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Complex organic molecules are widespread in different areas of the interstellar medium, including cold areas, such as molecular clouds, where chemical reactions occur in ice. Among the observed molecules are oxygen-bearing organic molecules, which are of high interest given their significant role in astrobiology. Despite the observed rich chemistry, the underlying molecular mechanisms responsible for molecular formation in such cold dilute areas are still not fully understood. In this paper, we study the unique chemistry taking place in astronomically relevant ices, where UV radiation is a central driving force for chemical reactions. Photofragmentation of ice components gives rise to highly reactive species, such as the O(1D) atom. These species provide a pathway for chemical complexity even in cold areas. Using quantum chemistry calculations, we demonstrate that O(1D) reacts barrierlessly with hydrocarbons. Moreover, photoprocessing of the reaction products (and other components of the ice), followed by radical recombination, is found to be an essential part of the overall mechanism. In ice containing O(1D) and hydrocarbons, the formation of formaldehyde in methane ice, acetaldehyde in ethane ice, and carbon monoxide in acetylene ice, and the consumption of alcohol in all systems, was predicted in agreement with experimental results. [ABSTRACT FROM AUTHOR]

Hydrogen cyanide (HCN) and its isomer hydrogen isocyanide (HNC) are omnipresent in the interstellar medium (ISM). The ratio between the two isomers serves as an indicator of the physical conditions in different areas of the ISM. As such, the isomerization process between the two isomers has been extensively studied on the neutral potential energy surface. Moreover, HCN and HNC are thought to be precursors of important organic molecules, such as adenine. Here, we use quantum chemistry calculations and ab initio molecular dynamics simulations to focus on the chemistry that occurs upon ionization of pure HNC clusters. We demonstrate that upon ionization of HNC clusters, a distonic ion CN⋯HCNH+ is formed, and this formation is accompanied by HNC-to-HCN isomerization. Moreover, we show that the cluster environment and the network of hydrogen bonds are crucial for the isomerization process to occur and for the stabilization of the clusters. We demonstrate that, in contrast to HNC clusters, isomerization of ionized HCN clusters can occur only for the larger clusters. In addition, we discuss the formation of aminonitrile cation in the clusters and propose a barrierless route for diaminonitrile, a known precursor of amino acids and nucleobases, to form. [ABSTRACT FROM AUTHOR]

The confinement of water molecules is vital in fields from biology to nanotechnology. The conditions allowing confinement in small finite polycyclic aromatic hydrocarbons (PAHs) are unclear, yet are crucial for understanding confinement in larger systems. Here, we report a computational study of water cluster confinement within PAHs dimers. Our results serve as a model for larger carbon allotropes and for understanding molecular interactions in confined systems. We identified size and structural motifs allowing confinement and demonstrated the motifs in various PAHs systems. We show that optimal OH⋯π interactions between water clusters and the PAH dimer permit optimal confinement to occur. However, the lack of such interactions leads to the formation of CH⋯O interactions, resulting in less ideal confinement. Confinement of layered clusters is also possible, provided that the optimal OH⋯π interactions are conserved. [ABSTRACT FROM AUTHOR]

Water-cluster interactions with polycyclic aromatic hydrocarbons (PAHs) are of paramount interest in many chemical and biological processes. We report a study of anthracene monomers and dimers with water (up to four)-cluster systems utilizing molecular beam vacuum-UV photoionization mass spectrometry and density functional calculations. Structural loss in photoionization efficiency curves when adding water indicates that various isomers are generated, while theory indicates only a slight shift in energy in photoionization states of different isomers. Calculations reveal that the energetic tendency of water is to remain clustered and not to disperse around the PAH. Theoretically, we observe water confinement exclusively in the case of four water clusters and only when the anthracenes are in a cross configuration due to optimal OH⋯π interactions, indicating dependence on the size and structure of the PAH. Furthermore theory sheds light on the structural changes that occur in water upon ionization of anthracene, due to the optimal interactions of the resulting hole and water hydrogen atoms. [ABSTRACT FROM AUTHOR]

Chemoselective reduction of nitro groups in multifunctional nitroaromatics is a challenging catalytic process with high interest due to the importance of the resulting anilines for the chemical industry. Molecular-level understanding of the ways by which adsorption geometry of nitroaromatics influence their affinity toward nitro reduction will enable the development of highly selective reactions. Herein, taking advantage of the well-ordered self-assembly of para- and ortho-nitrothiophenol (p-NTP and o-NTP, respectively) monolayers on Au(111), we examined the correlation between adsorption geometry and nitro reduction affinity. The anchoring geometry of NTPs and their nitro reduction affinity were determined by conducting polarized X-ray absorption spectroscopy while the influence of NTPs′ adsorption geometry on the interaction with the Au surface was analyzed by density functional theory (DFT) calculations. Exposure of surface anchored p-NTPs to reducing conditions led to their reorientation from a tilt angle of 52° to 25°, which enabled strong interactions between the π system of the molecules and the Au surface. Direct correlation was identified between the surface proximity of the nitro group, its parallel position to the surface and the resulting reduction yield. The asymmetric structure of o-NTP led to a tilted adsorption geometry in which the nitro group was rotated away from the plane of the aromatic ring and therefore was positioned parallel and in high proximity to the Au surface. This positioning led to surface-bonding that involved the oxygen atoms of o-NTP. The higher surface proximity and stronger surface interactions of the nitro group in o-NTP enabled nitro reduction already at 180 °C, while in p-NTP nitro reduction was achieved only at 230 °C, due to the longer distance between the NO2 group and the Au surface that led to weaker adsorbate-surface interactions. Thus, parallel positioning of the nitro group and high surface proximity were found as essential descriptors for nitro reduction affinity in both p-NTP and o-NTP on the Au surface. These findings provide explicit guidelines for tuning the reactant and surface properties in order to control the reactant's adsorption geometry for selective nitro reduction in multifunctional nitroaromatics. [ABSTRACT FROM AUTHOR]

Doubly occupied configuration interaction (DOCI) with optimized orbitals often accurately describes strong correlations while working in a Hilbert space much smaller than that needed for full configuration interaction. However, the scaling of such calculations remains combinatorial with system size. Pair coupled cluster doubles (pCCD) is very successful in reproducing DOCI energetically, but can do so with low polynomial scaling (N³, disregarding the two-electron integral transformation from atomic to molecular orbitals). We show here several examples illustrating the success of pCCD in reproducing both the DOCI energy and wave function and show how this success frequently comes about. What DOCI and pCCD lack are an effective treatment of dynamic correlations, which we here add by including higher-seniority cluster amplitudes which are excluded from pCCD. This frozen pair coupled cluster approach is comparable in cost to traditional closed-shell coupled cluster methods with results that are competitive for weakly correlated systems and often superior for the description of strongly correlated systems. [ABSTRACT FROM AUTHOR]

Coupled cluster theory with single and double excitations accurately describes weak electron correlation but is known to fail in cases of strong static correlation. Fascinatingly, however, pair coupled cluster doubles (p-CCD), a simplified version of the theory limited to pair excitations that preserve the seniority of the reference determinant (i.e., the number of unpaired electrons), has mean field computational cost and is an excellent approximation to the full configuration interaction (FCI) of the paired space provided that the orbital basis defining the pairing scheme is adequately optimized. In previous work, we have shown that optimization of the pairing scheme in the seniority zero FCI leads to a very accurate description of static correlation. The same conclusion extends to p-CCD if the orbitals are optimized to make the p-CCD energy stationary. We here demonstrate these results with numerous examples. We also explore the contributions of different seniority sectors to the coupled cluster doubles (CCD) correlation energy using different orbital bases. We consider both Hartree-Fock and Brueckner orbitals, and the role of orbital localization. We show how one can pair the orbitals so that the role of the Brueckner orbitals at the CCD level is retained at the p-CCD level. Moreover, we explore ways of extending CCD to accurately describe strongly correlated systems. [ABSTRACT FROM AUTHOR]

The growth mechanisms of organic molecules in an ionizing environment such as the interstellar medium are not completely understood. Here we examine by means of ab initio molecular dynamics (AIMD) simulations and density functional theory (DFT) computations the possibility of bond formation and molecular growth upon ionization of van der Waals clusters of pure HCN clusters, and mixed clusters of HCN and HCCH, both of which are widespread in the interstellar medium. Ionization of van der Waals clusters can potentially lead to growth in low temperature and low-density environments. Our results show, that upon ionization of the pure HCN clusters, strongly bound stable structures are formed that contain N⋯H bonds, and growth beyond pairwise HCN molecules is seen only in a small percentage of cases. In contrast, mixed clusters, where HCCH is preferentially ionized over HCN, can grow up to 3 or 4 units long with new carbon–carbon and carbon–nitrogen covalent bonds. Moreover, cyclic molecules formed, such as the radical cation of pyridine, which is a prebiotic molecule. The results presented here are significant as they provide a feasible pathway for molecular growth of small organic molecules containing both carbon and nitrogen in cold and relatively denser environments such as in dense molecular clouds but closer to the photo-dissociation regions, and protoplanetary disks. In the mechanism we propose, first, a neutral van der Waals cluster is formed. Once the cluster is formed it can undergo photoionization which leads to chemical reactivity without any reaction barrier. [ABSTRACT FROM AUTHOR]

The presence and formation of a large variety of organic molecules in the interstellar medium is evident from both astronomical data of absorption and emission bands at different regions of the spectrum. Specifically, polycyclic aromatic hydrocarbons (PAHs) are ubiquitous in the interstellar medium (ISM). The mechanism for their formation in ISM's low temperature environment is, as of yet, a mystery nonetheless. Understanding the mechanism of formation of complex molecules such as PAHs and nitrogen‐based PAHs (PANH) in the ISM is a long‐standing challenge which has been drawing a growing attention for the past several decades. In this review we wish to emphasize two things: Firstly, the essential role quantum chemistry can play in the study of astrochemical reactions. Secondly, we wish to demonstrate that said variety of possibilities for chemical reaction, starting upon ionization of van der Waals clusters. The potential for different chemical reactions to occur within a cluster environment arises from the fact that such processes can take place at low temperatures as the systems pose large amounts of energy upon ionization. Moreover, the spectator molecules in the cluster can provide a dissipation route for energy by detachment from the cluster, thus the system can stabilize efficiently even at low densities. The spectator molecules can also change the potential energy surface, by which it will pose a catalytic effect for certain reactions. We will demonstrate this by presenting Ab Initio Molecular Dynamic results on ionization of small acetylene clusters. [ABSTRACT FROM AUTHOR]

The use of gem‐diborylalkenes as radical‐reactive groups is explored for the first time. These reactions provide an efficient and general method for the photochemical conversion of gem‐diborylalkenes to rapidly access 1,1‐bisborylalkanes. This method exploits a novel photoredox decarboxylative radical addition to gem‐diborylalkenes to afford α‐gem‐diboryl carbon‐centered radicals, which benefit from additional stability by virtue of an interaction with the empty p‐orbitals on borons. The reaction offers a highly modular and regioselective approach to γ‐amino gem‐diborylalkanes. Furthermore, EPR spectroscopy and DFT calculations have provided insight into the radical mechanism underlying the photochemistry reaction and the stability of the bis‐metalated radicals, respectively. [ABSTRACT FROM AUTHOR]

We study the description of charge-transfer excitations in a series of coumarin-based donor-bridge-acceptor dyes. We show that excellent predictive power for the excitation energies and oscillator strengths in these systems is obtained by using a range-separated hybrid functional within the generalized Kohn–Sham approach to time-dependent density functional theory. Key to this success is a step for tuning the range separation parameter from first principles. We explore different methods for this tuning step, which are variants of a recently suggested approach for charge-transfer excitations [T. Stein et al., J. Am. Chem. Soc. 131, 2818 (2009)]. We assess the quality of prediction by comparing to excitation energies previously published for the same systems using the approximate coupled-cluster singles and doubles (CC2) method. [ABSTRACT FROM AUTHOR]

Studies have shown how charge transfer excitations at molecular complexes are calculated by using time-dependent density functional theory. Excellent performance of this method is obtained for a series of complexes composed of various aromatic donors and the tetracyanoethylene acceptor, thus providing ways for analyzing charge-transfer excitations in real systems.

Polycyclic aromatic hydrocarbons (PAHs) may comprise up to 20% of the carbon budget in our galaxy and most PAHs condense onto water-rich icy grain mantles. Benzene–water clusters have been invoked as model systems for studying the photo-processing of water ice mantles containing PAHs. However, there is a paucity of information on larger aromatics, where the extended π cloud could affect photo-processing. In this study, tunable vacuum ultraviolet (VUV) photoionization of naphthalene–water clusters Nx(H2O)y (N denotes naphthalene) is performed using synchrotron radiation and analyzed by reflectron time-of-flight mass spectrometry. Naphthalene clusters up to x = 4 are generated as are naphthalene–water clusters up to y = 25. At low photon energy (＜11 eV), the naphthalene moiety is ionized and there is no proton transfer from N+ to the water sub-cluster, which is very different from the benzene–water system. Protonated products, N[(H2O)xH]+ and OH radical addition product (NOH)[(H2O)xH]+ are generated above 11 eV, suggesting that water sub-clusters dominate the dynamics at high photon energies. Ab initio calculations are performed to decipher the experimental results. Energetics of the neutral structures N(H2O)1–4 and their photoionized counterparts are calculated, including ionization on the N moiety as well as on the water sub-cluster. Energy decomposition analysis (EDA) is performed to understand trends in the binding between the naphthalene and the water sub-cluster in the ionized species. [ABSTRACT FROM AUTHOR]

We investigated the formation mechanisms of the nucleobases adenine and guanine and the nucleobase analogues hypoxanthine, xanthine, isoguanine, and 2,6-diaminopurine in a UV-irradiated mixed 10:1 H2O:NH3 ice seeded with precursor purine by using ab initio and density functional theory computations. Our quantum chemical investigations suggest that a multistep reaction mechanism involving purine cation, hydroxyl and amino radicals, together with water and ammonia, explains the experimentally obtained products in an independent study. The relative abundances of these products appear to largely follow from relative thermodynamic stabilities. The key role of the purine cation is likely to be the reason why purine is not functionalized in pure ammonia ice, where cations are promptly neutralized by free electrons from NH3 ionization. Amine group addition to purine is slightly favored over hydroxyl group attachment based on energetics, but hydroxyl is much more abundant due to higher abundance of H2O. The amino group is preferentially attached to the 6 position, giving 6-aminopurine, that is, adenine, while the hydroxyl group is preferentially attached to the 2 position, leading to 2-hydroxypurine. A second substitution by hydroxyl or amino group occurs at either the 6 or the 2 position depending on the first substitution. Given that H2O is far more abundant than NH3 in the experimentally studied ices (as well as based on interstellar abundances), xanthine and isoguanine are expected to be the most abundant bi-substituted photoproducts. Key Words: Astrophysical ice-Abiotic organic synthesis-Nucleic acids-Origin of life-RNA world. Astrobiology 17, 771-785. [ABSTRACT FROM AUTHOR]

Mixed complexes of acetylene-ethylene are studied using vacuum-ultraviolet (VUV) photoionization mass spectrometry and theoretical calculations. These complexes are produced and ionized at different distances from the exit of a continuous nozzle followed by reflectron time-of-flight mass spectrometry detection. Acetylene, with a higher ionization energy (11.4 eV) than ethylene (10.6 eV), allows for tuning the VUV energy and initializing reactions either from a C2H2+ or a C2H4+ cation. Pure acetylene and ethylene expansions are separately carried out to compare, contrast, and hence identify products from the mixed expansion: these are C3H3+ (m/z = 39), C4H5+ (m/z = 53), and C5H5+ (m/z = 65). Intensity distributions of C2H2, C2H4, their dimers and reactions products are plotted as a function of ionization distance. These distributions suggest that association mechanisms play a crucial role in product formation closer to the nozzle. Photoionization efficiency (PIE) curves of the mixed complexes demonstrate rising edges closer to both ethylene and acetylene ionization energies. We use density functional theory (ωB97X-V/aug-cc-pVTZ) to study the structures of the neutral and ionized dimers, calculate their adiabatic and vertical ionization energies, as well as the energetics of different isomers on the potential energy surface (PES). Upon ionization, vibrationally excited clusters can use the extra energy to access different isomers on the PES. At farther ionization distances from the nozzle, where the number densities are lower, unimolecular decay is expected to be the dominant mechanism. We discuss the possible decay pathways from the different isomers on the PES and examine the ones that are energetically accessible. [ABSTRACT FROM AUTHOR]

Hartree–Fock(HF) is known to suffer from drawbacks in the description of the relativestabilities between the hemi-bonded (HB) and proton-transferred (PT)isomers of the water dimer cation, (H2O)2+. The energy difference predicted by HF is too large, approximately27 kcal/mol, which is lowered to 7 kcal/mol when correlation effectsare added. The error in HF has been previously attributed to the largedynamic correlation effects in the HB structure as well to the largesymmetry breaking this structure exhibits. In this study we use therecently developed projected Hartree–Fock (PHF) methods tostudy the relative stability of the two isomers of (H2O)2+as well as its second and third row analogs,namely, (H2S)2+and (H2Se)2+. In PHF, symmetries are broken and restoredin a variation-after-projection approach and thus can deal easilywith systems for which HF itself spontaneously breaks symmetry. Weuse different flavors of PHF (SUHF, KSUHF, SGHF, and KSGHF) to exploretheir ability in capturing dynamic correlation effects and to comparetheir performance to different wave function based methods. We studythe role of the symmetry-breaking in the above systems, using wavefunction based methods with unrestricted and restricted wave functionsas well as performing a single-shot symmetry restoration (a projection-after-variationscheme). [ABSTRACT FROM AUTHOR]

Polyaromatic hydrocarbons (PAHs) are widespread in the interstellar medium (ISM). The abundance and relevance of PAHs call for a clear understanding of their formation mechanisms, which, to date, have not been completely deciphered. Of particular interest is the formation of benzene, the basic building block of PAHs. It has been shown that the ionization of neutral clusters can lead to an intra-cluster ionic polymerization process that results in molecular growth. Ab-initio molecular dynamics (AIMD) studies in clusters consisting of 3–6 units of acetylene modeling ionization events under ISM conditions have shown maximum aggregation of three acetylene molecules forming bonded C6H6+ species; the larger the number of acetylene molecules, the higher the production of C6H6+. These results lead to the question of whether clusters larger than those studied thus far promote aggregation beyond three acetylene units and whether larger clusters can result in higher C6H6+ production. In this study, we report results from AIMD simulations modeling the ionization of 10 and 20 acetylene clusters. The simulations show aggregation of up to four acetylene units producing bonded C8H8+. Interestingly, C8H8+ bicyclic species were identified, setting a precedent for their astrochemical identification. Comparable reactivity rates were shown with 10 and 20 acetylene clusters. [ABSTRACT FROM AUTHOR]

Perdew et al. discovered two different properties of exact Kohn-Sham density functional theory (DFT): (i) The exact total energy versus particle number is a series of linear segments between integer electron points. (ii) Across an integer number of electrons, the exchange-correlation potential "jumps" by a constant, known as the derivative discontinuity (DD). Here we show analytically that in both the original and the generalized Kohn-Sham formulation of DFT the two properties are two sides of the same coin. The absence of a DD dictates deviation from piecewise linearity, but the latter, appearing as curvature, can be used to correct for the former, thereby restoring the physical meaning of orbital energies. A simple correction scheme for any semilocal and hybrid functional, even Hartree-Fock theory, is shown to be effective on a set of small molecules, suggesting a practical correction for the infamous DFT gap problem. We show that optimally tuned range-separated hybrid functionals can inherently minimize both DD and curvature, thus requiring no correction, and that this can be used as a sound theoretical basis for novel tuning strategies.

Excitation gaps are of considerable significance in electronic structure theory. Two different gaps are of particular interest. The fundamental gap is defined by charged excitations, as the difference between the first ionization potential and the first electron affinity. The optical gap is defined by a neutral excitation, as the difference between the energies of the lowest dipole-allowed excited state and the ground state. Within many-body perturbation theory, the fundamental gap is the difference between the corresponding lowest quasi-hole and quasi-electron excitation energies, and the optical gap is addressed by including the interaction between a quasi-electron and a quasi-hole. A long-standing challenge has been the attainment of a similar description within density functional theory (DFT), with much debate on whether this is an achievable goal even in principle. Recently, we have constructed and applied a new approach to this problem. Anchored in the rigorous theoretical framework of the generalized Kohn-Sham equation, our method is based on a range-split hybrid functional that uses exact long-range exchange. Its main novel feature is that the range-splitting parameter is not a universal constant but rather is determined from first principles, per system, based on satisfaction of the ionization potential theorem. For finite-sized objects, this DFT approach mimics successfully, to the best of our knowledge for the first time, the quasi-particle picture of many-body theory. Specifically, it allows for the extraction of both the fundamental and the optical gap from one underlying functional, based on the HOMO-LUMO gap of a ground-state DFT calculation and the lowest excitation energy of a linear-response time-dependent DFT calculation, respectively. In particular, it produces the correct optical gap for the difficult case of charge-transfer and charge-transfer-like scenarios, where conventional functionals are known to fail. In this perspective, we overview the formal and practical challenges associated with gap calculations, explain our new approach and how it overcomes previous difficulties, and survey its application to a variety of systems.

Förster Resonance Energy Transfer (FRET) between fluorescent proteins (FPs) is widely used to construct fluorescent sensor proteins, to study intracellular protein-protein interactions and to monitor conformational changes in multidomain proteins. Although FRET depends strongly on the orientation of the transition dipole moments (TDMs) of the donor and acceptor fluorophores, this orientation dependence is currently not taken into account in FRET sensor design. Similarly, studies that use FRET to derive structural constrains typically assume a κ(2) of 2/3 or use the TDM of green fluorescent protein, as this is the only FP for which the TDM has been determined experimentally. Here we used time-dependent density functional theory (TD-DFT) methods to calculate the TDM for a comprehensive list of commonly used fluorescent proteins. The method was validated against higher levels of calculation. Validation with model compounds and the experimentally determined TDM of GFP shows that the TDM is mostly determined by the structure of the π-conjugated fluorophore and is insensitive to non-conjugated side chains or the protein surrounding. Our calculations not only provide TDM for most of the currently used FPs, but also suggest an empirical rule that can be used to obtain the TDMs for newly developed fluorescent proteins in the future.

We address the conundrum posed by the well-known failure of time-dependent DFT (TDDFT) with conventional functionals for "charge-transfer-like" excitations in oligoacenes. We show that this failure is due to a small spatial overlap in orbitals obtained from the underlying single-electron orbitals by means of a unitary transformation. We further show that, as in true charge-transfer excitations, this necessarily results in failure of linear-response TDDFT with standard functionals. Range-separated hybrid functionals have been previously shown to mitigate such errors but at the cost of an empirically adjusted range-separation parameter. Here, we explain why this approach should succeed where conventional functionals fail. Furthermore, we show that optimal tuning of a range-separated hybrid functional, so as to enforce the DFT version of Koopmans' theorem, restores the predictive power of TDDFT even for such difficult cases, without any external reference data and without any adjustable parameters. We demonstrate the success of this approach on the oligoacene series and on related hydrocarbons. This resolves a long-standing question in TDDFT and extends the scope of molecules and systems to which TDDFT can be applied in a predictive manner.

We present a broadly applicable, physically motivated, first-principles approach to determining the fundamental gap of finite systems from single-electron orbital energies. The approach is based on using a range-separated hybrid functional within the generalized Kohn-Sham approach to density functional theory. Its key element is the choice of a range-separation parameter such that Koopmans' theorem for both neutral and anion is obeyed as closely as possible. We demonstrate the validity, accuracy, and advantages of this approach on first, second and third row atoms, the oligoacene family of molecules, and a set of hydrogen-passivated silicon nanocrystals. This extends the quantitative usage of density functional theory to an area long believed to be outside its reach.