Insertion of the Liquid Crystal 5CB into Monovacancy Graphene.

Interfacial interactions between liquid crystal (LC) and two-dimensional (2D) materials provide a platform to facilitate novel optical and electronic material properties. These interactions are uniquely sensitive to the local energy landscape of the atomically thick 2D surface, which can be strongly influenced by defects that are introduced, either by design or as a byproduct of fabrication processes. Herein, we present density functional theory (DFT) calculations of the LC mesogen 4-cyan-4'-pentylbiphenyl (5CB) on graphene in the presence of a monovacancy (MV-G). We find that the monovacancy strengthens the binding of 5CB in the planar alignment and that the structure is lower in energy than the corresponding homeotropic structure. However, if the molecule is able to approach the monovacancy homeotropically, 5CB undergoes a chemical reaction, releasing 4.5 eV in the process. This reaction follows a step-by-step process gradually adding bonds, inserting the 5CB cyano group into MV-G. We conclude that this irreversible insertion reaction is likely spontaneous, potentially providing a new avenue for controlling both LC behavior and graphene properties.

Synthesis and Structure of Sn14Cl6(CH2SiMe3)12: Toward Nanoclusters of 4-Coordinate α-Sn.

Orange crystals of a Sn14 cluster have been isolated in up to 22% yield from a reaction between Me3SiCH2SnCl3, SnCl4, and LiAlH4. The structure determined by single crystal X-ray diffraction shows three unique Sn atoms in a 6:6:2 ratio, with all Sn atoms 4-coordinate, similar to the tetrahedral bonding in elemental gray Sn. The solid state 117Sn MAS NMR spectrum shows the three types of distinct Sn atoms in the expected 3:3:1 intensity ratio with respective chemical shifts of 87.9, -66.6, and -607.1 ppm relative to Me4Sn. The chemical shift of the two Sn atoms without ligands (bonded only to Sn), at -607.1 ppm, is the most upfield, and is the closest to the chemical shift, reported here, of bulk gray tin (-910 ppm). First-principles density functional theory calculations of the chemical shielding tensors corroborate this assignment. While the core coordination is distorted from the ideal tetrahedral arrangement in the diamond structure of gray tin, this Sn14 cluster, as the largest reported cluster with all 4-coordinate Sn, represents a major incremental step toward being able to prepare atomically precise nanoparticles of gray tin.

Excited-state absorption in tetrapyridyl porphyrins: comparing real-time and quadratic-response time-dependent density functional theory.

Three meso-substituted tetrapyridyl porphyrins (free base, Ni(ii), and Cu(ii)) were investigated for their optical limiting (OL) capabilities using real-time (RT-), linear-response (LR-), and quadratic-response (QR-) time-dependent density functional theory (TDDFT) methods. These species are experimentally known to display a prominent reverse saturable absorption feature between the Q and B bands of the ground-state absorption (GSA), which has been attributed to increased excited-state absorption (ESA) relative to GSA. A recently developed RT-TDDFT based method for calculating ESA from a LR-TDDFT density was utilized with eight exchange-correlation functionals (BLYP, PBE, B3LYP, CAM-B3LYP, PBE0, M06, BHLYP, and BHandH) and contrasted with calculations of ESA using QR-TDDFT with five exchange-correlation functionals (BLYP, B3LYP, CAM-B3LYP, BHLYP, and BHandH). This allowed for comparison between functionals with varying amounts of exact exchange as well as between the ability of RT-TDDFT and QR-TDDFT to reproduce OL behavior in porphyrin systems. The absorption peak positions and intensities for GSA and ESA are significantly impacted by the choice of DFT functional, with the most critical factor identified as the amount of exact exchange in the functional form. Calculating ESA with QR-TDDFT is found to be significantly more sensitive to the amount of exact exchange than GSA and ESA with RT-TDDFT, as well as GSA with LR-TDDFT. An analogous behavior is also demonstrated for the polycyclic aromatic hydrocarbon coronene. This is problematic when using the same approximate functional for calculation of both GSA and ESA, as the LR- and QR-TDDFT excitation energies will not have similar errors. Overall, the RT-TDDFT method with hybrid functionals reproduces the OL features for the porphyrin systems studied here and is a viable computational approach for efficient screening of molecular complexes for OL properties.

Nonequilibrium Chemical Effects in Single-Molecule SERS Revealed by Ab Initio Molecular Dynamics Simulations.

Recent developments in nanophotonics have paved the way for achieving significant advances in the realm of single-molecule chemical detection, imaging, and dynamics. In particular, surface-enhanced Raman scattering (SERS) is a powerful analytical technique that is now routinely used to identify the chemical identity of single molecules. Understanding how nanoscale physical and chemical processes affect single-molecule SERS spectra and selection rules is a challenging task and is still actively debated. Herein, we explore underappreciated chemical phenomena in ultrasensitive SERS. We observe a fluctuating excited electronic state manifold, governed by the conformational dynamics of a molecule (4,4'-dimercaptostilbene, DMS) interacting with a metallic cluster (Ag20). This affects our simulated single-molecule SERS spectra; the time trajectories of a molecule interacting with its unique local environment dictates the relative intensities of the observable Raman-active vibrational states. Ab initio molecular dynamics of a model Ag20-DMS system are used to illustrate both concepts in light of recent experimental results.

Time-Domain Simulations of Transient Species in Experimentally Relevant Environments.

Simulating the spectroscopic properties of short-lived thermal and photochemical reaction intermediates and products is a challenging task, as these species often feature atypical molecular and electronic structures. The complex environments in which such species typically reside in practice add further complexity to the problem. Herein, we tackle this problem in silico using ab initio molecular dynamics (AIMD) simulations, employing iso-CHBr3, namely H(Br)C-Br-Br, as a prototypical system. This species was chosen because it features both a nonconventional C-Br-Br bonding pattern, as well as a strong dependence of its spectral features on the local environment in which it resides, as illustrated in recent experimental reports. We simulate the UV-vis and IR spectra of iso-CHBr3 in the gas phase, as well as in a Ne cluster (64 atoms) and in a methylcyclohexane cage (14 solvent molecules) representative of the previously characterized matrix isolated and solvated iso-CHBr3 species. We exclusively perform fully quantum mechanical static and dynamic simulations. By comparing our condensed phase simulations to their experimental analogues, we stress the importance of (i) conformational sampling, even at cryogenic temperatures, and (ii) using a fully quantum mechanical description of both solute and bath to properly account for the experimental observables.

Non-adiabatic molecular dynamics investigation of photoionization state formation and lifetime in Mn²âº-doped ZnO quantum dots.

The unique electronic structure of Mn(2+)-doped ZnO quantum dots gives rise to photoionization states that can be used to manipulate the magnetic state of the material and to generate zero-reabsorption luminescence. Fast formation and long non-radiative decay of this photoionization state is a necessary requirement for these important applications. In this work, surface hopping based non-adiabatic molecular dynamics are used to demonstrate the fast formation of a metal-to-ligand charge transfer state in a Mn(2+)-doped ZnO quantum dot. The formation occurs on an ultrafast timescale and is aided by the large density of states and significant mixing of the dopant Mn(2+) 3dt2 levels with the valence-band levels of the ZnO lattice. The non-radiative lifetime of the photoionization states is also investigated.

Surface hopping with Ehrenfest excited potential.

Given the exponentially scaling cost of full quantum calculations, approximations need to be employed for the simulation of the time evolution of chemical systems. We present a modified version of surface hopping that has the potential to treat larger systems. This is accomplished through an Ehrenfest-like treatment of the excited states, thereby reducing the dynamics to transitions between the ground state and a mean-field excited state. A simplified description of the excited states is achieved, while still allowing for an accurate description of disparate reaction channels. We test our mean-field approximation for the excited states on a series of model problems. Results are compared to the standard surface hopping procedure, with its explicit treatment of all excited states, and the traditional Ehrenfest approach, with its averaging together of all states.

Regarding the validity of the time-dependent Kohn-Sham approach for electron-nuclear dynamics via trajectory surface hopping.

The implementation of fewest-switches surface-hopping (FSSH) within time-dependent Kohn-Sham (TDKS) theory [Phys. Rev. Lett. 95, 163001 (2005)] has allowed us to study successfully excited state dynamics involving many electronic states in a variety of molecular and nanoscale systems, including chromophore-semiconductor interfaces, semiconductor and metallic quantum dots, carbon nanotubes and graphene nanoribbons, etc. At the same time, a concern has been raised that the KS orbital basis used in the calculation provides only approximate potential energy surfaces [J. Chem. Phys. 125, 014110 (2006)]. While this approximation does exist in our method, we show here that FSSH-TDKS is a viable option for computationally efficient calculations in large systems with straightforward excited state dynamics. We demonstrate that the potential energy surfaces and nonadiabatic transition probabilities obtained within the TDKS and linear response (LR) time-dependent density functional theories (TDDFT) agree semiquantitatively for three different systems, including an organic chromophore ligating a transition metal, a quantum dot, and a small molecule. Further, in the latter case the FSSH-TDKS procedure generates results that are in line with FSSH implemented within LR-TDDFT. The FSSH-TDKS approach is successful for several reasons. First, single-particle KS excitations often give a good representation of LR excitations. In this regard, DFT compares favorably with the Hartree-Fock theory, for which LR excitations are typically combinations of multiple single-particle excitations. Second, the majority of the FSSH-TDKS applications have been performed with large systems involving simple excitations types. Excitation of a single electron in such systems creates a relatively small perturbation to the total electron density summed over all electrons, and it has a small effect on the nuclear dynamics compared, for instance, with thermal nuclear fluctuations. In such cases an additional, classical-path approximation can be made. Third, typical observables measured in time-resolved experiments involve averaging over many initial conditions. Such averaging tends to cancel out random errors that may be encountered in individual simulated trajectories. Finally, if the flow of energy between electronic and nuclear subsystems is insignificant, the ad hoc FSSH procedure is not required, and a straightforward mean-field, Ehrenfest approach is sufficient. Then, the KS representation provides rigorously a convenient and efficient basis for numerically solving the TDDFT equations of motion.

Structural and theoretical studies of 4-chloro-2-methyl-6-oxo-3,6-dideuteropyrimidin-1-ium chloride (d 6).

The title compound, C5D6ClN2O+·Cl-, crystallizes in the ortho-rhom-bic space group, Pbcm, and consists of a 4-chloro-2-methyl-6-oxo-3,6-di-hydro-pyrimidin-1-ium cation and a chloride anion where both moieties lie on a crystallographic mirror. The cation is disordered and was refined as two equivalent forms with occupancies of 0.750 (4)/0.250 (4), while the chloride anion is triply disordered with occupancies of 0.774 (12), 0.12 (2), and 0.11 (2). Unusually, the bond angles around the C=O unit range from 127.2 (6) to 115.2 (3)° and similar angles have been found in other structures containing a 6-oxo-3,6-di-hydro-pyrimidin-1-ium cation, including the monclinic polymorph of the title compound, which crystallizes in the monoclinic space group P21/c [Kawai et al. (1973 ▸). Cryst. Struct. Comm. 2, 663-666]. The cations and anions pack into sheets in the ab plane linked by N-H⋯Cl hydrogen bonds as well as C-H⋯O and Cl⋯O inter-actions. In graph-set notation, these form R 3 3(11) and R 3 2(9) rings. Theoretical calculations seem to indicate that the reason for the unusual angles at the sp 2 C is the electrostatic inter-action between the oxygen atom and the adjacent N-H hydrogen.

First Principles Nonadiabatic Excited-State Molecular Dynamics in NWChem.

Computational simulation of nonadiabatic molecular dynamics is an indispensable tool for understanding complex photoinduced processes such as internal conversion, energy transfer, charge separation, and spatial localization of excitons, to name a few. We report an implementation of the fewest-switches surface-hopping algorithm in the NWChem computational chemistry program. The surface-hopping method is combined with linear-response time-dependent density functional theory calculations of adiabatic excited-state potential energy surfaces. To treat quantum transitions between arbitrary electronic Born-Oppenheimer states, we have implemented both numerical and analytical differentiation schemes for derivative nonadiabatic couplings. A numerical approach for the time-derivative nonadiabatic couplings together with an analytical method for calculating nonadiabatic coupling vectors is an efficient combination for surface-hopping approaches. Additionally, electronic decoherence schemes and a state reassigned unavoided crossings algorithm are implemented to improve the accuracy of the simulated dynamics and to handle trivial unavoided crossings. We apply our code to study the ultrafast decay of photoexcited benzene, including a detailed analysis of the potential energy surface, population decay timescales, and vibrational coordinates coupled to the excitation dynamics. We also study the photoinduced dynamics in trans-distyrylbenzene. This study provides a baseline for future implementations of higher-level frameworks for simulating nonadiabatic molecular dynamics in NWChem.

Ab initio nonadiabatic molecular dynamics of wet-electrons on the TiO(2) surface.

The electron transfer (ET) dynamics of wet-electrons on a TiO(2) surface is investigated using state-of-the-art ab initio nonadiabatic (NA) molecular dynamics (MD). The simulations directly mimic the time-resolved experiments [Science 2005, 308, 1154] and reveal the nature of ET in the wet-electron system. Focusing on the partially hydroxylated TiO(2) surface with 1-monolayer water coverage, and including electronic evolution, phonon motions, and electron-phonon coupling, the simulations indicate that the ET is sub-10 fs, in agreement with the experiment. Despite the large role played by low frequency vibrational modes, the ET is fast due to the strong coupling between the TiO(2) surface and water. The average ET for the system has equal contributions from the adiabatic and NA mechanisms, even though a very broad range of individual ET events is seen in the simulated ensemble. Thermal phonon motions induce a large fluctuation of the wet-electron state energy, generate frequent crossings of the donor and acceptor states, and drive the adiabatic mechanism. The rapid phonon-assisted NA tunneling from the wet-electron state to the TiO(2) surface is facilitated by the strong water-TiO(2) electronic interaction. The motions of molecular water have a greater effect on the ET dynamics than the hydroxyl vibrations. The former contribute to both the wet-electron state energy and the water-TiO(2) electronic coupling, while the latter changes only the energy and not the coupling. Delocalized over both water and TiO(2), wet-electrons are supported by a new type of state that is created at the interface due to the strong water-TiO(2) interaction and that cannot exist separately in either material. Similar states are present in a number of other systems with strong interfacial coupling, including certain dye-sensitized semiconductors and metal-liquid interfaces. The ET dynamics involving such interfacial states share many universal features, such as an ultrashort time scale and weak-dependence on temperature, surface defects, and other system details.

Analysis of Correlated Dynamics in the Grotthuss Mechanism of Proton Diffusion.

Using a large set of ab initio molecular dynamics trajectories we demonstrate that the mechanistic details of aqueous proton diffusion are insensitive to finite size effects. Furthermore, we show how correlation in the proton hopping direction is related to the presolvation of the hydronium ion. Specifically, we observe a dependence of the probability for the excess proton to return to its previous hydronium ion on whether that hydronium ion was accepting a hydrogen bond from a fourth water molecule at the time the excess proton left. The dynamics of this fourth water molecule was previously linked to the net displacement of the proton, and our analysis shows that this connection is due to the changes in the hopping probability that we calculate. Additionally, we show how our simulated dynamics with correlations that imply a faster time scale are compatible with recent spectroscopy results that point to a slower hopping time scale by looking closely at which proton transitions are being taken into consideration. Finally, we show that the correlation in proton hopping directions is not strongly influenced by interactions among hydronium ions.

Thermotropic liquid crystal (5CB) on two-dimensional materials.

We present ground-state electronic properties of the liquid crystal 4-cyano-4^{'}-pentylbiphenyl (5CB) on the two-dimensional materials monolayer graphene, hexagonal boron nitride, and phosphorene. Our density functional theory results show that the physisorption is robust on all surfaces with the strongest binding of 5CB on phosphorene. All surfaces exhibit flexural distortion, especially monolayer graphene and hexagonal boron nitride. While we find type-I alignment for all three substrates, meaning the Fermi level of the system is in the HOMO-LUMO gap of 5CB, the band structures are qualitatively different. Unlike for graphene and phosphorene, the HOMO-LUMO of 5CB appear as localized states within the band gap of boron nitride. In addition, we find that the valence band for boron nitride is sensitive to the orientation of 5CB relative to the surface. The qualitatively different band structures demonstrate the importance of substrate selection for tailoring the electronic and optoelectronic properties of nematic liquid crystals on two-dimensional materials.

Correlated dynamics in aqueous proton diffusion.

The aqueous proton displays an anomalously large diffusion coefficient that is up to 7 times that of similarly sized cations. There is general consensus that the proton achieves its high diffusion through the Grotthuss mechanism, whereby protons hop from one molecule to the next. A main assumption concerning the extraction of the timescale of the Grotthuss mechanism from experimental results has been that, on average, there is an equal probability for the proton to hop to any of its neighboring water molecules. Herein, we present ab initio simulations that show this assumption is not generally valid. Specifically, we observe that there is an increased probability for the proton to revert back to its previous location. These correlations indicate that the interpretation of the experimental results need to be re-examined and suggest that the timescale of the Grotthuss mechanism is significantly shorter than was previously thought.

Phase II trial of concurrent paclitaxel, carboplatin, and external-beam radiation followed by surgical resection in locally advanced non-small-cell lung cancer, protocol 99-444.

PURPOSE: We conducted a phase II study to evaluate the utility and outcomes of concurrent weekly low-dose chemotherapy with concurrent radiation in an effort to "downstage" patients with locally advanced non-small-cell lung cancer (NSCLC). PATIENTS AND METHODS: Eighteen patients with pathologically confirmed stage IIIA (T1-3 N2 or T3 N1) and 3 patients with stage IIB (T3 N0) NSCLC were enrolled. Seventeen of 18 patients with stage IIIA cancer had N2 disease. A chemotherapy/radiation schedule consisted of paclitaxel 50 mg/m(2 )and carboplatin administered at an area under the curve of 2 weekly for 5 weeks along with chest irradiation of 45 Gy. Patients with regressed or stable disease upon restaging were considered surgical candidates. Patients deemed inoperable were given additional radiation therapy. RESULTS: Twenty-one patients were enrolled from April 2000 to March 2004. Data from 21 patients were available for evaluation at the time of analysis. Grade 3/4 constitutional and pulmonary toxicity was

Excited-State Absorption from Real-Time Time-Dependent Density Functional Theory: Optical Limiting in Zinc Phthalocyanine.

Optical-limiting materials are capable of attenuating light to protect delicate equipment from high-intensity light sources. Phthalocyanines have attracted a lot of attention for optical-limiting applications due to their versatility and large nonlinear absorption. With excited-state absorption (ESA) being the primary mechanism for optical limiting behavior in phthalocyanines, the ability to tune the optical absorption of ground and excited states in phthalocyanines would allow for the development of advanced optical limiters. We recently developed a method for the calculation of ESA based on real-time time-dependent density functional theory propagation of an excited-state density. In this work, we apply the approach to zinc phthalocyanine, demonstrating the ability of our method to efficiently identify the optical limiting potential of a molecular complex.

Infrared and Raman Spectroscopy from Ab Initio Molecular Dynamics and Static Normal Mode Analysis: The C-H Region of DMSO as a Case Study.

Carbon-hydrogen (C-H) vibration modes serve as key probes in the chemical identification of hydrocarbons and in vibrational sum-frequency generation spectroscopy of hydrocarbons at the liquid/gas interface. Their assignments pose a challenge from a theoretical viewpoint. In this work, we present a detailed study of the C-H stretching region of dimethyl sulfoxide using a new ab initio molecular dynamics (AIMD) module that we have implemented in NWChem. Through a combination of AIMD simulations and static normal mode analysis, we interpret experimental infrared and Raman spectra and explore the role of anharmonic effects in this system. Comprehensive anharmonic normal mode analysis of the C-H stretching region casts doubt upon previous experimental assignments of the shoulder on the symmetric C-H stretching peak. In addition, our AIMD simulations also show significant broadening of the in-phase symmetric C-H stretching resonance, which suggests that the experimentally observed shoulder is due to thermal broadening of the symmetric stretching resonance.

Ice-nucleating bacteria control the order and dynamics of interfacial water.

Ice-nucleating organisms play important roles in the environment. With their ability to induce ice formation at temperatures just below the ice melting point, bacteria such as Pseudomonas syringae attack plants through frost damage using specialized ice-nucleating proteins. Besides the impact on agriculture and microbial ecology, airborne P. syringae can affect atmospheric glaciation processes, with consequences for cloud evolution, precipitation, and climate. Biogenic ice nucleation is also relevant for artificial snow production and for biomimetic materials for controlled interfacial freezing. We use interface-specific sum frequency generation (SFG) spectroscopy to show that hydrogen bonding at the water-bacteria contact imposes structural ordering on the adjacent water network. Experimental SFG data and molecular dynamics simulations demonstrate that ice-active sites within P. syringae feature unique hydrophilic-hydrophobic patterns to enhance ice nucleation. The freezing transition is further facilitated by the highly effective removal of latent heat from the nucleation site, as apparent from time-resolved SFG spectroscopy.

Excited State Absorption from Real-Time Time-Dependent Density Functional Theory.

The optical response of excited states is a key property used to probe photophysical and photochemical dynamics. Additionally, materials with a large nonlinear absorption cross-section caused by two-photon (TPA) and excited state absorption (ESA) are desirable for optical limiting applications. The ability to predict the optical response of excited states would help in the interpretation of transient absorption experiments and aid in the search for and design of optical limiting materials. We have developed an approach to obtain excited state absorption spectra by combining real-time (RT) and linear-response (LR) time-dependent density functional theory (TDDFT). Being based on RT-TDDFT, our method is aimed at tackling larger molecular complexes and materials systems where excited state absorption is predominantly seen and many time-resolved experimental efforts are focused. To demonstrate our method, we have calculated the ground and excited state spectra of H2⁺ and H2 due to the simplicity in the interpretation of the spectra. We have validated our new approach by comparing our results for butadiene with previously published results based on quadratic response (QR). We also present results for oligofluorenes, where we compare our results with both QR-TDDFT and experimental measurements. Because our method directly measures the response of an excited state, stimulated emission features are also captured; although, these features are underestimated in energy which could be attributed to a change of the reference from the ground to the excited state.

Trp-Cage Folding on Organic Surfaces.

Trp-cage is an artificial miniprotein that is small, stable, and fast folding due to concerted hydrophobic shielding of a Trp residue by polyproline helices. Simulations have extensively characterized Trp-cage; however, the interactions of Trp-cage with organic surfaces (e.g., membranes) and their effect on protein conformation are largely unknown. To better understand these interactions we utilized a combination of replica-exchange molecular dynamics (REMD) and metadynamics (MetaD), to investigate Trp-cage folding on self-assembled monolayers (SAMs). We found that, with REMD and MetaD, Trp-cage strongly binds to neutral CH3 surfaces (-25kT) and moderately adsorbs to anionic COOH interfaces (-7.6kT), with hydrophobic interactions driving CH3 adhesion and electrostatic attractions driving COOH adhesion. Similar to solid-state surfaces, SAMs facilitate a number of intermediate Trp-cage conformations between folded and unfolded states. Regarding Trp-cage's aromatic groups in neutral CH3 systems, Tyr becomes oriented parallel to the surface in order to maximize hydrophobic interactions while Trp remains caged perpendicular to the surface; however, Trp can reorient itself parallel to the interface as the miniprotein more closely binds to the surface. In contrast, Tyr and Trp are both repelled from COOH surfaces, though the Trp-cage still adheres to the anionic interface via Lys and its N-terminated Asn residue.