frequency generation (vSFG) spectroscopy is widely used to probe the protein structure at interfaces. Because protein vSFG spectra are complex, they can only provide detailed structural information if combined with computer simulations of protein molecular dynamics and spectra calculations. We show how vSFG spectra can be accurately modeled using a surface-specific velocity-velocity scheme based on ab initio normal modes. Our calculated vSFG spectra show excellent agreement with the experimental sum frequency spectrum of LTα14 peptide and provide insight into the origin of the characteristic α-helical amide I peak. Analysis indicates that the peak shape can be explained largely by two effects: (1) the uncoupled response of amide groups located on opposite sides of the α-helix will have different orientations with respect to the interface and therefore different local environments affecting the local mode vibrations and (2) vibrational splitting from nearest neighbor coupling evaluated as inter-residue vibrational correlation. The conclusion is consistent with frequency mapping techniques with an empirically based ensemble of peptide structures, thus showing how time correlation approaches and frequency mapping techniques can give independent yet complementary molecular descriptions of protein vSFG. These models reveal the sensitive relationship between protein structure and their amide I response, allowing exploitation of the complicated molecular vibrations and their interference to derive the structures of proteins under native conditions at interfaces.

The primary photo-dissociation dynamics of aqueous formamide and dimethylformamide.

We study the primary dissociation dynamics of aqueous formamide (HCONH2) and dimethylformamide (HCON(CH3)2) induced by photo-excitation at λ = 200 nm. The photolysis is recorded with sub-picosecond time resolution by UV pump-IR probe transient absorption spectroscopy. Formamide dissociates with a quantum yield of Φ(t = 20 ps) = 0.30 ± 0.05, t = 20 ps after the excitation. The rest of the excited formamide molecules return to the ground state within t = 1 ps and vibrationally relax towards equilibrium in t ≈ 10 ps. The only product observed is NH3. NH3 is produced with a yield of Φ(NH3) = 0.23 ± 0.10 on a timescale of τ = 3 ± 1 ps and likely constitutes the dominating product. The CO counter product to NH3 is not observed. Dimethylformamide is photolysed with a quantum yield of Φ(t = 30 ps) = 0.29 ± 0.05, t = 30 ps after the excitation. The photolysis of dimethylformamide produces CO on a time scale of τ ≈ 30 ps. The data indicate that dimethylamine and the N(CH3)2 radical are likely photoproducts.

Influence of Genetics, Immunity and the Microbiome on the Prognosis of Inflammatory Bowel Disease (IBD Prognosis Study): the protocol for a Copenhagen IBD Inception Cohort Study.

INTRODUCTION: Inflammatory bowel diseases (IBD), encompassing Crohn's disease and ulcerative colitis, are chronic, inflammatory diseases of the gastrointestinal tract. We have initiated a Danish population-based inception cohort study aiming to investigate the underlying mechanisms for the heterogeneous course of IBD, including need for, and response to, treatment. METHODS AND ANALYSIS: IBD Prognosis Study is a prospective, population-based inception cohort study of unselected, newly diagnosed adult, adolescent and paediatric patients with IBD within the uptake area of Hvidovre University Hospital and Herlev University Hospital, Denmark, which covers approximately 1 050 000 inhabitants (~20% of the Danish population). The diagnosis of IBD will be according to the Porto diagnostic criteria in paediatric and adolescent patients or the Copenhagen diagnostic criteria in adult patients. All patients will be followed prospectively with regular clinical examinations including ileocolonoscopies, MRI of the small intestine, validated patient-reported measures and objective examinations with intestinal ultrasound. In addition, intestinal biopsies from ileocolonoscopies, stool, rectal swabs, saliva samples, swabs of the oral cavity and blood samples will be collected systematically for the analysis of biomarkers, microbiome and genetic profiles. Environmental factors and quality of life will be assessed using questionnaires and, when available, automatic registration of purchase data. The occurrence and course of extraintestinal manifestations will be evaluated by rheumatologists, dermatologists and dentists, and assessed by MR cholangiopancreatography, MR of the spine and sacroiliac joints, ultrasonography of peripheral joints and entheses, clinical oral examination, as well as panoramic radiograph of the jaws. Fibroscans and dual-energy X-ray absorptiometry scans will be performed to monitor occurrence and course of chronic liver diseases, osteopenia and osteoporosis. ETHICS AND DISSEMINATION: This study has been approved by Ethics Committee of the Capital Region of Denmark (approval number: H-20065831). Study results will be disseminated through publication in international scientific journals and presentation at (inter)national conferences.

Asymmetric Dissociative Tunneling Ionization of Tetrafluoromethane in ω - 2ω Intense Laser Fields.

Dissociative ionization of tetrafluoromethane (CF4) in linearly polarized ω-2ω ultrashort intense laser fields (1.4 × 1014 W/cm2, 800 and 400 nm) has been investigated by three-dimensional momentum ion imaging. The spatial distribution of C F 3 + produced by CF4 → C F 3 + + F + e- exhibited a clear asymmetry with respect to the laser polarization direction. The degree of the asymmetry varies by the relative phase of the ω and 2ω laser fields, showing that 1) the breaking of the four equivalent C-F bonds can be manipulated by the laser pulse shape and 2) the C-F bond directed along the larger amplitude side of the ω-2ω electric fields tends to be broken. Weak-field asymptotic theory (WFAT) shows that the tunneling ionization from the 4t 2 second highest-occupied molecular orbital (HOMO-1) surpasses that from the 1t 1 HOMO. This predicts the enhancement of the tunneling ionization with electric fields pointing from F to C, in the direction opposite to that observed for the asymmetric fragment ejection. Possible mechanisms involved in the asymmetric dissociative ionization, such as post-ionization interactions, are discussed.

The primary photo-dissociation dynamics of lactic acid: decarboxylation as CO2 and CO2˙.

We study the primary photolysis dynamics of lactic acid induced by excitation at λ = 200 nm with the aim of elucidating how simple aqueous carboxyl acids react to the deep ultraviolet exposure on the prebiotic Earth. UV-IR transient absorption spectroscopy shows a photolysis quantum yield of Φ(100 ps) = 100 ± 5%. The primary products are CO2, CO2˙- and their counter products CH3CHOH˙ and CH3CHOH-. DFT calculations suggest that the dissociation takes place from the strongly acidic nπ* excited state. Dehydroxylation of lactic acid is not observed.

The oxygen-organic molecule photosystem: revisiting the past, recalibrating the present, and redefining the future.

Perturbation by a neighboring molecule M appreciably alters the properties of both the ground and excited states of molecular oxygen, as reflected in a variety of photophysical phenomena. In this article, we build upon the ~ 100 year history of work in this field, illustrating how the M-O2 system continues to challenge the scientific community, facilitating better insight into fundamental tenets of chemistry and physics.

Geometry Dependence of Spin-Orbit Coupling in Complexes of Molecular Oxygen with Atoms, H2, or Organic Molecules.

Studies of the interactions between molecular oxygen and a perturbing species, such as an organic solvent, have been an active research area for at least 70 years. In particular, interaction with a neighboring molecule or atom may perturb the electronic states of oxygen to such an extent that the O2(a1Δg) → O2(X3Σg-) transition, formally forbidden as an electric dipole process, achieves significant transition probability. We present a computational study of how the geometry of complexes consisting of molecular oxygen and different perturbing species influences the magnitude of spin-orbit coupling that facilitates the O2(a1Δg) → O2(X3Σg-) transition. We rationalize our results using a model based on orbital interactions: a non-zero spin-orbit coupling matrix element results from asymmetric transfer of charge to or from the 1πg orbitals on oxygen. Our results indicate that the atoms in a perturbing species closest to oxygen are responsible for the majority of the spin-orbit interactions, suggesting that large systems can be simplified appreciably. Furthermore, we infer and confirm that an estimate of the spin-orbit coupling matrix element can be obtained from the magnitude of the induced energy splitting of oxygen's 1πg orbitals. These results should provide further momentum in the long-standing issue of understanding phenomena that influence the O2(a1Δg) → O2(X3Σg-) transition.

Using atomic charges to model molecular polarization.

We review different models for introducing electric polarization in force fields, with special focus on methods where polarization is modelled at the atomic charge level. While electric polarization has been included in several force fields, the common approach has been to focus on atomic dipole polarizability. Several approaches allow modelling electric polarization by using charge-flow between charge sites instead, but this has been less exploited, despite that atomic charges and charge-flow is expected to be more important than atomic dipoles and dipole polarizability. A number of challenges are required to be solved for charge-flow models to be incorporated into polarizable force fields, for example how to parameterize the models and how to make them computational efficient.

The complex between molecular oxygen and an organic molecule: modeling optical transitions to the intermolecular charge-transfer state.

The collision complex between the ground electronic state of an organic molecule, M, and ground state oxygen, O2(X3Σg-), can absorb light to produce an intermolecular charge transfer (CT) state, often represented simply as the M radical cation, M+˙, paired with the superoxide radical anion, O2-˙. Aspects of this transition have been the subject of numerous studies for ∼70 years, many of which address fundamental concepts in chemistry and physics. We now examine the extent to which the combination of Molecular Dynamics simulations and electronic structure response methods can model transitions to the toluene-O2 CT state. To account for the experimental spectra, we consider (a) the distribution of toluene-O2 geometries that contribute to the transitions, (b) a quantitative description of intermolecular CT, and (c) oxygen-induced local transitions in toluene that complement the CT transitions, specifically transitions that populate toluene triplet states. We find that the latter oxygen-induced local transitions play a prominent role on the long wavelength side of the spectrum commonly attributed to the intermolecular CT transition. Our calculations provide a new perspective on the seminal discussion between R. S. Mulliken and D. F. Evans on the nature of O2-dependent transitions in organic molecules, and bode well for modeling transitions to excited states with CT character in noncovalent weakly-bonded molecular complexes.